bluuebunny/crossref_metadata_2025 huggingface dataset:
Exploring DNA movement through the application of droplet based high efficient chromatin conformation capture (DropHiChew) and loop velocity
Authors: Zhang Chen , Xie Yeming , Tan Chen , Chen Zhichao , Guo Mei , Tang Chong
Published: June 2024

This study presents a novel approach to understanding DNA movement dynamics through the development of a droplet-based, high-efficient chromatin conformation capture method, known as DropHiChew, and a new algorithm, loop velocity. DropHiChew, a user-friendly and cost-effective technique, employs the 10X single-cell systems allowing for easy experimental implementation. The loop velocity algorithm, on the other hand, enables the estimation of the speed and direction of cell development, providing a dynamic perspective on chromatin movement. Even with shallow sequencing, our loop velocity algorithm accurately gauges the trajectory of DNA motion and cellular states. The combined use of DropHiChew and loop velocity offers potential for a wide array of applications in future chromatin capture studies, including disease modeling, cellular differentiation studies, and developmental biology.
Massively Parallel Binding Assay (MPBA) reveals limited transcription factor binding cooperativity, challenging models of specificity
Authors: Lang Tamar Jana , Brodsky Sagie , Manadre Wajd , Vidavski Matan , Valinsky Gili , Mindel Vladimir , Ilan Guy , Carmi Miri , Barkai Naama
Published: June 2024

DNA binding domains (DBDs) within transcription factors (TFs) recognize short sequence motifs that are highly abundant in genomes.In vivo, TFs bind only a small subset of motif occurrences, which is often attributed to the cooperative binding of interacting TFs at proximal motifs. However, large-scale testing of this model is still lacking. Here, we describe a novel method allowing parallel measurement of TF binding to thousands of designed sequences within yeast cells and apply it to quantify the binding of dozens of TFs to libraries of regulatory regions containing clusters of binding motifs, systematically mutating all motif combinations. With few exceptions, TF occupancies were well explained by independent binding to individual motifs, with motif cooperation being of only limited effects. Our results challenge the general role of motif combinatorics in directing TF genomic binding and open new avenues for exploring the basis of protein-DNA interactions within cells.
A Message Passing Framework for Precise Cell State Identification with scClassify2
Authors: Ding Wenze , Cao Yue , Fu Xiaohang , Torkel Marni , Yang Jean
Published: June 2024

In single-cell analysis, the ability to accurately annotate cells is crucial for downstream exploration. To date, a wide range of approaches have been developed for cell annotation, spanning from classic statistical models to the latest large language models. However, most of the current methods focus on annotating distinct cell types and overlook the identification of sequential cell populations such as transitioning cells. Here, we propose a message-passing-neural-network-based cell annotation method, scClassify2, to specifically focus on adjacent cell state identification. By incorporating prior biological knowledge through a novel dual-layer architecture and employing ordinal regression and conditional training to differentiate adjacent cell states, scClassify2 achieves superior performance compared to other state-of-the-art methods. In addition to single-cell RNA-sequencing data, scClassify2 is generalizable to annotation from different platforms including subcellular spatial transcriptomics data. To facilitate ease of use, we provide a web server hosting over 30 human tissues.
Single-cell RNA Sequencing Reveals Methamphetamine Inhibits the Liver Immune Response with Involvement of the Dopamine D1 Receptor
Authors: Zhou Jin-Ting , Xu Yungang , Liu Xiao-Huan , Cheng Cheng , Fan Jing-Na , Li Xiaoming , Yu Jun , Li Shengbin
Published: June 2024

Methamphetamine (METH) is a highly addictive psychostimulant that causes physical and psychological damage and immune system disorder, especially in the liver, which contains a significant number of immune cells. Dopamine, which is a key neurotransmitter in METH addiction and immune regulation, plays a crucial role in this process. In this study, we developed a chronic METH administration model and conducted single-cell RNA sequencing to investigate the effect of METH on liver immune cells and the involvement of the dopamine receptor D1 (DRD1) in this process. Our findings revealed that chronic exposure to METH induced an immune cell shift from Ifitm3+Mac and Ccl5+Mac to Cd14+Mac, and from Fyn+CD4+Teff, CD8+T, and NKT to Fos+CD4+T and Rora+ILC2, along with suppression of multiple immune functional pathways. DRD1 was implicated in the regulation of some of these pathways and the shifts of hepatic immune cells. This research provides valuable insights into the development of therapies aimed at mitigating METH-induced immune impairment.
RNA-ligand interaction scoring via data perturbation and augmentation modeling
Authors: Ma Hongli , Gao Letian , Jin Yunfan , Bai Yilan , Liu Xiaofan , Bao Pengfei , Liu Ke , Xu Zhenjiang Zech , Lu Zhi John
Published: June 2024

