bluuebunny/crossref_metadata_2025 huggingface dataset:
A frog adaptive radiation: Ecomorphological evolution in Old-World shrub frogs (Rhacophoridae:Pseudophilautus)
Authors: Meegaskumbura Madhava , Ellepola Gajaba , Senevirathne Gayani , Manamendra-Arachchi Kelum , Wijayathillaka Nayana , Pie Marcio , Sun Dan , Pethiyagoda Rohan , Schneider Christopher J.
Published: August 2023

Ecomorphs result from divergent natural selection, leading to species-rich adaptive radiations. Identifying ecomorphs and the resulting adaptive radiations in frogs is challenging due to conserved morphology and high species diversity. In this study, we demonstrate the ecological and climate specializations that have driven the diversification of shrub frogs of the genusPseudophilautusin Sri Lanka, a tropical continental island. We use a time-calibrated phylogeny, morphometric analyses, and climate-niche evolution, and identify five ecomorphological categories, including Tree-shrub, Rock-boulder, Leaf-litter, Habitat Generalists, and Canopy forms, and describe their evolution. Body size is the primary factor separating species, and specific body features correlate with habitat type. Ecomorphs likely evolved multiple times in disparate lineages, and in different regions and altitudes, during cold climatic periods owing to monsoon cycles resulting from the Himalayan-Tibetan orogeny. The common ancestor was a medium-sized, wet-adapted, tree-shrub habitat specialist which originated in the late Oligocene. Extreme size classes (diminutive leaf litter forms and large canopy forms) evolved recently and suggest that morphological disparity arose late in diversification, possibly aided by favorable climates. This work will facilitate understanding of adaptive radiations in frogs, which possibly will help uncover the prevalence of subtle adaptive radiations in frogs, just as in tailed-vertebrates.
A vast repertoire of secondary metabolites influences community dynamics and biogeochemical processes in cold seeps
Authors: Dong Xiyang , Zhang Tianxueyu , Wu Weichao , Peng Yongyi , Liu Xinyue , Han Yingchun , Chen Xiangwei , Gao Zhizeng , Xia Jinmei , Shao Zongze , Greening Chris
Published: August 2023

In deep sea cold seeps, diverse microbial communities thrive on the geological seepage of hydrocarbons and inorganic compounds. These chemosynthetically-driven communities are unique in composition, ecology, and biogeochemical activities compared to photosynthetically-driven ecosystems. However, their biosynthetic capabilities remain largely unexplored. Here, we analyzed 81 metagenomes, 33 metatranscriptomes, and seven metabolomes derived from nine globally distributed areas of cold seeps to investigate the secondary metabolites produced by cold seep microbiomes. Cold seep microbiomes encode diverse, abundant, and novel biosynthetic gene clusters (BGCs). Most BGCs are affiliated with understudied bacteria and archaea, including key mediators of methane and sulfur cycling, and multiple candidate phyla. The BGCs encode diverse antimicrobial compounds (e.g. NRPS, PKSs, RiPPs) that potentially shape community dynamics, as well as compounds predicted to influence biogeochemical cycling, such as phosphonates, iron-acquiring siderophores, nitrogenase-protecting glycolipids, and methyl-CoM reductase-modifying proteins. BGCs from key players in cold seeps are widely distributed and highly expressed, with their abundance and expression levels varying with different sediment depths. Numerous unique natural products were detected through untargeted sediment metabolomics, demonstrating a vast, unexplored chemical space and validatingin situexpression of the BGCs in cold seep sediments. Overall, these results demonstrate cold seep sediments potentially serve as a reservoir of hidden natural products and provide insights into microbial adaptation in chemosynthetically-driven ecosystems.
Two-way feedback between chromatin compaction and histone modification state explainsS. cerevisiaeheterochromatin bistability
Authors: Movilla Miangolarra Ander , Saxton Daniel S , Yan Zhi , Rine Jasper , Howard Martin
Published: August 2023

Compact chromatin is closely linked with gene silencing in part by sterically masking access to promoters, inhibiting transcription factor binding and preventing polymerase from efficiently transcribing a gene. Here, we propose a broader view: chromatin compaction can be both a cause and a consequence of the histone modification state, and this tight bidirectional interaction can underpin bistable transcriptional states. To test this theory, we developed a mathematical model for the dynamics of the HMR locus inS. cerevisiae, that incorporates activating histone modifications, silencing proteins and a dynamic, acetylation-dependent, three-dimensional locus size. Chromatin compaction enhances silencer protein binding, which in turn feeds back to remove activating histone modifications, leading to further compaction. The bistable output of the model was in good agreement with prior quantitative data, including switching rates from expressed to silent states, and vice versa, and protein binding levels within the locus. We then tested the model by predicting changes in switching rates as the genetic length of the locus was increased, which were then experimentally verified. This bidirectional feedback between chromatin compaction and the histone modification state may be an important regulatory mechanism at many loci.

