bluuebunny/crossref_metadata_2025 huggingface dataset:
Temperature affects the host range of Rhabdochlamydia porcellionis and the infectivity of Waddlia chondrophila and Chlamydia trachomatis elementary bodies
Authors: Marquis Bastian , Ardissone Silvia , Greub Gilbert
Published: September 2022

The Rhabdochlamydiaceae family is a recent addition to the Chlamydiales order. Its members were discovered in cockroaches and woodlice but recent metagenomics surveys demonstrated the widespread distribution of this family in the environment. It was moreover estimated to be the largest family of the Chlamydiales order based on 16S rRNA encoding gene diversity. Unlike most chlamydia-like organisms, no Rhabdochlamydiaceae could be co-cultivated in amoebae and its host range remains largely unknown. Here, we tested the permissivity of various mammalian and arthropod cell lines to determine the host range of Rhabdochlamydia porcellionis, the only cultured representative of this family. While a growth could initially only be obtained in the Sf9 cell line, lowering the incubation temperature of the mammalian cells from 37 °C to 28 °C allowed R. porcellionis to grow in those cells. Furthermore, a 6 h exposure to 37 °C was sufficient to irreversibly block the replication of R. porcellionis, suggesting that this bacterium either lost or never acquired the ability to grow at 37 °C. We next sought to determine if temperature would also affect the infectivity of elementary bodies. Although we could not purify enough bacteria to reach a conclusive result for R. porcellionis, our experiment showed that the elementary bodies of Chlamydia trachomatis and Waddlia chondrophila lose their infectivity faster at 37 °C than at room temperature. Our results demonstrate that members of the Chlamydiales adapt to the temperature of their host organism and that this adaptation can in turn restrict their host range.

Importance

The Rhabdochlamydiaceae family is part of the Chlamydiales, a bacterial order that includes obligate intracellular bacteria sharing the same biphasic developmental cycle. This family have been shown to be highly prevalent in the environment, particularly in freshwater and soil and despite being estimated to be the largest family in the Chlamydiales order, is only poorly studied. Members of the Rhabdochlamydiaceae have been detected in various arthropods like ticks, spiders, cockroaches and woodlice, but the full host range of this family is currently unknown. In this study, we showed that R. porcellionis, the only cultured representative of the Rhabdochlamydiaceae family cannot grow at 37 °C and is quickly inactivated at this temperature. A similar temperature sensitivity was also observed for elementary bodies of chlamydial species adapted to mammals. Our work demonstrates that some chlamydiae adapt to the temperature of their reservoir, making a jump between species with different body temperatures unlikely.
Extensive cellular multitasking within Bacillus subtilis biofilms
Authors: Yannarell Sarah M. , Beaudoin Eric S. , Talley Hunter S. , Schoenborn Alexi A. , Orr Galya , Anderton Christopher R. , Chrisler William B. , Shank Elizabeth A
Published: September 2022

Bacillus subtilis is a soil-dwelling bacterium that can form biofilms, or communities of cells surrounded by a self-produced extracellular matrix. In biofilms, genetically identical cells often exhibit heterogeneous transcriptional phenotypes so that only subpopulations of cells carry out essential yet costly cellular processes that allow the entire community to thrive. Surprisingly, the extent of phenotypic heterogeneity and the relationships between subpopulations of cells within biofilms of even in well-studied bacterial systems like B. subtilis remains largely unknown. To determine relationships between these subpopulations of cells, we created 182 strains containing pairwise combinations of fluorescent transcriptional reporters for the expression state of 14 different genes associated with potential cellular subpopulations. We determined the spatial organization of the expression of these genes within biofilms using confocal microscopy, which revealed that many reporters localized to distinct areas of the biofilm, some of which were co-localized. We used flow cytometry to quantify reporter co-expression, which revealed that many cells ‘multi-task’, simultaneously expressing two reporters. These data indicate that prior models describing B. subtilis cells as differentiating into specific cell-types, each with a specific task or function, were oversimplified. Only a few subpopulations of cells, including surfactin and plipastatin producers, as well as sporulating and competent cells, appear to have distinct roles based on the set of genes examined here. These data will provide us with a framework with which to further study and make predictions about the roles of diverse cell phenotypes in B. subtilis biofilms.

IMPORTANCE

Many microbes differentiate, expressing diverse phenotypes to ensure their survival in various environments. However, studies on phenotypic differentiation have typically examined only a few phenotypes at one time, thus limiting our knowledge about the extent of differentiation and phenotypic overlap in the population. We investigated the spatial organization and gene expression relationships for genes important in B. subtilis biofilms. In doing so, we mapped spatial gene expression patterns and expanded the number of cell populations described in the B. subtilis literature. It is likely that other bacteria also display complex differentiation patterns within their biofilms. Studying the extent of cellular differentiation in other microbes may be important when designing therapies for disease-causing bacteria, where studying only a single phenotype may be masking underlying phenotypic differentiation relevant to infection outcomes.
Analysis of State-level Variation in Distribution of Oxycodone and its Adverse Effect Profile in the US from 2000-2021
Authors: Solgama Jay P. , Liu Edward Y. , Davis Mellar P. , Graham Jove , McCall Kenneth L. , Piper Brian J.
Published: September 2022

Objectives

Characterize oxycodone’s distribution in the US by state and its adverse effect profile from 2000-2021.

