bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular cloning and characterization of an AP2/ERF protein gene in cotton (Gossypium hirsutumL.)
Authors: Wu Chaofeng , Ma Xuemei , Li Shuyan 
Published: April 2023

AbstractUpland cotton (Gossypium hirsutumL.) is one of the most economically important crops worldwide due to the significant source of natural fiber, feed, oil and biofuel products. Cottonseed can also serve as an excellent source of edible protein and oil. However,the presence of gossypol in pigment gland has limited it utilization In the past few decades, some progress has been made in the understanding molecular mechanism of the formation of the pigment gland. However, little is known about the specific mechanism of pigment gland formation in cotton. In this study, the cDNA sequence of a ethylene transcription factor gene, designated GhERF105a, was cloned from upland cotton CCRI12. Sequence alignment revealed that GhERF105a gene contained a typical AP2/ERF domain of 61 amino acids, and belonged to the ERF subgroup of the ERF supfamily. It was highly expressed in the leaves and stems of glanded plants but had substantially lower expression of the glandless plants. GhERF105a, localized to the nucleus, could bind to GCC-box and DRE. Some development, phytohormone and stress related cis-elements were enriched in the promoters ofGhERF105a/d. Split ubiquitin assays in yeast and BiFC experiments showed extensive interactions between GhERF105a and Gh_A07G1044. In addition,GhERF105awas highly similar withGhERF105din the gene length, molecular weight, protein molecule, gene structure and expression pattern. The overall results suggested thatGhERF105amight participate in the pigment gland formation and stree-response processes.
Identification of the alternative sigma factor regulons ofChlamydia trachomatisusing multiplexed CRISPR interference
Authors: Hatch Nathan D. , Ouellette Scot P. 
Published: April 2023

AbstractC. trachomatisis a developmentally regulated, obligate intracellular bacterium that encodes three sigma factors: σ66, σ54, and σ28. σ66 is the major sigma factor controlling most transcription initiation during early and mid-cycle development as the infectious EB transitions to the non-infectious RB that replicates within an inclusion inside the cell. The roles of the minor sigma factors, σ54 and σ28, have not been well characterized to date – however, there are data to suggest each functions in late-stage development and secondary differentiation as RBs transition to EBs. As the process of secondary differentiation itself is poorly characterized, clarifying the function of these alternative sigma factors by identifying the genes regulated by them will further our understanding of chlamydial differentiation. We hypothesize that σ54 and σ28 have non-redundant and essential functions for initiating late gene transcription thus mediating secondary differentiation inChlamydia. Here, we demonstrate the necessity of each minor sigma factor in successfully completing the developmental cycle. We have implemented and validated multiplexed CRISPRi techniques novel to the chlamydial field to examine effects of knocking down each alternative sigma factor individually and simultaneously. In parallel, we also overexpressed each sigma factor. Altering transcript levels for either or both alternative sigma factors resulted in a severe defect in EB production as compared to controls. Furthermore, RNA sequencing identified differentially expressed genes during alternative sigma factor dysregulation, indicating the putative regulons of each. These data demonstrate the levels of alternative sigma factors must be carefully regulated to facilitate chlamydial growth and differentiation.ImportanceChlamydia trachomatisis a significant human pathogen in both developed and developing nations. Due to the organism’s unique developmental cycle and intracellular niche, basic research has been slow and arduous. However, recent advances in chlamydial genetics have allowed the field to make significant progress in experimentally interrogating the basic physiology ofChlamydia. Broadly speaking, the driving factors of chlamydial development are poorly understood, particularly regarding how the later stages of development are regulated. Here, we employ a novel genetic tool for use inChlamydiawhile investigating the effects of dysregulating the two alternative sigma factors in the organism that help control transcription initiation. We provide further evidence for both sigma factors’ essential roles in late-stage development and their potential regulons, laying the foundation for deeper experimentation to uncover the molecular pathways involved in chlamydial differentiation.
Deletion of the gene for the African swine fever virus BCL-2 family member A179L increases virus uptake and apoptosis, but decreases virus spread in macrophages and reduces virulence in pigs
Authors: Reis Ana Luisa , Rathakrishnan Anusyah , Goulding Leah V. , Barber Claire , Goatley Lynnette C. , Dixon Linda K. 
Published: April 2023

