bluuebunny/crossref_metadata_2025 huggingface dataset:
Zebrafish anterior segment mesenchyme progenitors are defined by function of tfap2a but not sox10
Authors: Vöcking Oliver , Van Der Meulen K , Patel M.K , Famulski J.K
Published: October 2022

The anterior segment is a critical component of the visual system. Developing independent of the retina, the AS relies partially on cranial neural crest cells (cNCC) as its earliest progenitors. The cNCCs are thought to first adopt a periocular mesenchyme (POM) fate and subsequently target to the AS upon formation of the rudimentary retina. AS targeted POM is termed anterior segment mesenchyme (ASM). However, it remains unknown when and how the switch from cNCC to POM or POM to ASM takes place. As such, we sought to visualize the timing of these transitions and identify the regulators of this process using the zebrafish embryo model. Using two color fluorescencein situhybridization, we tracked cNCC and ASM target gene expression from 12-24hpf. In doing so, we identified atfap2aandfoxc1aco-expression at 16hpf, identifying the earliest ASM to arrive at the AS. Interestingly, expression of two other key regulators of NCC,foxD3andsox10was not associated with early ASM. Functional analysis of tfap2a, foxd3 and sox10 revealed that tfap2a and foxd3 are both critical regulators of ASM specification and AS formation while sox10 was dispensable for either specification or development of the AS. Using genetic knockout lines, we show that in the absence of tfap2a or foxD3 function ASM cells are not specified, and subsequently the AS is malformed. Conversely, sox10 genetic mutants or CRISPR Cas9 injected embryos displayed no defects in ASM specification, migration or the AS. Lastly, using transcriptomic analysis, we show that GFP+ cNCCs derived from Tg[foxd3:GFP] and Tg[foxc1b:GFP] share expression profiles consistent with ASM development whereas cNCCs isolated from Tg[sox10:GFP] exhibit expression profiles associated with vasculogenesis, muscle function and pigmentation. Taken together, we identify the earliest stage of anterior segment mesenchyme (ASM) specification to be approximately 16hpf and involve tfap2a/foxc1a positive cNCCs.
High bacillary burden and the ESX-1 type VII secretion system promote MHC class I presentation byMycobacterium tuberculosisinfected macrophages to CD8 T-cells
Authors: Mott Daniel , Yang Jason , Baer Christina , Papavinasasundaram Kadamba , Sassetti Christopher M. , Behar Samuel M.
Published: October 2022

Mycobacterium tuberculosis(Mtb) subverts host defenses to persist in macrophages despite immune pressure. CD4 T-cells can recognize macrophages infected with a single bacillusin vitro. Under identical conditions, CD8 T-cells inefficiently recognize infected macrophages and fail to restrict Mtb growth, although they can inhibit Mtb growth during high burden intracellular infection. We show that high intracellular Mtb numbers cause macrophage death, leading other macrophages to scavenge cellular debris and cross-present the TB10.4 antigen to CD8 T-cells. Presentation by infected macrophages requires Mtb to have a functional ESX-1 type VII secretion system. These data indicate that phagosomal membrane damage and cell death promote class I MHC presentation of the immunodominant antigen TB10.4 by macrophages. Although this mode of antigen-presentation stimulates cytokine production that we presume would be host beneficial; killing of uninfected cells could worsen immunopathology. We suggest that shifting the focus of CD8 T-cell recognition to uninfected macrophages would limit the interaction of CD8 T-cells with infected macrophages and impair CD8 T-cell mediated resolution of tuberculosis.
Structural and molecular biology of Acheta domesticus segmented densovirus, the first parvovirus to harbor a bipartite genome
Authors: Penzes Judit J. , Pham Hanh T. , Chipman Paul , Smith Emmanuel W. , McKenna Robert , Tijssen Peter
Published: October 2022

Parvoviruses (familyParvoviridae) are defined by their linear monopartite ssDNA genome, T=1 icosahedral capsid, and distinct structural (VP) and non-structural (NS) protein expression cassettes within their genome. Here, we report the first parvovirus with a segmented genome, Acheta domesticus segmented densovirus (AdSDV), a house cricket (Acheta domesticus) pathogen. The AdSDV harbors its NS and VP cassettes on two separate segmented genomes. Its VP segment acquired a phospholipase A2-encoding gene via inter-subfamily recombination, which is absent from its capsid. The AdSDV evolved a transcription profile in response to its multipartite replication strategy that has diverged from itsBrevihamaparvovirusancestors. Furthermore, AdSDV assembles three capsid populations, which package one genome segment per particle. The cryoEM structures of these three capsids (2.3 to 3.3 Å resolution) reveal a genome packaging mechanism, which differs from other parvoviruses. This study provides a new perspective on ssDNA genome segmentation and on the plasticity of parvovirus biology.
Synaptotagmin-9 and Tomosyn-1 molecular complex regulates Stx1A SNAREs to inhibit insulin secretion from pancreatic β-cells
Authors: Rahman Md Mostafizur , Pathak Asmita , Schueler Kathryn L , Al Sharif Haifa , Michl Ava , Alexander Justin , Kim Jeonga-a , Chapman Edwin , Bhatnagar Sushant
Published: October 2022

Stimulus-coupled insulin secretion from β-cells involves the fusion of insulin granules to the plasma membrane (PM) via SNARE complex formation—a cellular process key for maintaining whole-body glucose homeostasis. Optimal insulin secretion depends on how the clamping of SNAREs is released, rendering granules fusogenic. We show that an insulin granule protein synaptotagmin-9 (Syt9) deletion in lean mice increased glucose clearance, random-fed plasma insulin levels, and insulin secretion (in vivo and ex vivo islets) without affecting insulin sensitivity. These outcomes demonstrate that Syt9 has an inhibitory function in insulin secretion. Moreover, Syt9 interacts with PM-Stx1A and soluble Tomosyn-1 proteins to form non-fusogenic complexes between PM and insulin granules, preventing Stx1A-SNARE formation and insulin secretion. Furthermore, Syt9 inhibits SNARE-complex formation by posttranscriptional regulation of Tomosyn-1. We conclude that Syt9 and Tomosyn-1 are endogenous inhibitors that modulate Stx1A availability to determine β-cell secretory capacity.

