bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Host miR-17-92 Cluster Negatively Regulates Mouse Mammary Tumor Virus (MMTV) Replication via miR-92a by Targeting the Viral Genome
Authors: Baby Jasmin , Gull Bushra , Ahmad Waqar , Khader Thanumol Abdul , Panicker Neena G. , Akhlaq Shaima , Rizvi Tahir A. , Mustafa Farah 
Published: September 2023

AbstractThe mouse mammary tumor virus (MMTV) induces mammary tumors in mice. Recently, we have shown that MMTV perturbs expression of the host miR-17-92 cluster in MMTV-infected mammary glands and MMTV-induced mammary tumors. Known as oncomiR-1, this cluster is often dysregulated in a number of cancers, especially breast cancer. Therefore, we investigated whether there was a functional interaction between MMTV and the cluster. Our results reveal that MMTV expression led to dysregulation of the cluster in both mammary epithelial HC11 and HEK293T cells with the expression of miR-92a cluster member being affected the most. Conversely, over-expression of the whole or partial cluster significantly repressed MMTV expression. Interestingly, overexpression of miR-92a alone resulted in MMTV repression to the same extent as observed with the whole or partial cluster. Inhibition of miR-92a led to nearly a complete recovery of MMTV gene expression. Deletion/substitution of the miR-92a seed sequence within the cluster rescued MMTV expression. Dual luciferase assays identified MMTV genomic RNA as the target of miR-92a. These results show that the miR-17-92 cluster acts as part of the cell’s well-known miRNA-based anti-viral response to thwart incoming MMTV infection. Interestingly, miR-92a expression was the least amongst cluster members in MMTV-induced breast tumors, suggesting that the elevated level of MMTV expression in tumors is due perhaps to MMTV subverting miR-92a overexpression, restricting its ability to control MMTV replication during tumorigenesis. Thus, our study provides the first evidence demonstrating the biological significance of host miRNAs in controlling MMTV replication and influencing the process of tumorigenesis.ImportanceMMTV is a non-acute, slow-transforming retrovirus that causes breast cancer and lymphomas in mice. Consequently, understanding how MMTV interacts with its host can reveal critical aspects of cellular anti-viral responses and the process of tumorigenesis. This study reveals that the host miR-17-92 cluster plays an anti-viral role during MMTV infection which seems to be counteracted by MMTV during tumorigenesis. This observation is significant since MMTV-induced tumors share similarity with human breast cancer and the MMTV/mouse model is the best mammalian animal model to study breast cancer initiation, progression, and therapy. Moreover, MMTV is increasingly (though controversial) being implicated in human breast cancer, leukemias/lymphomas, and biliary cirrhosis due to its potential zoonosis into humans. Thus, if proven true, understanding how miRNAs modulate MMTV replication will be critical in appreciating how hosts miRNAs affect virus replication/tumorigenesis, and towards the development of novel miRNA-based therapeutics (e.g., anti-miRs) to thwart MMTV replication in humans.
Structural basis of aggregate binding by the AAA+ disaggregase ClpG
Authors: Katikaridis Panagiotis , Simon Bernd , Jenne Timo , Moon Seongjoon , Lee Changhan , Hennig Janosch , Mogk Axel 
Published: September 2023

AbstractSevere heat stress causes massive loss of essential proteins by aggregation necessitating a cellular activity that rescues aggregated proteins. This activity is executed by ATP-dependent, ring-forming, hexameric AAA+ disaggregases. Little is known about the recognition principles of stress-induced protein aggregates. How can disaggregases specifically target aggregated proteins while avoiding binding to soluble non-native proteins? Here, we determined by NMR spectroscopy the core structure of the aggregate targeting N1 domain of the bacterial AAA+ disaggregase ClpG, which confers extreme heat resistance to bacteria. N1 harbors a Zn2+-coordination site that is crucial for structural integrity and disaggregase functionality. Conserved hydrophobic N1 residues located on a β-strand were found crucial for aggregate targeting and disaggregation activity. Mixing experiments with N1-truncated AAA+ hexamers revealed that a minimal number of four N1 domains must be present in a AAA+ ring for high disaggregation activity. We suggest that multiple N1 domains increase substrate affinity through avidity effects. These findings define the recognition principle of a protein aggregate by a disaggregase, involving simultaneous contacts with multiple hydrophobic substrate patches located in close vicinity on an aggregate surface. This binding mode ensures selectivity for aggregated proteins while sparing soluble, non-native protein structures from disaggregase activity.
The crystal structure of bacteriophage λ RexA provides novel insights into the DNA binding properties of Rex-like phage exclusion proteins
Authors: Adams Myfanwy C. , Schiltz Carl J. , Sun Jing , Hosford Christopher J. , Johnson Virginia M. , Pan Hao , Borbat Peter P. , Freed Jack H. , Thomason Lynn C. , Court Carolyn , Court Donald L. , Chappie Joshua S. 
Published: September 2023

