bluuebunny/crossref_metadata_2025_split huggingface dataset:
Host-symbiont-gene phylogenetic reconciliation
Authors: Menet Hugo , Trung Alexia Nguyen , Daubin Vincent , Tannier Eric 
Published: July 2022

AbstractMotivationBiological systems are made of entities organized at different scales (e.g.macro-organisms, symbionts, genes…) which evolve in interaction. These interactions range from independence or conflict to cooperation and coevolution, which results in them having a common history. The evolution of such systems is approached by phylogenetic reconciliation, which describes the common patterns of diversification between two different levels,e.g.genes and species, or hosts and symbionts for example. The limit to two levels hides the multi-level inter-dependencies that characterize complex systems.ResultsWe present a probabilistic model of evolution of three nested levels of organization which can account for the codivergence of hosts, symbionts and their genes. This model allows gene transfer as well as host switch, gene duplication as well as symbiont diversification inside a host, gene or symbiont loss. It handles the possibility of ghost lineages as well as temporary free-living symbionts.Given three phylogenetic trees, we devise a Monte Carlo algorithm which samples evolutionary scenarios of symbionts and genes according to an approximation of their likelihood in the model. We evaluate the capacity of our method on simulated data, notably its capacity to infer horizontal gene transfers, and its ability to detect hostsymbiont co-evolution by comparing host/symbiont/gene and symbiont/gene models based on their estimated likelihoods. Then we show in a aphid enterobacter system that some reliable transfers detected by our method, are invisible to classic 2-level reconciliation. We finally evaluate different hypotheses on human population histories in the light of their coevolvingHelicobacter pylorisymbionts, reconciled together with their genes.AvailabilityImplementation is available on GitHubhttps://github.com/hmenet/TALE. Data are available on Zenodohttps://doi.org/10.5281/zenodo.7667342.
Gene symbol recognition with GeneOCR
Authors: Geser Paul , Zhang Jitao David 
Published: July 2022

AbstractMotivationFigures in biomedical publications often contain lists of gene symbols. Human intelligence and manual curation is required to recognize, extract, and validate the symbols in order to reuse them. The task is laborious, error prone, and amenable to automation.ResultsWe introduce GeneOCR, a web-based software to recognize, extract, and check gene symbols from figures. It features both an interactive user interface and programmatic access. Simulation-based benchmark reveals that GeneOCR recognizes or suggests correct gene symbols in more than 80% cases. The performance qualifies GeneOCR as an enhancement to manual curation.AvailabilityThe source code of GeneOCR is available with GNU v3 license at https://github.com/bedapub/GeneOCR-UI (frontend) and https://github.com/bedapub/GeneOCR-API (backend). A Docker/Singularity image is available via BioContainers.Contactjitao_david.zhang@roche.com
Predicting leaf traits across functional groups using reflectance spectroscopy
Authors: Kothari Shan , Beauchamp-Rioux Rosalie , Blanchard Florence , Crofts Anna L. , Girard Alizée , Guilbeault-Mayers Xavier , Hacker Paul W. , Pardo Juliana , Schweiger Anna K. , Demers-Thibeault Sabrina , Bruneau Anne , Coops Nicholas C. , Kalacska Margaret , Vellend Mark , Laliberté Etienne 
Published: July 2022

SummaryPlant ecologists use functional traits to describe how plants respond to and influence their environment. Reflectance spectroscopy can provide rapid, non-destructive estimates of leaf traits, but it remains unclear whether general trait-spectra models can yield accurate estimates across functional groups and ecosystems.We measured leaf spectra and 22 structural and chemical traits for nearly 2000 samples from 104 species. These samples span a large share of known trait variation and represent several functional groups and ecosystems. We used partial least-squares regression (PLSR) to build empirical models for estimating traits from spectra.Within the dataset, our PLSR models predicted traits like leaf mass per area (LMA) and leaf dry matter content (LDMC) with high accuracy (R2>0.85; %RMSE<10). Models for most chemical traits, including pigments, carbon fractions, and major nutrients, showed intermediate accuracy (R2=0.55-0.85; %RMSE=12.7-19.1). Micronutrients such as Cu and Fe showed the poorest accuracy. In validation on external datasets, models for traits like LMA and LDMC performed relatively well, while carbon fractions showed steep declines in accuracy.We provide models that produce fast, reliable estimates of several widely used functional traits from leaf reflectance spectra. Our results reinforce the potential uses of spectroscopy in monitoring plant function around the world.
Characterization of DNA replicators of a 75-kb region of Chromosome 2 of fission yeast, Schizosacharomyces pombe
Authors: Yadav Mukesh Pratap , Dubey Dharani Dhar 
Published: July 2022

