bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative Analysis of Molecular Pathogenic Mechanisms and Antiviral Development Targeting Old and New World Hantaviruses
Authors: Jeyachandran Arjit Vijey , Irudayam Joseph Ignatius , Dubey Swati , Chakravarty Nikhil , Konda Bindu , Shah Aayushi , Su Baolong , Wang Cheng , Cui Qi , Williams Kevin J. , Srikanth Sonal , Shi Yanhong , Deb Arjun , Damoiseaux Robert , Stripp Barry R. , Ramaiah Arunachalam , Arumugaswami Vaithilingaraja 
Published: August 2023

ABSTRACTBackgroundHantaviruses – dichotomized into New World (i.e. Andes virus, ANDV; Sin Nombre virus, SNV) and Old-World viruses (i.e. Hantaan virus, HTNV) – are zoonotic viruses transmitted from rodents to humans. Currently, no FDA-approved vaccines against hantaviruses exist. Given the recent breakthrough to human-human transmission by the ANDV, an essential step is to establish an effective pandemic preparedness infrastructure to rapidly identify cell tropism, infective potential, and effective therapeutic agents through systematic investigation.MethodsWe established human cell model systems in lung (airway and distal lung epithelial cells), heart (pluripotent stem cell-derived (PSC-) cardiomyocytes), and brain (PSC-astrocytes) cell types and subsequently evaluated ANDV, HTNV and SNV tropisms. Transcriptomic, lipidomic and bioinformatic data analyses were performed to identify the molecular pathogenic mechanisms of viruses in different cell types. This cell-based infection system was utilized to establish a drug testing platform and pharmacogenomic comparisons.ResultsANDV showed broad tropism for all cell types assessed. HTNV replication was predominantly observed in heart and brain cells. ANDV efficiently replicated in human and mouse 3D distal lung organoids. Transcriptomic analysis showed that ANDV infection resulted in pronounced inflammatory response and downregulation of cholesterol biosynthesis pathway in lung cells. Lipidomic profiling revealed that ANDV-infected cells showed reduced level of cholesterol esters and triglycerides. Further analysis of pathway-based molecular signatures showed that, compared to SNV and HTNV, ANDV infection caused drastic lung cell injury responses. A selective drug screening identified STING agonists, nucleoside analogues and plant-derived compounds that inhibited ANDV viral infection and rescued cellular metabolism. In line with experimental results, transcriptome data shows that the least number of total and unique differentially expressed genes were identified in urolithin B- and favipiravir-treated cells, confirming the higher efficiency of these two drugs in inhibiting ANDV, resulting in host cell ability to balance gene expression to establish proper cell functioning.ConclusionsOverall, our study describes advanced human PSC-derived model systems and systems-level transcriptomics and lipidomic data to better understand Old and New World hantaviral tropism, as well as drug candidates that can be further assessed for potential rapid deployment in the event of a pandemic.
Nitrite secretion by cyanobacteria is controlled by the small protein NirP1
Authors: Kraus Alexander , Spät Philipp , Timm Stefan , Wilson Amy , Schumann Rhena , Hagemann Martin , Macek Boris , Hess Wolfgang R. 
Published: August 2023

ABSTRACTWhen the supply of inorganic carbon is limiting, photosynthetic cyanobacteria excrete nitrite, a toxic intermediate in the ammonia assimilation pathway from nitrate. While it has been hypothesized that the secreted nitrite represents excess nitrogen that could not be further assimilated due to the missing carbon, the underlying molecular mechanism has remained enigmatic. Here, we characterized a hitherto unannotated gene with homologs in the genomes of 485 different cyanobacteria that is upregulated under low carbon conditions and controlled by the transcription factor NtcA, a central regulator of nitrogen homeostasis. To understand its function, we ectopically overexpressed it inSynechocystissp. PCC 6803, which resulted in a chlorotic phenotype, delayed growth, severe changes in amino acid pools, and nitrite excretion. Coimmunoprecipitation experiments revealed that this protein targets nitrite reductase, a central enzyme in the assimilation of ammonia from nitrate/nitrite, and was re-named to nitrite reductase regulator protein 1 (NirP1). Our results reveal that NirP1 is widely conserved in cyanobacteria and plays a crucial role in the coordination of C/N primary metabolism by targeting one of the central enzymes. In natural environments, the excreted nitrite will be utilized by other microorganisms; therefore, NirP1 ultimately impacts the activities and composition of the surrounding microbiome.
PEX1 is essential for the glycosome biogenesis and trypanosomatid parasite survival
Authors: Mahadevan Lavanya , Arya Hemant , Schliebs Wolfgang , Erdmann Ralf , Kalel Vishal C. 
Published: August 2023

