bluuebunny/crossref_metadata_2025 huggingface dataset:
Site-specific length-biomass relationships of arctic arthropod families are critical for accurate ecological inferences
Authors: Versluijs Tom S.L. , Zhemchuzhnikov Mikhail K. , Kutcherov Dmitry , Roslin Tomas , Schmidt Niels Martin , van Gils Jan. A. , Reneerkens Jeroen
Published: April 2023

Arthropods play an essential role in terrestrial ecosystems, not least by forming the food base for insectivorous birds. To better understand such trophic interactions, it is essential to monitor seasonal trajectories in arthropod biomass. Because obtaining direct measurements of the body mass of individual specimens is laborious, these data are often indirectly acquired by utilizing allometric length-biomass relationships based on a correlative parameter, such as body length. Studies on insectivorous birds have often used such relationships with a low taxonomic resolution and/or small sample size and/or adopted regressions calibrated in different biomes. Despite the scientific interest in the ecology of arctic arthropods, no site-specific family-level length-biomass relationships have hitherto been published. Here we present 27 family-specific length-biomass relationships from two sites in the High Arctic: Zackenberg in northeast Greenland and Knipovich in north Taimyr, Russia. We show that length-biomass regressions from different sites within the same biome did not affect estimates of phenology but did result in substantially different estimates of arthropod biomass. Estimates of daily biomass at Zackenberg were on average 24% higher when calculated using regressions for Knipovich compared to using regressions for Zackenberg. Our results illustrate that the use of allometric relationships from different sites can significantly alter the biological interpretation of, for instance, the interaction between insectivorous birds and their arthropod prey. We conclude that length-biomass relationships should be locally established rather than being based on global relationships.

Subjects

Ecology, Entomology, Terrestrial ecology
Featural representation and internal noise underlie the eccentricity effect in contrast sensitivity
Authors: Xue Shutian , Fernández Antonio , Carrasco Marisa
Published: April 2023

Human visual performance for basic visual dimensions (e.g., contrast sensitivity and acuity) peaks at the fovea and decreases with eccentricity. The eccentricity effect is related to the larger surface area of the visual cortex corresponding to the fovea, but it is unknown if differential feature tuning contributes to this eccentricity effect. Here, we investigated two system-level computations underlying the eccentricity effect: featural representation (tuning) and internal noise. Observers (both sexes) detected a Gabor embedded in filtered white noise which appeared at the fovea or one of four perifoveal locations. We used psychophysical reverse correlation to estimate the weights assigned by the visual system to a range of orientations and spatial frequencies (SFs) in noisy stimuli, which are conventionally interpreted as perceptual sensitivity to the corresponding features. We found higher sensitivity to task-relevant orientations and SFs at the fovea than the perifovea, and no difference in selectivity for either orientation or SF. Concurrently, we measured response consistency using a double-pass method, which allowed us to infer the level of internal noise by implementing a noisy observer model. We found lower internal noise at the fovea than perifovea. Finally, individual variability in contrast sensitivity correlated with sensitivity to and selectivity for task-relevant features as well as with internal noise. Moreover, the behavioral eccentricity effect mainly reflects the foveal advantage in orientation sensitivity compared to other computations. These findings suggest that the eccentricity effect stems from a better representation of task-relevant features and lower internal noise at the fovea than at the perifovea.

Significance

Performance in many visual tasks worsens with eccentricity. Many studies attribute this eccentricity effect to retinal and cortical factors, like higher cone density and a larger cortical surface area representing the foveal than peripheral locations. We investigated whether system-level computations for task-relevant visual features also underlie this eccentricity effect. Measuring contrast sensitivity in visual noise, we showed that the fovea better represents task-relevant orientation and spatial frequency and has lower internal noise than the perifovea, and that individual variability in these two computations correlates with that in performance. These findings reveal that both representations of these basic visual features and internal noise underlie the difference in performance with eccentricity.
Small molecule chaperones facilitate the folding of long non-coding RNA G
Authors: Lejault Pauline , Prudent Louis , Terrier Michel-Pierre , Perreault Jean-Pierre
Published: April 2023

RNA G-quadruplexes (rG4) have recently emerged as major regulatory elements in both mRNA and non-coding RNA. To investigate the biological roles of the rG4 structures, chemists have developed a variety of highly specific and potent ligands. All these ligands bind to the rG4 by staking on their top, and the specificity of binding is demonstrated in comparison to other structures such as duplex or three-way junctions. It remains unclear whether rG4-ligands merely stabilize fully formed rG4 structures, or if they actively participate in the folding of the rG4 structure through their association with an unfolded RNA sequence. In order to access the innate steps of ligand-rG4 association and mechanisms, robustin vitrotechniques, including FRET, electrophoretic mobility shift assay and reverse transcriptase stalling assays, were used to examine the capacity of five well-known G4 ligands to induce rG4 structures derived from either long non-coding RNAs of from synthetic RNAs. It was found that both PhenDC3 and PDS induce rG4 formation in unfolded single RNA strands. This discovery has important implications for the interpretation of RNA-seq experiments. Overall,in vitrodata that can assist biochemists in selecting the optimal G4-ligands for their RNA cellular experiments are presented, while also considering the effects induced by these ligands of the rG4.