RNA-targeting drug discovery is undergoing an unprecedented revolution. Despite recent advances in this field, developing data-driven deep learning models remains challenging due to the limited availability of validated RNA-small molecule interactions and the scarcity of known RNA structures. In this context, we introduce RNAsmol, a novel sequence-based deep learning framework that incorporates data perturbation with augmentation, graph-based molecular feature representation and attention-based feature fusion modules to predict RNA-small molecule interactions. RNAsmol employs perturbation strategies to balance the bias between true negative and unknown interaction space thereby elucidating the intrinsic binding patterns between RNA and small molecules. The resulting model demonstrates accurate predictions of the binding between RNA and small molecules, outperforming other methods with average improvements of ∼8% (AUROC) in 10-fold cross-validation, ∼16% (AUROC) in cold evaluation (on unseen datasets), and ∼30% (ranking score) in decoy evaluation. Moreover, we use case studies to validate molecular binding hotspots in the prediction of RNAsmol, proving the model’s interpretability. In particular, we demonstrate that RNAsmol, without requiring structural input, can generate reliable predictions and be adapted to many RNA-targeting drug design scenarios.
Genetic variation modulates susceptibility to aberrant DNA hypomethylation and imprint deregulation in naïve pluripotent stem cells
Authors: Parikh C , Glenn RA , Shi Y , Chatterjee K , Swanzey EE , Singer S , Do SC , Zhan Y , Furuta Y , Tahiliani M , Apostolou E , Polyzos A , Koche R , Mezey JG , Vierbuchen T , Stadtfeld M
Published: June 2024

Naïve pluripotent stem cells (nPSC) frequently undergo pathological and not readily reversible loss of DNA methylation marks at imprinted gene loci. This abnormality poses a hurdle for using pluripotent cell lines in biomedical applications and underscores the need to identify the causes of imprint instability in these cells. We show that nPSCs from inbred mouse strains exhibit pronounced strain-specific susceptibility to locus-specific deregulation of imprinting marks during reprogramming to pluripotency and upon culture with MAP kinase inhibitors, a common approach to maintain naïve pluripotency. Analysis of genetically highly diverse nPSCs from the Diversity Outbred (DO) stock confirms that genetic variation is a major determinant of epigenome stability in pluripotent cells. We leverage the variable DNA hypomethylation in DO lines to identify several trans-acting quantitative trait loci (QTLs) that determine epigenome stability at either specific target loci or genome-wide. Candidate factors encoded by two multi-target QTLs on chromosomes 4 and 17 suggest specific transcriptional regulators that contribute to DNA methylation maintenance in nPSCs. We propose that genetic variants represent candidate biomarkers to identify pluripotent cell lines with desirable properties and might serve as entry points for the targeted engineering of nPSCs with stable epigenomes.

Highlights

Naïve pluripotent stem cells from distinct inbred mouse strains exhibit variable DNA methylation levels at imprinted gene loci.

The vulnerability of pluripotent stem cells to loss of genomic imprinting caused by MAP kinase inhibition strongly differs between inbred mouse strains.

Genetically diverse pluripotent stem cell lines from Diversity Outbred mouse stock allow the identification of quantitative trait loci controlling DNA methylation stability.

Genetic variants may serve as biomarkers to identify naïve pluripotent stem cell lines that are epigenetically stable in specific culture conditions.
CPI203, a BET inhibitor, down-regulates a consistent set of DNA synthesis genes across a wide array of glioblastoma lines
Authors: Garrett Matthew C. , Carnwath Troy , Albano Rebecca , Zhuang Yonghua , Behrmann Catherine A. , Pemberton Merissa , Barakat Farah , Lober Robert , Hoeprich Mark , Paravati Anthony , Reed Marilyn , Spry Hailey , Woo Daniel , O’Brien Eric , VanCauwenbergh Brett , Perentesis John , Nasser Rani , Medvedovic Mario , Plas David R.
Published: June 2024

Introduction

Glioblastomas utilize malignant gene expression pathways to drive growth. Many of these gene pathways are not directly accessible with molecularly targeted pharmacological agents. Chromatin-modifying compounds can alter gene expression and target glioblastoma growth pathways. In this study, we utilize a systematic screen of chromatin-modifying compounds on a panel of patient-derived glioblastoma lines to identify promising compounds and their associated gene targets.

Methods

Five glioblastoma cell lines were subjected to a drug screen of 106 chromatin-modifying compounds representing 36 unique drug classes to determine the twelve most promising drug classes and the best candidate inhibitors in each class. These twelve drugs were then tested with a panel of twelve patient-derived gliomasphere lines to identify growth inhibition and corresponding gene expression patterns. Overlap analysis and weighted co-expression network analysis (WCGNA) were utilized to determine potential target genes and gene pathways.

Results

The initial drug screen identified twelve candidate pharmacologic agents for further testing. Drug sensitivity testing indicated an overall high degree of variability between gliomasphere lines. However, CPI203 was the most consistently effective compound, and the BET inhibitor class was the most consistently effective class of compounds across the gliomasphere panel. Correspondingly, most of the compounds tested had highly variable effects on gene expression between gliomasphere lines. CPI203 stood out as the only compound to induce a consistent effect on gene expression across different gliomasphere lines, specifically down-regulation of DNA-synthesis genes. Amongst the twelve tested cell lines, high expression of CDKN2A and CDKN2B distinguished more drug sensitive from more drug resistant lines. WCGNA identified two oncogenic gene modules (FBXO5 and MELK) that were effectively downregulated by CPI203 (FBXO5) and ML228 (FBXO5 and MELK).

