bluuebunny/crossref_metadata_2025_split huggingface dataset:
Data stochasticity and model parametrisation impact the performance of species distribution models: insights from a simulation study
Authors: Lambert Charlotte , Virgili Auriane 
Published: January 2023

AbstractSpecies distribution models (SDM) are widely used to describe and explain how species relate to their environment, and predict their spatial distributions. As such, they are the cornerstone of most of spatial planning efforts worldwide. SDM can be implemented with wide array of data types (presence-only, presence-absence, count…), which can either be point- or areal-based, and use a wide array of environmental conditions as predictor variables. The choice of the sampling type as well as the resolution of environmental conditions to be used are recognized as of crucial importance, yet we lack any quantification of the effects these decisions may have on SDM reliability. In the present work, we fill this gap with an unprecedented simulation procedure. We simulated 100 possible distributions of two different virtual species in two different regions. Species distribution were modelled using either segment- or areal-based sampling and five different spatial resolutions of environmental conditions. The SDM performances were inspected by statistical metrics, model composition, shapes of relationships and prediction quality. We provided clear evidence of stochasticity in the modelling process (particularly in the shapes of relationships): two dataset from the same survey, species and region could yield different results. Sampling type had stronger effects than spatial resolution on the final model relevance. The effect of coarsening the resolution was directly related to the resistance of the spatial features to changes of scale: SDM failed to adequately identify spatial distributions when the spatial features targeted by the species were diluted by resolution coarsening. These results have important implications for the SDM community, backing up some commonly accepted choices, but also by highlighting some up-to-now unexpected features of SDM (stochasticity). As a whole, this work calls for carefully weighted decisions in implementing models, and for caution in interpreting results.Abstract Figure
Lemur gut microeukaryotic community variation is not associated with host phylogeny, diet, or habitat
Authors: Donohue Mariah E. , Hert Zoe L. , Karrick Carly E. , Rowe Amanda K. , Wright Patricia C. , Randriamanandaza Lovasoa J. , Zakamanana François , Nomenjanahary Stela , Everson Kathryn M. , Weisrock David W. 
Published: January 2023

ABSTRACTGut prokaryotic (GP) community variation is often associated with host evolutionary and ecological variables; whether these factors drive variation in other gut taxa remains largely untested. We present a one-to-one comparison of GP (16S rRNA metabarcoding) and microeukaryotic (GME) (18S rRNA metabarcoding) community patterning among 12 species of lemurs. Lemurs were sampled from dry forests and rainforests of southeastern Madagascar and display a range of phylogenetic and ecological diversity. We found that while lemur GPs vary with host taxonomy, diet, and habitat, GMEs have no association with these factors. As a mechanism, we suggest purifying selection purges microbes with negative and commensal associations, while positive selection promotes the persistence of beneficial microbes. It is therefore likely that a greater proportion of GMEs comprise taxa with commensal, transient, and parasitic symbioses compared with GPs, many of which are mutualists. Our study reveals different microbial taxa are shaped by unique selective pressures.
A tessellated lymphoid network provides whole-body T cell surveillance in zebrafish
Authors: Robertson Tanner F. , Hou Yiran , Shen Simone , Rindy Julie , Sauer John-Demian , Dinh Huy Q , Huttenlocher Anna 
Published: January 2023

