bluuebunny/crossref_metadata_2025 huggingface dataset:
The association of objectively and subjectively measuredmodifiablelifestyle factors with internalizing problems: The role of genetic confounding and shared method variancebias
Authors: Zhang Yingzhe , Choi Karmel , Frach Leonard , Robinson Elise , Ge Tian , Pingault Jean-Baptiste , Tiemeier Henning
Published: November 2024

Background

Sleep duration and physical activity have been associated with internalizing problems, such as depression, in observational studies. However, genetic confounding and measurement error may introduce bias. We assessed genetic confounding in the associations of sleep duration and physical activity with internalizing problems using both device-based and questionnaire assessments to estimate shared genetic risk across different assessment methods in adolescents.

Methods

In this preregistered study embedded in the Adolescents Brain Cognitive Development cohort, we included unrelated European adolescents with both self-reported and Fitbit-measured sleep duration devices data (N = 2283) and data on moderate to vigorous physical activity (days/week, N = 2772). Adolescents had a mean age of 12-year-old (SD = 0.65), with roughly 48% female. The internalizing problem scores were derived from self-reports of the Brief Problem Monitor A genetic sensitivity analysis was conducted to assess genetic confounding by combining polygenic scores and molecular-based heritability estimates of internalizing problems.

Results

Longer sleep duration was associated with lower internalizing problems using both self-reported (-0.15-SD, 95% CI, -0.19 to -0.11-SD) and objective (-0.10-SD, 95% CI, -0.15 to -0.06-SD) assessments. More frequent moderate/vigorous physical activity was associated with lower internalizing problems using both self-reported (-0.09-SD 95% CI, -0.13 to -0.05-SD) and device-based (-0.06-SD, 95% CI, -0.09 to -0.01-SD) assessments. A higher internalizing polygenic score was associated with more internalizing problems and shorter self-reported sleep duration but not device-based assessed sleep duration. Substantial genetic confounding (81%) was found between self-reported sleep duration and internalizing problems, predominantly among boys. No clear evidence of genetic confounding was found in the association between device-based measured sleep duration and internalizing problems. Similarly, no genetic confounding was observed for measures of physical activity in relation to internalizing problems.

Conclusion

The observed negative relationship between reported child sleep duration and internalizing problems may be partly due to genetic confounding, particularly among boys. This genetic influence likely captured some measurement error (i.e., shared method variance) in associations where exposure and outcome were assessed by self-reports. Observational studies relying on self-reports may overestimate the impact of adolescent sleep duration on internalizing problems, especially among boys. Questionnaire assessment of physical activity was less impacted.
Aeromedical Retrieval of Critically Ill Pulmonary Embolism Patients: A Protocol for a Retrospective Cohort Study of 10 Years in New South Wales
Authors: Vlok Ruan , Rassam Yousif , Partyka Christopher
Published: November 2024

Background

Pulmonary embolism is a common, time critical condition care requiring multidisciplinary care. Interhospital transport is a high-risk period in the patients’ care, but offers an opportunity for expedited risk stratification, resuscitation and transport to definitive care. Patients who require interhospital transfer to specialist centres for pulmonary embolism management have worse outcomes. Despite this, literature surrounding the medical retrieval practice and experience of pulmonary embolism is limited.

Methods

A retrospective cohort study over a 10-year period from January 2014-September 2024 from the database of a high-volume aeromedical retrieval service in New South Wales, Australia will be performed. The study aims to describe the experience in this service in the care of critically ill pulmonary embolism patients requiring interhospital transport.
Evaluating the Etiology of Metallic Taste During Head and Neck Cancer Treatments: A Study of Facial and Glossopharyngeal Nerve Interactions
Authors: Buiret Guillaume , Hélène Brignot , Chantal Septier , Gilles Feron , Thierry Thomas-Danguin
Published: November 2024

Metallic Taste (MT) is frequently described during head and neck cancer treatments but very little is known about its etiologies. One hypothesis to explain the MT is the removal of facial nerve inhibition on the glossopharyngeal nerve. Indeed, the decrease of taste afferents mediated by the facial nerve (anterior two-thirds of the tongue) due to cancer or its treatments, would reveal those mediated by the glossopharyngeal nerve (posterior one-third of the tongue) and thus lead to MT perception. The aim of this study was to evaluate the validity of this hypothesis.

Selective supraliminar taste tests on the tip and the base of the tongue were regularly performed on 44 patients with head and neck cancers before, during, and after their treatment. Sweet, salty, bitter, sour, and MT were tested. Patients were grouped based on whether they reported experiencing MT or not.

12 patients complained about MT (27.2%), always during the treatment phase. Most of them (83.3%) were treated by surgery and radiotherapy or radiochemotherapy. Supraliminar tastes were altered in every patient, especially during the treatment phase. Test results showed that perceived intensity was significantly reduced in patients reporting MT for salt, sweet and sour. This was observed more on the base of tongue than on the tip of the tongue. MT was significantly linked with mucositis (p=0.027) but with neither candidiasis (p=0.38) nor salivary flow (p=0.63).

