bluuebunny/crossref_metadata_2025 huggingface dataset:
Venous thromboembolism: diagnostic advances and unaddressed challenges in management
Authors: Mathews Rick , Hinds Monica T. , Nguyen Khanh P.
Published: February 2024

Purpose of review

This review summarizes recent advances in developing targeted diagnostics for venous thromboembolism (VTE) and unaddressed knowledge gaps in patient management. Without addressing these critical data needs, the morbidity in VTE patients will persist.

Recent findings

Recent studies investigating plasma protein profiles in VTE patients have identified key diagnostic targets to address the currently unmet need for low-cost, confirmatory, point-of-care VTE diagnostics. These studies and a growing body of evidence from animal model studies have revealed the importance of inflammatory and vascular pathology in driving VTE, which are currently unaddressed targets for VTE therapy. To enhance the translation of preclinical animal studies, clinical quantification of thrombus burden and comparative component analyses between modeled VTE and clinical VTE are necessary.

Lead candidates from protein profiling of VTE patients’ plasma offer a promising outlook in developing low cost, confirmatory, point-of-care testing for VTE. Additionally, addressing the critical knowledge gap of quantitatively measuring clinical thrombi will allow for an array of benefits in VTE management and informing the translatability of experimental therapeutics.
Iron Deficiency in Anemic Children Surviving Critical Illness: Post Hoc Analysis of a Single-Center Prospective Cohort in Canada, 2019–2022
Authors: Du Pont-Thibodeau Geneviève , Li Shu Yin Han , Ducharme-Crevier Laurence , Jutras Camille , Pantopoulos Kostas , Farrell Catherine , Roumeliotis Nadia , Harrington Karen , Thibault Céline , Roy Noémi , Shah Akshay , Lacroix Jacques , Stanworth Simon J.
Published: February 2024

OBJECTIVES:

Many children leave the PICU with anemia. The mechanisms of post-PICU anemia are poorly investigated, and treatment of anemia, other than blood, is rarely started during PICU. We aimed to characterize the contributions of iron depletion (ID) and/or inflammation in the development of post-PICU anemia and to explore the utility of hepcidin (a novel iron marker) at detecting ID during inflammation.

DESIGN:

Post hoc analysis of a single-center prospective study (November 2019 to September 2022).

SETTING:

PICU, quaternary center, Canada.

PATIENTS:

Children admitted to PICU with greater than or equal to 48 hours of invasive or greater than or equal to 96 hours of noninvasive ventilation. We excluded patients with preexisting conditions causing anemia or those admitted after cardiac surgery.

INTERVENTIONS:

None.

MEASUREMENTS AND MAIN RESULTS:

Hematological and iron profiles were performed at PICU discharge on 56 participants of which 37 (37/56) were diagnosed with anemia. Thirty-three children (33/56; 59%) were younger than 2 years. Median Pediatric Logistic Organ Dysfunction score was 11 (interquartile range, 6–16). Twenty-four of the 37 anemic patients had repeat bloodwork 2 months post-PICU. Of those, four (4/24; 16%) remained anemic. Hematologic profiles were categorized as: anemia of inflammation (AI), iron deficiency anemia (IDA), IDA with inflammation, and ID (low iron stores without anemia). Seven (7/47; 15%) had AI at discharge, and one had persistent AI post-PICU. Three patients (3/47; 6%) had IDA at discharge; of which one was lost to follow-up and the other two were no longer anemic but had ID post-PICU. Eleven additional patients developed ID post-PICU. In the exploratory analysis, we identified a diagnostic cutoff value for ID during inflammation from the receiver operating characteristic curve for hepcidin of 31.9 pg/mL. This cutoff would increase the detection of ID at discharge from 6% to 34%.

CONCLUSIONS:

The burden of ID in children post-PICU is high and better management strategies are required. Hepcidin may increase the diagnostic yield of ID in patients with inflammation.
Pediatric Emergency Physicians' Knowledge, Attitudes, and Behaviors Regarding Confidential Adolescent Care
Authors: Gutman Colleen K. , Koyama Atsuko , Pickett Michelle , Holmstrom Sara , Ahmad Fahd A. , Hoch Ariel , Lehto Elizabeth , Schneider Kari , Stukus Kristin S. , Weber Emily , Stich Cassandra , Chernick Lauren S.
Published: February 2024

Objectives

More than 19 million adolescents seek care in the emergency department (ED) annually. We aimed to describe the knowledge, attitudes, and behaviors related to confidential adolescent care among pediatric ED physicians.

Methods

We conducted a cross-sectional questionnaire of US physician members of the Pediatric Emergency Medicine Collaborative Research Committee survey listserv. The 24-item questionnaire assessed familiarity with adolescent confidentiality laws, attitudes toward providing confidential care, frequency of discussing behavioral health topics confidentially, and factors influencing the decision to provide confidential care. We dichotomized Likert responses and used χ2 to compare subgroups.

Results

Of 476 eligible physicians, 151 (32%) participated. Most (91. 4%) had completed pediatric emergency medicine fellowship. More participants reported familiarity with all sexual health-related laws compared with all mental health-related laws (64% vs 49%, P < 0.001). The median age at which participants thought it was important to begin routinely providing confidential care was 12 years; 9% thought confidential interviews should not be routinely conducted until older adolescence or at all. Their decision to provide confidential care was influenced by the following: chief complaint (97%), time (43%), language (24%), presence of family (23%) or friends (14%), and space (22%).

