bluuebunny/crossref_metadata_2025 huggingface dataset:
Rapid evolution of sex role specialization in a hermaphrodite under sex-limited selection
Authors: Nordén Anna K. , Ramm Steven A. , Abbott Jessica K.
Published: May 2022

The evolution of separate sexes from hermaphroditism is thought to have occurred independently many times, and is linked to the evolution of sex chromosomes. Even though we have a good understanding of the theoretical steps in the evolution of sex chromosomes from a hermaphrodite ancestor, the initial stages are still hard to study because many sex chromosome systems are old. We addressed this problem by experimentally selecting a hermaphrodite via sex-limited experimental evolution for several generations, simulating the early stages in the evolution of a sex chromosome. More specifically, we used a GFP (green fluorescent protein) marker as a proxy for a sex-determining locus, and selected replicate populations of the simultaneously hermaphroditic flatwormMacrostomum lignanofor fitness via the male sex role, female sex role, or both (i.e. a control). After 14 generations, a fitness assay revealed clear evidence for incipient sex role specialization, presumably reflecting the release from constraints usually imposed by selection on the other sex role. Importantly, however, this was not simply explained by differential sex allocation in the different selection regimes - insofar as morphological traits reflect the underlying trade-off over resource allocation to the male and female sex functions - because testis and ovary sizes did not diverge among treatments. Our study shows that sex role specialization can occur rapidly as a result of sex-limited selection, which is consistent with genetic constraints between sex-roles, and in line with the first predicted steps towards the evolution of a new sex chromosome system.
A highly diverse set of novel immunoglobulin-like transcript (NILT) genes in zebrafish indicates a wide range of functions with complex relationships to mammalian receptors
Authors: Wcisel Dustin J. , Dornburg Alex , McConnell Sean C. , Hernandez Kyle M. , Andrade Jorge , de Jong Jill L. O. , Litman Gary W. , Yoder Jeffrey A.
Published: May 2022

Multiple novel immunoglobulin-like transcripts (NILTs) have been identified from salmon, trout and carp. NILTs typically encode activating or inhibitory transmembrane receptors with extracellular immunoglobulin (Ig) domains. Although predicted to provide immune recognition in ray-finned fish, we currently lack a definitive framework of NILT diversity, thereby limiting our predictions for their evolutionary origin and function. In order to better understand the diversity of NILTs and their possible roles in immune function, we identified five NILT loci in the Atlantic salmon (Salmo salar) genome, defined 86 NILT Ig domains within a 3 Mbp region of zebrafish (Danio rerio) chromosome 1, and described 41 NILT Ig domains as part of an alternative haplotype for this same genomic region. We then identified transcripts encoded by 43 different NILT genes which reflect an unprecedented diversity of Ig domain sequences and combinations for a family of non-recombining receptors within a single species. Zebrafish NILTs include a sole putative activating receptor but extensive inhibitory and secreted forms as well as membrane-bound forms with no known signaling motifs. These results reveal a higher level of genetic complexity, interindividual variation and sequence diversity for NILTs than previously described, suggesting that this gene family likely plays multiple roles in host immunity.
Accurate and sensitive mutational signature analysis with MuSiCal
Authors: Jin Hu , Gulhan Doga C. , Geiger Benedikt , Ben-Isvy Daniel , Geng David , Ljungstrom Viktor , Park Peter J.
Published: May 2022

Mutational signature analysis is a recent computational approach for interpreting somatic mutations in the genome. Its application to cancer data has enhanced our understanding of mutational forces driving tumorigenesis and demonstrated its potential to inform prognosis and treatment decisions. However, methodological challenges remain for discovering new signatures and assigning proper weights to existing signatures, thereby hindering broader clinical applications. Here we present MuSiCal (Mutational Signature Calculator), a rigorous analytical framework with novel algorithms that solves major problems in the standard workflow. Our simulation studies demonstrate that MuSiCal outperforms state-of-the-art algorithms for both signature discovery and assignment. By reanalyzing over 2,700 cancer genomes, we provide an improved catalog of signatures and their assignments, discover nine indel signatures absent in the current catalog, resolve long-standing issues with the ambiguous ‘flat’ signatures, and give insights into signatures with unknown etiologies. We expect MuSiCal and the improved catalog to be a step towards establishing best practices for mutational signature analysis.
Single-cell mosaicism analysis reveals cell-type-specific somatic mutational burden in Alzheimer’s Dementia
Authors: Kousi Maria , Boix Carles , Park Yongjin P. , Mathys Hansruedi , Sledzieski Samuel , Peng Zhuyu , Bennett David A. , Tsai Li-Huei , Kellis Manolis
Published: May 2022

