sentences
stringlengths 139
8.91k
| labels
stringclasses 26
values |
|---|---|
An Entropy Approach for Choosing Gene Expression Cutoff Annotating cell types using single-cell transcriptome data usually requires binarizing the expression data to distinguish between the background noise vs. real expression or low expression vs. high expression cases. A common approach is choosing a "reasonable" cutoff value, but it remains unclear how to choose it. In this work, we describe a simple yet effective approach for finding this threshold value. | bioinformatics |
Genomic patterns of malignant peripheral nerve sheath tumour (MPNST) evolution correlate with clinical outcome and are detectable in cell-free DNA Malignant peripheral nerve sheath tumour (MPNST) is an aggressive soft-tissue sarcoma that arises in peripheral nerves. MPNST occurs either sporadically or in people with neurofibromatosis type 1 (NF1), a common cancer predisposition syndrome caused by germline pathogenic variants in NF1. Although MPNST is the most common cause of death and morbidity for individuals with NF1, the molecular underpinnings of MPNST pathogenesis remain unclear. Here, we report the analysis of whole-genome sequencing, multi-regional exome sequencing, transcriptomic and methylation profiling data for 95 MPNSTs and precursor lesions (64 NF1-related; 31 sporadic) from 77 individuals. Early events in tumour evolution include biallelic inactivation of NF1 followed by inactivation of CDKN2A and in some cases also TP53 and polycomb repressive complex 2 (PRC2) genes. Subsequently, both sporadic and NF1-related MPNSTs acquire a high burden of somatic copy number alterations (SCNAs). Our analysis revealed distinct pathways of tumour evolution and immune infiltration associated with inactivation of PRC2 genes and H3K27 trimethylation (H3K27me3) status. Tumours with loss of H3K27me3 evolve through extensive chromosomal losses with retention of chromosome 8 heterozygosity followed by whole genome doubling and chromosome 8 amplification. These tumours show lower levels of immune cell infiltration with low cytotoxic activity and low expression of immune checkpoints. In contrast, tumours with retention of H3K27me3 evolve through extensive genomic instability in the absence of recurrent alterations and exhibit an immune cell-rich phenotype. Specific SCNAs detected in both tumour samples and cell-free DNA (cfDNA) act as a surrogate for loss of H3K27me3 and immune infiltration, and predict prognosis. Our results suggest that SCNA profiling of tumour or cfDNA could serve as a biomarker for early diagnosis and to stratify patients into prognostic and treatment-related subgroups. | cancer biology |
Testing the link between isoaspartate and Alzheimer's disease etiology Isoaspartate (isoAsp) is a damaging amino acid residue formed in proteins as a result of spontaneous deamidation. IsoAsp disrupts the secondary and higher order structures of proteins, damaging their functions and making them prone to aggregation. An association has been suggested between isoAsp and Alzheimers Disease (AD). Here we strengthened the link between isoAsp and AD by novel approaches to isoAsp analysis in blood human serum albumin (HSA), the most abundant blood protein, a major carrier of amyloid beta (A{beta}) peptide and phosphorylated tau (pTau) protein in blood and a key participant in their clearance pathway. We discovered a reduced amount of anti-isoAsp antibodies (P < .0001), an elevated isoAsp level in HSA (P < .001), more HSA aggregates (P < .0001) and increased levels of free A{beta} (P < .01) in AD blood compared to healthy controls. We also found that deamidation significantly reduces HSA capacity to bind with A{beta} and pTau (P < .05). These findings support the presence in AD of a bottleneck in clearance of A{beta} and pTau leading to their increased concentrations in brain and facilitating their aggregations there.
RESEARCH IN CONTEXTO_LISystematic review: We reviewed the evidence that associates isoaspartate (isoAsp) residue in blood proteins with the etiology of Alzheimers disease (AD). However, the link between isoAsp in blood and aggregation of amyloid beta (A{beta}) peptide and phosphorylated tau (pTau) protein in brain remained unclear.
C_LIO_LIInterpretation: For the first time we demonstrate that isoAsp-containing human serum albumin (HSA) forms aggregates with reduced binding capacity toward A{beta} peptide and pTau protein. Using a novel ELISA, we discovered in AD blood elevated levels of isoAsp in HSA, together with reduced endogenous anti-isoAsp antibody levels, suggesting hampered A{beta} and pTau clearance in AD.
C_LIO_LIFuture directions: As degradation of the innate anti-isoAsp defenses may take years to develop, investigation of the isoAsp role in early stages of AD is warranted. And enrollment of different neurodegenerative disease cohorts will illustrate if isoAsp is AD-specific or universal to diseases related to aging.
C_LI
O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY | neuroscience |
Neutrophil-Mediated Stromal-Tumor IL-6/STAT-3 Signaling Underlies the Association between Neutrophil-to-Lymphocyte Ratio Dynamics and Chemotherapy Response in Localized Pancreatic Cancer: A Hybrid Clinical-Preclinical Study BackgroundPartial/complete pathologic response following neoadjuvant chemotherapy (NAC) in pancreatic cancer (PDAC) patients undergoing pancreatectomy is associated with improved survival. We sought to determine whether neutrophil-to-lymphocyte ratio (NLR) dynamics predict pathologic response following chemotherapy in PDAC, and if manipulating NLR impacts chemosensitivity in preclinical models and uncovers potential mechanistic underpinnings underlying these effects.
MethodsPathologic response in PDAC patients (n=94) undergoing NAC and pancreatectomy (7/2015-12/2019) was dichotomized as partial/complete or poor/absent (case-cohort design). Bootstrap-validated multivariable models assessed associations between pre-chemotherapy NLR (%neutrophils/%lymphocytes) or NLR dynamics during chemotherapy ({Delta}NLR=pre-surgery--pre-chemotherapy NLR) and pathologic response, disease-free survival (DFS), and overall survival (OS). To preclinically model effects of NLR attenuation on chemosensitivity, C57BL/6 mice (n=8-10/arm) were orthotopically injected with KrasG12D/+;Trp53fl/+;PdxCre(KPC)cells and randomized to vehicle, NLR-attenuating anti-Ly6G, gemcitabine/paclitaxel, or gemcitabine/paclitaxel+anti-Ly6G treatments.
ResultsIn 94 PDAC patients undergoing NAC (median:4 months), pre-chemotherapy NLR (P<0.001) and {Delta}NLR attenuation during NAC (P=0.002) were independently associated with partial/complete pathologic response. An NLR score=pre-chemotherapy NLR+{Delta}NLR correlated with DFS (P=0.006) and OS (P=0.002). Upon preclinical modeling, combining NLR-attenuating anti-Ly6G treatment with gemcitabine/paclitaxel--compared with gemcitabine/paclitaxel or anti-Ly6G alone--not only significantly reduced tumor burden and metastatic outgrowth, but also augmented tumor-infiltrating CD107a+-degranulating CD8+ T-cells (P<0.01) while dampening inflammatory cancer-associated fibroblast (CAF) polarization (P=0.006) and chemoresistant IL-6/STAT-3 signaling in vivo. Neutrophil-derived IL-1{beta} emerged as a novel mediator of stromal inflammation, inducing inflammatory CAF polarization and CAF-tumor cell IL-6/STAT-3 signaling in ex vivo co-cultures.
ConclusionsTherapeutic strategies to mitigate neutrophil-CAF-tumor cell IL-1{beta}/IL-6/STAT-3 signaling during NAC may improve pathologic responses and/or survival in PDAC. | immunology |
Antigenic characterization and pandemic risk assessment of North American H1 influenza A viruses circulating in swine The first pandemic of the 21st century was caused by an H1N1 influenza A virus (IAV) introduced from pigs into humans, highlighting the importance of swine as reservoirs for pandemic viruses. Two major lineages of swine H1 circulate in North America: the 1A classical swine lineage (including the 2009 pandemic H1N1) and 1B human seasonal-like lineage. Here, we investigated the evolution of these H1 IAV lineages in North American swine and their potential pandemic risk. We assessed the antigenic distance between the HA of representative swine H1 and human seasonal vaccine strains (1978-2015) in hemagglutination inhibition (HI) assays using a panel of monovalent anti-sera raised in pigs. Antigenic cross-reactivity varied by strain but was associated with genetic distance. Generally, swine 1A lineage viruses that seeded the 2009 H1 pandemic were antigenically most similar to H1 pandemic vaccine strains, with the exception of viruses in the genetic clade 1A.1.1.3 that had a two-amino acid deletion mutation near the receptor-binding site, dramatically reducing antibody recognition. The swine 1B lineage strains, which arose from previously circulating (pre-2009 pandemic) human seasonal viruses, were more antigenically similar to pre-2009 human seasonal H1 vaccine viruses than post-2009 strains. Human population immunity was measured by cross-reactivity in HI assays to representative swine H1 strains. There was a broad range of titers against each swine strain that was not associated with age, sex, or location. However, there was almost no cross-reactivity in human sera to the 1A.1.1.3 and 1B.2.1 genetic clades of swine viruses, and the 1A.1.1.3 and 1B.2.1 clades were also the most antigenically distant from all human vaccine strains. Our data demonstrate that antigenic distances of representative swine strains from human vaccine strains represent a rational assessment of swine IAV for zoonotic risk research and pandemic preparedness prioritization.
ImportanceHuman H1 influenza A viruses (IAV) spread to pigs in North America, resulting in sustained circulation of two major groups of H1 viruses in swine. We quantified the genetic diversity of H1 in swine and measured antigenic phenotypes. We demonstrated that swine H1 lineages were significantly different from human vaccine strains and this antigenic dissimilarity increased over time as the viruses evolved in swine. Pandemic preparedness vaccine strains for human vaccines also demonstrated a loss in similarity with contemporary swine strains. Human sera revealed a range of responses to swine IAV, including two groups of viruses with little to no immunity. Surveillance and risk assessment of IAV diversity in pig populations are essential to detect strains with reduced immunity in humans, providing critical information for pandemic preparedness. | microbiology |
Plasmodium falciparum genetic diversity in coincident human and mosquito hosts Population genetic diversity of P. falciparum antigenic loci is high despite large bottlenecks in population size during the parasite life cycle. The extent of this diversity in human blood-stage infections, following expansion from a small number of liver-stage schizonts, has been well described. However, little is known about parasite genetic diversity in the vector, where a similar bottleneck and expansion occurs following parasite mating and where parasite genotypes from several different human infections may accumulate. We assessed parasite genetic diversity within human and mosquito P. falciparum infections collected from the same households during a 14-month longitudinal cohort study using amplicon deep sequencing of two antigenic gene fragments (ama1 and csp). To a prior set of infected humans (n=1175/2813; 86.2% sequencing success) and mosquito abdomens (n=199/1448; 95.5% sequencing success), we added sequences from infected mosquito heads (n=134/1448; 98.5% sequencing success). Across all sample types we observed 456 ama1 and 289 csp unique haplotypes. While both hosts contained many rare haplotypes, population genetic metrics indicated that the overall and sample-level parasite populations were more diverse in mosquitoes than in humans, and infections were more likely to harbor a dominant haplotype in humans than in mosquitoes (based on relative read abundance). Finally, within a given mosquito there was little overlap in genetic composition of abdomen and head infections, suggesting that infections may be cleared from the abdomen during a mosquitos lifespan. Taken together, our observations provide evidence for the role of the mosquito vector in maintaining sequence diversity of malaria parasite populations.
Significance statementConcurrent infections with multiple strains of Plasmodium falciparum, the leading causative agent of death due to malaria, are common in highly endemic regions. During transitions within and between the parasites mosquito and human hosts, population bottlenecks occur, and distinct parasite strains may have differential fitness in the various environments encountered. These bottlenecks and fitness differences may lead to differences in strain prevalence and diversity between hosts. We investigated differences in genetic diversity between P. falciparum parasites in human and mosquito hosts and found that, compared to human parasite populations and infections, mosquito populations and infections were more diverse. This suggests that the mosquito vector may play a role in in maintaining sequence diversity in malaria parasite populations. | microbiology |
Controls of SAR11 subclade abundance, diversity, and growth in two Mid-Atlantic estuaries SAR11 is a dominant bacterial clade in marine oligotrophic ecosystems. SAR11 can also be dominant in estuarine systems, where they are not well-studied. We examined the effects of season, nutrient concentrations, and salinity in shaping SAR11 subclade abundance, diversity, function, and growth in two Mid-Atlantic estuaries, the Delaware and Chesapeake Bays. Using metagenome-assembled genomes, we identified twelve distinct genomospecies within the Ia, II, IIIa, and V subclades, which made up to 60% of the total bacterial community. The functional potential of all SAR11 genomospecies varied, especially in carbohydrate metabolism, transporters, and one-carbon metabolic pathways. Predicted growth rates, estimated by the Peak to Trough method, varied by season and genomospecies. SAR11 growth rates negatively correlated in the spring but positively correlated in the summer with chlorophyll a concentrations and bacterial production, as well as phosphate and ammonium concentrations. Genomospecies in Ia.1, IIIa.2, and IIIa.4 subclades had low growth rates, while genomospecies in Ia.3, Ia.5, Ia.6, II, and V subclades had higher and more variable growth rates that were positively correlated with phosphate concentrations and temperature. Growth rate variation between subclades was associated with carbohydrate metabolic gene repertoires, especially glycolysis and number of transporters. While total transcript to genome ratios generally mirrored growth rates, transcription of genes involved in phosphate and nitrogen transport were negatively associated with growth rates. These data suggest that SAR11 genomospecies abundance varies in these estuaries because of differences in growth rates and metabolic capacities in response to changes in environmental conditions.
ImportanceThe SAR11 clade is one of the most abundant bacterial groups in marine systems, including many estuaries. From the Delaware Bay and Chesapeake Bay environmental metagenomes, we reconstructed nearly complete SAR11 metagenome-assembled genomes representing ten genomospecies in four subclades, of which at least one is novel. Growth rate estimates of genomospecies correlated with functional gene repertoires of carbohydrate transporter and metabolism. Different SAR11 genomospecies dominated among the seasons, depending on their growth rates, biological productivity, and nutrient concentrations. Our RNAseq approach facilitated an understanding of the environmental controls on the abundance of SAR11 genomospecies in their natural habitat. This study is the first to combine multiple measures of diversity, abundance, functional potential, growth rates and activity of this important group, demonstrating a direct link between SAR11 genomospecies abundance and growth in the context of its environment. | microbiology |
An attempt to find the correlations between body weight and the composition of gut microbiota in Zhejiang and Shanghai Previous studies showed that the human gut microbiota was associated with metabolic diseases, but the interaction and mechanism between the gut microbiota and metabolic disease are still unclear. In this study, the gut microbiota of 58 persons living in Zhejiang and Shanghai area will be analyzed. Then, the potential contribution of the human gut microbiota to obesity/high Body Mass Index (BMI) will be explored. The gut microbiota was studied by high throughput sequencing analysis of bacterial 16S rRNA gene fragments, and the gut microbiota samples with different BMI were compared. Meanwhile, some gut microorganisms from faeces of a healthy individual were cultivated and isolated, and the classification was identified by 16S rRNA sequencing. The main microbes in human gut microbiota were assigned to the phyla of Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. Moreover, four strains were isolated from an individual fecal sample, of which one species was assigned to Escherichia fergusonii and the other three strains were assigned to Weissella cibaria. These four species belong to both abundant and low-abundant species revealed by high throughput sequencing. It was found that individuals with different BMI have different gut microbiota; while the differences are not significant. Also, the Firmicutes/Bacteroidetes ratio increases with the decrease of BMI, which is corresponding to previous results. In the future, more cohort gut microbiota in Zhejiang and Shanghai area will be collected and recovered, and the gut microbiota database of Zhejiang and Shanghai area will be built up in order to provide the basis for future gut microbiota modulation in this area. | microbiology |
Microbial paracetamol degradation involves a high diversity of novel amidase enzyme candidates Pharmaceuticals are relatively new to nature and often not completely removed in wastewater treatment plants (WWTPs). Consequently, these micropollutants end up in water bodies all around the world posing a great environmental risk. One exception to this recalcitrant conversion is paracetamol, whose full degradation has been linked to several microorganisms. However, the genes and corresponding proteins involved in microbial paracetamol degradation are still elusive. In order to improve our knowledge of the microbial paracetamol degradation pathway, we inoculated a bioreactor with sludge of a hospital WWTP (Pharmafilter, Delft, NL) and fed it with paracetamol as the sole carbon source. Paracetamol was fully degraded without any lag phase and the enriched microbial community was investigated by metagenomic and metatranscriptomic analyses, which demonstrated that the microbial community was very diverse. Dilution and plating on paracetamol-amended agar plates yielded two Pseudomonas sp. isolates: a fast-growing Pseudomonas sp. that degraded 200 mg/L of paracetamol in approximately 10 hours while excreting a dark brown component to the medium, and a slow-growing Pseudomonas sp. that degraded paracetamol without obvious intermediates in more than 90 days. Each Pseudomonas sp. contained a different highly-expressed amidase (31% identity to each other). These amidase genes were not detected in the bioreactor metagenome suggesting that other as-yet uncharacterized amidases may be responsible for the first biodegradation step of paracetamol. Uncharacterized deaminase genes and genes encoding dioxygenase enzymes involved in the catabolism of aromatic compounds and amino acids were the most likely candidates responsible for the degradation of paracetamol intermediates based on their high expression levels in the bioreactor metagenome and the Pseudomonas spp. genomes. Furthermore, cross-feeding between different community members might have occurred to efficiently degrade paracetamol and its intermediates in the bioreactor. This study increases our knowledge about the ongoing microbial evolution towards biodegradation of pharmaceuticals and points to a large diversity of (amidase) enzymes that are likely involved in paracetamol metabolism in WWTPs.
