bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatio-temporal distribution of rhinovirus types in Kenya: A retrospective analysis, 2014
Authors: Morobe John Mwita , Kamau Everlyn , Luka Martha M. , Murunga Nickson , Lewa Clement , Mutunga Martin , Bigogo Godfrey , Otieno Nancy , Nyawanda Bryan , Onyango Clayton , Nokes D. James , Agoti Charles N. , Munywoki Patrick K.
Published: April 2024

Rhinoviruses (RVs) are one of the most commonly detected viruses in people with acute respiratory illness (ARI). Despite their significant disease burden, RV epidemiology at national levels is underexplored. The circulation patterns of RV types throughout a population and the role of virus genotype in this distribution are ill-defined. We generated 803 VP4/VP2 gene sequences from rhinovirus-positive samples collected from ARI patients, including both in-patient and outpatient cases, between 1stJanuary and 31stDecember 2014 from eleven surveillance sites across Kenya and used phylogenetics to characterise virus introductions and spread. RVs were detected throughout the year, with the highest detection rates observed from January to March and June to July. We detected a total of 114 of the 169 currently classified types. Our analysis revealed numerous virus introductions into Kenya characterized by local expansion and extinction, and extensive spatial mixing of types within the country due to the widespread transmission of the virus after an introduction. This work demonstrates that in a single year, the circulation of rhinovirus in Kenya was characterized by substantial genetic diversity, multiple introductions, and extensive geographical spread.
Microvascular immunity is organ-specific and concealed in peripheral blood
Authors: Rixen Rebecca , Schütz Paula , Walter Carolin , Hüchtmann Birte , Marck Veerle Van , Heitplatz Barbara , Varghese Julian , Pavenstädt Hermann , Buscher Konrad
Published: April 2024

Blood tests are a common method for diagnosing and monitoring various health conditions. Nevertheless, the extent to which phlebotomy can offer insights into immune and organ dysfunction remains uncertain. Here, we conducted a comprehensive analysis of blood-borne leukocytes in the microvasculature of different mouse organs and compared it to peripheral blood and parenchymal samples. We observed that microvascular immune cells outnumber tissue-resident counterparts in the kidney, liver and lung. Classical monocytes and lymphocytes are diminished while nonclassical and SSC-high monocytes are enriched compared to blood. Utilizing single-cell sequencing, we identified specific cell populations up to 100-fold expanded in the kidney vasculature including macrophages, plasmacytoid dendritic cells, B cells, and innate lymphoid cells type 2. Microvascular enrichment could trigger a local phenotype switch as shown in glomerulus-restricted B cells. Peritonitis and acute kidney injury (AKI) elicited a multifaceted and systemic response of microvascular leukocytes. It involved remote organ effects, such as a 16-fold increase of leukocytes in the splenic circulation or 64-fold increase of SSC-high monocytes in the liver circulation that was not detectable in the peripheral blood or the tissue. Following full recovery from AKI, persistent and complex changes were observed predominantly in the renal vasculature, while most leukocytes in the peripheral blood had already returned to baseline levels. Collectively, our findings suggest a paradigm of organ- and disease-specific microvascular immunity that largely eludes conventional blood and tissue analysis.
A Facile LC-MS Method for Profiling Cholesterol and Cholesteryl Esters in Mammalian Cells and Tissues
Authors: Chandramouli Aakash , Kamat Siddhesh S.
Published: April 2024

Cholesterol is central to mammalian lipid metabolism and serves many critical functions in the regulation of diverse physiological processes. Dysregulation in cholesterol metabolism is causally linked to numerous human diseases, and therefore,in vivo, the concentrations and flux of cholesterol and cholesteryl esters (fatty acid esters of cholesterol) are tightly regulated. While mass spectrometry has been an analytical method of choice for detecting cholesterol and cholesteryl esters in biological samples, the hydrophobicity, chemically inert nature and poor ionization of these neutral lipids has often proved a challenge in developing lipidomics compatible liquid chromatography-mass spectrometry (LC-MS) methods to study them. To overcome this problem, here, we report a reverse-phase LC-MS method that is compatible with existing high-throughput lipidomics strategies, and capable of identifying and quantifying cholesterol and cholesteryl esters from mammalian cells and tissues. Using this sensitive yet robust LC-MS method, we profiled different mammalian cell lines and tissues, and provide a comprehensive picture of cholesterol and cholesteryl esters content in them. Specifically, amongst cholesteryl esters, we find that mammalian cells and tissues largely possess monounsaturated and polyunsaturated variants. Taken together, our lipidomics compatible LC-MS method to study this lipid class opens new avenues in understanding systemic and tissue-level cholesterol metabolism under various physiological conditions.