Abstract Figure

Graphical abstract

A schematic representation of the potential structures that may arise from unfolded RNA that is rich in G nucleotides. rG4 can be stabilized by K+either with or without G4 ligand and can be induced by a molecular chaperone in the presence of Li+.
Dynein-Powered Cell Locomotion Guides Metastasis of Breast Cancer
Authors: Tagay Yerbol , Kheirabadi Sina , Ataie Zaman , Singh Rakesh K. , Prince Olivia , Nguyen Ashley , Zhovmer Alexander S. , Ma Xuefei , Sheikhi Amir , Tsygankov Denis , Tabdanov Erdem D.
Published: April 2023

Metastasis is a principal cause of death in cancer patients, which remains an unresolved fundamental and clinical problem. Conventionally, metastatic dissemination is linked to the actomyosin-driven cell locomotion. However, locomotion of cancer cells often does not strictly line up with the measured actomyosin forces. Here, we identify a complementary mechanism of metastatic locomotion powered by the dynein-generated forces. These forces that arise within a non-stretchable microtubule network drive persistent contact guidance of migrating cancer cells along the biomimetic collagen fibers. We also show that dynein-powered locomotion becomes indispensable during invasive 3D migration within a tissue-like luminal network between spatially confining hydrogel microspheres. Our results indicate that the complementary contractile system of dynein motors and microtubules is always necessary and in certain instances completely sufficient for dissemination of metastatic breast cancer cells. These findings advance fundamental understanding of cell locomotion mechanisms and expand the spectrum of clinical targets against metastasis.
The ENCODE Uniform Analysis Pipelines
Authors: Hitz Benjamin C. , Lee Jin-Wook , Jolanki Otto , Kagda Meenakshi S. , Graham Keenan , Sud Paul , Gabdank Idan , Seth Strattan J. , Sloan Cricket A. , Dreszer Timothy , Rowe Laurence D. , Podduturi Nikhil R. , Malladi Venkat S. , Chan Esther T. , Davidson Jean M. , Ho Marcus , Miyasato Stuart , Simison Matt , Tanaka Forrest , Luo Yunhai , Whaling Ian , Hong Eurie L. , Lee Brian T. , Sandstrom Richard , Rynes Eric , Nelson Jemma , Nishida Andrew , Ingersoll Alyssa , Buckley Michael , Frerker Mark , Kim Daniel S , Boley Nathan , Trout Diane , Dobin Alex , Rahmanian Sorena , Wyman Dana , Balderrama-Gutierrez Gabriela , Reese Fairlie , Durand Neva C. , Dudchenko Olga , Weisz David , Rao Suhas S. P. , Blackburn Alyssa , Gkountaroulis Dimos , Sadr Mahdi , Olshansky Moshe , Eliaz Yossi , Nguyen Dat , Bochkov Ivan , Shamim Muhammad Saad , Mahajan Ragini , Aiden Erez , Gingeras Tom , Heath Simon , Hirst Martin , James Kent W. , Kundaje Anshul , Mortazavi Ali , Wold Barbara , Cherry J. Michael
Published: April 2023

The Encyclopedia of DNA elements (ENCODE) project is a collaborative effort to create a comprehensive catalog of functional elements in the human genome. The current database comprises more than 19000 functional genomics experiments across more than 1000 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of theHomo sapiensandMus musculusgenomes. All experimental data, metadata, and associated computational analyses created by the ENCODE consortium are submitted to the Data Coordination Center (DCC) for validation, tracking, storage, and distribution to community resources and the scientific community. The ENCODE project has engineered and distributed uniform processing pipelines in order to promote data provenance and reproducibility as well as allow interoperability between genomic resources and other consortia. All data files, reference genome versions, software versions, and parameters used by the pipelines are captured and availableviathe ENCODE Portal. The pipeline code, developed using Docker and Workflow Description Language (WDL;https://openwdl.org/) is publicly available in GitHub, with images available on Dockerhub (https://hub.docker.com), enabling access to a diverse range of biomedical researchers. ENCODE pipelines maintained and used by the DCC can be installed to run on personal computers, local HPC clusters, or in cloud computing environmentsviaCromwell. Access to the pipelines and dataviathe cloud allows small labs the ability to use the data or software without access to institutional compute clusters. Standardization of the computational methodologies for analysis and quality control leads to comparable results from different ENCODE collections - a prerequisite for successful integrative analyses.

Database URL:https://www.encodeproject.org/
Optogenetic control of medaka behavior with channelrhodopsin
Authors: Seki Takahide , Takeuchi Hideaki , Ansai Satoshi
Published: April 2023

Optogenetics enables the manipulation of neural activity with high spatiotemporal resolution in genetically defined neurons. The method is widely used in various model animals in the neuroscience and physiology fields. Channelrhodopsins are robust tools for optogenetic manipulation, but they have not yet been used for studies in medaka. In the present study, we used the CRISPR/Cas9-mediated knock-in approach to establish a transgenic medaka strain expressing theChloromonas oogamachannelrhodopsin (CoChR) in theISL LIM homeobox 1(isl1) locus. We demonstrated that light stimuli elicited specific behavioral responses such as bending or turning locomotion in the embryos and pectoral fin movements in the larvae and adults. The response probabilities and intensities of these movements could be controlled by adjusting the intensity, duration, or wavelength of each light stimulus. Furthermore, we demonstrated that the pectoral fin movements in the adult stage could be elicited using a laser pointer to irradiate only the hindbrain region. Our results indicate that CoChR allows for manipulation of medaka behaviors by activating targeted neurons, which will further our understanding of the detailed neural mechanisms of social behaviors in medaka.
TALLSorts: a T-cell acute lymphoblastic leukaemia subtype classifier using RNA-seq expression data
Authors: Gu Allen , Schmidt Breon , Lonsdale Andrew , Brown Lauren M. , Sadras Teresa , Ekert Paul G. , Oshlack Alicia
Published: April 2023

