Redox Regulation, Rather than Stress-Induced Phosphorylation, of a Hog1 Mitogen-Activated Protein Kinase Modulates Its Nitrosative-Stress-Specific Outputs

Data availability. The RNA sequencing dataset is available at EBI (www.ebi.ac.uk/arrayexpress/) under accession number E-MTAB-5990. Other data that support the findings of this study are available from the corresponding author upon reasonable request. ACKNOWLEDGMENTS We thank Debbie Smith for constructing the strains JC41 and JC310, Arnab Pradhan for help with DHE control experiments, and our colleagues in the Aberdeen Fungal Group and Newcastle Yeast Group for insightful discussions. We are also grateful to Mike Gustin for his advice. We are grateful to the Centre for Genome Enabled Biology and Medicine, Aberdeen Proteomics, the Iain Fraser Cytometry Centre, the Microscopy and Histology Facility, and the qPCR facility at the University of Aberdeen for their help, advice, and support. This work was funded by the UK Biotechnology and Biological Research Council (http://www.bbsrc.ac.uk) (grants BB/K017365/1 and BB/F00513X/1 to A.J.P.B. and grant BB/K016393/1 to J.Q.). This work was also supported by the European Research Council (http://erc.europa.eu/) (STRIFE advanced grant C-2009-AdG-249793 to A.J.P.B.), the UK Medical Research Council (http://www.mrc.ac.uk) (grant MR/M026663/1 to A.J.P.B. and grant MR/M000923/1 to P.S.S.), the Wellcome Trust (https://wellcome.ac.uk) (grant 097377 to A.J.P.B. and J.Q.), the MRC Centre for Medical Mycology and the University of Aberdeen (grant MR/M026663/1 to A.J.P.B.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewedPublisher PD

The Structure of an RNAi Polymerase Links RNA Silencing and Transcription

RNA silencing refers to a group of RNA-induced gene-silencing mechanisms that developed early in the eukaryotic lineage, probably for defence against pathogens and regulation of gene expression. In plants, protozoa, fungi, and nematodes, but apparently not insects and vertebrates, it involves a cell-encoded RNA-dependent RNA polymerase (cRdRP) that produces double-stranded RNA triggers from aberrant single-stranded RNA. We report the 2.3-Å resolution crystal structure of QDE-1, a cRdRP from Neurospora crassa, and find that it forms a relatively compact dimeric molecule, each subunit of which comprises several domains with, at its core, a catalytic apparatus and protein fold strikingly similar to the catalytic core of the DNA-dependent RNA polymerases responsible for transcription. This evolutionary link between the two enzyme types suggests that aspects of RNA silencing in some organisms may recapitulate transcription/replication pathways functioning in the ancient RNA-based world

Exploring design space: Machine learning for multi-objective materials design optimization with enhanced evaluation strategies

Discovering optimal material designs in the design space can be significantly accelerated by leveraging machine learning (ML) models for screening candidates. However, the quality of these designs depends on the prediction accuracy of the ML models and the efficiency of the optimization algorithms used. This study comprehensively compares different ML modeling strategies, optimization algorithms and evaluation strategies. Thereby, automated ML, tree-based ML models and neural networks were compared. Various optimization algorithms were analyzed, including random search, evolutionary and swarm-based methods. In addition, different strategies for evaluating the predictive performance of the ML models were investigated, which is particularly important as these models are expected to predict design parameters that deviate significantly from the known designs in the training data throughout the optimization. Our results highlight the capability of the proposed workflow to discover material designs that significantly outperform those within the training database and approach theoretical optima. Overall, this research contributes to advancing the field of material design optimization by providing a versatile and practical workflow that introduces automated ML into material design optimization and new model error assessment strategies tailored explicitly to optimization tasks

Structure of the RNA-dependent RNA polymerase P2 from the cystovirus φ8

The replication of RNA viruses relies on the activity of RNA-dependent RNA polymerases (RdRps). Despite large variations in their genomic sequences, viral RdRps share a common architecture generally known as a closed right hand. The P2 polymerase of cystovirus φ6 is currently among the best characterized viral RdRps. This polymerase is responsible for carrying out both replication and transcription of the viral double-stranded RNA genome using de novo initiation. Despite the extensive biochemical and structural studies conducted on φ6 P2, further structural information on other cystoviral RdRps is crucial to elucidate the structural and functional diversity of viral RdRps. Here, we have determined the atomic X-ray structure of the RdRp P2 from the φ6-related cystovirus φ8 at 3Å resolution. This structure completes the existing set of structural information on the φ8 polymerase complex and sheds light on the difference and similarities with related cystoviral RdRps