Highlights

Synaptotagmin-9 inhibits biphasic insulin secretion from β-cells.

Synaptotagmin-9, syntaxin-1A, and Tomosyn-1 forms a molecular complex that decreases the availability of syntaxin-1A to form SNARE complexes in insulin secretion.

Synaptotagmin-9–mediated inhibition of insulin secretion occurs through post-transcriptional regulation of Tomosyn-1.
Additivity predicts the efficacy of most approved combination therapies for advanced cancer
Authors: Hwangbo Haeun , Patterson Sarah , Dai Andy , Plana Deborah , Palmer Adam C.
Published: October 2022

Most advanced cancers are treated with drug combinations. Rational designs aim to identify synergistic drug interactions to produce superior treatments. However, metrics of drug interaction (i.e., synergy, additivity, antagonism) apply to pre-clinical experiments, and there has been no established method to quantify synergy versus additivity in clinical settings. Here, we propose and apply a model of drug additivity for progression-free survival (PFS) to assess if the clinical efficacies of approved drug combinations are more than, or equal to, the sum of their parts. This model accounts for the benefit from patient-to-patient variability in the best single drug response, plus the added benefit of the weaker drug per patient. Among FDA approvals for advanced cancers between 1995-2020, we identified 37 combinations across 13 cancer types where monotherapies and combination therapy could be compared. 95% of combination therapies exhibited progression-free survival times that were additive, or less than additive. Among a set of phase III trials with either positive or negative results published between 2014 and 2018, every combination that did improve PFS was expected to succeed by additivity (100% sensitivity) and most failures were expected to fail (78% specificity). This study has two key findings. First, a synergistic effect (more than additive) is neither a necessary nor even a common property of clinically effective drug combinations. Second, the predictable efficacy of many of the best drug combinations established over the past 25 years suggests that additivity can be used as a design principle for novel drug combinations and clinical trials.
Design of effective outpatient sentinel surveillance for COVID-19 decision-making: a modeling study
Authors: Toh Kok Ben , Runge Manuela , Richardson Reese AK , Hladish Thomas J , Gerardin Jaline
Published: October 2022

Background

Decision-makers impose COVID-19 mitigations based on public health indicators such as reported cases, which are sensitive to fluctuations in supply and demand for diagnostic testing, and hospital admissions, which lag infections by up to two weeks. Imposing mitigations too early has unnecessary economic costs, while imposing too late leads to uncontrolled epidemics with unnecessary cases and deaths. Sentinel surveillance of recently-symptomatic individuals in outpatient testing sites may overcome biases and lags in conventional indicators, but the minimal outpatient sentinel surveillance system needed for reliable trend estimation remains unknown.

Methods

We used a stochastic, compartmental transmission model to evaluate the performance of various surveillance indicators at reliably triggering an alarm in response to, but not before, a step increase in transmission of SARS-CoV-2. The surveillance indicators included hospital admissions, hospital occupancy, and sentinel cases with varying levels of sampling effort capturing 5, 10, 20, 50 or 100% of incident mild cases. We tested 3 levels of transmission increase, 3 population sizes, and condition of either simultaneous transmission increase, or lagged increase in older population. We compared the indicators’ performance at triggering alarm soon after, but not prior, to the transmission increase.

Results

Compared to surveillance based on hospital admissions, outpatient sentinel surveillance that captured at least 20% of incident mild cases could trigger alarm 2 to 5 days earlier for a mild increase in transmission and 6 days earlier for moderate or strong increase. Sentinel surveillance triggered fewer false alarms and averted more deaths per day spent in mitigation. When transmission increase in older populations lagged increase in younger populations by 14 days, sentinel surveillance extended its lead time over hospital admissions by an additional 2 days.

Conclusions

Sentinel surveillance of mild symptomatic cases can provide more timely and reliable information on changes in transmission to inform decision-makers in an epidemic like COVID-19.
Potential Misrepresentation of Inherited Breast Cancer Risk by Common Germline Alleles
Authors: Letsou William , Wang Fan , Moon Wonjong , Im Cindy , Sapkota Yadav , Robison Leslie L. , Yasui Yutaka
Published: October 2022