HighlightsO_LIParacetamol was fully degraded by activated sludge from hospital wastewater.
C_LIO_LILow paracetamol concentrations were removed by a diverse microbial community.
C_LIO_LIPseudomonas sp. dominated cultures with high paracetamol concentration.
C_LIO_LIUncharacterized amidases are probably involved in degrading paracetamol in WWTPs.
C_LIO_LIDeaminases and dioxygenases might be degrading paracetamol transformation products.
C_LI | microbiology |
VanRS and CroRS cross-talk revealed by coevolutionary modeling regulates antibiotic resistance in VanA-type vancomycin-resistant Enterococcus faecalis Enterococcus faecalis is an opportunistic pathogen that can cause bacteremia and endocarditis. Previous studies have shown that concurrent treatment with cephalosporin and vancomycin antibiotics exhibit synergy in vancomycin-resistant E. faecalis to render the bacterium susceptible to antibiotic treatment whereas treatment with each antibiotic separately was not successful. Proteins responsible for mediating vancomycin and cephalosporin resistance are classified as two-component systems (TCS). TCS consist of a histidine kinase that phosphorylates a response regulator after environmental activation. These signaling networks have been shown to exhibit cross-talk interactions, and through direct coupling analysis, we identify encoded specificity between vancomycin resistance TCS, which are horizontally acquired, and cephalosporin resistance TCS, which are endogenous to E. faecalis. To verify cross-talk between these pathways is responsible for vancomycin and cephalosporin synergy, we use RNA-Seq to identify differentially expressed genes in VanA- and VanB-type vancomycin resistant enterococci after treatment with the cephalosporin antibiotic, ceftriaxone, and also with vancomycin. We find that cross-talk between VanSA and CroR in strain HIP11704 may be responsible for synergy, demonstrating that horizontally acquired TCS can have large impacts on pre-existing signaling networks. The presence of encoded specificity between exogenous TCS and endogenous TCS show that the systems co-evolve, and cross-talk between these systems may be exploited to engineer genetic elements that disrupt antibiotic resistance TCS pathways.
Author SummaryBacteria may transmit genetic elements to other bacteria through the process known as horizontal gene transfer. In some enterococci, vancomycin resistance genes are acquired this way. Proteins encoded within the bacterial genome can interact with proteins acquired through horizontal gene transfer. The interaction that occurs between proteins VanSA and VanRA is known to mediate vancomycin antibiotic resistance in VanA-type vancomycin resistant enterococci (VRE), and the interaction between proteins CroS and CroR is an important pathway in cephalosporin antibiotic resistance. We show that the VanSA, which is obtained through horizontal gene transfer, inhibits CroR under treatment with antibiotics vancomycin and ceftriaxone. This interaction is responsible for the observed synergy between vancomycin and ceftriaxone in VanA-type VREs. These findings demonstrate how horizontally acquired genes may produce proteins that interrupt known protein interactions, including antibiotic resistance signaling pathways in bacteria. Furthermore, the specific mechanism found for VanA-type VREs provides a basis for engineering of horizontally acquired proteins that disrupt antibiotic resistance pathways. | microbiology |
Availability of abundant thiamine determines efficiency of thermogenic activation in human neck area derived adipocytes ObjectiveBrown/beige adipocytes are characterized by expression of uncoupling protein-1 (UCP1) that enables them to dissipate energy as heat instead of generating ATP. The activation of this process can alleviate obesity as it augments energy expenditure. Human brown adipose tissue is interspersed in distinct anatomical regions including the deep neck area. We found that UCP1 enriched adipocytes differentiated from progenitors of this depot highly expressed ThTr2 transporter of thiamine, the precursor of thiamine pyrophosphate (TPP) cofactor for mitochondrial fuel generating enzymes, and aimed to investigate the importance of thiamine availability during thermogenic activation.
MethodsHuman adipocytes were differentiated from subcutaneous and deep neck precursors and activated for thermogenesis by the cell permeable dibutyryl-cAMP, which mimics adrenergic stimulation. Proton leak respiration reflecting heat generation was monitored by Seahorse XF analyzer. Direct mitochondrial effect of TPP was observed in flux assay of permeabilized adipocytes. Expression of thermogenic genes and proteins was analyzed by RT-qPCR and immunoblotting, respectively.
ResultsInhibition of ThTr2 during thermogenic activation of deep and subcutaneous neck derived adipocytes by cAMP led to decreased proton leak respiration reflecting lower uncoupling activity. In the absence of thiamine, cAMP-induced elevation of proton leak respiration was diminished but restored by thiamine addition reaching highest levels in deep neck adipocytes and at concentrations larger than present in human blood plasma. Addition of TPP to permeabilized adipocytes increased proton leak respiration fueled by one of the TPP-dependent enzymes, pyruvate dehydrogenase. ThTr2 inhibition also hampered cAMP-dependent induction of UCP1, PGC1a and other browning marker genes, along with mitochondrial complex subunits, and thermogenic induction of these genes was potentiated by thiamine in a concentration dependent manner.
ConclusionOur study has revealed the importance of amply supplied thiamine during thermogenic activation in human adipocytes. Thiamine may increase heat generation by providing TPP for TPP-dependent enzymes which lack this cofactor and by potentiating the induction of UCP1 and other thermogenic genes.
HighlightO_LIAbundant thiamine is required for efficient activation of UCP1 dependent thermogenesis in human deep neck derived adipocytes
C_LIO_LIInhibition of thiamine transporters leads to decreased thermogenic response
C_LIO_LIIn stimulated adipocytes, thiamine supply provides extra thiamine pyrophosphate for increasing pyruvate dehydrogenase activity to generate sufficient fuel of UCP1 dependent respiration.
C_LIO_LIAdrenergic stimulation of thermogenic gene expression is potentiated by thiamine in a concentration dependent manner
C_LI | cell biology |
Inflammatory stress signaling via NF-kB alters accessible cholesterol to upregulate SREBP2 transcriptional activity in endothelial cells There is a growing appreciation that a tight relationship exists between cholesterol homeostasis and immunity in leukocytes, however, this relationship has not been deeply explored in the vascular endothelium. Endothelial cells (ECs) rapidly respond to extrinsic signals, such as tissue damage or microbial infection, by upregulating factors to activate and recruit circulating leukocytes to the site of injury and aberrant activation of ECs leads to inflammatory based diseases, such as multiple sclerosis and atherosclerosis. Here, we studied the role of cholesterol and its master regulator, SREBP2, in the EC responses to inflammatory stress. Treatment of ECs with pro-inflammatory cytokines upregulates SREBP2 cleavage and cholesterol biosynthetic gene expression within the late phase of the acute inflammatory response. Furthermore, SREBP2 activation was dependent on NF-{kappa}B DNA binding and canonical SCAP-SREBP2 processing. Mechanistically, inflammatory activation of SREBP was mediated by a reduction in accessible cholesterol, leading to heightened sterol sensing and downstream SREBP2 cleavage. Detailed analysis of NF-{kappa}B inducible genes that may impact sterol sensing resulted in the identification of a novel RELA-inducible target, STARD10, that mediates accessible cholesterol homeostasis in ECs. Thus, this study provides an in-depth characterization of the relationship between cholesterol homeostasis and the acute inflammatory response in EC. | cell biology |
The mechanism underlying redundant functions of the YTHDF proteins The YTH N6-methyladenosine RNA binding proteins (YTHDFs) mediate the functional effects of N6-methyladenosine (m6A) on RNA. Recently, a report proposed that all YTHDFs work redundantly to facilitate RNA decay, raising questions about the exact functions of individual YTHDFs, especially YTHDF1 and YTHDF2. We show that YTHDF1 and YTHDF2 differ in their low-complexity domains (LCDs) and exhibit different behaviors in condensate formation and subsequent physiological functions. Biologically, we also find that the global stabilization of RNA after depletion of all YTHDFs is driven by increased P-body formation and is not strictly m6A dependent. | cell biology |
Senescent Preosteoclast Secretome Promotes Metabolic Syndrome Associated Osteoarthritis through Cyclooxygenase 2 BackgroundMetabolic syndrome-associated osteoarthritis (MetS-OA) is a distinct osteoarthritis phenotype defined by the coexistence of MetS or its individual components. Despite the high prevalence of MetS-OA, its pathogenic mechanisms are unclear. The aim of this study was to determine the role of cellular senescence in the development of MetS-OA.
MethodsAnalysis of the human osteoarthritis initiative (OAI) dataset was conducted to investigate the MRI subchondral bone features of MetS-human OA participants. Joint phenotype and senescent cells were evaluated in two MetS-OA mouse models: high-fat diet (HFD)-challenged mice and STR/Ort mice. In addition, the molecular mechanisms by which preosteoclasts become senescent as well as how the senescent preosteoclasts impair subchondral bone microenvironment were characterized using in vitro preosteoclast culture system.
ResultsHumans and mice with MetS are more likely to develop osteoarthritis-related subchondral bone alterations than those without MetS. MetS-OA mice exhibited a rapid increase in joint subchondral bone plate and trabecular thickness before articular cartilage degeneration. Subchondral preosteoclasts undergo senescence at the pre- or early-osteoarthritis stage and acquire a unique secretome to stimulate osteoblast differentiation and inhibit osteoclast differentiation. Antagonizing preosteoclast senescence markedly mitigates pathological subchondral alterations and osteoarthritis progression in MetS-OA mice. At the molecular level, preosteoclast secretome activates COX2-PGE2, resulting in stimulated differentiation of osteoblast progenitors for subchondral bone formation. Administration of a selective COX2 inhibitor attenuated subchondral bone alteration and osteoarthritis progression in MetS-OA mice. Longitudinal analyses of the human Osteoarthritis Initiative (OAI) cohort dataset also revealed that COX2 inhibitor use, relative to non-selective nonsteroidal anti-inflammatory drug use, is associated with less progression of osteoarthritis and subchondral bone marrow lesion worsening in participants with MetS-OA.
ConclusionsOur findings suggest a central role of a senescent preosteoclast secretome-COX2/PGE2 axis in the pathogenesis of MetS-OA, in which selective COX2 inhibitors may have disease-modifying potential.
FundingThis work was supported by the National Institutes of Health grant R01AG068226 and R01AG072090 to M.W., R01AR079620 to S.D., and P01AG066603 to X.C. | cell biology |
An endolysosome membrane transformation process for engulfment of autophagosomes independently of ESCRT Endolysosome, usually regarded as the cellular recycling bin, digests materials from multiple origins. The materials from different origins are delivered to endolysosome through the vesicle fusion, kiss-and-run mechanisms, CMA or microautophagy. However, it remains unknown whether endolysosome can receive cargo via other ways. Here, we reported another endolysosomal process for receiving materials. In this, endolysosome receives materials by extending two arms which embraces autophagosomes and engulfs the autophagosomes ultimately, but not via the conventional fusion of autophagosomes with endolysosomes. We named this process as LEA (lysosome eats autophagosome) and the endolysosome arms as LF (endolysosome filopodia) provisionally. The endolysosomes with engulfed autophagosomes (LEA endolysosomes) get more autophagosomes via the fusion with other LEA endolysosomes. The engulfed autophagosomes are labelled by F-actin on their membranes and have ER protein Sec61{beta} and peroxisome protein Pex14 inside their lumens, but mitochondria are excluded outside endolysosome. Our discovery of LEA and LF reveal an unidentified endolysosome transformation process which is responsible for receiving cargoes. | cell biology |
Net-shaped DNA nanostructure designed for rapid/sensitive detection and potential inhibition of SARS-CoV-2 virus We present a net-shaped DNA nanostructure (called "DNA Net" herein) design strategy for selective recognition and high-affinity capture of the intact SARS-CoV-2 virions through spatial pattern-matching and multivalent interactions between the aptamers (targeting wild type spike-RBD) positioned on the DNA Net and the trimeric spike glycoproteins displayed on the viral outer surface. Carrying a designer nanoswitch, the DNA Net-aptamers releases fluorescent signal upon virus binding that is easily read by a hand-held fluorimeter for a rapid (in 10 mins), simple (mix- and-read), sensitive (PCR equivalent), room temperature compatible, and inexpensive ([~] $1.26/test) COVID-19 test assay. The DNA Net-aptamers also impede authentic wild-type SARS-CoV-2 infection in cell culture with a near 1x103-fold enhancement of the monomeric aptamer. Furthermore, our DNA Net design principle and strategy can be customized to tackle other life-threatening and economically influential viruses like influenza and HIV, whose surfaces carry class-I viral envelope glycoproteins like the SARS-CoV-2 spikes in trimeric forms. | bioengineering |
Network Thermodynamics of Biological Systems: A Bond Graph Approach Edmund Crampin (1973-2021) was at the forefront of Systems Biology research and his work will influence the field for years to come. This paper brings together and summarises the seminal work of his group in applying energy-based bond graph methods to biological systems. In particular, this paper: (a) motivates the need to consider energy in modelling biology; (b) introduces bond graphs as a methodology for achieving this; (c) describes extensions to modelling electrochemical transduction; (d) outlines how bond graph models can be constructed in a modular manner and (e) describes stoichiometric approaches to deriving fundamental properties of reaction networks. These concepts are illustrated using a new bond graph model of photosynthesis in chloroplasts. | systems biology |
Temporal and spatial patterns of vertebrate extinctions during the Anthropocene The human-induced annihilation of modern biodiversity is dragging the planet into a mass extinction that has already altered patterns of life globally. Among vertebrates, over 500 species have become extinct or possibly extinct in the last five centuries - an extinction rate that would have taken several millennia without human intervention. Vertebrate extinctions have often been quantified as cumulative counts that reveal sharp increases in losses over time. Here, we quantify global tetrapod extinctions since the 1400s using numbers of species losses across successive and independent time periods until present. Our results reveal that extinctions were low and fundamentally restricted to islands in pre-industrial times, experiencing a significant increase and spread over continental mainland following the onset of the industrial revolution. Recent amphibian extinctions alarmingly exceed the extinctions of all tetrapods, while extinctions of island birds account for a third of all extinctions. Finally, we quantified the relationship between human population growth (HPG, as a proxy for aggregate human effects on the environment) and extinctions between 1800-2000, to then predict that an estimated 838 tetrapod species will go extinct between 2030-2100 based on United Nations HPG projections. These findings further warn humanity about the need to sustainably control HPG and the destructive impacts of rapid environmental change on ecosystems worldwide. | ecology |
The characteristics of high-dark-diversity habitats derived from lidar A key aspect of nature conservation is knowledge of which aspects of nature to conserve or restore to favor the characteristic diversity of plants in a given area. Here, we used a large plant dataset with > 40.000 plots combined with airborne laser scanning (lidar) data to reveal the local characteristics of habitats having a high plant dark diversity - i.e., absence of suitable species - at national extent (> 43.000 km2). Such habitats have potential for reaching high realized diversity levels and hence are important in a conservation context. We calculated 10 different lidar based metrics (both terrain and vegetation structure) and combined these with 7 different field-based measures (soil chemistry and species indicators). We then used Integrated Nested Laplace Approximation for modelling plant dark diversity across 33 North European habitat types (open landscapes and forests) selected by the European communities to be important. In open habitat types high-dark-diversity habitats had relatively low pH, high nitrogen content, tall homogenous vegetation and overall relatively homogenous terrains (high terrain openness) although with a rather high degree of local microtopographical variations. High-dark-diversity habitats in forests had relatively tall vegetation, few natural-forest indicators, low potential solar radiation input and a low cover of small woody plants. Our results highlight important vegetation, terrain and soil related factors that managers and policymakers should be aware of in conservation and restoration projects to ensure a natural plant diversity, for example low nutrient loads, natural microtopography and open forests with old-growth elements such as dead wood and rot attacks. | ecology |
Acoustic cues and season affect mobbing responses in a bird community Heterospecific communication is common for birds when mobbing a predator. However, joining the mob should depend on the number of callers already enrolled, as larger mobs imply lower individual risks for the newcomer. In addition, some community informant species seem more reliable regarding the information transferred in mobbing calls. Birds should therefore rely on both the number of callers and the species identity of the caller(s) when mobbing. Given the large differences in social organization and environment throughout the year in passerine communities, the response to acoustic cues could be impacted by the season. In the present study, we tested the potential interaction between the number of callers, the species identity of the caller (i.e., coal tit or crested tit), and the season on birds mobbing response using a factorial playback experiment. Overall, we found that soundtracks with three callers triggered more mobbing than soundtracks with one caller and that soundtracks with coal tits calls triggered more mobbing than soundtracks with crested tits calls. However, this effect interacted with the season: in spring, only soundtracks with three coal tits triggered a mobbing response. We therefore confirm the hypothesis that birds consider both the species and the number of callers when joining a mobbing chorus. Moreover, our study demonstrates how seasonal context interacts with acoustic cues and illustrates the dynamic properties of heterospecific communication. | ecology |
Parental care allows genetic variation to accumulate by relaxing selection Benign social environments are thought to relax selection against deleterious mutations, enabling them to accumulate in the genome. However, it has not proved straightforward to demonstrate causality in this relationship. We allowed burying beetle populations to evolve with and without the benign effects of parental care for over 20 generations, before inbreeding lineages that were seeded from these experimental populations to expose any differences in their mutation load. We found that inbred lineages with a history of parental care went extinct most quickly, indicating that they harboured more recessive deleterious alleles. | evolutionary biology |
Rapid evolutionary change in trait correlations of a single protein Many organismal traits are genetically determined and covary in evolving populations. The resulting trait correlations can either help or hinder evolvability - the ability to bring forth new and adaptive phenotypes. The evolution of evolvability requires that trait correlations themselves must be able to evolve, but we know little about this ability. To learn more about it, we here study one of the simplest evolvable systems, a gene encoding a single protein, and two traits of this protein, namely the ability to emit yellow and green light. We show that correlations between these two traits can evolve rapidly through both mutation and selection on short evolutionary time scales. In addition, we show that these correlations are driven by a proteins ability to fold, because single mutations that alter foldability can dramatically change trait correlations. Since foldability is important for most proteins and their traits, mutations affecting protein folding may alter trait correlations mediated by many other proteins. Thus, mutations that affect protein foldability may also help shape the correlations of complex traits that are affected by hundreds of proteins. | evolutionary biology |
Loss of CD24 promotes radiation- and chemo-resistance by inducing stemness properties associated with a hybrid E/M state in breast cancer cells There is compelling evidence that cancer stem cells (CSCs) play an essential role in failure of conventional antitumor therapy. In breast cancer, CD24-/low/CD44+ phenotype as well as a high aldehyde dehydrogenase activity (ALDH+) are widely associated with CSC subtypes. Furthermore, CD24-/low/CD44+ pattern is also characteristic of the mesenchymal cells generated by an epithelial-mesenchymal transition (EMT). CD24 is a surface marker expressed in many tumor types, however, its biological functions and role in cancer progression and treatment resistance remain poorly documented. We have previously shown that loss of CD24 expression in breast cancer cells is associated with radiation resistance, in relationship with the control of oxidative stress. Because ROS are known to mediate the effects of anticancer drugs as well as ionizing radiation, we investigated if CD24 could be defined as an actor of both radiation- and chemo-resistance of breast cancer cells. Using the HMLE breast cancer cell model, we observed that loss of CD24 expression induces stemness properties associated with the acquisition of a hybrid E/M phenotype. The CD24-/low cells were intrinsically more resistant than CD24+ cells. The resistance was linked to a lower level of ROS, and CD24 controlled ROS levels through the regulation of mitochondrial functions independently of antioxidant activity. Together, these results suggest a key role of CD24 in de-differentiation process of breast cancer cells, promoting acquisition of therapeutic resistance properties. | cancer biology |
Mechanistic target of rapamycin (mTOR) regulates self-sustained quiescence, tumor indolence and late clinical metastasis in a Beclin-1-dependent manner. Self-sustained quiescence (SSQ) has been characterized as a stable but reversible non-proliferative cellular state that limits the cloning of cultured cancer cells. By developing refined clonogenic assays, we showed here that cancer cells in SSQ can be selected with anticancer agents and that culture at low cell density induced SSQ in pancreas and prostate adenocarcinoma cells. Pre-culture of cells in 3D or their pretreatment with pharmacological inhibitors of mechanistic target of rapamycin (mTOR) synergize with low cell density for induction of SSQ in a Beclin-1-dependent manner. Dissociated pancreatic adenocarcinoma (PAAD) cells rendered defective for SSQ by down-regulating Beclin-1 expression exhibit higher tumor growth rate when injected subcutaneously into mice. Conversely, dissociated PAAD cells in SSQ promote the formation of small indolent tumors that eventually transitioned to a rapid growth phase. Ex vivo clonogenic assays showed that up to 40% of clonogenic cancer cells enzymatically dissociated from resected growing mouse tumors could enter SSQ, suggesting that SSQ could significantly impact the proliferation of cancer cells naturally dispersed from tumors. Remarkably, the kinetics of clinical metastatic recurrence in 124 patients with pancreatic adenocarcinoma included in the TGCA-PAAD project could be predicted from the mRNA levels of Beclin-1 and Cyclin-A2, a marker of both cell proliferation and mTOR complex 1 activity, in their primary tumor. Overall, our data show that SSQ is likely to promote the late development of clinical metastases and provide a rationale for a better selection of patients eligible for intensive adjuvant chemotherapy. Additionally, they suggest that identifying new agents targeting cancer cells in SSQ could help improve patient survival.