Conclusions

Respondents reported moderate familiarity with adolescent confidentiality laws. Although they viewed confidential care as something they were comfortable providing, the likelihood of doing so varied. Barriers to confidential care were influenced by their assessment of adolescents' behavioral health risk, which may contribute to health inequity. Future efforts are needed to develop strategies that augment confidential ED care for adolescents.
Surgical Specialty Consultation for Pediatric Facial Laceration Repair
Authors: Miller Andrew F. , Levy Jason A. , Lyons Todd W.
Published: February 2024

Objective

We sought to describe patterns of and indications for surgical specialty consultation for facial laceration repair in pediatric emergency departments (PEDs).

Methods

We performed a multicenter survey of PED leadership throughout the United States and Canada evaluating the practice patterns of surgical specialty consultation for patients presenting for facial lacerations requiring repair. We measured demographics of PEDs, factors influencing the decision to obtain a surgical specialty consultation, and the presence and components of consultation guidelines. Factors related to consultation were ranked on a Likert scale from 1 to 5 (1 = Not at all important, 5 = Extremely important). We evaluated relationships between reported rates of surgical specialty consultation and PED region, annual PED volume, and reported factors associated with PED consultation.

Results

Survey responses were received from 67/124 (54%) queried PEDs. The median self-reported rate of surgical specialty consultation for facial lacerations was 10% and ranged from 1% to 70%, with resident physicians performing the repair 71% of the time a subspecialist was consulted. There was regional variability in specialty consultation, with the highest and lowest rate in the Midwest and Canada, respectively (P = 0.03). The top 4 influential factors prompting consultation with the highest percentage of responses of “Extremely Important” or “Very Important” were: discretion of the physician caring for the patient (95%), parental preference (39%), limited PED resources (32%), and patient requires sedation (32%). Surgical specialty consult guidelines were used in only 6% of PEDs with consensus that depth necessitating more than 2-layer repair or involvement of critical structures should prompt consultation.

Conclusions

Surgical specialty usage in the management of patients who present with facial lacerations to PEDs has significant variation related to patient, provider, and department-level factors that influence the decision to consult. Lack of consult guidelines represent a potential opportunity to standardize care delivery to this common presentation.
Updated Markov Model to Determine Optimal Management Strategy for Patients with Paraesophageal Hernia and Symptoms, Cameron Ulcer, or Comorbid Conditions
Authors: DeMeester Steven R , Bernard Lisa , Schoppmann Sebastian F , McKay Sarah C , Roth J Scott
Published: February 2024

BACKGROUND:

The current paradigm of watchful waiting (WW) in people 65 years or older with an asymptomatic paraesophageal hernia (PEH) is based on a now 20-year-old Markov analysis. Recently, we have shown that elective laparoscopic hernia repair (ELHR) provides an increase in life-years (L-Ys) compared with WW in most healthy patients aged 40 to 90 years. However, elderly patients often have comorbid conditions and may have complications from their PEH such as Cameron lesions. The aim of this study was to determine the optimal strategy, ELHR or WW, in these patients.

STUDY DESIGN:

A Markov model with updated variables was used to compare L-Ys gained with ELHR vs WW in hypothetical people with any type of PEH and symptoms, Cameron lesions, and/or comorbid conditions.

RESULTS:

In men and women aged 40 to 90 years with PEH-related symptoms and/or Cameron lesions, ELHR led to an increase in L-Ys over WW. The presence of comorbid conditions impacted life expectancy overall, but ELHR remained the preferred approach in all but 90-year-old patients with symptoms but no Cameron lesions.

CONCLUSIONS:

Using a Markov model with updated values for key variables associated with management options for patients with a PEH, we showed that life expectancy was improved with ELHR in most men and women aged 40 to 90 years, particularly in the presence of symptoms and/or Cameron lesions. Comorbid conditions increase the risk for surgery, but ELHR remained the preferred strategy in the majority of symptomatic patients. This model can be used to provide individualized management guidance for patients with a PEH.
Ogataea nonmethanolica f.a, sp. nov., a novel yeast species isolated from rotting wood in Brazil and Colombia
Authors: Garcia-Acero Angela M. , Morais Camila G. , Souza Gisele F. L. , Santos Ana Raquel O. , Lachance Marc-André , Velásquez-Lozano Mario E. , Rosa Carlos A.
Published: February 2024

