bluuebunny/crossref_metadata_2025_split huggingface dataset:
Retro-miRs: Novel and functional miRNAs originated from mRNA retrotransposition
Authors: Mercuri Rafael L. , Conceição Helena B. , Guardia Gabriela D. A. , Goldstein Gabriel , Vibranovski Maria D. , Hinske Ludwig C. , Galante Pedro A F 
Published: February 2023

ABSTRACTBackgroundReverse transcribed gene copies, or retrocopies, have emerged as a major source of evolutionary novelties. MicroRNAs (miRNAs) are small, highly conserved RNAs molecules among species that serve as key post-transcriptional regulators of gene expression. The birth and subsequent evolution of miRNAs have been addressed, but not fully.ResultsIn this study, we carried out a comprehensive investigation of miRNAs origination through retroduplicated mRNA sequences (retrocopies). We identified 17 retroduplicated miRNAs (retro-miRs) that emerged from mRNAs retrocopies. Four of these retro-miRs hadde novoorigination within retrocopied sequences, while 13 retro-miRNAs were located within exon regions and were duplicated along with their host mRNAs. We found that retro-miRs are primates specific, including 5 retro-miRs conserved among all primates and two human-specific retro-miRs. All of the retro-miRs were expressed and had predicted and experimentally validated target genes, with the exception of miR-10527. Notably, the target genes of retro-miRs are involved in key biological processes, such as metabolic processes, cell signaling and regulation of neurotransmitters in the central nervous system. Additionally, we found that these retro-miRs have a potential oncogenic role in cancer, targeting key cancer genes and being overexpressed in several cancer types, including Liver Hepatocellular Carcinoma and Stomach Adenocarcinoma.ConclusionOur findings demonstrate that mRNAs retrotransposition is a key mechanism for the generation of novel miRNAs (retro-miRs) in primates. These retro-miRs are expressed, conserved, have target genes with important cellular functions, and play roles in cancer.
Identifying the core genome of the nucleus-forming bacteriophage family and characterization ofErwiniaphage RAY
Authors: Prichard Amy , Lee Jina , Laughlin Thomas G. , Lee Amber , Thomas Kyle P. , Sy Annika , Spencer Tara , Asavavimol Aileen , Cafferata Allison , Cameron Mia , Chiu Nicholas , Davydov Demyan , Desai Isha , Diaz Gabriel , Guereca Melissa , Hearst Kiley , Huang Leyi , Jacobs Emily , Johnson Annika , Kahn Samuel , Koch Ryan , Martinez Adamari , Norquist Meliné , Pau Tyler , Prasad Gino , Saam Katrina , Sandhu Milan , Sarabia Angel Jose , Schumaker Siena , Sonin Aaron , Uyeno Ariya , Zhao Alison , Corbett Kevin , Pogliano Kit , Meyer Justin , Grose Julianne H. , Villa Elizabeth , Dutton Rachel , Pogliano Joe 
Published: February 2023

ABSTRACTWe recently discovered that some bacteriophages establish a nucleus-like replication compartment (phage nucleus), but the core genes that define nucleus-based phage replication and their phylogenetic distribution were unknown. By studying phages that encode the major phage nucleus protein chimallin, including previously sequenced yet uncharacterized phages, we discovered that chimallin-encoding phages share a set of 72 highly conserved genes encoded within seven distinct gene blocks. Of these, 21 core genes are unique to this group, and all but one of these unique genes encode proteins of unknown function. We propose that phages with this core genome comprise a novel viral family we term Chimalliviridae. Fluorescence microscopy and cryo-electron tomography studies ofErwiniaphage vB_EamM_RAY confirm that many of the key steps of nucleus-based replication encoded in the core genome are conserved among diverse chimalliviruses, and reveal that non-core components can confer intriguing variations on this replication mechanism. For instance, unlike previously studied nucleus-forming phages, RAY doesn’t degrade the host genome, and its PhuZ homolog appears to form a five-stranded filament with a lumen. This work expands our understanding of phage nucleus and PhuZ spindle diversity and function, providing a roadmap for identifying key mechanisms underlying nucleus-based phage replication.
Mycobacterium tuberculosis methyltransferase perturbs host epigenetic programming to promote bacterial survival
Authors: Singh Prakruti R , Dadireddy Venkatareddy , Udupa Shubha , Kalladi Shashwath Malli , Shee Somnath , Khosla Sanjeev , Rajmani Raju S , Singh Amit , Ramakumar Suryanarayanarao , Nagaraja Valakunja 
Published: February 2023