Conclusions

The bromodomain inhibitor CPI203 induced relatively consistent effects on gene expression and growth across a variety of glioblastoma lines, specifically down-regulating genes associated with DNA replication. We propose that clinically effective BET inhibitors have the potential to induce consistent beneficial effects across a spectrum of glioblastomas.
Loss ofasgr1aleads to the secretion of excess dietary cholesterol in zebrafish
Authors: Moll Tabea O.C. , Derrick Joshua T. , Sweeney Darby W. , Shin Jeffrey , Farber Steven A.
Published: June 2024

One of the major pathways to clear glycoproteins from circulation is via the liver-specific asialoglycoprotein receptor (ASGPR). Loss of asialoglycoprotein receptor 1 (ASGR1), the major subunit of ASGPR, was recently found to correlate with lower levels of plasma apolipoprotein B- containing lipoproteins (B-lps) and a profoundly reduced risk of cardiovascular disease in humans. We set out to identify the zebrafish ortholog ofASGR1(asgr1a) and generated two independent mutations inasgr1ausing CRISPR/Cas9. Neitherasgr1amutation displayed changes in larval, juvenile, and adult B-lp numbers or sizes. However, when challenged with a Western diet,asgr1amutant zebrafish exhibit less hepatic steatosis and lower hepatic triglyceride levels compared to control animals. Instead, the excess dietary cholesterol was excreted. While these results do not explain the cardioprotective nature of ASGR1 in humans, they indicate the importance of ASGR1 in modulating whole animal cholesterol flux.
Modeling of Rate Heterogeneity in Datasets Compiled for Use With Parsimony
Authors: Wright April M. , Wynd Brenen M.
Published: June 2024

Abstract

In recent years, there has been an increased interest in modeling morphological traits using Bayesian methods. Much of the work associated with modeling these characters has focused on the substitution or evolutionary model employed in the analysis. However, there are many other assumptions that researchers make in the modeling process that are consequential to estimated phylogenetic trees. One of these is how among-character rate variation (ACRV) is parameterized. In molecular data, a discretized gamma distribution is often used to allow different characters to have different rates of evolution. Morphological data are collected in ways that fundamentally differ from molecular data. In this paper, we appraise the use of standard parameters for ACRV and provide recommendations to researchers who work with morphological data in a Bayesian framework.
Short-term fluctuating and long-term divergent selection on sympatric Monkeyflowers: insights from decade-spanning reciprocal transplants
Authors: Dong Caroline M. , Aponte Rolón Bolívar , Sullivan Juj K. , Tataru Diana , Deleon Max , Dennis Rachael , Dutton Spencer , Machado Perez Fidel J. , Montano Lissette , Ferris Kathleen G.
Published: June 2024

Sympatric species are often locally adapted to distinct microhabitats. However, temporal variation may cause local maladaptation and species boundary breakdown, especially during extreme climatic events leading to episodic selection. Repeated reciprocal transplants can reveal the interplay between short and long-term patterns of natural selection. To examine evolutionary trajectories of sympatric Monkeyflowers adapted to different niches,Mimulus guttatusandM. laciniatus,we performed three replicated transplants and combined them with previous experiments to leverage a dataset of five transplants spanning 10 years. We performed phenotypic selection analyses on parents and hybrids in parental habitats in Yosemite NP, CA during years of drastically differing snowpack. If there is ecological isolation, then we predicted divergent phenotypic selection between habitats in line with species’ differences and local adaptation. We found interannual fluctuations in phenotypic selection, often in unpredicted directions. However, a combined-year analysis detected longer-term divergent selection on flowering time, a key temporally isolating and adaptative trait, suggesting that selection may reinforce species boundaries despite short-term fluctuations. Finally, we found temporal variation in local adaptation withM. laciniatuslocally adapted in low snowpack years, while an extremely high snowpack year contributed to average local maladaptation ofM. guttatus.
Rice novel useful semidwarf gened60on chromosome 2 causing pleiotropically gamete abortion
Authors: Tomita Motonori , Kamiya Daisuke , Okawa Keisuke , Nakayama Kohei
Published: June 2024

Rice semidwarf gened60is inherited according to a unique mode because it causes pleiotropically gamete abortion in the case of coexistence with the gamete lethal genegal. Namely, F2progenies of Koshihikari (D60D60galgal, long stem) × Hokuriku 100 (d60d60GalGal, short stem) segregated in the ratio of 1 semidwarf (1d60d60GalGal):2 tall and quarter sterile (2D60d60Galgal):6 tall (2D60d60GalGal:1D60D60GalGal:2D60D60Galgal:1D60D60galgal), which is skewed from the Mendelian 1 semidwarf:3 tall ratio. Firstly, genetic linkage was tested on the basis that the segregation ratios of the phenotypic marker genes linked tod60do not fit Mendelian ratio. F2of Koshihikari d60 line (d60d60GalGal)× lines carryingd30orgh2on chromosome 2, the segregation ratios of these alleles were deviated from 1:3 but well fitted to 5:4 whend30 and gh2were closely linked toD60. We then conducted molecular fine mapping ofd60by using DNA polymorphisms in F2of Koshihikari d60 line × line carrying the indica chromosome 2 segment in Koshihikari. As a result,d60was tightly linked with RM12970 by a recombination value 0.0 at the region 10.3 Mb away from the distal end of the short arm of chromosome 2. Whole genome sequencing of Koshihikari d60 revealed no SNPs and Indels around the 10.3 Mb region. RT-qPCR for ent-copalyl diphosphate synthase-like gene on 10.3 Mb indicated its transcription was reduced compared to that of Koshihikari.
The distribution and evolutionary dynamics of dopaminergic neurons in molluscs
Authors: Norekian Tigran P. , Moroz Leonid L.
Published: June 2024

