bluuebunny/crossref_metadata_2025 huggingface dataset:
Membrane composition and curvature in SNX9-mediated actin polymerization
Authors: Vaishnav Pankti , Shimo Kondo Hanae , Gadsby Jonathan R , Dobramysl Ulrich , Mason Julia , Atherton Joseph , Gallop Jennifer L
Published: September 2024

Membrane-binding adaptor protein Sorting nexin 9 (SNX9) contributes to viral uptake and inflammation and is associated with worse outcomes in several cancers. It is involved in endocytosis of epidermal growth factor receptors, β1-integrin and membrane type 1 matrix metalloprotease and in mitochondrial-derived vesicles. Its BAR-PX domain binds phosphatidylinositol phosphates (PIPs) and its SH3 domain interacts with dynamin and N-WASP to stimulate Arp2/3 complex actin polymerization during vesicle scission. Recent complexities have arisen in SNX9’s lipid specificity and its involvement both endocytic and filopodial membrane topologies. Here we use biolayer interferometry, cell-free reconstitution and superresolution microscopy to analyse the activities of SNX9. We find that more SNX9 binds membranes that contain PI(4,5)P2 and PI(3)P compared with PI(3,4)P2, despite having similar affinity, suggesting SNX9 can assemble into different macromolecular arrangements depending on the composition. Actin assembly requires the wider protein and lipid network provided by PX-BAR and SH3 interactions. 3D direct stochastic optical reconstruction microscopy on filopodia-like reconstitutions shows that SNX9 and related protein Transducer of Cdc42 activation-1 (TOCA-1) are competent to form both tubular and plaque-like organizations with the actin machinery. Finally, using cryo-electron tomography we show that SNX9 assembles both branched and bundled actin filaments demonstrating its multifunctional nature.
Interactions among Merlin, Arkadia, and SKOR2 mediate NF2-associated Schwann cell proliferation in human
Authors: Tang Pei-Ciao , Um Seyoung , Mayfield Anderson B. , Bracho Olena R. , Castillo Christian Del , Dinh Christine T. , Dykxhoorn Derek M. , Liu Xue Zhong
Published: September 2024

NF2-Related Schwannomatosis (previously referred to as Neurofibromatosis Type 2, or NF2) is a genetic-associated disease resulting from mutations in the gene,NF2.NF2encodes the merlin protein, which acts as a tumor suppressor. Bilateral vestibular schwannoma (VS) is a hallmark of NF2. Although the exactly molecular mechanism mediating NF2-driven schwannomatosis remain unclear, it is known that defective Merlin protein functionality leads to abnormal cell proliferation. Herein, we utilized a human induced pluripotent stem cell (hiPSC)-based Schwann cell (SC) model to investigate the role of merlin in human SCs. SCs were derived from hiPSCs carrying aNF2mutation (c.191 T > C; p. L64P), its isogenic wild-type control cell line, and a NF2 patient-derived hiPSC line. NF2 mutant SCs showed abnormal cellular morphology and proliferation. Proteomic analyses identified novel interaction partners for Merlin – Arkadia and SKOR2. Our results established a new model in which merlin interacts with Arkadia and SKOR2 and this interaction is required for the proper activation of the SMAD-dependent pathway in TGFβ signaling.
Biosynthetic Origin of the Methoxy Group in Quinine and Related Cinchona Alkaloids
Authors: Lombe Blaise Kimbadi , Zhou Tingan , Caputi Lorenzo , Ploss Kerstin , O’Connor Sarah E.
Published: September 2024

Quinine is a historically important natural product containing a methoxy group that is assumed to be incorporated at a late pathway stage. Here we show that the methoxy group in quinine and related Cinchona alkaloids is introduced onto the starting substrate tryptamine. Feeding studies with Cinchona plantlets definitively show that 5-methoxytryptamine is utilized as a quinine biosynthetic intermediatein planta. We discover the biosynthetic genes that encode the responsible oxidase and methyltransferase, and we use these genes to reconstitute the early steps of the Cinchona alkaloid biosynthetic pathway inNicotiana benthamianato produce a mixture of methoxylated and desmethoxylated Cinchona alkaloid intermediates. Importantly, we show that the co-occurrence of both tryptamine and 5-methoxytryptamine substrates, along with the substrate promiscuity of downstream pathway enzymes, enable parallel formation of both methoxylated and desmethoxylated alkaloids inCinchona pubescens.
Substrate stiffness dictates unique paths towards proliferative arrest in WI-38 cells
Authors: Kaiser Alyssa M. , Selahi Amirali , Kong Wenjun , Ruby J. Graham
Published: September 2024

Finite replicative potential is a defining feature of non-transformed somatic cells, first established by Leonard Hayflickin vitrousing WI-38 human lung fibroblasts. Once proliferative capacity is exhausted due to telomere shortening, cells enter into a state called replicative senescence, which can be avoided through ectopic expression of telomerase reverse transcriptase (hTERT). As WI-38 cells approach replicative arrest, molecular pathways linked to mechanotransduction are induced, including YAP signaling, but the potential interplay between replicative lifespan and the mechanical environment of the cell remains unexplored. Here, we investigate the influence of mechanosensation on the trajectory towards replicative arrest taken by WI-38 cells by growing cells on substrates of varying stiffnesses. Matrix softening slowed proliferation, altered cellular phenotypes, and shortened proliferative lifespan while hTERT expression abrogated or reduced these responses. Our analyses of bulk and single-cell RNA-sequencing and ATAC-sequencing revealed the emergence of a unique G1 transcriptional state on soft substrates, characterized by an AP-1 transcription factor program, which failed to manifest with hTERT expression. Together, these findings reveal how the mechanical environment alters WI-38 cell proliferative lifespan and dictates unique paths towards growth arrest.
Pooled nanoparticle screening using a chemical barcoding approach
Authors: Vaidya Katherine , Regan Michael S. , Lin James , Houle Jenna , Stopka Sylwia A. , Agar Nathalie Y. R. , Hammond Paula T. , Boehnke Natalie
Published: September 2024

