bluuebunny/crossref_metadata_2025_split huggingface dataset:
A shallow-scale phylogenomics approach reveals parallel patterns of diversification among sympatric populations of cryptic Neotropical aquatic beetles (Coleoptera: Noteridae)
Authors: Baca S.M. , Gustafson G.T. , DeRaad D.A. , Alexander A. , Hime P.M. , Short A.E.Z. 
Published: October 2023

AbstractTheNotomicrus trailispecies group (Coleoptera: Noteridae) is a lineage of aquatic beetles distributed throughout South America and extends into Mexico and the West Indies. Previous research has revealed a species complex within this group, with multiple distinct clades sharing overlapping distributions and lineages attributed toN. trailiand the closely relatedN. gracilipesrecovered as polyphyletic. Here, we perform targeted capture of ultraconserved elements (UCEs) to examine relationships and patterns of evolution within theN. trailigroup. First, we use short-read whole genome sequencing of four noterid genera to design a noterid-specific UCE probe set (Noteridae 3.4Kv1) targeting over 3,400 unique loci. Using this probe set, we capture UCE data from population-level sampling of 44trailigroup specimens from across the Neotropics, with an emphasis on the Guiana Shield where distributions of several putativeN. trailigroup populations overlap. We subject the resulting data matrix to various trimming and data completeness treatments and reconstruct the phylogeny with both concatenated maximum likelihood and coalescent congruent methods. We recover robust phylogenetic estimates that identify several phylogenetically distinct clades within thetrailigroup that share overlapping distributions. To test for the genetic distinctiveness of populations, we extract single nucleotide polymorphism (SNP) data from UCE alignments and examine patterns of genetic clustering using principal component analyses (PCAs) and STRUCTURE. Population genetic results are highly concordant with recovered phylogenetic structure, revealing a high degree of co-ancestry shared within identified clades, contrasting with limited ancestry sharing between clades. We recover a pattern consistent with repeated diversification and dispersal of thetrailigroup in the Neotropics, highlighting the efficacy of a tailored UCE approach for facilitating shallow-scale phylogenetic reconstructions and population genetic analyses, which can reveal novel aspects of coleopteran phylogeography.
Adaptation to space conditions of novel bacterial species isolated from the International Space Station revealed by functional gene annotations and comparative genome analysis
Authors: Szydlowski Lukasz M. , Bulbul Alper A. , Simpson Anna C. , Kaya Deniz E. , Singh Nitin K. , Sezerman Ugur O. , Łabaj Paweł P. , Kosciolek Tomasz , Venkateswaran Kasthuri J. 
Published: October 2023

AbstractBackgroundThe extreme environment of the International Space Station (ISS) puts selective pressure on microorganisms unintentionally introduced during its 20+ years of service as a low-orbit science platform and human habitat. Such pressure leads to the development of new features not found in the Earth-bound relatives, which enable them to adapt to unfavorable conditions.ResultsIn this study, we generated the functional annotation of the genomes of five newly identified species of Gram-positive bacteria, four of which are non-spore-forming and one spore-forming, all isolated from the ISS. Using a deep-learning based tool - deepFRI - we were able to functionally annotate close to 100% of protein-coding genes in all studied species, overcoming other annotation tools. Our comparative genomic analysis highlights common characteristics across all five species and specific genetic traits that appear unique to these ISS microorganisms. Proteome analysis mirrored these genomic patterns, revealing similar traits. The collective annotations suggest adaptations to life in space, including the management of hypoosmotic stress related to microgravity via mechanosensitive channel proteins, increased DNA repair activity to counteract heightened radiation exposure, and the presence of mobile genetic elements enhancing metabolism. In addition, our findings suggest the evolution of certain genetic traits indicative of potential pathogenic capabilities, such as small molecule and peptide synthesis and ATP-dependent transporters. These traits, exclusive to the ISS microorganisms, further substantiate previous reports explaining why microbes exposed to space conditions demonstrate enhanced antibiotic resistance and pathogenicity.ConclusionOur findings indicate that the microorganisms isolated from ISS we studied have adapted to life in space. Evidence such as mechanosensitive channel proteins, increased DNA repair activity, as well as metallopeptidases and novel S-layer oxidoreductases suggest a convergent adaptation among these diverse microorganisms, potentially complementing one another within the context of the microbiome. The common genes that facilitate adaptation to the ISS environment may enable bioproduction of essential biomolecules need during future space missions, or serve as potential drug targets, if these microorganisms pose health risks.
Removing bias in sequence models of protein fitness
Authors: Shaw Ada , Spinner Hansen , Shin June , Gurev Sarah , Rollins Nathan , Marks Debora 
Published: October 2023