Three yeast isolate candidates for a novel species were obtained from rotting wood samples collected in Brazil and Colombia. The Brazilian isolate differs from the Colombian isolates by one nucleotide substitution in each of the D1/D2 and small subunit (SSU) sequences. The internal transcribed spacer (ITS) and translation elongation factor 1-α gene sequences of the three isolates were identical. A phylogenetic analysis showed that this novel species belongs to the genus Ogataea. This novel species is phylogenetically related to Candida nanaspora and Candida nitratophila. The novel species differs from C. nanaspora by seven nucleotides and two indels, and by 17 nucleotides and four indels from C. nitratophila in the D1/D2 sequences. The ITS sequences of these three species differ by more than 30 nucleotides. Analyses of the sequences of the SSU and translation elongation factor 1-α gene also showed that these isolates represent a novel species of the genus Ogataea. Different from most Ogataea species, these isolates did not assimilate methanol as the sole carbon source. The name Ogataea nonmethanolica sp. nov. is proposed to accommodate these isolates. The holotype of Ogataea nonmethanolica is CBS 13485T. The MycoBank number is MB 851195.
Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses
Authors: Rahman Nadim , O'Cathail Colman , Zyoud Ahmad , Sokolov Alexey , Oude Munnink Bas , Grüning Björn , Cummins Carla , Amid Clara , Nieuwenhuijse David F. , Visontai Dávid , Yuan David Yu , Gupta Dipayan , Prasad Divyae K. , Gulyás Gábor Máté , Rinck Gabriele , McKinnon Jasmine , Rajan Jeena , Knaggs Jeff , Skiby Jeffrey Edward , Stéger József , Szarvas Judit , Gueye Khadim , Papp Krisztián , Hoek Maarten , Kumar Manish , Ventouratou Marianna A. , Bouquieaux Marie-Catherine , Koliba Martin , Mansurova Milena , Haseeb Muhammad , Worp Nathalie , Harrison Peter W. , Leinonen Rasko , Thorne Ross , Selvakumar Sandeep , Hunt Sarah , Venkataraman Sundar , Jayathilaka Suran , Cezard Timothée , Maier Wolfgang , Waheed Zahra , Iqbal Zamin , Aarestrup Frank Møller , Csabai Istvan , Koopmans Marion , Burdett Tony , Cochrane Guy
Published: February 2024

The COVID-19 pandemic has seen large-scale pathogen genomic sequencing efforts, becoming part of the toolbox for surveillance and epidemic research. This resulted in an unprecedented level of data sharing to open repositories, which has actively supported the identification of SARS-CoV-2 structure, molecular interactions, mutations and variants, and facilitated vaccine development and drug reuse studies and design. The European COVID-19 Data Platform was launched to support this data sharing, and has resulted in the deposition of several million SARS-CoV-2 raw reads. In this paper we describe (1) open data sharing, (2) tools for submission, analysis, visualisation and data claiming (e.g. ORCiD), (3) the systematic analysis of these datasets, at scale via the SARS-CoV-2 Data Hubs as well as (4) lessons learnt. This paper describes a component of the Platform, the SARS-CoV-2 Data Hubs, which enable the extension and set up of infrastructure that we intend to use more widely in the future for pathogen surveillance and pandemic preparedness.
HAIviz: an interactive dashboard for visualising and integrating healthcare-associated genomic epidemiological data
Authors: Permana Budi , Harris Patrick N. A. , Roberts Leah W. , Cuddihy Thom , Paterson David L. , Beatson Scott A. , Forde Brian M.
Published: February 2024

Existing tools for phylogeographic and epidemiological visualisation primarily provide a macro-geographic view of epidemic and pandemic transmission events but offer little support for detailed investigation of outbreaks in healthcare settings. Here, we present HAIviz, an interactive web-based application designed for integrating and visualising genomic epidemiological information to improve the tracking of healthcare-associated infections (HAIs). HAIviz displays and links the outbreak timeline, building map, phylogenetic tree, patient bed movements, and transmission network on a single interactive dashboard. HAIviz has been developed for bacterial outbreak investigations but can be utilised for general epidemiological investigations focused on built environments for which visualisation to customised maps is required. This paper describes and demonstrates the application of HAIviz for HAI outbreak investigations.
Predatory bacteria prevent the proliferation of intraocular Serratia marcescens and fluoroquinolone-resistant Pseudomonas aeruginosa
Authors: Romanowski Eric G. , Brothers Kimberly M. , Calvario Rachel C. , Stella Nicholas A. , Kim Tami , Elsayed Mennat , Kadouri Daniel E. , Shanks Robert M. Q.
Published: February 2024

Endogenous endophthalmitis caused by Gram-negative bacteria is an intra-ocular infection that can rapidly progress to irreversible loss of vision. While most endophthalmitis isolates are susceptible to antibiotic therapy, the emergence of resistant bacteria necessitates alternative approaches to combat intraocular bacterial proliferation. In this study the ability of predatory bacteria to limit intraocular growth of Pseudomonas aeruginosa, Serratia marcescens, and Staphylococcus aureus was evaluated in a New Zealand white rabbit endophthalmitis prevention model. Predatory bacteria Bdellovibrio bacteriovorus and Micavibrio aeruginosavorus were able to reduce proliferation of keratitis isolates of P. aeruginosa and to a lesser extent S. marcescens. However, it was not able to significantly reduce the number of intraocular S. aureus, which is not a productive prey for these predatory bacteria, suggesting that the inhibitory effect on P. aeruginosa and S. marcescens requires active predation rather than an antimicrobial immune response. Similarly, UV-inactivated B. bacteriovorus were unable to prevent proliferation of P. aeruginosa. Together, these data indicate in vivo inhibition of Gram-negative bacteria proliferation within the intra-ocular environment by predatory bacteria.
mTOR signaling regulates aberrant epithelial cell proliferative and migratory behaviors characteristic of airway mucous metaplasia in asthma
Authors: Kudrna Katrina , Staab Elizabeth B. , Eilers Evan , Thomes Paul , Maurya Shailendra , Brody Steven L. , Wyatt Todd A. , Bailey Kristina L. , Dickinson John D.
Published: February 2024