AbstractHomeostatic trafficking to lymph nodes allows T cells to efficiently survey the host for cognate antigen. Non-mammalian jawed vertebrates lack lymph nodes but maintain similarly diverse T cell pools. Here, we exploitin vivoimaging of transparent zebrafish to investigate how T cells organize and survey for antigen in an animal devoid of lymph nodes. We find that naïve-like T cells in zebrafish organize into a previously undescribed whole-body lymphoid network that supports streaming migration and coordinated trafficking through the host. This network has the cellular hallmarks of a mammalian lymph node, including naïve T cells and CCR7-ligand expressing non-hematopoietic cells, and facilitates rapid collective migration. During infection, T cells transition to a random walk that supports antigen presenting cell interactions and subsequent activation. Our results reveal that T cells can toggle between collective migration and individual random walks to prioritize either large-scale trafficking or antigen searchin situ. This novel lymphoid network thus facilitates whole-body T cell trafficking and antigen surveillance in the absence of a lymph node system.Significance StatementIn mammals, lymph nodes play a critical role in the initiation of adaptive immune responses by providing a dedicated place for T cells to scan antigen-presenting cells. Birds, reptiles, amphibians, and fish all maintain diverse repertoires of T cells but lack lymph nodes, raising questions about how adaptive immunity functions in lower jawed vertebrates. Here, we describe a novel network of lymphocytes in zebrafish that supports whole-body T cell trafficking and provides a site for antigen search, mirroring the function of mammalian lymph nodes. Within this network, T cells can prioritize large-scale trafficking or antigen scanning by toggling between two distinct modes of migration. This network provides valuable insights into the evolution of adaptive immunity.
Molecular Logic of Synaptic Diversity BetweenDrosophilaTonic and Phasic Motoneurons
Authors: Jetti Suresh K. , Crane Andrés B. , Akbergenova Yulia , Aponte-Santiago Nicole A. , Cunningham Karen L. , Whittaker Charles A. , Littleton J. Troy 
Published: January 2023

SummaryAlthough neuronal subtypes display unique synaptic organization and function, the underlying transcriptional differences that establish these features is poorly understood. To identify molecular pathways that contribute to synaptic diversity, single neuron PatchSeq RNA profiling was performed onDrosophilatonic and phasic glutamatergic motoneurons. Tonic motoneurons form weaker facilitating synapses onto single muscles, while phasic motoneurons form stronger depressing synapses onto multiple muscles. Super-resolution microscopy andin vivoimaging demonstrated synaptic active zones in phasic motoneurons are more compact and display enhanced Ca2+influx compared to their tonic counterparts. Genetic analysis identified unique synaptic properties that mapped onto gene expression differences for several cellular pathways, including distinct signaling ligands, post-translational modifications and intracellular Ca2+buffers. These findings provide insights into how unique transcriptomes drive functional and morphological differences between neuronal subtypes.
A predicted amphipathic helix contributes to the efficient S-acylation of theArabidopsis thalianaCalcineurin B-like protein 2
Authors: Wyganowski Thomas , Beckmann Linda , Batistič Oliver 
Published: January 2023

AbstractMembrane targeting of the Calcineurin B-like (CBL) calcium sensor proteins through protein S-acylation is crucial for various processes in plants, like nutrient uptake, plant development, and response to abiotic and biotic stresses. Certain CBLs target specifically to the vacuolar membrane, but which factors contribute to this particular localization and to the lipid modification efficiency are not yet known. Here, we examined the structural features of the N-terminus ofArabidopsis thalianaCBL2 and show that the lipid-modified cysteines are integrated within a predicted amphipathic helix. Mutations of amino acids, which contribute to the formation of this specific domain, affect S-acylation efficiency, membrane binding and function of CBL2. Interestingly, overexpression of the protein S-acyl transferase (PAT) 10 can compensate for the binding deficiency of a CBL2 mutant variant, which harbours a helix breaker mutation. This indicates that helix formation is rather involved in the S-acylation mechanism and is less important for membrane binding. Moreover, the introduction of basic residues resulted in a partial shift of the protein from the vacuolar to the plasma membrane, indicating that the underrepresentation of positively charged amino acids contributes to the vacuolar targeting specificity. Overall, our data suggest that helix formation is potentially an initial step in the S-acylation process and provides a deeper understanding of the mechanistic interplay between PATs and tonoplast targeted CBLs.
HiCLift: A fast and efficient tool for converting chromatin interaction data between genome assemblies
Authors: Wang Xiaotao , Yue Feng 
Published: January 2023