SignificanceThis study reveals that a particular state of cancer cell quiescence could largely determine delayed clinical metastasis, challenging current models of cancer cell persistence and offering new avenues for improving adjuvant chemotherapy. | cancer biology |
Hypoxia promotes an inflammatory phenotype of fibroblasts in pancreatic cancer Pancreatic ductal adenocarcinoma (PDAC) is characterized by an extensive fibroinflammatory stroma and often experiences conditions of insufficient oxygen availability, or hypoxia. Cancer-associated fibroblasts (CAF) are a predominant and heterogeneous population of stromal cells within the pancreatic tumor microenvironment. Here, we uncover a previously unrecognized role for hypoxia in driving an inflammatory phenotype in PDAC CAFs. We identify hypoxia as a strong inducer of tumor IL1 expression, which is required for inflammatory CAF (iCAF) formation. Notably, iCAFs preferentially reside in hypoxic regions of PDAC. Our data implicate hypoxia as a critical regulator of CAF heterogeneity in PDAC. | cancer biology |
NPC1 confers metabolic flexibility in Triple Negative Breast Cancer Triple negative breast cancer (TNBC) often undergoes at least partial epithelial-to-mesenchymal transition (EMT) to facilitate metastasis. Identifying EMT-associated characteristics can reveal novel dependencies that may serve as therapeutic vulnerabilities in this aggressive breast cancer subtype. We find that NPC1, which encodes the lysosomal cholesterol transporter Niemann-Pick Type C1 is highly expressed in TNBC as compared to estrogen receptor-positive (ER+) breast cancer and is significantly elevated in high grade disease. We demonstrate that NPC1 is directly targeted by microRNA-200c (miR-200c) a potent suppressor of EMT, providing a mechanism for its differential expression in breast cancer subtypes. Silencing of NPC1 in TNBC causes an accumulation of cholesterol-filled lysosomes and drives decreased growth on soft agar and invasive capacity. Conversely, overexpression of NPC1 in an ER+ cell line increases growth on soft agar. We further identify TNBC cell lines as cholesterol auxotrophs, however, they do not solely depend on NPC1 for adequate cholesterol supply. Genetic inhibition of NPC1 in TNBC cell lines led to altered mitochondrial function and morphology, suppression of mTOR signaling, and accumulation of autophagosomes. A small-molecule inhibitor of NPC1, U18666A, decreased TNBC proliferation and synergized with the chemotherapeutic drug, Paclitaxel. This work suggests that NPC1 promotes aggressive characteristics in TNBC and identifies NPC1 as a potential therapeutic target. | cancer biology |
Extensive patient-to-patient single nuclei transcriptome heterogeneity in pheochromocytomas and paragangliomas Pheochromocytomas (PC) and paragangliomas (PG) are rare neuroendocrine tumors of varied genetic makeup, associated with high cardiovascular morbidity and a variable risk of malignancy. The source of the transcriptional heterogeneity of the disease and the underlying biological processes determining the outcome in PCPG remains largely unclear. We focused on PCPG tumors with germline SDHB and RET mutations, representing distinct prognostic groups with worse or better prognoses, respectively. We applied single-nuclei RNA sequencing (snRNA-seq) on tissue samples from 11 patients and found high patient-to-patient transcriptome heterogeneity of the neuroendocrine tumor cells. The tumor microenvironment also showed heterogeneous profiles mainly contributed by macrophages of the immune cell clusters and Schwann cells of the stroma. Performing non-negative matrix factorization we identified common transcriptional programs active in RET and SDHB as well as distinct modules including neuronal development, hormone synthesis and secretion, and DNA replication. Comparison of the SDHB and RET transcriptomes with that of developmental stages of adrenal gland formation suggests different developmental stages at which PC and PG tumors appear to be arrested. | cancer biology |
Reconstructing the decline of Atlantic Cod with the help of environmental variability in the Scotia Shelf of Canada Ignoring environmental variability can lead to imprecise and inaccurate estimates of abundance and distribution of organisms. Fully embracing environmental variability can improve precision and accuracy of estimates of abundance and distribution, especially when it can be measured with lower costs. Using the example of Atlantic cod in the Scotian Shelf of the northwest Atlantic Ocean, we demonstrate the improved clarity of their historical population trends when such informative features are included. Further, the use of Bayesian spatiotemporal Conditional autoregressive models substantially improves our ability to understand the role of ecosystem variability upon cod, even when samples are incomplete or missing. Finally, by decomposing biomass into number, weight and a Hurdle process to estimate habitat conditions, we can extract much more information on what has occurred in the past and make reasoned inference on processes.
One-Sentence SummaryDeconstructing and reconstructing cod with environmental variability | ecology |
Resetting of H3K4me2 during mammalian parental-to-zygote transition Upon sperm and oocyte fertilization, drastic histone modification reprograming occurs during preimplantation development. However, the global H3K4me2 landscape and its dynamics reprogramming in this period remains largely unknown. Herein we investigate the erasure and re-establishment of H3K4me2 in mouse GV, MII and embryos using an improved approach called Cleavage Under Targets and Release Using Nuclease (CUT&RUN) for histone modification with high-throughput sequencing. We find H3K4me2 extensively exists as a non-canonical pattern in mouse GV oocytes and early embryos. Interestingly, H3K4me2 is erased in MII oocyte and re-established in late 2-cell stage. Importantly, mouse embryos acquire widespread H3K4me2 in CpG-rich and hypomethylated regulatory regions in 4-cell stage, as well as 8-cell stage, but drastic changes happen upon ICM, these CpG-rich H3K4me2 regulatory regions then resolve to either active or repressed states. In summary, our study not only unveil that H3K4me2 transition from parental to zygote, but also provide a H3K4me2 profile during early embryo development, and this will enhance our comprehension to epigenetic reprogramming during mouse early development and in vitro fertilization.
HighlightO_LIH3K4me2 present differential patterns in sperm and oocytes, as no-canonical pattern in GV oocytes but canonical of sperm in mouse.
C_LIO_LIGV H3K4me2 peaks were almost erased in MII oocytes, and reconstructed accompanying ZGA occurred, the first landscape of H3K4me2 during early mammalian development was provided.
C_LIO_LINon-canonical H3K4me2 in mammalian embryos and pervasive H3K4me2 in CpG-rich regulatory regions in 4 and 8-cell embryos.
C_LIO_LICpG-rich H3K4me2 regulatory regions resolve to either active or repressed states in ICM.
C_LI | genetics |
Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians Despite extensive efforts to address it, the vastness of uncharacterized dark matter microbial genetic diversity can impact short-read sequencing based metagenomic studies. Population-specific biases in genomic reference databases can further compound this problem. Leveraging advances in long-read and Hi-C technologies, we deeply characterized 109 gut microbiomes from three ethnicities in Singapore to comprehensively reconstruct 4,497 medium and high-quality metagenome assembled genomes, 1,708 of which were missing in short-read only analysis and with >28x N50 improvement. Species-level clustering identified 70 (>10% of total) novel gut species out of 685, improved reference genomes for 363 species (53% of total), and discovered 3,413 strains that are unique to these populations. Among the top 10 most abundant gut bacteria in our study, one of the species and >80% of all strains were not represented in existing databases. Annotation of biosynthetic gene clusters (BGCs) uncovered more than 27,000 BGCs with a large fraction (36-88%) not represented in current databases, and with several unique clusters predicted to produce bacteriocins that could significantly alter microbiome community structure. These results reveal the significant uncharacterized gut microbial diversity in Southeast Asian populations and highlight the utility of hybrid metagenomic references for bioprospecting and disease-focused studies. | genomics |
Autonomous untethered microinjectors for gastrointestinal delivery of insulin The delivery of macromolecular drugs via the gastrointestinal (GI) tract is challenging. Macromolecular drugs display low stability and poor absorption across the intestinal epithelium. While permeation-enhancing drug delivery methods can increase the bioavailability of low molecular weight drugs, the effective delivery of high molecular weight drugs across the tight epithelial cell junctions remains a formidable challenge. Here, we describe autonomous microinjectors that can efficiently penetrate the GI mucosa and deliver insulin systemically. In addition, we performed in vitro studies to characterize insulin release and the penetration capacity of microinjectors and measure in vivo release of insulin in live rats. We found that the microinjectors administered within the luminal GI tract could deliver insulin trans-mucosally to the systemic circulation at similar levels to intravenously administered insulin. Due to their small size, tunability in sizing and dosing, wafer-scale fabrication, and parallel, autonomous operation, we anticipate that these novel microinjectors could significantly advance drug delivery across the GI tract mucosa to the systemic circulation. | bioengineering |
A Self-Healing, Viscoelastic Hydrogel Promotes Healing of Brain Lesions Brain lesions can arise from traumatic brain injury, infection, and craniotomy. Although injectable hydrogels show promise for promoting healing of lesions and health of surrounding tissue, enabling cellular ingrowth and restoring neural tissue continue to be challenging. We hypothesized that these challenges arise in part from viscoelastic mismatch between the hydrogel and the brain parenchyma, and tested this hypothesis by developing and evaluating a self-healing hydrogel that mimicked both the composition and viscoelasticity of native brain parenchyma. The hydrogel was crosslinked by dynamic boronate ester bonds between phenylboronic acid grafted hyaluronic acid (HA-PBA) and dopamine grafted gelatin (Gel-Dopa). This HA-PBA/Gel-Dopa hydrogel could be injected into a lesion cavity in a shear-thinning manner with rapid hemostasis, high tissue adhesion and efficient self-healing. We tested this in an in vivo mouse model of brain lesions and found the hydrogel to support neural cell infiltration, decrease astrogliosis and glial scars, and close the lesions. The results suggest a role for viscoelasticity in brain lesion healing, and motivate additional experimentation in larger animals as the technology progresses towards potential application in humans. | bioengineering |
Single-cell genomic analysis of triple-negative breast cancer fibroblasts uncovers evolutionarily conserved features and potential therapeutic targets To explore cancer associated fibroblasts (CAFs) in triple-negative breast cancers (TNBC), we performed scRNA-seq analysis of fibroblasts from murine and human TNBCs. We observed three distinct CAF subtypes in mouse TNBC: two that are intermingled and adjacent to tumor cells, and one that is more distal. We present evidence that progression of CAFs from normal resident fibroblasts/pericytes involves upregulation of their Pdgf and Tgfb receptors along with reciprocal ligand upregulation in other cells within the tumor microenvironment. Additionally, extracellular matrix, glycolytic, and mitochondrial respiratory genes are strongly upregulated in all CAFs. Activation of extracellular matrix genes specifically in CAFs and not in normal fibroblasts provides numerous targets for CAF-based therapeutics, many of which are conserved in CAFs from human TNBC. In contrast, the subtype structure of CAFs was less conserved, which along with their transcriptional heterogeneity suggests that molecular targeting of CAFs is more practical than targeting CAF subtypes. | cancer biology |
Design and validation of the first family of photo-activatable ligands for melatonin receptors Melatonin is a neurohormone released in a circadian manner with peak levels during the night. In mammals, melatonin mediates its effects mainly through G protein-coupled MT1 and MT2 receptors. Drugs acting on melatonin receptors are indicated for circadian rhythm- and sleep-related disorders and major depression. Pharmacological tools to study the activation of these receptors with high temporal resolution are lacking. Here, we synthesized a family of light-activatable caged melatonin compounds by covalently attaching o-nitrobenzyl (o-NB) or coumarin photocleavable groups to the N-position of melatonin. All caged compounds showed the expected decrease in binding affinity for MT1 and MT2. Among them, the o-NB derivative MCS-0382 showed the best uncaging and biological properties upon light activation with a significant increase (2.5 log left-shift) in affinity and potency in melatonin receptor binding and signaling, respectively. Generation of biologically active melatonin from MCS-0382 was further demonstrated by its ability to modulate the excitation of SCN neurons in rat brain slices. MCS-0382 is now available to study melatonin effects in a temporally controlled manner in cellular and physiological settings. | pharmacology and toxicology |
A new, Critically Endangered species of Impatiens (Balsaminaceae) from the coastal plain of the Republic of Congo Impatiens moutsambotei is described from a herbarium specimen collected at a waterfall in forest on the coastal plain, below the Mayombe Mts of the Republic of Congo. Sharing many distinctive characters with Impatiens floretii of the Doudou Mts of Gabon, it is abundantly distinguished inter alia by the leaf-blades which are lanceolate or narrowly elliptic, not ovate, their bases acute, not obtuse or broadly rounded to truncate; the reduced, peduncular bracts bearing long, filiform setae, and not entire; the proximal (upper) of the lateral united petals are entire, not bifid; the spur is curved at the base and overlaps the lower sepal, not curved through its length to describe a semi-circle and held below the lower sepal. Both species are placed in the Impatiens macroptera species aggregate. Impatiens moutsambotei is known from a single site, where it was collected nearly 30 years ago and not seen since. The new species is assessed as Critically Endangered due to threats of habitat clearance from mining and road widening, and may be already be extinct. | plant biology |
Generating variability from motor primitives during infant locomotor development Motor variability is a fundamental feature of developing systems allowing motor exploration and learning. In human infants, leg movements involve a small number of basic coordination patterns called locomotor primitives, but whether and when motor variability could emerge from these primitives remains unknown. Here we longitudinally followed 10 neonates ([~]4 days old) until walking onset ([~]14 months old) and recorded the activity of their leg muscles during locomotor or rhythmic movements. Using unsupervised machine learning, we show that the structure of trial-to-trial variability changes during early development. In the neonatal period, infants own a minimal number of motor primitives but generate a maximal motor variability across trials thanks to variable activations of these primitives. A few months later, toddlers generate significantly less variability despite the existence of more primitives, due to more regularity within their activation. These results suggest that human neonates initiate motor exploration as soon as birth by variably activating a few basic locomotor primitives that later fraction and become more consistently activated by the motor system. | neuroscience |
Get the gist of the story: Neural map of topic keywords in multi-speaker environment Neural representation of lexico-semantics in speech processing has been revealed in recent years. However, to date, how the brain makes sense of the higher-level semantic gist (topic keywords) of a continuous speech remains mysterious. Capitalizing on a generative probabilistic topic modelling algorithm on speech materials to which participants listened while their brain activities were recorded by Magnetoencephalography (MEG), here we show spatio-temporal neural representation of topic keywords in a multi-speaker environment where task-relevant (attended) and -irrelevant (unattended) speech co-exits. We report the difference of neural representation between salient and less salient semantic gist of both attended and unattended speech. Moreover, we show that greater sensitivity to semantically salient unattended speech in the left auditory and motor cortices negatively mediates attended speech comprehension. | neuroscience |
Sigh breathing rhythm depends on intracellular calcium oscillations in a population of inspiratory rhythmogenic preBötzinger complex neurons in mice The preBotzinger Complex (preBotC) of the lower brainstem generates two breathing-related rhythms: one for inspiration on a timescale of seconds and another that produces larger amplitude sighs on the order of minutes. Their underlying mechanisms and cellular origins remain incompletely understood. We resolve these problems via a joint experiment and modeling approach. Blocking purinergic gliotransmission does not perturb either rhythm and imaging experiments show that both rhythms emanate from the same glutamatergic neuron population. We hypothesized that these two disparate rhythms emerge in tandem wherein recurrent excitation gives rise to inspiratory rhythm while a calcium oscillator generates sighs; there is no obligatory role for gliotransmission, hyperpolarization activated mixed cationic current (Ih) in neurons, or synaptic inhibition-mediated coupling of separate populations. We developed a mathematical model that instantiates our working hypothesis. Tests of model predictions validate the single-population rhythmogenic framework, reproducing disparate breathing-related frequencies and the ability for inspiratory and sigh rhythms to be separately regulated in support of respiration under a wide array of conditions. Here we show how a single neuron population exploits two cellular tool-kits: one involving voltage-dependent membrane properties and synaptic excitation for inspiratory breathing (eupnea) and an intracellular biochemical oscillator for sighs, which ventilate and maintain optimal function in the compliant mammalian lung.