ABSTRACTRexA and RexB function as an exclusion system that prevents bacteriophage T4rIImutants from growing onE. coliλ phage lysogens. Recent data established that RexA is a non-specific DNA binding protein that can act independently of RexB to bias the λ bistable switch toward the lytic state, preventing conversion back to lysogeny. The molecular interactions underlying these activities are unknown, owing in part to a dearth of structural information. Here we present the 2.05-Å crystal structure of the λ RexA dimer, which reveals a two-domain architecture with unexpected structural homology to the recombination-associated protein RdgC. Modelling suggests that our structure adopts a closed conformation and would require significant domain rearrangements to facilitate DNA binding. Mutagenesis coupled with electromobility shift assays, limited proteolysis, and double electron-electron spin resonance spectroscopy support a DNA-dependent conformational change. In vivophenotypes of RexA mutants suggest that DNA binding is not a strict requirement for phage exclusion but may directly contribute to modulation of the bistable switch. We further demonstrate that RexA homologs from other temperate phages also dimerize and bind DNAin vitro. Collectively, these findings advance our mechanistic understanding of Rex functions and provide new evolutionary insights into different aspects of phage biology.
Strain-specific differences in the interactions of the cucumber mosaic virus 2b protein with the viral 1a and host Argonaute 1 proteins
Authors: Crawshaw Sam , Watt Lewis G. , Murphy Alex M. , Carr John P. 
Published: September 2023

Abstract/SummaryThe cucumber mosaic virus (CMV) 2b protein is a potent counter-defense protein and symptom determinant that inhibits antiviral silencing by titration of short double-stranded RNAs. Expression of the 2b protein from the CMV Subgroup IA strain Fny-CMV in transgenicArabidopsis thalianaplants disrupts microRNA-mediated cleavage of host mRNAs by binding ARGONAUTE 1 (AGO1), leading to symptom-like phenotypes. This also triggers AGO2-mediated resistance against CMV and strong resistance to CMV’s aphid vectors, which would be deleterious to viral fitness. However, in authentic viral infections the Fny-CMV 1a protein modulates 2b-AGO1 interactions, which inhibits induction of AGO2-mediated virus resistance and resistance to aphid vectors. Contrastingly, the 2b proteins encoded by the Subgroup II LS-CMV strain or the recently discovered Subgroup IA strain Ho-CMV induce no apparent symptoms. Confocal laser scanning microscopy, bimolecular fluorescence complementation and co-immunoprecipitation showed that the Fny-CMV and Ho-CMV 2b proteins interact with the Fny-CMV and LS-CMV 1a proteins whilst the CMV-LS 2b protein does not. However, the Fny-CMV, Ho-CMV and LS-CMV 2b proteins all interacted with AGO1, but while AGO1-Fny2b complexes occurred in the host cell nucleus and cytoplasm, the corresponding AGO1-2b complexes for LS-CMV and Ho-CMV accumulated almost exclusively in nuclei.AGO2transcript accumulation was used to assess the inhibition of AGO1-mediated miRNA-regulated mRNA cleavage. While Fny-CMV 2b induced a five-fold increase inAGO2accumulation, the LS-CMV and Ho-CMV 2b proteins induced only two-fold increases. Thus, these 2b proteins bind AGO1 but are less effective at inhibiting AGO1 activity. We conclude that the intracellular localization sites of 2b-AGO1 complexes influences the degree to which a 2b protein can inhibit microRNA-mediated host mRNA degradation and that cytoplasmic AGO1 has the strongest influence on miRNA-mediated cellular mRNA turnover.
Single-cell transcriptomics reveals functional insights into a non-model aquatic phytoflagellate and its metabolically linked bacterial community
Authors: Florenza Javier , Jeevannavar Aditya , Divne Anna-Maria , Tamminen Manu , Bertilsson Stefan 
Published: September 2023