Hundreds of common variants have been found to confer small but significant differences in breast cancer risk, supporting the polygenic additive model of inherited risk. This widely accepted model is at odds with twin data indicating highly elevated risk in a subgroup of women. Using a novel closed-pattern-mining algorithm, we provide evidence that rare variants or haplotypes may underlie the association of breast cancer risk with common germline alleles. Our method, called Chromosome Overlap, consists in iteratively pairing chromosomes from affected individuals and looking for noncontiguous patterns of shared alleles without exhaustive enumeration. We applied Chromosome Overlap to haplotypes of genotyped SNPs from 9,011 female breast cancer cases from the UK Biobank (UKBB) at three topologically associating domains containing well-established common-allele “hits” for breast cancer. A total of 181,034 UKBB women of “white British” ancestry were used to assess the discovered haplotypes, and 55,346 cases and controls of European ancestry in the Discovery, Biology, and Risk of Inherited Variants in Breast Cancer (DRIVE) case-control study were used for replication. Out of twenty rare (frequency < ∼0.1%) risk haplotypes of large effect identified in UKBB atP< 1.0 × 10−5, four (hazard ratio: 4.22–20.2) were subsequently replicated in DRIVE (odds ratio: 2.13–11.9) atP< 0.05. Our results support the genetic heterogeneity and rare-variant/haplotype basis of breast cancer risk and suggest a novel type of “synthetic association” wherein common risk alleles on a rare risk haplotype may misrepresent disease risk through their tagging of many “false positive” haplotypes.

Significance

Chromosome Overlap reveals that common alleles identified by GWAS may be poor surrogates for underlying high-risk haplotypes, necessitating a reappraisal of the polygenic model of disease risk.
Career Self-Efficacy Disparities in Underrepresented Biomedical Scientist Trainees
Authors: Chatterjee Deepshikha , Jacob Gabrielle A. , Varvayanis Susi Sturzenegger , Wefes Inge , Chalkley Roger , Nogueira Ana T. , Fuhrmann Cynthia N. , Varadarajan Janani , Hubbard Nisan M. , Gaines Christiann H. , Layton Rebekah L. , Chaudhary Sunita
Published: October 2022

The present study examines racial, ethnic, and gender disparities in career self-efficacy amongst 6077 US citizens and US naturalized graduate and postdoctoral trainees. Respondents from biomedical fields completed surveys administered by the National Institutes of Health Broadening Experiences in Scientific Training (NIH BEST) programs across 17 US institutional sites. Graduate and postdoctoral demographic and survey response data were examined to evaluate the impact of intersectional identities on trainee career self-efficacy. The study hypothesized that race, ethnicity and gender, and the relations between these identities, would impact trainee career self-efficacy. The analysis demonstrated that racial and ethnic group, gender, specific career interests (academic principal investigator vs. other careers), and seniority (junior vs. senior trainee level) were, to various degrees, all associated with trainee career self-efficacy and the effects were consistent across graduate and postdoctoral respondents. Implications for differing levels of self-efficacy are discussed, including factors and events during training that may contribute to (or undermine) career self-efficacy. The importance of mentorship for building research and career self-efficacy of trainees is discussed, especially with respect to those identifying as women and belonging to racial/ethnic populations underrepresented in biomedical sciences. The results underscore the need for change in the biomedical academic research community in order to retain a diverse biomedical workforce.
Zebrafish Rif1 impacts zygotic genome activation, replication timing, and sex determination
Authors: Masser Emily A. , Noble Tyler D. , Siefert Joseph C. , Goins Duane , Sansam Courtney G. , Sansam Christopher L.
Published: October 2022

Deregulated DNA replication causes human developmental disorders and cancer, but we know little about how DNA replication is coordinated with changes in transcription and chromatin structure. The initiation of replication forks follows a spatiotemporal pattern called the replication timing program. We have developed the zebrafish into a model system to study the mechanisms by which the replication timing program changes during the extensive changes in the cell cycle, transcription, chromatin organization, and nuclear structure that occur during development. Our previous studies identified changes in DNA replication timing patterns occurring from the onset of zygotic transcription through gastrulation in zebrafish embryos. Rif1 is required for DNA replication timing in a wide range of eukaryotes. The broader role of Rif1 in establishing the replication timing program and chromatin structure during early vertebrate development remains unknown. We have generated Rif1 mutant zebrafish and have performed RNA sequencing and whole-genome replication timing analyses on multiple developmental stages. Rif1 mutants were viable but had a defect in female sex determination. Surprisingly, Rif1 loss predominantly affected DNA replication timing after gastrulation, while its impacts on transcription were more substantial during zygotic genome activation. Our results indicate that Rif1 has distinct roles in DNA replication and transcription control that manifest at different stages of development.
Barley MLA3 recognizes the host-specificity determinant PWL2 from rice blast (M. oryzae)
Authors: Brabham Helen J. , De La Cruz Diana Gómez , Were Vincent , Shimizu Motoki , Saitoh Hiromasa , Hernández-Pinzón Inmaculada , Green Phon , Lorang Jennifer , Fujisaki Koki , Sato Kazuhiro , Molnár István , Šimková Hana , Doležel Jaroslav , Russell James , Taylor Jodie , Smoker Matthew , Gupta Yogesh Kumar , Wolpert Tom , Talbot Nicholas J. , Terauchi Ryohei , Moscou Matthew J.
Published: October 2022