Abstract Figure

TOC Graphic
XOL-1 regulates developmental timing by modulating the H3K9 landscape inC. elegansearly embryos
Authors: Jash Eshna , Azhar Anati Alyaa , Mendoza Hector , Tan Zoey M. , Escher Halle Nicole , Kaufman Dalia S. , Csankovszki Györgyi
Published: April 2024

Sex determination in the nematodeC. elegansis controlled by the master regulator XOL-1 during embryogenesis. Expression ofxol-1is dependent on the ratio of X chromosomes and autosomes, which differs between XX hermaphrodites and XO males. In males,xol-1is highly expressed and in hermaphrodites,xol-1is expressed at very low levels. XOL-1 activity is known to be critical for the proper development ofC. elegansmales, but its low expression was considered to be of minimal importance in the development of hermaphrodite embryos. Our study reveals that XOL-1 plays an important role as a regulator of developmental timing during hermaphrodite embryogenesis. Using a combination of imaging and bioinformatics techniques, we found that hermaphrodite embryos have an accelerated rate of cell division, as well as a more developmentally advanced transcriptional program whenxol-1is lost. Further analyses reveal that XOL-1 is responsible for regulating the timing of initiation of dosage compensation on the X chromosomes, and the appropriate expression of sex-biased transcriptional programs in hermaphrodites. We found thatxol-1mutant embryos overexpress the H3K9 methyltransferase MET-2 and have an altered H3K9me landscape. Some of these effects of the loss ofxol-1gene were reversed by the loss ofmet-2. These findings demonstrate that XOL-1 plays an important role as a developmental regulator in embryos of both sexes, and that MET-2 acts as a downstream effector of XOL-1 activity in hermaphrodites.

Author Summary

Various organisms have differing ways of determining, at a molecular level, what the sex of a developing embryo is supposed to be. The two sexes in the nematodeC. elegans, hermaphrodite and male, have different numbers of X chromosomes. Hermaphrodites have two X chromosomes and males only have one. This mismatch raises an additional problem as hermaphrodites will have twice the amount of genes expressed from the X compared to males. This is solved by a process called dosage compensation, which equalizes gene expression between the sexes. A molecular sensor called XOL-1 detects the number of X chromosomes in an embryo and kick-starts the process of proper sexual development and/or dosage compensation. XOL-1 was known to be very important for activating male development but was believed to not have any role in the development of the hermaphrodite sex. We show that XOL-1 has some crucial roles in hermaphrodite embryos in controlling the rate of development of the embryo, and regulating the timing of dosage compensation. We also show that MET-2, a protein that deposits repressive methyl marks on DNA-bound histone proteins, is involved in this process.
HIV-1 Vpr causes separate cell cycle arrests in G2 and M that activate alternative DNA damage pathways
Authors: Hall Ross , Ahern Lucy M. , Yap Melvyn W. , Tsai Ming-Han C. , Boucherit Virginie C. , Takaki Tohru , Boulton Simon J. , Bishop Kate N.
Published: April 2024

Vpr is a conserved primate lentiviral accessory protein that induces cell cycle arrest in G2. The precise mechanism of this arrest and its benefit to viral replication is unknown. Here, we show that in addition to G2 arrest, Vpr from HIV-1/SIVcpz and HIV-2 lineages separately induce mitotic arrest through the spindle assembly checkpoint, in contrast to other Vpr proteins that only cause G2 arrest. The G2 arrest was mediated solely by ATR (ataxia telangiectasia and Rad3 related) and this activity caused elevated cellular dNTP levels. The mitotic arrest required ATM (ataxia-telangiectasia mutated) as well as ATR activity and resulted from the formation of HIV-1 Vpr-induced ultra-fine anaphase bridges. Moreover, ectopic expression of the DNA structure-specific endonuclease, MUS81, prevented mitotic but not G2 arrest. Importantly, virion-incorporated Vpr was sufficient to induce cellular changes within 12h post-infection, implying that these events benefit the early stages of HIV infection.

Author Summary

Vpr is an accessory protein found in primate lentiviruses. Like other retroviral accessory proteins, it is not absolutely required for viral replication but is thought to overcome a cellular factor that negatively regulates infection. The most well-documented effect of Vpr expression is cell cycle arrest in G2. This has been linked to activation of the DNA damage response (DDR) pathway but there are conflicting reports in the literature as to the mechanism behind this. Here, we show that Vpr from some lentiviruses, in fact, cause two separate cell cycle blocks, in G2 and M, that require different DDR pathways. Other Vpr proteins only cause arrest in G2. Furthermore, we show that degradation of one reported target of Vpr, MUS81, is specifically linked to M but not G2 arrest. This indicates that not all Vpr functions are conserved and helps explain contradictory published results. Additionally, we found that virion-incorporated Vpr protein was able to induce cellular changes, including elevated dNTP levels, within 12 hours of infection suggesting that these events enhance early HIV-1 replication events.
Cytosolic factors controlling PASTA kinase-dependent ReoM phosphorylation
Authors: Rothe Patricia , Wamp Sabrina , Rosemeyer Lisa , Rismondo Jeanine , Doellinger Joerg , Gründling Angelika , Halbedel Sven
Published: April 2024

