title: The effects of uncertain context inference on motor adaptation

abstract: Humans have been shown to adapt their movements when a sudden change to the dynamics of the environment is introduced, a phenomenon called motor adaptation. If the change is reverted, the adaptation is also quickly reverted. Human are also able to adapt to multiple changes in dynamics presented separately, and to be able to switch between adapted movements on the fly. Such switching relies on contextual information which is often noisy or misleading, which affects the switch between adaptations. In this work, we introduce a computational model to explain the behavioral phenomena effected by uncertain contextual information. Specifically, we present a hierarchical model for motor adaptation based on exact Bayesian inference. This model explicitly takes into account contextual information and how the dynamics of context inference affect adaptation and action selection. We show how the proposed model provides a unifying explanation for four different experimentally-established phenomena: (i) effects of sensory cues and proprioceptive information on switching between tasks, (ii) the effects of previously-learned adaptations on switching between tasks, (iii) the effects of training history on behavior in new contexts, in addition to (iv) the well-studied savings, de-adaptation and spontaneous recovery.


title: The enteric nervous system of C. elegans is specified by the Sine Oculis-like homeobox gene ceh-34

abstract: Overarching themes in the terminal differentiation of the enteric nervous system, an autonomously acting unit of animal nervous systems, have so far eluded discovery. We describe here the overall regulatory logic of enteric nervous system differentiation of the nematode C. elegans that resides within the foregut (pharynx) of the worm. A Caenorhabditis elegans homolog of the Drosophila Sine Oculis homeobox gene, ceh-34, is expressed in all 14 classes of interconnected pharyngeal neurons from their birth throughout their life time, but in no other neuron type of the entire animal. Constitutive and temporally controlled ceh-34 removal shows that ceh-34 is required to initiate and maintain the neuron type-specific terminal differentiation program of all pharyngeal neuron classes, including their circuit assembly, without affecting panneuronal features. Through additional genetic loss of function analysis, we show that within each pharyngeal neuron class, ceh-34 cooperates with different homeodomain transcription factors to individuate distinct pharyngeal neuron classes. Our analysis underscores the critical role of homeobox genes in neuronal identity specification and links them to the control of neuronal circuit assembly of the enteric nervous system. Together with the pharyngeal nervous system simplicity as well as its specification by a Sine Oculis homolog, our findings invite speculations about the early evolution of nervous systems.

category: neuroscience


title: Structure of Mycobacterium tuberculosis Cya, an evolutionary ancestor of the mammalian membrane adenylyl cyclases

abstract:
Mycobacterium tuberculosis adenylyl cyclase (AC) Rv1625c / Cya is an evolutionary ancestor of the mammalian membrane ACs and a model system for studies of their structure and function. Although the vital role of ACs in cellular signaling is well established, the function of their transmembrane (TM) regions remains unknown. Here we describe the cryo-EM structure of Cya bound to a stabilizing nanobody at 3.6 [A] resolution. The TM helices 1-5 form a structurally conserved domain that facilitates the assembly of the helical and catalytic domains. The TM region contains discrete pockets accessible from the extracellular and cytosolic side of the membrane. Neutralization of the negatively charged extracellular pocket Ex1 destabilizes the cytosolic helical domain and reduces the catalytic activity of the enzyme. The TM domain acts as a functional component of Cya, guiding the assembly of the catalytic domain and providing the means for direct regulation of catalytic activity in response to extracellular ligands.

One-Sentence SummaryStructure of M. tuberculosis membrane adenylyl cyclase Cya

category: biochemistry


title: SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessibility

abstract: The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has killed over 5 million people and is causing a devastating social and economic impact all over the world. The rise of new variants of concern (VOCs) represents a difficult challenge due to the loss vaccine and natural immunity, and increased transmissibility. All circulating VOCs contain mutations in the spike glycoprotein, which mediates fusion between the viral and host cell membranes, via its receptor binding domain (RBD) that binds to angiotensin-converting enzyme 2 (ACE2). In an attempt to understand the effect of RBD mutations in circulating VOCs, a lot of attention has been given to the RBD-ACE2 interaction. However, this type of analysis is limited, since it ignores more indirect effects, such as the conformational dynamics of the RBD itself. Observing that some VOCs mutations occur in residues that are not in direct contact with ACE2, we hypothesized that they could affect RBD conformational dynamics. To test this, we performed long atomistic (AA) molecular dynamics (MD) simulations to investigate the structural dynamics of wt RBD, and that of three circulating VOCs (alpha, beta, and delta). Our results show that in solution, wt RBD presents two distinct conformations: an "open" conformation where it is free to bind ACE2; and a "closed" conformation, where the RBM ridge blocks the binding surface. The alpha and beta variants significantly impact the open/closed equilibrium, shifting it towards the open conformation by roughly 20%. This shift likely increases ACE2 binding affinity. Simulations of the currently predominant delta variant RBD were extreme in this regard, in that a closed conformation was never observed. Instead, the system alternated between the before mentioned open conformation and an alternative "reversed" one, with a significantly changed orientation of the RBM ridge flanking the RBD. This alternate conformation could potentially provide a fitness advantage not only due to increased availability for ACE2 binding, but also by aiding antibody escape through epitope occlusion. These results support the hypothesis that VOCs, and particularly the delta variant, impact RBD conformational dynamics in a direction that simultaneously promotes efficient binding to ACE2 and antibody escape.

category: biophysics


title: Harbingers of Aggressive Prostate Cancer: Precision Oncology Case Studies

abstract:
Primary prostate cancer (PCa) can show marked molecular heterogeneity. However, systematic analyses comparing primary PCa and matched metastases in individual patients are lacking. We aimed to address the molecular aspects of metastatic progression while accounting for heterogeneity of primary PCa.

In this pilot study, we collected 12 radical prostatectomy (RP) specimens from men who subsequently developed metastatic castration-resistant prostate cancer (mCRPC). We used histomorphology (Gleason grade, focus size, stage) and immunohistochemistry (IHC) (ERG and p53) to identify independent tumors and/or distinct subclones of primary PCa. We then compared molecular profiles of these primary PCa areas to matched metastatic samples using whole exome sequencing (WES) and amplicon-based DNA and RNA sequencing. Based on combined pathology and molecular analysis, seven (58%) RP specimens harbored monoclonal and topographically continuous disease, albeit with some degree of intra-tumor heterogeneity; four (33%) specimens showed true multifocal disease; and one displayed monoclonal disease with discontinuous topography. Early (truncal) events in primary PCa included SPOP p.F133V (one patient), BRAF p.K601E (one patient), and TMPRSS2:ETS rearrangements (nine patients). Activating AR alterations were seen in eight (67%) mCRPC patients, but not in matched primary PCa. Hotspot TP53 mutations, found in metastases from three patients, were readily present in matched primary disease. Alterations in genes encoding epigenetic modifiers were observed in several patients (either shared between primary foci and metastases or in metastatic samples only).

WES-based phylogenetic reconstruction and/or clonality scores were consistent with the index focus designated by pathology review in six out of nine (67%) cases. The three instances of discordance pertained to monoclonal, topographically continuous tumors, which would have been considered as unique disease in routine practice.

Overall, our results emphasize pathologic and molecular heterogeneity of primary PCa, and suggest that comprehensive IHC-assisted pathology review and genomic analysis are highly concordant in nominating the "index" primary PCa area.

category: cancer biology


title: Dioxin Disrupts Thyroid Hormone and Glucocorticoid Induction of klf9, a Master Regulator of Frog Metamorphosis

abstract: Frog metamorphosis, the development of an air-breathing froglet from an aquatic tadpole, is controlled by thyroid hormone (TH) and glucocorticoids (GC). Metamorphosis is susceptible to disruption by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), an aryl hydrocarbon receptor (AHR) agonist. Kruppel-Like Factor 9 (klf9), an immediate early gene in the endocrine-controlled cascade of expression changes governing metamorphosis, can be synergistically induced by both hormones. This process is mediated by an upstream enhancer cluster, the klf9 synergy module (KSM). klf9 is also an AHR target. We measured klf9 mRNA following exposures to triiodothyronine (T3), corticosterone (CORT), and TCDD in the Xenopus laevis cell line XLK-WG. klf9 was induced 6-fold by 50 nM T3, 4-fold by 100 nM CORT, and 3-fold by 175 nM TCDD. Co- treatments of CORT and TCDD or T3 and TCDD induced klf9 7- and 11-fold, respectively, while treatment with all 3 agents induced a 15-fold increase. Transactivation assays examined enhancers from the Xenopus tropicalis klf9 upstream region. KSM-containing segments mediated a strong T3 response and a larger T3/CORT response, while induction by TCDD was mediated by a region [~]1 kb farther upstream containing 5 AHR response elements (AHREs). This region also supported a CORT response in the absence of readily-identifiable glucocorticoid responsive elements, suggesting mediation by protein-protein interactions. A functional AHRE cluster is positionally conserved in the human genome, and klf9 was induced by TCDD and TH in HepG2 cells. These results indicate that AHR binding to upstream AHREs represents an early key event in TCDDs disruption of endocrine-regulated klf9 expression and metamorphosis.

category: pharmacology and toxicology


title: Cytolysin-positive Enterococcus faecalis is elevated in patients with chronic alcoholic pancreatitis

abstract:
IntroductionPatients with alcoholic hepatitis have an increase in cytolysin-producing Enterococcus faecalis that correlates with disease severity and mortality.

AimTo determine whether patients with chronic alcoholic pancreatitis have an elevated abundance of cytolysin-producing E. faecalis.

MethodsQuantification by qPCR of cytolysin-producing E. faecalis in controls and patients with alcoholic hepatitis or pancreatitis.

ResultsPatients with alcoholic pancreatitis had a higher proportion of intestinal cytolysin-positive E. faecalis than healthy controls and patients with alcoholic hepatitis.