AbstractTrypanosomatid parasites are kinetoplastid protists that compartmentalize glycolytic enzymes in unique peroxisome-related organelles called glycosomes. The heterohexameric AAA-ATPase complex of PEX1-PEX6 is anchored to the peroxisomal membrane and functions in the export of matrix protein import receptor PEX5 from the peroxisomal membrane. Defects in PEX1, PEX6 or their membrane anchor causes dysfunction of peroxisomal matrix protein import cycle. In this study, we identified theTrypanosomaPEX1 orthologue using sequence and structural similarities. Using yeast two-hybrid analysis, we demonstrate thatTbPEX1 can bind toTbPEX6. Endogenously taggedTbPEX1 localizes to glycosomes in theT. bruceiparasites. Depletion of PEX1 gene expression by RNA interference causes lethality to bloodstream form trypanosomes, due to a partial mislocalization of glycosomal enzymes to the cytosol and ATP depletion.TbPEX1 RNAi leads to a selective proteasomal degradation of both matrix protein import receptorsTbPEX5 andTbPEX7. Unlike in yeast, PEX1 depletion did not result in an accumulation of ubiquitinatedTbPEX5 in trypanosomes. As PEX1 turned out to be essential for trypanosomatid parasites, it could provide a suitable drug target for parasitic diseases. The results also suggests that these parasites possess a highly efficient quality control mechanisms that export the import receptors from glycosomes to the cytosol, in the absence of a functionalTbPEX1-TbPEX6 complex.
Postzygotic barriers persist despite ongoing introgression in hybridizingMimulusspecies
Authors: Mantel Samuel J. , Sweigart Andrea L. 
Published: August 2023

SummaryThe evolution of postzygotic isolation is thought to be a key step in maintaining species boundaries upon secondary contact, yet the dynamics and persistence of hybrid incompatibilities in sympatric species are not well understood.Here, we explore these issues using genetic mapping in three populations of recombinant inbred lines between naturally hybridizing monkeyflowersMimulus guttatusandM. nasutusfrom the sympatric Catherine Creek population.The threeM. guttatusfounders differ dramatically in admixture history. Comparative genetic mapping also reveals three putative inversions segregating among theM. guttatusfounders, two due to admixture. We observe strong, genome-wide transmission ratio distortion, but patterns are highly variable among populations. Some distortion is explained by epistatic selection favoring parental genotypes, but tests of inter-chromosomal linkage disequilibrium also reveal multiple candidate Dobzhansky-Muller incompatibilities. We also map several genetic loci for hybrid fertility, including two interacting pairs coinciding with peaks of distortion.Remarkably, in this limited sample ofM. guttatus, we discover abundant segregating variation for hybrid incompatibilities withM. nasutus,suggesting this population harbors diverse contributors to postzygotic isolation. Moreover, even with substantial admixture, hybrid incompatibilities betweenMimulusspecies persist, suggesting postzygotic isolation might be a potent force in maintaining species barriers in this system.
Multiplexed amplicon sequencing reveals the heterogeneous spatial distribution of pyrethroid resistance mutations inAedes albopictusmosquito populations in Southern France
Authors: Fontaine Albin , Mignotte Antoine , Lacour Guillaume , Nguyen Agnès , Gomez Nicolas , Chanaud Lionel , L’Ambert Grégory , Briolant Sébastien 
Published: August 2023

