bluuebunny/crossref_metadata_2025 huggingface dataset:
Metastasis of ovarian dysgerminoma in a postmenopausal patient: a rare case report
Authors: Feng Ziren , Zhang Xinning , Wang Pan , Hu Qinglan , Lin Jinduan
Published: May 2024

Ovary dysgerminoma is one of the most good prognosis malignant tumor, which has a 5-year overall survival rate exceeding to 90%. Generally, the incidence of ovarian dysgerminoma (OD) is relatively low, accounting for ~0.6% of all ovarian tumors. Usually, it mainly occurs in very young women, about 85% of patients under 30 years old and is rare in middle-aged especially in elderly ones. This ovary dysgerminoma case report presents a 58-year-old menopausal postmenopausal woman which has a poor prognosis. Therefore, there may be differences between the elderly and young women in clinical characteristic that require separate management. This case reports a postmenopausal woman who was diagnosed with ovary dysgerminoma. After surgery, the patient was treated chemotherapy with bleomycin, etoposide, and cisplatin (BEP) according to the treatment guidelines. Unusually, the patient developed bone marrow suppression and lymph node metastasis in final. This report explored the clinical characteristic in postmenopausal woman dysgerminoma. Changes in lactate dehydrogenase (LDH) throughout the course of the disease are closely related to the progression. The patient had a disease progression when treated with the conventional treatment (BEP). The applicability of this treatment protocol to postmenopausal patients requires further research. Postmenopausal woman dysgerminoma is rare but rapid progress. Whether BEP is suitable for OD in middle-aged and elderly people remains to be further validated in the future. LDH may be a potential biomarker for monitoring the progression of OD in the elderly.
Superior mesenteric artery syndrome misdiagnosed and preceded by Helicobacter pylori-induced gastritis: a rare diagnosis with misleading features
Authors: Ismail Sawsan , Hasan Mohammad , Aljasem Muhamad , Darkaznli Mohamad Ismaeel , Habib Alice , Deeb Hala , Alkhalil Batool , Sheikh Mohamad Lalsh , Khalil Aleen , Kattash Shatha , Arja Joudi , Haydar Khalil
Published: May 2024

Introduction and importance:

Superior mesenteric artery (SMA) syndrome is a rare morbid vascular disorder that is defined as the decrease in the aortomesenteric angle and the compression of the third part of the duodenum. This disorder mainly affects young adult females, and severe weight loss represents a leading predisposing factor.

Case presentation:

The authors report the case of a 19-year-old male who was admitted to our hospital with a 3-month history of epigastric pain, nausea, and weight loss. Two months earlier, the patient was diagnosed with Helicobacter pylori-induced gastritis. Nevertheless, with complaints of severe headache and epigastric pain, the patient was admitted to our hospital for further investigations. Computed tomography (CT) scan with intravenous contrast injection was performed, and interestingly, the aortomesenteric angle was 19° accompanied by a compression of the third part of the duodenum, and a mild gastric dilatation. Accordingly, the diagnosis was confirmed as superior mesenteric artery syndrome.

Clinical discussion:

In the authors’ case, the non-specific clinical symptoms correlated with histopathological examinations led to the initial diagnosis of Helicobacter pylori-induced gastritis. Surprisingly, the lack of improvements led to performing CT scan, which confirmed the diagnosis of SMA syndrome. Subsequently, HP gastritis played a significant role in misleading and delaying the diagnosis.

Conclusion:

The authors report the first case report from Syria of s superior mesenteric artery syndrome that was misdiagnosed and preceded by HP-induced gastritis, highlighting the crucial role of detailed clinical and radiological examinations in the diagnosis of challenging cases with morbid complications.
Machine learning in heart failure diagnosis, prediction, and prognosis: review
Authors: Saqib Muhammad , Perswani Prinka , Muneem Abraar , Mumtaz Hassan , Neha Fnu , Ali Saiyad , Tabassum Shehroze
Published: May 2024

Globally, cardiovascular diseases take the lives of over 17 million people each year, mostly through myocardial infarction, or MI, and heart failure (HF). This comprehensive literature review examines various aspects related to the diagnosis, prediction, and prognosis of HF in the context of machine learning (ML). The review covers an array of topics, including the diagnosis of HF with preserved ejection fraction (HFpEF) and the identification of high-risk patients with HF with reduced ejection fraction (HFrEF). The prediction of mortality in different HF populations using different ML approaches is explored, encompassing patients in the ICU, and HFpEF patients using biomarkers and gene expression. The review also delves into the prediction of mortality and hospitalization rates in HF patients with mid-range ejection fraction (HFmrEF) using ML methods. The findings highlight the significance of a multidimensional approach that encompasses clinical evaluation, laboratory assessments, and comprehensive research to improve our understanding and management of HF. Promising predictive models incorporating biomarkers, gene expression, and consideration of epigenetics demonstrate potential in estimating mortality and identifying high-risk HFpEF patients. This literature review serves as a valuable resource for researchers, clinicians, and healthcare professionals seeking a comprehensive and updated understanding of the role of ML diagnosis, prediction, and prognosis of HF across different subtypes and patient populations.
WITHDRAWN: Multimolecular feature-based machine learning: system biology enhanced RF-QSAR modeling for the efficient prediction of the inhibitory potential of diverse SARS CoV-2 3CL Protease inhibitors
Authors: Manaithiya Ajay , Bhowmik Ratul , Ray Rajarshi , Kumar Sunil , Sharma Sameer , Mathew Bijo , Gong Wenping , Parkkila Seppo , Aspatwar Ashok
Published: May 2024