Design

Observational

Setting

More than 80,000 Americans died of an opioid overdose in 2021 as the United States (US) continues to struggle with an opioid crisis. Prescription opioids play a substantial role, introducing patients to opioids and providing a supply of drugs that can be redirected to those seeking to misuse them.

Methods

The Drug Enforcement Administration annual summary reports from the Automation of Reports and Consolidated Orders System (ARCOS) provided weights of oxycodone distributed per state by business type (pharmacies, hospitals, and practitioners). Weights were converted to Morphine Milligram Equivalents (MME) per capita and normalized for population.

Results

There was a sharp 280.13% increase in total MME/person of oxycodone from 2000-2010, followed by a slower 54.34% decrease from 2010-2021. Florida (2007-11), Delaware (2003-20), and Tennessee (2012-21) displayed consistent and substantial elevations in combined MME/person compared to other states. In the peak year (2010), there was a 15-fold difference between the highest and lowest states. MME/person from only pharmacies, which constituted >94% of the total, showed similar results. Hospitals in Alaska (2000-01, 2008, 2010-21), Colorado (2008-21), and DC (2000-11) distributed substantially more MME/person over many years compared to other states. Florida stood out in practitioner-distributed oxycodone, with an elevation of almost 15-fold the average state from 2006-2010. The percentage of consumer reports in the FDA Adverse Drugs Events Reporting System (FAERS) increased from 6.3% (2001) to 95% (2021). Adverse effects distribution remained constant by age and sex, with higher average proportions in males (55%) and the 18-65 age group (79%).

Conclusions

Oxycodone distribution across the US showed marked differences between states and business types over time. Investigation of opioid policies in states of interest may provide insight for future actions to mitigate opioid misuse.

Strengths and limitations of this study

ARCOS is publicly accessible, comprehensive, and includes institutions that are unavailable in other commonly used databases (i.e. IQVIA).

Diversion of oxycodone or whether the prescribed amounts were utilized cannot be determined from ARCOS data.

FAERS data includes duplicates, incomplete results, and non-verifiable data which cannot be used to suggest causation between oxycodone and adverse events.

These complementary results from two databases may not generalize to other countries with more restrictive oxycodone policies.
Aggregate expression of genes lacking CpG islands increases with age and is positively associated with human mortality
Authors: Kerber Richard A. , O’Brien Elizabeth , Cawthon Richard M.
Published: September 2022

In both mice and humans the misexpression of many genes lacking CpG islands (CGI- genes) increases with age, promoting inflammation and degenerative changes (Lee et al. 2021, ref. 1). In light of this recent discovery, we have revisited and expanded upon our previous work on gene expressions vs. aging and mortality in the three-generation CEPH (Centre d’Etudes du Polymorphisme Humain) Utah (CEU) families (Kerber et al. 2009, ref. 2). That study examined gene expressions in lymphoblastoid cell lines (LCLs) established in the early 1980s from all three CEU generations, in relation to age at blood draw, and in relation to the long-term survival of the grandparent generation. The 2009 study did not, however, consider the CGI status of genes, and it excluded from analysis genes not expressed in all of the subjects; therefore, the contribution to variation in age-at-death of inter-individual variation in the misexpression of genes with increasing age was not investigated. For the current study, after categorizing genes by their CGI status (- or +), we now find that most CGI- gene expressions in the LCLs increased with donor age, and after adjustment for donor age and sex, were positively associated with mortality risks. In contrast, most CGI+ gene expressions decreased with donor age, with higher expressions associated with decreased mortality risks. Of 7025 genes with known CGI status with expression detected in sufficient numbers of subjects from the grandparent generation to allow testing of association with mortality, 1834 genes were expressed in all subjects’ LCLs across all three generations, and 5191 were expressed in some, but not all subjects. We found the set of “not always expressed” genes to be highly enriched for CGI- genes. Furthermore, 49.4% of the CGI- genes were never expressed from ages 0-14, but expressed sometimes or always at older ages; in contrast, only 22.3% of the CGI+ genes were never expressed from ages 0-14, but expressed at older ages. These data support the model proposed by Lee et al. 2021, whereby tissue-restricted CGI- gene expressions become increasingly misexpressed during aging, contributing to loss of cellular identity, multiple aging-related pathologies, and ultimately death.
Heterogeneous aging across multiple organ systems and prediction of chronic disease and mortality
Authors: Tian Ye Ella , Cropley Vanessa , Maier Andrea B. , Lautenschlager Nicola T. , Breakspear Michael , Zalesky Andrew
Published: September 2022

Biological aging of human organ systems reflects the interplay of age, chronic disease, lifestyle and genetic risk. Using longitudinal brain imaging and physiological phenotypes from the UK Biobank, we establish normative models of biological age for 3 brain and 7 body systems. We find that an organ’s biological age selectively influences the aging of other organ systems, revealing a multiorgan aging network. We report organ age profiles for 16 chronic diseases, where advanced biological aging extends from the organ of primary disease to multiple systems. Advanced body age associates with several lifestyle and environmental factors, leucocyte telomere lengths and mortality risk, and predicts survival time (AUC=0.77) and premature death (AUC=0.86). Our work reveals the multisystem nature of human aging in health and chronic disease. It may enable early identification of individuals at increased risk of aging-related morbidity and inform new strategies to potentially limit organ-specific aging in such individuals.
Evaluation of QuantiFERON SARS-CoV-2 interferon-γ release assay following SARS-CoV-2 infection and vaccination
Authors: Johnson Síle A , Phillips Eloise , Adele Sandra , Longet Stephanie , Malone Tom , Mason Chris , Stafford Lizzie , Jamsen Anni , Gardiner Siobhan , Deeks Alexandra , Neo Janice , Blurton Emily J , White Jemima , Ali Muhammed , Kronsteiner-Dobramysl Barbara , Skelly Dónal T , Jeffery Katie , Conlon Christopher P , Goulder Philip ,   PITCH Consortium, Carroll Miles , Barnes Eleanor , Klenerman Paul , Dunachie Susanna J
Published: September 2022