Significance

Chromatin is the complex formed by proteins, including histones, and DNA to form chromosomes. Specific chromatin structures and states are thought to be key factors regulating transcription. A common view proposes that histone modifications activate or inhibit transcription either via specific activation or inhibition of RNA polymerase binding/elongation at a locus, or by expanding/compacting the locus, thereby modulating its accessibility to many macromolecules. In this work, we elucidated a broader hypothesis that chromatin compaction may both inhibit transcription, and feedback via silencing proteins to remove histone modifications that further control chromatin compaction and correlate with gene activity. We developed a model incorporating these ideas and showed that it explains quantitative experimental data for a silent locus in budding yeast.
Hyaluronan Hydrogel “Safety Nets” for 3D Cell Culture Applications
Authors: Wilson Russell T. , Bonteanu Andrei , Harrington Daniel A.
Published: August 2023

Polymeric hydrogels can mimic features of native extracellular matrix (ECM), and their facile production and characterization enable customizable cell encapsulation and 3-dimensional (3D) culture. These have applications relevant to dentistry such as soft tissue engineering, cancer modeling, and drug screening. Hyaluronan (HA), a biologically-derived polymer found in native ECM, offers an optimal platform for this use, as it can be modified covalently with adhesive ligands, enzyme-degradable crosslinkers, and other biorelevant moieties, yielding tailored physical properties and biological response. Cell-directed degradation of these encapsulating matrices can be a prerequisite for phenotype preservation, but degradation kinetics may not match desired timelines for drug screening applications. This study focused on optimizing hydrogel composition, network structure, and gelation kinetics to preserve z-distribution of physiologically relevant cells within high-throughput microfluidic plates. Hydrogels were formed from aqueous solutions of thiolated HA (HA-SH), bifunctional acrylated poly(ethylene glycol)-peptide crosslinkers, and pendant acrylated peptides (RGD or YIGSR sequences) to support cell adhesion. By varying the absolute crosslinker concentration and relative proportions of high:low crosslinker degradation kinetics, hydrogels could be tuned to desired moduli (G’: ∼10-120 Pa) and enzymatic degradation rate. Ratios of high:low degradable crosslinkers, at equivalent total crosslinker concentration, minimally impacted final modulus or gelation rate. Similarly, pendant adhesive ligands were swapped easily with negligible impact on hydrogel physical properties. Hydrogels with a 50:50 ratio of high:low degradable crosslinkers provided a “safety net” that preserved z-distribution of encapsulated bone marrow-derived fibroblasts, while maintaining expected phenotype. A comparable system supported the 3D co-culture of primary human salivary epithelial and mesenchymal cells within a perfusable microfluidic multiwell plate. This customizable bottom-up construction reduced confounding factors encountered in hybridoma-derived protein matrices, enabling modular customization of physiologically relevant, yet reproducible matrices to replicate native ECM. Our optimized model demonstrates workflows to improve future pharmaceutical screens, and tailor tissue engineering applications.
Nonlinear Parameter and State Estimation Approach for Intradialytic Measurement of Absolute Blood Volume
Authors: Abohtyra Rammah , Vincent Tyrone , Schneditz Daniel
Published: August 2023

Background

Managing blood and fluid volumes in chronic kidney disease (CKD) patients plays an essential role in dialysis therapy to replace kidney function.

Objective

This study aims to develop an estimation approach to provide predictable information on blood and fluid volumes during a regular dialysis routine.

Methods

The method utilizes a non-linear fluid volume model, an optimization technique, and the Unscented Kalman Filter (UKF). This method does not rely on specific ultrafiltration and dilution protocols and uses the Fisher information matrix to quantify the estimation error.

Results

The method was applied to 21 data sets of ten patients. A significant moderate correlation was obtained when estimated blood volumes were compared to a different method applied to the same data set. Average specific blood volumes were plausible and in the range of 78.7 and 75.9 mL/kg at the end of the high ultrafiltration rate pulse and above the critical level of 65 mL/kg. Critical blood volumes were only observed in four studies done on three patients.

Conclusion

The absolute blood volume estimated at the beginning and during every dialysis session offers the opportunity to detect critical blood volumes and to improve fluid management in CKD patients significantly.
Multi-omic stratification of the missense variant cysteinome
Authors: Desai Heta , Ofori Samuel , Boatner Lisa , Yu Fengchao , Villanueva Miranda , Ung Nicholas , Nesvizhskii Alexey I. , Backus Keriann
Published: August 2023

Cancer genomes are rife with genetic variants; one key outcome of this variation is gain-of-cysteine, which is the most frequently acquired amino acid due to missense variants in COSMIC. Acquired cysteines are both driver mutations and sites targeted by precision therapies. However, despite their ubiquity, nearly all acquired cysteines remain uncharacterized. Here, we pair cysteine chemoproteomics—a technique that enables proteome-wide pinpointing of functional, redox sensitive, and potentially druggable residues—with genomics to reveal the hidden landscape of cysteine acquisition. For both cancer and healthy genomes, we find that cysteine acquisition is a ubiquitous consequence of genetic variation that is further elevated in the context of decreased DNA repair. Our chemoproteogenomics platform integrates chemoproteomic, whole exome, and RNA-seq data, with a customized 2-stage false discovery rate (FDR) error controlled proteomic search, further enhanced with a user-friendly FragPipe interface. Integration of CADD predictions of deleteriousness revealed marked enrichment for likely damaging variants that result in acquisition of cysteine. By deploying chemoproteogenomics across eleven cell lines, we identify 116 gain-of-cysteines, of which 10 were liganded by electrophilic druglike molecules. Reference cysteines proximal to missense variants were also found to be pervasive, 791 in total, supporting heretofore untapped opportunities for proteoform-specific chemical probe development campaigns. As chemoproteogenomics is further distinguished by sample-matched combinatorial variant databases and compatible with redox proteomics and small molecule screening, we expect widespread utility in guiding proteoform-specific biology and therapeutic discovery.
Lymphatic vessel development in human embryos
Authors: Yamaguchi Shoichiro , Minamide Natsuki , Imai Hiroshi , Ikeda Tomoaki , Watanabe Masatoshi , Imanaka-Yoshida Kyoko , Maruyama Kazuaki
Published: August 2023