AbstractMycobacterium tuberculosis(Mtb) has evolved several mechanisms to counter host defense arsenal for its proliferation. We show thatMtbemploys multi-pronged approach to modify host epigenetic machinery for its survival upon infection. It secretes methyltransferase (MTase) Rv2067c into macrophages, trimethylating K79 of histone H3 in non-nucleosomal context. Rv2067c downregulates host MTase DOT1L, decreasing its H3K79me3 mark added nucleosomally on pro-inflammatory response genes. Consequent inhibition of caspase8 dependent apoptosis and enhancement of RIPK3 mediated necrosis results in increased pathogenesis. In parallel, Rv2067c enhances the expression of SESTRIN3, NLRC3 and TMTC1 enabling the pathogen to overcome host inflammatory and oxidative response. We provide structural basis for differential methylation of H3 by Rv2067c and DOT1L. The structure of Rv2067c and DOT1L explain how their action on H3K79 is temporally and spatially separated enabling Rv2067c to effectively intercept the host epigenetic circuit and downstream signalling.
Detection of Influenza virus andStreptococcus pneumoniaein air sampled from co-infected ferrets and analysis of their influence on pathogen stability
Authors: French Andrea J. , Rockey Nicole C. , Le Sage Valerie , Mueller Brown Karina , Shephard Meredith J. , Frizzell Sheila , Myerburg Mike M. , Hiller N. Luisa , Lakdawala Seema S. 
Published: February 2023

AbstractSecondary infection withStreptococcus pneumoniaehas contributed significantly to morbidity and mortality during multiple influenza virus pandemics and remains a common threat today. During a concurrent infection, both pathogens can influence the transmission of each other, but the mechanisms behind this are unclear. In this study, condensation air sampling and cyclone bioaerosol sampling were performed using ferrets first infected with the 2009 H1N1 pandemic influenza virus (H1N1pdm09) and secondarily infected withS. pneumoniaestrain D39 (Spn). We detected viable pathogens and microbial nucleic acid in expelled aerosols from co-infected ferrets, suggesting that these microbes could be present in the same respiratory expulsions. To assess whether microbial communities impact pathogen stability within an expelled droplet, we performed experiments measuring viral and bacterial persistence in 1 μL droplets. We observed that H1N1pdm09 stability was unchanged in the presence of Spn. Further, Spn stability was moderately increased in the presence of H1N1pdm09, although the degree of stabilization differed between airways surface liquid collected from individual patient cultures. These findings are the first to collect both pathogens from the air and in doing so, they provide insight into the interplay between these pathogens and their hosts.ImportanceThe impact of microbial communities on transmission fitness and environmental persistence is under-studied. Environmental stability of microbes is crucial to identifying transmission risks and mitigation strategies, such as removal of contaminated aerosols and decontamination of surfaces. Co-infection withS. pneumoniaeis very common during influenza virus infection, but little work has been done to understand whetherS. pneumoniaealters stability of influenza virus, or vice versa, in a relevant system. Here, we demonstrate that influenza virus andS. pneumoniaeare expelled by co-infected hosts. Our stability assays did not reveal any impact ofS. pneumoniaeon influenza virus stability, and a trend towards increased stability ofS. pneumoniaein the presence of influenza viruses. Future work characterizing environmental persistence of viruses and bacteria should include microbially-complex solutions to better mimic physiologically relevant conditions.
Escherichia coliB-strains are intrinsically resistant to colistin and not suitable for characterization and identification ofmcrgenes
Authors: Schumann Anna , Cohn Alexa R. , Gaballa Ahmed , Wiedmann Martin 
Published: February 2023