Despite significant advances in identifying genetic drivers of neurodegenerative disorders, the majority of affected individuals lack molecular genetic diagnosis, with somatic mutations proposed as one potential contributor to increased risk. Here, we report the first cell-type-specific map of somatic mosaicism in Alzheimer’s Dementia (AlzD), using 4,014 cells from prefrontal cortex samples of 19 AlzD and 17 non-AlzD individuals. We integrate full-transcript single-nucleus RNA-seq (SMART-Seq) with matched individual-level whole-genome sequencing to jointly infer mutational events and the cell-type in which they occurred. AlzD individuals show increased mutational burden, localized in excitatory neurons, oligodendrocytes, astrocytes and disease-associated “senescent” cells. High-mutational-burden cells showed mutational enrichment and similar single-cell expression profiles in AlzD cases versus non-AlzD individuals, indicating cellular-level genotype-to-phenotype correlation. Somatic mutations are specifically enriched for known AlzD genes, and implicate biologically meaningful cell-type specific processes, including: neuronal energy regulation, endocytic trafficking (NEFM), lipid metabolism (CNP, CRYAB), proteostasis (USP34), cytoskeleton, and microtubule dynamics (MACF1).
The kinase activity of the cancer stem cell marker DCLK1 drives gastric cancer progression by reprogramming the stromal tumor landscape
Authors: Afshar-Sterle Shoukat , Carli Annalisa L E , O’Keefe Ryan , Tse Janson , Fischer Stefanie , Azimpour Alexander I , Baloyan David , Elias Lena , Thilakasiri Pathum , Patel Onisha , Ferguson Fleur M , Eissmann Moritz F , Chand Ashwini L , Gray Nathanael S , Busuttil Rita , Boussioutas Alex , Lucet Isabelle S , Ernst Matthias , Buchert Michael
Published: May 2022

Gastric cancer (GC) is the 3rd leading cause of cancer mortality worldwide, therefore providing novel diagnostic and treatment options is crucial for at risk groups. The serine/threonine kinase doublecortin-like kinase 1 (DCLK1) is a proposed driver of GC with frequent amplification and somatic missense mutations yet the molecular mechanism how DCLK1 mediates tumorigenesis is poorly understood. We report how DCLK1 expression orchestrates complementary cancer cell intrinsic and extrinsic processes leading to a comprehensive pro-invasive and pro-metastatic reprogramming of cancer cells and tumor stroma in a DCLK1 kinase-dependent manner. Mechanistically, we identify the chemokine CXCL12 as a key promoter of the pro-tumorigenic properties downstream of DCLK1. Importantly, inhibition of the DCLK1 kinase domain reverses the pro-tumorigenic and pro-metastatic phenotype. Together, this study establishes DCLK1 as a promising, targetable master regulator of GC.

Teaser

DCLK1 is a druggable cancer driver of GC
Structure-based discovery and in vitro validation of selective inhibitors of Chloride Intracellular Channel 4 protein
Authors: Olotu Fisayo , Medina-Carmona Encarnacion , El-Hamdaoui Abdelaziz , Bishop Özlem Tastan , Ortega-Roldan Jose L. , Abdul-Salam Vahitha B.
Published: May 2022

Chloride Intracellular Channel Protein 4 (CLIC4) is a novel class of intracellular ion channel highly implicated in tumour and vascular biology. It regulates cell proliferation, apoptosis and angiogenesis; and is involved in multiple pathologic signaling pathways. Absence of specific inhibitors impedes its advancement to translational research. Here, we integrate structural bioinformatics and experimental research approach for the discovery and validation of small-molecule inhibitors of CLIC4. High-affinity allosteric binders were identified from a library of 1615 Food and Drug Administration (FDA)-approved drugs via a high-performance computing-powered blind-docking approach, resulting in the selection of amphotericin B and rapamycin. NMR assays confirmed the binding of the drugs. Both drugs reversed stress-induced membrane translocation of CLIC4 and inhibited endothelial cell migration. Structural and dynamics simulation studies further revealed that the inhibitory mechanisms of these compounds were hinged on the allosteric modulation of the catalytic glutathione (GSH)-like site loop and the extended catalytic β loop which may elicit interference with the catalytic activities of CLIC4. Structure-based insights from this study provide the basis for the selective targeting of CLIC4 to treat the associated pathologies.
The impact of sexual violence in mid-adolescence on mental health: a UK population-based longitudinal study.
Authors: Bentivegna Francesca , Patalay Praveetha
Published: May 2022

Background: A large gender gap appears in internalising mental health during adolescence. There is little high-quality longitudinal population-based research investigating the role of sexual violence experiences, which are disproportionately experienced by females. This study aims to estimate the mental health impact of sexual violence experiences in mid-adolescence. Methods: Longitudinal data from the UK Millennium Cohort Study (born 2000-02) in participants with information available on past-year sexual violence (sexual assault, unwelcome sexual approach) and mental health outcomes (psychological distress (K-6 questionnaire) in last 30 days, past-year self-harm, and lifetime attempted suicide) reported at age 17 years. Multivariable confounder adjusted regressions and propensity matching approaches were used, and population attributable fractions (PAFs) were calculated. Findings: Analyses were in 5,119 girls and 4,852 boys (mean age 17 years, 80.8% White). In the fully adjusted model, sexual violence was associated with greater mean psychological distress (mean difference girls: 2.09 [1.51; 2.68] boys: 2.56 [1.59; 3.53]) and higher risk of high distress (girls: 1.65 [1.37; 2.00] boys: 1.55 [1.00; 2.40]), self-harming (girls: 1.79 [1.52; 2.10] boys: 2.16 [1.63; 2.84]), and attempted suicide (girls: 1.75 [1.26; 2.41] boys: 2.73 [1.59; 4.67]). PAF estimates suggest that, in a scenario with no sexual violence, we could expect 3.7-10.5% (boys) to 14.0-18.7% (girls) fewer adverse mental health outcomes at this age. Interpretation: Our findings demonstrate the substantial role of sexual violence experiences for mid-adolescent mental health, especially for girls who are 4-5 times more likely to be victims. Changes are needed at societal and policy levels to prevent sexual violence and its wide-ranging impacts.
Adults’ self-reported barriers and enablers to riding a bike for transport: a systematic review
Authors: Pearson Lauren , Berkovic Danielle , Reeder Sandy , Gabbe Belinda , Beck Ben
Published: May 2022