AbstractThe risk of mosquito-borne diseases transmission is moving fast toward temperate climates with the colonization and proliferation of the Asian tiger mosquito vectorAedes albopictusand the rapid and mass transport of passengers returning from tropical regions where the viruses are endemic. The prevention of majorAedes-borne viruses heavily relies on the use of insecticides for vector control, mainly pyrethroids In Europe. High-throughput molecular assays can provide a cost-effective surrogate to phenotypic insecticide resistance assays when mutations have been previously linked to a resistance phenotype. Here, we screened for the spatial distribution ofkdrmutations at a large scale using a two-step approach based on multiplexed amplicon sequencing and an unprecedented collection of field-derived mosquitoes in South of France. We identified the presence of the V1016G allele in 14 sites. The V1016G allele was predominantly found in South-East France close to the Italian border with two additional isolated sites close to Bordeaux and Marmande. All mosquitoes were heterozygous for this mutation and should not be phenotypically resistant to pyrethroid insecticide. Four other mutations were identified in our targeted genomic sequence: I1532T, M1006L, M1586L, M995L. Sequencing a section of maternally inherited mitochondrial genome confirmed that the spread ofAe. albopictusin France originated from founders with haplogroup A1. These findings contribute to the broader understanding of resistance dynamics in Europe and can inform targeted approaches to mitigate the impact of resistance on vector control.
Determining the shelf life of an erythropoietin alfa biosimilar GBPD002 through stability study
Authors: Nag Kakon , Mohiuddin Mohammad , Kumar Samir , Khan Md. Maksudur Rahman , Sarker Md. Enamul Haq , Biswas Bipul Kumar , Roy Rony , Molla Md. Tarek , Roy Ratan , Bappi Md. Emrul Hasan , Rahman Arifur , Haq Sheik Rejaul , Sarker Md. Shofiquzzaman , Popy Priyanka Mollik , Mumu Raisa Ferdaushi , Barman Uttam , Oli Md. Shamsul Kaunain , Khoka Md. Sadek Hosen , Sarker Sourav , Alam Md. Firoz , Sultana Naznin 
Published: August 2023

AbstractGBPD002 is a recombinant human erythropoietin (rhEPO) produced by recombinant DNA technology using mammalian cell expression system. In this study, samples were analyzed according to current Good Laboratory Practice (cGLP) and regulatory guidelines to evaluate the quality of the product under the influence of variety of environmental factors in a time-dependent manner. Accelerated (25 ± 2 °C and relative humidity: 60 ± 5 %) and real-time (5 ± 3 °C) stability study were conducted up to 6 months and 12 months, respectively; samples were analyzed in every 3 months. After 12 months, real-time stability studies were performed with 6 months interval up to18 months, which to be continued up to 24 months. Appearance and pH were assessed using standard methods, and molecular weight was determined by Western blotting. Chromatographic identification and quantitative assays were performed by reversed- phase chromatography (RPC). High-molecular weight aggregatesand degradants were determined using size exclusion chromatography (SEC) and particle size distribution (PSD) analysis. Biofunctionality of the samples were evaluated byin vitroandin vivobioassays. Bacterial endotoxin and sterility test were performed as safety parameters. All samples met the acceptance criteria, and the data were extrapolated using the regulatory guideline to determine the shelf life. The data revealed that the GBPD002 is stable up to 24 months.
Transcriptional control of compartmental boundary positioning during Drosophila wing development
Authors: Aguilar Gustavo , Sickmann Michèle , Bieli Dimitri , Born Gordian , Affolter Markus , Müller Martin 
Published: August 2023

AbstractThe establishment of tissue axes is fundamental during embryonic development. In the Drosophila wing, the anterior/posterior (AP) and the dorsal/ventral (DV) compartment boundaries provide the basic coordinates around which the tissue develops. These boundaries arise as a result of two lineage decisions, the acquisition of posterior fate by the selector geneengrailed(en)and of dorsal fate by the selector geneapterous(ap). Whileenexpression domain is set up during embryogenesis,apexpression only starts during early wing development. Thus, the correct establishment ofapexpression pattern with respect toenmust be tightly controlled. Here we have functionally investigated the transcriptional inputs integrated by the “early”apenhancer (apE) and their requirement for correct boundary positioning. Detailed mutational analyses using CRISPR/Cas revealed a role of apE in positioning the DV boundary with respect to the AP boundary, with apE mutants often displaying mirror-image anterior wing duplications. We then accomplished tissue-specific enhancer disruption via dCas9 expression. This approach allowed us to dissect the spatio-temporal requirement of apE function, challenging the mechanism by which apE miss-regulation leads to AP defects. Base-pair resolution analyses of apE uncovered a single HOX binding site essential for wing development, which, when mutated, led to wingless flies. Along these lines, we found that the HOX gene Antennapedia (Antp) is fundamental forapexpression. In addition, we demonstrated that the transcription factors Pointed (Pnt), Homothorax (Hth) and Grain (Grn) are necessary for apE function. Together, our results provide a comprehensive molecular basis of earlyapactivation and the developmental consequences of its miss-regulation, shedding light on how compartmental boundaries are be set up during development.
Molecularly imprinted nanoparticles reveal regulatory scaffolding features in Pyk2 tyrosine kinase
Authors: Zanela Tania M. Palhano , Zangiabadi Milad , Zhao Yan , Underbakke Eric S. 
Published: August 2023