ABSTRACTAntimicrobial resistance is an increasing threat to human and animal health. Due to the rise of multi- and extreme drug resistance, last resort antibiotics, such as colistin, are extremely important in human medicine. While the distribution of colistin resistance genes can be tracked through sequencing methods, phenotypic characterization of putative antimicrobial resistance (AMR) genes is still important to confirm the phenotype conferred by different genes. While heterologous expression of AMR genes (e.g., inE. coli) is a common approach, so far, no standard method for heterologous expression and characterization ofmcrgenes exists.E. coliB-strains, designed for optimum protein expression, are frequently utilized. Here we report that fourE. coliB-strains are intrinsically resistant to colistin (MIC 8 – 16 μg/mL). Additionally, the three tested B-strains that encode T7 RNA show growth defects when transformed with empty or gene-expressing pET17b plasmids and grown in the presence of IPTG; K-12 or B-strains without T7 RNA polymerase do not show these growth defects. TheE. coliShuffle T7 express strain carrying empty pET17b also showed a heteroresistance phenotype when exposed to colistin in the presence of IPTG. These phenotypes could explain why B-strains were erroneously reported as colistin susceptible. Analysis of existing genome data identified one nonsynonymous change in eachpmrAandpmrBin all fourE. coliB-strains; the E121K change in PmrB has previously been linked to intrinsic colistin resistance. We conclude thatE. coliB-strains are not appropriate heterologous expression hosts for identification and characterization ofmcrgenes.
Structural Characterization of TRAF6 N-terminal for Therapeutic Uses
Authors: Guven Omur , Ciftci Halilibrahim , Tateishi Hiroshi , Koga Ryoko , Radwan Mohamed O. , Sever Belgin , Inoue Jun-ichiro , Otsuka Masami , Fujita Mikako , DeMirci Hasan 
Published: February 2023

AbstractTumor Necrosis Factor Receptor Associated Factors (TRAFs) are a protein family with a wide variety of roles and binding partners. Among them, TRAF6, a ubiquitin ligase, possesses unique receptor binding specificity and shows diverse functions in immune system regulation, cellular signaling, central nervous system (CNS), and tumor formation. TRAF6 consists of an N-terminal Really Interesting New Gene (RING) domain, multiple zinc fingers, and a C-terminal TRAF domain. RING domain and zinc fingers mediate the activation of nuclear factor kappa B (NF-κB), which has essential roles in the regulation of inflammatory responses, proliferation, differentiation, migration, cell adhesion, and apoptosis. Therefore, it has been found that TRAF6 is overexpressed in various types of cancer including pancreatic, liver, lung, head and neck, breast, colorectal cancers, and melanoma along with inflammatory, autoimmune and neurodegenerative disorders. Furthermore, TRAF6 is an important therapeutic target for numerous disorders and structural studies of this protein are crucial for the development of next-generation therapeutics. Here, we present a TRAF6 N-terminal structure determined at the Turkish Light Source “Turkish DeLight” to 2.6 Å resolution at cryogenic temperature. This structure offers insight into the domain organization and zinc-binding, which are critical for protein function. Since the RING domain and the zinc fingers are key targets for TRAF6 therapeutics, structural insights are crucial for future research.
Environmental drivers behind the genetic differentiation in mountain chickadees (Poecile gambeli)
Authors: Srikanthan P , Burg TM 
Published: February 2023

AbstractAnthropogenic climate change has a large impact on wildlife populations and the scale of the impacts have been increasing. In this study, we utilised ddRAD sequence data to investigate genetic divergence and identify the environmental drivers of genetic differentiation between 12 populations of mountain chickadees, family Paridae, sampled across North America. To delineate populations and identify potential zones of hybridisation, we conducted a discriminant analysis of principal components (DAPC), admixture analysis, and calculated pairwise Fst values. The DAPC revealed four clusters: southern California, eastern Rocky Mountains, northwestern Rocky Mountains and Oregon/northern California. We then used BayeScEnv to highlight significant outlier SNPs associated with the five environmental variables. We identified over 150 genes linked to outlier SNPs associated with more than 15 pathways, including stress response and circadian rhythm. We also found a strong signal of isolation by distance. Local temperature was highly correlated with genetic distance. Maxent simulations showed a northward range shift over the next 50 years and a decrease in suitable habitat, highlighting the need for immediate conservation action.
YAP-controlled MHC-I and CXCL10 expression potentiates antitumor immunity independently of IFNγ signaling
Authors: Peng Linyuan , Zhou Liang , Li Huan , Lu Desheng , Qian Minxian , Wang Zhongyuan 
Published: February 2023