T-cell acute lymphoblastic leukaemia (T-ALL) is an aggressive and heterogenous haematological malignancy affecting both children and adults. T-ALL subtype identification is an emerging area of active research, with several recent studies proposing potential subtypes based on transcriptomic and genomic analyses. Here we present TALLSorts, a machine-learning bioinformatic tool which classifies T-ALL samples by using bulk RNA sequencing (RNA-seq) data. Trained on four international cohorts totalling 264 samples, TALLSorts exhibits excellent accuracy when tested on holdout and independent test sets. TALLSorts is publicly available for use and will be constantly updated as the field of T-ALL classification further develops.
The Cauchy Process on Phylogenies: a Tractable Model for Pulsed Evolution
Authors: Bastide Paul , Didier Gilles
Published: April 2023

Phylogenetic comparative methods use random processes, such as the Brownian Motion, to model the evolution of continuous traits on phylogenetic trees. Growing evidence for non-gradual evolution motivated the development of complex models, often based on Lévy processes. However, their statistical inference is computationally intensive, and currently relies on approximations, high dimensional sampling, or numerical integration. We consider here the Cauchy Process (CP), a particular pure-jump Lévy process in which the trait increment along each branch follows a centered Cauchy distribution with a dispersion proportional to its length. In this work, we derive an exact algorithm to compute both the joint probability density of the tip trait values of a phylogeny under a CP, and the ancestral trait values and branch increments posterior densities in quadratic time. A simulation study shows that the CP generates patterns in comparative data that are distinct from any Gaussian process, and that Restricted Maximum Likelihood (REML) parameter estimates and root trait reconstruction are unbiased and accurate for trees with 200 tips or less. The CP has only two parameters but is rich enough to capture complex pulsed evolution. It can reconstruct posterior ancestral trait distributions that are multimodal, reflecting the uncertainty associated with the inference of the evolutionary history of a trait from extant taxa only. Applied on empirical datasets taken from the Evolutionary Ecology and Virology literature, the CP suggests nuanced scenarios for the body size evolution of Greater Antilles Lizards and for the geographical spread of the West Nile Virus epidemics in North America, both consistent with previous studies using more complex models. The method is efficiently implemented in C with an R interface in package cauphy, that is open source and freely available online. Cauchy process, Phylogenetic Comparative Methods, Evolutionary jumps, Quantitative traits, Phylogeography
RhoB promotesSalmonellasurvival by regulating autophagy
Authors: Kirchenwitz Marco , Halfen Jessica , von Peinen Kristin , Prettin Silvia , Kollasser Jana , Brakebusch Cord , Rottner Klemens , Steffen Anika , Stradal Theresia E.B.
Published: April 2023

Salmonella entericaserovar Typhimurium manipulates cellular Rho GTPases for host cell invasion by effector protein translocation via the Type III Secretion System (T3SS). The two Guanine nucleotide exchange (GEF) mimicking factors SopE and –E2 and the inositol phosphate phosphatase (PiPase) SopB activate the Rho GTPases Rac1, Cdc42 and RhoA, thereby mediating bacterial invasion.S.Typhimurium lacking these three effector proteins are largely invasion-defective. Type III secretion is crucial for both early and later phases of the intracellular life ofS.Typhimurium. Here we investigated whether and how the small GTPase RhoB, known to localize on endomembrane vesicles and at the invasion site ofS.Typhimurium, contributes to bacterial invasion and to subsequent steps relevant forS.Typhimurium lifestyle.

We show that RhoB is significantly upregulated within hours ofSalmonellainfection. This effect depends on the presence of the bacterial effector SopB, but does not require its phosphatase activity. Our data reveal that SopB and RhoB bind to each other, and that RhoB localizes on early phagosomes of intracellularS.Typhimurium. Whereas both SopB and RhoB promote intracellular survival ofSalmonella, RhoB is specifically required forSalmonella-induced upregulation of autophagy. Finally, in the absence of RhoB, vacuolar escape and cytosolic hyper-replication ofS.Typhimurium is diminished. Our findings thus uncover a role for RhoB inSalmonella-induced autophagy, which supports intracellular survival of the bacterium and is promoted through a positive feedback loop by theSalmonellaeffector SopB.
Spinal motoneurons respond aberrantly to serotonin in a rabbit model of cerebral palsy
Authors: Reedich E. J. , Genry L.T. , Steele P.R. , Avila E. Mena , Dowaliby L. , Drobyshevsky A. , Manuel M. , Quinlan K. A.
Published: April 2023