In asthma, the airway epithelium is hyperplastic, hypertrophied, and lined with numerous large MUC5AC-containing goblet cells (GC). Furthermore, the normal epithelial architecture is disorganized with numerous, what we here describe as, ectopic goblet cells (eGC) deep within the thickened epithelial layer disconnected from the lumenal surface. mTOR is a highly conserved pathway that regulates cell size and proliferation. We hypothesized that the balance between mTOR and autophagy signaling regulates key features of the asthma epithelial layer. Airway histological sections from subjects with asthma had increased frequency of eGC and increased levels of mTOR phosphorylation target-Ribosomal S6. Using human airway epithelial cells (hAECs) with IL-13 stimulation and timed withdrawal to stimulate resolution, we found that multiple key downstream phosphorylation targets downstream from the mTOR complex were increased during early IL-13-mediated mucous metaplasia, and then significantly declined during resolution. The IL-13-mediated changes in mTOR signaling were paralleled by morphologic changes with airway epithelial hypertrophy, hyperplasia, and frequency of eGC. We then examined the relationship between mTOR and autophagy using mice deficient in autophagy protein Atg16L1. Despite having increased cytoplasmic mucins, mouse AECs from Atg16L1 deficient mice had no significant difference in mTOR downstream signaling. mTOR inhibition with rapamycin led to a loss of IL-13-mediated epithelial hypertrophy, hyperplasia, ectopic GC distribution, and reduction in cytoplasmic MUC5AC levels. mTOR inhibition was also associated with a reduction in aberrant IL-13-mediated hAEC proliferation and migration. Our findings demonstrate that mTOR signaling is associated with mucous metaplasia and is crucial to the disorganized airway epithelial structure and function characteristic of muco-obstructive airway diseases such as asthma.

Graphical Abstract Key Concepts

The airway epithelium in asthma is disorganized and characterized by cellular proliferation, aberrant migration, and goblet cell mucous metaplasia.

mTOR signaling is a dynamic process during IL-13-mediated mucous metaplasia, increasing with IL-13 stimulation and declining during resolution.

mTOR signaling is strongly increased in the asthmatic airway epithelium.

mTOR signaling is associated with the development of key features of the metaplastic airway epithelium including cell proliferation and ectopic distribution of goblet cells and aberrant cellular migration.

Inhibition of mTOR leads to decreased epithelial hypertrophy, reduced ectopic goblet cells, and cellular migration.
Epigenome and early selection determine the tumour-immune evolutionary trajectory of colorectal cancer
Authors: Lakatos Eszter , Gunasri Vinaya , Zapata Luis , Househam Jacob , Heide Timon , Trahearn Nicholas , Swinyard Ottilie , Cisneros Luis , Lynn Claire , Mossner Maximilian , Kimberley Chris , Spiteri Inmaculada , Cresswell George D. , Llibre-Palomar Gerard , Mitchison Miriam , Maley Carlo C. , Jansen Marnix , Rodriguez-Justo Manuel , Bridgewater John , Baker Ann-Marie , Sottoriva Andrea , Graham Trevor A.
Published: February 2024

Immune system control is a major hurdle that cancer evolution must circumvent. The relative timing and evolutionary dynamics of subclones that have escaped immune control remain incompletely characterized, and how immune-mediated selection shapes the epigenome has received little attention. Here, we infer the genome- and epigenome-driven evolutionary dynamics of tumour-immune coevolution within primary colorectal cancers (CRCs). We utilise our existing CRC multi-region multi-omic dataset that we supplement with high-resolution spatially-resolved neoantigen sequencing data and highly multiplexed imaging of the tumour microenvironment (TME). Analysis of somatic chromatin accessibility alterations (SCAAs) reveals frequent somatic loss of accessibility at antigen presenting genes, and that SCAAs contribute to silencing of neoantigens. We observe that strong immune escape and exclusion occur at the outset of CRC formation, and that within tumours, including at the microscopic level of individual tumour glands, additional immune escape alterations have negligible consequences for the immunophenotype of cancer cells. Further minor immuno-editing occurs during local invasion and is associated with TME reorganisation, but that evolutionary bottleneck is relatively weak. Collectively, we show that immune evasion in CRC follows a “Big Bang” evolutionary pattern, whereby genetic, epigenetic and TME-driven immune evasion acquired by the time of transformation defines subsequent cancer-immune evolution.
Bisphenol A induces sex-dependent alterations in the dynamics of neuroendocrine seasonal adaptation in Djungarian hamsters
Authors: Moralia Marie-Azélie , Bothorel Béatrice , Andry Virginie , Simonneaux Valérie
Published: February 2024

In nature, species synchronize reproduction and energy metabolism with seasons to optimize survival and growth. While the effects of endocrine-disrupting chemicals (EDCs) exposure on conventional laboratory rodents are increasingly studied, their impacts on mammalian seasonal adaptation remain unexplored. This study investigates the effect of oral exposure to bisphenol A (BPA) on physiological and neuroendocrine seasonal adaptation in Djungarian hamsters. Adult female and male hamsters were orally exposed to BPA (5, 50, or 500 µg/kg/d) or vehicle during a 10-week transition from a long (LP) to short (SP) photoperiod (winter transition) or vice versa (summer transition). Changes in body weight, food intake, and pelage color were monitored weekly and, at the end of the exposure, gene expression of hypothalamic markers of photoperiodic, reproductive and metabolic integration, reproductive organ activity, and glycemia were assessed. Our results revealed sex-specific effects of BPA on acquiring SP and LP phenotypes. During LP to SP transition, females exposed to 500 µg/kg/d BPA exhibited delayed body weight loss and reduced feed efficiency associated with a lower expression ofsomatostatinin the arcuate nucleus (ARC), while males exposed to 5 µg/kg/d BPA showed an accelerated acquisition of SP-induced metabolic parameters. During SP to LP transition, females exposed to 5 µg/kg/d BPA displayed a faster LP adaptation in reproductive and metabolic parameters, along with quicker ARC kisspeptin downregulation and delayed ARCPomcupregulation, while males exposed to BPA exhibited decreased expression of central photoperiodic integrators without changes in the physiological LP acquisition. This pioneering study investigating EDC impacts on mammalian seasonal physiology shows that BPA alters the dynamic of metabolic adaptation to both SP and LP transitions with marked sex dimorphism, causing temporal discordance in seasonal adaptation between males and females. These findings emphasize the importance of investigating EDCs’ impact on non-conventional animal models, providing insights into wildlife physiology.