Lymphatic vessel development has been a subject of research for about 120 years. Studies employing mice and zebrafish models have elucidated that lymphatic endothelial cells (LECs) predominantly differentiate from venous endothelial cells via the expression of transcription factor Prospero homeobox protein 1 (Prox1), a master regulator of lymphatic vessel development. On the other hand, it has been found that LECs can also be generated from undifferentiated mesodermal or hemogenic endothelial cells, suggesting potential diversity in their origins depending on the organ or anatomical location. However, knowledge of human lymphatic vessel development remains limited. Here, we examined early lymphatic development in humans by analyzing 31 embryos and three 9-week old fetuses. We found that human embryos produce Prox1-expressing LECs in and around the cardinal veins, which converged to form initial lymph sacs. Furthermore, we also examined lymphatic vessel development in the heart, lungs, lower jaw, mesentery, intestines and kidneys. Lymphatic vessels appeared to develop at different rates in each organ and to display temporal differences in marker expression. These observation showed the possibility that there could exist different patterns of lymphatic vessel development across organs, which may reflect different cellular origins or developmental signaling in each organ.

Our research clarifies the early development of human lymphatic vessels, contributing to a better understanding of the evolution and phylogenetic relationships of lymphatic systems, and enriching our knowledge of the role of lymphatics in various human diseases.

Significance Statement

Lymphatic vessel development has been a focus of research for over a century. Recent studies across a variety of species have demonstrated that lymphatic endothelial cells originate from embryonic veins, and undifferentiated mesodermal cells. However, whether these findings are applicable to human has yet to be determined. In this study, we explored lymphatic vessel development in humans. Our analysis demonstrated that lymphatic endothelial cells in human embryos initially derived from embryonic veins. Notably, we found that lymphatic vessels in different organs displayed distinct developmental and marker expression patterns, suggesting a diversity in lymphatic vessel development across organs. Our research revealed the human lymphatic vessel development, contributing to the understanding of phylogenetics of lymphatic vessels and lymph-related diseases.
Engineered BCL6 BTB Domain of the Bcl-2 Protein Family shows Dynamic Structural Behavior: Insights from Molecular Dynamics Simulations
Authors: Saddam Md. , Habib Mohammad Ahsan , Fahim Md. Abrar , Mimi Afsana , Islam Saiful , Uddin Helal Md Mostofa
Published: August 2023

Apoptosis is crucially regulated by the Bcl-6 protein, and mutations in this protein can have a significant impact on many malignancies. In this study, we used molecular dynamics simulations to examine the effects of specific mutations (Q8C, R67C, and N84C) in the crystal structure of the BCL6 BTB domain in a compound with pyrazole-pyrimidine ligand. We concentrated on comprehending the dynamics of these alterations and their possible effects on the emergence of cancer. To explore the structural and dynamic changes induced by these mutations, we performed in silico simulations using the GROMACS software suite (version 5.2, 2020.1) on Google Colab’s Tesla T4 GPU. The crystal structure of the BCL6 BTB domain in complex with the pyrazole-pyrimidine ligand (PDB ID: 5N20) served as the wild-type reference structure. Mutations were imposed using the Rotamer functions of Chimera. The simulations were carried out for a total duration of 20 ns using a time step of 2 femtoseconds (0.002 ps). The Trajectory profiles of the BCL6 BTB domain protein and its three mutations, Q8C, R67C and N84C, were shown to differ from each other. Based on the analysis of RMSD, RMSF, and Rg, it was determined that the mutant 2 (R67C) protein exhibited increased instability and greater flexibility. In contrast, mutant 3 (N84C) demonstrates a heightened level of compactness and greater stability compared to the remaining protein mutant. PCA also provides information regarding the structural dynamics of these mutants. In addition, the SASA and SASA autocorrelation provides a distinct view of the solvent accessibility of these proteins.
Structure and function of the human mitochondrial MRS2 channel
Authors: He Zhihui , Tu Yung-Chi , Tsai Chen-Wei , Mount Jonathan , Zhang Jingying , Tsai Ming-Feng , Yuan Peng
Published: August 2023