Riding a bike for transport purposes is an effective way to improve population and environmental health. Despite this, participation levels in many countries are low. Identifying the barriers and enablers to riding a bike for transport is essential to developing interventions that encourage bike riding. In this mixed-methods systematic review, we aimed to identify the perceived barriers and enablers to adults riding a bike for transport in Organisation for Economic Development (OECD) countries. A systematic database search was conducted to identify relevant peer-reviewed and grey literature. Fifty-five papers/reports met eligibility criteria. There were 34 barriers and 21 enablers identified. The leading barriers related to riding on the road alongside motor vehicles. Other factors identified included the provision and quality of cycling infrastructure, personal factors such as physical fitness, attitudinal factors such as community perceptions of cyclists, and environmental factors. While this review highlights the complexity of factors that influence the uptake of riding a bike for transport, many of the leading factors could be overcome through the provision of high-quality protected infrastructure for bike riders. Other interventions to address other known barriers and enablers are needed to increase the uptake of bike riding.
Regional replacement of SARS-CoV-2 variant BA.1 with BA.2 as observed through wastewater surveillance
Authors: Boehm Alexandria B. , Hughes Bridgette , Wolfe Marlene K. , White Bradley J. , Duong Dorothea , Chan-Herur Vikram
Published: May 2022

An understanding of circulating SARS-CoV-2 variants can inform pandemic response, vaccine development, disease epidemiology, and use of monoclonal antibody treatments. We developed custom assays targeting characteristic mutations in SARS-CoV-2 variants Omicron BA.1 and BA.2 and confirmed their sensitivity and specificity in silico and in vitro. We then applied these assays to daily wastewater solids samples from eight publicly owned treatment works in the greater Bay Area of California, USA, over four months to obtain a spatially and temporally intensive data set. We documented regional replacement of BA.1 with BA.2 in agreement with, and ahead of, clinical sequencing data. This study highlights the utility of wastewater surveillance for real time tracking of SARS-CoV-2 variant circulation.

Synopsis

Wastewater surveillance was used to document regional emergence of SARS-CoV-2 variant Omicron BA.2 ahead of clinical surveillance.

Graphical Abstract
Benchmarking brain organoid recapitulation of fetal corticogenesis
Authors: Cheroni Cristina , Trattaro Sebastiano , Caporale Nicolò , López-Tobón Alejandro , Tenderini Erika , Troglio Flavia , Gabriele Michele , Bressan Raul Bardini , Pollard Steven M , Gibson William T , Testa Giuseppe
Published: May 2022

Brain organoids are becoming increasingly relevant to dissect the molecular mechanisms underlying psychiatric and neurological conditions. The in vitro recapitulation of key features of human brain development affords the unique opportunity of investigating the developmental antecedents of neuropsychiatric conditions in the context of the actual patients’ genetic backgrounds. Specifically, multiple strategies of brain organoid (BO) differentiation have enabled the investigation of human cerebral corticogenesis in vitro with increasing accuracy. However, the field lacks a systematic investigation of how closely the gene co-expression patterns seen in cultured BO from different protocols match those observed in fetal cortex, a paramount information for ensuring the sensitivity and accuracy of modeling disease trajectories. Here we benchmark BO against fetal corticogenesis by integrating transcriptomes from in-house differentiated cortical BO (CBO), other BO systems, human fetal brain samples processed in-house, and prenatal cortices from the BrainSpan Atlas. We identified co-expression patterns and prioritized hubs of human corticogenesis and CBO differentiation, highlighting both well-preserved and discordant trends across BO protocols, including different degrees of heterochronicity in differentiation across BO models compared to fetal cortex. Our approach provides a framework to directly compare the extent of in vivo/in vitro alignment of neurodevelopmentally relevant processes and their attending temporalities, structured as an accessible resource to query for modelling human corticogenesis and the neuropsychiatric outcomes of its alterations.
The genomic and transcriptomic landscape of advanced renal cell cancer for individualized treatment strategies
Authors: de Joode K. , van de Geer W.S. , van Leenders G.J.L.H. , Hamberg P. , Westgeest H.M. , Beeker A. , Oosting S.F. , van Rooijen J.M. , Beerepoot L.V. , Labots M. , Mathijssen R.H.J. , Lolkema M.P. , Cuppen E. , Sleijfer S. , van de Werken H.J.G. , van der Veldt A.A.M.
Published: May 2022

Background

Differences in the clinical course and treatment responses in individual patients with advanced renal cell carcinoma (RCC) can largely be explained by the different genomics of this disease. To improve the personalized treatment strategy and survival outcomes for patients with advanced RCC, the genomic make-up in patients with advanced RCC was investigated to identify putative actionable mutations and signatures.

Methods

In this prospective multicenter study (NCT01855477), whole-genome sequencing (WGS) data of locally advanced and metastatic tissue biopsies and matched whole-blood samples were collected from 91 patients with histopathologically confirmed RCC. WGS data were analyzed for small somatic variants, copy-number alterations and structural variants. For a subgroup of patients, RNA sequencing (RNA-Seq) data could be analyzed. RNA-Seq data were clustered on immunogenic and angiogenic gene expression patterns according to a previously developed angio-immunogenic gene signature.