AbstractSingle-cell transcriptomics is a vital tool for unraveling metabolism and tissue diversity in model organisms. Its potential for elucidating the ecological roles of microeukaryotes, especially non-model ones, remains largely unexplored. This study employed the Smart-seq2 protocol onOchromonas triangulata, a microeukaryote lacking a reference genome, showcasing how transcriptional states align with growth phases. Unexpectedly, a third transcriptional state was identified, across both growth phases. Metabolic mapping revealed a down-regulation trend in pathways associated with ribosome functioning, CO2 fixation, and carbohydrate catabolism from fast to slow growth to the third transcriptional state. Using carry-over rRNA reads, taxonomic identity ofOchromonas triangulatawas re-confirmed and distinct bacterial communities associated with transcriptional states were identified. This study underscores single-cell transcriptomics as a powerful tool for characterizing metabolic states in microeukaryotes without a reference genome, offering insights into unknown physiological states and individual-level interactions with different bacterial taxa. This approach holds broad applicability for uncovering ecological roles, surpassing alternative methods like metagenomics or metatranscriptomics.
Leaf and shoot apical meristem transcriptomes of quinoa (Chenopodium quinoaWilld.) in response to photoperiod and plant development
Authors: Maldonado-Taipe Nathaly , Rey Elodie , Tester Mark , Jung Christian , Emrani Nazgol 
Published: September 2023

AbstractOur study aimed to identify candidate genes for flowering time regulation and photoperiod response in quinoa. We investigated the timing of photoperiod-driven floral transition and analyzed the transcriptomes of leaf and shoot apical meristems in photoperiod-sensitive and -insensitive quinoa accessions. Histology analysis of the apical meristem showed that floral transition in quinoa initiates two to three weeks after sowing. We found four groups of differentially expressed genes responding to plant development and floral transition, which were annotated in the QQ74-V2 reference genome, including (i) 222 genes differentially responding to photoperiod in leaves, (ii) 1,812 genes differentially expressed between accessions under long-day conditions in leaves, (iii) 57 genes responding to developmental changes between weeks under short-day conditions in leaves, and (iv) 911 genes responding to floral transition within the shoot apical meristem. Interestingly, out of the thousands of candidates, two putativeFTorthologues and several others have been reported as key regulators of flowering time in other species (e.g.,SOC1,COL,AP1). Additionally, we used co-expression networks to associate novel transcripts to a putative biological process based on the annotated genes within the same co-expression cluster. The candidate genes in this study would benefit quinoa breeding by identifying and integrating their beneficial haplotypes in crossing programs to develop adapted cultivars to diverse environmental conditions.
An assessment of the prevalence and risk factors of hypertensive crisis in patients who visit the Emergency Outpatient Department (EOPD) at Adama Hospital Medical College, Adama, Oromia, Ethiopia: A 6-month prospective study
Authors: Abebe Abel Tezera , Kebede Yabets Tesfaye , Mohammed Bekri Delil 
Published: September 2023