AbstractDNA replication origins of a 75-kb region of chromosome 2 of Schizosacharomyces pombe, are well characterized. Here, we have further characterized two origins, ars2-3358 and ars2-3363 on plasmids using an Autonomous Replicating Sequences (ARS) assay. Sequence analysis of the five ARSs located within the 75-kb region revealed several asymmetric AT motifs ≥10 bp in each of these origins. Interestingly, we have also found a 29 bp AT-rich sequence (29W) in ars2-3358, which alone is not sufficient to provide DNA replication origins to plasmid. A genomic search for asymmetric AT motifs ≥10 bp gave a total 2309 near matches to 9 of these motifs in the genome. Majority (>65% to >77%) of six of these AT motifs overlapped with the earlier mapped genome-wide DNA replication origins. Moreover, functional comparison of these AT motifs to the deletion and mutational studies showed strong correlation with DNA replication origins efficiency. Therefore, we hypothesize that these sequences are important redundant core elements of S. pombe origins.
Local adaptation to hosts and parasitoids shapeHamiltonella defensagenotypes across aphid species
Authors: Wu Taoping , Monnin David , Lee Rene A. R. , Henry Lee M. 
Published: July 2022

AbstractFacultative symbionts are common in insects and are known to provide important adaptations that can drive rapid host evolution. Yet we still have a limited understanding of what shapes their distributions, such as why particular symbiont strains are common in some host species yet absent in other. To address this question, we genotyped the defensive symbiontHamiltonella defensain 26 aphid species that commonly carry this microbe. We found thatHamiltonellastrains were strongly associated with specific aphid species and that strains found in one host species rarely occurred in others. To explain these associations, we reciprocally transferred theHamiltonellastrains of 3 aphid species,Acyrthosiphon pisum, Macrosiphoniella artemisiaeandMacrosiphum euphorbiae, in the other host species, and assessed the impact ofHamiltonellastrain on: the stability of the symbiosis, aphid fecundity, and parasitoid resistance. We demonstrate that theHamiltonellaassociations found in nature are locally adapted both to the aphid host itself, and its ecology, in that aphids tend to carryHamiltonellastrains that provide strong protection against their dominant parasitoid species. Our results suggest thatHamiltonellastrains function as a horizontal gene pool that aphids draw from to rapidly adapt to pressures from different natural enemies.
The Genome of the Mustard Hill Coral,Porites astreoides
Authors: Wong Kevin H. , Putnam Hollie M. 
Published: July 2022

AbstractCoral reefs are threatened both locally and globally by anthropogenic impacts, which to date have contributed to substantial declines in coral cover worldwide. However, some corals are more resilient to these environmental changes and therefore have increased relative abundance on local scales and may represent prominent members shaping future reef communities. Here, we provide the first draft reference genome for one such reef-building coral, the mustard hill coral,Porites astreoides. This reference genome was generated from a sample collected in Bermuda, with DNA sequenced via Pacific Biosciences HiFi long-read technology to provide an initial draft reference genome assembly. Assembly of the PacBio reads with FALCON UnZip resulted in a 678 Mbp assembly with 3,051 contigs with an N50 of 412,256. The genome BUSCO completeness analysis resulted in 90.9% of the metazoan gene set. Anab initiotranscriptome was also produced with 64,636 gene models with a transcriptome BUSCO completeness analysis of 77.5% when compared to the metazoan gene set. The function annotation was obtained through a hierarchical approach of SwissProt, TrEMBL, and NCBI nr database of which 86.6% of proteins were annotated. Through ourab initiogene prediction for structural annotation and generation of a functional annotation for theP. astreoidesdraft genome assembly, we provide valuable resources for improving biological knowledge, which can facilitate comparative genomic analyses for corals, and enhance our capacity to test for the molecular underpinnings of adaptation and acclimatization to support evidence-based restoration and human assisted evolution of corals.ClassificationsGenetics and Genomics; Animal Genetics; Marine Biology
Nucleus of the lateral olfactory tract (NLOT): a hub linking water homeostasis-associated SON-AVP circuit and neocortical regions to promote social behavior under osmotic challenge
Authors: Hernández-Pérez Oscar R. , Hernández Vito S. , Zetter Mario A. , Eiden Lee E. , Zhang Limei 
Published: July 2022