Bacteria adapt the biosynthesis of their envelopes to specific growth conditions and prevailing stress factors. Peptidoglycan (PG) is the major component of the cell wall in Gram-positive bacteria, where PASTA kinases play a central role in PG biosynthesis regulation. Despite their importance for growth, cell division and antibiotic resistance, the mechanisms of PASTA kinase activation are not fully understood. ReoM, a recently discovered cytosolic phosphoprotein, is one of the main substrates of the PASTA kinase PrkA in the Gram-positive human pathogenListeria monocytogenes. Depending on its phosphorylation, ReoM controls proteolytic stability of MurA, the first enzyme in the PG biosynthesis pathway. The late cell division protein GpsB has been implicated in PASTA kinase signalling. Consistently, we show thatL. monocytogenes prkAandgpsBmutants phenocopied each other. Analysis ofin vivoReoM phosphorylation confirmed GpsB as an activator of PrkA leading to the description of structural features in GpsB that are important for kinase activation. We further show that ReoM phosphorylation is growth-phase dependent and that this kinetic is reliant on the protein phosphatase PrpC. ReoM phosphorylation was inhibited in mutants with defects in MurA degradation, leading to the discovery that artificial MurA overexpression prevented ReoM phosphorylation. Overexpressed MurA must adopt its substrate-bound closed conformation and interact with ReoM to exert this effect, but the extracellular PASTA domains of PrkA or MurJ flippases where not required. Our results indicate that intracellular signals control ReoM phosphorylation and extend current models describing the mechanisms of PASTA kinase activation.
Extracellular electrophysiology on clonal human β-cell spheroids
Authors: Puginier Emilie , Fischer Karen Leal , Gaitan Julien , Lallouet Marie , Scotti Pier-Arnaldo , Raoux Matthieu , Lang Jochen
Published: April 2024

Pancreatic islets are important in nutrient homeostasis and improved cellular models of clonal origin may very useful especially in view of relatively scarce primary material. Close 3D contact and coupling between β-cells are a hallmark of physiological function improving signal/noise ratios. Extracellular electrophysiology using micro-electrode arrays (MEA) is technically far more accessible than single cell patch clamp, enables dynamic monitoring of electrical activity in 3D organoids and recorded multicellular slow potentials (SP) provide unbiased insight in cell-cell coupling. We have therefore asked whether 3D spheroids enhance clonal β-cell function such as electrical activity and hormone secretion using human EndoC-βH1, EndoC-βH5 and rodent INS-1 cells. EndoC-βH1 spheroids exhibited increased signals in terms of SP frequency and especially amplitude as compared to monolayers and even single cell action potentials (AP) were quantifiable. Enhanced electrical signature in spheroids was accompanied by an increase in the glucose stimulated insulin secretion index. EndoC-βH5 monolayers and spheroids gave electrophysiological profiles similar to EndoC-βH1, except for a higher electrical activity at 3 mM glucose, and exhibited moreover a biphasic profile. Again, physiological concentrations of GLP-1 increased AP frequency. Spheroids also exhibited a higher secretion index. INS-1 cells did not form stable spheroids, but overexpression of connexin 36, required for cell-cell coupling, increased glucose responsiveness, dampened basal activity and consequently augmented the stimulation index. In conclusion, spheroid formation enhances physiological function of the human clonal β-cell lines and these models may provide surrogates for primary islets in extracellular electrophysiology.
Evaluating the efficacy of protein quantification methods on membrane proteins
Authors: Löptien Jana , Vesting Sidney , Dobler Susanne , Mohammadi Shabnam
Published: April 2024

Protein quantification is an important tool for a wide range of biological applications. The most common broadscale methods include the Lowry, bicinchoninic acid (BCA), and Coomassie Bradford assays. Despite their wide applicability, the mechanisms of action imply that these methods may not be ideal for large transmembrane proteins due to the proteins’ integration in the plasma membrane. Here, we investigate this problem by assessing the efficacy and applicability of these three common protein quantification methods on a candidate transmembrane protein – the Na,K-ATPase (NKA). We compared these methods to an ELISA, which we newly developed and describe here for the quantification of NKA. The use of a relative standard curve allows this ELISA to be easily adapted to other proteins and across the animal kingdom. Our results revealed that the three conventional methods significantly underestimate the concentration of NKA compared to the ELISA. Further, by applying the protein concentrations determined by the different methods to in vitro assays, we found that variation in the resulting data was consistently low when the assay reactions were prepared based on concentrations determined from the ELISA. Thus, when target protein concentrations vary across samples, the conventional quantification methods cannot produce reliable results in downstream applications. In contrast, the ELISA we describe here consistently provides robust results.
Antibody-dependent Intracellular neutralisation by TRIM21 is potentiated by HOIP and linear ubiquitin chains
Authors: Green Christopher , Winklhofer Konstanze F. , Fletcher Adam J. , James Leo C. , Skidmore John , Duce James , McEwan William A.
Published: April 2024

Antibody-dependent intracellular neutralisation (ADIN) promotes the rapid proteasomal degradation of viruses and other large substrates in the cytosol. It is dependent on detection of intracellular virus-bound antibodies by the Fc receptor and E3 ligase TRIM21, followed by disassembly of the virus by the unfoldase VCP/p97. It is not known how VCP is recruited to TRIM21. We performed a limited siRNA knock-down screen of known VCP adaptors to determine their involvement in ADIN. Knock-down of HOIP, the only ubiquitin E3 ligase capable of generating linear ubiquitin chains, resulted in impaired virus neutralisation. HOIPIN-8, a HOIP inhibitor, showed concentration-dependent reduction in virus neutralisation. We found that the activity of HOIP in ADIN is dependent on its ubiquitin binding domains and its PUB domain which recruits VCP. Knock-down of OTULIN, the only deubiquitinating enzyme that exclusively cleaves linear ubiquitin chains, potentiated neutralisation of the virus. Our results expand the role of HOIP and linear ubiquitin chains in proteostasis.
Regulation of fatty acid delivery to metastases by tumor endothelium
Authors: Edwards Deanna N. , Wang Shan , Song Wenqiang , Kim Laura C. , Ngwa Verra M. , Hwang Yoonha , Ess Kevin C. , Boothby Mark R. , Chen Jin
Published: April 2024