ABSTRACTBackgroundOver 1 billion people worldwide suffer from the common chronic medical condition of hypertension. A hypertensive crisis occurs when blood pressure exceeds 180/110 mmHg. Depending on whether the target organ is harmed, the situation may be presented as a hypertensive emergency or urgency.ObjectiveTo assess the prevalence and risk factors of patients with hypertensive crises who visited the Emergency Outpatient Department (EOPD) at Adama Hospital Medical College in Adama, Oromia, Ethiopia, between January 01 and August 31, 2021 G.C.MethodologyA cross sectional, prospective study on hypertensive crisis was conducted at Adama Hospital Medical College from January 01 to August 31, 2021 G.C. The data was collected using a standardized questionnaire, validated for completeness, and analyzed using SPSS. The findings were tabulated, and conclusions and recommendations were conveyed.ResultA total of 444 individuals with hypertension in crisis were identified. Of these, 56.8% were men, resulting in a M:F ratio of 1.31:1. Those between the ages of 66 and 75 were the most affected. At presentation, 91.0% of the study participants were known hypertensive patients. Of the known hypertensive patients, the majority (34.9%) were known to have been hypertensive for 5 to 10 years. Of the known hypertensive patients, 48.6% were found to be adherent. Hypertensive urgency was discovered to be far more common than hypertensive emergencies (63.5% vs. 36.5%). Headache was the most common presenting symptom, and most of the patients (36.5%) presented to the health setup in less than 24 hours. The main risk variables identified were drug discontinuation, family history of hypertension, salt consumption, and alcohol usage. The main excuse for lack of adherence was the cost of the medications. More than half of the patients do not have any additional comorbidities, and of those who do, diabetes mellitus is the most prevalent. A stroke was identified as a major complication.Conclusions and recommendationsHypertensive crises are one of the most prevalent reasons for EOPD admission and are linked to significant consequences. At presentation, most of the study subjects were known hypertension patients. Diabetes mellitus was discovered to be a comorbid condition in one quarter of them. Although more than half of the patients have improved, the death rate remains high. Infrastructure and capacity building to provide hospitals with the requisite baseline investigations are among the government’s recommendations. Health practitioners are expected to make improvements, such as educating the public about the need for lifestyle changes and evaluating and managing any hypertension problems.
Learning the sequence code of protein expression in human immune cells
Authors: Nicolet Benoît P. , Jurgens Anouk P. , Bresser Kaspar , Guislain Aurélie , Bradariç Antonia , Wolkers Monika C. 
Published: September 2023

ABSTRACTAccurate protein expression in human immune cells is essential for appropriate cellular function. The mechanisms that define protein abundance are complex and executed on transcriptional, post-transcriptional and post-translational level. Here, we present SONAR, a machine learning pipeline that learns the endogenous sequence code and that defines protein abundance in human cells. SONAR uses thousands of sequence features (SFs) to predict up to 63% of the protein abundance independently of promoter or enhancer information. SONAR uncovered the cell type-specific and activation-dependent usage of SFs. The deep knowledge of SONAR provides a map of biologically active SFs, which can be leveraged to manipulate the amplitude, timing, and cell type-specificity of protein expression. SONAR informed on the design of enhancer sequences to boost T cell receptor expression and to potentiate T cell function. Beyond providing fundamental insights in the regulation of protein expression, our study thus offers novel means to improve therapeutic and biotechnology applications.One Sentence SummarySONAR informs the design of cell type-specific protein expression in human cells
Phosphorylation bar-coding of Free Fatty Acid receptor 2 is generated in a tissue-specific manner
Authors: Barki Natasja , Jenkins Laura , Marsango Sara , Dedeo Domonkos , Bolognini Daniele , Dwomoh Louis , Abdelmalik Aisha M. , Nilsen Margaret , Stoffels Manon , Nagel Falko , Schulz Stefan , Tobin Andrew B. , Milligan Graeme 
Published: September 2023