The human Mitochondrial RNA Splicing 2 protein (MRS2) has been implicated in Mg2+transport across mitochondrial inner membranes, thus playing an important role in Mg2+homeostasis critical for mitochondrial integrity and function. However, the molecular mechanisms underlying its fundamental channel properties such as ion selectivity and regulation remain unclear. Here, we present structural and functional investigation of MRS2. Cryo-electron microscopy structures in various ionic conditions reveal a pentameric channel architecture and the molecular basis of ion permeation and potential regulation mechanisms. Electrophysiological analyses demonstrate that MRS2 is a Ca2+-regulated, non-selective channel permeable to Mg2+, Ca2+, Na+and K+, which contrasts with its prokaryotic ortholog, CorA, operating as a Mg2+-gated Mg2+channel. Moreover, a conserved arginine ring within the pore of MRS2 functions to restrict cation movements, likely preventing the channel from collapsing the proton motive force that drives mitochondrial ATP synthesis. Together, our results provide a molecular framework for further understanding MRS2 in mitochondrial function and disease.
Cooperative activities of dICA69N-BARand dCIP4F-BARdomain proteins regulate membrane tubule organizationin vivo
Authors: Mallik Bhagaban , Bhat Sajad , Kumar Vimlesh
Published: August 2023

Intracellular membrane tubules play a crucial role in diverse cellular processes, and their regulation is facilitated by Bin-Amphiphysin-Rvs (BAR) domain-containing proteins. This study investigates the roles of dICA69N-BARand dCIP4F-BARin vivo, focusing on their impact onin vivotubule organization. Through cell culture and immunofluorescence staining, we observed co-localization of endogenous dICA69 with dCIP4-induced membrane tubules, indicating their potential recruitment for tubule formation and maintenance. Additionally, dCIP4-positive tubules exhibit enrichment of actin regulatory proteins such as Wasp, SCAR, Arp2, Arp3, and Syndapin. Overexpressing dICA69N-BARin S2R+ cells reveals distinct punctate patterns in the perinuclear region. An earlier study indicated that F-BAR proteins spontaneously segregate from the N-BAR domain-containing proteins during membrane tubule formation. In contrast, our observation supports a model in which different BAR-domain family members can associate with the same tubule and cooperate to fine-tune the tubule width. Moreover, our analysis highlights how dCIP4F-BARfacilitates the redistribution of dICA69N-BARpunctae, leading to altered patterns within the cells. These cooperative activities of dICA69N-BARand dCIP4F-BARare vital for the precise organization of intracellular tubules. Understanding the underlying mechanisms governing this cooperation provides valuable insights into cellular dynamics and the organization of membrane tubules. The implications extend to various physiological and pathological conditions related to intracellular membrane dynamics.
Unveiling nesting strategies: Investigating visual concealment and nest-site selection in Yellow-wattled Lapwings,Vanellus malabaricus(Boddaert, 1783)
Authors: Jagati Vishwa , Ramaswami Geetha , Datta-Roy Aniruddha
Published: August 2023

Ground-nesting birds such as Yellow-wattled Lapwing,Vanellus malabaricus(Boddaert, 1783) employ several nesting and behavioral strategies to mitigate nest predation, which greatly influences their reproductive success and survival. Yet the breeding ecology of Yellow-wattled Lapwing has received relatively little research attention despite the species’ widespread presence in the Indian subcontinent. The objective of this study was to investigate the significance and impact of two visual concealment strategies commonly utilized by open ground-nesting birds: visual concealment through vegetative characteristics and camouflage using Yellow-wattled Lapwing as the model organism. We also assessed the nest-site selection of Yellow-wattled Lapwings in relation to vegetation cover and food availability, as well as their choice of nest substrate by using behavioral sampling, quadrat sampling, and digital image analysis techniques. We found that variation in hatching success could not be attributed to the analyzed camouflage mechanisms (disruptive markings and pattern complexity matching). Furthermore, the nesting pairs exhibited a preference for areas with high vegetation cover and low food availability while selecting nesting sites. We also showed that this species might exhibit an active behavioral preference for selecting nest substrates. It is important to note that this study was conducted during a single nesting season for the Yellow-wattled Lapwings, and further temporal replicates are necessary to validate and establish the findings over the long term.
Phylogenomic analyses support a new infrageneric classification ofPourthiaea(Maleae, Rosaceae) using multiple inference methods and extensive taxon sampling
Authors: Liu Guang-Ning , Ma Dai-Kun , Zhang Yu , Hodel Richard G.J. , Xie Si-Yu , Wang Hui , Jin Ze-Tao , Li Fu-Xing , Jin Shui-Hu , Zhao Liang , Xu Chao , Wei Yu , Liu Bin-Bin
Published: August 2023

In this comprehensive study, we conducted extensive taxon sampling and performed phylogenomic analyses based on plastome and nuclear ribosomal DNA (nrDNA) datasets. We employed multiple inference methods, including concatenated and coalescent-based strategies, to generate an accurate phylogeny of the woody Rosaceae genusPourthiaea. The nrDNA phylogeny ofPourthiaeastrongly supported three major clades, which were consistent with morphology. However, the plastid tree provided an alternative phylogenetic topology, indicating cytonuclear discordance. Frequent hybridizations between and among the species ofPourthiaeacould explain the cytonuclear discordance. Considering the evidence from morphology and phylogenomic data, we propose a new infrageneric classification forPourthiaea, consisting of three sections:P.sect.Pourthiaea,P.sect.AmphidoxaeB.B.Liu, andP.sect.ImpressivenaeB.B.Liu.
Search and Match across Spatial Omics Samples at Single-cell Resolution
Authors: Tang Zefang , Luo Shuchen , Zeng Hu , Huang Jiahao , Wu Morgan , Wang Xiao
Published: August 2023