ConclusionCytolytic E. faecalis may also be involved in this other alcohol-related complication and benefit from targeted microbiota editing strategies.

category: physiology


title: Chronic adolescent exposure to cannabis in mice leads to long-term sex-biased changes in gene expression networks across brain regions

abstract: During adolescence, frequent and heavy cannabis use can lead to serious adverse health effects and cannabis use disorders (CUD). Rodent models of adolescent exposure to the main psychoactive component of cannabis, delta-9-tetrahydrocannabinol (THC), mimic the behavioral alterations observed in adolescent users. However, the underlying molecular mechanisms remain largely unknown. Here, we treated female and male mice with high doses of THC during early adolescence and assessed their memory and social behaviors in late adolescence. We then profiled the transcriptome of five brain regions involved in cognitive and addiction-related processes. We applied gene coexpression network analysis and identified gene coexpression modules, termed cognitive modules, that simultaneously correlated with THC treatment and memory traits reduced by THC. The cognitive modules were related to endocannabinoid signaling in the female dorsal medial striatum, inflammation in the female ventral tegmental area, and synaptic transmission in the male nucleus accumbens. Moreover, cross-brain region module-module interaction networks uncovered intra- and inter-region molecular circuitries influenced by THC. Lastly, we identified key driver genes of gene networks associated with THC in mice and genetic susceptibility to CUD in humans. This analysis revealed a common regulatory mechanism linked to CUD vulnerability in the nucleus accumbens of females and males, which shared four key drivers (Hapln4, Kcnc1, Elav12, Zcchc12). These genes regulate transcriptional subnetworks implicated in addiction processes, synaptic transmission, brain development, and lipid metabolism. Our study provides novel insights into disease mechanisms regulated by adolescent exposure to THC in a sex- and brain region-specific manner.


title: Chronic adolescent exposure to cannabis in mice leads to sex-biased changes in gene expression networks across brain regions


title: Temporally stable beta sensorimotor oscillations and cortico-muscular coupling underlie force steadiness

abstract: As humans, we seamlessly hold objects in our hands, and may even lose consciousness of these objects. This phenomenon raises the unsettled question of the involvement of the cerebral cortex, the core area for voluntary motor control, in dynamically maintaining steady muscle force. To address this issue, we measured magnetoencephalographic brain activity from healthy adults who maintained a steady pinch grip. Using a novel analysis approach, we uncovered fine-grained temporal modulations in the [~]20-Hz sensorimotor brain rhythm and its coupling with muscle activity, with respect to several aspects of muscle force (rate of increase/decrease or plateauing high/low). These modulations preceded changes in force features by [~]40 ms and possessed behavioral relevance, as less salient or absent modulation predicted a more stable force output. These findings have consequences for the existing theories regarding the functional role of cortico-muscular coupling, and suggest that steady muscle contractions are characterized by a stable rather than fluttering involvement of the sensorimotor cortex.


title: Broad human and animal coronavirus neutralisation by SARS-CoV-2 S2-targeted vaccination

abstract: Several common-cold coronaviruses (HCoVs) are endemic in humans and several variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have emerged during the current Coronavirus disease 2019 (COVID-19) pandemic. Whilst antibody cross-reactivity with the Spike glycoproteins (S) of diverse coronaviruses has been documented, it remains unclear whether such antibody responses, typically targeting the conserved S2 subunit, contribute to or mediate protection, when induced naturally or through vaccination. Using a mouse model, we show that prior HCoV-OC43 S immunity primes neutralising antibody responses to otherwise subimmunogenic SARS-CoV-2 S exposure and promotes S2-targeting antibody responses. Moreover, mouse vaccination with SARS-CoV-2 S2 elicits antibodies that neutralise diverse animal and human alphacoronaviruses and betacoronaviruses in vitro, and protects against SARS-CoV-2 challenge in vivo. Lastly, in mice with a history of SARS-CoV-2 Wuhan-based S vaccination, further S2 vaccination induces stronger and broader neutralising antibody response than booster Wuhan S vaccination, suggesting it may prevent repertoire focusing caused by repeated homologous vaccination. The data presented here establish the protective value of an S2-targeting vaccine and support the notion that S2 vaccination may better prepare the immune system to respond to the changing nature of the S1 subunit in SARS-CoV-2 variants of concern (VOCs), as well as to unpredictable, yet inevitable future coronavirus zoonoses.

category: immunology


title: Community Composition of Bacteria Isolated from Swiss Banknotes Varies Depending on Collection Environment

abstract: Humans interact constantly with surfaces and associated microbial communities in the environment. The factors shaping the composition of these communities are poorly understood: some proposed explanations emphasize the influence of local habitat conditions (niche-based explanations), while others point to geographic structure and the distance among sampled locations (dispersal-based explanations). However, the relative roles of these different drivers for microbial community assembly on human-associated surfaces are not clear. Here, we used a combination of sampling, sequencing (16S rRNA) and culturing to show that the composition of banknote-associated bacterial communities varies depending on the local collection environment. Using banknotes collected from various locations and types of shops across Switzerland, we found taxonomic diversity dominated by families such as Pseudomonadaceae and Staphylococcaceae, but with banknote samples from particular types of shops (especially butcher shops) having distinct community structure. By contrast, we found no evidence of geographic structure: similarity of community composition did not decrease with increasing distance among sampled locations. These results show that microbial communities associated with banknotes, one of the most commonly encountered and exchanged human-associated surfaces, can reflect the local environmental conditions (in this case, the type of shop), and the signal for this type of variation was stronger than that for geographic structure among the locations sampled here.

category: microbiology


title: Regulation of dctA and DctA by cAMP-CRP and EIIAGlc at the transcriptional and post-translational levels in E. coli: Consequences for aerobic uptake and metabolism of C4-dicarboxylates

abstract: The expression of dctA, encoding the aerobic C4-dicarboxylate (C4-DC) transporter DctA of Escherichia coli, and its use in the presence of alternative carbon sources was characterized. dctA is regulated by cAMP-CRP and substrates that control cAMP levels, either through the phosphotransferase system (PTS), or through their metabolic link to PEP synthesis. The data indicates that phosphorylation of the regulator EIIAGlc of the glucose-specific PTS represents the mediator for regulation. The dctA promotor region contains a class I CRP-binding site (position -81.5) and a DcuR-binding site (position -105.5). The response regulator DcuR of the C4-DC-activated DcuS-DcuR two-component system is known to stimulate expression of dctA, and cAMP-CRP is known to stimulate expression of dcuS-dcuR. Thus, activation of dctA expression by cAMP-CRP and DcuR is organized in a coherent feed-forward loop (FFL) where cAMP-CRP positively regulates the expression of dctA by direct stimulation and by stimulating the expression of dcuR. Stimulation by DcuR is presumed to require DNA bending by cAMP-CRP. In this way, CRP-FFL integrates carbon catabolite control and C4-DC-specific regulation. Moreover, EIIAGlc of the glucose-specific PTS strongly interacts with DctA, which could lead to substrate exclusion of C4-DCs when preferred carbon substrates such as sugars are present. Since C4-DCs are perceived in the periplasmic space by the sensor DcuS, the substrate exclusion is not linked to inducer exclusion, contrasting classical inducer exclusion known for the lactose permease LacY. Thus, aerobic C4-DC metabolism is tightly regulated at the transcriptional and post-translational levels, whereas uptake of L-aspartate by DcuA is essentially unaffected. Overall, transcriptional and post-translational regulation of dctA expression and DctA function efficiently fine-tunes C4-DC catabolism in response to other preferred carbon sources.


title: A Co-abundant Gene Analysis for Identification of Gut Microbial Strains Associated with Immune Responses to Oral Cholera Vaccine

abstract:
BackgroundOral cholera vaccines (OCVs) are an important tool for reduction of the worldwide cholera burden, but some individuals who receive an OCV do not develop protective immune responses. The gut microbiota is a potential explanation for these differences. Components of the gut microbiota associated with differences in OCV response have not been identified.

ResultsWe used metagenomic sequencing to identify predicted protein-coding genes in the gut microbiota at the time of OCV administration, and then measured immune responses to vaccination. Vaccine recipients were classified as OCV "responders" if they developed a post{-}vaccination increase in memory B cell populations that produce IgA or IgG specific for cholera toxin and the V. cholerae O-specific polysaccharide. We next analyzed microbial genes seen at similar abundances across individual samples and classified these into co-abundant gene groupings (CAGs), and correlated CAGs with OCV responses. Next, to identify specific bacterial strains associated with OCV responses, we mapped CAGs to bacterial genomes and generated a "priority score" for each strain detected in the study population. This score reflects both the number of CAGs aligning to a specific bacterial genome and the strength of the association between the CAGs and the vaccine response. This strain-level analysis revealed relationships between the gut microbiota and immune response to OCV that were not detected at the genus or species level. Bacterial strains which produce short-chain fatty acids and those with sphingolipid-containing cell membranes were correlated with more robust immune responses to vaccination.