Tumor metastasis, the main cause of death in cancer patients, requires outgrowth of tumor cells after their dissemination and residence in microscopic niches. Nutrient sufficiency is a determinant of such outgrowth1. Fatty acids (FA) can be metabolized by cancer cells for their energetic and anabolic needs but impair the cytotoxicity of T cells in the tumor microenvironment (TME)2, 3, thereby supporting metastatic progression. However, despite the important role of FA in metastatic outgrowth, the regulation of intratumoral FA is poorly understood. In this report, we show that tumor endothelium actively promotes tumor growth and restricts anti-tumor cytolysis by transferring FA into developing metastatic tumors. This process uses transendothelial fatty acid transport via endosome cargo trafficking in a mechanism that requires mTORC1 activity. Thus, tumor burden was significantly reduced upon endothelial-specific targeted deletion of Raptor, a unique component of the mTORC1 complex (RptorECKO). In vivo trafficking of a fluorescent palmitic acid analog to tumor cells and T cells was reduced in RptorECKOlung metastatic tumors, which correlated with improved markers of T cell cytotoxicity. Combination of anti-PD1 with RAD001/everolimus, at a low dose that selectively inhibits mTORC1 in endothelial cells4, impaired FA uptake in T cells and reduced metastatic disease, corresponding to improved anti-tumor immunity. These findings describe a novel mechanism of transendothelial fatty acid transfer into the TME during metastatic outgrowth and highlight a target for future development of therapeutic strategies.
Enhanced delivery of protein therapeutics with a diphtheria toxin-like platform that evades pre-existing neutralizing immunity
Authors: Gill Shivneet K. , Sugiman-Marangos Seiji N. , Beilhartz Greg L. , Mei Elizabeth , Taipale Mikko , Melnyk Roman A.
Published: April 2024

Targeted intracellular delivery of therapeutic peptides and proteins remains an important but unresolved goal in biotechnology. A promising approach is to engineer bacterial exotoxins that deliver their cytotoxic enzymes into cells and can be engineered to target cancer cells as is the case with immunotoxins. The well-studied diphtheria toxin translocation domain is ideally suited as a delivery platform as it has been shown to be capable of delivering a wide range of macromolecular cargo. Widespread deployment of DT-based therapeutics in humans, however, is complicated by the prevalence of pre-existing anti-DT antibodies from childhood vaccinations that reduce the exposure, efficacy and safety of this important class of protein drugs. Thus, there is a great need for delivery platforms with no pre-existing immunity in humans. Here, we describe the discovery and characterization of a distant diphtheria toxin homolog from the ancient reptile pathogenAustwickia chelonaethat we have named Chelona Toxin (CT). We show that CT is comparable to DT structure and function in all respects except that it is not recognized by pre-existing anti-DT antibodies present in human sera. Moreover, we demonstrate that the CT translocase is superior to the DT translocase at delivering therapeutic protein cargo into target cells. These findings highlight CT as a potentially class-enabling new chassis for developing safer and more efficacious immunotoxins and intracellular protein delivery platforms for cancer therapy.
Does bumblebee preference of continuous over interrupted strings in string-pulling tasks indicate means-end comprehension?
Authors: Wen Chao , Lu Yuyi , Solvi Cwyn , Dong Shunping , Wang Cai , Wen Xiujun , Xiao Haijun , Dong Shikui , Wen Junbao , Peng Fei , Chittka Lars
Published: April 2024

Bumblebees (Bombus terrestris) have been shown to engage in string-pulling behavior to access rewards. The objective of this study was to elucidate whether bumblebees display means-end comprehension in a string-pulling task. We presented bumblebees with two options: one where a string is connected to an artificial flower containing a reward and the other presenting an interrupted string. Bumblebees displayed a consistent preference for pulling connected strings over interrupted ones after training with a stepwise pulling technique. When exposed to novel string colors, bees continued to exhibit a bias towards pulling the connected string. This suggests that bumblebees engage in featural generalization of the visual display of the string connected to the flower in this task. If the view of the string connected to the flower was restricted during the training phase, the proportion of bumblebees choosing the connected strings significantly decreased. Similarly, when the bumblebees were confronted with coiled connected strings during the testing phase, they failed to identify and reject the interrupted strings. This finding underscores the significance of visual consistency in enabling the bumblebees to perform the task successfully. Our results suggest that bumblebees’ ability to distinguish between continuous strings and interrupted strings relies on a combination of image matching and associative learning, rather than means-end understanding. These insights contribute to a deeper understanding of the cognitive processes employed by bumblebees when tackling complex spatial tasks.
Bridging Organ Transcriptomics for Advancing Multiple Organ Toxicity Assessment with a Generative AI Approach
Authors: Li Ting , Chen Xi , Tong Weida
Published: April 2024

Translational research in toxicology has significantly benefited from transcriptomic profiling, particularly in drug safety. However, its application has predominantly focused on limited organs, notably the liver, due to resource constraints. This paper presents TransTox, an innovative AI model using a Generative Adversarial Network (GAN) method to facilitate bidirectional translation of transcriptomic profiles between the liver and kidney under drug treatment. TransTox demonstrates robust performance, validated across independent datasets and laboratories. Firstly, the concordance between real experimental data and synthetic data generated by TransTox was demonstrated in characterizing toxicity mechanisms compared to real experimental settings. Secondly, TransTox proved valuable in gene expression predictive models, where synthetic data could be used to develop gene expression predictive models or serve as “digital twins” for diagnostic applications. The TransTox approach holds potential for multi-organ toxicity assessment with AI and advancing the field of precision toxicology.
Cryo-EM Structure of AAV2 Rep68 bound to integration site AAVS1: Insights into the mechanism of DNA melting
Authors: Jaiswal R. , Santosh V. , Braud B , Washington A. , Escalante Carlos R.
Published: April 2024