Background

T cells are important in preventing severe disease from SARS-CoV-2, but scalable and field-adaptable alternatives to expert T cell assays are needed. The interferon-gamma release assay QuantiFERON platform was developed to detect T cell responses to SARS-CoV-2 from whole blood with relatively basic equipment and flexibility of processing timelines.

Methods

48 participants with different infection and vaccination backgrounds were recruited. Whole blood samples were analysed using the QuantiFERON SARS-CoV-2 assay in parallel with the well-established ‘Protective Immunity from T Cells in Healthcare workers’ (PITCH) ELISpot, which can evaluate spike-specific T cell responses.

Aims

The primary aims of this cross-sectional observational cohort study were to establish if the QuantiFERON SARS-Co-V-2 assay could discern differences between specified groups and to assess the sensitivity of the assay compared to the PITCH ELISpot.

Findings

The QuantiFERON SARS-CoV-2 distinguished acutely infected individuals (12-21 days post positive PCR) from naïve individuals (p< 0.0001) with 100% sensitivity and specificity for SARS-CoV-2 T cells, whilst the PITCH ELISpot had reduced sensitivity (62.5%) for the acute infection group. Sensitivity with QuantiFERON for previous infection was 12.5% (172-444 days post positive test) and was inferior to the PITCH ELISpot (75%).

Although the QuantiFERON assay could discern differences between unvaccinated and vaccinated individuals (55-166 days since second vaccination), the latter also had reduced sensitivity (55.5%) compared to the PITCH ELISpot (66.6%).

Conclusion

The QuantiFERON SARS-CoV-2 assay showed potential as a T cell evaluation tool soon after SARS-CoV-2 infection but has lower sensitivity for use in reliable evaluation of vaccination or more distant infection.

Graphical abstract

With the exception of acute infection group, the PITCH ELISpot S1+S2 had greater sensitivity for SARS-CoV-2 specific T cell responses compared with the QuantiFERON SARS-CoV-2 assay tube Ag3.
Evaluation of a microRNA-based Risk Classifier Predicting Cancer-Specific Survival in Renal Cell Carcinoma with Tumor Thrombus of the Inferior Vena Cava
Authors: Kotlyar Mischa J. , Krebs Markus , Burger Maximilian , Kübler Hubert , Bargou Ralf , Kneitz Susanne , Otto Wolfgang , Breyer Johannes , Vergho Daniel C. , Kneitz Burkhard , Kalogirou Charis
Published: September 2022

(1)

Background

Clear cell renal cell carcinoma extending into the inferior vena cava (ccRCCIVC) represents a clinical high-risk setting. However, there is substantial heterogeneity within this patient subgroup regarding survival outcomes. Previously, members of our group developed a microRNA(miR)-based risk classifier – containing miR-21, miR-126 and miR-221 expression – which significantly predicted cancer-specific survival (CSS) of ccRCCIVCpatients.

(2)

Methods

Examining a single-center cohort of tumor tissue from n = 56 patients with ccRCCIVC, we measured expression levels of miR-21, miR-126 and miR-221 by qRT-PCR. Prognostic impact of clinicopathological parameters and miR expression were investigated via univariate and multivariate cox regression. Referring to the previously established risk classifier, we performed Kaplan Meier analyses for single miR expression levels and the combined risk classifier. Cut-off values and weights within the risk classifier were taken from the previous study.

(3)

Results

miR-21 and miR-126 expression were significantly associated with lymphonodal status at time of surgery, development of metastasis during follow-up, and cancer-related death. In Kaplan Meier analyses, miR-21 and miR-126 significantly impacted CSS in our cohort. Moreover, applying the miR-based risk classifier significantly stratified ccRCCIVCaccording to CSS.

(4)

Conclusions

In our retrospective analysis, we successfully validated the miR-based risk classifier within an independent ccRCCIVCcohort.
Accuracy of the diagnostic tests for the detection of Chagas disease: a systematic review and meta-analysis
Authors: Candia-Puma Mayron Antonio , Luque Laura Yesenia Machaca , Pumahuanca Brychs Milagros Roque , Galdino Alexsandro Sobreira , Giunchetti Rodolfo Cordeiro , Coelho Eduardo Antonio Ferraz , Chávez-Fumagalli Miguel Angel
Published: September 2022