Withdrawal Statement

The authors have withdrawn their manuscript owing to the inability to complete the revisions or follow up on the manuscript at this time, due to personal circumstances. 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.
Distinct gut microbiota profiles may characterize amyloid beta pathology and mild cognitive impairment
Authors: Rouskas Konstantinos , Mamalaki Eirini , Ntanasi Eva , Pantoura Marianna , Anezaki Maria , Emmanouil Christina , Novau-Ferré Nil , Bulló Mònica , Dimas Antigone S , Papandreou Christopher , Yannakoulia Mary , Argiriou Anagnostis , Scarmeas Nikolaos
Published: May 2024

Gut microbiome composition has been associated with early preclinical Alzheimer’s disease (AD), as reflected by cerebrospinal fluid (CSF) amyloid beta pathology, and with mild cognitive impairment (MCI). However, the presence of distinct microbiota across different disease stages has not been fully characterized. We profiled gut microbiota in 50 nondemented individuals by 16S ribosomal RNA sequencing and taxonomic profiles were compared between amyloid-based (amyloid-normal vs. amyloid-pathology) and clinically- based (cognitively normal vs. MCI) diagnosis groups using linear models (adjusted for sex, age and diet). Elastic net regression model was used to assess the discriminative performance of microbiota for amyloid-pathology and MCI. Microbial diversity measures did not differ across groups. We identified specific genera associated with amyloid-pathology and MCI such asOxalobacter, MarvinbryantiaandEscherichia-Shigella, mostly linked to inflammation. Distinct genera were found to be unique to amyloid-pathology and MCI. Microbiota was shown to have a fairly good discriminative performance. Overall, we suggest the presence of distinct microbiota in early preclinical stage of AD and MCI, which needs to be further explored.
The role of artificial intelligence in the application of the integrated electronic health records and patient-generated health data
Authors: Ye Jiancheng , Hai Jiarui , Song Jiacheng , Wang Zidan
Published: May 2024

Objective

This scoping review aims to identify and understand the role of artificial intelligence in the application of integrated electronic health records (EHRs) and patient-generated health data (PGHD) in health care, including clinical decision support, health care quality, and patient safety. We focused on the integrated data that combined PGHD and EHR data, and we investigated the role of artificial intelligence (AI) in the application in health care.

Methods

We used the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines to search articles in six databases: PubMed, Embase, Web of Science, Scopus, ACM Digital Library, and IEEE Computer Society Digital Library. In addition, we synthesized seminal sources, including other systematic reviews, reports, and white papers, to inform the context, history, and development of this interdisciplinary research field.

Results

Fifty-six publications met the review criteria after screening. The EHR-integrated PGHD introduces benefits to health care, including empowering patients and families to engage via shared decision-making, improving the patient-provider relationship, and reducing the time and cost of clinical visits. AI’s roles include cleaning and management of heterogeneous datasets, assisting in identifying dynamic patterns to improve clinical care processes, and providing more sophisticated algorithms to better predict outcomes and propose precise recommendations based on the integrated data. Challenges mainly stem from the large volume of integrated data, data standards, data exchange and interoperability, security and privacy, interpretation, and meaningful use.

Conclusion

The use of PGHD in health care is at a promising stage but needs further work for widespread adoption and seamless integration into health care systems. AI-driven, EHR-integrated PGHD systems can greatly improve clinicians’ abilities to diagnose patients’ health issues, classify risks at the patient level by drawing on the power of integrated data, and provide much-needed support to clinics and hospitals. With EHR-integrated PGHD, AI can help transform health care by improving diagnosis, treatment, and the delivery of clinical care, thus improving clinical decision support, health care quality, and patient safety.
Interferon-Inducible Guanylate-Binding Protein 5 Inhibits Replication of Multiple Viruses by Binding to the Oligosaccharyltransferase Complex and Inhibiting Glycoprotein Maturation
Authors: Wang Shaobo , Li Wanyu , Wang Lingling , Tiwari Shashi Kant , Bray William , Wu Lujing , Li Na , Hui Hui , Clark Alex E. , Zhang Qiong , Zhang Lingzhi , Carlin Aaron F. , Rana Tariq M.
Published: May 2024

Viral infection induces production of type I interferons and expression of interferon-stimulated genes (ISGs) that play key roles in inhibiting viral infection. Here, we show that the ISG guanylate-binding protein 5 (GBP5) inhibits N-linked glycosylation of key proteins in multiple viruses, including SARS-CoV-2 spike protein. GBP5 binds to accessory subunits of the host oligosaccharyltransferase (OST) complex and blocks its interaction with the spike protein, which results in misfolding and retention of spike protein in the endoplasmic reticulum likely due to decreasedN-glycan transfer, and reduces the assembly and release of infectious virions. Consistent with these observations, pharmacological inhibition of the OST complex with NGI-1 potently inhibits glycosylation of other viral proteins, including MERS-CoV spike protein, HIV-1 gp160, and IAV hemagglutinin, and prevents the production of infectious virions. Our results identify a novel strategy by which ISGs restrict virus infection and provide a rationale for targeting glycosylation as a broad antiviral therapeutic strategy.