Dopamine is one of the most versatile neurotransmitters in invertebrates. It’s distribution and plethora of functions is likely coupled to feeding ecology, especially in Euthyneura (the largest clade of molluscs), which presents the broadest spectrum of environmental adaptations. Still, the analyses of dopamine-mediated signaling were dominated by studies of grazers. Here, we characterize the distribution of dopaminergic neurons in representatives of two distinct ecological groups: the sea angel - obligate predatory pelagic molluscClione limacina(Pteropoda, Gymnosomata) and its prey - the sea devilLimacina helicina(Pteropoda, Thecosomata) as well as the plankton eaterMelibe leonina(Nudipleura, Nudibranchia). By using tyrosine hydroxylase-immunoreactivity (TH-ir) as a reporter, we showed that the dopaminergic system is moderately conservative among euthyneurans. Across all studied species, small numbers of dopaminergic neurons in the central ganglia contrast to significant diversification of TH-ir neurons in the peripheral nervous system, primarily representing sensory-like cells, which predominantly concentrated in the chemotactic areas and projecting afferent axons to the central nervous system. Combined with α-tubulin immunoreactivity, this study illuminates the unprecedented complexity of peripheral neural systems in gastropod molluscs, with lineage-specific diversification of sensory and modulatory functions.
Comparison of musculoskeletal robot biomechanical properties to human participants using motion study
Authors: Sander Iain L. , Sander Aidan C. , Stebbins Julie A. , Carr Andrew J. , Mouthuy Pierre-Alexis
Published: June 2024

Advanced robotic systems that replicate musculoskeletal structure and function have significant potential for a wide range of applications. Although they are proposed to be better platforms for biomedical applications, little is known about how well current musculoskeletal humanoid systems mimic the motion and force profiles of humans. This is particularly relevant to the field of tendon tissue engineering, where engineered grafts require advanced bioreactor systems that accurately replicate the kinetic and kinematic profiles experienced by the humansin vivo. A motion study was conducted comparing the kinetic and kinematic profiles produced by a musculoskeletal humanoid robot shoulder to a group of human participants completing abduction/adduction tasks. Results from the study indicate that the humanoid arm can be programed to either replicate the kinematic profile or the kinetic profile of human participants during task completion, but not both simultaneously. This study supports the use of humanoid robots for applications such as tissue engineering and highlights suggestions to further enhance the physiologic relevance of musculoskeletal humanoid robotic platforms.
GeneCOCOA: Detecting context-specific functions of individual genes using co-expression data
Authors: Zehr Simonida , Wolf Sebastian , Oellerich Thomas , Leisegang Matthias S. , Brandes Ralf P. , Schulz Marcel H. , Warwick Timothy
Published: June 2024

Extraction of meaningful biological insight from gene expression profiling often focuses on the identification of statistically enriched terms or pathways. These methods typically use gene sets as input data, and subsequently return overrepresented terms along with associated statistics describing their enrichment. This approach does not cater to analyses focused on a single gene-of-interest, particularly when the gene lacks prior functional characterization. To address this, we formulatedGeneCOCOA, a method which utilizes context-specific gene co-expression and curated functional gene sets, but focuses on a user-supplied gene-of-interest. The co-expression between the gene-of-interest and subsets of genes from functional groups (e.g. pathways, GO terms) is derived using linear regression, and resulting root-mean-square error values are compared against background values obtained from randomly selected genes. The resultingpvalues provide a statistical ranking of functional gene sets from any collection, along with their associated terms, based on their co-expression with the gene of interest in a manner specific to the context and experiment.GeneCOCOAthereby provides biological insight into both gene function, and putative regulatory mechanisms by which the expression of the gene-of-interest is controlled. Despite its relative simplicity,GeneCOCOAoutperforms similar methods in the accurate recall of known gene-disease associations.GeneCOCOAis formulated as an R package for ease-of-use, available athttps://github.com/si-ze/geneCOCOA.

Author summary

Understanding the biological functions of different genes and their respective products is a key element of modern biological research. While one can examine the relative abundance of a gene product in transcriptomics data, this alone does not provide any clue to the biological relevance of the gene. Using a type of analysis called co-expression, it is possible to identify other genes which have similar patterns of regulation to a gene-of-interest, but again, this cannot tell you what a gene does. Genes whose function has previously been studied are often assembled into groups (e.g. pathways, ontologies), which can be used to annotate gene sets of interest. However, if a gene has not yet been characterized, it will not appear in these gene set enrichment analyses. Here, we propose a new method -GeneCOCOA- which uses co-expression of a single gene with genes in functional groups to identify which functional group a gene is most similar too, resulting in a putative function for the gene, even if it has not been studied before. We testedGeneCOCOAby using it to find gene-disease links which have already been scientifically studied, and showed thatGeneCOCOAcan do this more effectively than other available methods.
Endosomal actin branching, fission and receptor recycling require FCHSD2 recruitment by MICAL-L1
Authors: Frisby Devin , Murakonda Ajay B. , Ashraf Bazella , Dhawan Kanika , Almeida-Souza Leonardo , Naslavsky Naava , Caplan Steve
Published: June 2024