Cerebral palsy (CP) is caused by a variety of factors that damage the developing central nervous system. Impaired motor control, including muscle stiffness and spasticity, is the hallmark of spastic CP. Rabbits that experience hypoxic-ischemic (HI) injuryin utero(at 70-80% gestation) are born with muscle stiffness, hyperreflexia, and, as recently discovered, increased serotonin (5-HT) in the spinal cord. To determine whether serotonergic modulation of spinal motoneurons (MNs) contributes to motor deficits, we performedex vivowhole cell patch clamp in neonatal rabbit spinal cord slices at postnatal day (P) 0-5. HI MNs responded to application of α-methyl 5-HT (a 5-HT1/5-HT2receptor agonist) and citalopram (a selective 5-HT reuptake inhibitor) with hyperpolarization of persistent inward currents and threshold voltage for action potentials, reduced maximum firing rate, and an altered pattern of spike frequency adaptation while control MNs did not exhibit any of these responses. To further explore the differential sensitivity of MNs to 5-HT, we performed immunohistochemistry for inhibitory 5-HT1Areceptors in lumbar spinal MNs at P5. Fewer HI MNs expressed the 5-HT1Areceptor compared to age-matched controls. This suggests many HI MNs lack a normal mechanism of central fatigue mediated by 5-HT1Areceptors. Other 5-HT receptors (including 5-HT2) are likely responsible for the robust increase in HI MN excitability. In summary, by directly exciting MNs, the increased concentration of spinal 5-HT in HI rabbits can cause MN hyperexcitability, muscle stiffness, and spasticity characteristic of CP. Therapeutic strategies that target serotonergic neuromodulation may be beneficial to individuals with CP.

Key points

After prenatal hypoxia-ischemia (HI), neonatal rabbits that show hypertonia are known to have higher levels of spinal serotonin

We tested responsivity of spinal motoneurons (MNs) in neonatal control and HI rabbits to serotonin using whole cell patch clamp

MNs from HI rabbits showed a more robust excitatory response to serotonin than control MNs, including hyperpolarization of the persistent inward current and threshold for action potentials, larger post-inhibitory rebound, and less spike frequency adaptation

Based on immunohistochemistry of lumbar MNs, fewer HI MNs express inhibitory 5HT1Areceptors than control MNs, which could account for the more robust excitatory response of HI MNs.

These results suggest that after HI injury, the increased serotonin could trigger a cascade of events leading to muscle stiffness and altered motor unit development
Statistical analysis of a Potts glass model of cortical dynamics
Authors: Ryom Kwang Il , Treves Alessandro
Published: April 2023

We introduce, in a previously studied Potts model of long-range cortical interactions, a differentiation between a frontal and a posterior subnetwork. “Frontal” units, representing patches of anterior cortex, are endowed with a higher numberSof attractor states, in keeping with the larger number of local synaptic contacts of neurons there, than in occipital cortex. A thermodynamic analysis and computer simulations confirm that disorder leads to glassy properties and slow dynamics but, surprisingly, the frontal network, which would be slower if isolated, becomes faster than the posterior network when interacting with it. From an abstract, drastically simplified model we take some steps towards approaching a neurally plausible one, and find that the speed inversion effect is basically preserved.
SPATIO-TEMPORAL DYNAMICS OF EARLY SOMITE SEGMENTATION IN THE CHICKEN EMBRYO
Authors: Maia-Fernandes Ana Cristina , Martins-Jesus Ana , Pais-de-Azevedo Tomás , Magno Ramiro , Duarte Isabel , Andrade Raquel P.
Published: April 2023

During vertebrate embryo development, the body is progressively segmented along the anterior-posterior (A-P) axis early in development. The rate of somite formation is controlled by the somitogenesis embryo clock (EC), which was first described as gene expression oscillations ofhairy1(hes4) in the presomitic mesoderm of chick embryos with 15-20 somites. Here, the EC displays the same periodicity as somite formation, 90 min, whereas the posterior-most somites (44-52) only arise every 150 minutes, matched by a corresponding slower pace of the EC. Evidence suggests that the rostral-most somites are formed faster, however, their periodicity and the EC expression dynamics in these early stages are unknown. In this study, we used time-lapse imaging of chicken embryos from primitive streak to somitogenesis stages with high temporal resolution (3-minute intervals). We measured the length between the anterior-most and the last formed somitic clefts in each captured frame and developed a simple algorithm to automatically infer both the length and time of formation of each somite. We found that the occipital somites (up to somite 5) form at an average rate of 75 minutes, while somites 6 onwards are formed approximately every 90 minutes. We also assessed the expression dynamics ofhairy1using half-embryo explants cultured for different periods of time. This showed that EChairy1expression is highly dynamic prior to somitogenesis and assumes a clear oscillatory behaviour as the first somites are formed. Importantly, usingex ovoculture and live-imaging techniques, we showed that thehairy1expression pattern recapitulates with the formation of each new pair of somites, indicating that somite segmentation is coupled with EC oscillations since the onset of somitogenesis.

Highlights

Time of early somite formation can be inferred from sequential length measurements

The cranial-most somites are formed faster than trunk somites

Oscillations ofhairy1expression are temporally coupled with early somite formation

GRAPHICAL ABSTRACT
Synthetic microbial sensing and biosynthesis of amaryllidaceae alkaloids
Authors: d’Oelsnitz Simon , Diaz Daniel , Acosta Daniel , Schechter Mason , Minus Matthew , Howard James , Loy James , Do Hannah , Alper Hal S. , Ellington Andrew D.
Published: April 2023