AbstractHomeostatic challenges increase the drive for social interaction. The neural activity that prompts this motivation remains poorly understood. Here, we identify direct projections from the hypothalamic supraoptic nucleus (SON) to the cortico-amygdalar nucleus of the lateral olfactory tract (NLOT). Dualin situhybridization (DISH) with probes for PACAP, and VGLUT1, VGLUT2, V1a and V1b revealed a population of vasopressin-receptive PACAPergic neurons in NLOT layer 2 (NLOT2). Water deprivation (48 hours, WD48) increased sociability compared to euhydrated subjects, assessed with the three-chamber social interaction test (3CST). Fos expression immunohistochemistry showed NLOT and its main efferent regions had further increases in rats subjected to WD48+3CST. These regions strongly expressed PAC1 mRNA. Microinjections of AVP into NLOT produced similar changes in sociability to water deprivation, and these were reduced by co-injection of V1a or V1b antagonists along with AVP. We conclude that during challenge to water homeostasis, there is a recruitment of a glutamatergic-multi-peptidergic cooperative circuit that promotes social behavior.
Complement receptor C5aR1 signaling in sensory neuron-associated macrophages drives neuropathic pain
Authors: Quadros Andreza U. , Maganin Alexandre G. M. , Silva Conceição E. A. , Damasceno Samara , Cavallini Maria C. M. , Davoli-Ferreira Marcela , Lopes Alexandre H. P. , Sagar Devi R. , Brandolini Laura , Lee Sang Hoon , Alves-Filho Jose C. , Cunha Fernando Q. , Berta Temugin , Köhl Jörg , Allegretti Marcello , Chapman Victoria , Cunha Thiago M. 
Published: July 2022

AbstractNeuroimmune interactions across the pain pathway play a predominant role in the development of neuropathic pain. Previous reports demonstrated that complement driven effector systems including the C5a/C5aR1 axis contribute to these neuro-immune mechanisms. However, the cellular and molecular mechanisms underlying C5a/C5aR1 signaling-mediated neuropathic pain development remain ill-identified. Here we show that neuropathic pain following peripheral nerve injury was attenuated in C5aR1-deficient male and female mice as well as in wild type mice treated with a selective allosteric C5aR1 antagonist. Using two complementary cell-specific C5aR1 knockout mouse strains, we identified C5a/C5aR1 driven-activation of sensory neuron-associated macrophages (sNAMs) located in the sensory ganglia as the key site of peripheral nerve injury-induced neuropathic pain, whereas activation of macrophages of the local of peripheral nerve injury was not involved. Mechanistically, we uncovered IL-1b the main mediator of pain hypersensitivity in response to C5aR1 signaling in sNAMs. Our findings highlight a crucial role of C5a/C5aR1 axis activation in sNAMs for the development of neuropathic pain and identify this pathway as a promising novel target for neuropathic pain therapy.
Backbone amides are key determinants of Cl− selectivity in CLC ion channels
Authors: Leisle Lilia , Lam Kin , Dehghani-Ghahnaviyeh Sepehr , Fortea Eva , Galpin Jason , Ahern Christopher A. , Tajkhorshid Emad , Accardi Alessio 
Published: July 2022