Endosome fission is required for the release of carrier vesicles and the recycling of receptors to the plasma membrane. Early events in endosome budding and fission rely on actin branching to constrict the endosomal membrane, ultimately leading to nucleotide hydrolysis and enzymatic fission. However, our current understanding of this process is limited, particularly regarding the coordination between the early and late steps of endosomal fission. Here we have identified a novel interaction between the endosomal scaffolding protein, MICAL-L1, and the human homolog of theDrosophilaNervous Wreck (Nwk) protein, FCH and double SH3 domains protein 2 (FCHSD2). We demonstrate that MICAL-L1 recruits FCHSD2 to the endosomal membrane, where it is required for ARP2/3-mediated generation of branched actin, endosome fission and receptor recycling to the plasma membrane. Since MICAL-L1 first recruits FCHSD2 to the endosomal membrane, and is subsequently responsible for recruitment of the ATPase and fission protein EHD1 to endosomes, our findings support a model in which MICAL-L1 orchestrates endosomal fission by connecting between the early actin-driven and subsequent nucleotide hydrolysis steps of the process.
Hypomorphic mutation in the large subunit of replication protein A affects mutagenesis by human APOBEC cytidine deaminases in yeast
Authors: Dennen Matthew S. , Kockler Zachary W. , Roberts Steven A. , Burkholder Adam B. , Klimczak Leszek J. , Gordenin Dmitry A.
Published: June 2024

Human APOBEC single-strand (ss) specific DNA and RNA cytidine deaminases change cytosines to uracils and function in antiviral innate immunity, RNA editing, and can cause hypermutation in chromosomes. The resulting uracils can be directly replicated, resulting in C to T mutations, or uracil-DNA glycosylase can convert the uracils to abasic (AP) sites which are then fixed as C to T or C to G mutations by translesion DNA polymerases. We noticed that in yeast and in human cancers, contributions of C to T and C to G mutations depends on the origin of ssDNA mutagenized by APOBECs. Since ssDNA in eukaryotic genomes readily binds to replication protein A (RPA) we asked if RPA could affect APOBEC-induced mutation spectrum in yeast. For that purpose, we expressed human APOBECs in the wild-type yeast and in strains carrying a hypomorph mutationrfa1-t33in the large RPA subunit. We confirmed that therfa1-t33allele can facilitate mutagenesis by APOBECs. We also found that therfa1-t33mutation changed the ratio of APOBEC3A-induced T to C and T to G mutations in replicating yeast to resemble a ratio observed in long-persistent ssDNA in yeast and in cancers. We present the data suggesting that RPA may shield APOBEC formed uracils in ssDNA from Ung1, thereby facilitating C to T mutagenesis through the accurate copying of uracils by replicative DNA polymerases. Unexpectedly, we also found that for uracils shielded from Ung1 by wild-type RPA the mutagenic outcome is reduced in the presence of translesion DNA polymerase zeta.
AntiCPs-CompML: A Comprehensive Fast Track ML method to predict Anti-Corona Peptides
Authors: Bist Prem Singh , Bhattarai Sadik , Tayara Hilal , Chong Kil To
Published: June 2024

This work introduces AntiCPs-CompML, a novel Machine learning framework for the rapid identification of anti-coronavirus peptides (ACPs). ACPs, acting as viral shields, offer immense potential for COVID-19 therapeutics. However, traditional laboratory methods for ACP discovery are slow and expensive. AntiCPs-CompML addresses this challenge by utilizing three primary features for peptide sequence analysis: Amino Acid Composition (AAC), Pseudo Amino Acid Composition (PAAC), and Composition-Transition-Distribution (CTD). The framework leverages 26 different machine learning algorithms to effectively predict potential anti-coronavirus peptides. This capability allows for the analysis of vast datasets and the identification of peptides with hallmarks of effective ACPs. AntiCPs-CompML boasts unprecedented speed and cost-effectiveness, significantly accelerating the discovery process while enhancing research efficiency by filtering out less promising options. This method holds promise for developing therapeutic drugs for COVID-19 and potentially other viruses. Our model demonstrates strong performance with an F1 Score of 92.12% and a Roc AUC of 76% in the independent test dataset. Despite these promising results, we are continuously working to refine the model and explore its generalizability to unseen datasets. Future enhancements will include featurebased and oversampling augmentation strategies addressing the limitation of anti-covid peptide data for comprehensive study, along with concrete feature selection algorithms, to further refine the model’s predictive power. AntiCPs-CompML ushers in a new era of expedited anti-covid peptides discovery, accelerating the development of novel antiviral therapies.
Acclimation temperature and parasite infection drive metabolic changes in a freshwater fish at different biological scales
Authors: Levet Marie , Killen Shaun S. , Bettinazzi Stefano , Mélançon Vincent , Breton Sophie , Binning Sandra A.
Published: June 2024

Environmental stressors such as elevated temperature and parasite infection can impact individual energy metabolism. However, organismal responses to co-occurring stressors and their effects across biological scales remain unexplored despite the importance of integrative studies for accurately predicting the resilience of natural populations in changing environments.

Using wild-caught, naturally parasitized pumpkinseed sunfish, Lepomis gibbosus, we quantified changes in cellular and whole-organism metabolism in response to temperature and parasite infection. We acclimated pumpkinseeds for three weeks at 20°C, 25°C, or 30°C before measuring whole-organism oxygen uptake (ṀO2) using intermittent flow-respirometry to quantify maximal and standard metabolic rates (MMR and SMR, respectively) and aerobic scope (AS). We also measured the maximal activity of enzymes (citrate synthase (CS), respiratory complexes I + III and IV of the electron transport system, and lactate dehydrogenase (LDH)) linked with cellular bioenergetics in fish heart, brain, spleen and gills using spectrophotometry.