AbstractFree Fatty Acid receptor 2 (FFA2) is activated by short-chain fatty acids and expressed widely, including in white adipocytes and various immune and enteroendocrine cells. Using both wild type human FFA2 and a Designer Receptor Exclusively Activated by Designer Drugs (DREADD) variant we explored the activation and phosphorylation profile of the receptor, both in heterologous cell lines and in tissues from transgenic knock-in mouse lines expressing either human FFA2 or the FFA2-DREADD. FFA2 phospho-site specific antisera targeting either pSer296/pSer297or pThr306/pThr310provided sensitive biomarkers of both constitutive and agonist-mediated phosphorylation as well as an effective means to visualise agonist-activated receptorsin situ. In white adipose tissue phosphorylation of residues Ser296/Ser297was enhanced upon agonist activation whilst Thr306/Thr310did not become phosphorylated. By contrast, in immune cells from Peyer’s patches Thr306/Thr310become phosphorylated in a strictly agonist-dependent fashion whilst in enteroendocrine cells of the colon both Ser296/Ser297and Thr306/Thr310were poorly phosphorylated. The concept of phosphorylation bar-coding has centred to date on the potential for different agonists to promote distinct receptor phosphorylation patterns. Here we demonstrate that this occurs for the same agonist-receptor pairing in different patho-physiologically relevant target tissues. This may underpin why a single G protein-coupled receptor can generate different functional outcomes in a tissue-specific manner.Significance StatementThe concept that agonist-occupancy of a G protein-coupled receptor can result in distinct patterns of phosphorylation of residues on the intracellular elements of the receptor in different tissues is referred to ‘bar-coding’. This has been challenging to demonstrate conclusively in native tissues. We now show this to be the case by using tissues from transgenic knock-in mouse lines expressing either wild type or a DREADD variant of human Free Fatty Acid Receptor 2 and a pair of phospho-site specific antisera. Clear differences in the pattern of phosphorylation of the receptor induced by the same ligand were observed in white adipose tissue and immune cells derived from Peyer’s patches. These outcomes provide direct evidence in tissues, at endogenous expression levels, of a well promoted hypothesis.
Attached to or stuck in? How resource attributes of i-deals influence the variation in continuance or affective commitment
Authors: Liu Yan , Zhou Miaodi , Hu Lingyan , Jaussi Kimberly S. 
Published: September 2023

PurposeThis study aims to identify when and why receiving i-deals will result in an increase in affective commitment rather than continuance commitment. As affective commitment yields long-term benefits for organizations than continuance commitment, this work will help organizations accrue maximum benefits from granting i-deals.Design/methodology/approachThis study develops a cognitive model delineating the process between i-deal receipt and the variation in i-dealers’ continuance or affective commitment.FindingsAfter receiving i-deals, i-dealers’ perceived valence may change with i-dealers’ evaluations of i-deal resources under the condition of coworkers' negative reactions or organizational investment. The i-deal valence changes trigger i-dealers’ internal or external attributions of coworkers' negative reactions or organizational investment, which leads to the variation in continuance or affective commitment. The changes of affective commitment also affect the variation in continuance commitment.Originality/valueIntegrating expectancy theory and attribution theory, this research addresses inconsistent findings about i-deals’ effect on continuance or affective commitment by revealing the critical factors that lead to the variation in the two types of commitment. The proposed model offers new theoretical rationale for why i-dealers may not reciprocate the goodwill of i-deals to their organizations. This study suggests i-dealers will engage in attributions rather than being passive recipients of their coworkers' negative reactions, which challenges previous view that the effectiveness of i-deals is ultimately determined by coworkers' acceptance. This research also extends the i-deal dynamics literature by depicting how i-deal valence changes arise and influence continuance or affective commitment.
Numerical simulation of true triaxial unilateral unloading effect of fractured rock
Authors: Zhang Chao , Fu Jianxin , Wang Yu 
Published: September 2023

PurposeThe interaction between rock mass structural planes and dynamic stress levels is important to determine the stability of rock mass structures in underground geotechnical engineering. In this work, the authors aim to focus on the degradation effects of fracture geometric parameters and unloading stress paths on rock mechanical properties.Design/methodology/approachA three-dimensional Particle Flow Code (PFC3D) was used for a systematic numerical simulation of the strength failure and cracking behavior of granite specimens containing prefabricated cracks under conventional triaxial compression and triaxial unilateral unloading. The authors demonstrated the unique mechanical response of prefabricated fractured rock under two conditions. The crack initiation, propagation, and coalescence process of pre-fissured specimens were analyzed in detail.FindingsThe authors show that the prefabricated cracks and unilateral unloading conditions not only deteriorate the mechanical strength but also have significant differences in failure modes. The degrading effect of cracks on model strength increases linearly with the decrease of the dip angle. Under the condition of true triaxial unilateral unloading, the deterioration effect of peak strength of rock is very significant, and unloading plays a role in promoting the instability failure of rock after peak, making the rock earlier instability failure. Associating with the particle vector diagram and crack coalescence process, the authors find that model failure mode under unilateral loading conditions is obviously distinct from that in triaxial loading. The peak strain in the unloading direction increases sharply, resulting in a new shear slip.Originality/valueThis study is expected to improve the understanding of the strength failure and cracking behavior of fractured rock under unilateral unloading.