A major challenge to achieving industry-scale biomanufacturing of therapeutic alkaloids is the slow process of biocatalyst engineering. Amaryllidaceae alkaloids, such as the Alzheimer’s medication galantamine, are complex plant secondary metabolites with recognized therapeutic value. Due to their difficult synthesis they are regularly sourced by extraction and purification from low-yielding plants, including the wild daffodilNarcissus pseudonarcissus. Engineered biocatalytic methods have the potential to stabilize the supply chain of amaryllidaceae alkaloids. Here, we propose a highly efficient biosensor-AI technology stack for biocatalyst development, which we apply to engineer amaryllidaceae alkaloid production inEscherichia coli. Directed evolution is used to develop a highly sensitive (EC50= 20 uM) and specific biosensor for the key amaryllidaceae alkaloid branchpoint 4-O’Methylnorbelladine. A machine learning model (MutComputeX) was subsequently developed and used to generate activity-enriched variants of a plant methyltransferase, which were rapidly screened with the biosensor. Functional enzyme variants were identified that yielded a 60% improvement in product titer, 17-fold reduced remnant substrate, and 3-fold lower off-product regioisomer formation.
Characterization of methionine dependence in melanoma cells
Authors: Garg Sarita , Morehead Lauren C. , Bird Jordan T. , Graw Stefan , Gies Allen , Storey Aaron J. , Tackett Alan J. , Edmondson Rick D. , Mackintosh Samuel G. , Byrum Stephanie D. , Miousse Isabelle R.
Published: April 2023

Dietary methionine restriction is associated with a reduction in tumor growth in preclinical studies and an increase in lifespan in animal models. The mechanism by which methionine restriction inhibits tumor growth while sparing normal cells is incompletely understood. We do know that normal cells can utilize methionine or homocysteine interchangeably (methionine independence) while most cancer cells are strictly dependent on methionine availability. Here, we compared a typical methionine dependent and a rare methionine independent melanoma cell line. We show that replacing methionine, a methyl donor, with its precursor homocysteine generally induced hypomethylation in gene promoters. This decrease was similar in methionine dependent and methionine independent cells. There was only a low level of pathway enrichment, suggesting that the hypomethylation is generalized rather than gene specific. Whole proteome and transcriptome were also analyzed. This analysis revealed that contrarily to the effect on methylation, the replacement of methionine with homocysteine had a much greater effect on the transcriptome and proteome of methionine dependent cells than methionine independent cells. Interestingly, methionine adenosyltransferase 2A (MAT2A), responsible for the synthesis of s-adenosylmethionine from methionine, was equally strongly upregulated in both cell lines. This suggests that the absence of methionine is equally detected but triggers different outcomes in methionine dependent versus independent cells. Our analysis reveals the importance of cell cycle control, DNA damage repair, translation, nutrient sensing, oxidative stress and immune functions in the cellular response to methionine stress in melanoma.
Chromatin conformation dynamics during CD4+ T cell activation implicates autoimmune disease-associated genes and regulatory elements
Authors: Pahl Matthew C. , Sharma Prabhat , Thomas Rajan M. , Thompson Zachary , Mount Zachary , Pippin James , Morawski Peter A. , Su Chun , Campbell Daniel J. , Grant Struan F.A. , Wells Andrew D.
Published: April 2023

Genome-wide association studies (GWAS) have identified hundreds of genetic signals associated with autoimmune disease. The majority of these signals are located in non-coding regions and likely impactcis-regulatory elements (cRE). Because cRE function is dynamic across cell types and states, profiling the epigenetic status of cRE across physiological processes is necessary to characterize the molecular mechanisms by which autoimmune variants contribute to disease risk. We localized risk variants from 15 autoimmune GWAS to cRE active during TCR-CD28 costimulation of naïve human CD4+ T cells. To characterize how dynamic changes in gene expression correlate with cRE activity, we measured transcript levels, chromatin accessibility, and promoter-cRE contacts across three phases of naive CD4+ T cell activation using RNA-seq, ATAC-seq, and HiC. We identified ∼1,200 protein-coding genes physically connected to accessible disease-associated variants at 423 GWAS signals, at least one-third of which are dynamically regulated by activation. From these maps, we functionally validated a novel stretch of evolutionarily conserved intergenic enhancers whose activity is required for activation-inducedIL2gene expression in human and mouse, and is influenced by autoimmune-associated genetic variation. The set of genes implicated by this approach are enriched for genes controlling CD4+ T cell function and genes involved in human inborn errors of immunity, and we pharmacologically validated eight implicated genes as novel regulators of T cell activation. These studies directly show how autoimmune variants and the genes they regulate influence processes involved in CD4+ T cell proliferation and activation.
Non-equilibrium antigen recognition in acute infections
Authors: Morán-Tovar Roberto , Lässig Michael
Published: April 2023

The immune response to an acute primary infection is a coupled process of antigen proliferation, molecular recognition by naive B-cells, and their subsequent proliferation and antibody shedding. Here we show B-cells can efficiently recognise new antigens by a tuned kinetic proofreading mechanism, where the number of proofreading steps and the characteristic rate of each step are set by the complexity of the immune repertoire. This process produces potent, specific and fast recognition of antigens, maintaining a spectrum of genetically distinct B-cell lineages as input for affinity maturation. We show that the proliferation-recognition dynamics of a primary infection can me mapped onto a generalised Luria-Delbrück process, akin to the dynamics of the classic fluctuation experiment. We derive the resulting statistics of the activated immune repertoire: antigen binding affinity, expected size, and frequency of active B-cell clones are related by power laws. Their exponents depend on the antigen and B-cell proliferation rate, the number of proofreading steps, and the lineage density of the naive repertoire. Empirical data of mouse immune repertoires are found to be consistent with activation involving at least three proofreading steps. Our model predicts key clinical characteristics of acute infections. The primary immune response to a given antigen is strongly heterogeneous across individuals; few elite responders are distinguished by early activation of high-affinity clones. Conversely, ageing of the immune system, by reducing the density of naive clones, degrades potency and speed of pathogen recognition.
Nanopore molecular trajectories of a eukaryotic reverse transcriptase reveal a long-range RNA structure sensing mechanism
Authors: Shaw Alan , Craig Jonathan M. , Amiri Hossein , Kim Jeonghoon , Upton Heather E. , Pimentel Sydney C. , Huang Jesse R. , Marqusee Susan , Collins Kathleen , Gundlach Jens H. , Bustamante Carlos J.
Published: April 2023