The hypothesis of removal of facial nerve inhibition on the glossopharyngeal nerve cannot explain MT in head and neck cancer.
Etomidate as an Effective Alternative Method of Euthanizing Adult Zebrafish (Danio Rerio)
Authors: Schwartz K , Byrd K , Huss M , Jampachaisri K , Sharp P , Pacharinsak C
Published: November 2024

We assessed the efficacy of etomidate in euthanizing adult zebrafish. The aims of this study were to investigate: 1) the efficacy of 2 concentrations and 2) the effects at 2 densities. Aim 1-Fish (n=10 fish/group) were immersed in either 6 mg/L (Eto-6) or 10 mg/L (Eto-10) etomidate. Aim 2– either 5 or 10 fish were immersed in Eto-6. Tanks were video recorded and scored by two blinded observers. The parameters monitored included: 1) loss of righting reflex (LORR); 2) undulation cessation; 3) cessation of operculation (COO); and 4) loss of startle reflex. After the 30 minute immersion, fish were transferred to recovery tanks and monitored once every 5 minutes for 60 minutes. Results – Aim 1, the time to undulation cessation, COO, and loss of startle reflex was significantly shorter in the Eto-10 group and there was no difference in LORR. Aim 2, the time to LORR and undulation cessation was significantly shorter in the 5 fish/L group and there was no significant difference in time to COO or loss of startle reflex. No aversive behaviors were noted and fish in all groups were effectively euthanized by 30 minutes. This study indicates that Eto-6 or Eto-10 effectively euthanizes adult zebrafish.
The Cryo-EM structure of TRPC1 and TRPC5 heterotetramer
Authors: Chen Yixiang , Che Tong , Cheng Xinyu , Yang Xiaoqiang , Fu Ying , Zhang Wei , Lv Sijia , Yang Tingting , Peng Qi , Nan Weiwei , Wan Shuangyan , Hua Yaoguang , Li Juncheng , Wu Xiaoyun , Hu Han , Zhang Yuting , Liu Yinzhen , Yang Mingxing , Zeng Shuqi , Li Jian , Xiong Bing , Zhang Jin
Published: November 2024

Ion channel heteromers display distinct electrophysiological and ligand-binding properties, allowing precise modulation of cellular functions in specific tissues. Among the TRPC subtypes, the TRPC1/4/5 heteromers are the most abundant isoform in the human brain and represent a primary target for treating anxiety and depression. However, the structural organization of TRPC1/4/5 heteromers remain unclear, limiting the advancement of research on these channels. Here, we report the cryo-EM structure of TRPC1/5 heterotatramer at a resolution of 2.84 Å. It consists of an asymmetric structure with three TRPC5 subunits and one TRPC1 subunit. Further structural and functional analysis revealed that the TRPC1 subunit contributes to an asymmetrical ion conduction pathway, a characteristic that differentiates it from TRPC5 homomers. The unique features of the TRPC1 pore loop and its interface interactions with TRPC5 were shown to play crucial roles in modulating the ion conduction properties and gating mechanisms of the heteromeric complex. In addition, we identified key residues within the gating regions that influence channel activation and ion permeability, elucidating the structural basis for the functional divergence between the TRPC1/C5 heterotetramer and TRPC5 homotetramer. Notably, TRPC5 residues were found to dominate gating mechanisms, underscoring the complex interplay between subunit composition and functional outcomes in TRPC channels. Our findings provide novel insights into the structural and functional dynamics of TRPC1/C5 heteromers, paving the way for targeted therapeutic strategies in TRPC5-related disorders.
Fascioliasis in north-central Vietnam: assessing community knowledge, attitudes, and practices
Authors: Hoang Vinh Quang , Levecke Bruno , Do Dung Trung , Vu Binh Thi Lam , Dung Le Thuy , Thuy Nguyen Duc , Thuyen Tran Thi , Hien Nguyen Thi Thu , Ha Nguyen Ngoc , Devleesschauwer Brecht , Goossens Kathy , de Jong Theodorus , Paredis Linda , Polman Katja , Callens Steven , Dorny Pierre , Dermauw Veronique
Published: November 2024

Background: Fascioliasis, caused by Fasciola hepatica and Fasciola gigantica, is a zoonotic disease that significantly impacts public health in agricultural communities, particularly in Vietnam. This study aims to assess the knowledge, attitudes, and practices (KAP) regarding fascioliasis among residents in a rural community in Vietnam. Methodology/Principal Findings: A cross-sectional study was conducted in Dong Thanh commune, north-central Vietnam. A random sample of 621 households was selected, and 1,398 individuals participated in this study. All participants were interviewed for individual KAP to assess KAP regarding fascioliasis. In contrast, household heads were also interviewed about household practices, including life cycle knowledge, health-seeking behavior, water and sanitation practices, livestock and crop management, and dietary habits. Descriptive statistics were used to assess KAP, and generalized linear models were applied to examine the associations between socio-demographic variables and KAP. Awareness of fascioliasis was low, with 85% (1,193/1,398) of respondents reporting no prior knowledge. Detailed understanding of transmission, symptoms, and prevention was limited. Only 9% (124/1,398) of participants could accurately identify the symptoms, while 12% (168/1,398) were knowledgeable about preventive measures. A high percentage of households treated drinking water (99%, 613/619), and consumption of raw vegetables was widespread, with 93% (1,083/1,168) of individuals and 95% of households reporting this practice. Males were less likely to engage in non-risky practices than females (odds ratio: 0.696; 95% confidence interval: 0.591-0.819). Most households (85%, 522/617) sourced plants from their own land, and 67% (395/588) used animal manure as fertilizer. Conclusion/Significance: The study reveals significant gaps in knowledge, attitudes, and practices related to fascioliasis in Dong Thanh commune. There is a pressing need for targeted educational programs to enhance community awareness and promote safer practices to mitigate the risk of fascioliasis transmission. Future interventions should emphasize gender-specific education and broader community involvement to address these gaps effectively.
Risk Perception, Behavior, and Knowledge of Typhoid Fever Diagnosis, Treatment, and Vaccination: Insights from Patients in Kano, Nigeria
Authors: Ravi Nirmal , Ayando Oluwaseunayo Deborah
Published: November 2024