Results

For papillary and clear cell RCC, putative actionable drug targets were detected by WGS in 100% of the patients. RNA-Seq data of clear cell and papillary RCC were clustered using a previously developed angio-immunogenic gene signature. Analyses of driver mutations and RNA-Seq data revealed clear differences among different RCC subtypes, showing the added value of WGS and RNA-Seq over clinicopathological data.

Conclusions

By improving both histological subtyping and the selection of treatment according to actionable targets and immune signatures, WGS and RNA-Seq may improve therapeutic decision making for most patients with advanced RCC, including patients with non-clear cell RCC for whom no standard treatment is available to data. Prospective clinical trials are needed to evaluate the impact of genomic and transcriptomic diagnostics on survival outcome for advanced RCC patients.
Engineered extracellular matrices reveal stiffness-mediated chemoresistance in patient-derived pancreatic cancer organoids
Authors: LeSavage Bauer L. , Gilchrist Aidan E. , Krajina Brad A. , Karlsson Kasper , Smith Amber R. , Karagyozova Kremena , Klett Katarina C. , Curtis Christina , Kuo Calvin J. , Heilshorn Sarah C.
Published: May 2022

Pancreatic ductal adenocarcinoma (PDAC) is characterized by its fibrotic and stiff extracellular matrix (ECM); however, the role that altered cell-ECM signaling may play in driving PDAC phenotype has historically been difficult to dissect. Here, we design an engineered matrix that recapitulates key hallmarks of the tumor ECM and show that patient-derived PDAC organoids develop gemcitabine chemoresistance when cultured within high stiffness matrices mechanically matched to in vivo tumors. Using genetic barcoding, we find that while matrix-specific clonal selection occurs, cellular heterogeneity is not the main driver of chemoresistance. Instead, stiffness-induced chemoresistance occurs due to the development of a plastic cancer stem cell phenotype – mediated by hyaluronan mechanosignaling – with increased expression of drug efflux transporters. Moreover, PDAC chemoresistance is reversible following transfer from high to low stiffness matrices, suggesting that mechanotherapeutics targeting the fibrotic ECM may sensitize chemoresistant tumors. Overall, we demonstrate the power of engineered matrices and patient-derived organoids to elucidate how ECM properties influence human disease pathophysiology.
A revised perspective on the evolution of troponin I and troponin T in vertebrates
Authors: Joyce William , Ripley Daniel M. , Gillis Todd , Black Amanda Coward , Shiels Holly A. , Hoffmann Federico G.
Published: May 2022

The troponin (Tn) complex, responsible for the Ca2+ activation of striated muscle, is composed of three interacting protein subunits: TnC, TnI, and TnT, encoded by TNNC, TNNI, and TNNT genes. TNNI and TNNT are sister gene families, and in mammals the three TNNI paralogs (TNNI1, TNNI2, TNNI3), which encode proteins with tissue-specific expression, are each in close genomic proximity with one of the three TNNT paralogs (TNNT2, TNNT3, TNNT1, respectively). It has been widely presumed that all vertebrates broadly possess genes of these same three classes, although earlier work has overlooked jawless fishes (cyclostomes) and cartilaginous fishes (chimaeras, rays and sharks), which are distantly related to other jawed vertebrates. With a new phylogenetic and synteny analysis of a diverse array of vertebrates including these taxonomic groups, we define five distinct TNNI classes (TNNI1-5), with TNNI4 and TNNI5 being only present in non-mammalian vertebrates and typically found in tandem, and four classes of TNNT (TNNT1-4). These genes are located in four genomic loci that were generated by the 2R whole-genome duplication events. TNNI3, encoding ‘cardiac TnI’ in mammals, was independently lost in cartilaginous and ray-finned fishes. Ray-finned fishes predominantly express TNNI1 in the heart. TNNI5 is highly expressed in shark hearts and contains an N-terminal extension similar to that of TNNI3 found in tetrapod hearts. Given that TNNI3 and TNNI5 are distantly related, this supports the hypothesis that the N-terminal extension may be an ancestral feature of vertebrate TNNI and not an innovation unique to TNNI3, as has been commonly believed.
Integrated optical device for Structured Illumination Microscopy
Authors: Calvarese Matteo , Paiè Petra , Candeo Alessia , Calisesi Gianmaria , Ceccarelli Francesco , Valentini Gianluca , Osellame Roberto , Gong Hai , Neil Mark A. , Bragheri Francesca , Bassi Andrea
Published: May 2022

Structured Illumination Microscopy (SIM) is a key technology for high resolution and super-resolution imaging of biological cells and molecules. The spread of portable and easy-to-align SIM systems requires the development of novel methods to generate a light pattern and to shift it across the field of view of the microscope. Here we show a miniaturized chip that incorporates optical waveguides, splitters, and phase shifters, to generate a 2D structured illumination pattern suitable for SIM microscopy. The chip creates three point-sources, coherent and controlled in phase, without the need for further alignment. Placed in the pupil of a microscope’s objective, the three sources generate a hexagonal illumination pattern on the sample, which is spatially translated thanks to thermal phase shifters. We validate and use the chip, upgrading a commercial inverted fluorescence microscope to a SIM setup and we image biological sample slides, extending the resolution of the microscope.
The molecular consequences of androgen activity in the human breast
Authors: Raths F. , Karimzadeh M. , Ing N. , Martinez A. , Qu Y. , Lee T.Y. , Mulligan B. , Devkota S. , Wang B. , Giuliano A.E. , Bose S. , Goodarzi H. , Ray E.C. , Cui X. , Knott S.R.V.
Published: May 2022