Spatial omics technologies characterize tissue molecular properties with spatial information, but integrating and comparing spatial data across different technologies and modalities is challenging. A comparative analysis tool that can search, match, and visualize both similarities and differences of molecular features in space across multiple samples is lacking. To address this, we introduce CAST (Cross-sampleAlignment ofSpaTial omics), a deep graph neural network (GNN)-based method enabling spatial-to-spatial searching and matching at the single-cell level. CAST aligns tissues based on intrinsic similarities of spatial molecular features and reconstructs spatially resolved single-cell multi-omic profiles. CAST enables spatially resolved differential analysis (ΔAnalysis) to pinpoint and visualize disease-associated molecular pathways and cell-cell interactions, and single-cell relative translational efficiency (scRTE) profiling to reveal variations in translational control across cell types and regions. CAST serves as an integrative framework for seamless single-cell spatial data searching and matching across technologies, modalities, and disease conditions, analogous to BLAST in sequence alignment.
A Pooled Cell Painting CRISPR Screening Platform Enables de novo Inference of Gene Function by Self-supervised Deep Learning
Authors: Sivanandan Srinivasan , Leitmann Bobby , Lubeck Eric , Sultan Mohammad Muneeb , Stanitsas Panagiotis , Ranu Navpreet , Ewer Alexis , Mancuso Jordan E. , Phillips Zachary F , Kim Albert , Bisognano John W. , Cesarek John , Ruggiu Fiorella , Feldman David , Koller Daphne , Sharon Eilon , Kaykas Ajamete , Salick Max R. , Chu Ci
Published: August 2023

Pooled CRISPR screening has emerged as a powerful method of mapping gene functions thanks to its scalability, affordability, and robustness against well or plate-specific confounders present in array-based screening1–6. Most pooled CRISPR screens assay for low dimensional phenotypes (e.g. fitness, fluorescent markers). Higher-dimensional assays such as perturb-seq are available but costly and only applicable to transcriptomics readouts7–11. Recently, pooled optical screening, which combines pooled CRISPR screening and microscopy-based assays, has been demonstrated in the studies of the NFkB pathway, essential human genes, cytoskeletal organization and antiviral response12–15. While the pooled optical screening methodology is scalable and information-rich, the applications thus far employ hypothesis-specific assays. Here, we enable hypothesis-free reverse genetic screening for generic morphological phenotypes by re-engineering the Cell Painting16technique to provide compatibility with pooled optical screening. We validated this technique using well-defined morphological genesets (124 genes), compared classical image analysis and self-supervised learning methods using a mechanism-of-action (MoA) library (300 genes), and performed discovery screening with a druggable genome library (1640 genes)17. Across these three experiments we show that the combination of rich morphological data and deep learning allows gene networks to emerge without the need for target-specific biomarkers, leading to better discovery of gene functions.
High quality genome assemblies reveal evolutionary dynamics of repetitive DNA and structural rearrangements in theDrosophila virilissub-group
Authors: Flynn Jullien M. , Ahmed-Braimah Yasir H. , Long Manyuan , Wing Rod A. , Clark Andrew G.
Published: August 2023

High-quality genome assemblies across a range of non-traditional model organisms can accelerate the discovery of novel aspects of genome evolution. TheDrosophila virilisgroup has several attributes that distinguish it from more highly studied species in theDrosophilagenus, such as an unusual abundance of repetitive elements and extensive karyotype evolution, in addition to being an attractive model for speciation genetics. Here we used long-read sequencing to assemble five genomes of three virilis group species and characterized sequence and structural divergence and repetitive DNA evolution. We find that our contiguous genome assemblies allow characterization of chromosomal arrangements with ease and can facilitate analysis of inversion breakpoints. We also leverage a small panel of resequenced strains to explore the genomic pattern of divergence and polymorphism in this species and show that known demographic histories largely predicts the extent of genome-wide segregating polymorphism. We further find that a neo-X chromosome inD. americanadisplays X-like levels of nucleotide diversity. We also found that unusual repetitive elements were responsible for much of the divergence in genome composition among species. Helitron-derived tandem repeats tripled in abundance on the Y chromosome inD. americanacompared toD. novamexicana, accounting for most of the difference in repeat content between these sister species. Repeats with characteristics of both transposable elements and satellite DNAs expanded by three-fold, mostly in euchromatin, in bothD. americanaandD. novamexicanacompared toD. virilis. Our results represent a major advance in our understanding of genome biology in this emerging model clade.