Background

Typhoid fever, caused bySalmonella entericaserovar Typhi andS. Paratyphi, remains a major public health issue in Nigeria, exacerbated by limited access to clean water, inadequate sanitation, and a lack of awareness about vaccination. To inform future interventions, this study investigates patients’ knowledge and perceptions of typhoid fever, including its diagnosis, treatment, and prevention.

Method

A prospective cross-sectional study was conducted among adults attending EHA Clinics in Kano, Nigeria. A structured survey assessed participants’ knowledge of typhoid fever, its transmission, its symptoms, and their attitudes toward the typhoid vaccine. Data were analyzed using R software, with descriptive statistics and associations between variables examined.

Results

Out of 443 participants, 71.4% were aware of typhoid fever, with 98% expressing confidence in its curability through appropriate treatment. Awareness of the typhoid vaccine, however, was low at 31.1%. Risk perception was high, with 75.5% of participants likely to trust a positive test result, and 63.4% believed they had a chance of contracting typhoid within the next year. Although antibiotics were widely regarded as beneficial (51.9%), misconceptions about vaccine harm persisted among some of the participants. Socio-demographic factors, particularly gender and education, were significantly associated with vaccine interest, with males and those with lower education levels showing greater interest in vaccination.

Conclusion

Despite high awareness of typhoid fever, misconceptions and limited knowledge about the vaccine pose challenges for prevention in Nigeria. Targeted educational campaigns could address these gaps and promote better attitudes toward vaccination and preventive behaviors.
The Maximal Expected Benefit of SARS-CoV-2 Interventions Among University Students: A Simulation Study Using Latent Class Analysis
Authors: Arnold Callum R.K. , Bharti Nita , Exten Cara , Small Meg , Srinivasan Sreenidhi , Kuchipudi Suresh V. , Kapur Vivek , Ferrari Matthew J.
Published: November 2024

Non-pharmaceutical public health measures (PHMs) were central to pre-vaccination efforts to reduce Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) exposure risk; heterogeneity in adherence placed bounds on their potential effectiveness, and correlation in their adoption makes assessing the impact attributable to an individual PHM difficult. During the Fall 2020 semester, we used a longitudinal cohort design in a university student population to conduct a behavioral survey of intention to adhere to PHMs, paired with an IgG serosurvey to quantify SARS-CoV-2 exposure at the end of the semester. Using Latent Class Analysis on behavioral survey responses, we identified three distinct groups among the 673 students with IgG samples: 256 (38.04%) students were in the most adherent group, intending to follow all guidelines, 306 (46.21%) in the moderately-adherent group, and 111 (15.75%) in the least-adherent group, rarely intending to follow any measure, with adherence negatively correlated with seropositivity of 25.4%, 32.2% and 37.7%, respectively. Moving all individuals in an SIR model into the most adherent group resulted in a 76-93% reduction in seroprevalence, dependent on assumed assortativity. The potential impact of increasing PHM adherence was limited by the substantial exposure risk in the large proportion of students already following all PHMs.
Long-term left atrial function after transcatheter device closure of patent foramen ovale in patients with cryptogenic stroke
Authors: Gil-Jiménez Teresa , García-Orta Rocía , Villegas-Rodriguez Inmaculada , Caballero-Borrego Juan , Moreno-Escobar Eduardo
Published: November 2024

Aims

The implantation of percutaneous atrial septal occluder (ASO) devices for patent foramen ovale (PFO) may affect left atrial (LA) function. Some studies have reported short- to mid-term impairment of this function, though it remains unclear whether this is a transient or permanent negative effect, nor if all patients are equally susceptible to these changes.

Methods and results

Observational, prospective study of consecutive patients with cryptogenic stroke (CS) undergoing percutaneous closure of PFO. Echocardiographic evaluation of evolving structural and functional parameters of the LA was carried out before procedure, inmediately after (within 24 hours), 6 and 18 months after device insertion.

From March 2019 to October 2023, 170 patients with CS were enrolled, 82 eligible for PFO closure and 65 undergoing percutaneous closure. Baseline structural and functional parameters were within normal limits. At 6 months follow-up, there is a significant increase in LA volumes and a deterioration of reservoir and conduit functions measured by strain. There is a subsequent trend toward normalization, but baseline parameters are not reached by 18 months.