The mammary gland has been extensively studied for estrogen and progesterone reactivity, but the molecular effects of androgen in the breast remain largely unexplored. Transgender men are recorded female at birth but identify as male and may undergo gender-affirming androgen therapy to align their physical characteristics and gender identity. Here we perform single cell resolution transcriptome, chromatin, and spatial profiling of androgen treated breasts from transgender men. We find male-biased androgen receptor gene targets are upregulated in cells expressing androgen receptor, and that paracrine signaling drives sex-relevant changes in other cell types. We observe an altered epithelium, shifts in immune populations, and a reduction of capillary vasculature. Finally, we find evidence of the metabolic impact of androgen and identify a gene regulatory network driving androgen-directed fat loss. This work elucidates the molecular consequences of androgen in the human breast at single cell resolution.
Identifying the best approximating model in Bayesian phylogenetics: Bayes factors, cross-validation or wAIC?
Authors: Lartillot Nicolas
Published: May 2022

Abstract

There is still no consensus as to how to select models in Bayesian phylogenetics, and more generally in applied Bayesian statistics. Bayes factors are often presented as the method of choice, yet other approaches have been proposed, such as cross-validation or information criteria. Each of these paradigms raises specific computational challenges, but they also differ in their statistical meaning, being motivated by different objectives: either testing hypotheses or finding the best-approximating model. These alternative goals entail different compromises, and as a result, Bayes factors, cross-validation and information criteria may be valid for addressing different questions. Here, the question of Bayesian model selection is revisited, with a focus on the problem of finding the best-approximating model. Several model selection approaches were re-implemented, numerically assessed and compared: Bayes factors, cross-validation (CV), in its different forms (k-fold or leave-one-out), and the widely applicable information criterion (wAIC), which is asymptotically equivalent to leave-one-out cross validation (LOO-CV). Using a combination of analytical results and empirical and simulation analyses, it is shown that Bayes factors are unduly conservative. In contrast, cross-validation represents a more adequate formalism for selecting the model returning the best approximation of the data-generating process and the most accurate estimates of the parameters of interest. Among alternative CV schemes, LOO-CV and its asymptotic equivalent represented by the wAIC, stand out as the best choices, conceptually and computationally, given that both can be simultaneously computed based on standard MCMC runs under the posterior distribution.
Membrane tension spatially organizes lysosomal exocytosis
Authors: Lachuer Hugo , Le Laurent , Lévêque-Fort Sandrine , Goud Bruno , Schauer Kristine
Published: May 2022

Lysosomal exocytosis is involved in many key cellular processes but its spatio-temporal regulation is poorly known. Using total internal reflection fluorescence microscopy (TIRFM) and spatial statistics, we observed that lysosomal exocytosis is not random at the adhesive part of the plasma membrane of RPE1 cells but clustered at different scales. Although the rate of exocytosis is regulated by the actin cytoskeleton, neither interfering with actin or microtubule dynamics by drug treatments alters its spatial organization. Exocytosis events partially co-appear at focal adhesions (FAs) and their clustering is reduced upon removal of FAs. Changes in membrane tension following a hypo-osmotic shock or treatment with methyl-β-cyclodextrin was found to increase clustering. To investigate the link between FAs and membrane tension, cells were cultured on adhesive ring-shaped micropatterns, which allows to control the spatial organization of FAs. By using a combination of TIRFM and fluorescence lifetime imaging microscopy (FLIM) microscopy, we revealed the existence of a radial gradient in membrane tension. By changing the diameter of micropatterned substrates, we further showed that this gradient as well as the extent of exocytosis clustering can be controlled. Together, our data indicate that the spatial clustering of lysosomal exocytosis relies on membrane tension patterning controlled by the spatial organization of FAs.
The contribution of mate-choice, couple convergence and confounding to assortative mating
Authors: Sjaarda Jennifer , Kutalik Zoltán
Published: May 2022

Increased phenotypic similarity between partners, termed assortative mating (AM), has been observed for many traits. However, it is currently unclear if these observations are due to mate choice for certain phenotypes, post-mating convergence, or a result of confounding factors such as shared environment or indirect assortment. To dissect these underlying phenomena, we applied Mendelian randomisation (MR) to 51,664 couples in the UK biobank to a panel of 118 phenotypes under AM. We found that 54% (64 of 118) of the tested traits had a causal relationship between partners, with female-to-male effects on average being larger. Forty traits, including systolic blood pressure, basal metabolic rate, weight and height, showed significantly larger phenotypic correlation than MR-estimates, suggesting the presence of confounders. Subsequent analyses revealed household income, overall health rating, education and tobacco smoking as major overall confounders, accounting for 29.8, 14.1, 11.6, and 4.78%, of cross-partner phenotypic correlations, respectively. We detected limited evidence for couple-correlation convergence (e.g. increased similarity with respect to smoking and medication use), measured by stratifying couples by their time spent together. Finally, mediation analysis revealed that the vast majority (>77%) of causal associations between one trait of an individual and a different trait of their partner is indirect. For example, the causal effect of the BMI of an individual on the overall health rating of their partner is entirely acting through the BMI of their partner. In summary, this study revealed many novel causal effects within couples, shedding light on the impact of confounding on couple phenotypic similarity.
Archaeal bundling pili of Pyrobaculum calidifontis reveal similarities between archaeal and bacterial biofilms
Authors: Wang Fengbin , Cvirkaite-Krupovic Virginija , Krupovic Mart , Egelman Edward H.
Published: May 2022