Significance statement

TheDrosophila virilissub-group is an emerging model with an enticing combination of attributes, including abundant and diverse repetitive DNA content, structural rearrangements, and hybridization capability. The lack of high-quality genome assemblies for this group have prevented detailed understanding of genome evolution. Here, we present five new long-read genome assemblies of three virilis sub-group species along with analyses of structural variants, polymorphisms, repetitive DNAs, and Y chromosome genes and repeats. We find that the expansion and mobilization of non-canonical repetitive elements accounts for most of the divergence in assembled genome sequence between these species, with an especially striking takeover of the Y chromosome by a single type of element in one of the three species. Overall, our study positions the virilis sub-group as a model for a variety of future studies.
Genomic signatures of adaptation to abiotic stress from a geographically diverse collection of chile peppers (Capsicum spp.) from Mexico
Authors: Bernau Vivian , Kantar Michael , Jardon Barbolla Lev , McCoy Jack , Mercer Kristin L. , McHale Leah K.
Published: August 2023

Extreme environmental variability requires the identification of genetic diversity that can help crops withstand difficult abiotic conditions. Understanding the genetic basis of adaptation to abiotic stress can provide tools for adapting agriculture to changing climates. Crop landraces and their wild ancestors from centers of domestication have often evolved across diverse environmental conditions and provide a unique opportunity to locate loci harboring alleles that could contribute to abiotic stress tolerance, among other traits. We collected chile peppers (Capsicumspp.) from farmers in southern Mexico along environmental transects crossing temperature, precipitation, and elevational gradients. Using 32,623 filtered SNPs generated from genotyping-by-sequencing (GBS), we conducted an environmental association analysis (EAA) combined with two outlier analyses, FSTand spatial ancestry analyses to detect priority candidate loci associated with climate and soil phenotypes relevant to drought tolerance. Even though cultivated species may be shielded from some environmental selection by management practices (e.g., irrigation), we found fifteen priority loci whose genetic variation covaried with environmental variation in our EAA and were also allele frequency outliers (i.e., Fst and/or SPA). Thirty-three percent of the priority loci were validated with phenotype in response to water deficit. The haplotype blocks associated with these loci identify unique genetic variants worthy of conservation and harbor genes with abiotic stress-related functions. This work provides valuable information to explore quantitative trait loci (QTLs) underlying abiotic stress tolerance in chile pepper and is a new resource for improving plant breeding around the world.

Article Summary

The extreme environmental variability faced by crops requires the identification of potentially adaptive loci for abiotic stressors. We conducted an environmental association analysis (EAA) environments using chile peppers collected in southern Mexico along environmental transects crossing temperature, precipitation, and elevational gradients. We combined EAA with outlier analyses FSTand spatial ancestry analysis to detect priority candidate loci associated with climate and soil phenotypes relevant to drought tolerance that may putatively contribute to abiotic stress adaptation.
Reduced brain glutathione levels during normal aging are associated with visuospatial memory
Authors: Hu Xin , Pan Keyu , Zhao Min , Lv Jiali , Wang Jing , Zhang Xiaofeng , Liu Yuxi , Song Yulu , Gudmundson Aaron T. , Edden Richard A.E. , Ren Fuxin , Zhang Tao , Gao Fei
Published: August 2023

During aging, the brain is subject to greater oxidative stress (OS), which is thought to play a critical role in cognitive impairment. Glutathione (GSH), as a major antioxidant in the brain, can be used to combatting OS. However, how brain GSH levels vary with age and their associations with cognitive function remain unclear. In this study, we combined point-resolved spectroscopy and edited spectroscopy sequences to investigate GSH levels in the anterior cingulate cortex (ACC), posterior cingulate cortex (PCC), and occipital cortex (OC) of 276 healthy participants (166 females, age range 20–70 years) and examined their relationships with age and cognitive function. The results revealed decreased GSH levels with age in the PCC among all participants. Notably, the timecourse of GSH level changes in the PCC and ACC differed between males and females. Additionally, positive correlations were observed between GSH levels in the PCC and OC and visuospatial memory. Taken together, these findings enhance our understanding of the brain GSH timecourse during normal aging and associations with sex and memory, which is an essential first step for understanding the neurochemical underpinnings of OS-related diseases.
F-box protein FBXB-65 regulates anterograde transport of UNC-104 through modification near the PH domain
Authors: Sabharwal Vidur , Boyanapalli Sri Padma Priya , Shee Amir , Nonet Michael L. , Nandi Amitabha , Chaudhuri Debasish , Koushika Sandhya P.
Published: August 2023

Axonal transport is essential for cargo movement between the neuronal cell body and synapses. UNC-104/KIF1A, a Kinesin-3 motor inC. elegansthat anterogradely transports precursors of synaptic vesicles (pre-SVs), is known to be degraded at synapses through the ubiquitin pathway. Knockdown of the E1 ubiquitin-activating enzyme,uba-1, leads to increased accumulation of UNC-104 at neuronal ends and at synapses of touch receptor neurons (TRNs). Loss of the F-box protein FBXB-65, a putative E3 ligase, leads to UNC-104 accumulation at distal ends of neurons, alters net anterograde movement of UNC-104, and the intensity of moving UNC-104 puncta likely bound to cargo without changes in synaptic UNC-104 levels. Using a theoretical model, we analyze the steady state distribution of the anterogradely moving UNC-104 motor. A good agreement between the model and the experimental distributions leads to a crucial hypothesis that UNC-104 may exhibit cooperative binding with moving motor puncta likely associated with cargo, which is regulated byfbxb-65. FBXB-65 regulates the modification of UNC-104 motor in a region besides the cargo binding PH-domain. Bothfbxb-65and UNC-104 motor independent of FBXB-65 regulate the extent of cargo transport in the axon and transport behaviour of cargo at branch points. Our study shows that modification of UNC-104 near its cargo-binding domain may regulate number of motors on the cargo surface and this regulation can fine-tune cargo transport to its destination, the synapse.
RasGEFX triggers spontaneous Ras excitation with RasGEFB/M/U for random cell migration
Authors: Iwamoto Koji , Matsuoka Satomi , Ueda Masahiro
Published: August 2023