Highlights

Djungarian hamster’s seasonal adaptation is disrupted by BPA oral exposure

BPA delays in females and accelerates in males the metabolic adaptation to short days

BPA accelerates in females, not in males, metabolic/reproductive adaptation to long days

BPA affects the photoperiodic expression of central reproductive and metabolic genes

Graphical abstract
Oncogenic KRAS cells use Wnt signalling and cell dormancy to override homeostatic cell elimination mechanisms in adult pancreas.
Authors: Salvador-Barbero Beatriz , Alatsatianos Markella , Morton Jennifer P , Sansom Owen J. , Hogan Catherine
Published: February 2024

Epithelial tissues use homeostatic defence mechanisms to actively expel aberrant or genetically mutant cells and prevent disease. When present in healthy tissues in low numbers, we show that cells expressing cancer-causing mutations (KrasG12D, p53R172H) compete with normal cells for survival and are often eliminated. Thus, tumour initiation must require mechanisms whereby mutant cells override tissue defence mechanisms to remain in a tissue; however, the biology of these initial events is poorly understood. Here, we use an in vivo model of sporadic tumorigenesis in the adult pancreas to show that a population of KrasG12D- or p53R172H-expressing cells are never eliminated from the epithelium. Using RNA sequencing of non-eliminated populations and quantitative fluorescence imaging, we show that beta-catenin-independent Wnt5a signalling, and cell dormancy are key features of surviving KrasG12D cells in vivo. We demonstrate that Wnt5a (and not Wnt3a) inhibits apical extrusion of RasV12 cells in vitro by promoting stable E-cadherin-based cell-cell adhesions at RasV12-normal cell-cell boundaries. Inhibition of Wnt5a signalling restores E-cadherin dynamics at normal-mutant boundaries and apical extrusion in vitro. RasV12 cells arrested in the cell cycle are not extruded and this is rescued when Wnt signalling is inhibited. In the pancreas, Wnt signalling, E-cadherin and beta-catenin are increased at cell-cell contacts between non-eliminated KrasG12D cells and normal neighbours. Importantly, we demonstrate that active Wnt signalling is a general mechanism required to promote KrasG12D and p53R172H cell survival in vivo. Treatment with porcupine inhibitor rescues pancreas tissue defence by switching mutant cell retention to cell expulsion. Our results suggest that RAS mutant cells activate Wnt and a dormant cell state to avoid cell expulsion and to survive in the adult pancreas.
A systematic quantitative approach comprehensively defines domain-specific functional pathways linked toSchizosaccharomyces pombeheterochromatin regulation
Authors: Muhammad Abubakar , Sarkadi Zsuzsa , van Emden Thomas , Mazumder Agnisrota , Capella Matias , Fekete Gergely , Sreechakram Vishnu N. Suma , Al-Sady Bassem , Papp Balázs , Barrales Ramón Ramos , Braun Sigurd
Published: February 2024

Heterochromatin plays a critical role in regulating gene expression and maintaining genome integrity. While structural and enzymatic components have been linked to heterochromatin establishment, a comprehensive view of the underlying pathways at diverse heterochromatin domains remains elusive. Here, we developed a systematic approach to identify factors involved in heterochromatin silencing at pericentromeres, subtelomeres, and the silent mating type locus inSchizosaccharomyces pombe. Using quantitative measures, iterative genetic screening, and domain-specific heterochromatin reporters, we identified 369 mutants with different degrees of reduced or enhanced silencing. As expected, mutations in the core heterochromatin machinery globally decreased silencing. However, most other mutants exhibited distinct qualitative and quantitative profiles that indicate domain-specific functions. For example, decreased mating type silencing was linked to mutations in heterochromatin maintenance genes, while compromised subtelomere silencing was associated with metabolic pathways. Furthermore, similar phenotypic profiles revealed shared functions for subunits within complexes. We also discovered that the uncharacterized protein Dhm2 plays a crucial role in maintaining constitutive and facultative heterochromatin, while its absence caused phenotypes akin to DNA replication-deficient mutants. Collectively, our systematic approach unveiled a landscape of domain-specific heterochromatin regulators controlling distinct states and identified Dhm2 as a previously unknown factor linked to heterochromatin inheritance and replication fidelity.
Characterization of Reconstructed Human Epidermis in a Chemically-defined, Animal Origin-free Cell Culture System
Authors: Bajsert Julia , De Glas Valerie , Faway Emilie , de Rouvroit Catherine Lambert , Perez-Aso Miguel , Cook Paul W. , Poumay Yves
Published: February 2024