Water-sediment physicochemical dynamics in a large reservoir in the Mediterranean region under multiple stressors

Nowadays, the Mediterranean freshwater systems face the threat of water scarcity, along with multiple other stressors (e.g., organic and inorganic contamination, geomorphological alterations, invasive species), leading to the impairment of their ecosystem services. All these stressors have been speeding up, due to climate variability and land cover/land use changes, turning them into a big challenge for the water management plans. The present study analyses the physicochemical and phytoplankton biomass (chlorophyll-a) dynamics of a large reservoir, in the Mediterranean region (Alqueva reservoir, Southern Portugal), under diverse meteorological conditions and land cover/land use real scenarios (2017 and 2018). The most important stressors were identified and the necessary tools and information for a more effective management plan were provided. Changes in these parameters were further related to the observed variations in the meteorological conditions and in the land cover/land use. The increase in nutrients and ions in the water column, and of potentially toxic metals in the sediment, were more obvious in periods of severe drought. Further, the enhancement of nutrients concentrations, potentially caused by the intensification of agricultural activities, may indicate an increased risk of water eutrophication. The results highlight that a holistic approach is essential for a better water resources management strategy

Cleavage of an engulfment peptidoglycan hydrolase by a sporulation signature protease in Clostridioides difficile

Funding Information: This work was supported by the European Union Marie Sklodowska Curie Innovative Training Networks (contract number 642068) to AOH and AF was the recipient of a PhD fellowship under that contract. This project was supported by award PTDC/BIA\u2010MIC/29293/2017 to MS. This work was also financially supported by Project LISBOA\u201001\u20100145\u2010FEDER\u2010007660 (\u201CMicrobiologia Molecular, Estrutural e Celular\u201D) funded by FEDER funds through COMPETE2020\u2014\u201CPrograma Operacional Competitividade e Internacionaliza\u00E7\u00E3o\u201D (POCI), by national funds through the FCT (\u201CFunda\u00E7\u00E3o para a Ci\u00EAncia e a Tecnologia\u201D). DM is the recipient of a PhD fellowship (PD/BD/143148/2019) within the scope of the PhD program INTERFACE funded by FCT. This project was supported by the Medical Research Council (grant number MR/V032151/1) awarded to PSS and ABS and the BBSRC (BB/W005557/1, BB/W013630/1) to WV. CGR is supported by a Barbour Foundation PhD Studentship from Faculty of Medical Science, Newcastle University. This project was also supported by awards R01AI116895 and R01AI172043 from the National Institute of Allergy and Infectious Diseases to JAS. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIAID. The funders had no role in study design, data collection, and interpretation, or the decision to submit the work for publication. Publisher Copyright: © 2024 The Author(s). Molecular Microbiology published by John Wiley & Sons Ltd.In the model organism Bacillus subtilis, a signaling protease produced in the forespore, SpoIVB, is essential for the activation of the sigma factor σK, which is produced in the mother cell as an inactive pro-protein, pro-σK. SpoIVB has a second function essential to sporulation, most likely during cortex synthesis. The cortex is composed of peptidoglycan (PG) and is essential for the spore's heat resistance and dormancy. Surprisingly, the genome of the intestinal pathogen Clostridioides difficile, in which σK is produced without a pro-sequence, encodes two SpoIVB paralogs, SpoIVB1 and SpoIVB2. Here, we show that spoIVB1 is dispensable for sporulation, while a spoIVB2 in-frame deletion mutant fails to produce heat-resistant spores. The spoIVB2 mutant enters sporulation, undergoes asymmetric division, and completes engulfment of the forespore by the mother cell but fails to synthesize the spore cortex. We show that SpoIIP, a PG hydrolase and part of the engulfasome, the machinery essential for engulfment, is cleaved by SpoIVB2 into an inactive form. Within the engulfasome, the SpoIIP amidase activity generates the substrates for the SpoIID lytic transglycosylase. Thus, following engulfment completion, the cleavage and inactivation of SpoIIP by SpoIVB2 curtails the engulfasome hydrolytic activity, at a time when synthesis of the spore cortex peptidoglycan begins. SpoIVB2 is also required for normal late gene expression in the forespore by a currently unknown mechanism. Together, these observations suggest a role for SpoIVB2 in coordinating late morphological and gene expression events between the forespore and the mother cell.publishersversionpublishe