Highlights

The interferon-stimulated gene GBP5 is induced by SARS-CoV-2 infection in vitro and in vivo.

ER-localized GBP5 restricts N-linked glycosylation of SARS-CoV-2 spike protein, leading to protein misfolding and preventing transport to the Golgi apparatus.

GBP5 binds to OST complex accessory proteins and potentially blocks access of the catalytic subunit to the spike protein.

GBP5 inhibits N-glycosylation of key proteins in multiple viruses, including SARS-CoV-2

Pharmacological inhibition of OST blocks host cell infection by SARS-CoV-2, variants of concern, HIV-1, and IAV.

Significance

Viral infection induces production of type I interferons and expression of interferon-stimulated genes (ISGs) that play key roles in inhibiting viral infection. We found that the interferon-stimulated gene GBP5 is induced by SARS-CoV-2 infection in vitro and in vivo. GBP5 inhibits N-glycosylation of key proteins in multiple viruses, including SARS-CoV-2. Importantly, pharmacological inhibition of Oligosaccharyltransferase (OST) Complex blocks host cell infection by SARS-CoV-2, variants of concern, HIV-1, and IAV, indicating future translational application of our findings.
Downstream metabolites of (+)-cis-12-oxo-phytodienoic acid function as noncanonical bioactive jasmonates inArabidopsis thaliana
Authors: Saito Rina , Nishizato Yuho , Kitajima Tsumugi , Nakayama Misuzu , Takaoka Yousuke , Kato Nobuki , Ueda Minoru
Published: May 2024

(+)-cis-12-oxo-phytodienoic acid (cis-OPDA) is a biosynthetic precursor of the plant hormone (+)-7-iso-jasmonoyl-L-isoleucine (JA-Ile). It functions as an endogenous chemical signal independent of the JA-Ile receptor COI1-JAZ inArabidopsis thaliana. The bioactive form ofcis-OPDA that induces COI1-JAZ-independent gene expression remains unknown.

In this study, we hypothesized that the genuine bioactive forms ofcis-OPDA are the downstream metabolites, which upregulate the expression of the OPDA marker genes such asZAT10/ERF5in a JA-Ile-independent manner. These downstream metabolites function independently of the JA-Ile-COI1-JAZ-MYCs canonical jasmonate signaling module, and its electrophilic nature is essential for its bioactivity.
Quantification ofLegionella pneumophilain building potable water systems: a meta-analysis comparing qPCR and culture-based detection methods
Authors: Sylvestre Émile , Rhoads William J. , Julian Timothy R. , Hammes Frederik
Published: May 2024

Quantitative polymerase chain reaction (qPCR) offers a rapid, automated, and potentially on-site method for quantifyingL. pneumophilain building potable water systems, complementing and potentially replacing traditional culture-based techniques. However, the application of qPCR in assessing human health risks is complicated by its tendency to overestimate such risks due to the detection of genomic copies that do not correspond to viable, infectious bacteria. This study examines the relationship betweenL. pneumophilameasurements obtained via qPCR and culture-based methods, aiming to understand and establish qPCR-to-culture concentration ratios needed to inform associated health risks. We developed a Poisson lognormal ratio model and a random-effects meta-analysis to analyze variations in qPCR-to-culture ratios within and across sites. Our findings indicate these ratios typically vary from 1:1 to 100:1, with ratios close to 1:1 predicted at all sites. Consequently, adopting a default 1:1 conversion factor appears necessary as a cautious approach to convert qPCR concentrations to culturable concentrations for use in models of associated health risks, for example, through quantitative microbial risk assessment (QMRA) frameworks. Where this approach may be too conservative, targeted sampling and the applications of viability-qPCR could improve the accuracy of qPCR-based QMRA. Standardizing qPCR and culture-based methods and reporting site-specific environmental factors that affect the culturability ofL. pneumophilawould improve the understanding of the relationship between the two methods. The ratio model introduced here shifts us beyond simple correlation analyses, facilitating investigations of temporal and spatial heterogeneities in the relationship. This analysis is a step forward in the integration of QMRA and molecular biology, as the framework demonstrated here forL. pneumphilais applicable to other pathogens monitored in the environment.
“I didn’t come into nursing to be attacked and constantly abused”: A qualitative study of exposure to violence for nurses across ethnic groups in the United Kingdom
Authors: Chui Zoe , Caton Emma , Naqvi Habib , Baker Edward , Onwumere Juliana , Lee Geraldine A , Hatch Stephani L
Published: May 2024

Background

Workplace violence is a serious threat to staff safety and leads to mental and physical health problems that have negative consequences for the recruitment and retention of nurses, amid the worst staffing crisis in the history of the National Health Service (NHS) in the United Kingdom.

Objectives

This study aims to explore the social context of violence for hospital-based and community nurses from different ethnic groups, the types of violence experienced or witnessed both in and outside the workplace, and the impact of violence on mental and physical health.

Methods

Semi-structured interviews were conducted online with 12 hospital-based and community nurses recruited across London. Interview data were analysed using reflexive thematic analysis.