ConclusionOur study demonstrates a method for translating metagenomic sequencing data into strain-specific results associated with a biological outcome. Using this approach, we identified strains for the study of bacterial-derived molecules or metabolites associated with immune responses; such agents might have potential utility as vaccine adjuvants.


title: Distinct ribosome states trigger diverse mRNA quality control pathways

abstract: Key protein adapters couple translation to mRNA decay on specific classes of problematic mRNAs in eukaryotes. Slow decoding on non-optimal codons leads to codon-optimality-mediated decay (COMD) and prolonged arrest at stall sites leads to no-go decay (NGD). The identities of the decay factors underlying these processes and the mechanisms by which they respond to translational distress remain open areas of investigation. We use carefully-designed reporter mRNAs to perform genetic screens and functional assays in S. cerevisiae. We characterize the roles of Hel2 and Syh1 in coordinating translational repression and mRNA decay on NGD reporter mRNAs, finding that Syh1 acts as the primary link to mRNA decay in NGD. Importantly, we observe that these NGD factors are not involved in the degradation of mRNAs enriched in non-optimal codons. Further, we establish that a key factor previously implicated in COMD, Not5, contributes modestly to the degradation of an NGD-targeted mRNA. Finally, we use ribosome profiling to reveal distinct ribosomal states associated with each reporter mRNA that readily rationalize the contributions of NGD and COMD factors to degradation of these reporters. Taken together, these results provide new mechanistic insight into the role of Syh1 in NGD and define the molecular triggers that determine how distinct pathways target mRNAs for degradation in yeast.

category: molecular biology


title: A Nascent Peptide Code for Translational Control of mRNA Stability in Human Cells

abstract: Stability of eukaryotic mRNAs is associated with their codon, amino acid, and GC content. Yet, coding sequence motifs that predictably alter mRNA stability in human cells remain poorly defined. Here, we develop a massively parallel assay to measure mRNA effects of thousands of synthetic and endogenous coding sequence motifs in human cells. We identify several families of simple dipeptide repeats whose translation triggers acute mRNA instability. Rather than individual amino acids, specific combinations of bulky and positively charged amino acids are critical for the destabilizing effects of dipeptide repeats. Remarkably, dipeptide sequences that form extended {beta} strands in silico and in vitro drive ribosome stalling and mRNA instability in vivo. The resulting nascent peptide code underlies ribosome stalling and mRNA-destabilizing effects of hundreds of endogenous peptide sequences in the human proteome. Our work reveals an intrinsic role for the ribosome as a selectivity filter against the synthesis of bulky and aggregation-prone peptides.


title: Age-related changes in microRNAs expression in cruciate ligaments of wild-stock house mice

abstract:
AimCruciate ligaments (CLs) of the knee joint are commonly injured following trauma or ageing. MicroRNAs (miRs) are potential therapeutic targets in musculoskeletal disorders. This study aimed to 1) identify if wild-stock house (WSH) mice are an appropriate model to study age-related changes of the knee joint and 2) investigate expression of miRs in ageing murine CLs.

MethodsKnee joints were collected from 6 and 24 months old C57BL/6 and WSH mice (Mus musculus domesticus) for histological analysis. RNA extraction and qPCR gene expression were performed on CLs in 6, 12, 24, and 30 month WSH old mice. Expression of miR targets in CLs was determined, followed by analysis of predicted mRNA target genes and Ingenuity Pathway Analysis.

ResultsHigher CL and knee OARSI histological scores were found in 24 month old WSH mice compared to 6 and 12 month old C57BL/6 and 6 month old WSH mice (p< 0.05). miR-29a and miR-34a were upregulated in 30 month-old WSH mice in comparison to 6, 12 and 24-month-old WSH mice (p<0.05). Ingenuity Pathway Analysis on miR-29a and 34a targets was associated with inflammation through interleukins, TGF{beta} and Notch genes and p53 signalling. Collagen type I alpha 1 chain (COL1A1) correlated negatively with both miR-29a (r= -0.35) and miR-34a (r= -0.33).

ConclusionThe findings of this study support WSH house mice as an accelerated ageing model of the murine knee joint. This study also indicated that miR-29a and 34a may be important regulators of COL1A1 gene expression in murine CLs.


title: Paracrine role for endothelial IGF-1 receptor in white adipocyte beiging

abstract: There are at least two distinct types of thermogenic adipocyte in mammals: a pre-existing form established during development, termed classical brown adipocytes and an inducible form,  beige adipocytes1-3. Various environmental cues can stimulate a process frequently referred to as  beiging of white adipose tissue (WAT), leading to enhanced thermogenesis and obesity resistance 4, 5. Whilst beiging of WAT as a therapeutic goal for obesity and obesity-related complications has attracted much attention6-9; therapeutics stimulating beiging without deleterious side-effects remain elusive10. The endothelium lines all blood vessels and is therefore in close proximity to all cells. Many studies support the possibility that the endothelium acts as a paracrine organ11-14. We explored the potential role of endothelial insulin-like growth factor-1 receptor (IGF-1R) as a paracrine modulator of WAT phenotype. Here we show that a reduction in endothelial IGF-1R expression in the presence of nutrient excess leads to white adipocyte beiging, increases whole-body energy expenditure and enhances insulin sensitivity via a non-cell autonomous paracrine mechanism. We demonstrate that this is mediated by endothelial release of malonic acid, which we show, using prodrug analogues, has potentially therapeutically-relevant properties in the treatment of metabolic disease.

category: cell biology


title: ESR2 regulates indian hedgehog signaling in neonatal rat ovary

abstract: The transcriptional regulatory function of estrogen receptor {beta} (ESR2) is essential for the regulation of primordial follicle activation (PFA). Increased PFA due to the loss of ESR2 becomes evident as early as postnatal day 8 (PND8). To identify the ESR2-regulated genes that control PFA, we performed RNA-seq analyses of wildtype, and Esr2 knockout (Esr2KO) neonatal rat ovaries collected on PND4, PND6, and PND8. Among the differentially expressed genes in Esr2KO ovaries, indian hedgehog (Ihh) displayed the highest downregulation among the ovary enriched genes. IHH regulated genes including Hhip as well as the steroidogenic enzymes were also downregulated in Esr2KO rat ovaries. Remarkably, the expression of Ihh in Esr2KO ovaries was not upregulated despite the high levels of Gdf9 and Bmp15, which are known regulators of Ihh expression in granulosa cells. Our findings suggest that indian hedgehog signaling in the neonatal rat ovary is dependent on ESR2.

category: developmental biology


title: Single-cell transcriptome reveals insights into the development and function of the zebrafish ovary

abstract: Zebrafish are an established research organism that has made many contributions to our understanding of vertebrate tissue and organ development, yet there are still significant gaps in our understanding of the genes that regulate gonad development, sex, and reproduction. Unlike the development of many organs, such as the brain and heart that form during the first few days of development, zebrafish gonads do not begin to form until the larval stage ([≥]5 dpf). Thus, forward genetic screens have identified very few genes required for gonad development. In addition, bulk RNA sequencing studies which identify genes expressed in the gonads do not have the resolution necessary to define minor cell populations that may play significant roles in development and function of these organs. To overcome these limitations, we have used single-cell RNA sequencing to determine the transcriptomes of cells isolated from juvenile zebrafish ovaries. This resulted in the profiles of 10,658 germ cells and 14,431 somatic cells. Our germ cell data represents all developmental stages from germline stem cells to early meiotic oocytes. Our somatic cell data represents all known somatic cell types, including follicle cells, theca cells and interstitial stromal cells. Further analysis revealed an unexpected number of cell subpopulations within these broadly defined cell types. To further define their functional significance, we determined the location of these cell subpopulations within the ovary. Finally, for select examples, we used gene knockout experiments to determine the role of newly identified genes. Our results reveal novel insights into ovarian development and function and the sequencing information will provide a valuable resource for future studies.


title: Demographic feedbacks can hamper the spatial spread of a gene drive

abstract: AO_SCPLOWBSTRACTC_SCPLOWThis paper is concerned with a reaction-diffusion system modeling the fixation and the invasion in a population of a gene drive (an allele biasing inheritance, increasing its own transmission to offspring). In our model, the gene drive has a negative effect on the fitness of individuals carrying it, and is therefore susceptible of decreasing the total carrying capacity of the population locally in space. This tends to generate an opposing demographic advection that the gene drive has to overcome in order to invade. While previous reaction-diffusion models neglected this aspect, here we focus on it and try to predict the sign of the traveling wave speed. It turns out to be an analytical challenge, only partial results being within reach, and we complete our theoretical analysis by numerical simulations. Our results indicate that taking into account the interplay between population dynamics and population genetics might actually be crucial, as it can effectively reverse the direction of the invasion and lead to failure. Our findings can be extended to other bistable systems, such as the spread of cytoplasmic incompatibilities caused by Wolbachia.

category: evolutionary biology


title: Barcode aware adaptive sampling for Oxford Nanopore sequencers.

abstract: Adaptive sampling enables selection of individual DNA molecules from sequencing libraries, a unique property of nanopore sequencing. Here we develop our adaptive sampling tool readfish to become "barcode-aware" enabling selection of different targets within barcoded samples or filtering out individual barcodes. We show that multiple human genomes can be assessed for copy number and structural variation on a single sequencing flow cell using sample specific customised target panels on both GridION and PromethION devices.

category: genomics


title: Barcode aware adaptive sampling for GridION and PromethION Oxford Nanopore sequencers.


title: An experimental test of chronic traffic noise exposure on parental behaviour and reproduction in zebra finches

abstract: Chronic traffic noise is increasingly recognised as a potential hazard to wildlife. Several songbird species have been shown to breed poorly in traffic noise exposed habitats. However, identifying whether noise is causal in this requires experimental approaches. We tested whether experimental exposure to chronic traffic noise affected parental behaviour and reproductive success in zebra finches (Taeniopygia guttata). In a counterbalanced repeated-measures design, breeding pairs were exposed to continuous playback of one of two types of highway noise previously shown to be either neutral (control) or aversive. Parental nest attendance positively correlated with feeding effort and was higher for the aversive than the control sound and this effect was more pronounced for parents attending larger broods. However, neither noise condition affected offspring number, growth or body mass. The absence of an effect held when we combined our data with data from two other comparable studies into a meta-analysis. We discuss whether the increased nest attendance could be a compensatory strategy that alleviated detrimental noise effects on the chicks, and whether it could be caused by impaired parent-offspring or within-pair communication. Future work should test these hypotheses and investigate potential long-term costs of increased parental engagement.

category: animal behavior and cognition


title: Allosteric Regulation of Human Plastins

abstract: Plastins/fimbrins are conserved actin-bundling proteins contributing to motility, cytokinesis, and other cellular processes by organizing actin assemblies of strikingly different geometries as in aligned bundles and branched networks. We propose that this unique ability stems from an allosteric communication between plastins two actin-binding domains (ABD1/2) engaged in a tight spatial association. We found that although ABD1 binds actin first, ABD2 can bind to actin three orders of magnitude stronger if not inhibited by an equally strong allosteric engagement with ABD1. Binding of ABD1 to actin lessened the inhibition, enabling weak bundling within aligned bundles. A mutation mimicking physiologically relevant phosphorylation at the ABD1-ABD2 interface strongly reduced their association, dramatically potentiating actin cross-linking. Cryo-EM reconstruction revealed the ABD1-actin interface and enabled modeling of the plastin bridge to confirm domain separation in parallel bundles. The characteristic domain organization with a strong allosteric inhibition imposed by ABD1 on ABD2 allows plastins to tune cross-linking, contributing to the assembly and remodeling of actin assemblies with different morphological and functional properties defining the unique place of plastins in actin organization.