AbstractMany efforts are underway to improve immune checkpoint blockade (ICB) therapy including potentiating MHC-I antigen processing and presentation. Accumulating evidence links the Hippo pathway to immunotherapy response, but the understanding of how the tumor-intrinsic Hippo signaling regulating antitumor immunity is limited. Here, we report that inhibition of the Hippo pathway coactivator YAP in tumor cells increases the expression of genes involving in MHC-I antigen processing and presenting machinery (APM) and CXCL10, promoting robust tumor-infiltrating of cytotoxic CD8+T lymphocytes (CTLs) and overcoming tumor resistance to anti-PD1 ICB therapy. Mechanically, we find that YAP/TEAD complex directly binds and recruits NuRD complex to the NLRC5 promoter to repress NLRC5 transcription, thereby blunting MHC-I antigen presentation. Patient cohort analysis revealed that YAP expression negatively correlated with the expression of NLRC5 and MHC-I APM and intratumoral infiltration of CTLs. Collectively, our results suggest that a novel tumor- promoting function of YAP depends on NLRC5 to impair MHC-I antigen processing and presentation and provide a rationale for inhibiting YAP activity in ICB therapy for cancer.
Light inducible protein degradation inE. coliwith the LOVdeg tag
Authors: Tague Nathan , Coriano-Ortiz Cristian , Sheets Michael B. , Dunlop Mary J. 
Published: February 2023

AbstractMolecular tools for optogenetic control allow for spatial and temporal regulation of cell behavior. In particular, light controlled protein degradation is a valuable mechanism of regulation because it can be highly modular, used in tandem with other control mechanisms, and maintain functionality throughout growth phases. Here, we engineered LOVdeg, a tag that can be appended to a protein of interest for inducible degradation inEscherichia coliusing blue light. We demonstrate the modularity of LOVdeg by using it to tag a range of proteins, including the LacI repressor, CRISPRa activator, and the AcrB efflux pump. Additionally, we demonstrate the utility of pairing the LOVdeg tag with existing optogenetic tools to enhance performance by developing a combined EL222 and LOVdeg system. Finally, we use the LOVdeg tag in a metabolic engineering application to demonstrate post-translational control of metabolism. Together, our results highlight the modularity and functionality of the LOVdeg tag system, and introduce a powerful new tool for bacterial optogenetics.
Confinement with Myosin-II suppression increases heritable loss of chromosomes, using live-cell ChReporters
Authors: Hayes Brandon H , Zhu Peter Kuangzheng , Wang Mai , Pfeifer Charlotte R , Xia Yuntao , Phan Steven , Andrechak Jason C , Du Junhong , Tobin Michael P , Anlas Alisya , Dooling Lawrence , Vashisth Manasvita , Irianto Jerome , Lampson Michael A. , Discher Dennis E 
Published: February 2023

ABSTRACTMatrix around cells exerts many effects, some of which depend on the putative tumor suppressor Myosin-II, but whether such factors affect DNA sequences in a cell remains unclear. Here, live-cell monitoring of changes to chromosome copy numbers is developed and studied under diverse perturbations, including Myosin-II inhibition in confined mitosis. Squeezing of mitotic cells is seenin vivoand killsin vitro, but stem cells and cancer cells that survive show heritable loss of mono-allelic GFP/RFP-tagged constitutive genes that function as novel Chromosome-reporters (ChReporters). Myosin-II suppression increases such loss in 3D & 2D confinement but not in standard 2D, with “lethal” multipolar divisions proving myosin-dependent. Viable chromosome loss after confined mitosis associates more with mis-segregation than with multipolars or division number. Solid human tumors and teratomas in mice also show ChReporter loss and a confinement-signature of Myosin-II suppression, although losses are selected against in 2D culture. Heritable loss in rigid-confinement also appears independent of a spindle assembly checkpoint that functions in 2D. Confinement and myosin-II thus regulate pathways of heritable mechanogenetic change.
Bed Nucleus of the Stria Terminalis GABA neurons are necessary for changes in foraging behavior following an innate threat
Authors: Ly Annie , Barker Alexandra , Prévost Emily D. , McGovern Dillon J. , Kilpatrick Zachary , Root David H. 
Published: February 2023