Results

The sample comprised seven hospital nurses and five community nurses. Four themes were identified from the analysis: i) the social context in which nurses from different ethnic groups are exposed to community violence; ii) the types of workplace violence experienced or witnessed by hospital-based and community nurses from different ethnic groups; iii) nurses’ perceptions of the factors contributing to workplace violence iv) how violence impacts mental and physical health outcomes for hospital-based and community nurses from different ethnic groups. Based on the social ecological framework and the sociological theory of stress, we have used these findings to present a conceptual stress process model of violence exposure for nurses.

Conclusions

Hospital-based and community nurses from different ethnic groups are exposed to violence both in and outside the workplace which negatively affects their mental and physical health. Whilst interventions aimed at improving personal safety and security measures in hospitals are valuable, interventions to address the social and institutional factors that put nurses at risk of violence exposure are needed. Further research using wider criteria for violence to include witnessing and hearing about violent events are needed to advance our understanding of how nurses are affected by multiple sources and types of violence in both their work and personal lives.

What is already known

Workplace violence is widespread and can lead to mental and physical health problems for healthcare staff.

Nurses are one of the occupational groups most vulnerable to workplace violence and are consistently in short supply.

What this paper adds

Findings informed the development of a conceptual stress process model of violence exposure for nurses.

Nurses perceived their gender, age and ethnicity as contributing factors to workplace violence.

Witnessing or experiencing violence both in and outside the workplace has serious negative consequences at the individual and organisational levels.
Potential Pathways of Spread of Highly Pathogenic Avian Influenza A/H5N1 Clade 2.3.4.4b Across Dairy Farms in the United States
Authors: Stone Haley , Jindal Mehak , Lim Samsung , Dawson Rebecca , Quigley Ashley , Scotch Matthew , MacIntyre C. Raina
Published: May 2024

The emergence of Highly Pathogenic Avian Influenza (HPAI) A/H5N1 clade 2.3.4.4b has led to an unprecedented intercontinental spread, affecting a broad spectrum of avian and mammalian species. Recent outbreaks in US dairy farms, underscore the urgent need to understand the transmission pathways. The study aimed to evaluate the modes of introduction and transmission to dairy farms, through geospatial and exposure analyses. Our findings favour a singular introduction over multiple independent introductions, with non-waterfowl species exhibiting the highest dairy farm exposure, which is a major shift from historical waterfowl spread. Moreover, bidirectional spread between cattle and poultry highlights the intricate nature of disease transmission within the agricultural ecosystem. Additional factors such as livestock trade, poultry litter feed and contaminated milking machinery likely contributed to the amplification of the outbreaks throughout the United States. As large-scale outbreaks persist in the United States, the likelihood of a human pandemic increases, making it imperative to enact and sustain heightened surveillance measures across all potentially impacted species.
TRMT1L-catalyzed m22G27 on tyrosine tRNA is required for efficient mRNA translation and cell survival under oxidative stress
Authors: Hwang Sseu-Pei , Liao Han , Barondeau Katherine , Han Xinyi , Herbert Cassandra , McConie Hunter , Shekar Amirtha , Pestov Dimitri , Limbach Patrick A , Chang Jeffrey T , Denicourt Catherine
Published: May 2024

tRNA modifications are critical for several aspects of their functions, including decoding, folding, and stability. Using a multifaceted approach encompassing eCLIP-seq and Nanopore tRNA-seq, we show that the human tRNA methyltransferase TRMT1L interacts with component of the Rix1 ribosome biogenesis complex and binds to the 28S rRNA, as well as to a subset of tRNAs. Mechanistically, we demonstrate that TRMT1L is responsible for catalyzing m22G solely at position 27 of tRNA-Tyr-GUA. Surprisingly, TRMT1L depletion also impaired the deposition of acp3U and dihydrouridine on tRNA-Tyr-GUA, Cys-GCA, and Ala-CGC. TRMT1L knockout cells have a marked decrease in tRNA-Tyr-GUA levels, coinciding with a reduction in global translation rates and hypersensitivity to oxidative stress. Our results establish TRMT1L as the elusive methyltransferase catalyzing the m22G27 modification on tRNA Tyr, resolving a long-standing gap of knowledge and highlighting its potential role in a tRNA modification circuit crucial for translation regulation and stress response.
DGCR8haploinsufficiency leads to primate-specific RNA dysregulation and pluripotency defects
Authors: Colomer-Boronat A , Knol LI , Peris G , Sanchez L , Peluso S , Tristan-Ramos P , Gazquez-Gutierrez A , Chin P , Gordon K , Barturen G , Hill RE , Garcia-Perez JL , Ivens A , Macias S , Heras SR
Published: May 2024

The 22q11.2 deletion syndrome (22qDS) is caused by a microdeletion in chromosome 22, includingDGCR8, an essential gene for miRNA production. The contribution of humanDGCR8hemizygosity to the disease is still unclear. In this study, we generated two human pluripotent cell models containing a single functionalDGCR8allele to elucidate its role on 22qDS.DGCR8+/-cells show increased apoptosis as well as self-renewal and differentiation defects in both the naïve and primed states. The expression of primate-specific miRNAs was largely affected, due to impaired miRNA processing and chromatin accessibility.DGCR8+/-cells also displayed a pronounced reduction in human endogenous retrovirus class H (HERVH) expression, a primate-specific retroelement essential for pluripotency maintenance. Importantly, the reintroduction of primate-specific miRNAs as well as the miR-371-3 cluster rescued the cellular and molecular phenotypes ofDGCR8+/-cells. Our results suggest thatDGCR8is haploinsufficient in humans and that miRNAs and transposable elements may have co-evolved in primates as part of an essential regulatory network to maintain stem cell identity.
Extracellular Vimentin is a Damage-Associated Molecular Pattern Protein Serving as an Agonist of TLR4 in Human Neutrophils
Authors: Suprewicz Łukasz , Fiedoruk Krzysztof , Skłodowski Karol , Zakrzewska Magdalena , Walewska Alicja , Deptuła Piotr , Lesiak Agata , Okła Sławomir , Galie Peter A. , Patteson Alison E. , Janmey Paul A. , Bucki Robert
Published: May 2024