Excitable systems of eukaryotic chemotaxis can generate asymmetric signals of Ras-GTP-enriched domains spontaneously to drive random cell migration without guidance cues. The molecules responsible for the spontaneous signal generation remain elusive. Here, we characterized RasGEFs encoded inDictyostelium discoideumby the live-cell imaging of the Ras dynamics and hierarchical clustering, finding that RasGEFX triggers symmetry breaking to generate a Ras-GTP-enriched domain and is essential for random migration in combination with RasGEFB/M/U but dispensable for chemotaxis. Among RasGEFs, RasGEFX and RasGEFB co-localize with Ras-GTP on oscillatory waves propagating along the membrane and regulate the temporal periods and spatial sizes, respectively, of the waves and thus the cytoskeletal dynamics differently. RasGEFU localized uniformly on the membrane and regulated cell adhesion. These findings provide mechanistic insights into the internal signal generation that operates independently of external chemotaxis signaling and suggest a coordinated control of the cytoskeletal dynamics by multiple RasGEFs for spontaneous motility.
A PD-1-ST2 axis controls Th2 effector function in tissue via a metabolic checkpoint
Authors: Heieis Graham A. , Everts Bart , Roberts Craig W. , Maizels Rick M. , Perona-Wright Georgia
Published: August 2023

Type 2 immune responses characterise both helminth infections and atopic disease such as allergy or asthma, but a better understanding of the mechanisms that regulate these responses is key to improving therapeutic and vaccination strategies. Immuno-metabolic studies over the last two decades have suggested T cell activation broadly requires rapid increases in glycolysis and oxidative phosphorylation. In contrast, we show that CD4+T helper 2 (Th2) cells activatedin vivo, using models of helminth infection, do not acquire a glycolytic metabolism. Instead, we show that Th2 cells solely increase their oxidative metabolism, associated with increased fatty acid uptake. Rather than contributing directly to effector function, our data reveal that Th2 cells switch to fatty acid oxidation downstream of PD-1 signalling to promote expression of the IL-33 receptor (ST2). These data provide insight into the spatial regulation of T cell metabolism, and suggest that PD-1 blockade therapies may be effective in Th2 disorders.
MYC and MAX drive the reactivation of the genome after mitosis
Authors: Gonzalez Inma , Chervova Almira , Escoll Pedro , Altamirano-Pacheco Luis , Mueller Florian , Dubois Agnès , Navarro Pablo
Published: August 2023

Shortly after cell division, a robust wave of hyper-transcription reactivates the genome1-3. This phenomenon is particularly pronounced in pluripotent cells4, which necessitate rapid transcrip-tome reactivation to maintain their undifferentiated state and prevent premature differentiation. While recent work has illuminated how specific groups of genes are reactivated4-8, the mechanisms enabling the global, efficient and accurate post-mitotic reactivation of the genome remain unknown. Here we elucidate the direct involvement of the MYC/MAX transcription factors in the post-mitotic reactivation of pluripotent mouse embryonic stem cells. While MYC undergoes extensive phosphorylation and largely dissociates from its DNA binding sites during mitosis, we report that MAX remains bound to its targets, preferentially at promoters, and facilitates early recruitment of MYC following mitosis. Through the application of MYC/MAX heterodimerization inhibitors, we demonstrate their indispensable role in sustaining hyper-transcription in ES cells, including during the critical transition from mitosis to G1 phase. Our findings uncover a novel role for MAX in mitotic book-marking, highlighting its pivotal role in post-mitotic MYC recruitment and the re-establishment of high global transcription levels. These findings hold significant implications for medically relevant contexts, particularly when cell proliferation is of paramount importance9. We anticipate that the study of mitotic bookmarking by MYC and MAX and of the effects of anticancer drugs targeting MYC/MAX interactions in such process10-12will be relevant for our understanding of cancer and its potential treatments.
Global and local adaptation to aridity in a desert plantGymnocarpos przewalskii
Authors: Fu Ruirui , Zhu Yuxiang , Liu Ying , Yang Zhaoping , Lu Ruisen , Qiu Yingxiong , Lascoux Martin , Li Pan , Chen Jun
Published: August 2023

In order to thrive and survive plant species need to combine stability in the long term and rapid response to environmental challenges in the short term. The former would be reflected by global adaptation across species and the latter by pronounced local adaptation among populations of the same species. It remains unclear how much overlap is to be expected between the parts of the genome associated to these two contrasted adaptation processes. In the present study, we generated a high-quality genome and re-sequenced 177 individuals forGymnocarpos przewalskii, an important desert plant species from North-West China, to detect local adaptation. To test for global adaptation to aridity at the molecular level we compared genomic data of 15 species that vary in their ability to withstand drought. A total of 118 genes were involved in global adaptation to aridity. Sixty-fiveG. przewalskiigenes were shared across all xerophytic species, of which sixty-three were under stabilizing selection and two under directional selection. While 20% ofG. przewalskiigenome showed signatures of local adaptation to aridity during population divergence, only 13 of those genes were also under global adaptation. Hence, our results suggest that long-term stability is crucial for adaptation to extreme environmental stress but is only maintained in a small group of highly pleiotropic genes while a rapid response to recent changes elicits a genome-wide response, including gene family expansion. The overlap between the two evolutionary mechanisms appears limited.
Orphan quality control by an SCF ubiquitin ligase directed to pervasive C-degrons
Authors: Kong Ka-Yiu Edwin , Shankar Susmitha , Rühle Frank , Khmelinskii Anton
Published: August 2023