AbstractMotivationWith the continuous effort to improve the quality of human reference genome and the generation of more and more personal genomes, the conversion of genomic coordinates between genome assemblies is critical in many integrative and comparative studies. While tools have been developed for such task for linear genome signals such as ChIP-Seq, no tool exists to convert genome assemblies for chromatin interaction data, despite the importance of three-dimensional (3D) genome organization in gene regulation and disease.ResultsHere, we present HiCLift, a fast and efficient tool that can convert the genomic coordinates of chromatin contacts such as Hi-C and Micro-C from one assembly to another, including the latest T2T genome. Comparing with the strategy of directly re-mapping raw reads to a different genome, HiCLift runs on average 42 times faster (hours vs. days), while outputs nearly identical contact matrices. More importantly, as HiCLift does not need to re-map the raw reads, it can directly convert human patient sample data, where the raw sequencing reads are sometimes hard to acquire or not available.AvailabilityHiCLift is publicly available athttps://github.com/XiaoTaoWang/HiCLift.
Nitrogen-limitation independent control ofglnA(glutamine synthetase) expression inEscherichia coliby urea, several amino acids, and post-transcriptional regulation
Authors: Urs Karthik , Zimmern Philippe E. , Reitzer Larry 
Published: January 2023

AbstractThe expression ofglnA(ammonia-assimilating glutamine synthetase) is high for uropathogenicE. coligrown in urine. BecauseglnAis part of an operon that codes for regulators of the nitrogen-regulated (Ntr) response, highglnAexpression has been interpreted to suggest nitrogen limitation, which is unexpected because of the high urinary ammonia concentration and the extremely rapid bacterial growth. We present evidence thatglnAexpression does not result from nitrogen limitation. First, in the presence of ammonia, urea induced expression ofglnAfrom the cAMP receptor protein (Crp)- dependentglnAp1promoter, which circumvents control from the nitrogen-regulatedglnAp2promoter. This urea effect onglnAexpression has not been previously described. Second, the most abundant amino acids in urine inhibited GS activity, based on reversal of the inhibition by glutamate and glutamine, and increasedglnAexpression. The relevance of these inhibitory amino acids in natural environments has not been previously demonstrated. Third, neither urea nor the inhibitory amino acids induced other Ntr genes, i.e., highglnAexpression can be independent of other Ntr genes. Finally, the urea-dependent induction did not result in GlnA synthesis because of a previously undescribed translational control. We conclude thatglnAexpression in urea-containing environments does not imply growth rate-limiting nitrogen restriction and is consistent with rapid growth of uropathogenicE. coli.SignificanceUrinary tract infections (UTIs), often caused byE. coli, frequently become resistant to antibiotic treatment. Expressed metabolic genes during an infection could guide development of urgently-needed alternate or adjunct therapies.glnA(glutamine synthetase) is expressed during growth in urine, which implies growth-restricting nitrogen limitation. We show thatglnAexpression results from urinary amino acids that inhibit GlnA activity and urea, but not from nitrogen limitation. Urinary components will vary greatly between individuals which suggests corresponding variations inglnAexpression. GlnA may be a metabolic vulnerability during UTIs, which may depend on a variable urinary composition.glnAexpression may be important in a complex host-pathogen interaction, but may not be a good therapeutic target.
HIV-PULSE: A long-read sequencing assay for high-throughput near full-length HIV-1 proviral genome characterization
Authors: Lambrechts Laurens , Bonine Noah , Verstraeten Rita , Pardons Marion , Noppe Ytse , Rutsaert Sofie , Van Nieuwerburgh Filip , Van Criekinge Wim , Cole Basiel , Vandekerckhove Linos 
Published: January 2023