Background

Vimentin is a type III intermediate filament protein, that plays an important role in cytoskeletal mechanics. It is now known that vimentin also plays important roles outside the cell. Recent studies show the controlled release of vimentin into the extracellular environment, where it functions as a signaling molecule. Such observations are expanding our current knowledge of vimentin as a structural cellular component towards additional roles as an active participant in cell signaling.

Methods

Our study investigates the immunological roles of extracellular vimentin (eVim) and its citrullinated form (CitVim) as a damage-associated molecular pattern (DAMP) engaging the Toll-like receptor 4 (TLR4) of human neutrophils. We usedin vitroassays to study neutrophil migration through endothelial cell monolayers and activation markers such as NADPH oxidase subunit 2 (NOX2/gp91phox). The comparison of eVim with CitVim and its effect on human neutrophils was extended to the induction of extracellular traps (NETs) and phagocytosis of pathogens.

Results

Both eVim and CitVim interact with and trigger TLR4, leading to increased neutrophil migration and adhesion. CitVim stimulated the enhanced migratory ability of neutrophils, activation of NF-κB, and induction of NET formation mainly mediated through reactive oxygen species (ROS)-dependent and TLR4-dependent pathways. In contrast, neutrophils exposed to non-citrullinated vimentin exhibited higher efficiency in favoring pathogen phagocytosis, such asEscherichia coliandCandida albicans, compared to CitVim.

Conclusions

Our study identifies new functions of eVim in its native and modified forms as an extracellular matrix DAMP and highlights its importance in the modulation of immune system functions. The differential effects of eVim and CitVim on neutrophil functions highlight their potential as new molecular targets for therapeutic strategies aimed at differential regulation of neutrophil activity in different pathological conditions. This, in turn, opens new windows of therapeutic intervention in inflammatory and immunological diseases characterized by immune system dysfunction, in which eVim and CitVim play a key role.
A neurometabolic mechanism involving dmPFC/dACC lactate in physical effort-based decision-making
Authors: Clairis N. , Barakat A. , Brochard Jules , Xin Lijing , Sandi C.
Published: May 2024

Motivation levels vary across individuals, yet the underlying mechanisms driving these differences remain elusive. The dorsomedial prefrontal cortex/dorsal anterior cingulate cortex (dmPFC/dACC) and the anterior insula (aIns) play crucial roles in effort-based decision-making. Here, we investigate the influence of lactate, a key metabolite involved in energy metabolism and signaling, on decisions involving both physical and mental effort, as well as its effects on neural activation. Using proton magnetic resonance spectroscopy and functional MRI in 63 participants, we find that higher lactate levels in the dmPFC/dACC are associated with reduced motivation for physical effort, a relationship mediated by neural activity within this region. Additionally, plasma and dmPFC/dACC lactate levels correlate, suggesting a systemic influence on brain metabolism. Supported by path analysis, our results highlight lactate’s role as a modulator of dmPFC/dACC activity, hinting at a neurometabolic mechanism that integrates both peripheral and central metabolic states with brain function in effort-based decision-making.
Dorsal prefrontal cortex drives perseverative behavior in mice
Authors: Lebedeva A. , Wang Y. , Funnell L. , Terry B. , Oh Y. J. , Miller K. , Harris K.D.
Published: May 2024

Perseveration – repeating one choice when others would generate larger rewards – is a common behavior, but neither its purpose nor neuronal mechanisms are understood. Here we demonstrate a neural correlate and causal role of dorsal prefrontal cortex (area MOs) in perseveration in mice performing a dynamic reward learning task. An auditory go cue signaled mice to turn a wheel either left or right, with the reward probability of each action switching in blocks. Mice perseverated, gaining suboptimal reward, but were faster when making repeated choices. Neuropixels recordings found neurons whose activity correlated with perseveration and predicted rapid reaction times, almost exclusively in MOs. Optogenetically inhibiting MOs reduced perseveration and slowed reaction times. In contrast, inactivating medial prefrontal cortex at choice time did not have any effect but impaired learning if delivered after reward delivery. In this task, therefore, MOs encodes a perseverative decision variable, and is necessary for mediating the effect of this decision variable on choice and reaction time.
Tn-seq of theCandida glabratareference strain CBS138 reveals epigenetic plasticity, structural variation, and intrinsic mechanisms of resistance to micafungin
Authors: Nickels Timothy J. , Gale Andrew P. , Harrington Abigail A. , Timp Winston , Cunningham Kyle W.
Published: May 2024