We report the development of a small molecule-based barcoding platform for pooled screening of nanoparticle delivery. Using aryl halide-based tags (halocodes), we achieve high-sensitivity detection via gas chromatography coupled with mass spectrometry or electron capture. This enables barcoding and tracking of nanoparticles with minimal halocode concentrations and without altering their physicochemical properties. To demonstrate the utility of our platform for pooled screening, we synthesized a halocoded library of polylactide-co-glycolide (PLGA) nanoparticles and quantified uptake in ovarian cancer cells in a pooled manner. Our findings correlate with conventional fluorescence-based assays. Additionally, we demonstrate the potential of halocodes for spatial mapping of nanoparticles using mass spectrometry imaging (MSI). Halocoding presents an accessible and modular nanoparticle screening platform capable of quantifying delivery of pooled nanocarrier libraries in a range of biological settings.
THOC1 complexes with SIN3A to regulate R-loops and promote glioblastoma progression
Authors: Budhiraja Shreya , Baisiwala Shivani , Cho Sia , Chojak Rafal , Kazi Hasaan A , Stepniak Amelia , Perrault Ella N , Chen Li , Park Cheol H. , Dmello Crismita , Lin Peiyu , Sonabend Adam M , Ahmed Atique U
Published: September 2024

ABSTRACT

Glioblastoma (GBM), the most common and aggressive malignant brain tumor in adults, has a median survival of 21 months. To identify drivers of GBM proliferation, we conducted a CRISPR-knockout screen, which revealed THO Complex 1 (THOC1) as a key driver. Knocking down THOC1 significantly reduced GBM cell viability across patient-derived xenograft (PDX) lines, enhancing survival (p<0.01) in primary PDX models. Conversely, overexpressing THOC1 in non-cancerous cells bolstered viability, decreasing survival and causing tumor engraftment in vivo (p<0.01). Further investigation revealed THOC1’s robust interaction with SIN3A, a histone deacetylase complex. Histone deacetylation has been previously shown to prevent the buildup of R-loops, structures that form normally during transcription but can be lethal in excess. We found that THOC1-knockdown leads to elevated R-loop levels and reduced histone deacetylation levels. Next, to understand the networks specifically regulated by THOC1-mediated R-loop prevention, we conducted unbiased RNA-sequencing on control and THOC1-knockdown GBM cells. We found that THOC1’s role in R-loop prevention primarily affects telomeres, critical regions for cell replication. We further show that THOC1-knockdown results in significantly increased telomeric R-loop levels and shortened telomeres. Ultimately, this study suggests that targeting THOC1 shows promise as a therapeutic strategy to disrupt the delicate R-loop landscape and undermine GBM’s replicative potential.
Distinct roles of the two BRCA2 DNA binding domains in DNA damage repair and replication fork preservation
Authors: Neal Francisco , Li Wenjing , Uhrig Mollie E. , Sharma Neelam , Syed Shahrez , Burma Sandeep , Hromas Robert , Mazin Alexander , Dray Eloise , Libich David , Olsen Shaun , Wasmuth Elizabeth , Zhao Weixing , Sørensen Claus S. , Wiese Claudia , Kwon Youngho , Sung Patrick
Published: September 2024

Homologous recombination (HR) is a highly conserved tool for the removal of DNA double-strand breaks (DSBs) and the preservation of stalled and damaged DNA replication forks. Successful completion of HR requires the tumor suppressor BRCA2. Germline mutations in BRCA2 lead to familial breast, ovarian, and other cancers, underscoring the importance of this protein for maintaining genome stability. BRCA2 harbors two distinct DNA binding domains, one that possesses three oligonucleotide/oligosaccharide binding (OB) folds (known as the OB-DBD), and with the other residing in the C-terminal recombinase binding domain (termed the CTRB-DBD) encoded by the last gene exon. Here, we employ a combination of genetic, biochemical, and cellular approaches to delineate contributions of these two DNA binding domains toward HR and the maintenance of stressed DNA replication forks. We show that OB-DBD and CTRB-DBD confer ssDNA and dsDNA binding capabilities to BRCA2, respectively, and that BRCA2 variants mutated in either DNA binding domain are impaired in the ability to load the recombinase RAD51 onto ssDNA pre-occupied by RPA. While the CTRB-DBD mutant is modestly affected for HR, it exhibits a strong defect in the protection of stressed replication forks. In contrast, the OB-DBD is indispensable for both BRCA2 functions. Our study thus defines the unique contributions of the two BRCA2 DNA binding domains in genome maintenance.
Grey Pineapple Mealybug,Dysmicoccus neobrevipesBeardsley: A New Devastating Pest of Tuberose in India
Authors: Firake D. M. , Joshi Sunil , Kumar P. Naveen , Saha T. N. , Dantuluri V.S. Raju , Prasad K. V.
Published: September 2024