The Rep68 protein from Adeno-Associated Virus (AAV) is a multifunctional SF3 helicase that performs most of the DNA transactions required for the viral life cycle. During AAV DNA replication, Rep68 assembles at the origin and catalyzes the DNA melting and nicking reactions during the hairpin rolling replication process to complete the second-strand synthesis of the AAV genome. Here, we report the Cryo-EM structures of Rep68 bound to double-stranded DNA (dsDNA) containing the sequence of the AAVS1 integration site in different nucleotide-bound states. In the apo state, Rep68 forms a heptameric complex around DNA, with three Origin Binding Domains (OBDs) bound to the Rep Binding Site (RBS) sequence and three other OBDs forming transient dimers with them. The AAA+domains form an open ring with no interactions between subunits and with DNA. We hypothesize the heptameric quaternary structure is necessary to load onto dsDNA. In the ATPγS-bound state, a subset of three subunits binds the nucleotide, undergoing a large conformational change, inducing the formation of intersubunit interactions interaction and interaction with three consecutive DNA phosphate groups. Moreover, the induced conformational change positions three phenylalanine residues to come in close contact with the DNA backbone, producing a distortion in the DNA. We propose that the phenylalanine residues can potentially act as a hydrophobic wedge in the DNA melting process.
Electric charge controls plasmodesma conductivity
Authors: Howell Alexander H. , Christensen Anneline H. , James Vincent , Vasina Viktoriya V. , Jensen Kaare H. , Foley James , Evans James E. , Stone Howard A. , Peters Winfried S. , Knoblauch Michael
Published: April 2024

While plant cells are enclosed by rigid cell walls that counteract intracellular hydrostatic pressure1, their plasma membrane, cytosol, and endoplasmic reticulum (ER) remain connected through plasmodesmata, nanoscopic cell wall pores2. Plasmodesmal cell-to-cell transport occurs in the cytosolic sleeve between the plasma membrane and the ER membrane3–5, and is generally thought to be limited by the size of the moving particle alone6. Given that biological membranes carry negative electric surface charges7–9, this steric notion conflicts with physical theory of ion diffusion in nanometer-sized pores with charged walls10. Quantifying the movements of differently sized and charged fluorescent dyes inTradescantiastamen hairs, we found that anionic fluorophores of up to 1 kDa traversed plasmodesmata whereas much smaller cationic ones did not. While this agrees with theoretical expectations of different size exclusion limits for cations and anions, it questions current dogma concerning plasmodesma function and also structure, as it implies positively rather than negatively charged surfaces within plasmodesmal pores. Our findings call for re-evaluations of current models of symplasmic transport, especially of charged molecules like the phytohormone auxin (indole-acetic acid) and certain amino acids.
Genome-wide identification of MAPK gene family and comparative transcriptional profiling among different organ and stress response in two jute species
Authors: Ahmed Borhan , Tabassum Anika , Bashar Kazi Khayrul , Ullah MW , Aktar Nasima , Roni MS , Hasan Fakhrul , Alam Mobashwer
Published: April 2024

Mitogen activated protein kinase (MAPK) cascade is evolutionary conserved universal signal transduction module that plays central role in the growth and development of plants as well as in biotic and abiotic stress response. Although, MAPKs have been investigated in several model plants, no systematic analysis has been conducted in jute species (Corchorus olitoriusandC. capsularis) even though, their genome sequencing has been completed. In the present study we identified 11 and 12 putative MAPKs inC. olitoriusandC. capsularisusing their genomic database, respectively. Here we provide a comprehensive bioinformatics analysis of the MAPK family from bothCorchorusspecies including identification and nomenclature, chromosomal localization, sequence alignment, domain and Motif, gene structure, phylogenetic, functional analysis and investigation of expression analysis in response to abiotic stress and fiber cell development. The phylogenetic analysis of predicted MAPKs were clustered into four different clades and assigned with specific name based on their orthology based evolutionary relationship withArabidopsis. Structural analysis of the MAPK genes revealed that there was a large variation among the exon number in bothCorchorusspecies ranged from 2 to 11 but genes with the same clade had similar exon-intron structure. The sequence alignment analysis concede the presence of several conserved domain and motif including crucial signature phosphorylation motif TDY or TEY where first one is harbor in group D sequence and rest of the sequence contain TEY motif in their activation loop. Transcriptome analysis against salinity, drought along with fiber cell formation showed that MAPK4-1 genes in both jute genome highly expressed and may play a potential role in jute on adverse condition as well as jute fiber formation. These findings yielded new insights into the transcriptional control of MAPK gene expression, provide an improved understanding of abiotic stress responses and signaling transduction in jute, that lead to potential applications in the genetic improvement of jute cultivars.
Investigating the Structural Impact and Conformational Dynamics of a Sequence Variant (c.242G>A) inTMIEGene Provoking Usher Syndrome
Authors: Ishaq Saqib , Usmani Shabir Ahmad , Habib Obaid , Tahir Raheel , Aziz Abdul , Rahman Siddiq Ur , Huiying Liang
Published: April 2024