SIGNIFICANCE STATEMENTBreathing consists of two vital rhythms: one for eupnea that serves periodic physiological gas exchange and the other for sighs, which are larger breaths that occur minutes apart and serve to optimize pulmonary function. These rhythms with disparate frequencies emerge via a mechanism that is simpler than previously envisaged: it results from one neuron population (not two as previously thought) without need for gliotransmission or synaptic inhibition-mediated coupling of neuronal populations. We show that a low-frequency intracellular calcium oscillation underlies sighs and functions in parallel with the higher-frequency voltage-dependent network oscillation that drives eupnea. Exploiting two separate cellular tool kits enables quasi-independent breathing rhythms, which are unique features of breathing in mammals with compliant lungs. | neuroscience |
Hierarchical cue control of drug seeking in the face of cost Addiction is characterized by intermittent drug seeking despite rising costs. This behavior is heavily influenced by environmental stimuli that signal drug availability and reinforce seeking. We aimed to establish the relationship between three key aspects of human drug use in rats: the intermittent, binge nature of drug intake, the motivational conflict of drug seeking in the face of escalating negative costs, and the ability of different drug cues to interact to modulate relapse. Rats were trained to self administer cocaine on an intermittent access schedule, where brief drug availability states were signaled by a shift in the ambient lighting of the environment and cocaine delivery was signaled by a separate proximal cue. Rats then went through a conflict procedure, where foot shock intensity associated with cocaine seeking was escalated until intake was suppressed. We completed relapse tests where the drug delivery cue was non contingently presented alone, or in the context of dynamic drug availability state transitions. Intermittent access spurred psychomotor sensitization and binge-like cocaine intake. The intensity of binge-like drug taking during training was predictive of later drug seeking despite escalating costs. In relapse tests, the ability of a proximal drug cue to trigger relapse was gated by the presence of a global cue signaling drug-availability state transitions. Our results suggest that the pattern of drug intake plays a role in many features of addiction, including modifying an individuals willingness to endure high costs associated with drug seeking. Further, our results indicate that drug-related sensory information can be hierarchically organized to exert a dynamic modulating influence on drug-seeking motivation. | neuroscience |
The ventral striatum contributes to energy balance Obesity-related pathologies and anorexia nervosa are increasingly considered as opposite ends of eating disorders (ED) spectrum. Accordingly, accumulating evidence points to opposite dysregulations of common brain systems in these pathologies, the Nucleus Accumbens (NAc) in particular. However, to which extent alterations in NAc activity are sufficient to elicit ED-like behavioral dimensions remains to be established. Using acute, bidirectional, chemogenetic modulation of each NAc medium spiny neuron (MSN) subpopulation, we found that D1-MSNs and D2-MSNs oppositely regulate the balance between food intake and exercise-induced energy expenditure. As opposed to the limited effect of repeated chemogenetic manipulations of each MSN subpopulation, the concomitant manipulation of both MSN subpopulation had sustained effects. Repeated activation of D1-MSNs combined with repeated inhibition of D2-MSNs biased behavior toward activity-related energy expenditure leading to weight/fat loss, whilst the opposite manipulations favored energy intake and hence weight/fat gain. These results suggest that dysregulations of NAc dopaminoceptive MSN network might be at the core of EDs. | neuroscience |
A Multidimensional Approach to Understanding the Emergence of Sex Differences in Internalizing Symptoms in Adolescence Women are more vulnerable to internalizing disorders (e.g., depression and anxiety). This study took an integrative, developmental approach to investigate multidimensional factors associated with the emergence of sex differences in internalizing symptoms, using data from the Adolescent Brain Cognitive Development (ABCD) study. Indices of sex hormone levels (dehydroepiandrosterone, testosterone, and estradiol), physical pubertal development, task-based functional brain activity, family conflict, and internalizing symptoms were drawn from the ABCD studys baseline sample (9-to 10-year-old; N = 11,844). Principal component analysis served as a data-driven dimensionality reduction technique on the internalizing subscales to yield a single robust measure of internalizing symptoms. Moderated mediation analyses assessed whether associations between known risk factors and internalizing symptoms vary by sex. Results revealed direct and indirect effects of physical pubertal development on internalizing symptoms through family conflict across sexes. No effects were found of sex hormone levels or amygdala response to fearful faces on internalizing symptoms. Females did not report overall greater internalizing symptoms relative to males, suggesting that internalizing symptoms have not yet begun to increase in females at this age. Findings provide an essential baseline for future longitudinal research on the endocrine, neurocognitive, and psychosocial factors associated with sex differences in internalizing symptoms. | neuroscience |
STEREOLOGICAL EVALUATION OF TISSUE PRESERVATION AFTERNEUROPROTECTIVE TREATMENTS FOR TRAUMATIC SPINAL CORDINJURY Spinal cord injury (SCI) is a major cause of permanent disability and its causes and pathophysiological effects are very variables between patients. The assessment of tissue damage extent and neurodegeneration degree correlated with the functional evaluation are the most accepted tools to diagnose and prognose the trauma severity. Animal models of SCI have been used for treatment development and in the present work we evaluate the potency of stereological tools to estimate damage degree for a diagnostic of neural degeneration and locomotor and sensorial disability after SCI and the efficacy of different types of therapeutic strategies. | neuroscience |
Lymph node-targeted vaccine boosting of TCR-T cell therapy enhances anti-tumor 1 function and eradicates solid tumors While T cell receptor (TCR)-modified T cell therapies have shown promise against solid tumors, overall therapeutic benefits in clinical practice have been modest due in part to suboptimal T cell persistence and activation in vivo, alongside the possibility of tumor antigen escape. In this study, we demonstrate an approach to enhance the in vivo persistence and activation of TCR-T cells through combination with Amphiphile (AMP)-vaccination including cognate TCR-T peptides. AMP-modification improves lymph node targeting of conjugated tumor immunogens and adjuvants, thereby coordinating a robust T cell-priming endogenous immune response. Vaccine combination with TCR-T cell therapy provided simultaneous in vivo invigoration of adoptively transferred TCR-T cells and in situ priming of the endogenous anti-tumor T cell repertoire. The resulting induction of an adoptive and endogenous anti-tumor effect led to durable responses in established murine solid tumors refractory to TCR-T cell monotherapy. Protection against recurrence was associated with antigen spreading to additional tumor-associated antigens not targeted by vaccination. Enhanced anti-tumor efficacy was further correlated with pro-inflammatory lymph node transcriptional reprogramming and increased antigen presenting cell maturation, resulting in TCR-T cell expansion and functional enhancement in lymph nodes and solid tumor parenchyma without lymphodepletion. In vitro evaluation of AMP-peptides with matched human TCR-T cells targeting NY-ESO-1, mutant KRAS, and HPV16 E7 illustrated the clinical potential of AMP-vaccination to enhance human TCR-T cell proliferation, activation, and anti-tumor activity. Taken together, these studies provide rationale and evidence to support clinical evaluation of the combination of AMP-vaccination with TCR-T cell therapies to augment anti-tumor activity.
SummaryAMP-vaccination targets the lymph nodes to enhance TCR-T cell therapy resulting in solid tumor eradication and durable protection against recurrence. | immunology |
Mechanical forces impair antigen discrimination by reducing differences in T cell receptor off-rates T cells use their T cell receptors (TCRs) to discriminate between lower-affinity self and higher-affinity foreign peptide major-histocompatibility-complexes (pMHCs) based on the TCR/pMHC off-rate. It is now appreciated that T cells generate mechanical forces during this process but how force impacts the TCR/pMHC off-rate remains unclear. Here, we measured the effect of mechanical force on the off-rate of multiple TCR/pMHC interactions. Unexpectedly, we found that lower-affinity pMHCs with faster solution off-rates were more resistant to mechanical force (weak slip or catch bonds) than higher-affinity interactions (strong slip bonds), and this was confirmed by molecular dynamic simulations. Consistent with these findings, we show that the best characterized catch-bond, involving the OT-I TCR, has a low affinity and an exceptionally fast solution off-rate. Our findings imply that reducing forces on the TCR/pMHC interaction improves antigen discrimination and we suggest this new force-shielding role for the adhesion receptors CD2 and LFA-1.
One sentence summaryMechanical forces disproportionately accelerate the off-rates of higher-affinity antigens reducing T cell antigen discrimination | immunology |
Measurement of Accumulation of Small Molecules into Gram-negative Bacteria Some of the most dangerous bacterial pathogens (Gram-negative and mycobacteria) deploy a formidable secondary membrane barrier to reduce the influx of exogenous molecules. For Gram-negative bacteria, this second exterior membrane is known as the Outer Membrane (OM) and its unique composition is generally what restricts the passive permeation of small molecules into bacterial cells. While it is well appreciated that the OM is a principal determinant of small molecule permeation, it has proven to be challenging to assess this feature in a robust and quantitative way. Herein, we describe the development of the Bacterial Chloro-Alkane Penetration Assay (BaCAPA), which employs the use of a genetically encoded protein called HaloTag, to measure the uptake and accumulation of molecules into Gram-negative bacteria. Directing the localization of the HaloTag protein to either the cytoplasm or periplasm of Escherichia coli (E. coli) enabled a compartmental analysis of permeation across individual cell membranes. Significantly, we also showed that BaCAPA can be used to analyze the permeation of molecules within the phagocytes of macrophages, which may prove critical in the analysis of intracellular pathogens. Together, our results show that BaCAPA can effectively report on the accumulation of molecules into bacterial cells and we anticipate that this will widen the set of tools available to generally measure permeability into bacterial cells. | microbiology |
The Ndc80-Cdt1-Ska1 complex constitute a minimal processive kinetochore-microtubule coupling unit The Ndc80 kinetochore complex is essential for robust kinetochore-microtubule (k-MT) attachments during mitosis. Ndc80 has been shown to recruit the Ska1 complex to kinetochores, where Ska1 is thought to aid in k-MT coupling by Ndc80. Our previous work has shown that Cdt1, a DNA replication licensing factor, is a novel mitotic spindle-associated protein that is also recruited to kinetochores via Ndc80 and is required for stabilizing k-MT attachments. In this study, we developed auxin-induced degron (AID)-tagging to validate the previously demonstrated mitotic role of Cdt1. We demonstrate a direct interaction between Cdt1 and Ska1 that is essential for proper recruitment of Cdt1 to kinetochores and spindle microtubules. We find that Cdk1dependent phosphorylation of Cdt1 during mitosis is critical for Ska1-binding, consequently regulating the stabilization of metaphase k-MT attachments and normal mitotic progression. Total internal reflection fluorescence microscopy (TIR-FM) experiments reveal that Cdt1 synergizes with the Ndc80 and the Ska1 complexes for microtubule-binding. Further, we show that single Cdt1 molecules form diffusive tripartite complexes with Ndc80 and Ska1 that can processively track the ends of dynamic microtubules in vitro. Taken together our data identifies a minimal molecular unit responsible for bidirectional processive tip tracking of kinetochores. | cell biology |
GliaMorph: A modular image analysis toolkit to quantify Müller glial cell morphology Cell morphology is critical for all cell functions. This is particularly true for glial cells as they rely on their complex shape to contact and support neurons. However, methods to quantify complex glial cell shape accurately and reproducibly are lacking. To address this gap in quantification approaches, we developed an analysis pipeline called "GliaMorph". GliaMorph is a modular image analysis toolkit developed to perform (i) image pre-processing, (ii) semi-automatic region-of-interest (ROI) selection, (iii) apicobasal texture analysis, (iv) glia segmentation, and (v) cell feature quantification. Muller Glia (MG) are the principal retinal glial cell type with a stereotypic shape linked to their maturation and physiological status. We here characterized MG on three levels, including (a) global image-level, (b) apicobasal texture, and (c) apicobasal vertical-to-horizontal alignment. Using GliaMorph, we show structural changes occurring in the developing retina. Additionally, we study the loss of cadherin2 in the zebrafish retina, as well as a glaucoma mouse disease model. The GliaMorph toolkit enables an in-depth understanding of MG morphology in the developing and diseased retina.
Graphical Abstract
O_FIG O_LINKSMALLFIG WIDTH=144 HEIGHT=200 SRC="FIGDIR/small/490765v1_ufig1.gif" ALT="Figure 1">
View larger version (73K):
[email protected]@5c54b4org.highwire.dtl.DTLVardef@1bd3221org.highwire.dtl.DTLVardef@2628e8_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIGlial morphology is complex, making it challenging to accurately quantify 3D cell shape.
C_LIO_LIWe developed the GliaMorph toolkit for image pre-processing, glial segmentation, and quantification of Muller glial cells.
C_LIO_LIMuller glia elaborate their morphology and rearrange subcellular features during embryonic development.
C_LIO_LIGliaMorph accurately identifies subcellular changes in models with disrupted glia cells, including zebrafish cadherin2 loss of function and a mouse glaucoma model.