We found no interactions between acclimation temperatures and parasite intensity on cellular or whole-organism metabolism. However, both stressors were independently related to fish metabolism, with differing impacts across biological scales.

Whereas MMR increased with acclimation temperature, this was not mirrored by increasing SMR or decreasing AS, suggesting thermal compensation across acclimation temperatures at the whole-organism level.

On a cellular level, acclimation responses were similar across organs, with maximal activity of all enzymes decreasing with increasing acclimation temperature. However, LDH activity remained higher than aerobic enzyme activities (CS, ETS complexes I + III and IV) across acclimation temperatures and organs, especially in gills, where LDH activity drastically increased at 30°C. This may indicate a stronger reliance on anaerobic metabolism to sustain whole-organism metabolic performance.

Fish with greater trematode infection had lower MMR and AS. There were no relationships between parasite intensity and SMR nor maximal enzyme activity.

Our work shows that co-occurring stressors have distinct impacts on fish metabolism: parasites are primarily related to whole-organism metabolism while temperature impacts metabolism across biological scales. This highlights that interactions among co-occurring stressors are important for ecological realism and accurate predictions regarding population resilience to environmental changes.
B lymphocytes acquire myeloid and autoimmune phenotypes via the downregulation of lymphocyte-specific protein-1
Authors: Lee Naeun , Hong Bong-Ki , You Sungyong , Kwon Riri , Kwon Jihoon , Choi Eunbyeol , Lee Kang-Gu , Kim Yu-Mi , Li Yingjin , Kim Jayhyun , Park Young-Jun , Chung Yeonseok , Im Sin-Hyeog , Sabbagh Laurent , Cho Chul-Soo , Kim Wan-Uk
Published: June 2024

Actin-binding proteins (ABPs) have been established as important mediators of immune homeostasis, but their effects on lymphocytes are poorly understood. Here, we demonstrated that LSP1, an ABP, is a master regulator for innate immune responses in B lymphocytes.Lsp1deficiency in B cells upregulated the expression of myeloid genes, including CD11b, CD11c, and myeloperoxidase, and bestowed myeloid morphology. Strikingly,Lsp1-deficient B cells exhibited dual functions, namely, strong phagocytic activity and high antibody (Ab) production, like ‘chimera’. The PKCβ-CEBPβ pathway was found to be required for such functional chimerism. Moreover,Lsp1deficiency induced the myeloid B cell phenotype and autoantibody production in B cells and consequently accelerated the progression of experimental lupus in mice. These changes were abrogated by retinoic acid, which upregulated LSP1 expression. In lupus patients, LSP1 expression in B cells was downregulated and inversely correlated with myeloperoxidase (MPO) expression. Overall, this study reveals a new role of the ABP LSP1 in B lymphocytes and emphasizes its critical involvement in promoting autoimmune responses, particularly by generating functionally chimeric B cells.
From Genes to Nanotubes: Exploring the UV-Resistome in the Andean ExtremophileExiguobacteriumSp. S17
Authors: Galván Fátima Silvina , Alonso-Reyes Daniel Gonzalo , Albarracín Virginia Helena
Published: June 2024

Exiguobacteriumsp. S17, a polyextremophile isolated from modern stromatolites in a High-Altitude Andean Lake, exhibits a remarkable multi-resistance profile against toxic arsenic concentrations, high levels of UV radiation (UV), and elevated salinity. Here, we perform a comprehensive characterization of the mechanisms underlying the UV resistance of S17 (UV-resistome/UVres) through comparative genomics within theExiguobacteriumgenus. Additionally, we describe the morphological and ultrastructural changes in the strain when exposed to different levels of UV.

UVresinExiguobacteriumspecies ranges from 112 to 132 genes, with a median of 117. While we anticipatedExiguobacteriumsp. S17 to lead the non-HAAL UVres, it ranked eleventh with 113 genes. This larger UVresinExiguobacteriumspp. aligns with their known adaptation to extreme environments. Morphological and ultrastructural analyses using Scanning Electron Microscopy (SEM) and Transmission Electron Microscopy (TEM) demonstrated significant changes in response to UV exposure in S17 cells. We observed the formation of nanotubes (NTs), a novel finding inExiguobacteriumspp., which increased with higher UV-B doses. These NTs, confirmed to be membranous structures through sensitivity studies and SEM/TEM imaging, suggest a role in cellular communication and environmental sensing. Genomic evidence supports the presence of essential NT biogenesis genes in S17, further elucidating its adaptive capabilities.