title: Mechanism of nucleotide discrimination by the translesion synthesis polymerase Rev1

abstract: Rev1 is a translesion DNA synthesis (TLS) polymerase involved in the bypass of adducted-guanine bases and abasic sites during DNA replication. During damage bypass, Rev1 utilizes a protein-template mechanism of DNA synthesis, where the templating DNA base is evicted from the Rev1 active site and replaced by an arginine side chain that preferentially binds incoming dCTP. Here, we utilize X-ray crystallography and molecular dynamics simulations to obtain structural insight into the dCTP specificity of Rev1. We show the Rev1 R324 protein-template forms sub-optimal hydrogen bonds with incoming dTTP, dGTP, and dATP that prevents Rev1 from adopting a catalytically competent conformation. Additionally, we show the Rev1 R324 protein-template forms optimal hydrogen bonds with incoming rCTP. However, the incoming rCTP adopts an altered sugar pucker, which prevents the formation of a catalytically competent Rev1 active site. This work provides novel insight into the mechanisms for nucleotide discrimination by the TLS polymerase Rev1.


title: Protein structure dynamic prediction: a Machine Learning/Molecular Dynamic approach to investigate the protein conformational sampling

abstract: Proteins exist in several different conformations. These structural changes are often associated with fluctuations at the residue level. Recent findings show that co-evolutionary analysis coupled with machine- learning techniques improves the precision by providing quantitative distance predictions between pairs of residues. The predicted statistical distance distribution from Multi Sequence Analysis (MSA) reveals the presence of different local maxima suggesting the flexibility of key residue pairs. Here we investigate the ability of the residue-residue distance prediction to provide insights into the protein conformational ensemble. We combine deep learning approaches with mechanistic modeling to a set of proteins that experimentally showed conformational changes. The predicted protein models were filtered based on energy scores, RMSD clustering, and the centroids selected as the lowest energy structure per cluster. The models were compared to the experimental-Molecular Dynamics (MD) relaxed structure by analyzing the backbone residue torsional distribution and the sidechain orientations. Our pipeline not only allows us to retrieve the global experimental folding but also the experimental structural dynamics. We show the potential correlation between the experimental structure dynamics and the predicted model ensemble demonstrating the susceptibility of the current state-of-the-art methods in protein folding and dynamics prediction and pointing out the areas of improvement.

category: bioinformatics


title: iDEP-assisted isolation of insulin secretory vesicles

abstract: Organelle heterogeneity and inter-organelle associations within a single cell contribute to the limited sensitivity of current organelle separation techniques, thus hindering organelle subpopulation characterization. Here we use direct current insulator-based dielectrophoresis (DC-iDEP) as an unbiased separation method and demonstrate its capability by identifying distinct distribution patterns of insulin vesicles from pancreatic {beta}-cells. A multiple voltage DC-iDEP strategy with increased range and sensitivity has been applied, and a differentiation factor (ratio of electrokinetic to dielectrophoretic mobility) has been used to characterize features of insulin vesicle distribution patterns. We observed a significant difference in the distribution pattern of insulin vesicles isolated from glucose-stimulated cells relative to unstimulated cells, in accordance with functional maturation of vesicles upon glucose stimulation, and interpret this to be indicative of high-resolution separation of vesicle subpopulation. DC-iDEP provides a path for future characterization of subtle biochemical differences of organelle subpopulations within any biological system.


title: Never cared for what they do. High structural stability of Guanine-quadruplexes in presence of strand-break damages

abstract: DNA integrity is an important factor to assure genome stability and, more generally, cells and organisms viability. In presence of DNA damage, the normal cell cycle is perturbed while cells activate their repair processes. Although efficient, the repair system is not always able to ensure the complete restoration of gene integrity. In these cases, not only mutations may occur, but the accumulation of lesions can either lead to carcinogenesis or reach a threshold which induces apoptosis and the programmed cell death. Among the different types of DNA lesions, strand breaks produced by ionizing radiations are the most toxic, due to their inherently difficult repair, which may lead to genomic instability. In this article we show, by using classical molecular simulations techniques, that differently from the canonical double-helical B-DNA, guanine-quadruplex (G4) arrangements show a remarkable structural stability, even in presence of two strand breaks. Since G4-DNA are recognized for their regulatory roles in cell senescence and gene expression, also involving oncogene, their stability can be related to an evolutionary cellular response aimed at minimizing the effects of ionizing radiation.


title: MSD2, an apoplastic Mn-SOD, contributes to root skotomorphogenic growth by modulating ROS distribution in Arabidopsis

abstract: Reactive oxygen species (ROS) play essential roles as a second messenger in various physiological processes in plants. Due to their oxidative nature, ROS can also be harmful. Thus, the generation and homeostasis of ROS are tightly controlled by multiple enzymes. Membrane-localized NADPH oxidases are well known to generate ROS during developmental and stress responses, but the metabolic pathways of the superoxide (O2{middle dot}-) generated by them in the apoplast are poorly understood, and the identity of the apoplastic superoxide dismutase (SOD) is unknown in Arabidopsis. Here, we show that a putative manganese SOD, MSD2 is secreted and possesses a SOD activity that can be inhibited by nitration at tyrosine 68. The expression of MSD2 in roots is light condition-dependent, suggesting that MSD2 may act on ROS metabolism in roots during the light-to-dark transition. Root architecture is governed by ROS distribution that exhibits opposite gradient of H2O2 and O2{middle dot}-, which is indeed altered in etiolated msd2 mutants and accompanied by changes in the onset of differentiation. These results provide a missing link in our understanding of ROS metabolism and suggest that MSD2 plays a role in root skotomorphogenesis by regulating ROS distribution, thereby playing a pivotal role in plant growth and development.

category: plant biology


title: Cellular selectivity of STING stimulation determines priming of tumor-specific T cell responses

abstract: T cells that recognize tumor antigens are crucial for anti-tumor immune responses. Induction of anti-tumor T cells in immunogenic tumors depends on STING, the intracellular innate immune receptor for cyclic guanosine monophosphate-adenosine monophosphate (cGAMP) and related cyclic dinucleotides (CDNs). However, the optimal way to leverage STING activation in non-immunogenic tumors is still unclear. Here, we show that cGAMP delivery by intra-tumoral injection of virus-like particles (cGAMP-VLP) leads to differentiation of tumor-specific T cells, decrease in tumor regulatory T cells (Tregs) and anti-tumoral responses that synergize with PD1 blockade. By contrast, intra-tumoral injection of synthetic CDN leads to tumor necrosis and systemic T cell activation but no differentiation of tumor-specific T cells, and a demise of immune cells in injected tumors. Analyses of cytokine responses and genetic models revealed that cGAMP-VLP preferentially targets STING in dendritic cells at a 1000-fold less dose than synthetic CDN. Sub-cutaneous administration of cGAMP-VLP showed synergy when combined with a tumor Treg-depleting antibody to elicit systemic tumor-specific T cells, leading to complete and lasting tumor eradication. These finding show that cell targeting of STING stimulation shapes the anti-tumor T cell response and reveal a therapeutic strategy with T cell modulators.


title: The AdcACB/AdcAII system is Essential for Zinc Homeostasis and an Important Contributor of Enterococcus faecalis Virulence

abstract: Bacterial pathogens require a variety of micronutrients for growth, including trace metals such as iron, manganese, and zinc (Zn). Despite their relative abundance in host environments, access to these metals is severely restricted during infection due to host-mediated defense mechanisms collectively known as nutritional immunity. Despite a growing appreciation of the importance of Zn in host-pathogen interactions, the mechanisms of Zn homeostasis and the significance of Zn to the pathophysiology of E. faecalis, a major pathogen of nosocomial and community-associated infections, have not been investigated. Here, we show that E. faecalis encoded an ABC-type transporter AdcACB and an orphan substrate-binding lipoprotein AdcAII that work cooperatively to maintain Zn homeostasis. Simultaneous inactivation of adcA and adcAII or the entire adcACB operon led to significant reduction in intracellular Zn under Zn-restricted conditions, heightened sensitivity to Zn-chelating agents including human calprotectin, aberrant cell morphology, and impaired fitness in serum ex vivo. Additionally, inactivation of adcACB and adcAII significantly reduced bacterial tolerance towards cell envelope-targeting antibiotics, which may be associated to altered fatty acid abundance and species. Lastly, we show that the AdcACB/AdcAII system contributes to E. faecalis virulence in an invertebrate (Galleria mellonella) infection model and in two catheter-associated mouse infection models that recapitulate many of the host conditions associated with enterococcal human infections. Collectively, this report reveals that high-affinity Zn import is essential for the pathogenesis of E. faecalis indicating that the surface-associated AdcA and AdcAII lipoproteins are potential therapeutic targets.


title: The influence of sponge-dwelling gobies (Elacatinus horsti) on the feeding efficiency of their Caribbean tube sponge (	Aplysina sp.) hosts

abstract: Mutualistic associations between benthic marine invertebrates and reef taxa are common. Sponge-dwelling gobies benefit from protection within sponge tubes and greater food availability. Sponge-dwelling gobies are hypothesized to increase sponge pump rates by consuming polychaete parasites, but such increases have not yet been demonstrated. We investigated the association between sponge-dwelling gobies (Elacatinus horsti) and two species of tube sponge (Aplysina lacunosa and Aplysina archeri) in Bonaire, Caribbean Netherlands. We visually assessed goby presence in sponges and used in situ methods with fluorescein dye to measure estimate feeding rates via pump rates. Aplysina archeri were more likely to host a goby than A. lacunosa. For both sponge species, pump rates of tubes with gobies were higher on average than those of tubes without gobies. Our observations, therefore, suggest that E. horsti associations with Aplysina are likely mutualistic relationships in which sponges benefit from higher feeding rates when gobies are present.