Usher syndrome (USH) is a retinal autosomal recessive genetic disorder, characterized by congenital severe-to-profound sensorineural hearing loss, retinitis pigmentosa (RP), and rarely vestibular dysfunction. A transmembrane inner ear gene TMIE causing autosomal recessive usher syndrome hearing loss, which may open up interesting perspectives into the function of this protein in inner ear. This disease is linked with mutations in TMIE gene. In this study delineates the pathogenic association, miss-fold aggregation, and conformational paradigm of a missense variant (c.242G>A) resulting into (p.Arg81His) in TMIE gene segregating usher syndrome through a molecular dynamics simulations approach. The transmembrane inner ear expressed protein assumes a critical role as its helices actively engage in binding with specific target DNA base pairs. The alteration observed in the mutant protein, characterized by an outward repositioning of the proximal helical portion, which is attributed to the absence of preceding beta-hairpins in the C-terminal region. This structural modification results in the loss of hydrogen bonds, exposure of hydrophobic residues to the solvent, and a consequential transformation of helices into loops, ultimately leading to functional impairment in the TMIE protein. These notable modifications in the stability and conformation of the mutant protein were verified through essential dynamics analysis, revealing that a point mutation induces distinct overall motions and correlations between proteins, ultimately resulting in usher syndrome. The current study provides insilico evidences of Usher syndrome hearing loss disease as protein folding disorder. The energy calculation also revealed that there is a difference of −251.211Kj/mol which also indicates that the SNP has significantly decreased the stability of protein consequently folding into Usher syndrome. This study contributes molecular insights into the structural correlation between the TMIE protein and usher syndrome. The docking analysis highlight various interaction between wild and mutant structure emphasizing key residues involved in hydrogen and hydrophobic interaction.
APOBEC shapes tumor evolution and age at onset of lung cancer in smokers
Authors: Zhang Tongwu , Sang Jian , Hoang Phuc H. , Zhao Wei , Rosenbaum Jennifer , Johnson Kofi Ennu , Klimczak Leszek J. , McElderry John , Klein Alyssa , Wirth Christopher , Bergstrom Erik N. , Díaz-Gay Marcos , Vangara Raviteja , Colon-Matos Frank , Hutchinson Amy , Lawrence Scott M. , Cole Nathan , Zhu Bin , Przytycka Teresa M. , Shi Jianxin , Caporaso Neil E. , Homer Robert , Pesatori Angela C. , Consonni Dario , Imielinski Marcin , Chanock Stephen J. , Wedge David C. , Gordenin Dmitry A. , Alexandrov Ludmil B. , Harris Reuben S. , Landi Maria Teresa
Published: April 2024

APOBEC enzymes are part of the innate immunity and are responsible for restricting viruses and retroelements by deaminating cytosine residues1,2. Most solid tumors harbor different levels of somatic mutations attributed to the off-target activities of APOBEC3A (A3A) and/or APOBEC3B (A3B)3–6. However, how APOBEC3A/B enzymes shape the tumor evolution in the presence of exogenous mutagenic processes is largely unknown. Here, by combining deep whole-genome sequencing with multi-omics profiling of 309 lung cancers from smokers with detailed tobacco smoking information, we identify two subtypes defined by low (LAS) and high (HAS) APOBEC mutagenesis. LAS are enriched for A3B-like mutagenesis andKRASmutations, whereas HAS for A3A-like mutagenesis andTP53mutations. UnlikeAPOBEC3A,APOBEC3Bexpression is strongly associated with an upregulation of the base excision repair pathway. Hypermutation by unrepaired A3A and tobacco smoking mutagenesis combined withTP53-induced genomic instability can trigger senescence7, apoptosis8, and cell regeneration9, as indicated by high expression of pulmonary healing signaling pathway, stemness markers and distal cell-of-origin in HAS. The expected association of tobacco smoking variables (e.g., time to first cigarette) with genomic/epigenomic changes are not observed in HAS, a plausible consequence of frequent cell senescence or apoptosis. HAS have more neoantigens, slower clonal expansion, and older age at onset compared to LAS, particularly in heavy smokers, consistent with high proportions of newly generated, unmutated cells and frequent immuno-editing. These findings show how heterogeneity in mutational burden across co-occurring mutational processes and cell types contributes to tumor development, with important clinical implications.
Metric Mirages in Cell Embeddings
Authors: Wang Hanchen , Leskovec Jure , Regev Aviv
Published: April 2024

Although biological studies increasingly rely on embeddings of single cell profiles, the quality of these embeddings can be challenging to assess. Such evaluations are especially important for avoiding misleading biological interpretations, assessing the accuracy of integration methods, and establishing the zero-shot capabilities of foundational models. Here, we posit that current evaluation metrics can be highly misleading. We show this by training a three-layer perceptron, Islander , which outperforms all 11 leading embedding methods on a diverse set of cell atlases, but in fact distorts biological structures, limiting its utility for biological discovery. We then present a metric, scGraph, to flag such distortions. Our work should help learn more robust and reliable cell embeddings.
Functional septate junctions between cyst cells are required for survival of transit amplifying male germ cells expressing Bag of marbles
Authors: Berry Cameron W. , Fuller Margaret T.
Published: April 2024