Conclusions

PFO device closure negatively impacts on LA function, resulting in increased atrial volumes, worsening of left ventricular diastolic function, decreased reservoir and conduit function, and a compensatory increase in pump function. These changes are significant at 6 months, with partial improvement but without full normalization of parameters at 18 months follow-up.
Microbes display broad diversity in cobamide preferences
Authors: Mok Kenny C. , Sokolovskaya Olga M. , Deutschbauer Adam M. , Carlson Hans K. , Taga Michiko E.
Published: November 2024

Cobamides, the vitamin B12(cobalamin) family of cofactors, are used by most organisms but produced by only a fraction of prokaryotes, and are thus considered key shared nutrients among microbes. Cobamides are structurally diverse, with multiple different cobamides found in most microbial communities. The ability to use different cobamides has been tested for several bacteria and microalgae, and nearly all show preferences for certain cobamides. This approach is limited by the commercial unavailability of cobamides other than cobalamin. Here, we have extracted and purified seven commercially unavailable cobamides to characterize bacterial cobamide preferences based on growth in specific cobamide-dependent conditions. The tested bacteria include engineered strains ofEscherichia coli, Sinorhizobium meliloti, andBacillus subtilisexpressing native or heterologous cobamide-dependent enzymes, cultured under conditions that functionally isolate specific cobamide-dependent processes such as methionine synthesis. Comparison of these results to previous studies of diverse bacteria and microalgae revealed that a broad diversity of cobamide preferences exists not only across different organisms, but also between different cobamide-dependent metabolic pathways within the same organism. The microbes differed in the cobamides that support growth most efficiently, cobamides that do not support growth, and the minimum cobamide concentrations required for growth. The latter differ by up to four orders of magnitude across organisms from different environments and by up to 20-fold between cobamide-dependent enzymes within the same organism. Given that cobamides are shared, required for use of specific growth substrates, and essential for central metabolism in certain organisms, cobamide preferences likely impact community structure and function.
dArc1controls sugar reward valuation inDrosophila melanogaster
Authors: Bervoets Sven , Jacob Miles Solomon , Devineni Anita V. , Mahoney Brennan Dale , Sullivan Kaelan R. , Butts Andrew R. , Sung Hayeon , Einstein Jenifer , Metzstein Mark M. , Dus Monica , Shepherd Jason D. , Caron Sophie Jeanne Cécile
Published: November 2024

TheArcgenes — which includeDrosophila Arc1andArc2(dArc) — evolved from Ty3 retrotransposons and encode proteins that form virus-like capsids. These capsids enable a novel form of intercellular communication by transferring RNAs between cells. However, the specific neuronal circuits and brain processes Arc intercellular signaling regulates remain unknown. Here, we show that loss of bothdArcgenes inDrosophila melanogasterenhances associative learning in an appetitive conditioning paradigm, where flies associate an odor with sugar rewards. This increased learning performance arises from an increased valuation of sugar rewards: unlike wild-type flies,dArc-/-flies form abnormally strong associations even when the sugar reward is small or has no caloric value. We found that the γ5-dopaminergic neurons of the protocerebral anterior medial (PAM) cluster, which encode the positive valence of sugar rewards, show heightened activity in response to sucrose indArc-/-flies. We further show that the learning phenotype ofdArc-/-flies depends on the formation of capsids, underscoring a direct role for capsid-mediated Arc signaling in sugar valuation. Our findings establishdArcgenes as critical regulators of reward valuation inD. melanogaster, acting through a non-cell autonomous mechanism that relies on capsid-mediated communication between cells.
Compressive forces induce epigenetic activation of aged human dermal fibroblasts through ERK signaling pathway
Authors: Liu Hui , Yuan Luezhen , Baldi Lucrezia , Sornapudi Trinadha Rao , Shivashankar G.V.
Published: November 2024

Age-related changes in human dermal fibroblasts (HDFs) contribute to impaired wound healing and skin aging. While these changes result in altered mechanotransduction, the epigenetic basis of rejuvenating aging cells remains a significant challenge. This study investigates the effects of compressive forces on nuclear mechanotransduction and epigenetic rejuvenation in aged HDFs. Using a compressive force application model, the activation of HDFs through alpha-smooth muscle actin (ɑ-SMA) is demonstrated. Sustained compressive forces induce significant epigenetic modifications, including chromatin remodeling and altered histone methylation patterns. These epigenetic changes correlate with enhanced cellular migration and rejuvenation. Small-scale drug screening identifies the extracellular signal-regulated kinase (ERK) signaling pathway as a key mediator of compression-induced epigenetic activation. Furthermore, implanting aged cell spheroids to an aged skin model and subjecting the tissue with compressing forces resulted in increased collagen I protein levels. Collectively, these findings demonstrate that applying compressive force to aged fibroblasts activates global epigenetic changes through the ERK signaling pathway, ultimately rejuvenating cellular functions with potential applications for wound healing and skin tissue regeneration.