Eukaryotic reverse transcriptases (RTs) can have essential or deleterious roles in normal human physiology and disease. Compared to well-studied helicases, it remains unclear how RTs overcome the ubiquitous RNA structural barriers during reverse transcription. Herein, we describe the development of a Mycobacterium smegmatis porin A (MspA) nanopore technique to sequence RNA to quantify the single-molecule kinetics of an RT fromBombyx moriwith single-nucleotide resolution. By establishing a quadromer map that correlates RNA sequence and MspA ion current, we were able to quantify the RT’s dwell time at every single nucleotide step along its RNA template. By challenging the enzyme with various RNA structures, we found that during cDNA synthesis the RT can sense and actively destabilize RNA structures 11-12 nt downstream of its front boundary. The ability to sequence single molecules of RNA with nanopores paves the way to investigate the single-nucleotide activity of other processive RNA translocases.
Fast genome-based species delimitation: Enterobacterales and beyond
Authors: Hernández-Salmerón Julie E. , Irani Tanya , Moreno-Hagelsieb Gabriel
Published: April 2023

Average Nucleotide Identity (ANI) is becoming a standard measure for bacterial species delimitation. However, its calculation can take orders of magnitude longer than fast similarity estimates based on sampling of short nucleotides, compiled into so-called sketches. These estimates are widely used and correlate well with ANI. However, they might not be as accurate. Thus, we compared two sketching programs, mash and dashing, against ANI, in delimiting species among publicly available Esterobacterales genomes. Receiver Operating Characteristic (ROC) curve analysis found all three programs to be highly accurate, with Area Under the Curve (AUC) values of 0.99, indicating almost perfect species discrimination. Subsampling to reduce over-represented species, reduced these AUC values to 0.92. Focused tests with ten genera represented by more than three species, also showed almost identical results for all methods.Shigellashowed the lowest AUC values (0.68), followed byCitrobacter(0.80). All other genera,Dickeya, Enterobacter, Escherichia, Klebsiella, Pectobacterium, Proteus, ProvidenciaandYersinia, produced AUC values above 0.90. The species delimitation thresholds varied, with species distance ranges in a few genera overlapping the genus ranges of other genera. Mash was able to separate theE. coli+Shigellacomplex into 25 apparent phylogroups. Testing mash for species separation in genera outside Enterobacterales showed AUCs above 0.95, again with different thresholds for species delimitation within each genus. Overall, our results suggest that fast estimates of genome similarity are as good as ANI for species delimitation. Therefore, these fast estimates might suffice for determining the role of genomic similarity in bacterial taxonomy.
Innate attraction and aversion to odors in locusts
Authors: Ray Subhasis , Sun Kui , Stopfer Mark
Published: April 2023

Many animals display innate preferences for some odors, but the physiological mechanisms underlying these preferences are poorly understood. Here, with behavioral tests, we establish a model system well suited to investigating olfactory mechanisms, the locustSchistocerca americana. We conducted open field two-choice tests with purely olfactory stimuli. In these tests, newly hatched locusts navigated toward, and spent time near, the source of a food odor blend, crushed wheat grass. In similar tests, we found that hatchlings avoided moderate concentrations of major individual components of the food blend odor, 1-hexanol and hexanal. They were neither attracted nor repelled by a lower concentration of 1-hexanol, but were moderately attracted to a low concentration of hexanal. These results establish that hatchlings have a strong, innate preference for food odor blend, but the valence of the blend’s individual components may be different and may change depending on the concentration. This suggests innate odor preferences may emerge from more complex processing pathways than labeled lines. Our results provide a useful entry point for an analysis of physiological mechanisms underlying innate sensory preferences.
Dehydrated snakes reduce postprandial thermophily
Authors: Azzolini Jill L. , Roderick Travis B. , DeNardo Dale F.
Published: April 2023

Transient thermophily in ectothermic animals is a common response during substantive physiological events. For example, ectotherms often elevate body temperature after ingesting a meal. In particular, the increase in metabolism during the postprandial period of pythons - known as specific dynamic action – is supported by a concurrent increase in preferred temperature. The objective of this study was to determine whether hydration state influenced digestion-related behavioral thermophily. Sixteen (8 male and 8 female) Children’s pythons (Antaresia childreni) with surgically implanted temperature data loggers were housed individually and provided a thermal gradient of 25-45 °C. Body temperature was recorded hourly beginning 6 days prior to feeding and for 18 days post-feeding, thus covering pre-feeding, postprandial, and post-absorptive stages. Each snake underwent this 24-day trial twice, once when hydrated and once when dehydrated. Our results revealed a significant interaction between temperature preference, digestive stage, and hydration state. Under both hydrated and dehydrated conditions, snakes similarly increased their body temperature shortly after consuming a meal, but during the later period of the postprandial stage, snakes selected significantly lower (~1.5°C) body temperature when they were dehydrated compared to when they were hydrated. Our results demonstrate a significant effect of hydration state on postprandial thermophily, but the impact of this dehydration-induced temperature reduction on digestive physiology (e.g., passage time, energy assimilation) is unknown and warrants further study.