Plant nucleotide-binding leucine-rich repeat immune receptors (NLRs) directly or indirectly recognize pathogen-secreted effector molecules to initiate plant defense. Recognition of multiple pathogens by a single NLR is rare and usually occurs via monitoring for changes to host proteins; few characterized NLRs have been shown to recognize multiple effectors. The barley NLRMlahas undergone functional diversification andMlaalleles recognize host-adapted isolates of barley powdery mildew (Blumeria graminisf. sp.hordei; Bgh). Here, we show thatMla3also confers resistance to rice blast (Magnaporthe oryzae) in a dosage dependent manner. Using a forward genetic screen, we discovered that the recognized effector fromM. oryzaeisPWL2, a host range determinant factor that preventsM. oryzaefrom infecting weeping lovegrass (Eragrostis curvula).Mla3has therefore convergently evolved the capacity to recognize effectors from diverse pathogens.
Lineage plasticity in SCLC generates non-neuroendocrine cells primed for vasculogenic mimicry
Authors: Pearsall Sarah M , Williamson Stuart C , García Marqués Fernando J , Humphrey Sam , Hughes Ellyn , Shue Yan Ting , Bermudez Abel , Frese Kristopher K , Galvin Melanie , Carter Mathew , Priest Lynsey , Kerr Alastair , Zhou Cong , Oliver Trudy G. , Humphries Jonathan D , Humphries Martin J. , Blackhall Fiona , Cannell Ian G , Pitteri Sharon J , Hannon Gregory J , Sage Julien , Simpson Kathryn L , Dive Caroline
Published: October 2022

Introduction

Vasculogenic mimicry (VM), the process of tumor cell trans-differentiation to endow endothelial-like characteristics supportingde novovessel formation, is associated with poor prognosis in several tumor types, including small cell lung cancer (SCLC). In genetically engineered mouse models (GEMMs) of SCLC, NOTCH and MYC co-operate to drive a neuroendocrine (NE) to non-NE phenotypic switch and co-operation between NE and non-NE cells is required for metastasis. Here, we define the phenotype of VM-competent cells and molecular mechanisms underpinning SCLC VM using circulating tumor cell-derived explant (CDX) models and GEMMs.

Methods

We analysed perfusion within VM vessels and their association with NE and non-NE phenotypes using multiplex immunohistochemistry in CDX and GEMMs. VM-proficient cell subpopulations inex vivocultures were molecularly profiled by RNA sequencing and mass spectrometry. We evaluated their 3D structure and defined collagen-integrin interactions.

Results

We show that VM vessels are present in 23/25 CDX models and in 2 GEMMs. Perfused VM vessels support tumor growth and only Notch-active non-NE cells are VM-competentin vivoandex vivo, expressing pseudohypoxia, blood vessel development and extracellular matrix (ECM) organization signatures. On Matrigel, VM-primed non-NE cells re-model ECM into hollow tubules in an integrin β1-dependent process.

Conclusions

We identify VM as an exemplar of functional heterogeneity and plasticity in SCLC and these findings take significant steps towards understanding the molecular events that enable VM. These results support therapeutic co-targeting of both NE and non-NE cells to curtail SCLC progression and to improve SCLC patient outcomes in future.
Memory phase-specific genes in the Mushroom Bodies identified using CrebB-target DamID
Authors: Sgammeglia Noemi , Widmer Yves F. , Kaldun Jenifer C. , Fritsch Cornelia , Bruggmann Rémy , Sprecher Simon G.
Published: October 2022

The formation of long-term memories requires changes in the transcriptional program andde novoprotein synthesis. One of the critical regulators for long-term memory (LTM) formation and maintenance is the transcription factor CREB. Genetic studies have dissected the requirement of CREB activity within memory circuits, however less is known about the genetic mechanisms acting downstream of CREB and how they may contribute defining LTM phases. To better understand the downstream mechanisms, we here used a targeted DamID approach (TaDa). We generated a CREB-Dam fusion protein using the fruit flyDrosophila melanogasteras model. Expressing CREB-Dam in the mushroom bodies (MBs), a brain center implicated in olfactory memory formation, we identified genes that are differentially expressed between paired and unpaired appetitive training paradigm. Of those genes we selected candidates for an RNAi screen in which we identified genes causing increased or decreased LTM.
Brain DNA methylomic analysis of frontotemporal lobar degeneration revealsOTUD4in shared dysregulated signatures across pathological subtypes
Authors: Fodder Katherine , Murthy Megha , Rizzu Patrizia , Toomey Christina E. , Hasan Rahat , Humphrey Jack , Raj Towfique , Lunnon Katie , Mill Jonathan , Heutink Peter , Lashley Tammaryn , Bettencourt Conceição
Published: October 2022

Frontotemporal lobar degeneration (FTLD) is an umbrella term describing the neuropathology of a clinically, genetically and pathologically heterogeneous group of diseases, including frontotemporal dementia (FTD) and progressive supranuclear palsy (PSP). Among the major FTLD pathological subgroups, FTLD with TDP-43 positive inclusions (FTLD-TDP) and FTLD with tau positive inclusions (FTLD-tau) are the most common, representing about 90% of the cases. Although alterations in DNA methylation have been consistently associated with neurodegenerative diseases, including Alzheimer’s disease and Parkinson’s disease, little is known for FTLD and its heterogeneous subgroups and subtypes. The main goal of this study was to investigate DNA methylation variation in FTLD-TDP and FTLD-tau. We used frontal cortex genome-wide DNA methylation profiles from three FTLD cohorts (234 individuals), generated using the Illumina 450K or EPIC microarray. We performed epigenome-wide association studies (EWAS) for each cohort followed by meta-analysis to identify shared differential methylated loci across FTLD subgroups/subtypes. Additionally, we used weighted gene correlation network analysis to identify co-methylation signatures associated with FTLD and other disease-related traits. Wherever possible, we also incorporated relevant gene/protein expression data. After accounting for a conservative Bonferroni multiple testing correction, the EWAS meta-analysis revealed two differentially methylated loci in FTLD, one annotated to OTUD4 (5’UTR-shore) and the other to NFATC1 (gene body-island). Of these loci, OTUD4 showed consistent upregulation of mRNA and protein expression in FTLD. Additionally, in the three independent co-methylation networks,OTUD4-containing modules were enriched for EWAS meta-analysis top loci and were strongly associated with the FTLD status. These co-methylation modules were enriched for genes implicated in the ubiquitin system, RNA/stress granule formation and glutamatergic synaptic signalling. Altogether, our findings identified novel FTLD-associated loci, and support a role for DNA methylation as a mechanism involved in the dysregulation of biological processes relevant to FTLD, highlighting novel potential avenues for therapeutic development.
Targeting the Human Papillomavirus 16 E6 Oncoprotein with Antibodies
Authors: Dayer Guillem , Faulkner Ashley , Talwar Tanu , Togtema Melissa , Zehbe Ingeborg
Published: October 2022