AbstractPyk2 is a multi-domain non-receptor tyrosine kinase that serves dual roles as signaling enzyme and scaffold. Pyk2 activation involves a multi-stage cascade of conformational rearrangements and protein interactions initiated by autophosphorylation of a linker site. Linker phosphorylation recruits Src kinase, and Src-mediated phosphorylation of the Pyk2 activation loop confers full activation. The regulation and accessibility of the initial Pyk2 autophosphorylation site remains unclear. We employed peptide-binding molecularly imprinted nanoparticles (MINPs) to probe the regulatory conformations controlling Pyk2 activation. MINPs differentiating local structure and phosphorylation state revealed that the Pyk2 autophosphorylation site is protected in the autoinhibited state. Activity profiling of Pyk2 variants implicated FERM and linker residues responsible for constraining the autophosphorylation site. MINPs targeting each Src docking site disrupt the higher-order kinase interactions critical for activation complex maturation. Ultimately, MINPs targeting key regulatory motifs establish a useful toolkit for probing successive activational stages in the higher-order Pyk2 signaling complex.Abstract Figure
Accelerated social representational drift in the nucleus accumbens in a model of autism
Authors: Zhao Pingping , Chen Xing , Bellafard Arash , Murugesan Avaneesh , Quan Jonathan , Aharoni Daniel , Golshani Peyman 
Published: August 2023

SummaryImpaired social interaction is one of the core deficits of autism spectrum disorder (ASD) and may result from social interactions being less rewarding. How the nucleus accumbens (NAc), as a key hub of reward circuitry, encodes social interaction and whether these representations are altered in ASD remain poorly understood. We identified NAc ensembles encoding social interactions by calcium imaging using miniaturized microscopy. NAc population activity, specifically D1 receptor-expressing medium spiny neurons (D1-MSNs) activity, predicted social interaction epochs. Despite a high turnover of NAc neurons modulated by social interaction, we found a stable population code for social interaction in NAc which was dramatically degraded in Cntnap2-/-mouse model of ASD. Surprisingly, non-specific optogenetic inhibition of NAc core neurons increased social interaction time and significantly improved sociability in Cntnap2-/-mice. Inhibition of D1- or D2-MSNs showed reciprocal effects, with D1 inhibition decreasing social interaction and D2 inhibition increasing interaction. Therefore, social interactions are preferentially, specifically and dynamically encoded by NAc neurons and social representations are degraded in this autism model.
Exploiting Activation and Inactivation Mechanisms in Type I-C CRISPR-Cas3 for Genome Editing Applications
Authors: Hu Chunyi , Myers Mason T. , Zhou Xufei , hou Zhonggang , Lozen Macy L. , Zhang Yan , Ke Ailong 
Published: August 2023

AbstractType I CRISPR-Cas systems utilize the RNA-guided Cascade complex to identify matching DNA targets, and the nuclease-helicase Cas3 to degrade them. Among seven subtypes, Type I-C is compact in size and highly active in creating large-sized genome deletions in human cells. Here we use four cryo-electron microscopy snapshots to define its RNA-guided DNA binding and cleavage mechanisms in high resolution. The non-target DNA strand (NTS) is accommodated by I-C Cascade in a continuous binding groove along the juxtaposed Cas11 subunits. Binding of Cas3 further traps a flexible bulge in NTS, enabling efficient NTS nicking. We identified two anti-CRISPR proteins AcrIC8 and AcrIC9, that strongly inhibitN. lactamicaI-C function. Structural analysis showed that AcrIC8 inhibits PAM recognition through direct competition, whereas AcrIC9 achieves so through allosteric inhibition. Both Acrs potently inhibit I-C-mediated genome editing and transcriptional modulation in human cells, providing the first off-switches for controllable Type I CRISPR genome engineering.
CRISPR-DIPOFF: An Interpretable Deep Learning Approach for CRISPR Cas-9 Off-Target Prediction
Authors: Toufikuzzaman Md. , Samee Md. Abul Hassan , Rahman M Sohel 
Published: August 2023