ABSTRACTUnsupervised sequence models for protein fitness have emerged as powerful tools for protein design in order to engineer therapeutics and industrial enzymes, yet they are strongly biased towards potential designs that are close to their training data. This hinders their ability to generate functional sequences that are far away from natural sequences, as is often desired to design new functions. To address this problem, we introduce a de-biasing approach that enables the comparison of protein sequences across mutational depths to overcome the extant sequence similarity bias in natural sequence models. We demonstrate our method’s effectiveness at improving the relative natural sequence model predictions of experimentally measured variant functions across mutational depths. Using case studies proteins with very low functional percentages further away from the wild type, we demonstrate that our method improves the recovery of top-performing variants in these sparsely functional regimes. Our method is generally applicable to any unsupervised fitness prediction model, and for any function for any protein, and can thus easily be incorporated into any computational protein design pipeline. These studies have the potential to develop more efficient and cost-effective computational methods for designing diverse functional proteins and to inform underlying experimental library design to best take advantage of machine learning capabilities.
QUANTIFYING INTRASPECIFIC VARIATION IN HOST RESISTANCE AND TOLERANCE TO A LETHAL PATHOGEN
Authors: Hardy Bennett M. , Muths Erin , Funk W. Chris , Bailey Larissa L. 
Published: October 2023

ABSTRACTDue to the ubiquity of disease in natural systems, hosts have evolved strategies of disease resistance and tolerance to defend themselves from further harm once infected. Resistance strategies directly limit pathogen growth, typically leading to lower infection burdens in the host. A tolerance approach limits the fitness consequences caused by the pathogen but does not directly inhibit pathogen growth. Testing for intraspecific variation in wild host populations is important for informing conservation decisions about captive breeding, translocation, and disease treatment. Here, we test for the relative importance of tolerance and resistance in multiple populations of boreal toads (Anaxyrus boreas boreas) againstBatrachochytrium dendrobatidis(Bd), the amphibian fungal pathogen responsible for the greatest host biodiversity loss due to disease. Boreal toads have severely declined in Colorado (CO) due to Bd, but toad populations challenged with Bd in western Wyoming (WY) appear to be less affected. We used a common garden infection experiment to expose post-metamorphic toads sourced from four populations (2 in CO and 2 in WY) to Bd and monitored changes in mass, pathogen burden, and survival for eight weeks. We used a multi-state modeling approach to estimate weekly survival and transition probabilities between infected and cleared states, reflecting a dynamic infection process that traditional approaches fail to capture. We found that WY boreal toads are highly tolerant to Bd infection with higher survival probabilities than those in CO when infected with identical pathogen burdens. WY toads also had higher probabilities of clearing infections and took an average of five days longer to reach peak infection burdens. Our results demonstrate strong intraspecific differences in tolerance and resistance that explain why population declines vary regionally across the species. We used a robust, multi-state framework to gain inference on typically hidden disease processes when testing for host tolerance or resistance and demonstrated that describing an entire species as ‘tolerant’ or ‘resistant’ is unwise without testing for intraspecific variation in host defenses.
Isolation and Identification of possible pathogenic bacteria on carrots sold at community market, Ahmadu Bello University, Zaria
Authors: Ojodomo Blessing , Ashar Saaondo James 
Published: October 2023