AbstractChloride homeostasis is tightly regulated in cellular compartments by dedicated channels and transporters. Whereas CLC-type channels select for Cl− over other anions, all other ‘chloride’ channels are indiscriminate in their anionic permeability. Pore-lining side chains are thought to determine Cl− selectivity in CLC channels. However, orientation and functional roles of these side chains is not conserved among CLCs. All CLC pores are lined by backbone amides in a conserved structural arrangement, suggesting a role of mainchain groups in selectivity. We replaced pore-lining residues in the CLC-0 and bCLC-k channels with their respective α-hydroxy acid counterparts using nonsense suppression method. This exchanges peptide-bond amides with ester-bond oxygens, incapable of hydrogen-bonding with permeating anions. Backbone substitutions functionally degrade inter-anion discrimination in a site-specific manner. These effects depend on the presence of a glutamate side chain that competes with ions permeating through the pore. Molecular dynamics simulations show that ion energetics within the bCLC-k pore are primarily determined by interactions with backbone amides. Insertion of an α-hydroxy acid significantly alters ion selectivity and global pore hydration. We propose that backbone amides are conserved determinants of Cl− specificity in CLC channels in a mechanism reminiscent of that described for K+ channels.
Reducing chlorophyll level in seed filling stages results in higher seed nitrogen without impacting canopy carbon assimilation
Authors: Cho Young B. , Boyd Ryan A. , Ren Yudong , Lee Moon-Sub , Jones Sarah I. , Ruiz-Vera Ursula M. , McGrath Justin , Masters Michael D. , Ort Donald R. 
Published: July 2022

ABSTRACTChlorophyll is the major light absorbing pigment for plant photosynthesis. While evolution has selected for higher chlorophyll content in leaves, previous work suggests that domesticated crops grown in modern agricultural environments overinvest in chlorophyll production thereby lowering light use and nitrogen use efficiency. To investigate the potential benefits of reducing chlorophyll level, we created ethanol inducible RNAi tobacco mutants that suppress Mg-chelatase subunit I (CHLI) with small RNA (sRNA) within 3 hours of induction and reduce chlorophyll within 5 days in field conditions. We initiated chlorophyll reduction later in plant development to avoid the highly sensitive seedling stage, and to allow young plants to have full green leaves to maximize light interception before canopy formation. This study demonstrated that >60% reduction of leaf chlorophyll could be tolerated without penalty on above-ground biomass or canopy photosynthesis in field conditions. Leaf chlorophyll reduction during seed filling stages increased tobacco seed nitrogen concentration as much as 17%, while biomass and seed yields were maintained. These results indicate that time-specific reduction of chlorophyll could be a niche strategy that decouples the inverse relationship between yield and seed nitrogen by utilizing saved nitrogen from the reduction of chlorophyll while maintaining full carbon assimilation capacity.
Frequent sexual reproduction limits adaptation in outcrossed populations of the algaChlamydomonas reinhardtii
Authors: Moerman Felix , Colegrave Nick 
Published: July 2022

AbstractSexual reproduction can facilitate adaptation by reshuffling genetic variation. However, sexual reproduction can also bear costs. Such costs come in two forms: direct costs and evolutionary costs. Direct costs are associated with the cost of producing males (twofold cost of sex), the cost of meiosis, and the typically slower cell division during sexual reproduction of single-celled organisms. Evolutionary costs occur when too frequent sexual reproduction would hinder adaptation, by breaking apart adaptive allele combinations. Whereas the direct costs of sexual reproduction have been studied repeatedly in theoretical studies, the evolutionary costs of sex remain less well understood. We investigate here how the frequency of sexual reproduction affects adaptation to a non-stressful and a stressful environment in populations of the green alga Chlamydomonas reinhardtii, while minimizing the direct costs of sexual reproduction. Contrary to several previous studies, we found that an increasing frequency of sexual reproduction hindered adaptation of populations. In populations experiencing the highest frequency of sexual reproduction, adaptation was entirely prevented. These findings suggest that there were strong evolutionary costs associated with too frequent sexual reproduction in our populations. This observation may help to explain why in many facultative sexual species, there is a low frequency of sexual reproduction.
Transcription factors regulating the fate and developmental potential of a multipotent progenitor in C. elegans
Authors: Soukup Evan M. , Bettinger Jill C. , Mathies Laura D. 
Published: July 2022