Tuberose (Agave amica) is a highly valued flower crop in India, known for its consistently high returns and ability to thrive in various climatic conditions. Severe outbreaks of the grey pineapple mealybug,Dysmicoccus neobrevipesBeardsley (Hemiptera: Pseudococcidae), have been observed in several villages of the Pune district, Maharashtra (India), since 2021, leading to significant economic losses. This report provides an illustrative morphological diagnosis ofD. neobrevipesand basic information on its field establishment, impact on tuberose crops, nature of the damage and field symptoms etc. Surveys conducted in major tuberose-growing areas of Pune district (Maharashtra) revealed that the mealybug primarily infests the underground and basal portion of tuberose plants, causing stunted growth, drooping, and ultimately death of the plants.D. neobrevipesproduces honeydew, fostering sooty mold growth that impairs photosynthesis, reduces flower yield. It also infests tuberose bulbs, spoiling them in storage. Based on primary scientific literature, this study represents the first scientifically confirmed record ofD. neobrevipesas a new pest of tuberose in India. The ant speciesSolenopsis geminatawas found attending to mealybug colonies, aiding their spread and creating a nuisance for farmers during routine field activities. A total of 87.09% of the surveyed fields (n=62) showed mealybug infestation, ranging from 68% to 97%. Raising awareness among the farmers and implementing regular monitoring in tuberose-growing areas are crucial steps for developing effective management practices and preventing the further spread of this pest to other regions.
Bergeyella cardium variant induces unique cytoplasmic vacuolization cell death
Authors: Mao Rudi , Pan Hongwei , Yang Luyu , Li Zhen , Yu Xinran , Li Yanfeng , Chen Ying , Yu Yang , Wang Wei , Gao Chengjiang , Peng Jun , Xu Tao , Zhang Yi , Qi Xiaopeng
Published: September 2024

Bacterial pathogens have evolved multiple mechanisms to modulate host cell death, evade host immunity, and establish persistent infection. Here, we show that an emerging pathogen Bergeyella cardium variant (BCV) survives serum killing, inducing unique cytoplasmic vacuolization cell death in the majority of cells and apoptosis in a small number of bystanders. The cytoplasmic vacuolization cell death triggered by BCV is characterized by fused lysosome-associated termination and is inhibited by the sodium channel inhibitor amiloride. Endosomal solute carrier family 9 member A9 (SLC9A9) was identified as a critical regulator in the process of BCV-triggered cytoplasmic vacuolization cell death. Moreover, outer membrane vesicles (OMVs) or transfection of barrel-like membrane proteins lipocalin, b-barrel, and PorV dramatically induced cytoplasmic vacuolization. BCV hijacked SLC9A9 by maintaining its high expression, increasing cytoplasmic vacuolization, and enhancing pathogenicity. These findings contribute to the development of novel approaches to modulate cytoplasmic vacuolization cell death and treat infectious diseases.
Association between national action and trends in antibiotic resistance: an analysis of 73 countries from 2000 to 2023
Authors: Søgaard Jørgensen Peter , Nguyen Thanh Luong , Pehlivanoglu Ege , Klein Franziska , Wernli Didier , Jasovsky Dusan , Aktipis Athena , Dunn Robert R. , Gröhn Yrjo , Lhermie Guillaume , Scott H. Morgan , Klein Eili Y.
Published: September 2024

Background

The world’s governments have agreed both global and national actions to address the challenge of antimicrobial resistance. This raises the importance of understanding to what degree national action so far has been effective. Answering this question is challenged by variation in data availability and quality as well as disruptive events such as the COVID-19 pandemic. We investigate the association between a survey of self-reported action based on the first Global Database for Tracking Antimicrobial Resistance (TrACSS) survey and trends in multiple indicators related to the DPSEEA framework leading up to the survey.

Methods and findings

We apply regression methods across 73 countries between actions in 2016 and the trend in indicators of health system development (drivers), antibiotic use (pressures, ABU), absolute rates of resistance (state, ABR) and relative rates of resistance (exposure, Drug Resistance Index, DRI) from 2000 to 2016. We find that action is consistently associated with improved linear and categorical trend in health systems, ABU, ABR and DRI. Reductions are associated with relatively high levels of action (0-4) for ABU (median 2.8, 25-75% quartile 2.6-3.3), ABR (3.0, 2.4-3.4), and DRI (3.5, 3.1-3.6). These associations are robust to the inclusion of other contextual factors such as health system and socio-economic status, human population density, animal production and climate. Since 2016, a majority of both Low-Middle Income Countries (LMICs) and High-Income Countries (HICs) report increased action on repeated questions, while one third of countries report reduced action. The main limitations in interpretation are heterogeneity in data availability and the recency of action.

Conclusions

Our findings highlight the importance of national action to address the domestic situation related to antibiotic resistance and indicate the value of both incremental changes in reducing adverse outcomes and the need for high levels of action in delivering improvements.
Ruminant-dense environments increase risk of Shiga toxin-producingEscherichia coliindependently of ruminant contact
Authors: Ward Caitlin , Finical William , Smith Kirk , Rounds Joshua M. , Klumb Carrie A. , Tarr Gillian A.M.
Published: September 2024

Abstract

Cattle and other domestic ruminants are the primary reservoirs of O157 and non-O157 Shiga toxin-producingEscherichia coli(STEC). Living in areas with high ruminant density has been associated with excess risk of infection, which could be due to both direct ruminant contact and residual environmental risk, but the role of each is unclear. We investigated whether there is any meaningful risk to individuals living in ruminant-dense areas if they do not have direct contact with ruminants. Using a Bayesian spatial framework, we investigated the association between the density of ruminants on feedlots and STEC incidence in Minnesota from 2010 to 2019, stratified by serogroup and season, and adjusting for direct ruminant contact. For every additional head of cattle or sheep per 10 acres, the incidence of O157 STEC infection increased by 30% (IRR 1.30; 95% CrI 1.18, 1.42) or 135% (IRR 2.35; 95% CrI 1.14, 4.20), respectively, during the summer months. Sheep density was also associated with O157 STEC risk during winter (IRR 4.28; 95% CrI 1.40, 8.92). The risk of non-O157 STEC infection was only elevated in areas with goat operations during summer (IRR 19.6; 95% CrI 1.69, 78.8). STEC risk associated with ruminant density was independent of direct ruminant contact across serogroups and seasons. Our findings demonstrate that living in a ruminant-dense area increases an individual’s risk of O157 and non-O157 STEC infection even without direct ruminant contact, indicating that prevention efforts need to extend to community strategies for averting indirect transmission from local ruminant populations.