Diagnósticos de enfermagem identificados em pacientes internados em Unidade de Terapia Intensiva Adulto

Estudo descritivo para identificar nos registros de prontuários de pacientes internados em uma Unidade de Terapia Intensiva de Adultos os diagnósticos de enfermagem e mapear os diagnósticos mais frequentes às Necessidades Humanas Básicas. Obteve-se uma amostra de 44 prontuários. Identificaram-se 1.087 diagnósticos de enfermagem. Após exclusão de repetições, encontraram-se 28 diferentes títulos de diagnósticos. Vinte e cinco diagnósticos estavam relacionados às necessidades psicobiológicas, e três, às necessidades psicossociais. Sugere-se a realização de estudos que identifiquem, entre os diagnósticos de enfermagem formulados e as necessidades humanas afetadas, quais foram solucionados e para quais necessidades são predominantemente elaborados os cuidados. Os resultados deste estudo são importantes para a organização de conteúdos de ensino para alunos e enfermeiros, preparando-os para que, ao prestar o cuidado, considerem o ser humano, tanto nos aspectos biológicos, como emocionais e espirituais

The Structure of an RNAi Polymerase Links RNA Silencing and Transcription

RNA silencing refers to a group of RNA-induced gene-silencing mechanisms that developed early in the eukaryotic lineage, probably for defence against pathogens and regulation of gene expression. In plants, protozoa, fungi, and nematodes, but apparently not insects and vertebrates, it involves a cell-encoded RNA-dependent RNA polymerase (cRdRP) that produces double-stranded RNA triggers from aberrant single-stranded RNA. We report the 2.3-Å resolution crystal structure of QDE-1, a cRdRP from Neurospora crassa, and find that it forms a relatively compact dimeric molecule, each subunit of which comprises several domains with, at its core, a catalytic apparatus and protein fold strikingly similar to the catalytic core of the DNA-dependent RNA polymerases responsible for transcription. This evolutionary link between the two enzyme types suggests that aspects of RNA silencing in some organisms may recapitulate transcription/replication pathways functioning in the ancient RNA-based world

The cause of urinary symptoms among Human T Lymphotropic Virus Type I (HLTV-I) infected patients: a cross sectional study

BACKGROUND: HTLV-I infected patients often complain of urinary symptomatology. Epidemiological studies have suggested that these individuals have a higher prevalence and incidence of urinary tract infection (UTI) than seronegative controls. However, the diagnosis of UTI in these studies relied only on patient information and did not require confirmation by urine culture. The purpose of this study was to investigate the role of urinary tract infection (UTI) as the cause of urinary symptoms in HTLV-I infected patients. METHODS: In this cross sectional study we interviewed, and cultured urine from, 157 HTLV-I seropositive individuals followed regularly at a specialized clinic. All patients were evaluated by a neurologist and classified according to the Expanded Disability Status Scale (EDSS). Urodynamic studies were performed at the discretion of the treating physician. RESULTS: Sixty-four patients complained of at least one active urinary symptom but UTI was confirmed by a positive urine culture in only 12 of these patients (19%); the majority of symptomatic patients (81%) had negative urine cultures. To investigate the mechanism behind the urinary complaints in symptomatic individuals with negative urine cultures, we reviewed the results of urodynamic studies performed in 21 of these patients. Most of them (90.5%) had abnormal findings. The predominant abnormalities were detrusor sphincter hyperreflexia and dyssynergia, findings consistent with HTLV-I-induced neurogenic bladder. On a multivariate logistic regression, an abnormal EDSS score was the strongest predictor of urinary symptomatology (OR 9.87, 95% CI 3.465 to 28.116, P < 0.0001). CONCLUSION: Urinary symptomatology suggestive of UTI is highly prevalent among HTLV-I seropositive individuals but true UTI is responsible for the minority of cases. We posit that the main cause of urinary symptoms in this population is neurogenic bladder. Our data imply that HLTV-I infected patients with urinary symptomatology should not be empirically treated for UTI but rather undergo urine culture; if a UTI is excluded, further investigation with urodynamic studies should be considered