The Reconstructed Human Epidermis (RHE) model derived from epidermal keratinocytes offers an ethical and scientifically valid alternative to animal experimentation, particularly in cutaneous toxicology and dermatological research, where elimination of animal cruelty is of paramount importance. Moreover, safer cell- and tissue-based cutaneous therapies are also possible, where the removal of animal-originated products from the RHE culture media lessens the risk of adverse clinical events. Thus, we compared chemically-define animal origin-free (cdAOF) supplements and the historically utilized supplement (HKGS), which contains growth factors and bovine pituitary extract. Herein we present the first extended characterization of RHE using cdAOF culture systems with newborn, adult, and immortalized N/TERT keratinocytes. Culture of RHE in the cdAOF media produced histological features that were nearly identical to that produced using HKGS, with the exception that the basal keratinocytes were less cylindrical, and with some immunolocalization of involucrin in the basal layer. Additionally, increased mRNA expression of several inflammatory-proliferative markers was observed in the cdAOF RHEs as well. Importantly, in RHEs cultured in cdAOF media, expression and immunolocalization of other expected markers of keratinization, as well as monitoring of barrier function revealed results equal or close to those observed in RHE cultured in HKGS.
Unique growth and morphology properties of Clade 5Clostridioides difficilestrains revealed by single-cell time-lapse microscopy
Authors: Ribis John W. , Nieto César , DiBenedetto Nicholas V. , Mehra Anchal , Dong Qiwen , Nagawa Irene , Meouche Imane El , Aldridge Bree B. , Dunlop Mary J. , Tamayo Rita , Singh Abhyudai , Shen Aimee
Published: February 2024

Clostridioides difficileis a major One Health threat as a gastrointestinal pathogen of both humans and agricultural animals. TheC. difficilespecies consists of five main clades, with Clade 5 currently undergoing speciation from Clades 1-4. Notably, Clade 5 strains are highly prevalent in agricultural animals and can cause zoonotic infections, suggesting that Clade 5 strains have evolved phenotypes that distinguish them from Clade 1-4 strains. Here, we compare the growth properties of Clade 5 strains to Clade 1, 2, and 4 strains using anaerobic time-lapse microscopy coupled with automated image analysis. These analyses reveal that Clade 5 strains grow faster than Clade 1, 2, and 4 strains and are more likely to form long chains of cells. Comparative genomic analyses revealed that the orientation of the invertiblecmrswitch sequence likely drives the cell chaining phenotype of Clade 5 strains during growth in rich media. Interestingly, during murine infection, Clade 5 strains with a high frequency of thecmrswitch in the ON orientation shifted to a largelycmrOFF state, suggesting that thecmrOFF state may be positively selected during infection. Taken together, our data suggest that Clade 5 strains have distinct growth properties that allow them to inhabit diverse ecological niches.

Importance

The Clade 5 strains of theClostridioides difficilespecies are so phylogenetically divergent that they almost meet the threshold of being a distinct species. Although these strains are ubiquitously isolated from agricultural and environmental settings and an important source of zoonotic and community-acquired infections, it is unclear whether they have distinct phenotypic properties that allow them to efficiently colonize diverse hosts or persist in the environment. By combining a novel anaerobic time-lapse microscopy method with automated image analysis, we discovered that Clade 5 strains grow faster than strains from otherC. difficileclades and that they frequently form long chains. These chaining properties appear to be driven by the environmentally responsive expression of a non-canonical signal transduction system, which we also found is likely selected against during growth in mice. Collectively, our analyses reveal that Clade 5 strains have distinct growth properties that may promote their persistence in the environment.
Differential associations between SARS-CoV-2 infection, perceived burden of the pandemic and mental health in the German population-based cohort for digital health research
Authors: Steinmann Lavinia A. , Claaß Luise V. , Rau Moritz , Massag Janka , Diexer Sophie , Klee Bianca , Gottschick Cornelia , Binder Mascha , Sedding Daniel , Frese Thomas , Girndt Matthias , Hoell Jessica , Moor Irene , Rosendahl Jonas , Gekle Michael , Mikolajczyk Rafael , Opel Nils
Published: February 2024

Introduction

Understanding the potential adverse effects of the Covid-19-pandemic remains a challenge for public mental health. In this regard, the differentiation between potential consequences of actual infection with SARS-CoV-2 and the subjective burden of the pandemic due to measures and restrictions to daily life remains elusive.

Methods

Here we investigated the differential association between infection with SARS-Cov-2 and subjective burden of the pandemic in a study cohort of 7601 participants from the German population-based cohort for digital health research (DigiHero), who were recruited between March 4thand April 25th2022. Data was collected using the online survey tool LimeSurvey® between March and October 2022 in consecutive surveys, which included questionnaires on infection status and symptoms following COVID-19 as well as retrospective assessment of the subjective burden of the pandemic.

Results

We observed an association of a past SARS-CoV-2 infection on deteriorated mental health related symptoms, whereas no association or interaction with burden of the pandemic occurred. The association was driven by participants with persistent symptoms 12 weeks after acute infection. On a symptom specific level, neuropsychiatric symptoms such as exhaustion and fatigue, concentration deficits as well as problems with memory function were the primary drivers of the association.