Importance

STEC are zoonotic enteric bacteria responsible for 2.5 million illnesses each year. Infections in young children can be especially devastating, causing hemolytic uremic syndrome (HUS), a debilitating and sometimes fatal form of acute kidney injury. STEC’s primary reservoirs are cattle and other domestic ruminants, and transmission can occur through food, water, animal contact, and person-to-person. Living near ruminants poses a significant risk of STEC infection; however, the proportion of that risk due to direct ruminant contact or other routes of transmission is unknown. Our research demonstrates that direct ruminant contact is a substantial risk irrespective of location, and that individuals living in ruminant-rich regions are at high risk of STEC infection regardless of whether they come into contact with ruminants. These findings indicate a need for multi-pronged prevention efforts that emphasize control of contamination in the environments surrounding ruminant populations, in addition to biosafety precautions when contacting ruminants directly.
Neural correlates of β-lactam exposure in intensive care unit patients: an observational, prospective cohort study
Authors: Zalta Arnaud , Trébuchon Agnès , Daquin Géraldine , Velly Lionel , Leone Marc , Blin Olivier , Lagarde Stanislas , Guilhaumou Romain
Published: September 2024

Background

Β-Lactam-induced neurotoxicity in critical care patients can compromise clinical outcomes. Despite the growing use of therapeutic drug monitoring (TDM) for β-lactams, clear toxicity thresholds remain undefined, leaving clinicians uncertain about dosing adjustments when adverse effects occur. Identifying a relevant and easily detectable neurophysiological biomarker for β-lactam exposure would improve monitoring and prevent serious complications.

Methods

In a prospective multicenter, non-interventional study, we analysed electroencephalographic (EEG) signals of 56 patients hospitalized in intensive care units (ICUs) receiving continuous infusions of five β-lactams (meropenem, piperacillin/tazobactam, cefepime, cefotaxime, or ceftazidime). We applied a time frequency decomposition on these EEG data to investigate quantitatively the power of neural dynamics across frequencies ranging from 1 to 45 Hz. We used a multivariate pattern decoding method to correlate the β-lactam exposure and Sepsis-related Organ Failure Assessment (SOFA) scores with the neural activity.

Results

β-lactam exposure correlated with increased β-low γ neural dynamics (20–40 Hz) (p < 0.001, FDR corrected), independent of other clinical factors or medications. Β neural activity was most pronounced in central electrodes (C3 : r = 0.20, p < 0.01; C4 : r = 0.26, p < 0.01) and the right frontal electrode (Fp2 : r = 0.12, p = 0.02). Lower θ-α activity (3.5-5 Hz and 12-18 Hz) was associated with higher SOFA scores (p < 0.001, FDR corrected). No significant correlations were observed between other drugs (opioids, antiseizure medications, psychotropics) and β or θ-α dynamics.

Conclusions

These results suggest that β neural dynamics represent a potential biomarker for β-lactam exposure in ICU patients. They highlight the potential of quantitative EEG and advanced multivariate decoding methods to identify subtle neurophysiological features that are otherwise difficult to detect.

Trial registration

ClinicalTrials.govIDNCT03339869. Registered 14 September 2017.
Arsenic exposure is associated with elevated sweat chloride concentration and airflow obstruction among adults in Bangladesh: a cross sectional study
Authors: Lee Mi-Sun S. , North Crystal M. , Choudhuri Irada , Biswas Subrata K. , Fleisch Abby F. , Farooque Afifah , Bao Diane , Afroz Sakila , Mow Sadia , Husain Nazmul , Islam Fuadul , Mostafa Md Golam , Biswas Partha Pratim , Ludwig David S. , Digumarthy Subba R. , Hug Christopher , Quamruzzaman Quazi , Christiani David C. , Mazumdar Maitreyi
Published: September 2024

Arsenic is associated with lung disease and experimental models suggest that arsenic-induced degradation of the chloride channel CFTR (cystic fibrosis transmembrane conductance regulator) is a mechanism of arsenic toxicity. We examined associations between arsenic exposure, sweat chloride concentration (measure of CFTR function), and pulmonary function among 285 adults in Bangladesh. Participants with sweat chloride ≥ 60 mmol/L had higher arsenic exposures than those with sweat chloride < 60 mmol/L (water: median 77.5 µg/L versus 34.0 µg/L,p= 0.025; toenails: median 4.8 µg/g versus 3.7 µg/g,p= 0.024). In linear regression models, a one-unit µg/g increment in toenail arsenic was associated with a 0.59 mmol/L higher sweat chloride concentration, p < 0.001. We found that toenail arsenic concentration was associated with increased odds of airway obstruction (OR: 1.97, 95%: 1.06, 3.67,p= 0.03); however, sweat chloride concentration did not mediate this association. Our findings suggest that sweat chloride concentration may be a novel biomarker for arsenic exposure and also that arsenic likely acts on the lung through mechanisms other than CFTR dysfunction.
Red blood cell distribution as Potential Predictor of Mortality in Diabetic Foot Patients
Authors: Gou Chunmei , Huang Siyi , Huang Li , Wang Tinggang , Huang Guangtao
Published: September 2024

Background

Red blood cell distribution width (RDW) reflects the heterogeneity of red blood cell volume, which reflects the variable width of red blood cell (RBC). RDW has been proved as predictor of mortality among several diseases. The purpose of this study is to analyze the relationship between RDW and mortality of diabetic foot patients.