Significance Statement

Partial rejuvenation of aging cells is desirable but is still a major challenge. In this paper, we demonstrate that aged human dermal fibroblasts, embedded in a 3D collagen hydrogel matrix as spheroids, subjected to external static compressive force exhibit partial rejuvenation. Through immunofluorescence, small-scale inhibitor screen and gene expression analysis, we identify some of the critical mechanotransduction pathways in this process. Collectively, our results provide compelling evidence that tissue compression results in the activation of potential rejuvenation pathways in aging cells.
Modulating Neurotoxic Effects of Prenatal Chlorpyrifos Exposure Through Probiotic and Vitamin D Gestational Supplementation: Unexpected Effects on Neurodevelopment and Sociability
Authors: Coca Mario , Perez-Fernandez Cristian , Abreu Ana C. , Salmerón Ana M. , Morales-Navas Miguel , Ruiz-Sobremazas Diego , Colomina Teresa , Fernández Ignacio , Sanchez-Santed Fernando
Published: November 2024

Autism is a neurodevelopmental disorder characterized by impairments in sociability and communication. Prenatal exposure to Chlorpyrifos has been associated with autism-like behaviors in preclinical models. Interest has grown in the gut-brain axis and the role of microbiota modulation through dietetic supplementation to reduce this ASD-like phenotype. This study examines the effects of prenatal CPF exposure in Wistar Rats and assesses the potential of gestational probiotic and vitamin D supplementation to mitigate these effects in offspring. CPF exposure significantly impaired sociability in adolescence, and supplementation did not reverse these deficits. However, in control animals, supplementation induced neurodevelopmental changes, including alterations in metabolic status, the pattern of expression of ASD-related genes, the regulation of oxytocin and vasopressin receptors, and the GABAergic system in the brain. Additionally, supplementation accelerated overall development, increased ultrasonic vocalization emission and modified the typical responses to social novelty. CPF exposure blocked most of these effects at both behavioral and molecular levels. While supplementation did not block CPF-induced impairments, CPF exposure altered the observed effects of supplementation in controls, possibly indicating shared molecular mechanisms. These findings highlight the need for further research into the safety of probiotic and vitamin D supplementation during pregnancy.
Chromatin mimicry by human JC virus
Authors: Schaefer Uwe , Miroshnikova Yekaterina A. , Xie Wei , Larson Adam G. , Lu Ziyu , Chen Shoudeng , Bradic Martina , Goldgur Yehuda , Chen Kexin , Sharma Ved P. , Cao Junyue , Patel Dinshaw J. , Narlikar Geeta J. , Wickström Sara A. , Tarakhovsky Alexander
Published: November 2024

Chronically persistent viruses are integral components of the organismal ecosystem in humans and animals12. Many of these viruses replicate and accumulate within the cell nucleus3. The nuclear location allows viruses to evade cytoplasmic host viral sensors and promotes viral replication4. One of the unexplored and puzzling aspects of the viral nuclear lifecycle involves the virus’s ability to deal with the physical constraints of nuclear architecture. To replicate and accumulate within the nucleus in large numbers sufficient for infection spreading, DNA viruses need to overcome the spatial limitations imposed by chromatin and the nuclear matrix. We found that one of the most widespread and potentially lethal human viruses, the JC polyomavirus5, interferes with nuclear heterochromatin to create virus-occupied space. The JC virus’s impact on heterochromatin is mediated by the viral nonstructural protein, Agnoprotein (Agno). Agno’s interference with heterochromatin is governed by structurally diverse mimics of host epigenetic regulators that facilitate virus-induced chromatin reorganization and a dramatic decline in nuclear stiffness in the infected cells. The JCV epigenetic mimicry is critical for the virus infection, as evident from reduced replication of mimic-mutant viruses. Our data suggest that modulation of nuclear mechanical properties is a novel strategy enabling chronicity of the JC and possibly other nuclear virus infections.
Identification of Novel FosX Family Determinants from Diverse Environmental Samples
Authors: Kieffer Nicolas , Böhm Maria-Elisabeth , Berglund Fanny , Marathe Nachiket P. , Gillings Michael R , Larsson D. G. Joakim
Published: November 2024

Objectives

This study aimed to identify novel fosfomycin resistance genes across diverse environmental samples, ranging in levels of anthropogenic pollution. We focused on fosfomycin resistance, and given its increasing clinical importance, explored the prevalence of these genes within different environmental contexts.

Methods

Metagenomic DNA was extracted from wastewater and sediment samples collected from sites in India, Sweden, and Antarctica. Class 1 integron gene cassette libraries were prepared, and resistant clones were selected on fosfomycin-supplemented media. Long-read sequencing was performed, followed by bioinformatics analysis to identify novel fosfomycin resistance genes. The genes were cloned and functionally characterized inE. coli, and the impact of phosphonoformate on the enzymes was assessed.

Results

Four novel fosfomycin resistance genes were identified. Phylogenetic analysis placed these genes within the FosX family, a group of metalloenzymes that hydrolyse fosfomycin without thiol conjugation. The genes were subsequently renamedfosE2, fosI2, fosI3, andfosP. Functional assays confirmed that these genes conferred resistance to fosfomycin inE. coli, with with MIC ranging from 32 μg/ml to 256μg/ml. Unlike FosA/B enzymes, these FosX-like proteins were resistant to phosphonoformate inhibitory action. AfosI3homolog was identified inPseudomonas aeruginosa, highlighting potential clinical relevance.