The human papillomavirus (HPV) 16 genome encodes two oncoproteins, E6 and E7, which are essential for viral carcinogenesis. While E7 promotes cell proliferation, E6 abolishes the resulting p53-dependent apoptotic response. Due to this specific function, E6 is considered a suitable target for the development of a variety of therapeutic agents such as antibodies. Here, we review anti-E6 antibodies/antibody fragments generated by us and others, as well as present our latest results withCamelidae-derived single-domain antibodies (sdAbs). We had previously isolated a pool of anti-E6 sdAbs to identify E6 binders with the potential to be used clinically and in research. While our previous work has focused on recombinant E6 proteins, here we evaluated these sdAbs’ binding capacity to the endogenous E6 protein using co-immunoprecipitation and immunofluorescence. We obtained reproducible results in these applications with two sdAbs, filling a gap in HPV research. Despite their apparent E6 binding ability, these sdAbs do not raise p53 levels or induce apoptosis. Thus, while these reagents are valuable diagnostic and detection tools, identifying their therapeutic potential will require further development and testing.
Improving fine-mapping by modeling infinitesimal effects
Authors: Cui Ran , Elzur Roy A , Kanai Masahiro , Ulirsch Jacob C , Weissbrod Omer , Daly Mark J , Neale Benjamin M , Fan Zhou , Finucane Hilary K
Published: October 2022

Fine-mapping aims to identify causal variants for phenotypes. Bayesian fine-mapping algorithms (e.g.: SuSiE, FINEMAP, ABF, and COJO-ABF) are widely used, but assessing posterior probability calibration remains challenging in real data, where model misspecification likely exists, and true causal variants are unknown. We introduce Replication Failure Rate (RFR), a metric to assess fine-mapping consistency by down-sampling. SuSiE, FINEMAP and COJO-ABF show high RFR, indicating potential under-conservative mis-calibration. Simulations reveal that non-sparse genetic architecture can lead to miscalibration, while imputation noise, non-uniform distribution of causal variants, and QC filters have minimal impact. We present SuSiE-inf and FINEMAP-inf, novel fine-mapping methods modeling infinitesimal effects alongside fewer larger causal effects. Our methods exhibit improved calibration, RFR and functional enrichment, competitive recall and computational efficiency. Notably, using our methods’ posterior effect sizes substantially increases PRS accuracy over SuSiE and FINEMAP. Our work improves causal variants identification for complex traits, a fundamental goal of human genetics.
Rapamycin rescues loss-of-function in blood-brain barrier-interacting regulatory T cells
Authors: Baeten Paulien , Hamad Ibrahim , Hoeks Cindy , Hiltensperger Michael , Van Wijmeersch Bart , Popescu Veronica , Aly Lilian , Somers Veerle , Korn Thomas , Kleinewietfeld Markus , Hellings Niels , Broux Bieke
Published: October 2022

In many autoimmune diseases, FOXP3+regulatory T cells (Tregs) skew towards a pro-inflammatory and non-suppressive phenotype and are therefore unable to control the exaggerated autoimmune response. This may largely impact the success of autologous Treg therapy which is currently under investigation for treatment of autoimmune diseases, including multiple sclerosis (MS). Thus, there is a need to ensurein vivostability of Tregs before successful Treg therapy can be applied. Using a murine genetic fate-mapping model, we demonstrate that inflammatory exFOXP3 T cells accumulate in the central nervous system (CNS) during experimental autoimmune encephalomyelitis (EAE). In a humanin vitroBBB model, we discovered that interaction with inflamed blood-brain barrier (BBB)-endothelial cells induces loss of suppressive function in Tregs. Transcriptome analysis further revealed that Tregs which migrated across inflamed BBB-endothelial cellsin vitrohave a pro-inflammatory Th1/17 signature and upregulate the mTORC1 signaling pathway compared to non-migrated Tregs. These findings suggest that interaction with BBB-endothelial cells is sufficient to affect Treg function, and that transmigration triggers an additive pro-inflammatory phenotype switch, which was also seen in CNS-derived exFOXP3 T cells of EAE mice.In vitrotreatment of migrated human Tregs with the clinically-approved mTORC1 inhibitor rapamycin completely restored the loss of suppressive function. Finally, flow cytometric analysis indicated an enrichment of inflammatory, less suppressive CD49d+Tregs in the cerebrospinal fluid of MS patients, thereby underscoring the relevance of our findings for human disease. In sum, our findings provide firm evidence that the inflamed BBB affects human Treg stability, which can be restored using a mTORC1 inhibitor. These insights can help in significantly improving the efficacy of autologous Treg therapy of MS.
The Nuclear RNAi Pathway Regulates DAF-16/FOXO to ControlC. elegansLongevity andDauerEntry
Authors: Sarmah Sweta , De-Souza Evandro A. , Pinto Silas , Antebi Adam , Mori Marcelo A.
Published: October 2022