C. glabratais an opportunistic pathogen that can resist common antifungals and rapidly acquire multidrug resistance. A large amount of genetic variation exists between isolates, which complicates generalizations. Portable Tn-seq methods can efficiently provide genome-wide information on strain differences and genetic mechanisms. Using theHermestransposon, the CBS138 reference strain and a commonly studied derivative termed 2001 were subjected to Tn-seq in control conditions and after exposure to varying doses of the clinical antifungal micafungin. The approach revealed large differences between these strains, including a 131 kb tandem duplication and a variety of fitness differences. Additionally, both strains exhibited up to 1000-fold increased transposon accessibility in subtelomeric regions relative to the BG2 strain, indicative of open subtelomeric chromatin in these isolates and large epigenetic variation within the species. Unexpectedly, the Pdr1 transcription factor conferred resistance to micafungin through targets other thanCDR1. Other micafungin resistance pathways were also revealed including mannosyltransferase activity and biosynthesis of the lipid precursor sphingosine, the drugging of which by SDZ 90-215 or myriocin enhanced the potency of micafunginin vitro. These findings provide insights into complexity of theC. glabrataspecies as well as strategies for improving antifungal efficacy.

Candida glabrata is an emerging pathogen with large genetic diversity and genome plasticity. The type strain CBS138 and a laboratory derivative were mutagenized with theHermestransposon and profiled using Tn-seq. Numerous genes that regulate innate and acquired resistance to an important clinical antifungal were uncovered, including a pleiotropic drug resistance gene (PDR1) and a duplication of part of one chromosome. Compounds that target PDR1 and other genes may augment the potency of existing antifungals.
Higher multiplication rates ofPlasmodium falciparumin isolates from hospital cases compared with community infections
Authors: Stewart Lindsay B. , Escolar Elena Lantero , Philpott James , Claessens Antoine , Amambua-Ngwa Alfred , Conway David J.
Published: May 2024

Background

Parasite multiplication rates vary amongPlasmodium falciparumisolates from patients with malaria, suggesting differences in virulence potential, although direct comparisons between hospital-based clinical cases and community infections are needed.

Methods

Cryopreserved blood samples from malaria cases presenting to a district hospital in The Gambia and infections detected in local communities were introduced to continuous culture under the same conditions. Thirty-four isolates (23 hospital-based and 11 community-based) were successfully established and then tested under exponential growth conditions over six days to derive estimatedP. falciparummultiplication rates per cycle based on a 48-hour typical cycle length.

Results

A range of parasite multiplication rates in culture was seen across isolates, from 1.5-fold to 5.0-fold per cycle. Multiplication rates were significantly higher in the hospital-based isolates than the community-based isolates. There was a significantly positive correlation between parasitaemia in peripheral blood and multiplication rates in culture. There was no significant difference in multiplication rates between isolates with single or multiple parasite genotypes.

Conclusions

These findings are consistent with a hypothesis that intrinsic natural variation in parasite multiplication rate may affect levels of parasitaemia achieved during infection, and that this affects likelihood of hospital presentation. Results do not support a hypothesis that parasites modify their multiplication rates in response to competing parasites with different genotypes.

Relevant to understanding parasite virulence, this study finds higherPlasmodium falciparummultiplication rates in cultured isolates from malaria cases presenting to hospital than in isolates from local community infections, and positive correlation with parasitaemia in peripheral blood of individuals.
Decoding scalp health and microbiome dysbiosis in dandruff
Authors: Rasheedkhan Regina Viduthalai , Chopra Tarun , Weihao Kwok , Cheruvalli Sreelakshmi , Sabrina Ang , Fatimah Binte Jamal Mohamed Hashmath , Ramasamy Kesava Priyan , Sarah Kay , Yan Chong Yik , Kaliyamoorthi Eganathan , Williams Rohan , Xianghui Liu , Krishna Vedula , Bourokba Nasrine , Jhingan Anjali , Thng Tien Guan Steven , Da Cruz Olivier , Riu Sylvie , De Dormael Romain , Abed Kahina , Touriguine Olivia , Jourdain Roland , Cupferman Sylvie , Aguilar Luc , Rice Scott A.
Published: May 2024

A balanced scalp microbiome is crucial for scalp health, yet the mechanisms governing this balance and the etiology of dysbiosis in scalp disorders remain elusive. We conducted a detailed investigation of the scalp and hair follicles, in healthy individuals and those with dandruff/seborrheic dermatitis (D/SD). It was demonstrated that the microbiome inhabiting hair follicles serves as a reservoir for the scalp microbiome, thereby integrating the scalp, follicle, and the hair into one functional unit. Using in vitro models, we further elucidated mechanisms governing the assembly and interactions of the follicular microbiome under healthy and D/SD conditions. We show that propionic acid, produced byC. acnes, plays a pivotal role in maintaining microbiome balance, with implications for scalp health, which was validated through a clinical study.
Imaging flow cytometry enables label-free cell sorting of morphological variants from unculturable bacterial populations
Authors: Vocelle Daniel , Thompson Lindsey , Bernard Matthew P. , Wale Nina
Published: May 2024