category: ecology


title: Chromosome-level reference genomes for two strains of Caenorhabditis briggsae: an improved platform for comparative genomics

abstract: The publication of the Caenorhabditis briggsae reference genome in 2003 enabled the first comparative genomics studies between C. elegans and C. briggsae, shedding light on the evolution of genome content and structure in the Caenorhabditis genus. However, despite being widely used, the currently available C. briggsae reference genome is substantially less complete and structurally accurate than the C. elegans reference genome. Here, we used high-coverage Oxford Nanopore long-read and chromosome conformation capture data to generate chromosomally resolved reference genomes for two C. briggsae strains: QX1410, a new reference strain closely related to the laboratory AF16 strain, and VX34, a highly divergent strain isolated in China. We also sequenced 99 recombinant inbred lines (RILs) generated from reciprocal crosses between QX1410 and VX34 to create a recombination map and identify chromosomal domains. Additionally, we used both short- and long-read RNA sequencing (RNA-seq) data to generate high-quality gene annotations. By comparing these new reference genomes to the current reference, we reveal that hyper-divergent haplotypes cover large portions of the C. briggsae genome, similar to recent reports in C. elegans and C. tropicalis. We also show that the genomes of selfing Caenorhabditis species have undergone more rearrangement than their outcrossing relatives, which has biased previous estimates of rearrangement rate in Caenorhabditis. These new genomes provide a substantially improved platform for comparative genomics in Caenorhabditis and narrow the gap between the quality of genomic resources available for C. elegans and C. briggsae.


title: An in vitro, in utero and in silico framework of oxygen diffusion in intricate vascular networks of the placenta

abstract: AO_SCPLOWBSTRACTC_SCPLOWThe placenta is a temporary and complex organ critical for fetal development through its subtle but convoluted harmonization of endocrine, vascular, haemodynamic and exchange adaptations. Yet, due to experimental, technological and ethical constraints, this unique organ remains poorly understood. In silico tools are emerging as a powerful means to overcome these challenges and have the potential to actualize novel breakthroughs. Here, we present an interdisciplinary framework combining in vitro experiments used to develop an elegant and scalable in silico model of oxygen diffusion. We then use in utero imaging of placental perfusion and oxygenation in both control and growth-restricted rodent placentas for validation of our in silico model. Our framework revealed the structure-function relationship in the feto-placental vasculature; oxygen diffusion is impaired in growth-restricted placentas, due to the diminished arborization of growth-restricted feto-placental vasculature and the lack of decelerated flow for adequate oxygen diffusion and exchange. We highlight the mechanisms of impairment in a rat model of growth restriction, underpinned by placental vascular impairment. Our framework reports and validates the prediction of blood flow deceleration impairment in growth restricted placentas with the placentas oxygen transfer capability being significantly impaired, both globally and locally.

category: bioengineering


title: A druggable addiction to de novo pyrimidine biosynthesis in diffuse midline glioma

abstract: Diffuse midline glioma (DMG) is a uniformly fatal pediatric cancer driven by oncohistones that do not readily lend themselves to drug development. To identify therapeutic targets for DMG, we conducted a genome-wide CRIPSR screen for DMG metabolic vulnerabilities, which revealed a DMG selective dependency on the de novo pathway for pyrimidine biosynthesis. The dependency is specific to pyrimidines as there is no selectivity for suppression of de novo purine biosynthesis. A clinical stage inhibitor of DHODH (a rate limiting enzyme in the de novo pathway) generates DNA damage and induces apoptosis through suppression of replication forks--an "on target" effect, as shown by uridine rescue. MALDI mass spectroscopy imaging demonstrates that BAY2402234 accumulates in brain at therapeutically relevant concentrations, suppresses de novo pyrimidine biosynthesis in vivo, and prolongs survival of mice bearing intracranial DMG xenografts. Our results highlight BAY2402234, a brain-penetrant DHODH inhibitor, as a promising therapy against DMGs.


title: Zoledronic acid targets the mevalonate pathway causing reduced cell recruitment and attenuation of pulmonary fibrosis

abstract:
Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease causing irreparable scarring of lung tissue, resulting in most patients succumbing rapidly after diagnosis. With limited treatment options available, repurposing of current pharmaceuticals offers an expeditious option to address this dire need. The mevalonate pathway, which is involved in the regulation of cell proliferation, survival and motility, is targeted by the bisphosphonate zoledronic acid (ZA). In this study, administration of ZA reduced myofibroblast transition and blocked NF-kB signaling in macrophages leading to impaired immune cell recruitment. ZA treatment of mice with bleomycin-induced lung damage displayed decreased levels of cytokines in the BALF, plasma, and lung tissue, resulting in less histologically visible fibrotic scarring. Additionally, bleomycin induced production of the ZA target, farnesyl diphosphate synthase (FDPS), was reduced in lung tissue and fibroblasts upon ZA treatment. Therefore, ZA administration offers an expedient and efficacious treatment option against IPF in a clinical setting.

TeaserRepurposing of zoledronic acid potentially offers a clinically viable treatment for idiopathic pulmonary fibrosis


title: Revising the Role of Cortical Cytoskeleton During Secretion: Actin and Myosin XI Function in Vesicle Tethering

abstract: In plants, secretion of cell wall components and membrane proteins plays a fundamental role in growth and development as well as survival in diverse environments. Exocytosis, as the last step of the secretory trafficking pathway, is a highly ordered and precisely controlled process involving tethering, docking, and fusion of vesicles at the plasma membrane (PM) for cargo delivery. Although the exocytic process and machinery are well characterized in yeast and animal models, the molecular players and specific molecular events that underpin late stages of exocytosis in plant cells remain largely unknown. Here, by using the delivery of functional, fluorescent-tagged cellulose synthase (CESA) complexes (CSCs) to the PM as a model system for secretion, as well as single-particle tracking in living cells, we describe a quantitative approach for measuring the frequency of vesicle tethering events. Genetic and pharmacological inhibition of cytoskeletal function, reveal that the initial vesicle tethering step of exocytosis is dependent on actin and myosin XI. In contrast, treatments with the microtubule inhibitor, oryzalin, did not significantly affect vesicle tethering or fusion during CSC exocytosis but caused a minor increase of transient or aborted tethering events. With data from this new quantitative approach and improved spatiotemporal resolution of single particle events during secretion, we generate a revised model for the role of the cortical cytoskeleton in CSC trafficking.


title: CURT1A and CURT1C mediate distinct stages of plastid conversion in Arabidopsis

abstract: The crystalline structure of prolamellar bodies (PLBs) and light-induced etioplasts-to-chloroplasts transformation have been investigated with electron microscopy methods. However, these studies suffer from chemical fixation artifacts and limited volumes of tomographic reconstruction. We have examined Arabidopsis thaliana cotyledon samples preserved by high-pressure freezing with scanning transmission electron tomography to visualize larger volumes in etioplasts and their conversion into chloroplasts. PLB tubules were arranged in a zinc blende-type lattice like carbon atoms in diamonds. Within 2 hours after illumination, the lattice collapsed from the PLB exterior and the disorganized tubules merged to form fenestrated sheets that eventually matured into lamellar thylakoids. These planar thylakoids emerging from PLBs overlapped or folded into grana stacks in PLBs vicinity. Since the nascent lamellae had curved membrane at their tips, we examined the localization of CURT1 proteins. CURT1A transcript was most abundant in de-etiolating cotyledon samples, and CURT1A concentrated at the peripheral PLB. In curt1a mutant etioplasts, thylakoid sheets were swollen and failed to develop stacks. In curt1c mutant, however, PLBs had cracks in their lattices, indicating that CURT1C contributes to cubic crystal growth under darkness. Our data provide evidence that CURT1A and CURT1C play distinct roles in the etioplast and chloroplast biogenesis.


title: Overexpression of NDR1 Leads to Pathogen Resistance at Elevated Temperatures

abstract:
Abiotic and biotic environments influence a myriad of plant-related processes, including growth, development, and the establishment and maintenance of interaction(s) with microbes. As a driver of this signaling between plants and microbes, the role of plant hormones in both surveillance and signaling has emerged as a point of intersection between plant-abiotic and -biotic responses. In the current study, we elucidate a role for NON-RACE-SPECIFIC DISEASE RESISTANCE1 (NDR1) by exploiting effector-triggered immunity (ETI) to define the regulation of plant host immunity in response to both pathogen infection and elevated temperature. We generated time-series RNA sequencing data of WT Col-0, a NDR1 overexpression line, as well as ndr1 and ics1-2 mutant plants under elevated temperature. Not surprisingly, the NDR1-overexpression line showed genotype-specific gene expression changes related to defense response and immune system function. Interestingly, overexpression of NDR1 revealed a role for NDR1 in immune system function; specifically, we describe a mechanism that intersects with Pseudomonas syringae, type-III effector translocation, R-protein signaling complex stabilization, and sustained levels of SA at elevated temperature during ETI. The results described herein support a role for NDR1 in maintaining cell signaling during simultaneous exposure to elevated temperature and avirulent pathogen stressors.