Summary statement

Dehydration suppresses the extent to which python increase body temperature after ingesting a meal, thus demonstrating a physiological conflict between optimizing body temperature and water balance.
Polarized vesicle transport requires AP-1-mediated recruitment of KIF13A and KIF13B at the trans-Golgi network
Authors: Montgomery Andrew C. , Mendoza Christina S. , Garbouchian Alex , Quinones Geraldine B. , Bentley Marvin
Published: April 2023

Neurons are polarized cells that require accurate membrane trafficking to maintain distinct protein complements at dendritic and axonal membranes. The Kinesin-3 family members KIF13A and KIF13B are thought to mediate dendrite-selective transport, but the mechanism by which they are recruited to polarized vesicles and the differences in the specific trafficking role of each KIF13 have not been defined. We performed live-cell imaging in cultured hippocampal neurons and found that KIF13A is a dedicated dendrite-selective kinesin. KIF13B confers two different transport modes, both dendrite- and axon-selective transport. Both KIF13s are maintained at the trans-Golgi network by interactions with the heterotetrameric adaptor protein complex AP-1. Interference with KIF13 binding to AP-1 resulted in disruptions to both dendrite- and axon- selective trafficking. We conclude that AP-1 is the molecular link between the sorting of polarized cargoes into vesicles and the recruitment of kinesins that confer polarized transport.
Cross-talk between QseBC and PmrAB two-component systems is crucial for regulation of motility and colistin resistance in EnteropathogenicEscherichia coli
Authors: Fernandez-Ciruelos Blanca , Potmis Tasneemah , Solomin Vitalii , Wells Jerry M.
Published: April 2023

The quorum sensing two-component system (TCS) QseBC has been linked to virulence, motility and metabolism regulation in multiple Gram-negative pathogens, including EnterohaemorrhagicEscherichia coli(EHEC), UropathogenicE. coli(UPEC) andSalmonella enterica.In EHEC, the sensor histidine kinase (HK) QseC detects the quorum sensing signalling molecule AI-3 and also acts as an adrenergic sensor binding host epinephrine and norepinephrine. Downstream changes in gene expression are mediated by phosphorylation of its cognate response regulator (RR) QseB, and ʻcross-talk’ with non-cognate regulators KdpE and QseF to activate motility and virulence. In UPEC, cross-talk between QseBC and TCS PmrAB is crucial in the regulation and phosphorylation of QseB RR that acts as a repressor of multiple pathways, including motility. Here, we investigated QseBC regulation of motility in the atypical EnteropathogenicE. coli(EPEC) strain O125ac:H6, causative agent of persistent diarrhoea in children, and its possible cross-talk with the KdpDE and PmrAB TCS. We showed that in EPEC QseB acts as a repressor of genes involved in motility, virulence and stress response, and in absence of QseC HK, QseB is activated by the non-cognate PmrB HK, similarly to UPEC. We show that in absence of QseC, phosphorylated QseB activates its own expression, and is responsible for the low motility phenotypes seen in a QseC deletion mutant. Furthermore, we showed that KdpD HK regulates motility in an independent manner to QseBC and through a third unidentified party different to its own response regulator KdpE. We showed that PmrAB has a role in iron adaptation independent to QseBC. Finally, we showed that QseB is the responsible for activation of colistin and polymyxin B resistance genes while PmrA RR acts by preventing QseB binding to the promoter of polymyxin resistance genes.

Author summary

EnteropathogenicEscherichia coli(EPEC) is a human pathogen and the leading cause of diarrhoea in children under 5 years in low-income countries. EPEC, and specially the subgroup denominated atypical EPEC, has been associated with community-acquired persistent diarrhoea and also is an important agent of post-weaning diarrhoea in young piglets. Two-component systems (TCS) are signalling system used by bacteria to sense and adapt to different stimuli. Bacteria use TCS to detect host signals as queues to exert virulence in their preferred niche. QseBC is a TCS that has been linked to regulation of motility and virulence in other pathogenicE. coli.In this study we broaden our understanding of QseBC TCS and its role in regulating virulence traits such as motility in atypical EPEC. We also investigate its capabilities to interact with other TCS, named KdpDE and PmrAB, and how these interactions are responsible for regulation of motility and resistance to antimicrobials such as colistin.
Insights into the ISG15 transfer cascade by the UBE1L activating enzyme
Authors: Wallace Iona , Baek Kheewoong , Prabu Jesuraj R. , Vollrath Ronnald , von Gronau Susanne , Schulman Brenda A. , Swatek Kirby N.
Published: April 2023