Caenorhabditis eleganswith impaired insulin/IGF-1 receptor signalling (IIS) or with germline ablation live longer and this phenomenon is entirely dependent on the transcription factor DAF-16 - theC. eleganshomolog of the class O of the forkhead box transcription factors (FoxO). In a candidate RNAi screen designed to search for new modifiers of DAF-16 function among genes involved in histone modification and/or small RNA-mediated silencing pathways, we foundnrde-1, wago-1, andadr-1as positive regulators of DAF-16. We confirmed by several methods and in different models that DAF-16 translocation to the nucleus and, subsequently, its function is tightly controlled by these genes and narrowed down to components of the NRDE complex and the nuclear RNAi pathway as key DAF-16 modulators. Importantly, we found that the NRDE pathway controls DAF-16-mediated longevity anddauerentry. Our epistasis data indicate thatnrde-1interacts withakt-1to control lifespan. We also demonstrated that NRDE-1 acts downstream of AGE-1/PI3K and partially requires mTORC2 and AKT-1 to control DAF-16 translocation. These results unveil a mechanism of regulation ofdauerformation and longevity inC. elegansvia nuclear RNAi-mediated modulation of DAF-16 function in a manner that involves the mTORC2-AKT axis.
Influence of mimicry on extinction risk in Aculeata: a theoretical approach
Authors: Boutin Maxime , Costa Manon , Fontaine Colin , Perrard Adrien , Llaurens Violaine
Published: October 2022

Abstract

Positive ecological interactions can play a role in community structure and species co-existence. A well-documented case of mutualistic interaction is Mullerian mimicry, the convergence of colour pattern in defended species living in sympatry. By reducing predation pressure, Mullerian mimicry may limit local extinction risks of defended species, but this positive effect can be weakened by undefended mimics (Batesian mimicry). While mimicry was well-studied in neotropical butterflies, it remains surprisingly poorly studied in wasps and bees (Hymenoptera: Aculeata). However, only females are defended in Aculeata and this female-limited defence may modulate the effect of Mullerian mimicry on extinction risks. Here, we focus on the effect of Mullerian mimicry on extinction risk in Aculeata, using a population dynamics model for two species. We show that Mullerian mimicry has a positive effect on species co-existence, but this effect depends on the sex-ratio. We found that the probability of extinction increases as the proportion of undefended males increases in the population, however co-existence still occurs if females are sufficiently abundant or noxious. Furthermore, we detected a destabilising effect of dual sex-limited mimicry (when each sex resembles a different model) on species co-existence. In a context of massive population decline caused by anthropic activities, our findings highlight the potential importance of Mullerian mimicry as an overlooked mechanism linked to extinction risk in wasp and bee species.
Tmem117 in AVP neurons regulates the counterregulatory response to hypoglycemia
Authors: Gaspari Sevasti , Labouèbe Gwenaël , Picard Alexandre , Berney Xavier , Sanchez-Archidona Ana Rodriguez , Thorens Bernard
Published: October 2022

The counterregulatory response to hypoglycemia (CRR), which ensures a sufficient glucose supply to the brain, is an essential survival function. It is orchestrated by incompletely characterized glucose-sensing neurons, which trigger a coordinated autonomous and hormonal response that restores normoglycemia. Here, we investigated the role of hypothalamicTmem117, identified in a genetic screen as a regulator of CRR. We show thatTmem117is expressed in vasopressin magnocellular neurons of the hypothalamus.Tmem117inactivation in these neurons increases hypoglycemia-induced vasopressin secretion leading to higher glucagon secretion, an estrus cycle phase-dependent effect in female mice.Ex vivoelectrophysiological analysis, in-situ hybridization andin vivocalcium imaging reveal thatTmem117inactivation does not affect the glucose-sensing properties of vasopressin neurons but increases ER-stress, ROS production and intracellular calcium levels accompanied by increased AVP production and secretion. Thus,Tmem117in vasopressin neurons is a physiological regulator of glucagon secretion and highlight the role of these neurons in the coordinated response to hypoglycemia.
Heritable and sex-specific variation in the development of social behavior in a wild primate
Authors: Lange Elizabeth C. , Griffin Madison , Fogel Arielle S. , Archie Elizabeth A. , Tung Jenny , Alberts Susan C.
Published: October 2022

Affiliative social bonds are linked to fitness components in many social mammals. However, despite their importance, little is known about how the tendency to form social bonds develops in young animals, or if the development of social behavior is heritable and thus can evolve. Using four decades of longitudinal observational data from a wild baboon population, we assessed the environmental determinants of an important social developmental milestone in baboons—the age at which a young animal first grooms a conspecific—and we assessed how mother-offspring grooming reciprocity develops during the juvenile period. We found that grooming development differs between the sexes: female infants groom at an earlier age and reach reciprocity in grooming with their mother earlier than males. Using the quantitative genetic ‘animal model’, we also found that age at first grooming behavior for both sexes is weakly heritable (h2= 4.3%). These results show that sex differences in grooming emerge at a young age; that strong, reciprocal social relationships between mothers and daughters begin very early in life; and that age at first grooming is heritable and therefore can be shaped by natural selection.
Phylogenetic reconstructions of Polynesian medicinal plant use reveal adaptive strategies to meet health needs
Authors: Thompson Jamie , Jordan Fiona , Hawkins Julie
Published: October 2022