ABSTRACTAfrican swine fever virus encodes proteins that inhibit apoptosis including one member of the BCL-2 family, A179L. Deletion of the A179L gene from the virulent genotype I isolate Benin 97/1 compared to Benin 97/1 expressing A179L or mock-infected macrophages, resulted in increased Caspase 3 and 7 activity, annexin V binding to surface phosphatidyl serine and DNA fragmentation, measured by terminal deoxynucleotidyl transferase nick-end labelling. These results confirmed that apoptosis was induced earlier in macrophages infected with the BeninΔA179L virus. Increased cell entry of the A179L gene-deleted virus was indicated at early times since up to double the numbers of cells expressed fluorescent protein from the virus genome. Yields of infectious virus were similar over a single cycle but were significantly lower for the A179L gene-deleted virus over a multi-step growth cycle. Pigs immunised and boosted with the BeninΔA179L virus showed no clinical signs, although a weak cellular response to ASFV was observed showing that the virus had replicated. The immunised pigs were not protected against challenge with the virulent parental virus Benin 97/1 although viremia was lower at 3 days post-challenge compared to the control non-immune pigs. The reduced levels of virus replication in macrophages probably limited induction of a protective immune response. The results show an important role for the A179L protein in virus replication in macrophages and virulence in pigs.IMPORTANCEAfrican swine fever virus (ASFV) causes a lethal disease of pigs that has spread extensively in Africa, Europe and Asia. The virus codes for more than 150 proteins, many of which help the virus to evade the host’s defences following infection. We investigated the effect of deleting one of these genes, A179L, from the genome of an ASFV isolate that causes death of infected pigs. A179L belongs to the BCL-2 protein family, consisting of members which promote or inhibit apoptosis with A179L belonging to the latter. Deleting the A179L gene reduced ASFV replication and spread between macrophages, its main target cells. This was correlated with an increase in cell death. Pigs infected with the virus with A179L gene deleted did not show signs of disease and no virus replication was detected in blood. A low immune response was generated but the immunised pigs were not protected when challenged with the parental deadly virus. The results show that the A179L gene is important for ASFV to replicate efficiently in cells and in animals.
Development of two mouse strains conditionally expressing bright luciferases with distinct emission spectra as new tools for in vivo imaging
Authors: Nakashiba Toshiaki , Ogoh Katsunori , Iwano Satoshi , Sugiyama Takashi , Mizuno-Iijima Saori , Nakashima Kenichi , Mizuno Seiya , Sugiyama Fumihiro , Yoshiki Atsushi , Miyawaki Atsushi , Abe Kuniya 
Published: April 2023

AbstractIn vivo bioluminescence imaging (BLI) has been an invaluable noninvasive method to visualize molecular and cellular behaviors in laboratory animals. Bioluminescent reporter mice possessing luciferases for general use have been limited to a classical luciferase, Luc2, fromPhotinus pyralis, and have been extremely powerful for various in vivo studies. However, applicability of reporter mice for in vivo BLI could be further accelerated by increasing light intensity using other luciferases and/or improving the biodistribution of their substrates in animal body. Here, we created two Cre-dependent reporter mice incorporating luciferases: oFluc derived fromPyrocoeli matsumuraiand Akaluc, both of which had been reported previously to be brighter than Luc2 when using appropriate substrates; we then tested their bioluminescence in neural tissues and other organs in living mice. When expressed throughout the body, both luciferases emitted an intense yellow (oFluc) or far-red (Akaluc) light easily visible to the naked eye. Moreover, oFluc and Akaluc were similarly bright in the pancreas for in vivo BLI. However, Akaluc was superior to oFluc for brain imaging, because its substrate, AkaLumine-HCl, was distributed to the brain more efficiently than the oFluc substrate, D-luciferin. We also demonstrated that the light produced by oFluc and Akaluc was sufficiently spectrally distinct for dual-color imaging in a single living mouse. Taken together, these novel bioluminescent reporter mice are an ideal source of cells with bright bioluminescence and may facilitate the in vivo BLI of various tissues/organs for preclinical and biomedical research in combination with a wide variety of Cre-driver mice.
Synthetic neuromelanin as a trigger of inflammation in the brain – new mouse model of Parkinson’s disease
Authors: Tejchman-Skrzyszewska Anna , Strzelec Martyna , Kot Marta , Chlebanowska Paula , Badyra Bogna , Sobocińska Małgorzata , Zecca Luigi , Majka Marcin 
Published: April 2023