C_LI | developmental biology |
Maintenance of neurotransmitter identity by Hox proteins through a homeostatic mechanism Hox transcription factors play fundamental roles during early patterning, but they are also expressed continuously - from embryo through adulthood - in the nervous system. The functional significance of their sustained expression remains unclear. In C. elegans motor neurons (MNs), we find that LIN-39 (Scr/Dfd/Hox4-5) is continuously required during post-embryonic life to maintain neurotransmitter identity, a core element of neuronal function. LIN-39 acts directly to co-regulate genes that define cholinergic identity (e.g., unc-17/VAChT, cho-1/ChT). We further show that LIN-39, MAB-5 (Antp/Hox6-8) and the transcription factor UNC-3 (Collier/Ebf) operate in a positive feedforward loop to ensure continuous and robust expression of cholinergic identity genes. Finally, we identify a two-component, design principle (Hox transcriptional autoregulation counterbalanced by negative UNC-3 feedback) for homeostatic control of Hox gene expression in adult MNs. These findings uncover a noncanonical role for Hox proteins during post-embryonic life, critically broadening their functional repertoire from early patterning to the control of neurotransmitter identity. | developmental biology |
RanBP1 plays an essential role in directed migration of neural crest cells during development. Collective cell migration is essential for embryonic development, tissue regeneration and repair, and has been implicated in pathological conditions such as cancer metastasis. It is, in part, directed by external cues that promote front-to-rear polarity in individual cells. However, our understanding of the pathways that underpin the directional movement of cells in response to external cues remains incomplete. To examine this issue we made use of neural crest cells (NC), which migrate as a collective during development to generate vital structures including bones and cartilage. Using a candidate approach, we found an essential role for Ran-binding protein 1 (RanBP1), a key effector of the nucleocytoplasmic transport pathway, in enabling directed migration of these cells. Our results indicate that RanBP1 is required for establishing front-to-rear polarity, so that NCs are able to chemotax. Moreover, our work suggests that RanBP1 function in chemotaxis involves the polarity kinase LKB1/PAR4. We envisage that regulated nuclear export of LKB1 through Ran/RanBP1 is a key regulatory step required for establishing front-to-rear polarity and thus chemotaxis, during NC collective migration. | developmental biology |
Tbx2 is essential for cochlear inner hair cell development and regeneration Atoh1 is essential for the development of outer hair cells (OHCs) and inner hair cells (IHCs) in the mammalian cochlea. Whereas Ikzf2 is necessary for OHC development, the key gene for IHC development remains unknown. We found that deleting Tbx2 in neonatal IHCs led to their trans-differentiation into OHCs, by repressing 26.7% of IHC and inducing 56.3% of OHC genes, including Ikzf2. More importantly, persistent expression of Tbx2 together with transient Atoh1 effectively reprogramed non-sensory supporting cells into new IHCs expressing functional IHC marker vGlut3. The differentiation status of these new IHCs is much more advanced than those previously reported. Thus, Tbx2 is essential for IHC development, and its co-upregulation with Atoh1 in supporting cells represents a new approach for treating IHC degeneration-related deafness. | developmental biology |
Failure of digit tip regeneration in the absence of <Lmx1b> suggests Lmx1b functions disparate from dorsoventral polarity Mammalian digit tip regeneration is linked to the presence of nail tissue, but a nail-explicit model is missing. Here, we report that nail-less double-ventral digits of {Delta}LARM1/2 mutants that lack limb-specific Lmx1b enhancers fail to regenerate. To separate the nails effect from the lack of DV polarity, we also interrogate double-dorsal double-nail digits and show that they regenerate. Thus, DV polarity is not a prerequisite for regeneration and the nail requirement is supported. Transcriptomic comparison between wild-type and non-regenerative{Delta} LARM1/2 mutant blastemas reveals differential up-regulation of vascularization and connective tissue functional signatures in wild-type versus upregulation of inflammation in the mutant. These results, together with the finding of uniform Lmx1b expression in the wild-type blastema and in the dorsal dermis underneath the nail, indicate that, in addition of the nails effect, a direct role for Lmx1b in driving the progression of digit tip regeneration is likely. | developmental biology |
Soil microbe-induced plant resistance alters aphid inter-genotypic competition leading to rapid evolution with consequences for plant growth and aphid abundance O_LIPlants and insect herbivores are two of the most diverse multicellular groups in the world, and both are strongly influenced by interactions with the belowground soil microbiome. Effects of reciprocal rapid evolution on ecological interactions between herbivores and plants have been repeatedly demonstrated, but it is unknown if (and how) the soil microbiome could mediate these eco-evolutionary processes.
C_LIO_LIWe tested the role of a plant-beneficial soil bacterium (Acidovorax radicis) in altering eco-evolutionary interactions between sap-feeding aphid herbivores (Sitobion avenae) feeding on barley (Hordeum vulgare). We reared two aphid genotypes separately or together on three barley varieties that were inoculated with or without A. radicis bacteria. In the first experiment we counted the aphid number and plant biomass after 7, 14 and 21 days of aphid growth, while in a second experiment we counted and removed offspring every 1-2 days to assess aphid longevity and fecundity.
C_LIO_LIResults showed that A. radicis increased plant growth and suppressed aphids of both genotypes. The strength of effect was dependent on aphid genotype and barley variety, while the direction of effect was altered by aphid population mixture. Fescue aphids experienced increased growth when they were sharing the plant with Sickte aphids on inoculated plants; this increase was not seen in the control plants without A. radicis and was only apparent after 14 days of aphid population growth.
C_LIO_LIPlant inoculation with A. radicis reduced aphid survival (reduced number of reproductive days) and fecundity (reduced daily reproductive output for surviving aphids). In the second experiment, when density was controlled, Fescue aphids did not experience increased reproduction in mixed populations, suggesting this is a density-dependent effect. Using Lotka-Volterra modelling, we demonstrated that A. radicis inoculation decreased aphid population stability as it increased inter-genotype competition but decreased the intra-genotype competition (likely through reduced population density).
C_LIO_LIOur work demonstrates the important role that plant-associated microbiomes can have in mediating eco-evolutionary interactions between herbivores and host plants.
C_LI | ecology |
A quantitative eDNA-based method to monitor fish spawning in lakes: application to European perch and whitefish There is an urgent need to evaluate the effects of anthropogenic pressures and climatic change on fish populations dynamics. When monitored in lakes, the spawning of fish is generally assessed using traditional, mostly destructive or damaging, methods as gillnetting and collection of fertilized eggs.
Over the last decade, environmental DNA (eDNA) based methods have been widely developed for the detection of aquatic species, offering a non-invasive alternative method to conventional biomonitoring tools. In particular, the emergence of new methods as the droplet digital PCR (ddPCR) offer the possibility to quantify an absolute eDNA signal in a very sensitive way and at a low cost.
Here, we developed and implemented a quantitative eDNA method to monitor the spawning activity of two fish species, European perch and whitefish. ddPCR protocols were formalized based on existing and newly designed COI primers, and were applied during four spawning periods in lake Geneva.
The results demonstrate the efficiency of eDNA coupled with ddPCR to identify the timing and duration of the spawning periods, as well as the peak of the spawning activity for the targeted species. In addition, the use of a control species (i.e., quantification of the eDNA signal of a fish that does not reproduce during the monitoring period) was shown to be relevant to clearly discriminate fluctuations of the eDNA signal associated to the spawning activity from the baseline eDNA signal. For future implementation, we recommend using an integrative sampling strategy (e.g., pooled samples for a give station) to smooth the local variability of the eDNA signal. These results show that we reached an operational level to use these non-invasive eDNA methods to monitor the spawning periods of these two fish species in large lakes. | ecology |
Bayesian prediction of multivariate ecology from phenotypic data yields novel insights into the diets of extant and extinct taxa Morphology often relates to ecology in a well-defined manner, enabling prediction of ecological roles for taxa that lack direct observations, such a fossils. Diet is a particularly important component of a species ecology. However, in order to predict diet it must first be codified, and establishing metrics that effectively summarize dietary variability without excessive information loss remains challenging. We employed a dietary item relative importance coding scheme to derive multivariate dietary classifications for a sample of extant carnivoran mammals, and then used Bayesian multilevel modeling to assess whether these scores could be predicted from a set of dental metrics, with body size as a covariate. There is no "one size fits all" model for predicting dietary item importance; different topographical features best predict different foods at different body sizes, and model-averaged estimates perform especially well. We show how models derived from living taxa can be used to provide novel insights into the dietary diversity of extinct carnivoran species. Our approach need not be limited to diet as an ecological trait of interest, to these phenotypic traits, or to carnivorans. Rather, this framework serves as a general approach to predicting multivariate ecology from phenotypic traits. | evolutionary biology |
Limiting distribution of X-chromosomal coalescence times under first-cousin consanguineous mating By providing additional opportunities for coalescence within families, the presence of consanguineous unions in a population reduces coalescence times relative to non-consanguineous populations. First-cousin consanguinity can take one of six forms differing in the configuration of sexes in the pedigree of the male and female cousins who join in a consanguineous union: patrilateral parallel, patrilateral cross, matrilateral parallel, matrilateral cross, bilateral parallel, and bilateral cross. Considering populations with each of the six types of first-cousin consanguinity individually and a population with a mixture of the four unilateral types, we examine coalescent models of consanguinity. We previously computed, for first-cousin consanguinity models, the mean coalescence time for X-chromosomal loci and the limiting distribution of coalescence times for autosomal loci. Here, we use the separation-of-time-scales approach to obtain the limiting distribution of coalescence times for X-chromosomal loci. This limiting distribution has an instantaneous coalescence probability that depends on the probability that a union is consanguineous; lineages that do not coalesce instantaneously coalesce according to an exponential distribution. We study the effects on the coalescence time distribution of the type of first-cousin consanguinity, showing that patrilateral-parallel and patrilateral-cross consanguinity have no effect on X-chromosomal coalescence time distributions and that matrilateral-parallel consanguinity decreases coalescence times to a greater extent than does matrilateral-cross consanguinity. | genetics |
Temporal analysis suggests a reciprocal relationship between 3D chromatin structure and transcription To infer potential causal relationships between 3D chromatin structure, enhancers, and gene transcription, we mapped each feature in a genome-wide fashion across eight narrowly-spaced timepoints of macrophage activation. Enhancers and genes connected by loops exhibited stronger correlations between histone H3K27 acetylation and expression than can be explained by genomic distance or physical proximity alone. Changes in acetylation at looped distal enhancers preceded changes in gene expression. Changes in gene expression exhibit a directional bias at differential loop anchors; gained loops are associated with increased expression of genes oriented away from the center of the loop, while lost loops were often accompanied by high levels of transcription with the loop boundaries themselves. Taken together, these results are consistent with a reciprocal relationship in which loops can facilitate increased transcription by connecting promoters to distal enhancers while high levels of transcription can impede loop formation.
HIGHLIGHTSO_LILPS + IFN{gamma} triggers genome-wide changes in chromatin looping, enhancer acetylation, and gene expression
C_LIO_LILooped enhancer-promoter pairs exhibit ordered and correlated changes in acetylation and expression
C_LIO_LIChanges in gene expression exhibit a directional bias at differential loop anchors
C_LIO_LILost loops are associated with high levels of transcription within loop boundaries
C_LI | genomics |
Differential regulation of mRNA stability modulates transcriptional memory and facilitates environmental adaptation Transcriptional memory, by which cells respond faster to repeated stimuli, is key for cellular adaptation and organism survival. Factors related to chromatin organization and activation of transcription have been shown to play a role in the faster response of those cells previously exposed to a stimulus (primed). However, the contribution of post-transcriptional regulation is not yet explored. Here, combining flow cytometry and high throughput sequencing, we perform a genome-wide screen to identify novel factors modulating transcriptional memory in S. cerevisiae in response to galactose nutrition sources. In addition to the well-known chromatin factors modulating transcriptional memory, we find that depletion of the nuclear RNA exosome increases GAL1 expression in primed cells. We perform a genome-wide characterisation of this process and show that changes in nuclear surveillance factor association can enhance both gene induction and repression in primed cells. Finally, we show that in addition to nuclear mRNA degradation, differences in cytoplasmic mRNA decay also modulate transcriptional memory and contribute to faster gene expression remodelling in primed cells. Our results demonstrate that mRNA post-transcriptional regulation, and not only transcription regulation, should be considered when investigating gene expression memory. | genomics |
Generalisation of early learned tutor song preferences in female zebra finches (Taeniopygia guttata) Song learning is a prime example for a culturally transmitted mating signal. Local or individual song variants are socially learned early in life and adults sing and prefer these songs. An unresolved issue in this context is the question of how learned preferences for specific variants generalise to songs sufficiently similar to the original model. Here we asked whether female zebra finches would generalise early learned song preferences along a similarity gradient based on syllables sharing between test and tutor songs. For each female, this gradient consisted of their tutors (fathers) song (F), two variants of unfamiliar songs edited to share 2/3 (F2/3) and 1/3 (F1/3) of syllables with fathers song and an unfamiliar song (UF). Females preferences were measured in a 4-way operant choice arena where the birds could perch on different operant perches to trigger playbacks of the four different songs. Number and duration of perch visits were positively associated with the number of syllables that the assigned stimuli shared with fathers songs. These results suggest that female zebra finches generalise early learned song preferences to songs sharing syllables (and/or voice characteristics) with songs learned early in life. | animal behavior and cognition |
The iron-sulfur cluster is critical for DNA binding by human DNA polymerase ϵ DNA polymerase {varepsilon} (Pol{varepsilon}) is a key enzyme for DNA replication in eukaryotes. It is attached to a helicase and performs DNA synthesis on the leading strand. Recently it was shown that the catalytic domain of yeast Pol{varepsilon} (Pol{varepsilon}CD) contains a [4Fe-4S] cluster located at the base of the processivity domain (P-domain) and coordinated by four conserved cysteines. In this work, we have shown that human Pol{varepsilon}CD (hPol{varepsilon}CD) expressed in bacterial cells also contains an iron-sulfur cluster. In comparison, recombinant hPol{varepsilon}CD produced in insect cells contains an eight-fold-lower level of iron. Interestingly, the iron content correlates with the level of DNA-binding molecules, which suggests an important role of the iron-sulfur cluster in hPol{varepsilon} interaction with DNA. Indeed, mutation of two conserved cysteines that coordinate the cluster abolished template:primer binding and, therefore, DNA polymerase and proofreading exonuclease activities. We propose that the cluster regulates the conformation of the P-domain, which, like a gatekeeper, controls access to a DNA-binding cleft for a template:primer. In addition, we performed kinetic and binding studies of hPol{varepsilon}CD. The binding studies demonstrated low affinity of hPol{varepsilon}CD to DNA and a strong effect of salt concentration on stability of the hPol{varepsilon}CD/DNA complex. Pre-steady-state kinetic studies have shown a maximal polymerization rate constant of 51.5 s-1 and a relatively low affinity to incoming dNTP with an apparent KD of 105 M. This work provides notable insight into the role of a [4Fe-4S] cluster in Pol{varepsilon} function. | biochemistry |
A microfluidic droplet array demonstrating high-throughput screening in individual lipid-producing microalgae Microalgae are a group of photoautotrophic microorganisms which could use carbon dioxide for autosynthesis. They have been envisioned as one of the most prospective feedstock for renewable oil. However, great endeavors will still be needed to increase their economic feasibility; the screening of competitive species and suitable culture conditions are such issues. To greatly accelerate these rather laborious steps and also improve their experimental lump-sum-manner, we developed a microfluidic droplet-based 2x103 resolution "identification card", which allowed high throughput real-time monitoring of individual algae among population. A novel fluid-blocking-based droplet generating and trapping performance were integrated in the platform which made it excellent in operational simplicity, rapidity and stability and full of the potentials in single-cell-isolation/screening. The developed platform was successfully used to screen three unicellular algae, namely, Isochrysis zhanjiangensis, Platymonas subcordiformis and Platymonas helgolandica var. tsingtaoensis. In situ bioassays of the lipid accumulation and cell proliferation at single cell level for interspecies comparison were possible. Nitrogen stress condition can be indentified that induce positive-skewed frequency distribution of lipid content. | bioengineering |
SOPHIE: viral outbreak investigation and transmission history reconstruction in a joint phylogenetic and network theory framework Genomic epidemiology is now widely used for viral outbreak investigations. Still, this methodology faces many challenges. First, few methods account for intra-host viral diversity. Second, maximum parsimony principle continues to be employed, even though maximum likelihood or Bayesian models are usually more consistent. Third, many methods utilize case-specific data, such as sampling times or infection exposure intervals. This impedes study of persistent infections in vulnerable groups, where such information has a limited use. Finally, most methods implicitly assume that transmission events are independent, while common source outbreaks violate this assumption.
We propose a maximum likelihood framework SOPHIE (SOcial and PHilogenetic Investigation of Epidemics) based on integration of phylogenetic and random graph models. It infers transmission networks from viral phylogenies and expected properties of inter-host social networks modelled as random graphs with given expected degree distributions. SOPHIE is scalable, accounts for intra-host diversity and accurately infers transmissions without case-specific epidemiological data. SOPHIE code is freely available at https://github.com/compbel/SOPHIE/ | bioinformatics |
MobsPy: A Meta-Species Language for Chemical Reaction Networks Chemical reaction networks are widely used to model biochemical systems. However, when the complexity of these systems increases, the chemical reaction networks are prone to errors in the initial modeling and subsequent updates of the model.