Modern migrants using plants to meet their health needs are known to conserve traditional knowledge, but also to innovate to adapt to their new environment. The voyage into Polynesia is amongst the most remarkable of human migrations, resulting in the peopling of isolated, difficult to reach archipelagos. We use this context to determine the role for adaptation in plant-based healthcare at pre-historic timescales. Testing the extent to which the new floristic environments encountered, cultural ancestry or geographic proximity predict the composition of ethnopharmacopoeias, we reveal adaptation to new floristic environments across seven oceanic ethnolinguistic groups. Reconstructions using data that encompass therapeutic applications and plant parts reveal more than three quarters of the plants used cross-culturally have use likely to be innovations by the first migrants into Oceania. For the other plants, there are non-tree-like patterns in therapeutic applications and plant parts used, showing that even when plants have continuity of use there is lability in how they are used. Applying linguistic criteria to the plants with putatively deep cultural uses, we find two, qaoa (Ficus) and walo-walo (Premna), that are highly conserved in therapeutic use, plant part used and with cognate names. Our study highlights the remarkable flexibility of Polynesian people seeking to meet health needs.
Gene expression profile of the developing endosperm in durum wheat provides insight into starch biosynthesis
Authors: Chen Jiawen , Watson-Lazowski Alexander , Vickers Martin , Seung David
Published: October 2022

Durum wheat (Triticum turgidumsubsp.durum) is widely grown for pasta production, and more recently, is gaining additional interest due to its resilience to warm, dry climates and its use as an experimental model for wheat research. Like in bread wheat, the starch and protein accumulated in the endosperm during grain development are the primary contributors to the calorific value of durum grains. To enable further research into endosperm development and storage reserve synthesis, we generated a high-quality transcriptomics dataset from developing endosperms of variety Kronos, to complement the extensive mutant resources available for this variety. Endosperms were dissected from grains harvested at eight timepoints during grain development (6 to 30 days post anthesis (dpa)), then RNA sequencing was used to profile the transcriptome at each stage. The largest changes in gene expression profile were observed between the earlier timepoints, prior to 15 dpa. We detected a total of 29,925 genes that were significantly differentially expressed between at least two timepoints, and clustering analysis revealed nine distinct expression patterns. We demonstrate the potential of our dataset to provide new insights into key processes that occur during endosperm development, using starch metabolism as an example. Overall, we provide a valuable resource for studying endosperm development in this increasingly important crop species.
The mechanism of nicotinamide phosphoribosyltransferase whereby positive allosteric modulation elevates cellular NAD+
Authors: Ratia Kiira M. , Shen Zhengnan , Gordon-Blake Jesse , Lee Hyun , Laham Megan S. , Krider Isabella S. , Christie Nicholas , Ackerman-Berrier Martha , Penton Christopher , Knowles Natalie G. , Musku Soumya Reddy , Fu Jiqiang , Velma Ganga Reddy , Xiong Rui , Thatcher Gregory R J
Published: October 2022

In aging and disease, cellular NAD+is depleted by catabolism to nicotinamide (NAM) and NAD+supple-mentation is being pursued to enhance human healthspan and lifespan. Activation of nicoti namide phosphoribosyl -transferase (NAMPT), the rate-limiting step in NAD+biosynthesis, has potential to increase salvage of NAM. Novel NAMPT positive allosteric modulators (N-PAMs) were discovered in addition to demonstration of NAMPT activati on by biogenic phenols. The mechanism of activation was revealed through synthesis of novel chemical probes, new NAMPT co-crystal structures, and enzyme kinetics. Binding to a rear channel in NAMPT regulates NAM binding and turnover, with biochemical observations being replicated by NAD+measurements in human cells. The mechanism of action of N-PAMs identifies, for the first time, the role of the rear channel in regulation of NAMPT turnover coupled to feedback inhibition by NAM. N-PAM inhibition of low affinity, non-productive NAM binding via the rear channel, causes a right-shif t in KI(NAM) that accompanies an increase in enzyme activity. Conversion of an N-PAM to a high-affinity l igand blocks both high and low affinity NAM binding, ablating enzyme activity. In the presence of an N-PAM, NAMPT boosts NAD+biosynthesis at higher NAM concentrations, in addition to relieving inhibition by NAD+. Since cellular stress often leads to enhanced catabolism of NAD+to NAM, this mechanism is relevant to supporting cellular N AD+levels in aging and disease. The tight regulation of cellular NAMPT is differentially regulated by N-PAMs and other activators, indicating that different classes of pharmacological activators may be engineered for cell and tissue selectivity.
Disentangling leaf structural and material properties in relation to their anatomical and chemical compositional traits in oaks (QuercusL.)
Authors: Alonso-Forn David , Sancho-Knapik Domingo , Fariñas María Dolores , Nadal Miquel , Martín-Sánchez Rubén , Ferrio Juan Pedro , Resco de Dios Víctor , Peguero-Pina José Javier , Onoda Yusuke , Cavender-Bares Jeannine , Gómez Álvarez Arenas Tomás , Gil-Pelegrín Eustaquio
Published: October 2022