AbstractA deep understanding of the composition of the HIV-1 reservoir is necessary for the development of targeted therapies and the evaluation of curative efforts. However, current near full-length (NFL) HIV-1 proviral genome sequencing assays are based on labor-intensive and costly principles of repeated PCRs at limiting dilution, restricting their scalability. To address this, we developed a high-throughput, long-read sequencing assay called HIV-PULSE (HIVProviralUMI-mediatedLong-readSequencing). This assay uses unique molecular identifiers (UMIs) to tag individual HIV-1 genomes, allowing for the omission of the limiting dilution step and enabling long-range PCR amplification of many NFL genomes in a single PCR reaction, while simultaneously overcoming poor single-read accuracy. We optimized the assay using HIV-infected cell lines and then applied it to blood samples from 18 individuals living with HIV on antiretroviral therapy, yielding a total of 1,308 distinct HIV-1 genomes. Benchmarking against the widely applied Full-Length Individual Proviral Sequencing assay revealed similar sensitivity (11% vs 18%) and overall good concordance, though at a significantly higher throughput. In conclusion, HIV-PULSE is a cost-efficient and scalable assay that allows for the characterization of the HIV-1 proviral landscape, making it an attractive method to study the HIV-1 reservoir composition and dynamics.
Spatial transcriptomics reveals unique gene expression changes in different brain regions after sleep deprivation
Authors: Vanrobaeys Yann , Peterson Zeru J. , Walsh Emily. N. , Chatterjee Snehajyoti , Lin Li-Chun , Lyons Lisa C. , Nickl-Jockschat Thomas , Abel Ted 
Published: January 2023

AbstractSleep deprivation has far-reaching consequences on the brain and behavior, impacting memory, attention, and metabolism. Previous research has focused on gene expression changes in individual brain regions, such as the hippocampus or cortex. Therefore, it is unclear how uniformly or heterogeneously sleep loss affects the brain. Here, we use spatial transcriptomics to define the impact of a brief period of sleep deprivation across the brain. We find that sleep deprivation induced pronounced differences in gene expression across the brain, with the greatest changes in the hippocampus, neocortex, hypothalamus, and thalamus. Both the differentially expressed genes and the direction of regulation differed markedly across regions. Importantly, we developed bioinformatic tools to register tissue sections and gene expression data into a common anatomical space, allowing a brain-wide comparison of gene expression patterns between samples. Our results suggest that distinct molecular mechanisms acting in discrete brain regions underlie the biological effects of sleep deprivation.Graphical AbstractHighlightsSpatial transcriptomics using the Visium platform reveals the transcriptional signature across the brain, recapitulating the anatomy of the mouse brainSleep deprivation induces transcriptomic changes unique to each brain regionThe hippocampus is the brain region impacted the most by acute sleep deprivation, with most differentially regulated genes significantly downregulatedThe neocortex exhibits layer-specific changes in gene expression, with most differentially regulated genes significantly upregulatedRegistration of spatial transcriptomic data to a common anatomical reference space (Allen Common Coordinate Framework) allows statistical analysis of gene expression across regions of the brain and for multi-sample analysis
Hierarchical Deviant Processing in Auditory Cortex of Awake Mice
Authors: Luo Dan , Liu Ji , Auksztulewicz Ryszard , Wing Yip Tony Ka , Kanold Patrick O. , Schnupp Jan W. 
Published: January 2023

AbstractDetecting patterns, and noticing unexpected pattern changes, in the environment is a vital aspect of sensory processing. Adaptation and prediction error responses are two components of neural processing related to these tasks, and previous studies in the auditory system in rodents show that these two components are partially dissociable in terms of the topography and latency of neural responses to sensory deviants. However, many previous studies have focused on repetitions of single stimuli, such as pure tones, which have limited ecological validity. In this study, we tested whether the auditory cortical activity shows adaptation to repetition of more complex sound patterns (bisyllabic pairs). Specifically, we compared neural responses to violations of sequences based on single stimulus probability only, against responses to more complex violations based on stimulus order. We employed an auditory oddball paradigm and monitored the auditory cortex (ACtx) activity of awake mice (N=8) using wide-field calcium imaging. We found that cortical responses were sensitive both to single stimulus probabilities and to more global stimulus patterns, as mismatch signals were elicited following both substitution deviants and transposition deviants. Notably, A2 area elicited larger mismatch signaling to those deviants than primary ACtx (A1), which suggests a hierarchical gradient of prediction error signaling in the auditory cortex. Such a hierarchical gradient was observed for late but not early peaks of calcium transients to deviants, suggesting that the late part of the deviant response may reflect prediction error signaling in response to more complex sensory pattern violations.
Genome wide clustering on integrated chromatin states and Micro-C contacts reveals chromatin interaction signatures
Authors: Sexton Corinne E. , Han Mira V. 
Published: January 2023