We present the Meta-species-oriented Biochemical Systems Language (MobsPy), a language designed to simplify the definition of chemical reaction networks in Python. MobsPy is built around the notion of meta-species, which are sets of species that can be multiplied to create higher-dimensional orthogonal characteristics spaces and inheritance of reactions. Reactions can modify these characteristics. For reactants, queries allow to select a subset from a meta-species and use them in a reaction. For products, queries specify the dimensions in which a modification occurs. We demonstrate the simplification capabilities of the MobsPy language at the hand of a running example and a circuit from literature. The MobsPy Python package includes functions to perform both deterministic and stochastic simulations, as well as easily configurable plotting. The MobsPy package is indexed in the Python Package Index and can thus be installed via pip. | bioinformatics |
Physical limits to acceleration of chemical reactions inside phase-separated compartments We present a theoretical analysis of phase separated compartments as a means to facilitate chemical reactions. We find that the attractive interactions that concentrate reactants within the dense phase inhibit reactions by lowering the chemical potential and mobility of the reactants. Therefore, condensed phases are only beneficial if mobility in the condensed phase can be maintained. This can be achieved in multi-step reactions, where the proximity between enzymatic steps results in higher efficiency with less unreacted substrate, but does not increase the reaction rate. Alternatively, mobility can be maintained if recruitment to the condensed phase is driven by multiple attractive moieties that can bind and release independently. However, the spacers necessary to ensure independence between stickers are prone to entangle with the dense phase scaffold. We find an optimal sticker affinity that balances the need for rapid binding/unbinding kinetics and minimal entanglement. Reaction rates can be accelerated by shrinking the size of the dense phase with a corresponding increase in the number of stickers to enhance recruitment. | biophysics |
Insights into Long-term Acclimation Strategies of Grapevines in Response to Multi-decadal Cyclical Drought The Australian wine industry is currently under pressure to sustain its profitability due to climate change. Therefore, there is a pressing need to explore grapevine genetic diversity and identify superior clones with improved drought resistance. We previously characterised more than 15,000 dry-farmed (for over 65 years) Cabernet Sauvignon clones in a vineyard and identified three drought-tolerant (DT) clones, which can maintain significantly higher intrinsic water use efficiency (WUEi) under limited soil moisture than drought-sensitive (DS) clones. To understand whether DT clones grown under multi-decadal cyclical drought can prime their vegetatively-propagated clonal progenies for future drought events, in this study, all DT and DS vegetative progenies were propagated with commercial clones in the glasshouse. Their physiological and molecular responses were investigated under well-watered and two recurrent drought (D1 and D2) conditions. We observed that concentration of a natural priming agent, {gamma}-amino butyric acid (GABA), were significantly higher in all DT progenies relative to other progenies under drought. Both commercial and DT progenies exhibited improved gas exchange, photosynthetic performance and WUEi under recurrent drought events relative to DS progenies. Our results suggest that DT progenies have adapted to be in a "primed state" to withstand future drought events. | physiology |
Lipodystrophy can be uncoupled from detrimental metabolic consequences SUMMARYAdipose tissue has at least two major functions: storing metabolic energy as triacylglycerols (TG) and coordinating metabolism by secreting hormones, such as leptin. In lipodystrophies, defects of storing TG are typically accompanied by metabolic abnormalities, such as hepatic steatosis, and endocrine perturbations. Thus, the concept emerged that the endocrine function of adipose tissue is coordinated with, and requires, TG stores. To test this notion, we selectively depleted adipose TG stores by deleting the TG synthesis enzymes, DGAT1 and DGAT2, in murine adipose tissue (ADGAT DKO mice). Despite markedly reduced TG storage, ADGAT DKO mice maintained ample adipose tissue endocrine function and surprisingly did not develop metabolic perturbations, even when fed a high-fat diet, owing to increased energy expenditure and beiging of white adipose tissue. These findings, thus, reveal that adipose tissue performs TG storage and endocrine functions largely independently from each other. | physiology |
A Versatile Enhanced Freeze-Substitution Protocol for Volume Electron Microscopy Volume electron microscopy, a powerful approach to generate large three-dimensional cell and tissue volumes at electron microscopy resolutions, is rapidly becoming a routine tool for understanding fundamental and applied biological questions. One of the enabling factors for its adoption has been the development of conventional fixation protocols with improved heavy metal staining. However, freeze-substitution with organic solvent-based fixation and staining has not realized the same level of benefit. Here, we report a straightforward approach including 2% osmium tetroxide, acetone and up to 3% water substitution fluid (compatible with traditional or fast freeze-substitution protocols), warm-up and transition from organic solvent to aqueous 2% OsO4. Once fully hydrated, samples were processed in aqueous based potassium ferrocyanide, thiocarbohydrazide, osmium tetroxide, uranyl acetate and lead acetate before resin infiltration and polymerization. We observed a consistent and substantial increase in heavy metal staining across diverse and difficult-to-fix test organisms and tissue types, including plant tissues, nematodes, yeast, and bacteria. Our approach opens new possibilities to combine the benefits of cryo-preservation with enhanced contrast for volume electron microscopy in diverse organisms. | plant biology |
Sucrose rather than GA transported by AtSWEET13 and AtSWEET14 supports pollen fitness at late anther development stages SummaryO_LIBoth sugar and hormone gibberellin (GA) are essential for anther-enclosed pollen development and thus for plant productivity in flowering plants. Arabidopsis (Arabidopsis thaliana) AtSWEET13 and AtSWEET14, which are expressed in anthers and associated with seed yield, transport both sucrose and GA. However, it is still unclear which substrate transported by them directly affects anther development and seed yield.
C_LIO_LIHistochemical staining, cross-sectioning and microscopy imaging techniques were used to investigate and interpret the phenotypes of AtSWEET13 and AtSWEET14 double mutant during anther development. Genetic complementation of atsweet13;14 using AtSWEET9 that transports sucrose but not GA was conducted to test the substrate preference relevant to the biological process.
C_LIO_LIThe loss of AtSWEET13 and AtSWEET14 resulted in reduced pollen viability and therefore decreased pollen germination. AtSWEET9 fully rescued
C_LIO_LIthe defects in pollen fertility of atsweet13;14, indicating AtSWEET13/14 mediated sucrose rather than GA is essential to pollen fertility.
C_LIO_LIAtSWEET13 and AtSWEET14 mainly function at the anther wall during late anther development stages and are likely responsible for sucrose efflux into locules to support pollen development to maturation, which is vital for subsequent pollen viability and germination.
C_LI | plant biology |
Dynamic regulation of neural variability during working memory reflects dopamine, functional integration, and decision-making The regulation of moment-to-moment neural variability may permit effective responses to changing cognitive demands. However, the mechanisms that support variability regulation are unknown. In the context of working memory, we leverage the largest available PET and fMRI dataset to jointly consider three lenses through which neural variability regulation could be understood: dopamine capacity, network-level functional integration, and flexible decision processes. We show that with greater working memory load, upregulation of variability was associated with elevated dopamine capacity and heightened functional integration, effects dominantly expressed in the striato-thalamic system rather than cortex. Strikingly, behavioral modeling revealed that working memory load evoked substantial decision biases during evidence accumulation, and those who jointly expressed a more optimal decision bias and higher dopamine capacity were most likely to upregulate striato-thalamic variability under load. We argue that the ability to align striato-thalamic variability to level of demand may be a hallmark of a well-functioning brain. | neuroscience |
Periodic Time Cells in Human Entorhinal Cortex The representation of time in the brain is a fundamental component of cognition. Here we investigated how the human brain represents time during a temporally continuous uninterrupted experience by presenting fifteen neurosurgical patients with an audiovisual video while recording neurons activity from multiple brain regions. We report on a set of units that modulate their activity in a strikingly periodic manner across different timescales--from seconds to many minutes. These cells were most prevalent in the entorhinal cortex and time could be decoded from their population activity. Furthermore, these cells remapped their dominant periodicity to shorter timescales during a subsequent recognition memory task. When the audiovisual sequence was presented at two different speeds (regular and faster), a significant percentage of these periodic time cells (PTCs) maintained their timescales, suggesting a degree of invariance with respect to the narrative content. The temporal periodicity of PTCs may complement the spatial periodicity of grid cells, thereby providing scalable spatiotemporal metrics for encoding and retrieval of human experience. | neuroscience |
Developmental dynamics of the postsynaptic proteome to understand synaptic maturation and dysmaturation The postsynaptic density (PSD) is a protein condensate composed of [~]1,000 proteins beneath the postsynaptic membrane of excitatory synapses. The number, shape, and plasticity of synapses are altered during development. However, the dynamics of synaptic protein composition across development have not been fully understood. Here we show alterations of PSD protein composition in mouse and primate brains during development. Proteins involved in synapse regulation are enriched in the differentially expressed (288 decreased and 267 increased) proteins on mouse PSD after a 2-week-old. We find that the changes in PSD protein abundance in mouse brains correlate with gene expression levels in postnatal mice and perinatal primates. This alteration of PSD composition is likely to be defective in the brains of mouse models or patients with autism spectrum disorder (ASD). Finally, we demonstrate that the brain of the common marmoset (Callithrix jacchus) changes PSD composition after the juvenile period. The alteration of PSD composition after 2-month-old is distinct from that observed in mice. Our results provide a comprehensive architecture of the remodeling of PSD composition across development, which may explain the molecular basics of synapse maturation and the pathology of psychiatric disorders, such as ASD. | neuroscience |
Spinal cord extracts from sporadic ALS induce and propagate TDP-43 pathology in cerebral organoids Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder caused by progressive loss of motor neurons and there is currently no effective therapy. Cytoplasmic mislocalization and aggregation of TAR DNA-binding protein 43 kDa (TDP-43) within the CNS is a pathological hallmark in sporadic ALS and prion-like propagation of pathogenic TDP-43 is thought to be implicated in disease progression. However, cell-to-cell transmission of pathogenic TDP-43 in the human CNS has not been confirmed experimentally.
Here we used induced pluripotent stem cells (iPSCs)-derived cerebral organoids as recipient CNS tissue model that are anatomically relevant human brain. We injected postmortem spinal cord protein extracts individually from three non-ALS or five sporadic ALS patients containing pathogenic TDP-43 into the cerebral organoids to validate the templated propagation and spreading of TDP-43 pathology in human CNS tissue.
We first demonstrated that the administration of spinal cord extracts from an ALS patient induced the formation of TDP-43 pathology that progressively spread in a time-dependent manner in cerebral organoids, suggesting that pathogenic TDP-43 from ALS functioned as seeds and propagated cell-to-cell to form de novo TDP-43 pathology. We also reported that the administration of ALS patient-derived protein extracts caused astrocyte proliferation to form astrogliosis in cerebral organoids, reproducing the pathological feature seen in ALS. Moreover, we showed pathogenic TDP-43 induced cellular apoptosis and that TDP-43 pathology correlated with genomic damage due to DNA double-strand breaks.
Thus, our results provide evidence that patient-derived pathogenic TDP-43 can mimic the prion-like propagation of TDP-43 pathology in human CNS tissue. Our findings indicate that our assays with human cerebral organoids that replicate ALS pathophysiology have a promising strategy for creating readouts that could be used in future drug discovery efforts against ALS. | neuroscience |
Interacting cortical gradients of neural timescales and functional connectivity and their relationship to perceptual behavior Cognitive acts take place over a large range of temporal scales. Numerous corresponding gradients in neurodynamic timescales and long-range cortical interactions are believed to provide organizational constraints to the brain and influence neural populations' roles in cognition. However, it is unclear if gradients in various types of neural timescales and functional connectivity arise from related or distinct neurophysiological processes and if they influence behavior. Here, intracranial recordings from 4,090 electrode contacts in 35 individuals were used to systematically map gradients of multiple aspects of neurodynamics, neural timescales, and functional connectivity, and assess their interactions along category-selective ventral temporal cortex. Opposing functional connectivity gradients, with decreasing connectivity to visually responsive regions and increasing connectivity to regions that were not visually responsive, were observed along the ventral visual hierarchy. Endogenous neural timescales were correlated with functional connectivity to visually responsive regions after removing the effects of shared anatomical gradients, suggesting that these properties influence one another. Different stimulus evoked and endogenous timescales exhibited gradients with longer dynamics along the ventral visual hierarchy, but none of these timescales were significantly correlated with one another. This suggests that local neural timescales depend on neural and cognitive context and different timescales may arise through distinct neurophysiological processes. Furthermore, activity from neural populations with faster endogenous timescales and stronger functional connectivity to visually responsive regions was more predictive of perceptual behavior during a visual repeat detection task. These results reveal interrelationships and key distinctions among neural timescale and functional connectivity gradients that together can influence behavior. | neuroscience |
The modulation of acute stress on Model-Free and Model-Based reinforcement learning in Gambling Disorder Background and aimsExperiencing acute stress is common in behavioral addictions such as gambling disorder. Additionally, like most substance-induced addictions, aberrant decision-making wherein a reactive habit-induced response (conceptualized as a Model-free [MF] in reinforcement learning) suppresses a flexible goal-directed response (conceptualized as a Model-based [MB]) is also common in gambling disorder. In the current study we investigated the influence of acute stress on the balance between habitual response and the goal-directed system.
MethodsA sample of N = 116 pathological gamblers (PG) and healthy controls (HC) performed an acute stress task - the Socially Evaluated Cold pressure task (SECPT) - or a control task. Self-reported stress and salivary cortisol were collected as measures of acute stress. Following the SECPT, participants performed the Two-Step Markov Task to account for the relative contribution of MB and MF strategies. Additionally, verbal working-memory and IQ measures were collected to account for their mediating effects on the orchestration between MB/MF and the impact of stress.
ResultsBoth groups had comparable baseline and stress-induced cortisol response to the SECPT. Non-stressed PG displayed lower MB learning than HC. MANOVA and regression analyses showed a deleterious effect of stress-induced cortisol response on the orchestration between MB and MF learning in HC but not in PG. Neither working memory nor IQ mediated these effects.
Discussion and ConclusionsDespite normal cortisol response to stress, we found an abnormal pattern of modulation of stress on the orchestration between MB and MF learning among PG. | neuroscience |
TMEM106B is increased in Multiple Sclerosis plaques, and deletion causes accumulation of lipid after demyelination During inflammatory, demyelinating diseases such as multiple sclerosis (MS) axonal damage is prevalent early in the disease course. Axonal damage includes swellings, defects in transport, and failure to clear damaged intracellular proteins, all of which affect recovery and compromise the integrity of neurons and remyelination. Autophagy and the clearance of damaged cell components by the proteasome are important for the maintenance of normal cellular turnover; and the restoration of cellular homeostasis. The gradual accumulation of insoluble proteins in the brain is known to impair recovery from several neurodegenerative diseases. In this study, we used mass spectrometry to identify insoluble proteins within high-speed, mercaptoethanol/sarcosyl-insoluble pellets from purified white matter plaques isolated from the brains of individuals with MS. We determined that insoluble transmembrane protein106B (TMEM106B), expressed in neurons and glia and normally lysosomal-associated, is increased in MS plaques relative to normal-appearing white matter from individuals with Alzheimers disease and non-neurologic controls. We found that decreased TMEM106B protein in mice results in significant axonal damage and lipid droplet accumulation in the spinal cord following chronic myelin oligodendrocyte glycoprotein-induced experimental autoimmune encephalomyelitis. When TMEM106Bt/t mice were treated with cuprizone to experimentally induce demyelination, a significant increase in lipid deposition was observed in the corpus callosum of TMEM106Bt/t mice post-cuprizone withdrawal. Our study shows that the brain and spinal cord from challenged TMEM106Bt/t mice accumulate OilRedO+/Perilipin2+ lipid droplets. We postulate that increased insolubility of TMEM106B in MS plaques limits debris clearance by the lysosome which over time contributes to failed remyelination and axonal defects.
Abbreviated AbstractTransmembrane protein106B (TMEM106B), a lysosome-associated protein, is significantly less soluble in multiple sclerosis plaques than in white matter controls. Decreased TMEM106B produces significant axonal damage and lipid accumulation in mouse models of demyelinating diseases. TMEM106B insolubility and likely loss of function may limit lysosome transport and contribute to CNS pathology. | neuroscience |
Pathophysiology of Dyt1 dystonia is mediated by spinal cord dysfunction Dystonia, a neurological disorder defined by abnormal postures and disorganised movements, is thought to be a neural circuit disorder with dysfunction arising within and between multiple brain regions. Given that spinal circuits are the de facto final common pathway for motor control, we sought to determine their contribution to the movement disorder. We confined a dystonia-related mutation to the spinal cord, which led to behavioural and physiological recapitulation of a severe form of inherited, early-onset, generalised dystonia. These data challenge our current understanding of dystonia, and lead to broader insights into spinal cord function and its involvement in movement disorder pathophysiology.