Conclusions

This study expands the understanding of fosfomycin resistance by identifying new FosX family members across diverse environments. The lack of phosphonoformate inhibition underscores the clinical importance of these poorly studied enzymes, which warrant further investigation, particularly in pathogenic contexts.
Spatial characterizations of bacterial dynamics for food safety: Modeling for shared water processing environments
Authors: Munther Daniel , Ryan Shawn D. , Kothapalli Chandrasekhar R. , Zekaj Nerion
Published: November 2024

Bacterial dynamics occurring in shared water environments during food processing are typically modeled assuming a homogeneous mixing profile. However, given the tank configurations, and water recirculation and reuse specifications used in many facilities, uniform mixing is not always applicable. Towards this goal, we here developed a novel reaction-diffusion-advection model that captures temporal and spatial variations in the water tanks under dynamic conditions. We utilize the dynamics involved in poultry chilling as an example, as this process features a comprehensive interplay of bacteria, water chemistry and water flow dynamics, as well as determining bacteria levels on carcasses moving into final phases of the food production chain, thus directly influencing public health risk. Well-posedness, existence and uniqueness of positive steady-state solutions with global stability are proved, as well as an estimation of the time scale of convergence to the steady-state solution provided. Simulations are used to verify the analytical results incorporating parameters informed by experimental data from generic, non-pathogenicE. coli, and predictively estimate the time to equilibrium. We show that during a typical 8 h processing shift, the model reaches steady state within 2 h, applying this result to validate model simulations against commercial data. The calibrated model predicts a distribution ofE. colilevels on post-chill carcasses with mean and standard deviation of 3.35 ± 0.56 Log10 CFU/carcass, which closely compares to the experimentally observed distribution of 3.55 ± 0.64 Log10 CFU/carcass in an industrial setting. Our results reinforce the key role of space in quantifying essential mechanisms that govern water chemistry andE. colidynamics during poultry chilling. Our model is an important tool to improve decision making for pathogen control during poultry chilling, as well as a blueprint from which models for processing other commodities like fresh produce and pork can be established.
Perisomatic Synaptic Targeting by Cholecystokinin-Basket Interneurons through NrCAM and Ankyrin B
Authors: Oldre Erik N. , Webb Barrett D. , Sperringer Justin E. , Maness Patricia F.
Published: November 2024

The perisomatic region of cortical pyramidal neurons (PNs) integrates local and long-range inputs and regulates firing.This domain receives GABAergic inputs from cholecystokinin (CCK)- and parvalbumin (PV)-expressing basket cells (BCs) but how synaptic contacts are established is unclear. Neuron-glial related cell adhesion molecule (NrCAM) is a homophilic transmembrane protein that binds the scaffold protein Ankyrin B. Here we show that NrCAM and Ankyrin B mediate perisomatic synaptic contact between CCK-BCs and PNs in mouse prefrontal cortex (PFC). Immunolabeling of CCK-BC terminals for vesicular glutamate transporter-3 (VGlut3) or vesicular glutamate transporter (VGAT) revealed a significant decrease in CCK-BC synaptic puncta on PN soma in NrCAM-null mice, however no decrease in PV-BC puncta, or cell loss. VGlut3+ CCK-BC puncta were also decreased by Ankyrin B deletion from PNs in Nex1Cre-ERT2:Ank2flox/flox:EGFP mice. A novel CCK-BC reporter mouse expressing tdTomato (tdT) at the Synuclein-γ (Sncg) locus showed NCAM localized to presynaptic Sncg+ CCK-BCs, as well as to postsynaptic PN soma of WT mice. Results implicate NrCAM homophilic interactions and Ankyrin B binding with development of inhibitory connectivity between CCK-BCs and excitatory neurons of the PFC.
Non-gonadal PIWI protein, Aubergine, regulates regenerative stem cell proliferation and tumourigenesis in theDrosophilaadult intestine
Authors: Bellec Karen , Carroll Lynsey R , Pennel Kathryn AF , Tian Yuanliangzi , Yu Yachuan , Cameron Alexander R , Herédia Fabiana , Gontijo Alisson M , Edwards Joanne , Hayashi Rippei , Cordero Julia B
Published: November 2024

Somatic stem cells are executors of physiological and pathological proliferation of adult self-renewing tissues, such as the intestine. The actions of intestinal stem cells (ISCs) rely on the integration of cell intrinsic and niche-derived signals, which are necessary to achieve a balanced response to the multiple stimuli that constantly challenge tissue homeostasis and organismal health. Disruption of such balance is causative of age-associated tissue dysfunction and hyperproliferative conditions, including inflammation and cancer.

The highly conserved PIWI-interacting RNAs (piRNAs) biosynthesis pathway, also known as the PIWI pathway, has been classically studied in theDrosophilagermline for its role in the repression of transposable elements (TEs) and the regulation of germline stem cell homeostasis. Recent reports have emerged on a role of Piwi, the founding member of the pathway, in the maintenance of ISC homeostasis in the adultDrosophilamidgut. The implications of these findings regarding a general role of the PIWI pathway and piRNAs in the intestine remain to be addressed. Here, we characterise a cell autonomous role of the PIWI family protein Aubergine (Aub) in ISCs. We show that, while dispensable for homeostatic self-renewal of the midgut, inducible Aub is essential to regulate ISC proliferation following acute damage of the intestinal epithelium and in oncogenic settings. Our work suggests that the role of Aub in ISCs is independent of its piRNAs regulatory function. Instead, Aub drives ISC proliferation through the regulation of protein synthesis, including induction of regenerative stem cell factors Myc and Sox21a, and a parallel pathway involving the eukaryotic initiation factor 3 complex (eIF3). In summary, our results discover a role for Aub in damage-induced proliferation of the adultDrosophilaintestine involving the regulation of major regenerative pathways and the protein translation machinery. Furthermore, we present genetically defined hyperplastic settings fostering distinct functions of Aub in intestinal tumourigenesis.
MINT: a toolbox for the analysis of multivariate neural information coding and transmission
Authors: Lorenz Gabriel Matías , Engel Nicola M. , Celotto Marco , Kocillari Loren , Curreli Sebastiano , Fellin Tommaso , Panzeri Stefano
Published: November 2024