AbstractChromatin states based on various histone modifications are a common annotation for genomes, and have been shown to correspond to regulatory functions such as enhancers and transcription start sites. With the advent of Hi-C and other chromatin conformation capture technologies, we now have the ability to analyze 3-dimensional physical interactions of chromatin regions, in addition to the 1-dimensional regulatory annotation, but methods to integrate this information are lacking. We present a framework for integrating the chromatin state of interacting regions into a numeric vector through the contact-weighted sum of chromatin states. Unsupervised clustering on integrated chromatin states and Micro-C contacts reveals common patterns of chromatin interaction which we call chromatin interaction signatures. Our results indicate that most chromatin interaction signatures are found in all four cell types investigated here. Between 12-40% of the regions change chromatin interaction signatures between the cell types despite maintaining chromatin state, hinting at the dynamic nature of chromatin conformation. Although regions with similar chromatin states are often in contact as expected, subcategories of enhancers and transcription start sites have distinct chromatin interaction signatures that are associated with gene expression. The integrated information on the chromatin states that the region is in contact with adds another layer of annotation beyond chromatin state or Hi-C contact separately. In summary, we present the first set of chromatin interaction signatures for the human genome that provides an integrated view of the complex dynamics of concurrent change occurring in chromatin state and in chromatin interaction.
Cyclic and pseudo-cyclic electron pathways play antagonistic roles during nitrogen deficiency inChlamydomonas reinhardtii
Authors: Dao Ousmane , Burlacot Adrien , Buchert Felix , Bertrand Marie , Auroy Pascaline , Stoffel Carolyne , Irby Jacob , Hippler Michael , Peltier Gilles , Li-Beisson Yonghua 
Published: January 2023

AbstractNitrogen (N) scarcity is a frequently encountered situation that constrains global biomass productivity. In response to N deficiency, cell division stops and photosynthetic electron transfer is downregulated, while carbon storage is enhanced. However, the molecular mechanism downregulating photosynthesis during N deficiency and its relationship with carbon storage are not fully understood. The Proton Gradient Regulator-like 1 (PGRL1) controlling cyclic electron flow (CEF) and Flavodiiron proteins involved in pseudo-(CEF) are major players in the acclimation of photosynthesis. To determine the role of PGRL1 or FLV in photosynthesis under N deficiency, we measured photosynthetic electron transfer, oxygen gas exchange and carbon storage inChlamydomonas pgrl1andflvBknockout mutants. Under N deficiency,pgrl1maintains higher net photosynthesis and O2photoreduction rates, whileflvBshows a similar response compared to control strains. Cytochromeb6fand PSI are maintained at a higher abundance inpgrl1. The photosynthetic activity offlvBandpgrl1 flvBdouble mutants decreases in response to N deficiency similar to the control strains. Furthermore, the preservation of photosynthetic activity inpgrl1is accompanied by an increased accumulation of triacylglycerol depending on the genetic background. Taken together, our results suggest that in the absence of PGRL1-controlled CEF, FLV-mediated PCEF maintains net photosynthesis at a high level and that CEF and PCEF play antagonistic roles during N deficiency. It further illustrates how nutrient status and genetic makeup of a strain can affect the regulation of photosynthetic energy conversion in relation to carbon storage and provides new strategies for improving lipid productivity in algae.Significance statementNitrogen (N) deficiency, an often-encountered phenomenon in nature, results in growth arrest, downregulation of photosynthesis and massive carbon storage in microalgae. However, more mechanistic insights involved in tuning photosynthetic electron transfer during N deficiency are required. Here, we provide evidence that a well-conserved protein in chlorophytes, the Proton Gradient Regulator-like 1 (PGRL1), is a key regulator of photosynthesis during N deficiency. In its absence, cells exhibited sustained photosynthesis thanks to the Flavodiiron (FLV) proteins. We propose that both PGRL1 and FLV, by having antagonistic roles in N deficiency, manage the redox landscape, carbon storage and biomass production. Our work revolves around the current paradigm of photosynthesis regulation during N deficiency and provides a new framework for improving biomass production and carbon storage in microalgae for biotechnological purposes.