The present systematic review and meta-analysis about the accuracy of diagnostic tests aim to describe the findings of literature over the last thirty years for the diagnosis of Chagas disease (CD). This work aimed to determine the accuracy of diagnostic techniques for CD in the disease’s acute and chronic phases. The PubMed database was searched for studies published between 1990 and 2021 on CD diagnostic. Fifty-six published studies that met the criteria were analyzed and included in the meta-analysis, evaluating diagnostic accuracy through sensitivity and specificity. For Enzyme-Linked Immunosorbent Assay (ELISA), Fluorescent Antibody Technique (IFAT), Hemagglutination Test (HmT), Polymerase Chain Reaction (PCR) and (Real-Time Polymerase Chain Reaction qPCR diagnosis methods, the sensitivity had a median of 99.0%, 78.0%, 75.0%, 76.0% and 94.0%, respectively; while specificity presented a median of 99.0%, 99.0%, 99.0%, 98.0% and 98.0%, respectively. This meta-analysis showed that ELISA and qPCR techniques had a higher performance compared to other methods of diagnosing CD in the chronic and acute phases, respectively. It was concluded by means of the AUC restricted to the false positive rates, that the ELISA diagnostic test presents the highest performance in diagnosing acute and chronic CD, compared to serological and molecular tests. Future studies focusing on new CD diagnostics approaches should be targeted.
Novel subgroups of type 2 diabetes based on multi-Omics profiling: an IMI-RHAPSODY Study
Authors: Li Shiying , Dragan Iulian , Fung Chun Ho , Kuznetsov Dmitry , Hansen Michael K. , Beulens Joline W.J. , ’t Hart Leen M. , Slieker Roderick C. , Donnelly Louise A. , Gerl Mathias J. , Klose Christian , Mehl Florence , Simons Kai , Elders Petra JM , Pearson Ewan R. , Rutter Guy A. , Ibberson Mark
Published: September 2022

Type 2 diabetes is a complex, multifactorial disease with varying presentation and underlying pathophysiology. Recent studies using data-driven cluster analysis have led to a stratification of type 2 diabetes into novel subgroups based on six clinical measurements. Whether these subgroups truly correspond to the underlying phenotypic differences is nevertheless unclear. Here, we apply an unsupervised, data-driven clustering method (Similarity Network Fusion) to characterize type 2 diabetes in two independent cohorts involving 1,134 subjects in total based on integrated plasma lipidomics and peptidomics data without pre-selection. Logistic regression was then used to explore clustering based on ≥ 180 circulating lipids and 1,195 protein biomarkers, alongside clinical signatures. Two subgroups were identified, one of which associated with elevated C-peptide levels, diabetic complications and more severe insulin resistance compared to the other. GWAS analysis against 403 type 2 diabetes risk variants revealed associations of several SNPs with clusters and altered molecular profiles. We thus demonstrate that heterogeneity in type 2 diabetes can be captured by circulating omics alone using an unsupervised bottom-up approach. Such multiomics signatures could reflect pathological mechanisms underlying type 2 diabetes and thus may help inform on precision medicine approaches to disease management.
Clinical predictors of treatment outcome in Melanesian adults with Tuberculous Meningitis at the Kundiawa General Hospital in Papua New Guinea
Authors: Aiwara Stanley , Aglua Izzard
Published: September 2022

Background

Tuberculous meningitis is the most severe form of extrapulmonary TB and accounted for 5% of 10 million global TB cases in the WHO 2018 report, with mortality as high as 19% in children and 30% in adults. Clinicians in resource-poor settings are often challenged by limited diagnostic and therapeutic options for optimal patient care, and often rely on clinical parameters for diagnosis, treatment, monitoring and outcome.

Aim

This study was done to identify potential clinical predictors of i) 28-day mortality and ii) length of hospitalization, amongst Melanesian adults with TB meningitis at a provincial hospital in Papua New Guinea.

Method

A retrospective observational study was conducted on 65 Melanesian adults with TB meningitis at a provincial hospital in Papua New Guinea between 2015 and 2019.

Result

High case fatality (49%) and mortality rates (2.22 per 100 000 per year) for TB Meningitis were observed in this study. Even higher case fatality of 93% observed for HIV-TBM co-infection. 28-day mortality associated with HIV-TBM co-infection (p-value=0.007, 95% CI 2.49-289.19), positive fluid balance 24-hours after admission (p-value=0.019, 95% CI 1.23-10.19) and admission GCS ≤10 (p-value=0.049, 95% CI 1.01-16.58).

Conclusion

Study showed high case fatality (49%) and mortality rates (2.22 per 100,000 per year) for TB Meningitis in Melanesian adults, with significantly high case fatality (93%) for HIV-TBM co-infection. HIV-TBM co-infection was strongly associated with 28-day mortality whilst a positive fluid balance 24-hours after admission and admission-GCS ≤10 were weakly associated with 28-day mortality.
The Impact of Variance in Carnitine Palmitoyltransferase-1 Expression on Breast Cancer Prognosis is Stratified by Clinical and Anthropometric Factors
Authors: Liu Ryan , Ospanova Shyryn , Perry Rachel J.
Published: September 2022

1.