ABSTRACTCarrots (Daucus carota) are root vegetables that can be purple, red, yellow or white colour based on their pigmentation and variety. Due to the awareness of its high nutritional content such as vitamins, minerals and carotene, they are mainly consumed raw, possibly exposing one to the risk of being infected. Studies on the pathogenic Bacteria associated with fresh carrots sold in the community market at Ahmadu Bello University, main campus Samaru Zaria, were carried out using cultural techniques. Salmonella Shigella agar, MacConkey agar and Eosin methylene blue agar were the growth media for the isolation of the pathogenic Bacteria. Twelve fresh carrots were randomly bought from different food vendors in the community market, and then 10g of the outer layer (epidermal) scrapings were collected from each sample and homogenized in 90 ml of buffered peptone water. It was then serially diluted and 0.1ml of each 104and 105dilutions were plated on EMB, SSA, and MacConkey agar. Isolates were identified by gram staining and biochemical tests. The bacteria were identified to beProteusspecies,Citrobacterspecies,Klebsiellaspecies, andSalmonellaspecies.Proteusspp was predominantly isolated among the bacterial isolates (41%) followed byCitrobacterspp (25%),Klebsiellaspp (17%) andSalmonellaspp (17%). These organisms may have been introduced to the carrots during growth, harvesting, handling, storage and distribution. The presence of the organisms is a public health risk because of the diseases known to be caused by them. It is therefore imperative that adequate hygienic practices be put in place during the cultivating and handling of carrots. A high level of susceptibility was observed in Ciprofloxacin at (100%) and Augmentin at (50%), while the high level of resistance was observed to be high in Gentamicin at (100%).
Phylogenetic analysis ofABCEgenes across the plant kingdom
Authors: Jakobson Liina , Mõttus Jelena , Suurväli Jaanus , Sõmera Merike , Tarassova Jemilia , Nigul Lenne , Smolander Olli-Pekka , Sarmiento Cecilia 
Published: October 2023

AbstractATP-BINDING CASSETTE SUBFAMILY E MEMBER (ABCE) proteins are one of the most conserved proteins across eukaryotes and archaea. Yeast and the vast majority of animals possess a singleABCEgene encoding the vital ABCE1 protein. We retrievedABCEgene sequences of 76 plant species from public genome databases and analyzed them with the reference toArabidopsis thaliana ABCE2gene (AtABCE2). Over half of the studied plant species possess two or moreABCEgenes. There can be as many as eightABCEgenes in a plant species. This suggest thatABCEgenes in plants can be classified as a low-copy gene family, rather than a single-copy gene family. Plant ABCE proteins showed overall high sequence conservation, sharing at least 78% of amino acid sequence identity with AtABCE2. The phylogenetic trees of full-length ABCE amino acid and CDS sequences demonstrated thatBrassicaceaeandPoaceaefamilies have independently undergone lineage-specific split of the ancestralABCEgene. Other plant species have gainedABCEgene copies through more recent duplication events. Deeper analysis ofAtABCE2and its paralogueAtABCE1from 1135Arabidopsis thalianaecotypes revealed 4 and 35 non-synonymous SNPs, respectively. The lower natural variation inAtABCE2compared toAtABCE1is in consistence with its crucial role for plant viability. Overall, while the sequence of the ABCE protein family is highly conserved in the plant kingdom, many plants have evolved to have more than one copy of this essential translational factor.Significance statementIn most eukaryotes there is a single ABCE protein, which is involved in many vital processes in cells. However, less is known about ABCEs specifically in plants. Here we show that while the sequence of ABCE proteins is highly conserved in plants, they have evolved to often have multiple copies of this essential translational factor. By studying 76 species from the entire plant kingdom, we observed as many as eightABCEgenes being present at a time, although most species have less. SomeABCEcopies appeared earlier than others and were found in multiple species. Thus, our findings indicate that ABCE genes in plants are not a single-copy gene family and should instead be re-classified as a low-copy gene family.
Human eukaryotic initiation factor 4G directly binds the 40S ribosomal subunit to promote efficient translation
Authors: Villa Nancy , Fraser Christopher S. 
Published: October 2023