While biofilms formed by bacteria have received great attention due to their importance in pathogenesis, much less research has been focused on the biofilms formed by archaea. It has been known that extracellular filaments in archaea, such as Type IV pili, hami and cannulae, play a part in the formation of archaeal biofilms. We have used cryo-electron microscopy to determine the atomic structure of a previously uncharacterized class of archaeal surface filaments from hyperthermophilic Pyrobaculum calidifontis. These filaments, which we call archaeal bundling pili (ABP), assemble into highly ordered bipolar bundles. The bipolar nature of these bundles most likely arises from the association of filaments from at least two different cells. The component protein shows homology, both at the sequence and structural level, to the bacterial protein TasA, a major component of the extracellular matrix in bacterial biofilms, contributing to biofilm stability. We show that ABP forms very stable filaments in a manner similar to the donor-strand exchange of bacterial TasA fibers and chaperone-usher pathway pili where a β-strand from one subunit is incorporated into a β-sheet of the next subunit. Our results reveal mechanistic similarities and evolutionary connection between bacterial and archaeal biofilms, and suggest that there could be many other archaeal surface filaments that are as yet uncharacterized.

Significance

Biofilms are communities of microbes where cells attach to each other as well as to surfaces, and bacterial biofilms have been intensively studied due to their importance in many infections. Much less has been known about archaeal biofilms, where archaea are a third domain of life. Using cryo-electron microscopy, we have determined the atomic structure of a surface filament in archaea that forms bi-polar bundles connecting cells. We show that this protein has common ancestry with a protein known to be an important component of bacterial biofilms. This adds to our understanding of the evolutionary relationship between bacteria and archaea and may provide new insights into bacterial biofilms.
Neural connectivity molecules best identify the heterogeneous clock and dopaminergic cell types in theDrosophilaadult brain
Authors: Ma Dingbang , Herndon Nicholas , Le Jasmine Quynh , Abruzzi Katharine C. , Rosbash Michael
Published: May 2022

Our recent single cell sequencing of most adultDrosophilacircadian neurons indicated striking gene expression heterogeneity, about 2-3 cells per clock neuron group. To extend this characterization to other adult fly brain neurons, we used the identical plate-based methods to generate single cell data from a similar subset of dopaminergic neurons. To minimize batch effects and to apply an additional sequencing strategy, we also assayed these two populations together with 10X Chromium. An unsupervised clustering algorithm indicates that dopaminergic neurons are comparably heterogeneous, suggesting that the transcriptomic diversity of adult fly brain neurons parallels its EM connectome. The results here further indicate that connectivity molecules like cell surface molecules best characterize all neuron groups. We suggest that these surprising features are general and make major contributions to neuronal identity and connectivity of the adult central brain as well as underlie the complex behavioral repertoire ofDrosophila.
De novo phytosterol synthesis in animals
Authors: Michellod Dolma , Bien Tanja , Birgel Daniel , Jensen Marlene , Kleiner Manuel , Fearn Sarah , Zeidler Caroline , Gruber-Vodicka Harald R , Dubilier Nicole , Liebeke Manuel
Published: May 2022

Sterols are lipids that regulate multiple processes in eukaryotic cells, and are essential components of cellular membranes. Sterols are currently assumed to be kingdom specific, with phytosterol synthesis restricted to plants while animals are only able to synthesize cholesterol. Here, we challenge this assumption by demonstrating that the marine annelids Olavius and Inanidrilus synthesize the phytosterol sitosterol de novo. Using multi-omics, high-resolution metabolite imaging, heterologous gene expression and enzyme assays, we show that sitosterol is the most abundant (60%) sterol in these animals and characterize its biosynthetic pathway. We show that phytosterol synthesis partially overlaps with cholesterol synthesis and involves a non-canonical C-24 sterol methyltransferase (C24-SMT). C24-SMT is an essential enzyme for sitosterol synthesis in plants, but not known from animals with bilateral symmetry (bilaterians). Our comparative phylogenetic analyses of C24-SMT homologs revealed that these are widely distributed across annelids and other animal phyla, including sponges and rotifers. Our findings show that phytosterol synthesis and use is not restricted to the plant kingdom, and indicate that the evolution of sterols in animals is more complex than previously assumed.
IL-17A-mediated alterations in gut microbiota composition, particularly changes in Prevotella abundance, impact Treg function in CNS Autoimmunity
Authors: Shahi Shailesh K. , Ghimire Sudeep , Jensen Samantha N. , Lehman Peter , Rux Allison G , Turner Ti-Ara , Borcherding Nicholas , Gibson-Corley Katherine N. , Ganesan Sukirth M. , Karandikar Nitin J. , Mangalam Ashutosh K.
Published: May 2022