One-sentence summaryNDR1 is required for Pst-AvrRpt2 triggered ETI at elevated temperature.


title: A Comparison of Macaque Hair Hormone Concentration Following Enhanced Cognitive Experiences or Standard Nonhuman Primate Environmental Enrichment

abstract: Experience with enriched environments positively impacts the health and wellbeing of nonhuman animals ranging from rodents to primates. Little is known, however, about the specific effects of enhanced cognitive enrichment (ECE) on nonhuman primates. The study reported here used archival samples to provide preliminary analysis of ECE on hormones associated with stress and wellbeing, as well as evaluation of persistent effects of infant social rearing. Hair samples from 24 adult male rhesus macaques were analyzed via LC-MS/MS technique for the main stress response hormones: cortisol, cortisone, and dehydroepiandrosterone. The ECE and care-as-usual (CAU) groups did not significantly differ in any of the mean analyte values. Cortisol and dehydroepiandrosterone were strongly and positively correlated in the ECE group. By contrast, for the CAU group the two analytes were weakly correlated. Within the ECE group, cortisol and dehydroepiandrosterone were significantly and positively correlated in the mother-reared group, but not in the nursery-reared group. Overall, these results provide preliminary evidence that experience with ECE could help to maintain a balanced cortisol:dehydroepiandrosterone ratio, possibly indicative of a healthy stress response. Further examination of this ratio in hair is needed to support this hypothesis. These observations may also suggest that nursery rearing could have persistent effects, including dysregulation of the hypothalamic-pituitary-adrenal axis, apparent in the unbalanced cortisol:dehydroepiandrosterone ratio. Together these findings are consistent with the growing literature that supports the use of ECE to promote nonhuman primate wellbeing and healthy development.

category: zoology


title: Ikaros family proteins regulate developmental windows in the mouse retina through convergent and divergent transcriptional programs

abstract: Temporal identity factors regulate the competence of neural progenitors to generate specific cell types in a time-dependent manner, but how they operate remains poorly defined. In the developing mouse retina, the Ikaros zinc finger transcription factor Ikzf1 regulates the production of early-born cell types, except cone photoreceptors. In this study we show that Ikzf4, another Ikaros family protein, cooperates with Ikzf1 to control cone photoreceptor production during early stages of retinal development, whereas at late stages, when Ikzf1 is no longer expressed in progenitors, Ikzf4 is instead required for Muller glia production. Using CUT&RUN sequencing, we find that both Ikzf1 and Ikzf4 generally bind to the same genes involved in cone development and other early-born fates, but at different cis-regulatory elements. In late-stage progenitors, Ikzf4 re-localizes to bind target genes involved in Muller glia development and regulate their expression. Specifically, we show that Ikzf4 maintains Hes1 expression in differentiating cells using two Ikzf GGAA binding sites at the Hes1 promoter, thereby favouring Muller glia fate commitment. These results uncover a combinatorial role for Ikaros family members in nervous system development and provide mechanistic insights on how they temporally regulate cell fate output.


title: High Efficiency Recombinant Protein Purification Using mCherry and YFP Nanobody Affinity Matrices

abstract: Mammalian cell lines are important expression systems for large proteins and protein complexes, particularly when the acquisition of post-translational modifications in the proteins native environment is desired. However, low or variable transfection efficiencies are challenges that must be overcome to use such an expression system. Expression of recombinant proteins as a fluorescent protein fusion enables real-time monitoring of protein expression, and also provides an affinity handle for one-step protein purification using a suitable affinity reagent. Here we describe a panel of anti-GFP and anti-mCherry nanobody affinity matrices and their efficacy for purification of GFP/YFP or mCherry fusion proteins. We define the molecular basis by which they bind their target protein using X-ray crystallography. From these analyses we define an optimal pair of nanobodies for purification of recombinant protein tagged with GFP/YFP or mCherry, and demonstrate these nanobody-sepharose supports are stable to many rounds of cleaning and extended incubation in denaturing conditions. Finally, we demonstrate the utility of the mCherry-tag system by using it to purify recombinant human Topoisomerase 2 expressed in HEK293F cells. The mCherry-tag and GFP/YFP-tag expression systems can be utilized for recombinant protein expression individually or in tandem for mammalian protein expression systems where real-time monitoring of protein expression levels and a high-efficiency purification step is needed.

category: biochemistry


title: Fatigue Metabolites of Large Yellow Croaker and Construction of Swimming Model

abstract: A trend in large yellow croaker (Larimichthys crocea) aquaculture is to establish new production sites that are suitable for extreme weather conditions. However, continuous and strong currents can harm fish welfare. To determine the location of the net cage, it is necessary to assess the swimming ability of large yellow croaker. Currently, our research on large yellow croakers is focusing on behavior analysis. This article investigates the effect of swimming large yellow croakers on metabolites in the body by examining the preferred speed of the group and the endurance swimming ability of single-tailed fish. We evaluated the factors that influence the large yellow croakers swimming fatigue by quantifying the content of metabolites and constructed the endurance swimming model using those results. Various results showed large yellow croaker populations tend to grow in low-velocity environments, and this matches their traditional habitat. The samples were taken at different swimming times at a flow rate of 0.35 m/s. According to the results of the metabolite content determination, blood glucose levels is closely related to swimming ability in large yellow croakers. The content of liver glycogen, which regulates blood glucose concentration, decreases in a certain linear relationship. The endurance swimming model of large yellow croaker was constructed according to the changes of liver glycogen content. The goals of this article are to provide a deeper understanding of the physiological characteristics of large yellow croaker swimming, and to provide a reference for choosing fishing and cage sites for large yellow croaker.


title: Transplantable human thyroid organoids generated from embryonic stem cells to rescue hypothyroidism

abstract: The function of the thyroid gland is to capture iodide in order to synthesize hormones that act on almost all tissues and are essential for normal growth and metabolism. Low plasma levels of thyroid hormones lead to hypothyroidism, which is one of the most common disorder in humans which is not always satisfactorily treated by lifelong hormone replacement. Therefore, in addition to the lack of in vitro tractable models to study human thyroid development, differentiation and maturation, there is a need for new therapeutic approaches that involve replacement of thyroid tissue responsive to changing demands for thyroid hormone. Here we report the first transplantable thyroid organoids derived from human embryonic stem cells capable of restoring plasma thyroid hormone to athyreotic mice as a proof of concept for future therapeutic development.


title: Intron dynamics reveal principles of gene regulation during the maternal-to-zygotic transition

abstract: The maternal-to-zygotic transition (MZT) is a conserved embryonic process in animals where developmental control shifts from the maternal to zygotic genome. A key step in this transition is zygotic transcription, and deciphering the MZT requires classifying newly transcribed genes. However, due to current technological limitations, this starting point remains a challenge for studying many species. Here we present an alternative approach that characterizes transcriptome changes based solely on RNA-seq data. By combining intron-mapping reads and transcript-level quantification, we characterized transcriptome dynamics during the Drosophila melanogaster MZT. Our approach provides an accessible platform to investigate transcriptome dynamics that can be applied to the MZT in non-model organisms. In addition to classifying zygotically transcribed genes, our analysis revealed that over 300 genes express different maternal and zygotic transcript isoforms due to alternative splicing, polyadenylation, and promoter usage. The vast majority of these zygotic isoforms have the potential to be subject to different regulatory control, and over two-thirds encode different proteins. Thus, our analysis reveals an additional layer of regulation during the MZT, where new zygotic transcripts can generate additional proteome diversity.


title: Mechanisms of modulation of pre-mRNA 3D structural scaffolds for splicing substrate definition

abstract: Coordination of different serine-arginine-rich (SR) proteins - a class of critical splicing activators - facilitates recognition of the highly degenerate mammalian splice signal sequences against the background sequences. Yet, the mechanistic details of their actions remain unclear. Here we show that cooperative binding of SR proteins to exonic and intronic motifs remodels the pre-mRNA 3D structural scaffold. The scaffold generated by the pre-mRNA-specific combinations of different SR proteins in an appropriate stoichiometry is recognized by U1 snRNP - the 5' splice site recognizing factor. A large excess of U1 snRNP particles displaces majority of the bound SR protein molecules from the remodeled pre-mRNA. A higher than optimal stoichiometry of SR proteins occludes the binding sites on the pre-mRNA, raising the U1 snRNP levels required for SR protein displacement and potentially impeding spliceosome assembly. This novel splicing-related function of U1 snRNP is important for distinguishing the substrate and the non-substrate by U2AF65 - the primary 3' splice site-recognizing factor. Overall, this work elucidates early regulatory steps of mammalian splicing substrate definition by SR proteins.


title: Mechanisms of splicing substrate definition by modulation of pre-mRNA 3D structural scaffolds


title: Automated identification of cell-type-specific genes and alternative promoters

abstract:
BackgroundIdentifying key transcriptional features, such as genes or transcripts, involved in cellular differentiation remains a challenging problem. Current methods for identifying key transcriptional features predominantly rely on pairwise comparisons among different cell types. These methods also identify long lists of differentially expressed transcriptional features. Combining the results from many such pairwise comparisons to find the transcriptional features specific only to one cell type is not straightforward. Thus, one must have a principled method for amalgamating pairwise cell type comparisons that makes full use of prior knowledge about the developmental relationships between cell types.

MethodWe developed Cell Lineage Analysis (CLA), a computational method which identifies transcriptional features with expression patterns that discriminate cell types, incorporating Cell Ontology knowledge on the relationship between different cell types. CLA uses random forest classification with a stratified bootstrap to increase the accuracy of binary classifiers when each cell type have a different number of samples. Regularized random forest results in a classifier that selects few but important transcriptional features. For each cell type pair, CLA runs multiple instances of regularized random forest and reports the transcriptional features consistently selected. CLA not only discriminates individual cell types but can also discriminate lineages of cell types related in the developmental hierarchy.

ResultsWe applied CLA to Functional Annotation of the Mammalian Genome 5 (FANTOM5) data and identified discriminative transcription factor and long non-coding RNA(lncRNA) genes for 71 human cell types.With capped analysis of gene expression (CAGE) data, CLA identified individual cell-type-specific alternative promoters for cell surface markers. Compared to random forest with a standard bootstrap approach, CLAs stratified bootstrap approach improved the accuracy of gene expression classification models for more than 95% of 2060 cell type pairs examined. Applied on 10X Genomics single-cell RNA-seq data for CD14+ monocytes and FCGR3A+ monocytes, CLA selected only 13 discriminative genes. These genes included the top 9 out of 370 significantly differentially expressed genes obtained from conventional differential expression analysis methods.

DiscussionOur CLA method combines tools to simplify the interpretation of transcriptome datasets from many cell types. It automates the identification of the most differentially expressed genes for each cell type pairs CLAs lineage score allows easy identification of the best transcriptional markers for each cell type and lineage in both bulk and single-cell transcriptomic data.