ABSTRACTMessenger RNA (mRNA) recruitment to the 40S ribosomal subunit is mediated by eukaryotic initiation factor 4F (eIF4F). This complex includes 3 subunits: eIF4E (m7G cap binding protein), eIF4A (DEAD box helicase), and eIF4G. Mammalian eIF4G is a scaffold that coordinates the activities of eIF4E and eIF4A and provides a bridge to connect the mRNA and 40S ribosomal subunit through its interaction with eIF3. While the roles of many eIF4G binding domains are relatively clear, the precise function of RNA binding by eIF4G remains to be elucidated. In this work, we used an eIF4G-dependent translation assay to reveal that the RNA binding domain (eIF4G-RBD; amino acids 682–720) stimulates translation. This stimulating activity is observed when eIF4G is independently tethered to an internal region of the mRNA, suggesting that the eIF4G-RBD promotes translation by a mechanism that is independent of the m7G cap and mRNA tethering. Using a kinetic helicase assay, we show that the eIF4G-RBD has a minimal effect on eIF4A helicase activity, demonstrating that the eIF4G-RBD is not required to coordinate eIF4F-dependent duplex unwinding. Unexpectedly, native gel electrophoresis and fluorescence polarization assays reveal a previously unidentified direct interaction between eIF4G and the 40S subunit. Using binding assays, our data show that this 40S subunit interaction is separate from the previously characterized interaction between eIF4G and eIF3. Thus, our work reveals how eIF4F can bind to the 40S subunit using eIF3-dependent and eIF3-independent binding domains to promote translation initiation.
An updated model of shoot apical meristem regulation by ERECTA family and CLAVATA3 signaling pathways
Authors: Uzair Muhammad , Urquidi Camacho Ricardo Andres , Liu Ziyi , Overholt Alex M. , DeGennaro Daniel , Zhang Liang , Herron Brittani S. , Hong Tian , Shpak Elena D. 
Published: October 2023

ABSTRACTThe shoot apical meristem (SAM) gives rise to above-ground organs. The size of the SAM is relatively constant due to the balance of stem cell replenishment versus cell recruitment into developing organs. In angiosperms, the transcription factor WUSCHEL (WUS) promotes stem cell identity in the central zone of the SAM. WUS forms a negative feedback loop with a signaling pathway activated by CLAVATA3 (CLV3). In the periphery of the SAM, the ERECTA family (ERf) receptors promote cell differentiation and constrain the expression ofWUSandCLV3. Here, we show that four ligands of ERfs redundantly inhibitCLV3andWUSexpression. Transcriptome analysis confirmed thatWUSandCLV3are the main targets of ERf signaling and uncovered several new ones. Analysis of promoter reporters indicated that in the vegetative meristem, theWUSexpression domain mostly overlapped with theCLV3domain and did not shift along the apical-basal axis inclv3. A 3D mathematical model reproduced the experimentally observedCLV3andWUSexpression patterns with fewer assumptions than earlier models. Based on these findings, we propose that CLV3 regulates cellular levels ofWUSexpression through autocrine signaling, while ERfs regulateWUSspatial expression, preventing its encroachment into the peripheral zone.One Sentence SummaryThrough autocrine signaling, CLV3 regulates the level ofWUSexpression in the vegetative SAM but not its location, while ERfs regulate theWUSspatial pattern, preventing its expansion into the peripheral zone.
BiP/GRP78 is a pro-viral factor for diverse dsDNA viruses that promotes the survival and proliferation of cells upon KSHV infection
Authors: Najarro Guillermo , Brackett Kevin , Woosley Hunter , Faeldonea Catya , Moreno Osvaldo Kevin , Negron Adriana Ramirez , Love Christina , Ward Ryan , Langelier Charles , Gardner Brooke M. , Arias Carolina 
Published: October 2023