AbstractMultipotent stem and progenitor cells have the capacity to generate a limited array of related cell types. The two C. elegans somatic gonadal precursors (SGPs) are multipotent progenitors that generate all 143 cells of the somatic gonad, including complex tissues and specialized signaling cells. To screen for candidate regulators of cell fate and multipotency, we identified transcription factor genes with higher expression in SGPs than in their differentiated sister, the head mesodermal cell. We used RNA interference or genetic mutants to reduce the function of 183 of these genes and examined the worms at two developmental stages. Eight genes were identified that regulate the SGP fate, including the Ci/GLI homolog tra-1, which is the terminal regulator of sex determination. We show that tra-1 regulates SGP fate independently of its role in sex determination, supporting the idea that tra-1 retains ancestral functions. Four genes were necessary for SGPs to generate the correct number and type of descendant cells. We show that the E2F homolog, efl-3, regulates the cell fate decision between distal tip cells and the sheath/spermathecal precursor. We find that the FACT complex gene hmg-4 is required for the generation of the correct number of SGP descendants, and we define an earlier role for the nhr-25 nuclear hormone receptor-encoding gene, in addition to its previously described role in regulating the asymmetric division of SGPs. Overall, our data show that genes regulating cell fate are largely different from genes regulating developmental potential, demonstrating that these processes are genetically separable.
State-specific morphological deformations of the lipid bilayer explain mechanosensitive gating of MscS ion channels
Authors: Park Yein Christina , Reddy Bharat , Bavi Navid , Perozo Eduardo , Faraldo-Gómez José D. 
Published: July 2022

ABSTRACTThe force-from-lipids hypothesis of cellular mechanosensation posits that membrane channels open and close in response to changes in the physical state of the lipid bilayer, induced for example by lateral tension. Here, we investigate the molecular basis for this transduction mechanism by studying the mechanosensitive ion channel MscS fromEscherichia coliand its eukaryotic homolog, MSL1 fromArabidopsis thaliana. First, we use single-particle cryo-EM to determine the structure of a novel open conformation of wild-type MscS, stabilized in a thinned lipid nanodisc. Compared with the closed state, the structure shows a reconfiguration of helices TM1, TM2 and TM3a, and widening of the central pore. Based on these structures, we examined how the morphology of the lipid bilayer is altered upon gating, using molecular dynamics simulations. The simulations reveal that closed-state MscS causes drastic protrusions in the inner leaflet of the lipid bilayer, both in the absence and presence of lateral tension, and for different lipid compositions. These deformations arise to provide adequate solvation to hydrophobic features of the protein surface in this conformation, and clearly reflect a high energy conformation for the membrane, particularly under tension. Strikingly, these protrusions are largely eradicated upon channel opening. An analogous computational study of open and closed MSL1 recapitulates these findings. The gating equilibrium of MscS channels thus appears to be dictated by two opposing conformational preferences, namely those of the lipid membrane and of the protein structure. We propose a membrane deformation model of mechanosensation, which posits that tension shifts the gating equilibrium towards the conductive state not because it alters the mode in which channel and lipids interact but because it increases the energetic cost of the morphological perturbations in the membrane induced by to the closed state.
Injectable hydrogel embedded with mesenchymal stem cells repairs severe spinal cord injury
Authors: Chen Xiangfeng , Lu Wujie , Zuo Yanming , Ye Jingjia , Li Xiaodan , Wu Zhonghan , Jin Shuang , Cai Wanxiong , Abdelrahman Zeinab , Zhang Tianfang , Gu Xiaosong , Yu Bin , Chen Zuobing , Wang Xuhua 
Published: July 2022

AbstractMesenchymal stem cell (MSC) transplantation was suggested as a promising approach to treat spinal cord injury (SCI). However, the heterogeneity of MSC and the lack of appropriate delivery methods impede its clinical application. To tackle these challenges, we first generated human MSCs derived from a single cell with a great homogeneity of batch quality and then developed a biocompatible injectable hydrogel to embed these cells to treat severe SCI. In a clinically relevant rat severe SCI model, we showed that the injection of MSCs with injectable hydrogel into the lesion site promoted robust functional recovery, while the intrathecal delivery of MSCs only resulted in limited therapeutic effects. Mechanistically, the hydrogel protected MSCs from the damage of harmful neuroinflammatory microenvironment in the spinal cord lesion. The hydrogel with the survived MSCs ameliorates the neuroinflammatory microenvironment of spinal cord lesion, preventing cavity formation and leads to the remnant of spared axons/tissues, which results in a better prognosis in the end.