In adult stem cell lineages, the cellular microenvironment plays essential roles to ensure the proper balance of self-renewal, differentiation and regulated elimination of differentiating cells. Although regulated death of progenitor cells undergoing proliferation or early differentiation is a feature of many tissues, mechanisms that initiate this pruning remain unexplored, particularly in the male germline, where up to 30% of the germline is eliminated before the meiotic divisions. We conducted a targeted screen to identify functional regulators required in somatic support cells for survival or differentiation at early steps in the male germ line stem cell lineage. Cell type-specific knockdown in cyst cells uncovered novel roles of genes in germline stem cell differentiation, including a previously unappreciated role of the Septate Junction (SJ) in preventing cell death of differentiating germline progenitors. Loss of the SJ in the somatic cyst cells resulted in elimination of transit-amplifying spermatogonia by the 8-cell stage. Germ cell death was spared in males mutant for the differentiation factorbamindicating that intact barriers surrounding transit amplifying progenitors are required to ensure germline survival once differentiation has initiated.
DNA-free and genotype-independent CRISPR/Cas9 system in soybean
Authors: Kuwabara Chikako , Miki Ryuji , Maruyama Nobuyuki , Yasui Masanori , Hamada Haruyasu , Nagira Yozo , Imai Ryozo , Taoka Naoaki , Yamada Tetsuya
Published: April 2024

The CRISPR/Cas9 system has revolutionized the field of plant genetic engineering. Here we report a smart genome editing system of soybean by using iPB-RNP method without introducing foreign DNA and requiring traditional tissue culture processes such as embryogenesis and organogenesis. Shoot apical meristem (SAM) of embryonic axes was used the target tissue for genome editing, because the SAM in soybean mature seeds has stem cells and specific cell layer developing germ cells during reproductive growth stage. In the iPB-RNP method, the complex of ribonucleoprotein (RNP) and Cas9 protein was directly delivered into SAM stem cells via particle bombardment and genome-edited plants were generated from these SAMs. Soybean allergenic geneGly m Bd 30K, which we previously generated genome-editing soybean by usingAgrobacterium-mediated transformation and particle bombardment in our previous studies, was targeted in this study. Many E0(the first generation of genome-edited) plants in this experiment harbored mutant alleles at the targeted locus. Editing frequency of inducing mutations transmissible to the E1generation was approximately 0.4 to 4.6 % of all E0plants utilized in various soybean varieties. Furthermore, Gly m Bd 30K protein in mature seeds was not detected by western blot analysis due to flame-sift mutations. Our results offer a practical approach for both plant regeneration- and DNA-free genome editing achieved by delivering RNP into the SAM of dicotyledonous plants.
Kidney toxicology of a novel compound Lithium Bis(trifluoromethanesulfonyl)imide (LiTFSI, ie. HQ-115) used in energy applications: an Epigenetic evaluation
Authors: Sands Mia , Zhang Xing , Irudayaraj Joseph
Published: April 2024

Exposure to emerging energy-based environmental contaminants such as lithium bis(trifluoromethanesulfonyl)imide (LiTFSI), more commonly known as HQ-115, poses a significant threat to human health, yet its impact on kidney function and epigenetic regulation remains poorly understood. Here, we investigated the effects of LiTFSI exposure on kidney-related biochemical parameters, renal injuries, and epigenetic alterations in male CD-1 mice under both 14-day and 30-day exposure durations. Our study revealed that LiTFSI exposure led to changes in kidney-related biochemical indicators, notably affecting serum bicarbonate levels, while relative kidney weight remained unaffected. Histological analysis unveiled tubule dilation, inflammation, and loss of kidney structure in LiTFSI-exposed mice, alongside dysregulated expression of genes associated with inflammation, renal function, and uric acid metabolism. Epigenetic analysis further identified widespread DNA methylation changes in the two exposure regimes. Functional analysis revealed that differentially methylated regions are implicated in cell apoptosis and cancer-related pathways and are enriched with development-related transcription factor binding motifs, suggesting a potential mechanism of action that can lead to kidney injury. These findings underscore the intricate interplay between environmental exposures, epigenetic modulation, and kidney health, emphasizing the need for additional research to unravel precise mechanisms that can help in the development of targeted interventions to mitigate the adverse effects of LiTFSI exposure on human health.

SYNOPSIS

LiTFSI (HQ-115), an emerging environmental contaminant, impacts kidney health in male CD-1 mice by altering biochemical indicators, to result in renal injuries, and inducing epigenetic changes, highlighting environmental health concerns.
The flavivirus protein NS4B recruits thecis-Golgi protein ACBD3 to modify ER-Golgi trafficking for virion release
Authors: Yau Wai-Lok , Peters Marie B. A. , Sorin Marie , Rönfeldt Sebastian , Pulkkinen Lauri I. A. , Carlson Lars-Anders , Överby Anna K. , Lundmark Richard
Published: April 2024

Flavivirus infection involves extensive remodeling of the endoplasmic reticulum (ER), which is key to both the replication of the viral RNA genome as well as the assembly and release of new virions. Yet, little is known about how viral proteins and host factors cooperatively facilitate such a vast transformation of the ER, and how this influences the different steps of the viral life cycle. In this study, we screened for host proteins that interact with the tick-borne encephalitis virus (TBEV) protein NS4B and found that the top candidates were coupled to trafficking between ER exit sites (ERES) and the Golgi. We characterized the role of ACBD3, one of the identified proteins, in flavivirus infection and show that it interacts with NS4B to promote infection across multiple flavivirus species. Using ACBD3 knockout cells, we found that the depletion of ACBD3 inhibited TBEV replication by preventing the trafficking of virions from the cell. We found that ACBD3 promotes flavivirus infection via a different mechanism than its previously described role in picornavirus infection. ACBD3 was enriched at modified ERES-Golgi contact sites to support virus replication. Therefore, we propose that ACBD3 promotes flavivirus replication by modifying the trafficking between the ERES and the Golgi to enable the release of new virions.