Methods

We first collect clinic data from the public database MIMIC-III. Kruskal Wallis rank sum test was used to analyze the association between RDW and DF mortality, and to evaluate the relationship between them. Univariate and multivariate logistic regression analysis was used for determining the risk factors and prognosis of DF patients.

Results

A total of 283 patients were included in this study, with an average age of 64.0 [54.0,70.5] years, including 193 males and 90 females. We divided RDW into three groups (high, moderate and low) according to RDW tertiles and then compared the mortality of the three groups. The high RDW group (RDW > 16.8%) had significant higher mortality (P = 0.031). In multivariate logistic regression analysis, RDW, SOFA score and APS are risk factors for death in diabetic foot. After adjusting for confounding factors in model II, RDW remains a particularly strong predictor of mortality.

Conclusions

A total of 283 patients were included in this study, with an average age of 64.0 [54.0,70.5] years, including 1We confirm that RDW is an independent predictor of mortality in DF patients,and the higher the RDW, the higher the mortality of DF patients.
In-Hospital and Long-Term Outcomes in Spontaneous Coronary Artery Dissection (SCAD) with Concurrent Cardiac Arrest: A Systematic Review and Meta-Analysis
Authors: Baqal Omar , Karikalan Suganya A. , Hasabo Elfatih A. , Tareen Haseeb , Futela Pragyat , Qasba Rakhtan K. , Shafqat Areez , Qasba Ruman K. , Hayes Sharonne N. , Tweet Marysia S. , El Masry Hicham Z. , Lee Kwan S. , Shen Win-Kuang , Sorajja Dan
Published: September 2024

Background

Spontaneous coronary artery dissection (SCAD) is increasingly recognized as an important cause of myocardial infarction (MI). However, our understanding of clinical characteristics that predispose patients to worse outcomes, such as concurrent sudden cardiac arrest (CA), remains limited.

Objective

We performed a systematic review and meta-analysis of studies assessing clinical outcomes among SCAD patients with aconcurrent CA.

Methods

This study was performed according to PRISMA guidelines. PubMed, Cochrane, and Scopus were systematically searched using relevant search terms, such as “Spontaneous Coronary Artery Dissection”, “Ventricular Tachycardia”, “Ventricular Fibrillation”, “Sudden Cardiac Death” and “Cardiac Arrest”. The search was conducted from database inception to July 2024. Studies assessing the clinical outcomes of SCAD patients with concurrent CA were included. RevMan 5.4 was used for meta-analysis.

Results

After removal of duplicates, 269 studies underwent screening, out of which 10 studies were included (n= 3978 patients, 357 with CA). In-hospital mortality, post-discharge mortality, recurrent MI and recurrent SCAD occurred in 20%, 3%, 12% and 9% of SCAD patients with CA, respectively. When compared to SCAD patients without CA, SCAD patients with CA were at significantly higher risk of in-hospital mortality (RR = 6.75, 95% CI [4.50, 10.14], I2= 0%), post-discharge mortality (RR = 5.86, 95% CI [1.72, 19.91], I2=0%), recurrent MI (RR =3.31, 95% CI [2.03, 5.39], I2=56%), recurrent SCAD (RR = 1.91, 95% CI [1.11, 3.27], I2= 43%), acute heart failure (RR = 4.82, 95% CI [3.22, 7.20], I2=42%), and cardiogenic shock (RR = 6.11, 95% CI [4.07, 9.19], I2=64%). Out of a pooled 24 implanted cardiac defibrillators (ICDs) and 11 wearable cardiac defibrillators (WCDs), there was only one appropriate and one inappropriate ICD discharge recorded over the follow-up period.

Conclusion

In this cohort, SCAD with concurrent CA was associated with worse in-hospital and long-term outcomes including in-hospital and post-discharge mortality, acute heart failure, and recurrent MI and SCAD. There was a low long-term rate of administered defibrillator therapies among patients discharged from the hospital with an ICD or WCD. Further research is needed to better delineate optimal management approaches toward this high-risk patient population, including secondary prevention of sudden cardiac death.

Graphical abstract
A Comparison of the Sexual Expression, Biomass, Cannabinoid Content, and Seed Production in XXX and XXY Triploid Cannabis
Authors: Paul Nathan , Yanush Ben , Monthony Adrian , Hall Braydon , Babaei Mehdi , Torkamaneh Davoud , Jones AMP
Published: September 2024

Cannabis is a multi-billion dollar industry reliant on unpollinated genetically female (XX) plants, as pollination reduces cannabinoid yields and flower quality. The mechanism behind the sexual expression ofC. sativais unclear. This study examines the sexual characteristics of homo- and hetero-gametic triploid cannabis plants (XX(X/Y)) to understand the role of the Y chromosome in cannabis sex determination. Heterogametic triploids were produced by crossing a male diploidC. sativacv. Durban Poison (2n = 2x = 18 + XY) with a tetraploid femaleC. sativacv. Higher Education (2n = 4x = 36 + XXXX) confirmed by flow cytometry and PCR. Measurements include fresh and dry plant weight, dry flower weight, seed counts, seed weights, and cannabinoids quantified using liquid chromatography. Results showed 44.4% of plants were XXY (n= 8), with 75% presenting a monoecious phenotype (n= 6). Of these, 50% produced predominately male flowers (n= 3), while the rest produced predominately female flowers. Plants with predominately female flowers had higher yields and cannabinoids compared to predominantly male plants. XXX genotypes outperformed XXY in several metrics. This study enhances our understanding ofC. sativasex determination and offers insight into breeding and cultivation strategies utilizing triploid cannabis.
Oxytocin receptor controls promiscuity and development in prairie voles
Authors: Sharma Ruchira , Berendzen Kristen M. , Everitt Amanda , Wang Belinda , Williams Gina , Wang Shuyu , Quine Kara , Larios Rose D. , Long Kimberly L. P. , Hoglen Nerissa , Sulaman Bibi Alika , Heath Marie C. , Sherman Michael , Klinkel Robert , Cai Angela , Galo Denis , Caamal Lizandro Chan , Goodwin Nastacia L. , Beery Annaliese , Bales Karen L. , Pollard Katherine S. , Willsey Arthur Jeremy , Manoli Devanand S.
Published: September 2024