Selective protein degradation typically involves substrate recognition via short linear motifs known as degrons. Various degrons can be found at protein termini from bacteria to mammals. While N-degrons have been extensively studied, our understanding of C-degrons is still limited. Towards a comprehensive understanding of eukaryotic C-degron pathways, we performed an unbiased survey of C-degrons in budding yeast. We identified over 5000 potential C-degrons by stability profiling of random peptide libraries and of the yeast C-terminome. Combining machine learning, high-throughput mutagenesis and genetic screens revealed that the SCF ubiquitin ligase targets ∼40% of degrons using a single F-box substrate receptor Das1. Although sequence-specific, Das1 is highly promiscuous, recognizing a variety of C-degron motifs. By screening for endogenous substrates, we implicate SCFDas1in degradation of orphan protein complex subunits. Altogether, this work provides a comprehensive view of a eukaryotic C-degronome and uncovers how an SCF/C-degron pathway of broad specificity contributes to proteostasis.
Sensory representations and pupil-indexed listening effort provide complementary contributions to multi-talker speech intelligibility
Authors: McHaney Jacie R. , Hancock Kenneth E. , Polley Daniel B. , Parthasarathy Aravindakshan
Published: August 2023

Optimal speech perception in noise requires successful separation of the target speech stream from multiple competing background speech streams. The ability to segregate these competing speech streams depends on the fidelity of bottom-up neural representations of sensory information in the auditory system and top-down influences of effortful listening. Here, we use objective neurophysiological measures of bottom-up temporal processing using envelope-following responses (EFRs) to amplitude modulated tones and investigate their interactions with pupil-indexed listening effort, as it relates to performance on the Quick speech in noise (QuickSIN) test in young adult listeners with clinically normal hearing thresholds. We developed an approach using ear-canal electrodes and adjusting electrode montages for modulation rate ranges, which extended the rage of reliable EFR measurements as high as 1024Hz. Pupillary responses revealed changes in listening effort at the two most difficult signal-to-noise ratios (SNR), but behavioral deficits at the hardest SNR only. Neither pupil-indexed listening effort nor the slope of the EFR decay function independently related to QuickSIN performance. However, a linear model using the combination of EFRs and pupil metrics significantly explained variance in QuickSIN performance. These results suggest a synergistic interaction between bottom-up sensory coding and top-down measures of listening effort as it relates to speech perception in noise. These findings can inform the development of next-generation tests for hearing deficits in listeners with normal-hearing thresholds that incorporates a multi-dimensional approach to understanding speech intelligibility deficits.
CryoEM structures of the human CLC-2 voltage gated chloride channel reveal a ball and chain gating mechanism
Authors: Xu Mengyuan , Neelands Torben , Powers Alexander S. , Liu Yan , Miller Steven D. , Pintilie Grigore , Bois J. Du , Dror Ron O. , Chiu Wah , Maduke Merritt
Published: August 2023

CLC-2 is a voltage-gated chloride channel that contributes to electrical excitability and ion homeostasis in many different mammalian tissues and cell types. Among the nine mammalian CLC homologs, CLC-2 is uniquely activated by hyperpolarization, rather than depolarization, of the plasma membrane. The molecular basis for the divergence in polarity of voltage gating mechanisms among closely related CLC homologs has been a long-standing mystery, in part because few CLC channel structures are available, and those that exist exhibit high conformational similarity. Here, we report cryoEM structures of human CLC-2 at 2.46 – 2.76 Å, in the presence and absence of the potent and selective inhibitor AK-42. AK-42 binds within the extracellular entryway of the Cl--permeation pathway, occupying a pocket previously proposed through computational docking studies. In the apo structure, we observed two distinct apo conformations of CLC-2 involving rotation of one of the cytoplasmic C-terminal domains (CTDs). In the absence of CTD rotation, an intracellular N-terminal 15-residue hairpin peptide nestles against the TM domain to physically occlude the Cl--permeation pathway from the intracellular side. This peptide is highly conserved among species variants of CLC-2 but is not present in any other CLC homologs. Previous studies suggested that the N-terminal domain of CLC-2 influences channel properties via a “ball-and-chain” gating mechanism, but conflicting data cast doubt on such a mechanism, and thus the structure of the N-terminal domain and its interaction with the channel has been uncertain. Through electrophysiological studies of an N-terminal deletion mutant lacking the 15-residue hairpin peptide, we show that loss of this short sequence increases the magnitude and decreases the rectification of CLC-2 currents expressed in mammalian cells. Furthermore, we show that with repetitive hyperpolarization WT CLC-2 currents increase in resemblance to the hairpin-deleted CLC-2 currents. These functional results combined with our structural data support a model in which the N-terminal hairpin of CLC-2 stabilizes a closed state of the channel by blocking the cytoplasmic Cl--permeation pathway.