AbstractParkinson’s disease (PD) is a neurodegenerative disease that is an increasing threat to an aging society. The idiopathic form of PD accounts for over 90% of all cases, and the current etiology is still unknown. One of the reasons hindering research on this form of PD is the lack of an appropriate animal models. Among mouse models of the disease, those based on the administration of neurotoxins such as 1-methyl-4-phenyl-1,2,3,6- tetrahydropyridine (MPTP) or 6-hydroxydopamine (6-OHDA) to the substantia nigra pars compacta (SNpc) or striatum are predominantly used. In these models, there are metabolic disturbances causing oxidative stress in the SNpc or striatum, which ultimately leads to the death of dopaminergic neurons. However, the models used so far have serious limitations, most of all they do not fully reflect the processes occurring in the course of the disease and do not consider the involvement of inflammation in the etiology and pathogenesis of PD. In this study we show that the administration of synthetic neuromelanin, which activates astrocytes and microglia, induces the inflammation and may be involved in degeneration of dopaminergic neurons. Neuromelanin under physiological conditions acts as a neuroprotector, however, released from dying dopaminergic neurons is an important factor activating astrocytes, microglia and causing neuroinflammation. Since one of the causes of Parkinson’s appear to be the death of dopaminergic neurons overloaded with neuromelanin and consequent pathological activation of microglia, the use of synthetic neuromelanin reflect the natural pathological processes occurring during the development of the disease.
CyAbrB2 is a nucleoid-associated protein inSynechocystiscontrolling hydrogenase expression during fermentation
Authors: Kariyazono Ryo , Osanai Takashi 
Published: April 2023

AbstractThehoxoperon inSynechocystissp. PCC 6803, encoding bidirectional hydrogenase responsible for H2production, is transcriptionally upregulated under microoxic conditions. Although several regulators forhoxtranscription have been identified, their dynamics and higher-order DNA structure ofhoxregion in microoxic conditions remain elusive. We focused on key regulators for thehoxoperon: cyAbrB2, a conserved regulator in cyanobacteria, and SigE, an alternative sigma factor. Chromatin immunoprecipitation-sequencing revealed that cyAbrB2 binds to thehoxpromoter region under aerobic conditions, with its binding being flattened in microoxic conditions. Concurrently, SigE exhibited increased localization to thehoxpromoter under microoxic conditions. Genome-wide analysis revealed that cyAbrB2 binds broadly to AT-rich genome regions and represses gene expression. Moreover, we demonstrated the physical interactions of thehoxpromoter region with its distal genomic loci. Both the transition to microoxic conditions and the absence of cyAbrB2 influenced the chromosomal interaction. From these results, we propose that cyAbrB2 is a cyanobacterial nucleoid-associated protein (NAP), modulating chromosomal conformation, which blocks RNA polymerase from thehoxpromoter in aerobic conditions. We further infer that cyAbrB2, with altered localization pattern upon microoxic conditions, modifies chromosomal conformation in microoxic conditions, which allows SigE-containing RNA polymerase to access thehoxpromoter. The coordinated actions of this NAP and the alternative sigma factor are crucial for the properhoxexpression in microoxic conditions. Our results highlight the impact of cyanobacterial chromosome conformation and NAPs on transcription, which have been insufficiently investigated.
Cell-attribute aware community detection improves differential abundance testing from single-cell RNA-Seq data
Authors: Maity Alok K. , Teschendorff Andrew E. 
Published: April 2023