Oxytocin receptor (Oxtr) signaling influences complex social behaviors in diverse species, including social monogamy in prairie voles. How Oxtr regulates specific components of social attachment behaviors and the neural mechanisms mediating them remains unknown. Here, we examine prairie voles lacking Oxtr and demonstrate that pair bonding comprises distinct behavioral modules: the preference for a bonded partner, and the rejection of novel potential mates. Our longitudinal study of social attachment shows that Oxtr sex-specifically influences early interactions between novel partners facilitating the formation of partner preference. Additionally, Oxtr suppresses promiscuity towards novel potential mates following pair bonding, contributing to rejection. Oxtr function regulates coordinated patterns of gene expression in regions implicated in attachment behaviors and regulates the expression of oxytocin in the paraventricular nucleus of the hypothalamus, a principal source of oxytocin. Thus, Oxtr controls genetically separable components of pair bonding behaviors and coordinates development of the neural substrates of attachment.
Failure of colonization following gut microbiota transfer exacerbates DSS-induced colitis
Authors: Gustafson Kevin L. , Rodriguez Trevor R. , McAdams Zachary L. , Coghill Lyndon M. , Ericsson Aaron C. , Franklin Craig L.
Published: September 2024

To study the impact of differing specific pathogen-free gut microbiomes (GMs) on a murine model of inflammatory bowel disease, selected GMs were transferred using embryo transfer (ET), cross-fostering (CF), and co-housing (CH). Prior work showed that the GM transfer method and the microbial composition of donor and recipient GMs can influence microbial colonization and disease phenotypes in dextran sodium sulfate-induced colitis. When a low richness GM was transferred to a recipient with a high richness GM via CH, the donor GM failed to successfully colonize, and a more severe disease phenotype resulted when compared to ET or CF, where colonization was successful. By comparing CH and gastric gavage for fecal material transfer, we isolated the microbial component of this effect and determined that differences in disease severity and survival were associated with microbial factors rather than the transfer method itself. Mice receiving a low richness GM via CH and gastric gavage exhibited greater disease severity and higher expression of pro-inflammatory immune mediators compared to those receiving a high richness GM. This study provides valuable insights into the role of GM composition and colonization in disease modulation.
Concurrent single-pulse (sp) TMS/fMRI to reveal the causal connectome in healthy and patient populations
Authors: Glick Cameron , Gajawelli Niharika , Sun Yinming , Badami Faizan , Saggar Manish , Etkin Amit
Published: September 2024

Neuroimaging and cognitive neuroscience studies have identified neural circuits linked to anxiety, mood, and trauma-related symptoms and focused on their interaction with the medial prefrontal default mode circuitry. Despite these advances, developing new neuromodulatory treatments based on neurocircuitry remains challenging. It remains unclear which nodes within and controlling these circuits are affected and how their impairment is connected to psychiatric symptoms. Concurrent single-pulse (sp) TMS/fMRI offers a promising approach to probing and mapping the integrity of these circuits. In this study, we present concurrent sp-TMS/fMRI data along with structural MRI scans from 152 participants, including both healthy and depressed individuals. The sp-TMS was administered to 11 different cortical sites, providing a dataset that allows researchers to investigate how brain circuits are modulated by spTMS.
The unique contributions of Rab11 and Rab35 to the completion of cell division
Authors: Gibieža Paulius , Ratkevičiūtė Emilija , Dabkevičiūtė Girstautė , Petrikaitė Vilma
Published: September 2024

Rab11 and Rab35 were shown to be responsible for wide-scale intracellular membrane trafficking during the last phases of the cell cycle. Even though data suggests that Rab11 and Rab35 are abscission-related, each gives a different phenotype to dividing cells. Moreover, nobody has ever looked at both and systematically compared the two during the regulation of cancer cell division. Hence, the molecular interplay and compensatory mechanisms between Rab11 and Rab35 remain to be established. Our data shows that depletion of Rab11 or Rab35 inhibits cytokinetic abscission and is associated with aberrant levels of F-actin at the intercellular bridge. In contrast, overexpression of functionally similar Rab protein cannot rescue downregulation-associated cytokinetic defects in cancer cells. We also demonstrate that even though Rab11 and Rab35 function in the same molecular pathway, the input that each individual Rab11 and Rab35 carries out during a distinct mitotic M-phase stage differs. Thus, this research study is dedicated to getting a more in-depth understanding of molecular machinery behind Rab11- and Rab35-mediated cell progression from late anaphase to cytokinesis.
Influenza A viruses induce tunnelling nanotube-like structures through the onset of apoptosis
Authors: Weir Daniel , Bentley-Abbot Calum , McCowan Jack , Loney Colin , Roberts Edward , Hutchinson Edward
Published: September 2024

As well as spreading through virions, influenza A viruses (IAVs) can evade antiviral drugs and neutralising antibodies by spreading directly from cell to cell. In cell culture this can occur by the induction of intercellular membrane connections known as tunnelling nanotube-like structures (TLSs), which are capable of trafficking the viral genome between cells. Here, we showed that TLSs are present at the site of IAV infectionsin vivo, and then usedin vitromodels to ask how IAVs induce their formation. We found that TLS induction cannot be induced by cytokine signalling from infected to uninfected cells, but requires IAV replication within cells. IAV replication can form filamentous virions with structural similarities to TLSs, but we found that TLS induction is independent of virion morphology. We therefore looked at the intracellular responses to infection. Using a pan-caspase inhibitor, we found that TLS induction by IAVs requires the onset of apoptosis. Our results, which suggest that IAVs control their ability to spread directly from cell to cell by driving infected cells into apoptosis, identifies a new way in which a virus can manipulate its host to evade antiviral immune responses.