CPT1A is a rate-limiting enzyme in fatty acid oxidation and is upregulated in high-risk breast cancer. Obesity and menopausal status’ relationship with breast cancer prognosis is well established, but its connection with fatty acid metabolism is not. We performed an observational study on anonymized RNA sequencing data in the Xena Functional Genomics Explorer, to explore CPT1A’s effect on breast cancer patients’ survival probability. Using [18F]-fluorothymidine positron emission tomography-computed tomography images from The Cancer Imaging Archive, we segmented these analyses by obesity and menopausal status. In 1214 patients, higher CPT1A expression is associated with lower breast cancer survivability. We confirmed a previously observed protective relationship between obesity and breast cancer in pre-menopausal patients and supported this data using two-sided Pearson correlations. Taken together, these analyses using open-access, deidentified databases bolster the potential role of CPT1A-dependent fatty acid metabolism as a pathogenic factor in breast cancer.
Higher level of Quinolones residue in poultry meat and eggs; an alarming public health issue in Nepal
Authors: Shrestha Nabaraj , Layalu Sundar , Amatya Serene , Shrestha Samrat , Basnet Shobha , Shrestha Manash , Shrestha Upendra Thapa
Published: September 2022

Background

With extensive use of antimicrobial agents in poultry production to prevent and treat diseases and as growth promoters, there has been an increase in antibiotic residue in the poultry meat and eggs. Quinolones are one of the highly prioritized, critically important drugs, whose residue in poultry can cause transmission of resistant zoonotic pathogens to humans. This study was conducted to assess the qualitative and quantitative residue of the quinolone in meat and eggs supplied to Kathmandu Valley, Nepal.

Methods

A standard questionnaire was used to identify the trend of antibiotic application in the poultry industry. Epicollect+ android application was used for the survey. A total of 120 meat samples and 120 egg samples were collected from the specified five sectors. Enzyme Linked Immuno Sorbant Assay was employed to screen antimicrobial residues in the samples. Only the samples with antimicrobial residues above maximum residual limit value were quantified with High Performance Liquid Chromatography.

Result

About 88.33% of chicken meat and 80% egg samples were positive for Quinolone residue. Three meat samples from Kathmandu had residues above the maximum residue level (MRL). One sample each from commercial and education sector showed Enrofloxacin residues while 1 sample from the health sector showed residues of both Enrofloxacin and Ciprofloxacin. The egg samples of Kathmandu, Bhaktapur and Lalitpur district contained 83.9%, 76.9% and 65% Quinolone residues respectively. While the eggs collected from household sector had the highest (100%) Quinolone residues than eggs from any other sectors followed by the lowest (66.6%) in eggs from the education sector (p=0.005).

Conclusion

A high level of Quinolone residue in the chicken meat and egg samples in the study indicates the imprudent and haphazard use of antibiotics which is a cause of emergence of antimicrobial resistant poultry pathogens alarming the potential transmission of resistance to human pathogens.
Motion of single molecular tethers reveals dynamic subdomains at ER-mitochondria contact sites
Authors: Obara Christopher J. , Nixon-Abell Jonathon , Moore Andrew S. , Riccio Federica , Hoffman David P. , Shtengel Gleb , Xu C. Shan , Schaefer Kathy , Pasolli H. Amalia , Masson Jean-Baptiste , Hess Harald F. , Calderon Christopher P. , Blackstone Craig , Lippincott-Schwartz Jennifer
Published: September 2022

To coordinate cellular physiology, eukaryotic cells rely on the inter-organelle transfer of molecules at specialized organelle-organelle contact sites1,2. Endoplasmic reticulum-mitochondria contact sites (ERMCSs) are particularly vital communication hubs, playing key roles in the exchange of signaling molecules, lipids, and metabolites3. ERMCSs are maintained by interactions between complementary tethering molecules on the surface of each organelle4,5. However, due to the extreme sensitivity of these membrane interfaces to experimental perturbation6,7, a clear understanding of their nanoscale structure and regulation is still lacking. Here, we combine 3D electron microscopy with high-speed molecular tracking of a model organelle tether, VAPB, to map the structure and diffusion landscape of ERMCSs. From EM reconstructions, we identified subdomains within the contact site where ER membranes dramatically deform to match local mitochondrial curvature. In parallel live cell experiments, we observed that the VAPB tethers that mediate this interface were not immobile, but rather highly dynamic, entering and leaving the site in seconds. These subdomains enlarged during nutrient stress, indicating ERMCSs can readily remodel under different physiological conditions. An ALS-associated mutation in VAPB altered the normal fluidity of contact sites, likely perturbing effective communication across the contact site and preventing remodeling. These results establish high speed single molecule imaging as a new tool for mapping the structure of contact site interfaces and suggest that the diffusion landscape of VAPB is a crucial component of ERMCS homeostasis.
Structural rearrangements of a caspase-like protease TPR-CHAT govern virus-host discrimination during type III-E CRISPR-Caspase immunity
Authors: Cui Ning , Zhang Jun-Tao , Li Zhuolin , Liu Xiao-Yu , Wang Chongyuan , Huang Hongda , Jia Ning
Published: September 2022

The RNA-targeting type III-E CRISPR-gRAMP effector forms a complex with a caspase-like protease TPR-CHAT, but the mechanistic details of their functional relationship remain unknown. Here, we report on cryo-EM structures of gRAMPcrRNA and gRAMPcrRNA-TPR-CHAT complexes, before and after either self or non-self RNA target binding, elucidating mechanisms underlying RNA-targeting and non-self RNA-induced protease activation. Noteworthy, the associated TPR-CHAT adopts a strikingly distinct conformation on self versus non-self RNA targets, with nucleotides at position −1 and −2 of crRNA serving as a sensor. Only binding of non-self RNA target activates TPR-CHAT protease, leading to the cleavage of Csx30 protein. Furthermore, given that TPR-CHAT structurally resembles eukaryotic separase, our results implicate an ancient mechanism for separase regulation. Our findings should not only facilitate the development of gRAMP-based RNA manipulation tools, but also lead to a mechanistic understanding of the virus-host discrimination process governed by a caspase-like protease during type III-E CRISPR-Caspase immunity.
Revisiting the burden borne by fumarase: enzymatic hydration of an olefin
Authors: Bellur Asutosh , Das Soumik , Jayaraman Vijay , Behera Sudarshan , Suryavanshi Arpitha , Balasubramanian Sundaram , Balaram Padmanabhan , Jindal Garima , Balaram Hemalatha
Published: September 2022