One sentence summarySpinal Tor1a deletion causes severe early onset generalised dystonia, exposing spinal circuitopathy as a key factor in its pathophysiology. | neuroscience |
Manipulating the rapid consolidation periods in a learning task affects general skills more than statistical learning Memory consolidation processes have always been thought to cover up extended periods and have traditionally been investigated from the perspective of hours or days. However, the latest developments in memory research showed that memory stabilization processes could occur even within seconds. Here, we investigate this rapid form of consolidation during statistical learning. We aim to answer (a) whether this rapid offline improvement occurs in implicit statistical learning and general skill learning and (b) whether the duration of rest periods affects these two learning types differently. Participants performed a widely used statistical learning task - the Alternating Serial Reaction Time (ASRT) task - that enables us to measure implicit statistical and general skill learning separately. The ASRT task consisted of 25 learning blocks with a rest period between the blocks. In a between-subjects design, the length of the rest periods was fixed at 15 or 30 seconds, or the participants could control the length themselves. We found that the duration of rest periods does not affect the acquisition of statistical knowledge, but they do change the dynamics of learning in a way that learning is more likely to occur online in the case of certain fixed breaks. Moreover, we found weaker general skill learning in the self-paced group than in the fixed rest period groups (i.e., 15 and 30-second breaks). These results suggest that distinct learning processes are differently affected by the duration of short rest periods. | neuroscience |
Inter-scanner brain MRI volumetric biases persist even in a harmonized multi-subject study of multiple sclerosis Background/PurposeMulticenter study designs involving a variety of MRI scanners have become increasingly common. However, these present the issue of biases in image-based measures due to scanner or site differences. To assess these biases, we imaged 11 volunteers with multiple sclerosis (MS) with scan and rescan data at 4 sites.
Materials and MethodsImages were acquired on Siemens or Philips scanners at 3-tesla. Automated white matter lesion detection and whole brain, gray and white matter, and thalamic volumetry were performed, as well as expert manual delineations of T1 and T2 (FLAIR) lesions. Random effect and permutation-based nonparametric modeling was performed to assess differences in estimated volumes within and across sites.
ResultsRandom effect modeling demonstrated model assumption violations for most comparisons of interest. Non-parametric modeling indicated that site explained > 50% of the variation for most estimated volumes. This expanded to > 75% when data from both Siemens and Philips scanners were included. Permutation tests revealed significant differences between average inter- and intra-scanner differences in most estimated brain volumes (P < .05). The automatic activation of spine coil elements during some acquisitions resulted in a shading artifact in these images. Permutation tests revealed significant differences between thalamic volume measurements from acquisitions with and without this artifact.
ConclusionDifferences in brain volumetry persisted across MR scanners despite protocol harmonization. These differences were not well explained by variance component modeling; however, statistical innovations for mitigating inter-scanner differences show promise in reducing biases in multi-center studies of MS. | neuroscience |
Feature-space selection with banded ridge regression Encoding models provide a powerful framework to identify the information represented in brain recordings. In this framework, a stimulus representation is expressed as a feature space and is used in a regularized linear regression to predict brain activity. To account for a potential complementarity of different feature spaces, a joint model is fit on multiple feature spaces simultaneously. To adapt regularization strength to each feature space, ridge regression is extended to banded ridge regression, which optimizes a different regularization hyperparameter per feature space. The present paper proposes a method to decompose over feature spaces the variance explained by a banded ridge regression model. It also describes how banded ridge regression performs a feature-space selection, effectively ignoring non-predictive and redundant feature spaces. This feature-space selection leads to better prediction accuracy and to better interpretability. Banded ridge regression is then mathematically linked to a number of other regression methods with similar feature-space selection mechanisms. Finally, several methods are proposed to address the computational challenge of fitting banded ridge regressions on large numbers of voxels and feature spaces. All implementations are released in an open-source Python package called Himalaya. | neuroscience |
Multicomponent Pseudomonas aeruginosa vaccines eliciting Th17 cells and functional antibody responses confer enhanced protection against experimental acute pneumonia in mice The Gram-negative pathogen Pseudomonas aeruginosa is a common cause of pneumonia in hospitalized patients. Its increasing antibiotic resistance and widespread occurrence present a pressing need for vaccines. We previously showed that a P. aeruginosa type III secretion system protein, PopB elicits a strong Th17 response in mice after intranasal (IN) immunization and confers antibody-independent protection against pneumonia in mice. In the current study, we evaluated the immunogenicity and protective efficacy in mice of the combination of PopB (purified with its chaperone protein PcrH) and OprF/I, an outer membrane hybrid fusion protein, compared to immunization with the proteins individually either by the intranasal (IN) or subcutaneous (SC) routes. Our results show that after vaccination, a Th17 recall response from splenocytes was detected only in mice vaccinated with PopB/PcrH, either alone or in combination with OprF/I. Mice that were immunized with the combination of PopB/PcrH and OprF/I had enhanced protection in an acute lethal P. aeruginosa pneumonia model, regardless of vaccine route, compared to the mice vaccinated the with either alone or adjuvant control. Immunization generated IgG titers against the vaccine proteins and whole P. aeruginosa cells. Interestingly, none of these antisera had opsonophagocytic killing activity, but antisera from mice immunized with vaccines containing OprF/I had the ability to block IFN-{gamma} binding to OprF/I, a known virulence mechanism. Hence, vaccines combining PopB/PcrH with OprF/I that elicit functional antibodies lead to a broadly and potently protective vaccine against P. aeruginosa pulmonary infections. | immunology |
Non-invasive Fluorescence Imaging of Gut Commensal Bacteria in Live Mice In mammals, gut commensal microbiota interact extensively with the host and the same interactions can be dysregulated in diseased states. The development of methods to monitor gut microbiota in vivo can lead to improved foundational understanding of the biological events underpinning these interactions. The current standard for non-invasive monitoring of gut bacteria entails classification by 16S rRNA sequencing from fecal samples. This method has many advantages but also has serious limitations, especially for monitoring dynamic changes in the gut of live animals. In recent years, several imaging techniques have been widely adopted that afford non-invasive assessment of animal subjects - most notably in cancer biology; however, these technical gains have not translated to the imaging of gut bacterial communities. Herein, we describe a method to non-invasively image commensal bacteria based on the specific metabolic labeling of bacterial cell walls to illuminate the gut bacteria of live mice. This tagging strategy may additionally provide unprecedented insight into cell wall turnover of gut commensals, which has implications for bacterial cellular growth and division, in a live animal. | microbiology |
The microtubule minus end-binding protein CAMSAP2 does not regulate microtubule dynamics in primary pancreatic β-cells but facilitates insulin secretion Glucose stimulation induces the remodeling of microtubules in Islet {beta}-cells to potentiate glucose-stimulated insulin secretion. CAMSAP2 is a microtubule minus-end binding protein and is reported to stabilize and position microtubules in several non-{beta}-cells, such as human retinal pigment epithelium cells. In immortalized insulinoma MIN6 cells, CAMSAP2 binds to and forms short stretches at microtubule minus ends in the cytoplasm, which is consistent with the reported subcellular localization and functions of CAMSAP2 in non-{beta}-cells. Surprisingly, we found that CAMSAP2 expressed in primary islet {beta}-cells does not form short stretches in the cytoplasm, but instead is localized to the Golgi apparatus. This novel localization is specific to {beta}-but not -cells in islets and it is independent of MT-binding. Knockdown of CAMSAP2 by shRNA impairs Golgi-ER trafficking, reduces total insulin content, and attenuates GSIS without affecting the MT dynamics or releasability of insulin granules in islet {beta}-cells. Corresponding to these results, we found that primary islets and MIN6 cells express different CAMSAP2 isoforms. We propose that primary islet {beta} cells use a novel CAMSAP2 isoform for a MT-independent non-canonical function, which is to promote Golgi-ER trafficking that supports efficient production of insulin secretory granules. | cell biology |
Testicular macrophages are recruited during a narrow time window by fetal Sertoli cells to promote organ-specific developmental functions While macrophages are most commonly known for their roles in innate immunity, a growing body of evidence supports the idea that fetal-derived tissue-resident macrophages play developmental roles during organogenesis. In the testis, it has long been proposed that macrophages are important players in steroidogenesis and other testicular functions, but which macrophage populations are involved is unclear. We previously showed that macrophages play critical roles in fetal testis morphogenesis and reported the presence of 2 unique adult testicular macrophage populations, interstitial and peritubular. There has been some debate regarding the hematopoietic origins of testicular macrophages and whether distinct macrophage populations promote specific testicular functions. Here we have undertaken an extensive lineage-tracing study of mouse hematopoietic cells. We found that, while yolk-sac-derived macrophages comprise the earliest testicular macrophages, fetal hematopoietic stem cells (HSCs) give rise to monocytes that colonize the gonad during a narrow time window in mid-gestation, after which time HSCs no longer contribute to testicular macrophages. These long-lived monocytes, over the course of fetal and postnatal life, differentiate into testicular macrophages. Our data indicate that Sertoli cells, and not germ cells, are required for recruitment of immune cells and peritubular macrophage differentiation. Finally, we show that yolk-sac-derived macrophages and HSC-derived macrophages play distinct roles in testis cord morphogenesis, whereas interstitial macrophages promote adult Leydig cell proliferation and steroid production. Overall, our findings offer clarity regarding the origins of testicular macrophages and provide insight into the diversity of their tissue-specific developmental roles. | developmental biology |
Field margins as substitute habitat for the conservation of birds in agricultural wetlands Breeding birds in agricultural landscapes have declined considerably since the 1950s and the beginning of agricultural intensification in Europe. Given the increasing pressure on agricultural land, it is necessary to identify conservation measures that consume little productive land. We tested the hypothesis that field margins represent substitute habitats for bird species in agricultural wetlands. We monitored bird species in 86 crop fields in rice paddy landscapes of Camargue (southern France), a wetland of international importance for birds. We investigated whether the area of three types of field margins (grass strips, hedgerows and reed strips) within a 500 m buffer around each studied crop field had an effect on the abundance of three groups of birds defined based on their primary habitat (reedbeds, grasslands, and forest edge species). We controlled for the area of each semi-natural habitat (wetlands, grasslands, and woodlands), crop diversity and mean crop field size. Our study confirms that bird guilds are favored by the cover of their primary habitat but are also influenced by the cover of field margins. Reedbed birds are favored by the cover of wetlands and reed strips, grassland birds are favored by the cover of grasslands and wetlands and negatively impacted by the cover of woodlands and hedgerows, while forest edge birds are favored by the cover of hedgerows and negatively impacted by the cover of reed strips. These results suggest that field margins may represent substitute habitats for reedbed and forest edge bird species and highlight their importance for biodiversity conservation in wetland agricultural landscapes. However, our results also suggest that increasing the area of hedgerows and reed strips may have a negative effect on grassland birds and forest edge birds, respectively. Recommendations for field margin management in agricultural wetlands should therefore be tailored to local conservation priorities. | ecology |
Association of variants in ACE, ACTN3, AGT, IL6 and BDKRB2 genes with athlete status and playing position in Colombian amateur rugby athletes Genetic polymorphisms are involved in different metabolic pathways that are manifested at the physiological level and have been associated with specific phenotypes in sport from anthropometric and functional characterizations that pose conditional and physiological demands for the rugby athlete. The identification of this type of polymorphisms in athletes represents a resource that contributes significantly to the processes of training, selection and sports orientation.
The purpose of this study was to describe type and frequencies of allelic and genotypic variants in ACTN3, ACE, AGT, BDRKB2 and IL6 genes in sub elite rugby athletes in Colombia. Additionally, the polymorphisms found were compared with a control population, as well as contrasted according to playing position backs and forwards.
In this research, 47 individuals from the Vallecaucana rugby league and 67 from a control group (non-athletes) were sampled. All were analyzed for polymorphisms in the ACE, AGT, ACTN3, IL6 and BDKRB2 genes, using the PCR RFLPs technique. The significance of the differences between the experimental and control groups was tested by the X2 test (p <0.05).
In rugby athletes we found a higher frequency of allele D (0.883) ACE gene, allele R (0.63) ACTN3 gene, allele G (0.819) IL6 gene, all associated with strength and power sports. There are significant genotypic differences between athletes and the control population in all the genes analyzed and significant allelic differences in the ACE, ACTN3, BDRKB2 and IL6 genes. When comparing the playing positions (backs vs. forwards), significant genotypic differences were observed in the ACTN3, BDRKB2, AGT and IL6 genes. At the allelic level, the R and X alleles of the ACTN3 gene and the I allele of the ACE gene show significant differences.
In conclusion, in the polymorphisms analyzed, an association with strength sports, explosive strength and rugby is observed. Significant genotypic and allelic differences were also recorded between the backs and forwards positions, as well as significant differences in the allelic and genotypic structure between the group of athletes and the control population. | genetics |
Optical mapping compendium of structural variants across global cattle breeds Structural variants (SV) have been linked to several important bovine disease phenotypes, but due to the difficulty of their accurate detection with standard sequencing approaches, their role in shaping economically important traits across global cattle breeds is largely unexplored. Optical mapping is an alternative approach for mapping SVs that has been shown to have higher sensitivity than DNA sequencing approaches. The aim of this project was to use optical mapping to develop a high quality database of structural variation across cattle breeds from different geographical regions and origins, to enable further studies of the important roles of SV in cattle.
To do this we generated 100X Bionano optical mapping data for 18 cattle of nine different ancestries, three continents and covering both major cattle lineages. In total we identified 13,457 SVs, of which 1,200 putatively overlap a coding region. This resource therefore provides a high-quality set of optical mapping-based SV calls that can be used across studies, from validating DNA sequencing based SV calls to prioritising candidate functional variants in genetic association studies and expanding our understanding of the role of SVs in the evolution of cattle. | genomics |
Promiscuous feeding across multiple honey bee hosts amplifies the vectorial capacity of Varroa destructor Varroa destructor is a cosmopolitan pest and leading cause of colony loss of the European honey bee. Historically described as a competent vector of honey bee viruses, this arthropod vector is cause for the global pandemic of Deformed wing virus, now endemic in honeybee populations. Our work shows viral spread is driven by Varroa actively switching from one adult bee to another as they feed. Assays using fluorescent microspheres were used to show the movement of fluids in both directions between host and vector when Varroa feed. Therefore, Varroa could be in either an infectious or naive state dependent upon the disease status of their host. We tested this and confirm that the relative risk of a Varroa feeding was dependent on the infectiousness of their previous host. Varroa exhibit remarkable heterogeneity in their host switching behavior, with some Varroa switching infrequently while others switch at least daily. As a result, relatively few of the most active Varroa parasitize the majority of bees. This multiple feeding behavior has analogs in vectorial capacity models of other systems, where promiscuous feeding by individual vectors is a leading driver of vectorial capacity. We propose that the honeybee-Varroa relationship offers a unique opportunity to apply principles of vectorial capacity to a social organism, as virus transmission is both vectored and occurs through multiple host-to-host routes common to a crowded society. | animal behavior and cognition |
Structure and mechanism of a novel cytomegaloviral DCAF mediating interferon antagonism Human cytomegalovirus (CMV) is a highly relevant pathogen, and its rodent counterparts serve as common infection models. Global proteome profiling of rat CMV-infected cells uncovered a pronounced loss of the transcription factor STAT2, which is crucial for interferon signalling. Deletion mutagenesis documented that STAT2 is targeted by the viral protein E27. Cellular and in vitro analyses showed that E27 exploits host-derived Cullin4-RING ubiquitin ligases (CRL4) to induce poly-ubiquitylation and proteasomal degradation of STAT2. Cryo-electron microscopic structure determination revealed how E27 mimics molecular surface properties of cellular CRL4 substrate receptors (DDB1- and Cullin4-associated factors, DCAFs) to displace them from the CRL4 catalytic core. Moreover, structural analyses elucidated the mechanism of STAT2 recruitment and indicate that E27-binding additionally disturbs STAT2 activation by occupying the IRF9 binding interface. For the first time, these data provide structural insights into cytomegalovirus-encoded interferon antagonism and establish an atomic model for STAT2 counteraction by CRL4 misappropriation with important implications for viral immune evasion. | biochemistry |
Gaining insight into the allometric scaling of trees by utilizing 3d reconstructed tree models - a SimpleForest study Forestry utilizes volume predictor functions utilizing as input the diameter at breast height. Some of those functions take the power form Y = a * Xb. In fact this function is fundamental for the biology field of allometric scaling theories founded round about a century ago. The theory describes the relationships between organs/body parts and the complete body of organisms.
With digital methods we can generate 3d forest point clouds non destructively in short time frames. SimpleForest is one free available tool which generates fully automated ground and tree models from high resoluted forest plots. Generated topological ordered cylinder models are called commonly QSMs.
We use SimpleForest QSMs an build a function which estimates the total supported wood volume at any given point of the tree. As input we use the supported soft wood volume for those query points. Instead of measuring directly the soft wood volume we use as a proxy the number of supported twigs. We argue with the pipe model theory for the correctness of the proxy.
We can use the named relationship to also filter our QSMs made of an open data set of tree clouds. The filter corrects overestimated radii. And we compare the corrected QSM volume against the harvested reference data for 66 felled trees. We also found QSM data of TreeQSM, a competitive and broadly accepted QSM modeling tool. Our RMSE was less than 40% of the tree QSM RMSE. And for other error measures, the r2adj. and the CCC, the relative improvement looked even better with 27% and 21% respectively.