Conclusion

Our findings underscore the impact of SARS-CoV-2 infections on mental health in patients suffering from ongoing symptoms 12 weeks after infection. As the association between SARS-CoV-2 infection and mental health appeared more pronounced in populations with higher vulnerability for mental disorders, increased attention should be dedicated towards these subgroups regarding the prevention of infection.
Changes in diet quality across life transitions from adolescence to early adulthood: a latent growth analysis
Authors: Tao Yinhua , Wall Melanie , Larson Nicole , Neumark-Sztainer Dianne , Winpenny Eleanor M
Published: February 2024

Background

Adolescence to early adulthood is a period of multiple education-, employment- and family-related life transitions. Changing resources and food environments within the context of these transitions could contribute to significant changes in diet, which persist into later adulthood. This study investigated diet quality trajectories from age 15 to 31 years and changes in diet quality associated with life transitions, by sex.

Methods

Data from the Project EAT (Eating and Activity in Teens and Young Adults) study were used to examine diet quality among a longitudinal cohort (n=2,524) across four waves (mean ages of 15, 19, 25 and 31 years). Diet quality was evaluated using the DASH (Dietary Approaches to Stop Hypertension) index. Life transitions were assessed by changes in life circumstances between pairs of waves, including leaving the parental home, leaving full-time education, beginning full-time employment, cohabitating with a partner, and becoming a parent. Average within-person changes in DASH scores were analysed by sex-specific latent growth models, incorporating underlying growth trajectories, five life transitions and baseline socio-demographic characteristics.

Results

Both sexes followed a quadratic trajectory of DASH scores, showing decreases in diet quality from waves 1 to 2 followed by increases until wave 4. Compared to females, males had worse diet quality at wave 1, and this sex difference widened at wave 4. Leaving the parental home between waves 1 and 2 was associated with transient decreases in diet quality at wave 2 only for males. For females, cohabitating with a partner and becoming a parent between waves 3 and 4 were respectively related to decreases and increases in diet quality at wave 4. Leaving full-time education and starting full-time employment respectively had long-term negative and positive associations with diet quality for both sexes.

Conclusions

Diet quality remained suboptimal throughout adolescence but to some extent improved across early adulthood. A sex-sensitive approach in public health policy is welcome for addressing sex differences in diet quality and dietary changes associated with family-related life transitions. Targeted dietary interventions are beneficial for young people who leave their parental home early or who do not enter into a structured school or workplace environment.
Feasibility and acceptability of collecting dried blood spots (DBS) from children after vaccination during Supplementary Immunization Activities to estimate measles and rubella seroprevalence
Authors: Carcelen Andrea C. , Prosperi Christine , Hamahuwa Mutinta , Kapungu Kelvin , Chongwe Gershom , Mwansa Francis D. , Ndubani Phillimon , Simulundu Edgar , Bwalya Innocent C. , Matakala Kalumbu H. , Musukwa Gloria , Mutale Irene , Betha Evans , Chaavwa Nchimunya , Kampamba Lombe , Matoba Japhet , Munachoonga Passwell , Mufwambi Webster , Situtu Ken , Thuma Philip E. , Sakala Constance , Kayeye Princess , Truelove Shaun A. , Winter Amy K. , Ferrari Matthew J , Moss William J. , Mutembo Simon
Published: February 2024

Nested serosurveys within routine service delivery platforms such as planned supplemental immunization activities (SIAs) provide an opportunity to collect information that can be used to answer valuable questions on the effectiveness and efficiency of the delivery model to inform future activities. However, integrating research data collection in SIAs is rarely done due to concerns it will negatively impact the program.

We conducted a serosurvey nested within the November 2020 measles-rubella SIA integrated with the Child Health Week activities in Zambia to evaluate this approach. In-depth interviews with the study teams and vaccination campaign staff at the vaccination sites were conducted. Recorded interviews were transcribed, transcripts were coded and then grouped into themes based on a process evaluation framework. A multi-methods analytical approach was used to assess the feasibility and acceptability of collecting dried blood spots from children during the SIA. This included a quantitative assessment of participant enrollment.

The serosurvey successfully enrolled 90% of children from Child Health Week due to close coordination and teamwork between the vaccination teams and serosurvey team, in addition to substantial social mobilization efforts. Continually adjusting the sampling interval that was used to select eligible children allowed us to enroll throughout the SIA and capture a representative sample of children in attendance although it was challenging for the staff involved.

As vaccination programs aim to tailor their approaches to reach the hardest-to-reach children, embedding research questions in SIAs will allow evaluation of the successes and challenges and compare alternative approaches. Lessons learned from this experience collecting data during an SIA can be applicable to future research activities embedded in SIAs or other delivery platforms.
Gene Discovery and Biological Insights into Anxiety Disorders from a Multi-Ancestry Genome-wide Association Study of >1.2 Million Participants
Authors: Friligkou Eleni , Løkhammer Solveig , Cabrera-Mendoza Brenda , Shen Jie , He Jun , Deiana Giovanni , Zanoaga Mihaela Diana , Asgel Zeynep , Pilcher Abigail , Di Lascio Luciana , Makharashvili Ana , Koller Dora , Tylee Daniel S. , Pathak Gita A. , Polimanti Renato
Published: February 2024