Fumarate hydratase (FH) is a remarkable catalyst that decreases the free energy of the catalyzed reaction by 30 kcal mol−1, much larger than most exceptional enzymes with extraordinary catalytic rates. Two classes of FH are observed in nature: class-I and class-II, that have different folds, yet catalyze the same reversible hydration/dehydration reaction of the dicarboxylic acids fumarate/malate, with equal efficiencies. Using class-I FH from the hyperthermophilic archaeon Methanocaldococcus jannaschii (Mj) as a model along with comparative analysis with the only other available class-I FH structure from Leishmania major (Lm), we provide insights into the molecular mechanism of catalysis in this class of enzymes. The structure of MjFH apo-protein has been determined, revealing that large inter-subunit rearrangements occur across apo- and the holo-protein forms, with a largely preorganized active site for substrate binding. Site-directed mutagenesis of active site residues, kinetic analysis and computational studies including DFT and natural population analysis, together show that residues interacting with the carboxylate group of the substrate play a pivotal role in catalysis. Our study establishes that an electrostatic network at the active site of class-I FH, polarizes the substrate fumarate through interactions with its carboxylate groups, thereby permitting an easier addition of a water molecule across the olefinic bond. We propose a mechanism of catalysis in FH that occurs through transition state stabilization involving the distortion of the electronic structure of the substrate olefinic bond mediated by the charge polarization of the bound substrate at the enzyme active site.

Abstract Figure
Structural basis of substrate recognition by human tRNA splicing endonuclease TSEN
Authors: Sekulovski Samoil , Sušac Lukas , Stelzl Lukas S. , Tampé Robert , Trowitzsch Simon
Published: September 2022

The heterotetrameric human transfer RNA (tRNA) splicing endonuclease (TSEN) catalyzes the excision of intronic sequences from precursor tRNAs (pre-tRNAs)1. Mutations in TSEN and its associated RNA kinase CLP1 are linked to the neurodegenerative disease pontocerebellar hypoplasia (PCH)2–8. The three-dimensional (3D) assembly of TSEN/CLP1, the mechanism of substrate recognition, and the molecular details of PCH-associated mutations are not fully understood. Here, we present cryo-electron microscopy structures of human TSEN with intron-containing pre-tRNATyrgta and pre-tRNAArgtct. TSEN exhibits broad structural homology to archaeal endonucleases9 but has evolved additional regulatory elements that are involved in handling and positioning substrate RNA. Essential catalytic residues of subunit TSEN34 are organized for the 3’ splice site which emerges from a bulge-helix configuration. The triple-nucleotide bulge at the intron/3’-exon boundary is stabilized by an arginine tweezer motif of TSEN2 and an interaction with the proximal minor groove of the helix. TSEN34 and TSEN54 define the 3’ splice site by holding the tRNA body in place. TSEN54 adapts a bipartite fold with a flexible central region required for CLP1 binding. PCH-associated mutations are located far from pre-tRNA binding interfaces explaining their negative impact on structural integrity of TSEN without abrogating its catalytic activity in vitro10. Our work defines the molecular framework of pre-tRNA recognition and cleavage by TSEN and provides a structural basis to better understand PCH in the future.
WITHDRAWN:In vivoCRISPR screen definesSlc25a37as an organ-specific regulator of antioxidant metabolism in metastasis
Authors: Cuadros Alejandro M. , Fernández-Garcia Juan , Planque Mélanie , Altea-Manzano Patricia , Schalley Tessa , Vermeire Ines , Broekaert Dorien , Wu Qi , Van Brussel Thomas , Leduc Sophia , Maetens Marion , Nguyen Ha-Linh , Van Baelen Karen , Darzi Naama , Floris Giuseppe , Wildiers Hans , Desmedt Christine , Lambrechts Diether , Fendt Sarah-Maria
Published: September 2022

Withdrawal Statement

The authors have withdrawn their manuscript owing to the detection of inaccurate data analysis in some figure panels that leads in some but not all cases to a different interpretation of the data after corrected analysis. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
The Role of the Posterior Medial Network in Language Comprehension: Dissociating Construction of Episodic versus Semantic Representations
Authors: Branzi Francesca M. , Lambon Ralph Matthew A.
Published: September 2022

Language comprehension involves the construction of complex mental representations, i.e., “event representations”, reflecting current events or situation models. The construction of these representations requires manipulation of both semantic and episodic content and has been widely associated with the functioning of the posterior medial network, a subsystem of the default network. However, it is still unknown the extent to which activity in posterior medial network reflects construction of the variable episodic versus semantic content of event representations. In this fMRI study, we establish the unique neural correlates of (1) episodic richness and (2) semantic coherence measured during a narrative reading task. Interestingly, we observed a functional fractionation within the posterior medial network in terms of brain regions whose activity was modulated by semantic or episodic content. Specifically, the number of episodic details in the narratives modulated the activity in the left angular gyrus and the retrosplenial cortex/ventral posterior cingulate cortex. Semantic coherence, in contrast, modulated neural responses in the right anterior temporal lobe/middle temporal gyrus, but also in brain regions within the posterior medial network, such as the dorsal posterior cingulate cortex. These results provide the first demonstration of functional dissociations within the posterior medial network in terms of brain regions involved in the construction of semantic versus episodic representational content during a language comprehension task.