Our study highlights the complex interplay of genetic and phenotypic adaptations enablingExiguobacteriumsp. S17 to thrive in extreme UV environments. The novel discovery of NTs under UV stress presents a new avenue for understanding bacterial survival strategies in harsh conditions.
Climatic predictors of prominent honey bee (Apis mellifera) disease agents:Varroa destructor,Melissococcus plutonius, andVairimorphaspp
Authors: McAfee Alison , Alavi-Shoushtari Niloofar , Tran Lan , Labuschagne Renata , Cunningham Morgan , Tsvetkov Nadejda , Common Julia , Higo Heather , Pernal Stephen F. , Giovenazzo Pierre , Hoover Shelley E. , Guzman-Novoa Ernesto , Currie Robert W. , Veiga Patricia Wolf , French Sarah K. , Conflitti Ida M. , Pepinelli Mateus , Borges Daniel , Walsh Elizabeth M. , Bishop Christine A. , Zayed Amro , Duffe Jason , Foster Leonard J. , Guarna M. Marta
Published: June 2024

Improving our understanding of how climate influences honey bee parasites and pathogens is critical as weather patterns continue to shift under climate change. While the prevalence of diseases vary according to regional and seasonal patterns, the influence of specific climatic predictors has rarely been formally assessed. To address this gap, we analyzed how occurrence and intensity of three prominent honey bee disease agents (Varroa destructor― hereonVarroa―Melissococcus plutonius, andVairimorphaspp.) varied according to regional, temporal, and climatic factors in honey bee colonies across five Canadian provinces. We found strong regional effects for all disease agents, with consistently highVarroaintensity and infestation probabilities and highM. plutoniusinfection probabilities in British Columbia, and year-dependent regional patterns ofVairimorphaspp. spore counts. Increasing wind speed and precipitation were linked to lowerVarroainfestation probabilities, whereas warmer temperatures were linked to higher infestation probabilities. Analysis of an independent dataset shows that these trends forVarroaare consistent within a similar date range, but temperature is the strongest climatic predictor of season-long patterns.Vairimorphaspp. intensity decreased over the course of the summer, with the lowest spore counts found at later dates when temperatures were warm.Vairimorphaspp. intensity increased with wind speed and precipitation, consistent with inclement weather limiting defecation flights. Probability ofM. plutoniusinfection generally increased across the spring and summer, and was also positively associated with inclement weather. These data contribute to building a larger dataset of honey bee disease agent occurrence that is needed in order to predict how epidemiology may change in our future climate.
Stochastic Gene Expression in Proliferating Cells: Differing Noise Intensity in Single-Cell and Population Perspectives
Authors: Zhang Zhanhao , Zabaikina Iryna , Nieto César , Vahdat Zahra , Bokes Pavol , Singh Abhyudai
Published: June 2024

Random fluctuations (noise) in gene expression can be studied from two complementary perspectives: following expression in a single cell over time or comparing expression between cells in a proliferating population at a given time. Here, we systematically investigated scenarios where both perspectives lead to different levels of noise in a given gene product. We first consider a stable protein, whose concentration is diluted by cellular growth, and the protein inhibits growth at high concentrations, establishing a positive feedback loop. For a stochastic model with molecular bursting of gene products, we analytically predict and contrast the steady-state distributions of protein concentration in both frameworks. Although positive feedback amplifies the noise in expression, this amplification is much higher in the population framework compared to following a single cell over time. We also study other processes that lead to different noise levels even in the absence of such dilution-based feedback. When considering randomness in the partitioning of molecules between daughters during mitosis, we find that in the single-cell perspective, the noise in protein concentration is independent of noise in the cell cycle duration. In contrast, partitioning noise is amplified in the population perspective by increasing randomness in cell-cycle time. Overall, our results show that the commonly used single-cell framework that does not account for proliferating cells can, in some cases, underestimate the noise in gene product levels. These results have important implications for studying the inter-cellular variation of different stress-related expression programs across cell types that are known to inhibit cellular growth.
PKA Activity-Driven Modulation of Bidirectional Long-Distance transport of Lysosomal vesicles During Synapse Maintenance
Authors: Badal Kerriann K. , Zhao Yibo , Raveendra Bindu L , Lozano-Villada Sebastian , Miller Kyle E. , Puthanveettil Sathyanarayanan V.
Published: June 2024

The bidirectional long-distance transport of organelles is crucial for cell body-synapse communication. However, the mechanisms by which this transport is modulated for synapse formation, maintenance, and plasticity are not fully understood. Here, we demonstrate through quantitative analyses that maintaining sensory neuron-motor neuron synapses in theAplysiagill-siphon withdrawal reflex is linked to a sustained reduction in the retrograde transport of lysosomal vesicles in sensory neurons. Interestingly, while mitochondrial transport in the anterograde direction increases within 12 hours of synapse formation, the reduction in lysosomal vesicle retrograde transport appears three days after synapse formation. Moreover, we find that formation of new synapses during learning induced by neuromodulatory neurotransmitter serotonin further reduces lysosomal vesicle transport within 24 hours, whereas mitochondrial transport increases in the anterograde direction within one hour of exposure. Pharmacological inhibition of several signaling pathways pinpoints PKA as a key regulator of retrograde transport of lysosomal vesicles during synapse maintenance. These results demonstrate that synapse formation leads to organelle-specific and direction specific enduring changes in long-distance transport, offering insights into the mechanisms underlying synapse maintenance and plasticity.
A small number of point mutations confer formate tolerance inShewanella oneidensis
Authors: Cross Megan C Gruenberg , Aboulnaga Elhussiny , TerAvest Michaela A
Published: June 2024