AbstractVariations of cell-type proportions within tissues could be informative of biological aging and disease risk. Single-cell RNA-sequencing offers the opportunity to detect such differential abundance (DA) patterns, yet this task can be statistically challenging due to the noise in single-cell data, inter-sample variability and because DA patterns are often of small effect size. Here we present a DA-testing paradigm called ELVAR that uses cell attribute aware clustering when inferring differentially enriched communities within the single-cell manifold. Using simulated and real single-cell and single-nucleus RNA-Seq datasets, we benchmark ELVAR against an analogous DA algorithm that uses Louvain for clustering, as well as local neighborhood-based DA-testing methods, demonstrating that ELVAR improves the sensitivity to detect DA-shifts in relation to aging, precancerous states and Covid-19 phenotypes. In effect, leveraging cell attribute information when inferring cell communities can denoise single-cell data, avoid the need for batch correction and help retrieve more robust cell states for subsequent DA-testing. ELVAR is available as an open-source R-package.
xQTLbiolinks: a comprehensive and scalable tool for integrative analysis of molecular QTLs
Authors: Ding Ruofan , Zou Xudong , Qin Yangmei , Chen Hui , Ma Xuelian , Yu Chen , Wang Gao , Li Lei 
Published: April 2023

ABSTRACTGenome-wide association studies (GWAS) have identified thousands of disease-associated non-coding variants, posing urgent needs for functional interpretation. Molecular quantitative trait loci (xQTLs) such as eQTLs serve as an essential intermediate link between these non-coding variants and disease phenotypes and have been widely used to discover disease-risk genes from many population-scale studies. However, mining and analyzing the xQTLs data presents several significant bioinformatics challenges, particularly when it comes to integration with GWAS data. Here, we developed xQTLbiolinks as the first comprehensive and scalable tool for xQTLs data retrieval, quality controls, and pre-processing from 75 human tissues and cell types. In addition, xQTLbiolinks provided a robust colocalization module through integration with GWAS data. The result generated by xQTLbiolinks can be flexibly visualized or stored in standard R objects that can easily be integrated with other R packages and custom pipelines. We applied xQTLbiolinks to cancer GWAS summary statistics as case studies and demonstrated its robust utility and reproducibility. xQTLbiolinks will profoundly accelerate the interpretation of disease-associated variants, thus promoting a better understanding of disease etiologies. xQTLbiolinks is available athttps://github.com/lilab-bioinfo/xQTLbiolinks.
An ancient ecospecies ofHelicobacter pylorifound in Indigenous populations and animal adapted lineages
Authors: Tourrette Elise , Torres Roberto C. , Svensson Sarah L. , Matsumoto Takashi , Miftahussurur Muhammad , Fauzia Kartika Afrida , Alfaray Ricky Indra , Vilaichone Ratha-Korn , Tuan Vo Phuoc ,   HelicobacterGenomicsConsortium, Wang Difei , Yadegar Abbas , Olsson Lisa M. , Zhou Zhemin , Yamaoka Yoshio , Thorell Kaisa , Falush Daniel 
Published: April 2023

AbstractThe colonization of our stomachs byHelicobacter pyloriis believed to predate the oldest splits between extant human populations. We identify a “Hardy” ecospecies ofH. pyloriassociated with indigenous groups, isolated from people in Siberia, Canada, USA and Chile. The ecospecies shares the ancestry of “Ubiquitous”H. pylorifrom the same geographical region in most of the genome but has nearly fixed SNP differences in 100 genes, many of which encode outer membrane proteins and host interaction factors. For these parts of the genome, the ecospecies has a separate, independently evolving gene pool with a distinct evolutionary history.H. acinonychis, found in big cats, and a newly identified primate-associated lineage both belong to the Hardy ecospecies and both represent human to animal host jumps. Most strains from the ecospecies encode an additional iron-dependent urease that is shared byHelicobacterfrom carnivorous hosts, as well as a tandem duplication ofvacA, encoding the vacuolating toxin. We conclude thatH. pylorisplit into two highly distinct ecospecies in Africa and that both dispersed around the globe with humans, but the Hardy ecospecies has gone extinct in most parts of the world. Our analysis also pushes back the likely length of the association betweenH. pyloriand humans.
Role of the NO-GC/cGMP signaling pathway in platelet biomechanics
Authors: Rodríguez Johanna G. , Balmes Aylin , Seifert Jan , Pinto-Quintero Daniel , Khawaja Akif A. , Boffito Marta , Frye Maike , Friebe Andreas , Emerson Michael , Seta Francesca , Feil Robert , Feil Susanne , Schäffer Tilman E. 
Published: April 2023