We leveraged information from more than 1.2 million participants to investigate the genetics of anxiety disorders across five continental ancestral groups. Ancestry-specific and cross-ancestry genome-wide association studies identified 51 anxiety-associated loci, 39 of which are novel. Additionally, polygenic risk scores derived from individuals of European descent were associated with anxiety in African, Admixed-American, and East Asian groups. The heritability of anxiety was enriched for genes expressed in the limbic system, the cerebral cortex, the cerebellum, the metencephalon, the entorhinal cortex, and the brain stem. Transcriptome- and proteome-wide analyses highlighted 115 genes associated with anxiety through brain-specific and cross-tissue regulation. We also observed global and local genetic correlations with depression, schizophrenia, and bipolar disorder and putative causal relationships with several physical health conditions. Overall, this study expands the knowledge regarding the genetic risk and pathogenesis of anxiety disorders, highlighting the importance of investigating diverse populations and integrating multi-omics information.
Genetic Mechanisms underlying Preference-Performance Mismatches: Insights from a Specialized Native Herbivore on an Invasive Toxic Plant
Authors: Ravikanthachari Nitin , Boggs Carol L
Published: February 2024

Specialist phytophagous insects have a narrow hostplant range for optimal development and survival. Mismatches between female oviposition preference and larval performance can lead to high fitness costs. Understanding the mechanistic basis of this decoupling can help us understand evolutionary constraints and aid in predicting outcomes of error-prone oviposition. We investigated the causes for preference-performance mismatches in a specialist native herbivore laying eggs on an invasive toxic plant. Transcriptomic analyses revealed no differential gene expression in gustatory/olfactory organs of adult females with different oviposition preference, but larvae exhibit host-plant-specific gene expression signatures. The larvae feeding on toxic plants showed lower expression of specialized detoxification enzymes and higher expression of general digestive enzymes, indicating the inability of larvae to detoxify toxic compounds present in the toxic plants. We additionally found that genes related to successful detoxification and adaptive feeding were enriched in larvae feeding on native plants, while genes related to toxic responses, apoptosis and accelerated development were enriched in larvae feeding on toxic plants. Our findings dissect genetic mechanisms behind preference-performance mismatches, quantifying the impact of error-prone oviposition on larval performance in specialized species interaction.
Inhibition of epithelial Na+transport: novel mechanism ofUreaplasma-driven lung disease
Authors: Glaser Kirsten , Rieger Carl-Bernd , Paluszkiewicz Elisabeth , Thome Ulrich H. , Laube Mandy
Published: February 2024

Background

Respiratory tract colonisation withUreaplasmaspecies has been associated with the development of acute and long-term pulmonary morbidity in preterm infants. Apart from inflammation, the underlying mechanisms ofUreaplasma-driven lung disease are mainly unknown. The present investigation is the first to examine the influence of acuteUreaplasmainfection on critical mechanisms of alveolar fluid clearance in the immature lung.

Methods

Primary rat fetal distal lung epithelial (FDLE) cells were incubated with viableUreaplasmain the absence or presence of the urease inhibitor flurofamide. Na+transport and activity of the epithelial Na+channel (ENaC) and the Na,K-ATPase were determined in Ussing chambers. Barrier integrity, metabolic activity, gene expression, and kinase signalling were also assessed.

Results

We found a 30-90% decrease of epithelial Na+transport upon 24 hours ofUreaplasmainfection resulting from significant inhibition of ENaC and Na,K-ATPase activities. Notably,Ureaplasmainduced phosphorylation of Erk1/2 – a well-known inhibitor of ENaC activity. Moreover,Ureaplasma-driven NH3production - and not the accompanying pH shift - inhibited the epithelial Na+transport. Co-incubation with flurofamide entirely restored Na+transport inUreaplasma-infected FDLE cells.

Conclusion

Our data demonstrate thatUreaplasmainfection significantly impairs epithelial Na+transport and subsequent fluid clearance in fetal alveolar cells – most likely by Erk1/2 phosphorylation. We identified NH3as the mediating virulence factor and were able to restore Na+transport by inhibiting theUreaplasma-specific urease. This is the first study to show a functional impairment of pulmonary epithelial cells uponUreaplasmainfection, revealing a potential mechanism ofUreaplasma-driven preterm lung disease.

Take Home

We reportUreaplasma-induced inhibition of epithelial Na+transport as a potential mechanism ofUreaplasma-driven preterm lung disease. NH3is identified as a virulence factor offering a potential therapeutic role for urease inhibitors in colonised infants.
Derepression of transposable elements enhances interferon beta signaling and stem/progenitor cell activity after proton irradiation
Authors: Cinat Davide , van der Wal Ryan , Baanstra Mirjam , Soto-Gamez Abel , Jellema-de Bruin Anne L. , van Goethem Marc-Jan , van Vugt Marcel A.T.M. , Barazzuol Lara , Coppes Rob P.
Published: February 2024

The release and subsequent detection of nucleic acids into the cytoplasm constitute a hallmark of the radiation-induced DNA damage response. However, different radiation types, such as photons and protons, may elicit distinct DNA damage responses, uniquely influencing normal stem cell activity and tissue regeneration. Here, we show that proton irradiation leads to enhanced derepression of transposable elements (TEs) with consequent activation of salivary gland stem/progenitor cells. This response is mediated by a pronounced loss of heterochromatin regulators and accumulation of cytoplasmic TE-derived dsRNA, resulting in upregulation of RIG-I and augmented interferon-beta (IFN-β) signaling. Single cell RNA sequencing (scRNA-seq) and TE dynamics analyses corroborate these findings, specifically in a subpopulation ofSox9-expressing stem/progenitor cells with increased INF-β response. These data reveal that the presence of TE-derived IFN-β in the microenvironment of irradiated organoids increases stem/progenitor cell activity and organoid growth, pointing to advantages of proton therapy over photon-based radiotherapy.