Author Summary

Influenza A viruses (IAVs) spread efficiently through the respiratory tract in the form of extracellular virus particles, but can be restricted by neutralising antibodies and antiviral drugs. IAVs can avoid this restriction by transporting viral genomes directly from one cell to the next. They can do this by inducing the formation of long, thin intercellular connections known as tunnelling nanotube-like structures, which are capable of trafficking viral genomes. In this study, we demonstrate for the first time that tunnelling-nanotube like structures form within IAV infected lungs. We then asked how IAVs induce these structures. We found that cell death pathways triggered by IAV replication induce the formation of tunnelling nanotube-like structures, thereby establishing routes of infection spread to other cells. In this way, the virus exploits the cell death response of its host to ensure that its infection can continue to spread even within the restrictive environment of the respiratory tract.
DNA methylation and demethylation driven regulation of sepsis
Authors: Saini Akhilesh , Kumar Jitendra , Tyagi Purnima , Gautam Vipul , Khanna Rajeev , Kumar Vijay
Published: September 2024

During dysregulated inflammation and sepsis, there is a sudden surge of cytokines, such as TNF alpha, IL6, and IL10, which disrupts the body homeostasis. This sudden and rapid increase in cytokine gene expression cannot be explained by the conventional central dogma mechanism. DNA methylation is one of the most significant epigenetic modifications. DNA methylation is mostly associated with the suppression of gene activity, and DNA demethylation is associated with the activation of gene activity. There are numerous transcription factors, such as CREB1, c-FOS, AP-1, IRF1, and EGR1, that play pivotal roles in regulating inflammation. Thus, it was hypothesized that changes in the DNA methylation patterns of cytokine promoter regions or in the promoter regions of these specific transcription factors might be the potential reasons for the increase in cytokine levels during sepsis. During endotoxin stimulation, DNA methyltransferases were suppressed, and DNA methylation levels were altered at the global level. Bisulfite sequencing revealed no change in the DNA methylation patterns of the TNF-alpha, IL6 and IL10 cytokine promoters. The CREB1 and c-FOS transcription factor promoters were demethylated after LPS stimulation and in clinical sepsis samples. Overall, this study highlights the importance of the role of DNA methylation in sepsis.
A mix-and-match reverse genetics system for evaluating genetic determinants of orthobunyavirus neurological disease
Authors: Miettinen Heini M. , Abbott Matthew J. , Evans Alyssa B.
Published: September 2024

The encephalitic orthobunyaviruses have tri-segmented, negative sense RNA genomes and can cause severe neurological disease in humans, including La Crosse virus (LACV), which is the leading cause of pediatric arboviral encephalitis in the United States. However, little is known about the genetic factors that drive neuropathogenesis. Reverse genetics (RG) systems are valuable tools for studying viral genetics and pathogenesis. Plasmid-based cDNA RG systems are available for LACV, however the plasmid backbones are medium-copy number and have a propensity for recombination. We therefore generated a plasmid-based cDNA RG system for LACV utilizing a more stable and high-copy number plasmid backbone. Additionally, we created the first full RG systems for two closely related orthobunyaviruses, Jamestown Canyon virus (JCV), and Inkoo virus (INKV), which have differing reported disease incidences in humans and differing neuropathogenic phenotypes in mice compared to LACV. We compared wild type (wt) viruses with RG-derived viruses in human neuronal cells and in mice, and found that RG-derived viruses maintained the replication and neuropathogenic phenotypes of their wt counterpart. Additionally, we demonstrated that reverse genetics plasmids from different parental viruses can be readily mix-and-matched to generate reassortant viruses. This system provides a valuable genetic tool utilizing viruses with differing neuropathogenic phenotypes to investigate the genetic determinants of orthobunyavirus neuropathogenesis.
A haplotype-resolved chromosome-level genome assembly ofUrochloa decumbenscv. Basilisk resolves its allopolyploid ancestry and composition
Authors: Ryan Camilla , Fraser Fiona , Irish Naomi , Barker Tom , Knitlhoffer Vanda , Durrant Alex , Reynolds Gillian , Kaithakottil Gemy , Swarbreck David , De Vega Jose J.
Published: September 2024

Haplotyped-resolved phased assemblies aim to capture the full allelic diversity in heterozygous and polyploid species to enable accurate genetic analyses. However, building non-collapsed references still presents a challenge. Here, we used long-range interaction Hi-C reads (high-throughput chromatin conformation capture) and HiFi PacBio reads to assemble the genome of the apomictic cultivar Basilisks fromUrochloa decumbens(2n = 4x = 36), an outcrossed tetraploid Paniceae grass widely cropped to feed livestock in the tropics. We identified and removed Hi-C reads between homologous unitigs to facilitate their scaffolding and employed methods for the manual curation of rearrangements and misassemblies. Our final phased assembly included the four haplotypes in 36 chromosomes. We found that 18 chromosomes originated from diploidU. brizanthaand the other 18 from eitherU. ruziziensisor diploidU. decumbens.We also identified a chromosomal translocation between chromosomes 5 and 32, as well as evidence of pairing exclusively within subgenomes, except for a homoeologous exchange in chromosome 21. Our results demonstrate that haplotype-aware assemblies accurately capture the allelic diversity in heterozygous species, making them the preferred option over collapsed-haplotype assemblies.
High-Sensitivity Analysis of Native Bacterial Biofilms Using Dynamic Nuclear Polarization-Enhanced Solid-State NMR
Authors: Byeon Chang-Hyeock , Kinney Ted , Saricayir Hakan , Hansen Kasper Holst , Scott Faith , Srinivasa Sadhana , Wells Meghan K. , Mentink-Vigier Frederic , Kim Wook , Akbey Ümit
Published: September 2024