AbstractCyclic guanosine monophosphate (cGMP) is a second messenger produced by the NO-sensitive guanylyl cyclase (NO-GC) enzyme. In platelets, the NO-GC/cGMP pathway inhibits aggregation. One aspect of the inhibitory mechanism involves changes in the cytoskeleton; however, the molecular mechanisms underlying platelet inhibition and its correlation with cytoskeletal cellular stiffness are poorly understood.We measured the cellular stiffness of individual platelets after treatment with the NO-GC stimulator riociguat or the NO-GC activator cinaciguat, using scanning ion conductance microscopy (SICM). We quantified changes in platelet shape using deep learning-based platelet morphometry. Cytoskeletal actin polymerization and platelet activation were measured by co-immunostaining F-actin and P-selectin, respectively. To test for clinical applicability of NO-GC stimulators in the context of increased thrombogenicity risk, we investigated the effect of riociguat on platelets from human immunodeficiency virus (HIV)-positive patients taking abacavir sulphate (ABC)-containing regimens, compared with HIV-negative volunteers.Stimulation of human and murine platelets with the NO-GC stimulator riociguat or with the NO-GC activator cinaciguat downregulated P-selectin expression, decreased F-actin polymerization, and decreased cellular stiffness by ≈50%, compared to vehicle control. In addition, platelets became more circular, indicating decreased activation. Riociguat did not cause any change in platelet aggregation or circularity in HIV-positive patients taking ABC-containing regimens.These results corroborate a functional role of the NO-GC enzyme in platelet biomechanics (cellular stiffness) in correlation with the inhibition of platelet activation and morphological changes. The observed changes in stiffness and platelet shape therefore demonstrate the possibility of pharmacologically targeting the NO-GC/cGMP pathway.
Age-associated elevated inflammation and immune pathways in the mice heart are linked to Adiponectin-Adipor1-RelA signaling
Authors: Gupta Tinku , Gujaral Akash , Chandan Shivanshu 
Published: April 2023

AbstractInflammatory gene profiles using RNA seq analysis were studied by measuring pro-inflammatory cytokines and chemokines levels. qRT-PCR and Western blot analysis were used to validate the expression profile of these inflammatory mediators. Using flow cytometry analysis, CD11b+ monocytes and CD64+ Ly6C were quantified in the young and old hearts. The inflammatory response, Adipor1 and Adipor2 gene expression, RelA nuclear translocation and the effects of adiponectin in LPS-stimulated or Adipor1 silenced H9C2 cells were studied. Gene ontology analysis using differentially expressed genes revealed an enrichment of immune response pathways in the old mice hearts when compared to young mice hearts. Western blot analysis confirmed the down regulation of several anti-inflammatory proteins and the upregulation of pro-inflammatory proteins including CD68, NF-kB1 and Rel-A, in the old mice hearts. Flow cytometry suggested an infiltration of CD11b+monocytes and CD64+ Ly6C-high macrophages in the old mice hearts compared to younger hearts confirming an increased inflammation in the older hearts. Mechanistically, to understand if the Adiponectin-Adipor1-NFkB axis regulates inflammation in the aging heart, Adipor1 and Adipor2 genes were silenced in H9c2 cardiomyocytes. Immune response genes were elevated in the Adipor1 silenced H9c2 cells but not in Adipor2 silenced cells. Pretreatment with Adiponectin (APN) attenuated the Adipor1 silenced or lipopolysaccharides (LPS)-stimulated expression of inflammatory genes in H9c2 cardiomyocytes. APN also attenuated the nuclear translocation of RelA and induction of immune response genes in Adipor1 silenced or LPS-challenged H9c2 cardiomyocytes. APN-AdipoR1-RelA signaling might be a novel therapeutic target for the treatment of inflamed elderly hearts.