AbstractThe Endoplasmic Reticulum (ER)-resident HSP70 chaperone BiP (HSPA5) plays a crucial role in maintaining and restoring protein folding homeostasis in the ER. BiP’s function is often dysregulated in cancer and virus-infected cells, conferring pro-oncogenic and pro-viral advantages. We explored BiP’s functions during infection by the Kaposi’s sarcoma-associated herpesvirus (KSHV), an oncogenic gamma-herpesvirus associated with cancers of immunocompromised patients. Our findings reveal that BiP protein levels are upregulated in infected epithelial cells during the lytic phase of KSHV infection. This upregulation occurs independently of the unfolded protein response (UPR), a major signaling pathway that regulates BiP availability. Genetic and pharmacological inhibition of BiP halts KSHV viral replication and reduces the proliferation and survival of KSHV-infected cells. Notably, inhibition of BiP limits the spread of other alpha- and beta-herpesviruses and poxviruses with minimal toxicity for normal cells. Our work suggests that BiP is a potential target for developing broad-spectrum antiviral therapies against double-stranded DNA viruses and a promising candidate for therapeutic intervention in KSHV-related malignancies.
Spatial Patterning of Laminin and N-Cadherin for Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes (hiPSC-CMs)
Authors: Lane Kerry V. , Dow Liam P. , Castilloa Erica A. , Boros Rémi , Feinstein Sam D. , Pardon Gaspard , Pruitt Beth L. 
Published: October 2023

AbstractControlling cellular shape with protein micropatterning can mimic physiological morphologies and has been shown to improve reproducibility, enhancing our ability to collect statistics on single-cell behaviors. It has also advanced efforts in developing human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) as a promising human model for studies of heart structure and function. hiPSC-CMs have key physiological differences from primary human cardiomyocytes (CMs), including lower sarcomere alignment and contractility, smaller area and lower aspect ratio, and lower force production. Protein micropatterning has been demonstrated to make hiPSC-CMs behave more like primary human CMs across these metrics. However, these micropatterned models typically use only extracellular matrix (ECM) proteins and have not investigated whether providing a protein associated with CM-CM interactions, such as N-cadherin, further enhances hiPSC-CM structure and function. Here, we developed a novel dual-protein patterning process to geometrically control single-cell CM placement on deformable hydrogels suitable for traction force microscopy (TFM). The patterns were comprised of rectangular laminin islands for attachment across the majority of the cell area, with N-cadherin “end-caps” imitating cell-cell interactions. We first photopatterned two proteins on a glass coverslip using a two-step process with photomolecular adsorption of proteins. After both photopatterning steps were complete, we transferred the pattern from the coverslip to a physiologically relevant ∼10-kPa polyacrylamide hydrogel. We seeded α-actinin-tagged hiPSC-CMs on the dual-protein-patterned hydrogels and verified interaction between the hiPSC-CMs and the N-cadherin end-caps via immunofluorescent staining. We found hiPSC-CMs on dual-protein patterns have a higher cell area and contractility in the direction of sarcomere organization than those on laminin-only patterns, but no difference in sarcomere organization or force production. While N-cadherin modestly improves the single-cell patterned hiPSC-CM model, it is not sufficient to replicate the role of cell-cell contacts in CM development for in vitro hiPSC-CM systems.
Eccentricity strongly modulates visual processing delays
Authors: Burge Johannes , Dyer Callista M. 
Published: October 2023

AbstractThe temporal dynamics of visual information processing varies with the stimulus being processed and with the retinal location that initiates the processing. Here, we present psychophysical data with sub-millisecond precision showing that increasing eccentricity decreases the delay with which stimuli are processed. We show that, even within the central +/-6º of the visual field, processing delays change by a factor of up to three times. A simple model, grounded in retinal physiology, provides a good account of the data. The relative delays are on the order of only milliseconds. But if later processing leaves the delays unresolved, they can cause dramatic misperceptions of motion and 3D layout. We discuss the implications for how the human visual system solves the temporal binding problem across eccentricity. The results highlight the severe computational challenge of obtaining accurate, temporally-unified percepts of the environment with spatiotemporally-staggered processing across the visual field.