The existence of sclerophyllous plants has been considered an adaptive strategy against different environmental stresses. As it literally means “hard-leaved”, it is essential to quantify the leaf mechanical properties to understand sclerophylly. However, the relative importance of each leaf trait on mechanical properties is not yet well established. The genusQuercusis an excellent system to shed light on this since it minimizes phylogenetic variation while having a wide variation in sclerophylly. Thus, leaf anatomical traits and cell wall composition were measured, analyzing their relationship with LMA and leaf mechanical properties in a set of 25 oak species. Outer wall contributed strongly to leaf mechanical strength. Moreover, cellulose plays a critical role in increasing leaf strength and toughness. The PCA plot based on leaf trait values clearly separatedQuercusspecies into two groups corresponding to evergreen and deciduous species. SclerophyllousQuercusspecies are tougher and stronger due to their thicker epidermis outer wall and/or higher cellulose concentration. Furthermore, sectionIlexspecies share common traits regardless of they occupy quite different climates. In addition, evergreen species living in Mediterranean-type climates share common leaf traits irrespective of their different phylogenetic origin.
Neuronal birthdate reveals topography in a vestibular brainstem circuit for gaze stabilization
Authors: Goldblatt Dena , Huang Stephanie , Greaney Marie R. , Hamling Kyla R. , Voleti Venkatakaushik , Perez-Campos Citlali , Patel Kripa B. , Li Wenze , Hillman Elizabeth M. C. , Bagnall Martha W. , Schoppik David
Published: October 2022

Across the nervous system, neurons with similar attributes are topographically organized. This topography reflects developmental pressures. Oddly, vestibular (balance) nuclei are thought to be disorganized. By measuring activity in birthdated neurons, we revealed a functional map within the central vestibular projection nucleus that stabilizes gaze in the larval zebrafish. We first discovered that both somatic position and stimulus selectivity follow projection neuron birthdate. Next, with electron microscopy and loss-of-function assays, we found that patterns of peripheral innervation to projection neurons were similarly organized by birthdate. Lastly, birthdate revealed spatial patterns of axonal arborization and synapse formation to projection neuron outputs. Collectively, we find that development reveals previously hidden organization to the input, processing, and output layers of a highly-conserved vertebrate sensorimotor circuit. The spatial and temporal attributes we uncover constrain the developmental mechanisms that may specify the fate, function, and organization of vestibulo-ocular reflex neurons. More broadly, our data suggest that, like invertebrates, temporal mechanisms may assemble vertebrate sensorimotor architecture.
Chemical diversity in some biofouling organisms from the western coastal waters of Sri Lanka
Authors: Weerasinghe R L , Ranatunga R R M K P , Chinthaka S D M
Published: October 2022

Sri Lanka occupies a strategic position in the Indian Ocean, making the surrounding ocean one of the busiest in the region. The lack of fundamental studies has created a void regarding the physical and chemical behaviour of the fouling community. A few studies have been conducted to assess the subtidal biofouling communities and invasive threats in key ports and surrounding coastal waters. This study explores the chemical diversity and environmental resilience of nine marine macrofouling organisms through secondary metabolite-induced impacts on biofilm formation and volatile component analysis. The anti-settlement assay revealed thatSchizoporella errata, Botrylloides violaceus, Callyspongia diffusa, andAcanthella cavernosashowed significant resistance againstEscherichia colisettlement within the first 12 h (OD600< 0.1). The identification of known compounds with a higher degree of antimicrobial activity, such as dodecanoic acid, methyl palmitate, β-caryophyllene and β-asarone, further supports the findings of anti-settlement activity of macrofouling organisms and likely plays a role in environmental resilience.
Natural history and ecological effects on the establishment and fate of Florida carpenter ant cadavers infected by the parasitic manipulatorOphiocordyceps camponoti-floridani
Authors: Will Ian , Linehan Sara , Jenkins David G. , de Bekker Charissa
Published: October 2022

Ophiocordycepsfungi manipulate the behavior of their ant hosts to produce a summit disease phenotype, thereby establishing infected ant cadavers onto vegetation at elevated positions suitable for fungal growth and transmission. Multiple environmental and ecological factors have been proposed to shape the timing, positioning, and outcome of these manipulations.

We conducted a long-term field study ofOphiocordyceps camponoti-floridaniinfections ofCamponotus floridanusants – the Florida zombie ants. We propose and refine hypotheses on the factors that shape infection outcomes by tracking the occurrence of and fungal growth from hundreds of ant cadavers. We modeled and report these data in relation to weather, light, vegetation, and attack by hyperparasites.

We investigated environmental factors that could affect the occurrence and location of newly manipulated ant cadavers. New cadaver occurrence was preferentially biased toward epiphyticTillandsiabromeliads, canopy openness, and summer weather conditions (an interactive effect of temperature, humidity, and precipitation). Furthermore, we suggest that incident light at the individual cadaver level reflects microhabitat choice by manipulated ants or selective pressure on cadaver maintenance for conditions that improve fungal survival.

We also asked which environmental conditions affect fungal fitness. Continued fungal development of reproductive structures and putative transmission increased with moist weather conditions (interaction of humidity and precipitation) and canopy openness, while being reduced by hyperparasitic mycoparasite infections. Moreover, under the most open canopy conditions, we found an atypicalOphiocordycepsgrowth morphology that could represent a plastic response to conditions influenced by high light levels.

Taken together, we explore general trends and the effects of various ecological conditions on host and parasite disease outcomes in the Florida zombie ant system. These insights from the field can be used to inform experimental laboratory setups that directly test the effects of biotic and abiotic factors on fungus-ant interactions or aim to uncover underlying molecular mechanisms.