Bacterial populations often display remarkable morphological heterogeneity. Flow cytometric cell sorting (often called FACS) is an important tool for understanding this diversity. FACs allows researchers to obtain pure samples of each morphological variant (or morphotype) that is present within a mixed population of cells and thus permits each morphotype to be phenotyped. In FACS, cells are first labeled with fluorescent markers such as antibodies or transgenic constructs, and then separated out based on their possession of these labels. However, since the development of fluorescent labels requiresa prioriknowledge of bacterial biology, it is often impossible to apply FACS to understudied and/or unculturable bacteria. This challenge has limited our capacity to investigate the biology of bacterial size and shape in all but a small, largely culturable subset of bacterial taxa. Here, we present an innovative strategy that permits label-free cell sorting of bacterial morphotypes, using an unculturable, pleiomorphic pathogen (Pasteuria ramosa) as a model bacterium. We show that imaging flow cytometry (IFC) can be used to systematically identify light-scattering and autofluorescence “signatures” of bacterial morphotypes, on which basis cell sorting can be conducted. Critically, our IFC-enabled cell sorting strategy yields samples of sufficient purity (>90%) for common downstream analyses e.g., “-omics” analyses. Our work represents an innovative application of IFC and provides an economical, widely applicable solution to a central problem in the study of bacterial diversity.

Importance

Bacteria come in many different shapes and sizes. Why this morphological variation exists is a longstanding question in microbiology, but it remains difficult to answer. To phenotype different morphological variants (morphotypes) within a bacterial population, we need to separate them from one another. This is normally achieved using flow cytometric cell-sorting, whereby morphotypes are labelled with fluorescent antibodies and separated on the basis of their differential fluorescence. Unfortunately, it is difficult to develop fluorescent-labels specific to unculturable or poorly studied bacteria because of the limited availability of appropriate molecular tools. Here, we demonstrate that imaging flow cytometry can be used to design and validate label-free cell sorting strategies. Recently, there has been a resurgence of interest in bacterial morphological diversity and a call to expand its study across the tree of life. Our work will help microbiologists to answer this call.
Rationally Designed Pooled CRISPRi-Seq Uncovers an Inhibitor of Bacterial Peptidyl-tRNA Hydrolase
Authors: Rahman A. S. M. Zisanur , Syroegin Egor A. , Novomisky Nechcoff Julieta , Devarajan Archit , Polikanov Yury S. , Cardona Silvia T.
Published: May 2024

Pooled knockdown libraries of essential genes are useful tools for elucidating the mechanisms of action of antibacterial compounds, a pivotal step in antibiotic discovery. However, achieving genomic coverage of antibacterial targets poses a challenge due to the uneven proliferation of knockdown mutants during pooled growth, leading to the unintended loss of important targets. To overcome this issue, we describe the construction of CIMPLE (CRISPRi-mediatedpooled library ofessential genes), a rationally designed pooled knockdown library built in a model antibiotic-resistant bacteria,Burkholderia cenocepacia.By analyzing growth parameters of clonal knockdown populations of an arrayed CRISPRi library, we predicted strain depletion levels during pooled growth and adjusted mutant relative abundance, approaching genomic coverage of antibacterial targets during antibiotic exposure. We first benchmarked CIMPLE by chemical-genetic profiling of known antibacterials, then applied it to an uncharacterized bacterial growth inhibitor from a new class. CRISPRi-Seq with CIMPLE, followed by biochemical validation, revealed that the novel compound targets the peptidyl-tRNA hydrolase (Pth). Overall, CIMPLE leverages the advantages of arrayed and pooled CRISPRi libraries to uncover unexplored targets for antibiotic action.

Bacterial mutant libraries in which antibiotic targets are downregulated are useful tools to functionally characterize novel antimicrobials. These libraries are used for chemical-genetic profiling as target-compound interactions can be inferred by differential fitness of mutants during pooled growth. Mutants that are functionally related to the antimicrobial mode of action are usually depleted from the pool upon exposure to the drug. Although powerful, this method can fail when the unequal proliferation of mutant strains before exposure causes mutants to fall below the detection level in the library pool. To address this issue, we constructed an arrayed essential gene mutant library (EGML) in the antibiotic-resistant bacteriumBurkholderia cenocepaciausing CRISPR interference (CRISPRi) and analyzed the growth parameters of individual mutant strains. We then modelled depletion levels during pooled growth and used the model to rationally design an optimized CRISPR interference-mediated pooled library of essential genes (CIMPLE). By adjusting the initial inoculum of the knockdown mutants, we achieved coverage of the bacterial essential genome with mutant sensitization. We exposed CIMPLE to a recently discovered antimicrobial of a novel class and discovered it inhibits the peptidyl-tRNA hydrolase, an essential bacterial enzyme. In summary, we demonstrate the utility of CIMPLE and CRISPRi-Seq to uncover the mechanism of action of novel antimicrobial compounds.

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Systematic large-scale application of ClinGen InSiGHTAPC-specific ACMG/AMP variant classification criteria substantially alleviates the burden of variants of uncertain significance in ClinVar and LOVD databases
Authors: Yin Xiaoyu , Richardson Marcy , Laner Andreas , Shi Xuemei , Ognedal Elisabet , Vasta Valeria , Hansen Thomas v. O. , Pineda Marta , Ritter Deborah , den Dunnen Johan T. , Hassanin Emadeldin , Lyman Lin Wencong , Borras Ester , Krahn Karl , Nordling Margareta , Martins Alexandra , Mahmood Khalid , Nadeau Emily A.W. , Beshay Victoria , Tops Carli , Genuardi Maurizio , Pesaran Tina , Frayling Ian M. , Capellá Gabriel , Latchford Andrew , Tavtigian Sean V. , Maj Carlo , Plon Sharon E. , Greenblatt Marc S. , Macrae Finlay A. , Spier Isabel , Aretz Stefan
Published: May 2024

Background

Pathogenic constitutionalAPCvariants underlie familial adenomatous polyposis, the most common hereditary gastrointestinal polyposis syndrome. To improve variant classification and resolve the interpretative challenges of variants of uncertain significance (VUS), APC-specific ACMG/AMP variant classification criteria were developed by the ClinGen-InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (VCEP).