AbstractCRISPR Cas-9 is a groundbreaking gene-editing tool that harnesses bacterial defense systems to alter DNA sequences accurately. This innovative technology holds vast promise in multiple domains like biotechnology, agriculture, and medicine. However, such power does not come without its own peril, and one such issue is the potential for unintended modifications (Off-Target), which highlights the need for accurate prediction and mitigation strategies. Though previous studies have demonstrated improvement in Off-Target prediction capability with the application of deep learning, they often struggle with the precision-recall trade-off, limiting their effectiveness and do not provide proper interpretation of the complex decision-making process of their models. To address these limitations, we have thoroughly explored deep learning networks, particularly the recurrent neural network (RNN) and transformer based models, leveraging their established success in handling sequence data. Furthermore, we have employed genetic algorithm for hyperparameter tuning to optimize these models’ performance. The results from our experiments demonstrate significant performance improvement compared to the current state-of-the-art in Off-Target prediction, highlighting the efficacy of our approach. Furthermore, leveraging the power of the integrated gradient method, we make an effort to interpret our models resulting in a detailed analysis and understanding of the underlying factors that contribute to Off-Target predictions, in particular the presence of two sub-regions in the seed region of sgRNA which extends the established biological hypothesis of Off-Target effects. To the best of our knowledge, our model can be considered as the first model combining high efficacy, interpretability, and a desirable balance between precision and recall.
Enterovirus-A71 exploits Rab11 to recruit chaperones for virus morphogenesis
Authors: Yong Ng Qing , Mahendran Vikneswari , Lim Ze Qin , Chu Justin Jang Hann , Chow Vincent Tk , Sze Newman Siu Kwan , Alonso Sylvie 
Published: August 2023

ABSTRACTEnterovirus 71 (EV-A71) causes Hand, Foot and Mouth Disease (HFMD) in children and has been associated with neurological complications. A siRNA screen in EV-A71 infected-motor neurons identified small GTPase Rab11a as a pro-viral host factor. Rab11a and Rab11b isoforms were interchangeably exploited by strains from major EV-A71 genogroups and Coxsackievirus 16, another major causative agent of HFMD. We showed that Rab11 did not play a role in viral entry, IRES-mediated protein translation, or viral genome replication, although it co-localized with replication organelles. GTPase-defective Rab11 mutants had no effect on EV-A71 replication, ruling out Rab11 involvement in intracellular trafficking of viral or host components. Instead, reduced VP2:VP0 ratio in siRab11-treated cells supported a role in provirion maturation. Co-immunoprecipitation and mass spectrometry revealed chaperones as Rab11 top interacting partners during infection. Among which, CCT8 subunit of the chaperone complex TRiC/CCT was found to interact with viral structural proteins specifically. Together, this study describes a novel, unconventional role for Rab11 during viral infection, where it participates in the complex process of virus morphogenesis by recruiting essential chaperone proteins.
osl-dynamics: A toolbox for modelling fast dynamic brain activity
Authors: Gohil C. , Huang R. , Roberts E. , van Es M.W.J. , Quinn A.J. , Vidaurre D. , Woolrich M.W. 
Published: August 2023

AbstractNeural activity contains rich spatio-temporal structure that corresponds to cognition. This includes oscillatory bursting and dynamic activity that span across networks of brain regions, all of which can occur on timescales of a tens of milliseconds. While these processes can be accessed through brain recordings and imaging, modelling them presents methodological challenges due to their fast and transient nature. Furthermore, the exact timing and duration of interesting cognitive events is often a priori unknown. Here we present the OHBA Software Library Dynamics Toolbox (osl-dynamics), a Python-based package that can identify and describe recurrent dynamics in functional neuroimaging data on timescales as fast as tens of milliseconds. At its core are machine learning generative models that are able to adapt to the data and learn the timing, as well as the spatial and spectral characteristics, of brain activity with few assumptions.osl-dynamicsincorporates state-of-the-art approaches that can be, and have been, used to elucidate brain dynamics in a wide range of data types, including magneto/electroencephalography, functional magnetic resonance imaging, invasive local field potential recordings and electrocorticography. It also provides novel summary measures of brain dynamics that can be used to inform our understanding of cognition, behaviour and disease. We hopeosl-dynamicswill further our understanding of brain function, through its ability to enhance the modelling of fast dynamic processes.HighlightsAn open-source toolbox for identifying and describing brain dynamics in neuroimaging data on fast timescales.Includes visualisation and quantification of oscillatory bursting and network dynamics.Provides novel summary measures and group analysis tools of brain dynamics that can be used to inform our understanding of cognition, behaviour and disease.Implemented in Python and makes use ofTensorFlow.Includes comprehensive documentation and tutorials.