We consider this manuscript as highly impactful because of the magnitude of quality improvement we do. The relation between soft volume and total volume distributions seems to be really strong and tree data can easily also be used as example data for the generic field of allometric scaling. | bioinformatics |
Auxin Plays a Role in the Adaptation of Rice to Anaerobic Germination and Seedling Establishment Auxin is well known to stimulate coleoptile elongation and rapid seedling growth in the air. However, its role in regulating rice germination and seedling establishment under submergence is largely unknown. Previous studies have shown that excessive levels of IAA frequently cause the inhibition of plant growth and development. In the present study, the high-level accumulation of endogenous IAA is observed under submergence in the dark, stimulating rice coleoptile elongation but limiting the root and primary leaf growth during anaerobic germination (AG). We found that oxygen and light can reduce IAA levels, promote the seedling establishment and enhance rice AG tolerance. miRNA microarray profiling and RNA gel blot analysis results show that the expression of miR167 is negatively regulated by submergence; it subsequently modulates the accumulation of free IAA through the miR167-ARF-GH3 pathway. The OsGH3-8 encodes an IAA-amido synthetase that functions to prevent free IAA accumulation. Reduced miR167 levels or overexpressing OsGH3-8 increase auxin metabolism, reduce endogenous levels of free IAA and enhance rice AG tolerance. The present study reveals that poor seed germination and seedling growth inhibition resulting from excessive IAA accumulation would cause intolerance to submergence in rice, suggesting that a certain threshold level of auxin is essential for rice AG tolerance. | plant biology |
Cross-link assisted spatial proteomics to map sub-organelle proteomes and membrane protein topology The specific functions of cellular organelles and sub-compartments depend on their protein content, which can be characterized by spatial proteomics approaches. However, many spatial proteomics methods are limited in their ability to resolve organellar sub-compartments, profile multiple sub-compartments in parallel, and/or characterize membrane-associated proteomes. Here, we develop a cross-link assisted spatial proteomics (CLASP) strategy that addresses these shortcomings. Using human mitochondria as a model system, we show that CLASP can elucidate spatial proteomes of all mitochondrial sub-compartments and provide topological insight into the mitochondrial membrane proteome in a single experiment. Biochemical and imaging-based follow-up studies demonstrate that CLASP allows discovering mitochondria-associated proteins and revising previous protein sub-compartment localization and membrane topology data. This study extends the scope of cross-linking mass spectrometry beyond protein structure and interaction analysis towards spatial proteomics, establishes a method for concomitant profiling of sub-organelle and membrane proteomes, and provides a resource for mitochondrial spatial biology. | systems biology |
Commonality of Odorant Receptor Choice Mechanism Revealed by Analysis of a Highly Represented Odorant Receptor Transgene In the mouse, more than 1,100 odorant receptors (ORs) are expressed in a monogenic and monoallelic fashion, referred to as singular gene expression. Using a 21bp singular-choice enhancer (x21), we radically increase representation of olfactory sensory neurons (OSNs) choosing a 5x21 enhanced OR transgene, but not overexpression of its mRNA on a per cell basis. RNA-sequencing and differential expression analysis identified 425 differentially expressed genes (DEGs). ORs make up 86% of all DEGs, of which 325 have decreased representation and 40 have increased representation. Underrepresented ORs include Class I, Class II and TAAR genes and within each of their respective olfactory bulb domains: DI, DII, and DIII (TAAR) we committedly observe multiple homogeneous glomeruli with an OR1A1-identity. The underrepresentation of endogenous, class-specific ORs across evolutionarily distinct cell types in favor of the expression of the 5x21-OR1A1 transgene argues that a common mechanism of singular gene choice is present for all OR-expressing OSNs. | neuroscience |
Nitrogen palaeo-isoscapes: Changing spatial gradients of faunal δ15N in late Pleistocene and early Holocene Europe Nitrogen isotope ({delta}15N) analysis of animal tissue is widely used in archaeology and palaeoecology to investigate diet and ecological niche. Data interpretations require an understanding of nitrogen isotope compositions at the base of the food web (baseline {delta}15N). Significant variation in animal {delta}15N has been recognised at various spatiotemporal scales and linked to changes both in baseline {delta}15N and animal ecology. Isoscapes (models of isotope spatial variation) have proved a useful tool for investigating spatial variability in biogeochemical cycles in present-day marine and terrestrial ecosystems, but so far, their application to palaeo-data has been limited. Here, we present time-sliced nitrogen isoscapes for late Pleistocene and early Holocene Europe (c. 50,000 to 10,000 years BP) using herbivore collagen {delta}15N data. This period covers the Last Glacial-Interglacial Transition, during which significant variation in the terrestrial nitrogen cycle occurred. Our results show clear changes in spatial gradients of {delta}15N through time. Prediction of the lowest faunal {delta}15N values in northern latitudes after, rather than during, the Last Glacial Maximum is consistent with the Late Glacial Nitrogen Excursion (LGNE). We consider the potential of incorporating climatic covariate data into isoscape models but find their inclusion does not improve model performance. These findings have implications for investigating the drivers of the LGNE, which has been linked to increased landscape moisture and permafrost thaw, and for understanding changing isotopic baselines, which are fundamental for studies investigating diets, niche partitioning, and migration of higher trophic level animals. | biochemistry |
The PCI domains are "winged" HEAT domains The HEAT domains are a family of helical hairpin repeat domains, composed of four or more hairpins. HEAT is derived from the names of four family members: huntingtin, eukaryotic translation elongation factor 3 (eEF3), protein phosphatase 2 regulatory A subunit (PP2A), and mechanistic target of rapamycin (mTOR). HEAT domain-containing proteins play roles in a wide range of cellular processes, such as protein synthesis, nuclear transport and metabolism, and cell signaling. The PCI domains are a related group of helical hairpin domains, with a "winged-helix" (WH) subdomain at their C-terminus, which is responsible for multi-subunit complex formation with other PCI domains. The name is derived from the complexes, where these domains are found: the Proteasome "lid" regulatory subcomplex, the COP9 signalosome (CSN), and eukaryotic translation initiation factor 3 (eIF3). We noted that in structure homology searches using HEAT domains, sometimes PCI domains appeared in the search results ahead of other HEAT domains, which indicated that the PCI domains could be members of the HEAT domain family, and not a related but separate group. Here, we report extensive structure homology analysis of HEAT and PCI domains, both within and between the two groups of proteins. We present evidence that the PCI domains as a group have greater structural homology with individual groups of HEAT domains than some of the HEAT domain groups have among each other. Therefore, our results indicate that the PCI domains have evolved from a HEAT domain that acquired a WH subdomain. The WH subdomain in turn mediated selfassociation into a multi-subunit complex, which eventually evolved into the common ancestor of the Proteasome lid/CSN/eIF3. | bioinformatics |
Comparative study between radiofrequency- and muscimol-induced inhibition of cultured networks of cortical neuron Previous studies have shown that spontaneously active cultured networks of cortical neuron grown planar microelectrode array are sensitive to radiofrequency (RF) fields and exhibit an inhibitory response more pronounced as the exposure time and power increase. To better understand the mechanism behind the observed effects, we aimed at identifying similarities and dissimilarities between the inhibitory effect of RF fields (continuous wave, 1800 MHz) to the {gamma}-Aminobutyric acid type A (GABAA) receptor agonist muscimol (MU). Inhibition of network bursting activity in response to RF exposure became apparent at an SAR level of 28.6 W/kg and co-occurred with an elevation of the culture medium temperature of [~]1 {degrees}C. Differently to a pharmacological inhibition with MU, exposure to RF fields preferentially inhibits bursting over spiking activity and exerts less constrains on neural network bursting synchrony. Network rebound excitation, a phenomenon relying on intrinsic properties of cortical neurons, was observed consecutively to the removal of tonic hyperpolarization after washout of MU but not in response to cessation of RF exposure which implies that hyperpolarization is not the main driving force mediating the inhibitory effects of RF fields. At the level of single neurons, network inhibition induced by MU and RF fields occurred with reduced action potential (AP) half-width. As change in AP waveform tightly influence efficiency of synaptic transmission, the narrowing effect on AP seen under RF exposure might contribute to reduce network bursting activity. By pointing only to a partial overlap between the inhibitory hallmarks of these two forms of inhibition, our data suggest that the inhibitory mechanisms of action of RF fields differ from the ones mediated by the activation of GABAA receptor. The rapid onset of the inhibitory effect of RF fields and its reversibility strikingly similar to MU are in favour of a mechanism interacting with fast operating targets at the membrane such as ion channels. | neuroscience |
RORβ modulates a gene program that is protective against articular cartilage damage Osteoarthritis (OA) is the most prevalent chronic joint disease which increases in frequency with age eventually impacting most people over the age of 65. OA is the leading cause of disability and impaired mobility, yet the pathogenesis of OA remains unclear. Treatments have focused mainly on pain relief and reducing joint swelling. Currently there are no effective treatments to slow the progression of the disease and to prevent irreversible loss of cartilage. Here we demonstrate that stable expression of ROR{beta} in cultured cells results in alteration of a gene program that is supportive of chondrogenesis and is protective against development of OA. Specifically, we determined that ROR{beta} regulates the balance of FGFRs signaling on FGFR1/FGFR3 that ERK1/2-MAPK signaling was suppressed by FGFR1(cartilage destruction) and AKT signaling was enhanced by FGFR3 (cartilage protection). These results suggest a critical role for ROR{beta} in chondrogenesis and suggest that identification of mechanisms that control the expression of ROR{beta} in chondrocytes could lead to the development of disease modifying therapies for the treatment of OA. | cell biology |
Single cell transcriptomics of ferrets reveal a common temporal pattern of progenitors in brain development of gyrencephalic mammals The diversity of neural stem cells is a hallmark of gyrencephalic brains, including that in humans. Ferrets are an excellent model to study the complex brain development in gyrencephalic mammals, but information on their neural progenitor subtypes is fragmentary. Here, we investigated the temporal series of single-cell transcriptomes of progenitors in developing cortices in ferrets for comparison with human datasets. We found that the diversity and temporal trajectory of neural progenitors, termed radial glia (RG), are well conserved between ferrets and humans. Truncated RG (tRG), a progenitor subtype previously described in humans, and outer RG-like cells were assigned to ferret transcriptomes. In vivo and transcriptome analyses indicated that ferret tRG are generated via asymmetric RG divisions during late neurogenesis, and suggested that tRG is eventually fated to ependymal and glial populations. Therefore, the combined analyses of human and ferret transcriptomes enable the determination of progenitor fate sequences in vivo. | developmental biology |
Histone deacetylase 1 maintains lineage integrity through histone acetylome refinement during early embryogenesis Histone acetylation is a pivotal epigenetic modification that controls chromatin structure and regulates gene expression. It plays an essential role in modulating zygotic transcription and cell lineage specification of developing embryos. While the outcomes of many inductive signals have been described to require enzymatic activities of histone acetyltransferases and deacetylases (HDACs), the mechanisms by which HDACs confine the utilization of the zygotic genome remain to be elucidated. Here, we show that histone deacetylase 1 (Hdac1) progressively binds to the zygotic genome from mid blastula and onward. The recruitment of Hdac1 to the genome at blastula is instructed maternally. Cis-regulatory modules (CRMs) bound by Hdac1 possess epigenetic signatures underlying distinct functions. We highlight a dual function model of Hdac1 where Hdac1 not only represses gene expression by sustaining a histone hypoacetylation state on inactive chromatin, but also maintains gene expression through participating in dynamic histone acetylation-deacetylation cycles on active chromatin. As a result, Hdac1 maintains differential histone acetylation states of bound CRMs between different germ layers and reinforces the transcriptional program underlying cell lineage identities, both in time and space. Taken together, our study reveals a comprehensive role for Hdac1 during early vertebrate embryogenesis. | genomics |
Spermine inhibits PAMP- elicited ROS and Ca2+ burst and reshapes the transcriptional landscape of PTI in Arabidopsis Polyamines are small polycationic amines which levels increase during defense. Previous studies support the contribution of the polyamine spermine (Spm) to the establishment of the hypersensitive response (HR) during incompatible plant-pathogen interactions. However, the potential contribution of Spm to other layers of defense, and pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) in particular, was not completely established. Here we compared the contribution of Spm and putrescine (Put) to early and late PTI responses. We find that Put and Spm show opposite effects on PAMP-elicited reactive oxygen species (ROS) production, with Put increasing whereas Spm lowering flg22-stimulated ROS burst. Through genetic and pharmacological approaches, we find that the inhibitory effect of Spm on flg22-elicited ROS is independent of polyamine oxidation and EDS1 (ENHANCED DISEASE SUSCEPTIBILITY 1), PAD4 (PHYTOALEXIN DEFICIENT 4), salicylic acid and NPR1 (NONEXPRESSER OF PR GENES 1) defense components but resembles chemical inhibition of RBOHD (RESPIRATORY BURST OXIDASE HOMOLOG D) function. Remarkably, Spm can also suppress ROS elicited by FLS2-independent but RBOHD-dependent pathways, thus pointing to compromised RBOHD function. Consistent with this, we find that Spm dampens flg22-stimulated cytosolic Ca2+ influx necessary for RBOHD function and reshapes the transcriptional landscape of PTI and defense responses against Pseudomonas syringae pv. tomato DC3000. Overall, we provide molecular evidence for the differential contribution of Put and Spm to PTI with an impact on plant defense. | plant biology |
Chemotherapy drugs induce different gut microbiota disorder pattern and NODs/RIP2/NF-κB signaling pathway activation that lead to different degrees of intestinal injury 5-Fluorouracil (5-FU), irinotecan (CPT-11), oxaliplatin (L-OHP) and calcium folinate (CF) are the widely used chemotherapy drugs to treat colorectal cancer. However, the use of chemotherapy is often accompanied by intestinal inflammation and gut microbiota disorder. Moreover, the change of gut microbiota may lead to destruction of the intestinal barrier, which contributes to the severity of intestinal injury. There was no detailed comparison of intestinal injury and gut microbiota disorder among 5-FU, CPT-11, L-OHP and CF, which is not benefit for the development of targeted detoxification therapy after chemotherapy. In this project, a model of chemotherapy-induced intestinal injury in tumor-bearing mice was established by intraperitoneal injection of chemotherapy drugs at a clinically equivalent dose. 16S rDNA sequencing was used to detect gut microbiota. We found that 5-FU, CPT-11 and L-OHP caused intestinal injury, inflammatory cytokine (IFN-{gamma}, TNF-, IL-1{beta}, and IL-6) secretion, and gut microbiota disorder. Importantly, we established a complex but clear network between the gut microbiota change pattern and intestinal damage degree induced by different chemotherapy drugs. L-OHP caused the most severe damage in intestine and disorder of gut microbiota, and showed considerable overlap of the microbiota change pattern with 5-FU and CPT-11. The phylogenetic investigation of communities by reconstruction of unobserved states, V1.0 (PICRUSt) analysis showed that the microbiota disorder pattern induced by 5-FU, CPT-11 and L-OHP was related to the NOD like signaling pathway. Therefore, we detected the protein expression of the NODs/RIP2/NF-{kappa}B signaling pathway and found that L-OHP activated that pathway highest. Furthermore, by RDA/CCA analysis, we found that Bifidobacterium, Akkermansia, Allobaculum, Catenibacterium, Mucispirillum, Turicibacter, Helicobacter, Proteus, Escherichia Shigella, Alloprevotealla, Vagococcus, Streptococcus and Candidatus Saccharimonas were highly correlated with the NODs/RIP2/NF-{kappa}B signaling pathway, and influenced by chemotherapy drugs.
IMPORTANCEThe chemotherapy-induced intestinal injury limit drugs clinical use. Intestinal injury involves multiple signaling pathways and the disruption of microbiota. Our results suggest that the degree of intestinal injury caused by different drugs of the first-line colorectal chemotherapy regimen is related to the change pattern of microbiota. Moreover, the NODs/RIP2/NF-{kappa}B signaling pathway was activated in different degrees is also related to the change pattern of microbiota. We found L-OHP caused the most severe change of gut microbiota, and showed considerable overlap of the microbiota changes pattern with 5-FU and CPT-11. Here, we have established a network of different chemotherapy drugs, gut microbiota and NODs/RIP2/NF-{kappa}B signaling pathway, which may provide a new basis for further elucidating the mechanism and clinical treatment of intestinal injury caused by chemotherapy. | molecular biology |
Semi-automated protocol to quantify and characterize fluorescent, 3D vascular images The microvasculature facilitates gas exchange, provides nutrients to cells, and regulates blood flow in response to stimuli. Vascular abnormalities are an indicator of pathology for various conditions, such as compromised vessel integrity in small vessel disease and angiogenesis in tumors. Traditional immunohistochemistry enables visualization of tissue cross-sections containing exogenously labeled vasculature. Although this approach can be utilized to quantify vascular changes within small fields-of-view, it is not a practical way to study the vasculature on the scale of whole organs. Three-dimensional (3D) imaging presents a more appropriate method to visualize the vascular architecture in tissue. Here we describe the complete protocol that we use to characterize the vasculature of different organs in mice encompassing the methods to fluorescently label vessels, optically clear tissue, collect 3D vascular images, and quantify these vascular images with a semi-automated approach. To validate the automated segmentation of vascular images, one user manually segmented fifty random regions of interest across different vascular images. The automated segmentation results had an average sensitivity of 80{+/-}8% and an average specificity of 90{+/-}5% when compared to manual segmentation. Applying this procedure of image analysis presents a method to reliably quantify and characterize vascular networks in a timely fashion. This procedure is also applicable to other methods of tissue clearing and vascular labels that generate 3D images of microvasculature. | bioengineering |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.