Information theory has deeply influenced the conceptualization of brain information processing and is a mainstream framework for analyzing how neural networks in the brain process information to generate behavior. Information theory tools have been initially conceived and used to study how information about sensory variables is encoded by the activity of small neural populations. However, recent multivariate information theoretic advances have enabled addressing how information is exchanged across areas and used to inform behavior. Moreover, its integration with dimensionality-reduction techniques has enabled addressing information encoding and communication by the activity of large neural populations or many brain areas, as recorded by multichannel activity measurements in functional imaging and electrophysiology. Here, we provide a Multivariate Information in Neuroscience Toolbox (MINT) that combines these new methods with statistical tools for robust estimation from limited-size empirical datasets. We demonstrate the capabilities of MINT by applying it to both simulated and real neural data recorded with electrophysiology or calcium imaging, but all MINT functions are equally applicable to other brain-activity measurement modalities. We highlight the synergistic opportunities that combining its methods afford for reverse engineering of specific information processing and flow between neural populations or areas, and for discovering how information processing functions emerge from interactions between neurons or areas. MINT works on Linux, Windows and macOS operating systems, is written in MATLAB (requires MATLAB version 2018b or newer) and depends on 5 native MATLAB toolboxes. The calculation of one possible way to compute information redundancy requires the installation and compilation of C files (made available by us also as pre-compiled files). MINT is freely available athttps://github.com/panzerilab/MINTwith DOI 10.5281/zenodo.13998526 and operates under a GNU GPLv3 license.
Validation of DXS as an attractive drug target in mycobacteria
Authors: Maila T , Nicolaai M , Mbau R.D , Mashabela G.T.M
Published: November 2024

A rapid emergence in the incidences of Tuberculosis (TB) drug resistance undermines efforts to eradicate the disease and strengthens calls for development of new drugs with novel mechanisms of action. In drug discovery, finding an attractive drug target is as important as finding a good drug candidate. Hence more efforts are made to identify, validate and prioritize drug targets in TB drug discovery. Here, using CRISPRi technology, we showed thatdxs1transcriptional knockdown attenuated growth of bothMycobacterium smegmatisandMycobacterium tuberculosiscultures, and the effect was more profound in the latter. Chemical supplementation of the growth medium with 10 μM of isoprenoid pyrophosphates, thiamine and thiamine pyrophosphate failed to rescue growth ofM. smegmatiscultures, while partial rescue was observed with addition of menatetrenone, a menaquinone derivative with four isoprenyl groups. Similarly, culture growth could not be rescued by the addition of prenol and isoprenol, which suggested the lack of isoprenoid salvage pathway in mycobacteria. Importantly, and in the context of drug discovery,dxs1depleted mutants displayed four-fold more sensitive towards a mixture of isoniazid, rifampicin and ethambutol, suggesting that inhibitors of DXS enzyme or other MEP pathway enzymes could potentiate antimycobacterial effect of the first-line TB drugs. Additionally,dxs1depletion increased growth retardation of the mutant in acidic pH and under oxidative stress, conditions that are encountered in activated macrophage compartments. Taken together, our results validated DXS as an attractive drug target that should be prioritized for developments on new antitubercular agents.
Nucleus accumbens D2-expressing neurons: Balancing reward and licking disruption through rhythmic optogenetic stimulation
Authors: Requejo-Mendoza Nikte , Arias-Montaño José-Antonio , Gutierrez Ranier
Published: November 2024

Dopamine D1 receptor-expressing neurons in the nucleus accumbens (NAc) are known to be critical for processing reward and regulating food intake. However, the role of D2-expressing neurons in this region remains less understood. This study employed optogenetic manipulations to investigate the role of NAc D2-expressing neurons in reward processing and sucrose consumption. Optogenetic activation of these neurons decreased sucrose preference (at 20 Hz), disrupted licking patterns (particularly at 8 and 20 Hz), and increased self-stimulation. Conversely, synchronizing stimulation with the animal’s licking rhythm mitigated licking disruption and even increased sucrose intake, suggesting a rewarding effect. Furthermore, 20 Hz stimulation (but not 8 Hz) induced place preference in a real-time place preference (RTPP) test. In contrast, inhibiting D2 neurons produced a negative hedonic state, although not reaching a complete aversion, influencing food choices in specific contexts. For instance, while the RTPP test per se was not sensitive enough to observe place aversion when mice could choose between consuming a high-fat diet (HFD) pellet in a context associated with or without inhibition of D2 neurons, they preferred to consume HFD on the non-inhibited side. This suggests that the palatability of HFD can unmask (but also overshadow) the negative hedonic state associated with D2 neuron inhibition. A negative reinforcement paradigm further confirmed the active avoidance behavior induced by D2 neuron inhibition. In conclusion, NAc D2 neuron inhibition induces a negative hedonic state, while activation has a dual effect—it is rewarding yet disrupts licking behavior—highlighting its complex role in reward and consummatory behavior. Importantly, self-paced stimulation, where the animal controls the timing of the stimulation by its licking behavior, offers a more efficient and natural approach for stimulating NAc activity.
A rare HSC-derived megakaryocyte progenitor accumulates via enhanced survival and contributes to exacerbated thrombopoiesis upon aging
Authors: Manso Bryce A. , Medina Paloma , Smith-Berdan Stephanie , Rodriguez y Baena Alessandra , Bachinsky Elmira , Mok Lydia , Deguzman Angela , Avila Sarah Beth , Chattopadhyaya Saran , Rommel Marcel G.E. , Jönsson Vanessa D. , Forsberg E. Camilla
Published: November 2024