Bacterial biofilms cause persistent infections that are difficult to treat and contribute greatly to antimicrobial resistance. However, high-resolution structural information on native bacterial biofilms remain very limited. This limitation is primarily due to methodological constraints associated with analyzing complex native samples. Although solid-state NMR (ssNMR) is a promising method in this regard, its conventional applications typically suffer from sensitivity limitations, particularly for unlabeled native samples. Through the use of Dynamic Nuclear Polarization (DNP), we applied sensitivity enhanced ssNMR to characterize nativePseudomonas fluorescenscolony biofilms. The increased ssNMR sensitivity by DNP enabled ultrafast structural characterization of the biofilm samples without isotope-labelling, and chemical or physical modification. We collected 1D13C and15N, and 2D1H-13C,1H-15N and13C-13C ssNMR spectra within seconds/minutes or hours, respectively which enabled us to identify biofilm components as polysaccharides, proteins, and eDNA effectively. This study represents the first application of ultrasensitive DNP ssNMR to characterize a native bacterial biofilm and expands the technical scope of ssNMR towards obtaining insights into the composition and structure of a wide array ofin vitroandex vivobiofilm applications. Such versatility should greatly boost efforts to develop structure-guided approaches for combating infections caused by biofilm-forming microbes.
Uncovering hundreds of exogenous and endogenous RNA viral RdRp sequences amongst uncharacterised sequences in public protein databases
Authors: Brown K. , Firth A. E.
Published: September 2024

Public databases of protein sequences, such as the National Center for Biotechnology Information (NCBI) Protein repository and UniProt, contain millions of proteins identified in samples from specific species but named as uncharacterised, hypothetical or unclassified due to a lack of information about their function. It has been demonstrated previously that many such sequences show high similarity to genes from RNA viruses, either due to viral infection of the original sample, contamination or endogenous viral elements (EVEs) integrated into the genome of the sample species. Many proteins from RNA virus discovery research are also deposited into these repositories but, for various reasons, can only be labelled as uncharacterised and classified taxonomically at a superkingdom or realm level. Sequences from protein repositories not labelled specifically as being derived from the RNA viral RNA dependent RNA polymerase (RdRp) protein are often used as negative controls when looking to identify viral RdRp sequences, so the presence of unlabelled viruses amongst these datasets is problematic.

In this study, we screened uncharacterised proteins from two large public protein repositories - NCBI Protein and UniProt - to identify sequences likely to be derived from RNA viral RdRp. 3,560 such sequences were identified, many derived from EVEs. Many previously unknown EVEs were identified and led to characterisation of additional, related sequences. For example, a group of orbivirus-like viruses infecting nematodes was uncovered which appears to have both ancient endogenous and circulating exogenous members. Many recent integrations of mito-like viruses into plant genomes were identified, indicative of current or recent RNA viral activity. In several taxonomic groups, the first example of an EVE, and in some cases the first example of any RNA virus, was uncovered. The large number of EVEs uncovered by this relatively small-scale search suggests that only a fraction of the true diversity of EVEs is currently known.

We also explore uncharacterised proteins further by providing provisional taxonomic annotations for RdRps which are currently only listed as members of the Riboviria realm. A number of sequences are identified which are indistinguishable from known, pathogenic viruses but are labelled as bacteria, seemingly as a result of mislabelling or contamination. Sequences which are not RNA viral but show some similarity to RdRp are also analysed, as a potential source of false positives in virus discovery research. Finally, recommendations are made for generating useful negative controls.
Senataxin and DNA-PKcs Redundantly Promote Non-Homologous End Joining Repair of DNA Double Strand Breaks During V(D)J Recombination
Authors: Chen Bo-Ruei , Pham Thu , Reynolds Lance D. , Dang Nghi , Zhang Yanfeng , Manalang Kimberly , Matos-Rodrigues Gabriel , Neidigk Jason Romero , Nussenzweig Andre , Tyler Jessica K. , Sleckman Barry P.
Published: September 2024

Non-homologous end joining (NHEJ) is required for repairing DNA double strand breaks (DSBs) generated by the RAG endonuclease during lymphocyte antigen receptor gene assembly by V(D)J recombination. The Ataxia telangiectasia mutated (ATM) and DNA-dependent protein kinase catalytic subunit (DNA-PKcs) kinases regulate functionally redundant pathways required for NHEJ. Here we report that loss of the senataxin helicase leads to a significant defect in RAG DSB repair upon inactivation of DNA-PKcs. The NHEJ function of senataxin is redundant with the RECQL5 helicase and the HLTF translocase and is epistatic with ATM. Co-inactivation of ATM, RECQL5 and HLTF results in an NHEJ defect similar to that from the combined deficiency of DNA-PKcs and senataxin or losing senataxin, RECQL5 and HLTF. These data suggest that ATM and DNA-PKcs regulate the functions of senataxin and RECQL5/HLTF, respectively to provide redundant support for NHEJ.