AvailabilityCLA is available at https://cla.hoffmanlab.org. We deposited the version of the CLA source with which we ran our experiments at https://doi.org/10.5281/zenodo.3630670. We deposited other analysis code and results at https://doi.org/10.5281/zenodo.5735636.


title: A temporal sequence of thalamic activity unfolds at transitions in behavioral arousal state

abstract: The moment of awakening from sleep reflects a profound transformation in neural activity and behavior. The thalamus is a key controller of arousal state, but whether its diverse nuclei exhibit coordinated or distinct activity at transitions in behavioral arousal state is not known. Using fast fMRI at ultra-high field (7 Tesla), we measured sub-second activity across thalamocortical networks and within nine thalamic nuclei to delineate these dynamics during spontaneous transitions in behavioral arousal state. We discovered a stereotyped sequence of activity across thalamic nuclei that preceded behavioral arousal after a period of inactivity, followed by widespread cortical deactivation. These thalamic dynamics were linked to whether participants remained awake or fell back asleep, with unified thalamic activation reflecting subsequent maintenance of awake behavior. These results provide an outline of the complex interactions across thalamocortical circuits that orchestrate arousal state transitions, and additionally, demonstrate that fast fMRI can resolve sub-second subcortical dynamics in the human brain.

category: neuroscience


title: Distributed processing for action control by prelimbic circuits targeting anterior-posterior dorsal striatal subregions.

abstract:
Fronto-striatal circuits have been extensively implicated in the cognitive control of behavioral output for both social and appetitive rewards. The functional diversity of prefrontal cortical populations is strongly dependent on their synaptic targets, with control of motor output strongly mediated by connectivity to the dorsal striatum. Despite evidence for functional diversity along the anterior-posterior axis of the dorsomedial striatum (DMS), it is unclear how distinct fronto- striatal sub-circuits support neural computations essential for action selection. Here we identify prefrontal populations targeting distinct DMS subregions and characterize their functional roles. We first performed neural circuit tracing to reveal segregated prefrontal populations defined by anterior/posterior dorsomedial striatal target. We then probed the functional relevance of these parallel circuits via in vivo calcium imaging and temporally precise causal manipulations during a feedback-based 2-alternative choice task. Single-photon imaging revealed circuit-specific representations of task-relevant information with prelimbic neurons targeting anterior DMS (PL::A- DMS) uniquely encoded choices and responses to negative outcomes, while prelimbic neurons targeting posterior DMS (PL::P-DMS) encoded internal representations of value and positive outcomes contingent on prior choice. Consistent with this distributed coding, optogenetic inhibition of PL::A-DMS circuits strongly impacted choice monitoring and behavioral control in response to negative outcomes while perturbation of PL::P-DMS signals impaired task engagement and strategies following positive outcomes. Di-synaptic retrograde tracing uncovered differences in afferent connectivity that may underlie these pathways functional divergence. Together our data uncover novel PL populations engaged in distributed processing for action control.

SUMMARYO_LIPrelimbic cortex engages A- and P-DMS via distinct circuits
C_LIO_LIPL::A-DMS and PL::P-DMS pathways encode divergent aspects of a simple goal-directed task
C_LIO_LIPL::A-DMS pathways shape responding to negative outcomes via multiple mechanisms
C_LIO_LIPL::P-DMS pathways guide engagement and choices in response to positive outcomes
C_LIO_LIAfferent connectomes of PL neurons defined by A-P DMS target are distinct
C_LI


title: Input-specific control of interneuron numbers in nascent striatal networks

abstract: The assembly of functional neuronal circuits requires appropriate numbers of distinct classes of neurons, but the mechanisms through which their relative proportions are established remain poorly defined. Investigating the mouse striatum, here we found that the two most prominent subtypes of striatal interneurons, parvalbumin-expressing (PV+) GABAergic and cholinergic (ChAT+) interneurons, undergo extensive programmed cell death between the first and second postnatal weeks. Remarkably, the survival of PV+ and ChAT+ interneurons is regulated by distinct mechanisms mediated by their specific afferent connectivity. While long-range cortical inputs control PV+ interneuron survival, ChAT+ interneuron survival is regulated by local input from the medium spiny neurons. Our results identify input-specific circuit mechanisms that operate during the period of programmed cell death to establish the final number of interneurons in nascent striatal networks.


title: Genomic architecture controls spatial structuring in Amazonian birds

abstract: Large rivers are ubiquitously invoked to explain the distributional limits and speciation of the Amazon Basins mega-diversity. However, inferences on the spatial and temporal origins of Amazonian species have narrowly focused on evolutionary neutral models, ignoring the potential role of natural selection and intrinsic genomic processes known to produce heterogeneity in differentiation across the genome. To test how genomic architecture impacts our ability to reconstruct patterns of spatial diversification across multiple taxa, we sequenced whole genomes for populations of bird species that co-occur in southeastern Amazonian. We found that phylogenetic relationships within species and demographic parameters varied across the genome in predictable ways. Genetic diversity was positively associated with recombination rate and negatively associated with the species tree topology weight. Gene flow was less pervasive in regions of low recombination, making these windows more likely to retain patterns of population structuring that matched the species tree. We further found that approximately a third of the genome showed evidence of selective sweeps and linked selection skewing genome-wide estimates of effective population sizes and gene flow between populations towards lower values. In sum, we showed that the effects of intrinsic genomic characteristics and selection can be disentangled from the neutral processes to elucidate how speciation hypotheses and biogeographic patterns are sensitive to genomic architecture.


title: Unraveling the kinetochore nanostructure in Schizosaccharomyces pombe using multi-color single-molecule localization microscopy

abstract:
The key to ensuring proper chromosome segregation during mitosis is the kinetochore complex. This large and tightly regulated multi-protein complex links the centromeric chromatin to the microtubules attached to the spindle pole body and as such leads the segregation process. Understanding the architecture, function and regulation of this vital complex is therefore essential. However, due to its complexity and dynamics, only its individual subcomplexes could be studied in high-resolution structural detail so far.

In this study we construct a nanometer-precise in situ map of the human-like regional kinetochore of Schizosaccharomyces pombe (S. pombe) using multi-color single-molecule localization microscopy (SMLM). We measure each kinetochore protein of interest (POI) in conjunction with two reference proteins, cnp1CENP-A at the centromere and sad1 at the spindle pole. This arrangement allows us to determine the cell cycle and in particularly the mitotic plane, and to visualize individual centromere regions separately. From these data, we determine protein distances within the complex using Bayesian inference, establish the stoichiometry of each POI for individual chromosomes and, consequently, build an in situ kinetochore model for S.pombe with so-far unprecedented precision. Being able to quantify the kinetochore proteins within the full in situ kinetochore structure, we provide valuable new insights in the S.pombe kinetochore architecture.


title: Direct lysis RT-qPCR of SARS-CoV-2 in cell culture supernatant allows for fast and accurate quantification of virus, opening a vast array of applications

abstract: An enormous global effort is being made to study SARS-CoV-2 and develop safe and effective treatments. Studying the entire virus replication cycle of SARS-CoV-2 is essential to identify host factors and treatments to combat the infection. However, quantification of released virus often requires lengthy procedures, such as endpoint dilution assays or reinfection with engineered reporter viruses. Quantification of viral RNA in cell supernatant is faster and can be performed on clinical isolates. However, viral RNA purification is expensive in time and resources and often unsuitable for high-throughput screening. Here, we show a direct lysis RT-qPCR method allowing sensitive, accurate, fast, and cheap quantification of SARS-CoV-2 in culture supernatant. During lysis, the virus is completely inactivated, allowing further processing in low containment areas. This protocol facilitates a wide array of high- and low-throughput applications from basic quantification to studying the biology of SARS-CoV-2 and to identify novel antiviral treatments in vitro.


title: SARS-CoV-2 Delta derivatives impact on neutralization of Covishield recipient sera

abstract: The emergence of SARS-CoV-2 Delta variant and its derivatives has created grave public health problem worldwide. The high transmissibility associated with this variant has led to daily increase in the number of SARS-CoV-2 infections. Delta variant has slowly dominated the other variants of concern. Subsequently, Delta has further mutated to Delta AY.1 to Delta AY.126. Of these, Delta AY.1 has been reported from several countries including India and considered to be highly infectious and probable escape mutant. Considering the possible immune escape, we had already evaluated the efficacy of the BBV152 against Delta and Delta AY.1 variants. Here, we have evaluated the neutralizing potential of sera of COVID-19 naive vaccinees (CNV) immunized with two doses of vaccine, COVID-19 recovered cases immunized with two doses of vaccine (CRV) and breakthrough infections (BTI) post immunization with two doses of vaccine against Delta, Delta AY.1 and B.1.617.3 using 50% plaque reduction neutralization test (PRNT50). Our study observed low NAb titer in CNV group against all the variants compared to CRV and BTI groups. Delta variant has shown highest reduction of 27.3-fold in NAb titer among CNV group compared to other groups and variants. Anti-S1-RBD IgG immune response among all the groups was also substantiated with NAb response. Compromised neutralization was observed against Delta and Delta AY.1 compared B.1 in all three groups. However, it provided protection against severity of the disease and fatality.


title: X-MyoNET: Biometric Identification using Deep Processing of Transient Surface Electromyography

abstract: The rapid development of the Internet and various applications such as the Internet of Medical Things (IoMT) has raised substantial concerns about personal information security. Conventional methods (e.g., passwords) and classic biological features (e.g., fingerprints) are security deficient because of potential information leakage and hacking. Biometrics that express behavioral features suggest a robust approach to achieving information security because of the corresponding uniqueness and complexity. In this paper, we consider identifying human subjects based on their transient neurophysiological signature captured using multichannel upper-limb surface electromyography (sEMG). An explainable artificial intelligence (XAI) approach is proposed to process the internal dynamics of temporal sEMG signals. We propose and prove the suitability of "transient sEMG" as a biomarker that can identify individuals. For this, we utilize the Gradient-weighted Class Activation Mapping (Grad-CAM) analysis to explain the networks attention. The outcome not only decodes and makes the unique neurophysiological pattern (i.e., motor unit recruitment during the transient phase of contraction) associated with each individual visualizable but also generates an optimizing two-dimensional (2D) spectrotemporal mask used to significantly reduce the size of the model and the trainable parameters. The resulting mask selectively and systematically samples the spectrotemporal characteristics of the users neurophysiological responses, discarding 40% of the input space while securing the accuracy of about 74% with much shallower neural network architecture. In the systematic comparative study, we find that our proposed model outperforms several state-of-the-art algorithms. For broader impacts, we anticipate our design of a compact, practical, interpretable, and robust identification system that requires only a minimal number of gestures and sensors (only 7% of the entire data set) to be a starting point for small and portable identification hardware.


title: Dynamic Resting State Motor Network Connectivity of Neurotypical Children, the Groundwork for Network-Guided Therapy in Childhood Movement Disorders

abstract:
BackgroundNormative childhood motor network resting-state fMRI effective connectivity is undefined, yet necessary for translatable dynamic resting-state network informed treatments in pediatric movement disorders.