Significance Statement

The construction of “event representations”, which is crucial to understand the world around us, predict the future and make plans, requires manipulation of both semantic and episodic information. The functioning of the posterior medial network has been tightly linked to formation of event representations. However, it is unclear the extent to which activity in this network reflects construction of the variable episodic versus semantic content of event representations. The present study provides the first demonstration of functional dissociations within posterior medial network in terms of brain regions involved in construction of semantic versus episodic representational content during language comprehension. These findings represent a first step towards understanding how episodic and semantic memory systems operate during the construction of event representations.
Structural insights into the formation of repulsive Netrin guidance complexes
Authors: Priest Jessica M. , Nichols Ev L. , Mendoza Juan L. , Shen Kang , Özkan Engin
Published: September 2022

Netrins can dictate attractive and repulsive responses during axon growth and cell migration, where presence of the receptor UNC-5 on target cells results in Netrin-mediated repulsion. Molecular details of Netrin–UNC-5 interactions and how they signal remain elusive. Here, we show that nematode UNC-5 is a heparin-binding protein, and the UNC-5–heparin affinity can be modulated using directed evolution or via rational design using our novel structure of UNC-5 with a heparin fragment. Furthermore, UNC-5 and nematode UNC-6/Netrin form a large, stable and rigid oligomeric complex in the presence of heparin, which can incorporate the attractive UNC-40/DCC receptor, demonstrating binary and ternary ectodomain complexes at preparative scale.C. eleganswith a heparin-binding deficient UNC-5 fail to establish proper gonad morphology due to abrogated distal tip cell migration, which relies on repulsive UNC-5 signaling in response to UNC-6. Our findings establish Netrin responses to be mediated through glycosaminoglycan-regulated large macromolecular complexes.
Assembly of neuron- and radial glial cell-derived extracellular matrix molecules promotes radial migration of developing cortical neurons
Authors: Mubuchi Ayumu , Takechi Mina , Nishio Shunsuke , Matsuda Tsukasa , Itoh Yoshifumi , Sato Chihiro , Kitajima Ken , Kitagawa Hiroshi , Miyata Shinji
Published: September 2022

Radial neuronal migration is a key neurodevelopmental event for proper cortical laminar organization. The multipolar-to-bipolar transition, a critical step in establishing neuronal polarity during radial migration, occurs in the subplate/intermediate zone (SP/IZ), a distinct region of the embryonic cerebral cortex. It has been known that the extracellular matrix (ECM) molecules are enriched in the SP/IZ. However, the molecular constitution and functions of the ECM formed in this region remain poorly understood. Here, we identified neurocan (NCAN) as a major chondroitin sulfate proteoglycan in the SP/IZ. NCAN binds to both radial glial cell-derived tenascin-C (TNC) and hyaluronan (HA), a large linear polysaccharide, forming a ternary complex of NCAN, TNC, and HA in the SP/IZ. Developing cortical neurons make contact with the ternary complex during migration. The enzymatic or genetic disruption of the ternary complex impairs radial migration by suppressing the multipolar-to-bipolar transition. Furthermore, both TNC and NCAN promoted the morphological maturation of cortical neuronsin vitro. The present results provide evidence for the cooperative role of neuron- and radial glial cell-derived ECM molecules in cortical development.
Frequency and Risk Factors of Resident Burnout Before and During the COVID19 Pandemic
Authors: Türk Sevcan , Kalyoncu Anıl , Karabilgin Öztürkçü Özlem Sürel , Elbi Hayriye , Orman Mehmet Nurullah , Yaman Aziz Cem , Toptaş Muratcan , Bekki Yaşar Çağlar , Özlütaş Murat , Esentürk Mehmet Burak , Bapuraj Jayapalli , Özbek Süha Süreyya
Published: September 2022

Objective

To explore the prevalence and contributing factors of resident burnout in a University Hospital before and during the COVID 19 pandemic.

Methods

Thirty Faculty of Medicine departments were included in the survey, where 400 university hospital residents filled out the Maslach Burnout Inventory (MBI) in January 2018 and April 2020. Related scores of emotional exhaustion (EE), decreased accomplishment (DA) and depersonalization (DP) were calculated and compared between the different groups. Correlation between scores and possible contributing factors, including demographics, work-life circumstances, exposure to workplace violence, were investigated. Contributing factors were compared between the time points.

Results

The EE and DA scores were significantly higher in junior residents than in senior residents. Both scores were higher among residents who had experienced abuse or violence. The emergency medicine residents had significantly higher DP scores, while the EE scores of radiology residents were lower than others. Thirty percent of all residents smoked cigarettes. This percentage was even higher among the residents of the departments of surgery and emergency medicine (45-50%). A significant correlation was demonstrated between the scores of MBI and smoking, while analysis with other demographics did not yield any relation. According to the study results, basic science residents had significantly increased scores in all MBI subgroups during the pandemic.