Distinct routes of cellular production from hematopoietic stem cells (HSCs) have defined our current view of hematopoiesis. Recently, we challenged classical views of platelet generation, demonstrating that megakaryocyte progenitors (MkPs), and ultimately platelets, can be specified via an alternate and additive route of HSC-direct specification specifically during aging. This “shortcut” pathway generates hyperactive platelets likely to contribute to age-related platelet-mediated morbidities. Here, we used single-cell RNA/CITEseq to demonstrate that these age-unique, non-canonical (nc)MkPs can be prospectively defined and experimentally isolated from wild type mice. Surprisingly, this revealed that a rare population of ncMkPs also exist in young mice. Young and aged ncMkPs are functionally distinct from their canonical (c)MkP counterparts, with aged ncMkPs paradoxically and uniquely exhibiting enhanced survival and platelet generation capacity. We further demonstrate that aged HSCs generate significantly more ncMkPs than their younger counterparts, yet this is accomplished without strict clonal restriction. Together, these findings reveal significant phenotypic, functional, and aging-dependent heterogeneity among the MkP pool and uncover unique features of megakaryopoiesis throughout life, potentially offering cellular and molecular targets for mitigation of age-related adverse thrombotic events.
xIV-LDDMM Toolkit: A Suite of Image-Varifold Based Technologies for Representing and Mapping 3D Imaging and Spatial-omics Data Simultaneously Across Scales
Authors: Stouffer Kaitlin , Chen Xiaoyin , Zeng Hongkui , Charlier Benjamin , Younes Laurent , Trouve Alain , Miller Michael I
Published: November 2024

Advancements in imaging and molecular techniques enable the collection of subcellular-scale data. Diversity in measured features, resolution, and physical scope of capture across technologies and experimental protocols pose numerous challenges to integrating data with reference coordinate systems and across scales. This resource paper describes a collection of technologies that we have developed for cross-modality 3D mapping for the alignment of transcriptomics at the micron scales of genes and cells to the anatomical tissue scales. Our collection of technologies include (i) an explicit censored data representation for the partial matching problem mapping whole brains to subsampled subvolumes, (ii) image-varifold measure norms for supporting nearly universal crossing of modality, (iii) a multi, scale-space optimization technology for generating resampling grids optimized to represent spatial geometry at fixed complexities, and (iv) mutual-information based functional feature selection. Collectively, these methods afford efficient representations of peta-scale imagery providing the algorithms for mapping from the nano to millimeter scales which we term cross-modality image-varifold LDDMM (xIV-LDDMM).
Biochemical evidence for the diversity of LHCI proteins in PSI-LHCI from the red algaGaldieria sulphurariaNIES-3638
Authors: Nagao Ryo , Ogawa Haruya , Suzuki Takehiro , Dohmae Naoshi , Kato Koji , Nakajima Yoshiki , Shen Jian-Ren
Published: November 2024

Red algae are photosynthetic eukaryotes whose light-harvesting complexes (LHCs) associate with photosystem I (PSI). In this study, we examined characteristics of PSI-LHCI, PSI, and LHCI isolated from the red algaGaldieria sulphurariaNIES-3638. The PSI-LHCI supercomplexes were purified using anion-exchange chromatography followed by hydrophobic interaction chromatography, and finally by trehalose density gradient centrifugation. PSI and LHCI were similarly prepared following the dissociation of PSI-LHCI with Anzergent 3-16. Polypeptide analysis of PSI-LHCI revealed the presence of PSI and LHC proteins, along with a red-lineage chlorophylla/b-binding-like protein (RedCAP), which is distinct from LHC proteins within the LHC protein superfamily. RedCAP, rather than LHC proteins, exhibited tight binding to PSI. Carotenoid analysis of LHCI identified zeaxanthin,β-cryptoxanthin, andβ-carotene, with zeaxanthin particularly enriched, which is consistent with other red algal LHCIs. A Qy peak of chlorophyllain the LHCI absorption spectrum was blue-shifted compared with those of PSI-LHCI and PSI, and a fluorescence emission peak was similarly shifted to shorter wavelengths. Based on these results, we discuss the diversity of LHC proteins, including RedCAP, in red algal PSI-LHCI supercomplexes.