Author summary

Flaviviruses including dengue virus and tick-borne encephalitis virus are group of viruses that widely affecting the health of human. During infection, flavivirus particles enter host cells and transform the endoplasmic reticulum (ER), which is the main structure for protein synthesis in cells. New flaviviral particles are produced in the transformed ER and then released to the Golgi apparatus, which is the main structure for protein transport in cells. It is unclear how the particles are transported from the ER to Golgi. Here we screened the factors that interact with viral proteins and identified a Golgi protein called ACBD3 as an important factor supporting flavivirus particles release from ER to Golgi. We showed that ACBD3 is recruited by flavivirus to a modified connection between ER and Golgi for viral particles release from the ER. Our work provides new insights into the fine coordination of virus replication and viral particles transport between organelles inside host cells.
Superfast quarks in deuterium
Authors: Kim Dmitriy N. , Miller Gerald A.
Published: April 2024

An extension to our previous study on nuclear parton distribution functions (nPDFs) [Kim and Miller, ] using light-front holographic quantum chromodynamics (LFHQCD) [Brodsky, de Teramond, Dosch, and Erlich, ] is presented. We apply the effects of nucleon motion inside the nucleus (Fermi motion/smearing) to deuterium, extending our deuterium nPDFs to the , x>1, region [Frankfurt and Strikman, ] where we estimate our results to be reasonable up to x≈1.7. We utilize four different deuteron wave functions (AV18, NijmI, NijmII, Nijm93). We find that our model, with no additional new parameters, shows very good agreement with deuterium EMC ratio data obtained from the BONuS experiment [Fenker , ; Baillie (CLAS Collaboration), ; ; Tkachenko (CLAS Collaboration), ; ; Griffioen , ]. Looking beyond conventional nuclear physics, and in anticipation of 12 GeV experiments at Jefferson Lab, we use a LFHQCD ansatz to predict the contributions of an exotic six-quark state to the deuteron F2 structure function, F2D, in the superfast region. We find that the effects of using other potentials are about the same magnitude as six-quark effects—both have small effects in x<1, but have significant contributions at x>1.

Published by the American Physical Society
2024
Coherent Control of Bloch Oscillations in a Superconducting Circuit
Authors: Song Pengtao , Xiang Zhongcheng , Zhang Yu-Xiang , Wang Zhan , Guo Xueyi , Ruan Xinhui , Song Xiaohui , Xu Kai , Gao Yvonne Y. , Fan Heng , Zheng Dongning
Published: April 2024

Bloch oscillations (BOs) are oscillations of electrons under external constant forces in a lattice, revealing the wavelike behavior of electrons. BOs lead to the localization of the wave packet that is called Wannier-Stark localization (WSL), resulting in the inhibition of conductivity. We simulate BOs experimentally in a one-dimensional superconducting circuit with nine qubits. The nine qubits form a one-dimensional lattice and an electron is mapped to a photon. We experimentally realize the coherent control of BOs by applying a well-controlled driving force with a frequency close to BOs. We observe the competition between localization and delocalization of the wave pocket by changing the drive parameters. Our study demonstrates the visualized wave behavior of electrons and proves a way to modulate electron transport in a perfect lattice.

Published by the American Physical Society
2024
Navigating the generative AI travel landscape: the influence of ChatGPT on the evolution from new users to loyal adopters
Authors: Li Yu , Lee Soyeun Olivia
Published: April 2024

Purpose

This study, rooted in affordance-actualization theory and communication theory, aims to critically examine how ChatGPT influences users’ transition from new adopters to loyal advocates within the context of travel decision-making. It incorporates constructs including communication quality, personalization, anthropomorphism, cognitive and emotional trust (ET), loyalty and intention to adopt into a comprehensive model.

Design/methodology/approach

This study used quantitative methods to analyze data from 477 respondents, collected online through a self-administered questionnaire by Embrain, a leading market research company in South Korea. Lavaan package within R studio was used for evaluating the measurement model through confirmatory factor analysis and using structural equation modeling to examine the proposed hypotheses.

Findings

The findings reveal a pivotal need for enhancing ChatGPT’s communication quality, particularly in terms of accuracy, currency and understandability. Personalization emerges as a key driver for cognitive trust, while anthropomorphism significantly impacts ET. Interestingly, the study unveils that in the context of travel recommendations, users’ trust in ChatGPT predominantly operates at the cognitive level, significantly impacting loyalty and subsequent adoption intentions.

Practical implications

The findings of this research provide valuable insights for improving Generative AI (GenAI) technology and management practices in travel recommendations.

Originality/value

As one of the few empirical research papers in the burgeoning field of GenAI, this study proposes a highly explanatory model for the process from affordance to actualization in the context of using ChatGPT for travel recommendations.