Methods

A streamlined algorithm using theAPC-specific criteria was developed and applied to assess allAPCvariants in ClinVar and the InSiGHT international referenceAPCLOVD variant database.

Results

A total of 10,228 uniqueAPCvariants were analysed. Among the ClinVar and LOVD variants with an initial classification of (Likely) Benign or (Likely) Pathogenic, 94% and 96% remained in their original categories, respectively. In contrast, 41% ClinVar and 61% LOVD VUS were reclassified into clinically actionable classes, the vast majority as (Likely) Benign. The total number of VUS was reduced by 37%. In 21 out of 36 (58%) promisingAPCvariants that remained VUS despite evidence for pathogenicity, a data mining-driven work-up allowed their reclassification as (Likely) Pathogenic.

Conclusions

The application ofAPC-specific criteria substantially reduced the number of VUS in ClinVar and LOVD. The study also demonstrated the feasibility of a systematic approach to variant classification in large datasets, which might serve as a generalisable model for other gene-/disease-specific variant interpretation initiatives. It also allowed for the prioritization of VUS that will benefit from in-depth evidence collection. This subset ofAPCvariants was approved by the VCEP and made publicly available through ClinVar and LOVD for widespread clinical use.
Facultative endosymbiosis between cellulolytic protists and methanogenic archaea in the gut of the Formosan termiteCoptotermes formosanus
Authors: Kaneko Masayuki , Omori Tatsuki , Igai Katsura , Mabuchi Takako , Sakai-Tazawa Miho , Nishihara Arisa , Kihara Kumiko , Yoshimura Tsuyoshi , Ohkuma Moriya , Hongoh Yuichi
Published: May 2024

Anaerobic protists frequently harbour methanogenic archaea, which apparently contribute to the hosts’ fermentative metabolism by consuming excess H2. However, the ecological properties of endosymbiotic methanogens remain elusive in many cases. Here we investigated the ecology and genome of the endosymbiotic methanogen of theCononymphaprotists in the hindgut of the termiteCoptotermes formosanus. Microscopic and 16S rRNA amplicon sequencing analyses revealed that a single species, designated here ‘CandidatusMethanobrevibacter cononymphae’, is associated with bothCononympha leidyiandCononympha koidzumiiand that its infection rate inCononymphacells varied from 0.0 to 99.8% among termite colonies. Fine-scale network analysis indicated that multiple 16S rRNA sequence variants coexisted within a single host cell and that identical variants were present in bothCononymphaspecies and also on the gut wall. Thus, ‘Ca.Methanobrevibacter cononymphae’ is a facultative endosymbiont, transmitted vertically with frequent exchanges with the gut environment. Indeed, transmission electron microscopy showed escape or uptake of methanogens from/by aCononymphacell. The genome of ‘Ca.Methanobrevibacter cononymphae’ showed features consistent with its facultative lifestyle: i.e., the genome size (2.7 Mbp) comparable to those of free-living relatives; the pseudogenization of the formate dehydrogenase genefdhA, unnecessary within the non-formate-producing host cell; the dependence on abundant acetate in the host cell as an essential carbon source; and the presence of a catalase gene, required for colonization on the microoxic gut wall. Our study revealed a versatile endosymbiosis between the methanogen and protists, which may be a strategy responding to changing conditions in the termite gut.
The avian and human influenza A virus receptors sialic acid (SA)-α2,3 and SA-α2,6 are widely expressed in the bovine mammary gland
Authors: Kristensen Charlotte , Jensen Henrik E. , Trebbien Ramona , Webby Richard J. , Larsen Lars E.
Published: May 2024

An outbreak of H5N1 highly pathogenic influenza A virus (HPIAV) has been detected in dairy cows in the United States. Influenza A virus (IAV) is a negative-sense, single-stranded, RNA virus that has not previously been associated with widespread infection in cattle. As such, cattle are an extremely under-studied domestic IAV host species. IAV receptors on host cells are sialic acids (SAs) that are bound to galactose in either an α2,3 or α2,6 linkage. Human IAVs preferentially bind SA-α2,6 (human receptor), whereas avian IAVs have a preference for α2,3 (avian receptor). The avian receptor can further be divided into two receptors: IAVs isolated from chickens generally bind more tightly to SA-α2,3-Gal-β1,4 (chicken receptor), whereas IAVs isolated from duck to SA-α2,3-Gal-β1,3 (duck receptor). We found all receptors were expressed, to a different degree, in the mammary gland, respiratory tract, and cerebrum of beef and/or dairy cattle. The duck and human IAV receptors were widely expressed in the bovine mammary gland, whereas the chicken receptor dominated the respiratory tract. In general, only a low expression of IAV receptors was observed in the neurons of the cerebrum. These results provide a mechanistic rationale for the high levels of H5N1 virus reported in infected bovine milk and show cattle have the potential to act as a mixing vessel for novel IAV generation.

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