Microbial electrosynthesis (MES) is a sustainable approach to chemical production from CO2and clean electricity. However, limitations in electron transfer efficiency and gaps in understanding of electron transfer pathways in MES systems prevent full realization of this technology.Shewanella oneidensiscould serve as an MES biocatalyst because it has a well-studied, efficient transmembrane electron transfer pathway. A key first step in MES in this organism could be CO2reduction to formate. However, wild-typeS. oneidensisdoes not tolerate high levels of formate. In this work, we created and characterized formate-tolerant strains ofS. oneidensisfor further engineering and future use in MES systems through adaptive laboratory evolution. Two different point mutations in a sodium-dependent bicarbonate transporter and a DUF2721-contianing protein separately confer formate tolerance toS. oneidensis. The mutations were further evaluated to understand their role in improving formate tolerance. We also show that the wild-type and mutant versions of theS. oneidensissodium-dependent bicarbonate transporter improves formate tolerance ofZymomonas mobilis, indicating the potential for the transfer of this formate tolerance phenotype to other organisms.

Importance

Shewanella oneidensisis a bacterium with a well-studied, efficient extracellular electron transfer pathway. This capability could make this organism a suitable host for microbial electrosynthesis using CO2or formate feedstocks. However, formate is toxic toS. oneidensis, limiting the potential for its use in these systems. In this work, we evolve several strains ofS. oneidensisthat have improved formate tolerance and we investigate some mutations that confer this phenotype. The phenotype is confirmed to be attributed to several single point mutations by transferring the wild- type and mutant versions of each gene to the unmutated strain. Finally, the formate tolerance mechanism of one mutation is studied using structural modeling and expression in another host. This study therefore presents a simple method for conferring formate tolerance to bacterial hosts.
Structural basis for transcription activation through cooperative recruitment of MntR
Authors: Shi Haoyuan , Fu Yu , Kodyte Vilmante , Andreas Amelie , Sachla Ankita J. , Miller Keiki , Shrestha Ritu , Helmann John D. , Glasfeld Arthur , Ahuja Shivani
Published: June 2024

The manganese transport regulator (MntR) fromB. subtilisis a dual regulatory protein that responds to heightened Mn2+availability in the cell by both repressing the expression of uptake transporters and activating the expression of efflux proteins. Recent work indicates that, in its role as an activator, MntR binds several sites upstream of the genes encoding Mn2+exporters, leading to a cooperative response to manganese. Here, we use cryo-EM to explore the molecular basis of gene activation by MntR and report a structure of four MntR dimers bound to four 18-base pair sites across an 84-base pair regulatory region of themnePpromoter. Our structures, along with solution studies including mass photometry andin vivotranscription assays, reveal that MntR dimers employ polar and non-polar contacts to bind cooperatively to an array of low-affinity DNA-binding sites. These results reveal the molecular basis for cooperativity in the activation of manganese efflux.
Electrical and G-protein Regulation of CaV2.2 (N-type) Channels
Authors: Nilsson Michelle , Wang Kaiqian , Mínguez-Viñas Teresa , Angelini Marina , Berglund Stina , Olcese Riccardo , Pantazis Antonios
Published: June 2024

How G-proteins inhibit N-type, voltage-gated, calcium-selective channels (CaV2.2) during presynaptic inhibition is a decades-old question. G-proteins Gβγ bind to intracellular CaV2.2 regions, but the inhibition is voltage-dependent. Using the hybrid electrophysiological and optical approach voltage-clamp fluorometry, we show that Gβγ acts by selectively inhibiting a subset of the four different CaV2.2 voltage-sensor domains (VSDs I-IV). During regular “willing” gating, VSDs I and IV activation resemble pore opening, VSD III activation is hyperpolarized, and VSD II appears unresponsive to depolarization. In the presence of Gβγ, CaV2.2 gating is “reluctant”: pore opening and VSD-I activation are strongly and proportionally inhibited, VSD IV is modestly inhibited while VSD III is not. We propose that Gβγ inhibition of VSD-I and -IV underlies reluctant CaV2.2 gating and subsequent presynaptic inhibition.
A novel family of lncRNAs relate facioscapulohumeral muscular dystrophy to nucleolar architecture and protein synthesis
Authors: Salsi Valentina , Losi Francesca , Fosso Bruno , Ferrarini Marco , Pini Sara , Manfredi Marcello , Vattemi Gaetano , Mongini Tiziana , Maggi Lorenzo , Pesole Graziano , Henras Anthony K. , Kaufman Paul D. , McStay Brian , Tupler Rossella
Published: June 2024

Facioscapulohumeral muscular dystrophy (FSHD) is a hereditary myopathy linked to deletions of the tandemly arrayed D4Z4 macrosatellite repeats at human chromosome 4q35. These deletions accompany local chromatin changes and the anomalous expression of nearby transcriptsFRG2A, DBET,andD4Z4.We discovered thatFRG2Ais one member of a family of long non-coding RNAs (lncRNAs) expressed at elevated levels in skeletal muscle cells with distinct amounts detected in individual patients. We found thatFRG2AlncRNA preferentially associates with rDNA sequences and centromeres and promotes the three-dimensional association of centromeres with the nucleolar periphery in FSHD cells. Furthermore, we demonstrate that the elevatedFRG2Aexpression in cells from FSHD patients reduces rDNA transcription and global protein synthesis. Our results frame an entirely unanticipated new disease model in which elevated lncRNAs levels mediated by deletions of D4Z4 macrosatellite repeats leads to a diminished protein synthesis capacity, thereby contributing to muscle wasting.