MethodCross-spectral dynamic causal modelling of resting-state fMRI was investigated in 19 neurotypically developing 5-7-year-old children. Fully connected six-node motor network models were created for each hemisphere including primary motor cortex, striatum, subthalamic nucleus, globus pallidus internus, thalamus, and contralateral cerebellum. Parametric Empirical Bayes with exhaustive Bayesian model reduction and Bayesian modeling averaging were used to create a group model for each hemisphere; Purdue Pegboard Test (PPBT) scores for relevant hand motor behavior were also entered as a covariate at the group level to determine the brain-behavior relationship.

ResultsOverall, the resting-state functional MRI effective connectivity of motor cortico-basal ganglia-cerebellar networks was similar across hemispheres, with greater connectivity in the left hemisphere. The motor network effective connectivity relationships between the nodes were consistent and robust across subjects. Additionally, the PPBT score for each hand was positively correlated with the thalamus to contralateral cerebellum connection.

DiscussionThe normative effective connectivity from resting-state functional MRI in children largely reflect the direction of inter-nodal signal predicted by other prior modalities and was consistent and robust across subjects, with differences from these prior task-dependent modalities that likely reflect the motor rest-action state during acquisition. Effective connectivity of the motor network was correlated with motor behavior, indicating effective connectivity brain-behavior relationship has physiological meaning in the normally developing. Thus, it may be helpful for future studies in children with movement disorders, wherein comparison to normative effective connectivity will be critical for network-targeted intervention.

Impact StatementThis is the first study to use pediatric resting-state functional MRI to create a normative effective connectivity model of the motor network and to also show correlation with behavior, which may have therapeutic implications for children with movement disorders.


title: Effect of spatiotemporally changing environment on serial dependence in ensemble representations

abstract: The recent visual past has a strong impact on our current perception. Recent studies of serial dependence in perception show that low-level adaptation repels our current perception away from previous stimuli1-5 whereas post-perceptual decision attracts perceptual report toward the immediate past6-12. In their studies, these repulsive and attractive biases were observed with different task demands perturbing ongoing sequential process. Therefore, it is unclear whether the opposite biases arise naturally in navigating complex real-life environments. Here we only manipulated the environmental statistics to characterize how serially dependent perceptual decisions unfold in spatiotemporally changing visual environments. During sequential mean orientation adjustment task on the array of Gabor patches, we found that the repulsion effect dominated only when ensemble variance increased across consecutive trials whereas the attraction effect prevailed when ensemble variance decreased or remained the same. The observed attractive bias by high- to-low-variance stimuli and repulsive bias by low-to-high-variance stimuli were reinforced by the repeated exposure to the low and the high ensemble variance, respectively. Further, this variance-dependent differential pattern of serial dependence in ensemble representation remained the same regardless of whether observers had a prior knowledge of environmental statistics or not. We used a Bayesian observer model constrained by visual adaptation13,14 to provide a unifying account of both attractive and repulsive bias in perception. Our results establish that the temporal integration and segregation of visual information is flexibly adjusted through variance adaptation.


title: Identifying potential key genes and existing drugs for Multiple sclerosis, Schizophrenia, and Autism- an in silico approach

abstract: Nowadays, neurological conditions are a major concern as it not only preys on a patients health but also is a huge economic burden that is placed on the patients family. The diagnosis and treatment of disease sometimes cause methodological limitations. This is mainly common for individuals who have the signs of MS and schizophrenia (SZ). Patients suffering from multiple sclerosis are more likely to develop schizophrenia. Besides, a significant portion of patients who have been diagnosed with Autism Spectrum Disorder (ASD) later acquire the symptoms of Schizophrenia. In this study, we used bioinformatics tools to determine differentially expressed genes (DEGs) in all these diseases, and then we created a protein-protein interaction network using the online software STRING and identified 15 significant genes with the help of Cytohubba a plug-in tool in Cytoscape, the offline software (version3.8.2). We then used a drug-gene interaction database to conduct a drug-gene interaction study of the 15 hub genes and from there we identified 37 FDA-approved drugs. These findings may provide a new and common therapeutic approach for MS, SZ, and ASD therapy.


title: Temporal-sensitive prefrontal involvement in associating confidence with task performance illustrates metacognitive introspection in Old World monkeys (Macaca mulatta)

abstract: Metacognition refers to the ability to be aware of ones own cognition. Ample evidence indicates that metacognition in the human primate is highly dissociable from cognition, specialized across domains, and subserved by distinct neural substrates. However, these aspects remain relatively understudied in macaque monkeys. In the present study, we investigated the functionality of macaque metacognition by combining a confidence proxy, hierarchical Bayesian meta-d' computational modelling, and a single-pulse transcranial magnetic stimulation technique. We found that Brodmann area 46d (BA46d) played a critical role in supporting metacognition independent of task performance; we also found that the critical role of this region in meta-calculation was time-sensitive. Additionally, we report that macaque metacognition is highly domain-specific with respect to memory and perception decisions. These findings carry implications for our understanding of metacognitive introspection within the primate lineage.


title: Time-sensitive prefrontal involvement in associating confidence with task performance illustrates metacognitive introspection in monkeys


title: AraC binds the p75NTR transmembrane domain to induce neurodegeneration in mature neurons.

abstract:
BackgroundCytosine arabinoside (AraC) is one of the main therapeutic treatments for several types of cancer including acute myeloid leukaemia. However, after high dose AraC chemotherapy regime, patients develop severe neurotoxicity and neurodegeneration in the central nervous system leading to cerebellar ataxia, dysarthria, nystagmus, somnolence and drowsiness. AraC induces apoptosis in dividing cells, however, the mechanism by which it leads to neurite degeneration and cell death in mature neurons remains unclear. We hypothesized that the upregulation of the death receptor p75NTR is responsible for AraC-mediated neurodegeneration and cell death in leukemia patients undergoing AraC treatment.

MethodsTo determine the role of AraC-p75NTR signalling in degeneration of mature cerebellar granule neurons, we used primary cultures from p75NTR knockout and p75NTRCys259 mice. Evaluation of neurodegeneration, cell death and p75NTR signalling was done by immunohistochemistry and immunoblotting. To assess the direct interaction between AraC and p75NTR, we performed isothermal dose response-cellular thermal shift and AraTM assays as well as Homo-FRET anisotropy imaging.

ResultsWe show that AraC induces neurite degeneration and programmed cell death of mature cerebellar granule neurons in a p75NTR-dependent manner. Mechanistically, AraC binds to Proline 252 and Cysteine 256 of the p75NTR transmembrane domain and selectively uncouples p75NTR from the NF{kappa}B survival pathway. This in turn, exacerbates the activation of the cell death/JNK pathway by recruitment of TRAF6 to p75NTR.

ConclusionOur findings identify p75NTR as a novel molecular target to develop treatments to counteract AraC-mediated neurodegeneration.


title: Maternal parity affects Day 8 embryo gene expression in old mares

abstract:
As sport career is a priority in most of equine breeds, mares are frequently bred for the first time at an advanced age. Both age and first gestation were shown to have a deleterious effect on reproduction outcomes, respectively on fertility and offspring weight but the effect mares parity in older mares on embryo quality has never been considered. The aim of this project was to determine the effect of old mares nulliparity on gene expression in embryos. Day 8 post ovulation embryos were collected from old (10-16 years old) nulliparous (ON, N=5) or multiparous (OM, N=6) non-nursing Saddlebred mares, inseminated with the semen of one stallion. Pure (TE_part) or inner cell mass enriched (ICMandTE) trophoblast were obtained by embryo bisection and paired end, non-oriented RNA sequencing (Illumina, NextSeq500) was performed on each hemi-embryo. To discriminate gene expression in the ICM from that in the TE, deconvolution (DeMixT R package) was used on the ICMandTE dataset. Differential expression was analyzed (DESeq2) with embryo sex and diameter as cofactors using a false discovery rate <0.05 cutoff. Although the expression of only a few genes was altered by mares nulliparity (33 in ICM and 23 in TE), those genes were related to nutrient exchanges and responses to environment signaling, both in ICM and TE, suggesting that the developing environment from these mares are not optimal for embryo growth. In conclusion, being nulliparous and old does not seem to be the perfect match for embryonic development in mares.

Summary sentenceMares parity in old mares impacts the expression of genes related to development and molecule exchanges in ICM and TE of blastocysts suggesting an adaptation to an altered environment.


title: Characterising genome architectures using Genome Decomposition Analysis

abstract:
Genome architecture describes how genes and other features are arranged in genomes. These arrangements reflect the evolutionary pressures on genomes and underlie biological processes such as chromosomal segregation and the regulation of gene expression. We present a new tool called Genome Decomposition Analysis (GDA) that characterises genome architectures and acts as an accessible approach for discovering hidden features of a genome assembly. With the imminent deluge of high quality genome assemblies from projects such as the Darwin Tree of Life and the Earth BioGenome Project, GDA has been designed to facilitate their exploration and the discovery of novel genome biology. We highlight the effectiveness of our approach in characterising the genome architectures of single-celled eukaryotic parasites from the phylum Apicomplexa and show that it scales well to large genomes.

SignificanceGenome sequencing has revealed that there are functionally important arrangements of genes, repetitive elements and regulatory sequences within chromosomes. Identifying these arrangements requires extensive computation and analysis. Furthermore, improvements in genome sequencing technology and the establishment of consortia aiming to sequence all species of eukaryotes mean that there is a need for high throughput methods for discovering new genome biology. Here we present a software pipeline, named GDA, which determines the patterns of genomic features across chromosomes and uses these to characterise genome architecture. We show that it recapitulates the known genome architecture of several Apicomplexan parasites and use it to identify features in a recently sequenced, less well-characterised genome. GDA scales well to large genomes and is freely available.