Conclusion

Resident physician burnout was found to be related to the work environment, smoking cigarettes and exposure to violence at workplace.
A rapid review of the effectiveness of remote consultations versus face-to-face consultations in secondary care surgical outpatient settings
Authors: Edwards Deborah , Csontos Judit , Gillen Liz , Carrier Judith , Lewis Ruth , Cooper Alison , Edwards Adrian
Published: September 2022

The use of remote consultations and telemedicine approaches significantly increased over the pandemic. There is evidence that some patients still prefer this mode of care delivery and time saving may also enable additional consultations and help to reduce waiting lists. However, the effectiveness of remote consulting for certain specialities, such as surgery, is unclear.

The aim of this review was to investigate the effectiveness of video or telephone consultations, particularly focusing on clinical, patient reported and safety outcomes, in adult secondary surgical outpatient care during the COVID-19 pandemic.

14 studies were identified. These were published in 2021-2022. Evidence is low or very-low quality due to observational study designs, small sample sizes and patient selection.

Policy and practice implications: Evidence is of low quality but suggests that for many surgical outpatient consultations, remote consultations are as effective as in-person consultations. There is potential for time and cost savings for remote consultations compared to in-person consultations. High quality research is needed to evaluate the effectiveness of remote consultations to understand which patients and which surgical specialities would benefit most.

Funding statement

The Wales Centre for Evidence Based Care was funded for this work by the Wales COVID-19 Evidence Centre, itself funded by Health & Care Research Wales on behalf of Welsh Government.
Association between visit-to-visit lipid variability and incident cancer: a population-based cohort study
Authors: Chan Jeffrey Shi Kai , Satti Danish Iltaf , Lee Yan Hiu Athena , Waleed Khalid Bin , Tang Pias , Mahalwar Gauranga , Minhas Abdul Mannan Khan , Roever Leonardo , Biondi-Zoccai Giuseppe , Leung Fung Ping , Wong Wing Tak , Liu Tong , Zhou Jiandong , Tse Gary
Published: September 2022

Background

Dyslipidaemia is associated with increased cancer risk. However, the prognostic value of visit-to-visit lipid variability (VVLV) is unexplored in this regard.

Objective

To investigate the associations between VVLV and the risk of incident cancer.

Design

Retrospective cohort study.

Setting

Family medicine clinics.

Patients

Adults attending a family medicine clinic in Hong Kong during 2000-2003, excluding those with <3 tests for low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), triglycerides, and total cholesterol (TC) each, those with prior cancer diagnosis, and those with <1 year of follow-up.

Measurements

Visit-to-visit LDL-C, HDL-C, TC, and triglycerides variabilities were measured by the coefficient of variation (CV). Patients were followed up until 31stDecember 2019 for the primary outcome of incident cancer.

Results

Altogether, 69,186 patients were included (26,679 males (38.6%); mean age 60±13 years; mean follow-up 16±3 years); 7958 patients (11.5%) had incident cancer. Higher variability of LDL-C, HDL-C, TC, and TG was associated with higher risk of incident cancer. Patients in the third tercile of the CV of LDL-C (adjusted hazard ratio (aHR) against first tercile 1.06 [1.00, 1.12], p=0.049), HDL-C (aHR 1.37 [1.29, 1.44], p<0.001), TC (aHR 1.10 [1.04, 1.17], p=0.001), and TG (aHR 1.11 [1.06, 1.18], p<0.001) had the highest risks of incident cancer. Among these, only HDL-C variability remained associated with the risk of incident cancer in users of statins/fibrates.

Limitations

Due to the observational nature of this study, there may be residual and unmeasured confounders. Patient data could not be individually adjudicated, implying that coding errors may be possible.

Conclusion

Higher VVLV was associated with significantly higher long-term risks of incident cancer. VVLV may be a clinically useful tool for cancer risk stratification.
Anticholinergic burden in middle and older age is associated with lower cognitive function, but not with brain atrophy
Authors: Mur J. , Marioni R. E. , Russ T. C. , Muniz-Terrera G. , Cox S. R.
Published: September 2022

Background

Anticholinergic drugs block muscarinic receptors in the body. They are commonly prescribed for a variety of indications and their use has previously been associated with dementia and cognitive decline.

Methods

UK Biobank participants with linked health-care records (n=163,043, aged 40-71 at baseline), for about 17,000 of which MRI data was available, we calculated the total anticholinergic drug burden according to 15 different anticholinergic scales and due to different classes of drugs. We then used linear regression to explore the associations between anticholinergic burden and various measures of cognition and structural MRI, including general cognitive ability, 9 separate cognitive domains, brain atrophy, volumes of 68 cortical and 14 subcortical areas, and fractional anisotropy and median diffusivity of 25 white-matter tracts.

Results

Anticholinergic burden was modestly associated with poorer cognition across most anticholinergic scales and cognitive tests (7/9 FDR-adjusted significant associations, standardised betas (β) range: −0.039, −0.003). When using the anticholinergic scale exhibiting the strongest association with cognitive functions, anticholinergic burden due to only some classes of drugs exhibited negative associations with cognitive function, with β-lactam antibiotics (β=-0.035, pFDR<0.001) and opioids (β=-0.026, pFDR<0.001) exhibiting the strongest effects. Anticholinergic burden was not associated with any measure of brain macro- or microstructure (pFDR>0.08).

Discussion

Anticholinergic burden is weakly associated with poorer cognition, but there is little evidence for associations with brain structure. Future studies might focus more broadly on polypharmacy or more narrowly on distinct drug classes, instead of using purported anticholinergic action to study the effects of drugs on cognitive ability.