A disrupted equilibrium among gut microbiota, IL-17A-producing CD4 T-cells (Th17), and regulatory CD4 T-cells (Treg) have been linked with the pathobiology of multiple sclerosis (MS). While gut microbiota can regulate both Treg and Th17 cells, the impact of IL-17A on this gut-immune connection remains unclear. Utilizing HLA-DR3 transgenic mouse model of MS, we show that IL-17A deficiency (HLA-DR3.IL17A-/-) resulted in milder disease characterized by increased Tregs and expansion of Treg-promoting gut microbes, includingPrevotella. Cohousing HLA-DR3 mice with HLA-DR3.IL17A-/-transferred the milder disease phenotype and associated microbiota changes to DR3 mice, highlighting the dominant role of gut microbiota in Treg induction and disease amelioration. DR3.IL17A-/-mice also showed a higher abundance of functional pathways linked with short-chain fatty acid synthesis and elevated IL-10 in dendritic cells. Enrichment of the Treg-promoting PPAR signaling pathway expression in the colon of HLA-DR3.IL17A-/-mice and followingPrevotellaadministration in HLA-DR3 mice underscores the importance of gut microbiota in IL-17A-mediated immune regulation. Thus, our study uncovers a previously unappreciated role for IL-17A in shaping gut microbiota and immune regulation, with far-reaching implications for MS treatment.

One-Sentence Summary

IL-17A modulates Treg and gut microbiota to control EAE
The effect of sleep continuity disruption on multimodal emotion processing and regulation: a laboratory-based, randomized, controlled experiment in good sleepers
Authors: Reid MJ. , Omlin X. , Espie CA. , Sharman R. , Tamm S. , Kyle SD.
Published: May 2022

Previous research shows that experimental sleep deprivation alters emotion processing, suggesting a potential mechanism linking sleep disruption to mental ill-health. Extending previous work, we experimentally disrupted sleep continuity in good sleepers and assessed next-day emotion processing and regulation using tasks with established sensitivity to depression. In a laboratory-based study, 51 good sleepers (37 female; mean age = 24 years, SD= 3.63) were randomized to one night (23:00-07:00) of uninterrupted sleep (n=24) or sleep continuity disruption (n=27). We assessed emotion perception, attention, and memory the following day. Participants also completed an emotion regulation task and measures of self-reported affect, anxiety, sleepiness, overnight declarative memory consolidation, and psychomotor vigilance. Confirming the effects of the manipulation, sleep continuity disruption led to a marked decrease in polysomnography-defined total sleep time (229.98 mins vs 434.57 mins), increased wake-time after sleep onset (260.66 mins vs 23.84 mins) and increased sleepiness (d=0.81). Sleep continuity disruption led to increased anxiety (d=0.68), decreased positive affect (d=-0.62), reduced overnight declarative memory consolidation (d=-1.08) and reduced psychomotor vigilance [longer reaction times (d=0.64) and more lapses (d=0.74)], relative to control. However, contrary to our hypotheses, experimental sleep disruption had no effect on perception of, or bias for, emotional facial expressions, emotional memory for words, or emotion regulation following worry induction. In conclusion, one night of sleep continuity disruption had no appreciable effect on objective measures of emotion processing or emotion regulation in response to worry induction, despite clear effects on memory consolidation, vigilance, and self-reported affect and anxiety.
A Chalcone Synthase-Like Bacterial Protein Catalyzes Heterocyclic C-Ring Cleavage of Naringenin to Alter Bioactivity Against Nuclear Receptors in Colonic Epithelial Cells
Authors: Gülşan Ebru Ece , Nowshad Farrhin , Leigh Meredith Davis , Crott Jimmy W , Safe Stephen , Jayaraman Arul , Lee Kyongbum
Published: May 2022

The human gut microbiota contributes enzymatic functions that are unavailable to host cells and play crucial roles in host metabolism, nutrient processing and regulating immune functions. As dietary compounds that are only partially absorbed, flavonoids are available for metabolism by gut microbiota, leading to diverse bioactive products. Combining prediction of enzyme promiscuity, metabolomics, and in vitro model systems, we identified a bacterial enzyme that can catalyze heterocyclic C-ring cleavage of naringenin. Culture experiments using a wild-type and mutant strain of Bacillus subtilis confirmed that the enzyme is a chalcone synthase-like polyketide synthase. The prediction-validation methodology developed in this work could be used to systematically characterize the products of gut bacterial flavonoid metabolism and identify the responsible enzymes and species. Further, we demonstrated that naringenin and its ring cleavage metabolites differentially engage the AhR and NR4A in intestinal epithelial cells. Our results suggest that the abundance of selected gut bacterial species impacts the profile of bioactive flavonoids and flavonoid-derived metabolites and thereby influences inflammatory responses in the intestine. These results are significant for understanding the mechanisms of gut microbiota-dependent effects of dietary flavonoids.
Polarly Localized WPR Proteins Interact With PAN Receptors And The Actin Cytoskeleton During Maize Stomatal Development
Authors: Nan Qiong , Char Si Nian , Yang Bing , Bennett Eric J. , Yang Bing , Facette Michelle R.
Published: May 2022