The attachment of the ubiquitin-like protein ISG15 to substrates is a well-established antiviral signalling mechanism of the innate immune response. However, despite the identification of thousands of substrates and clear roles in antiviral immunity, a molecular understanding of ISG15 selection and transfer through its cognate E1-E2- E3 enzyme cascade is largely unknown. Here, we present a 3.45 Å cryo-EM structure of a chemically trapped UBE1L-UBE2L6 complex bound to activated ISG15. This structure reveals the details of the first steps of ISG15 recognition and UBE2L6 recruitment by UBE1L. Taking advantage of viral effector proteins from severe acute respiratory coronavirus 2 (SARS-CoV-2) and influenza B virus (IBV), we validated the structure and confirmed the importance of the ISG15 C-terminal ubiquitin-like domain in the adenylation reaction. Moreover, biochemical characterization of the UBE1L-ISG15 and UBE1L-UBE2L6 interactions enabled the design of ISG15 and UBE2L6 mutants with altered selectively for the ISG15 and ubiquitin conjugation pathways. Together, our study provides much needed insight into the specificity determinants that ensure the fidelity of ISG15 signalling during the antiviral response.
Interaction studies of Gut metabolite; Trimethylene amine Oxide with Bovine Serum Albumin through Spectroscopic, DFT and Molecular Docking Approach
Authors: Verma Awadhesh Kumar , Gulati Payal , Lakshmi GBVS , Solanki Pratima R , Kumar Anil
Published: April 2023

Trimethyleneamine N-oxide (TMAO); a gut microbiota derived metabolite has been involved in human health and diseases. It is enhanced by insulin resistivity and linked with various metabolic syndromes in human being such as renal, neuro-degenerative, and cardiovascular diseases. The primary mechanism through which TMAOs promotes disease is not clear yet. TMAO with MW= 75.11 g/mol is a small biomolecule hence, it becomes crucial to develop the conjugate of TMAO with BSA for aptamer synthesis. The binding interactions among TMAO and BSA were investigated using spectroscopic methods like UV-Vis, photoluminescence, Fourier transform infrared and circular dichroism. Hydrophilicity/Hydrophobicity of the conjugate was monitored by using contact angle (Ɵ) measurement. Sodium dodecyl sulphate polyacryl amide gel electrophoresis (SDS-PAGE) confirmed the different ratio of conjugate formation with the help of band size. This interaction study reveals that TMAO bind with BSA on two sites and with high affinity on one site. Docking studies also showed TMAO is involved in non-covalent interaction with bovine serum albumin forming stable docking complex with binding score of –3.6 kcal/mol obtained from the docking simulation. TMAO is involved in interaction with BSA via amino acid residues forming the stable docking complex through hydrogen bond and electrostatic interaction. This kind of interaction study may be helpful in making strategies to break the conjugation between serum albumin and uremic toxin and pave the way for the treatment for CKD and other diseases wherein TMAO is implicated. Also, conjugation of TMAO and BSA studied here may also serve as premise to develop aptamers for the detection of TMAO in the body fluids.
The BOD1L subunit of the mammalian SETD1A complex sustains the expression of DNA damage repair genes despite restraining H3K4 trimethylation
Authors: Ciotta Giovanni , Singh Sukhdeep , Gupta Ashish , Torres Davi Coe , Fu Jun , Choudhury Rupam , Chu Wai Kit , Choudhary Chuna , Gahurova Lenka , Al-Fatlawi Ali , Schroeder Michael , Aasland Rein , Poetsch Anna R. , Anastassiadis Konstantinos , Stewart A. Francis
Published: April 2023

SETD1A is the histone 3 lysine 4 (H3K4) methyltransferase central to the mammalian version of the highly conserved eight subunit Set1 complex (Set1C) that apparently conveys H3K4 trimethylation (H3K4me3) onto all active Pol II promoters. Accordingly, mouse embryonic stem cells (ESCs) die when SETD1A is removed. We report that death is accompanied by loss of expression of DNA repair genes and accumulating DNA damage. BOD1L and BOD1 are homologs of the yeast Set1C subunit, Shg1, and subunits of the mammalian SETD1A and B complexes. We show that the Shg1 homology region binds to a highly conserved central α-helix in SETD1A and B. Like mutagenesis ofShg1in yeast, conditional mutagenesis ofBod1lin ESCs promoted increased H3K4 di- and tri-methylation but also, like loss of SETD1A, loss of expression of DNA repair genes, increased DNA damage and cell death. In contrast to similar losses of gene expression, the converse changes in H3K4 methylation implies that H3K4 methylation is not essential for expression of the DNA repair network genes. Because BOD1L becomes highly phosphorylated after DNA damage and acts to protect damaged replication forks, the SETD1A complex and BOD1L in particular are key nodes for the DNA damage repair network.
StocSum: stochastic summary statistics for whole genome sequencing studies
Authors: Wang Nannan , Yu Bing , Jun Goo , Qi Qibin , Durazo-Arvizu Ramon A. , Lindstrom Sara , Morrison Alanna C. , Kaplan Robert C. , Boerwinkle Eric , Chen Han
Published: April 2023

Genomic summary statistics, usually defined as single-variant test results from genome-wide association studies, have been widely used to advance the genetics field in a wide range of applications. Applications that involve multiple genetic variants also require their correlations or linkage disequilibrium (LD) information, often obtained from an external reference panel. In practice, it is usually difficult to find suitable external reference panels that represent the LD structure for underrepresented and admixed populations, or rare genetic variants from whole genome sequencing (WGS) studies, limiting the scope of applications for genomic summary statistics. Here we introduce StocSum, a novel reference-panel-free statistical framework for generating, managing, and analyzing stochastic summary statistics using random vectors. We develop various downstream applications using StocSum including single-variant tests, conditional association tests, gene-environment interaction tests, variant set tests, as well as meta-analysis and LD score regression tools. We demonstrate the accuracy and computational efficiency of StocSum using two cohorts from the Trans-Omics for Precision Medicine Program. StocSum will facilitate sharing and utilization of genomic summary statistics from WGS studies, especially for underrepresented and admixed populations.