ABSTRACTForaging is a universal behavior that has co-evolved with predation pressure. We investigated the role of bed nucleus of the stria terminalis (BNST) GABA neurons in robotic and live predator threat processing and their consequences in post-threat encounter foraging. Mice were trained to procure food in a laboratory-based foraging apparatus in which food pellets were placed at discrete and incrementally greater distances from a nest zone. After mice learned to forage, they were exposed to either a robotic or live predator threat, while BNST GABA neurons were chemogenetically inhibited. Post-robotic threat encounter, mice spent more time in the nest zone, but other foraging parameters were unchanged compared to pre-encounter behavior. Inhibition of BNST GABA neurons had no effect on foraging behavior post-robotic threat encounter. Following live predator exposure, control mice spent significantly more time in the nest zone, increased their latency to successfully forage, and their overall foraging performance was significantly a ltered. I nhibition o f BNST GABA neurons during live predator exposure prevented changes in foraging behavior from developing after live predator threat. BNST GABA neuron inhibition did not alter foraging behavior during robotic or live predator threat. We conclude that while both robotic and live predator encounter effectively intrude on foraging behavior, the perceived risk and behavioral consequence of the threats are distinguishable. Additionally, BNST GABA neurons may play a role in the integration of prior innate predator threat experience that results in hypervigilance during post-encounter foraging behavior.
Recent developments in the production of 2D- and 3D colon and stomach adenocarcinomas primary cell models
Authors: Tokarchuk Igor , Mushii Oleksandr , Dreus Alona , Koziaruk Anastasia A. , Shapochka Dmyto O. , Ryzhak Oleg A. , Venhryk Serhii O. , Golovko Iurii S. , Ryabuhin Sergey V. , Hanopolskyi Anton I. , Judd Duncan B. , Volochnyuk Dmitriy M. 
Published: February 2023

AbstractGastric and colorectal cancer models are essential for the advancement of precision medicine discovery and development. 2D attached monolayer, spheroid and organoid approaches have all been used in the formation of biobanks containing primary patient-derived cells. Here, we report an assessment of those procedures for a panel of nine patient-derived adenocarcinoma samples, along with the most applicable method for the bio-banking of these cell types. A live cell biobank of tumour specimens would facilitate drug discovery laboratories to evaluate drugs on the population of cell cultures, prior to the clinical phase.
External audit quality: its meaning, representations and potential conflict in practice
Authors: Sulaiman Noor Adwa 
Published: February 2023

PurposeThis study provides insights into the meanings given to audit quality (AQ) by audit partners responsible for delivering audit services. It explores the influence of contextual factors in the auditing setting on constructing such meanings and its representations.Design/methodology/approachDrawing on a symbolic-interactionist framework, this study takes an interpretive approach, employing semi-structured interviews with audit partners from the United Kingdom (UK).FindingsThree primary meanings of AQ are identified. First, in contradiction to that offered by “mainstream” AQ research, audit partners in this study predominantly regarded the meaning of AQ as an economic concept in the context of the “business” of auditing, delivering the service quality (e.g. value-added auditing and value-for-money) that is expected by their audit clients. Second, the audit partners also espouse the meaning of AQ to be “fit for purpose” audit documentation and adherence to quality control that meets the standards of compliance demanded by independent audit inspections. Third, and similar to the classic convention of AQ, audit partners consider “inputs” to AQ, attributes related to individual auditors (e.g. qualifications, experience and training) as one of the key AQ meanings. A range of stimuli underlies AQ meaning construction, including the audit firm's commercial interests, legitimacy, image management and social identity resulting from audit partners' interactions with audit clients, regulators, and their own self-reflexivity. Interestingly, this study identifies a considerable potential conflict between the meanings assigned to AQ, which suggests that auditors are struggling to strike a balance between the competing demands of those meanings.Research limitations/implicationsThis exploratory study addresses only the audit partners' perceptions concerning the meaning of AQ. Findings of this study are relevant to auditors and other parties, such as regulators, in addressing competing dimensions of AQ and potential choices involving conduct and content in any individual audit engagement.Originality/valueThe study complements existing research into AQ by exposing the rationales and potential behaviours that underlie commitments to quality by those involved in commissioning audit engagements. It also adds detailed evidence of how contextual factors in the auditing environment interact with auditors' notions of AQ.