Polarization of cells prior to asymmetric cell division is crucial for correct cell divisions, cell fate and tissue patterning. In maize stomatal development, polarization of subsidiary mother cells prior to asymmetric division is controlled by the BRK-PAN-ROP pathway. Two catalytically inactive receptor-like kinases, PAN2 and PAN1, are required for correct division plane positioning. Proteins in the BRK-PAN-ROP pathway are polarized in subsidiary mother cells, with the polarization of each protein dependent on the previous one. As most of the known proteins in this pathway do not physically interact, possible interactors that might participate in the pathway are yet to be described. We identified WPR proteins as new players during subsidiary mother cell polarization. WPRs physically interact with PAN receptors, and polarly accumulate in subsidiary mother cells. The polarized localization of WPR proteins depends on PAN2 but not PAN1. CRISPR-Cas9- induced mutations result in division plane defects in subsidiary mother cells, and ectopic expression of WPR-RFP results in stomatal defects and alterations to the actin cytoskeleton. We show certain WPR proteins directly interact with F-actin through their N-terminus. Our data implicate WPR proteins as potentially regulating actin filaments, which providing insight into their molecular function. Together, these results demonstrate that WPR proteins are important for cell polarization.

One-sentence summary

Four related proteins, identified via their physical interaction with the receptor PAN2, are polarly localized prior to asymmetric division in stomatal lineage cells, and interact with F-actin.
Run-on sequencing reveals nascent transcriptomics of the human microbiome
Authors: Vill Albert C. , Rice Edward J. , De Vlaminck Iwijn , Danko Charles G. , Brito Ilana L.
Published: May 2022

Precise regulation of transcription initiation and elongation enables bacteria to control cellular responses to environmental stimuli. RNAseq is the most common tool for measuring the transcriptional output of bacteria, comprising predominantly mature transcripts. To gain further insight into transcriptional dynamics, it is necessary to discriminate actively transcribed loci from those represented in the total RNA pool. One solution is to capture RNA polymerase (RNAP) in the act of transcription, but current methods are restricted to culturable and genetically tractable organisms. Here, we apply precision run-on sequencing (PRO-seq) to profile nascent transcription, a method amenable to diverse species. We find that PRO-seq is well-suited to profile small, structured, or post-transcriptionally modified RNAs, which are often excluded from RNAseq libraries. When PRO-seq is applied to the human microbiome, we identify taxon-specific RNAP pause motifs. We also uncover concurrent transcription and cleavage of guide RNAs and tRNA fragments at active CRISPR and tRNA loci. We demonstrate the specific utility of PRO-seq as a tool for exploring transcriptional dynamics in diverse microbial communities.
Implications for food safety of the size and location of fragments of lead shotgun pellets embedded in hunted carcasses of small game animals intended for human consumption
Authors: Green Rhys E. , Taggart Mark A. , Pain Deborah J. , Smithson Keturah
Published: May 2022

Carcasses of common pheasants (Phasianus colchicus) killed by hunters using shotguns are widely used or sold in the United Kingdom and elsewhere for human consumption. Almost all of the birds are shot using shotgun pellets composed principally of lead (Pb). Lead shotgun pellets often fragment on impact within the bodies of gamebirds, leaving small lead particles in the meat that are difficult for consumers to detect and remove and from which a greater proportion of lead is likely to be absorbed. Chronic exposure to even low levels of lead is associated with negative health effects in humans and especially in groups particularly vulnerable to the effects of lead, which include young children and pregnant women. Our study used a high-resolution computerised tomography X-ray scanner to locate, in three dimensions, metal fragments embedded within carcasses of eight pheasants sold for human consumption in the UK. Small radio-dense fragments (<2 mm diameter), assumed to be metallic lead, were present in all of the pheasant carcasses examined (mean number: 39 per carcass) and many were too small (<0.1 mm diameter) and too distant from the nearest large shotgun pellet for it to be practical for consumers to detect and remove them without discarding a large proportion of otherwise usable meat. Consumers of carcasses of pheasants killed using lead shotgun ammunition are likely to be exposed to elevated levels of dietary lead, even if careful food preparation is practiced to remove shotgun pellets and the most damaged tissue.
Quantifying the fraction of new mutations that are recessive lethal
Authors: Wade Emma E. , Kyriazis Christopher C. , Cavassim Maria Izabel A. , Lohmueller Kirk E.
Published: May 2022

The presence and impact of recessive lethal mutations has been widely documented in diploid outcrossing species. However, precise estimates in different species of the proportion of mutations that are recessive lethal remain limited. Here, we attempt to quantify the fraction of new mutations that are recessive lethal using Fit∂a∂i, a commonly-used method for inferring the distribution of fitness effects (DFE) using the site frequency spectrum. Using simulations, we demonstrate that Fit∂a∂i cannot accurately estimate the fraction of recessive lethal mutations, as expected given that Fit∂a∂i assumes that all mutations are additive by default. Consistent with the idea that mis-specification of the dominance model can explain this performance, we find that Fit∂a∂i can accurately infer the fraction of additive lethal mutations. Moreover, we demonstrate that in both additive and recessive cases, inference of the deleterious non-lethal portion of the DFE is minimally impacted by a small proportion (<10%) of lethal mutations. Finally, as an alternative approach to estimate the proportion of mutations that are recessive lethal, we employ models of mutation-selection-drift balance using existing genomic parameters and segregating recessive lethals estimates for humans and Drosophila melanogaster. In both species, we find that the segregating recessive lethal load can be explained by a very small fraction (<1%) of new nonsynonymous mutations being recessive lethal. Our results refute recent assertions of a much higher recessive lethal mutation fraction (4-5%), while highlighting the need for additional information on the joint distribution of selection and dominance coefficients.