bluuebunny/crossref_metadata_2025 huggingface dataset:
ImputeBench: Benchmarking Single Imputation Methods
Authors: Richter Robin , Tavares Juliana F. , Miloschewski Anne , Breteler Monique M. B. , Mukherjee Sach
Published: February 2025

Biomedical data often contain missing values and in many applications missing value imputation (MVI) is an important part of the data analysis work-flow. However, the performance of MVI methods depends on details of the joint distribution of data and missingness patterns that are typically unknown in practice, making ana priorichoice of MVI method challenging. Furthermore, technical assumptions underlying MVI methods can be hard to directly verify in practice. Motivated by these issues, in this paper, we propose an approach for the context-specific selection of MVI methods. Due to the fact that different methods may work well in different cases we argue for a move away from a “one size fits all” view and put forward in this paper a standardized, empirical approach in which MVI methods are benchmarked in the specific context of a problem of interest. We connect our work to the large body of MVI research, along the way refining definitions of missing at random and missing not at random and providing a detailed review of existing work on benchmarking. Our approach can be tailored to reflect specific assumptions on missingness patterns, allowing for application in diverse applied problems. Furthermore, in addition to using real data, we study benchmarking via data simulation spanning a broad range of properties, such as latent factors, non-linearity and multi-modality, with interpretable simulation parameters that are amenable to user specification. The approaches we propose can be used to (i) select an MVI method for a given data set or (ii) benchmark a novel MVI method across a range of regimes. Alongside the general protocol, we provide a specific, reproducible implementation (in the R-packageImputeBench, available under github.com/richterrob/ImputeBench) that gives users a ready-to-use tool for MVI selection and assessment. We illustrate the use ofImputeBenchto study the behaviour of a range of existing imputation methods (k-nn, soft impute, missForest, MICE) in the context of real data from an ongoing large-scale population-level study.
Worm Perturb-Seq: massively parallel whole-animal RNAi and RNA-seq
Authors: Zhang Hefei , Li Xuhang , Song Dongyuan , Yukselen Onur , Nanda Shivani , Kucukural Alper , Li Jingyi Jessica , Garber Manuel , Walhout Albertha J.M.
Published: February 2025

The transcriptome provides a highly informative molecular phenotype to connect genotype to phenotype and is most frequently measured by RNA-sequencing (RNA-seq). Therefore, an ultimate goal is to perturb every gene and measure changes in the transcriptome. However, this remains challenging, especially in intact organisms due to different experimental and computational challenges. Here, we present ‘Worm Perturb-Seq (WPS)’, which provides high-resolution RNA-seq profiles for hundreds of replicate perturbations at a time in a living animal. WPS introduces multiple experimental advances that combine strengths of bulk and single cell RNA-seq, and that further provides an analytical framework, EmpirDE, that leverages the unique power of the large WPS datasets. EmpirDE identifies differentially expressed genes (DEGs) by using gene-specific empirical null distributions, rather than control conditions alone, thereby systematically removing technical biases and improving statistical rigor. We applied WPS to 103Caenhorhabditis elegansnuclear hormone receptors (NHRs) to delineate a Gene Regulatory Network (GRN) and found that this GRN presents a striking ‘pairwise modularity’ where pairs of NHRs regulate shared target genes. We envision that the experimental and analytical advances of WPS should be useful not only forC. elegans, but will be broadly applicable to other models, including human cells.
Accidental and Regulated Cell Death in Yeast Colony Biofilms
Authors: Netherwood Daniel J. , Tam Alexander K. Y. , Gourlay Campbell W. , Knežević Tea , Gardner Jennifer M. , Jiranek Vladimir , Binder Benjamin J. , Green J. Edward F.
Published: February 2025

The yeast speciesSaccharomyces cerevisiaeis one of the most intensively studied organisms on the planet due to being an excellent eukaryotic model organism in molecular and cell biology. In this work, we investigate the growth and morphology of yeast colony biofilms, where proliferating yeast cells reside within a self-produced extracellular matrix. This research area has garnered significant scientific interest due to its applicability in the biological and biomedical sectors. A central feature of yeast colony biofilm expansion is cellular demise, which is onset by one of two independent mechanisms: either accidental cell death (ACD) or regulated cell death (RCD). In this article, we generalise a recently developed continuum model for the nutrient-limited growth of a yeast colony biofilm to include the effects of ACD and RCD. This new model involves a system of four coupled nonlinear reaction–diffusion equations for the yeast-cell density, the nutrient concentration, and two species of dead cells. Numerical solutions of the spatially one and two-dimensional governing equations reveal the impact that ACD and RCD have on expansion speed, morphology and cell distribution within the colony biofilm. Our results show good qualitative agreement with our own experiments.
Genetic liability to physical health conditions influences comorbidities in individuals with severe mental illness
Authors: Kappel Djenifer B. , Smart Sophie E. , Owen Michael J. , O’Donovan Michael C. , Pardiñas Antonio F. , Walters James T. R.
Published: February 2025

Background

Individuals with severe mental illness (SMI), including schizophrenia and bipolar disorder, have elevated rates of physical health conditions, leading to increased morbidity and mortality. While environmental factors such as adverse effects of medication and lifestyle changes contribute to this burden, the role of genetic liability to physical health conditions remains underexplored. We assessed whether genetic risk for physical health conditions influences comorbidities in individuals with SMI and compared these effects to those observed in the general population.

Methods

We utilized data from two SMI cohorts from the UK: CardiffCOGS (n=721) and the National Centre for Mental Health (NCMH; n=1011). We tested whether polygenic risk scores (PRS) for six physical health conditions (high cholesterol, type 2 diabetes, hypertension, asthma, heart disease, and rheumatoid arthritis) were associated with having the corresponding condition in those with SMI. Models were adjusted for demographic and clinical covariates. Associations between psychiatric PRSs (schizophrenia, bipolar disorder, major depressive disorder, and ADHD) and presence of physical comorbidities were also evaluated.

Results

PRS for physical health conditions were associated with the presence of the corresponding conditions in SMI cohorts, with effect sizes comparable to those reported in the general population. Adjustments for environmental factors had minimal impact on these associations. Psychiatric PRS showed weaker and less consistent associations with physical comorbidities.

Discussion

This study provides robust evidence supporting the role of genetic risk in the development of common physical health conditions in individuals with SMI. Our findings indicate that the occurrence of physical health comorbidities was much more strongly associated with genetic liability to physical health conditions, than with psychiatric genetic liability. The genetic risk for physical health conditions contributes additively to environmental and clinical factors in driving comorbidities among individuals with SMI. These findings indicate there would be value in incorporating genetic risk information into predictive algorithms for physical health comorbidities in those with SMI, and that PRS should be included in research studies developing and validating such algorithms.
High agreement between lean mass assessed by dual-energy X-ray absorptiometry and bioelectrical impedance analysis across the adult lifespan
Authors: Kristensen T. , Kamper R.S. , Haddock B. , Nygaard H. , Nørst T. , Hovind P. , Suetta C.
Published: February 2025

Background

Bioelectrical impedance analysis (BIA) is considered a portable alternative to Dual-energy X-ray absorptiometry (DXA) when assessing deficient muscle mass, a major concern for older adults associated with increased risks of falls, fractures, disability, and mortality. However, several studies have demonstrated that BIA overestimates muscle mass in the older population and that estimates of muscle mass may depend on the BIA and DXA devices utilized. This study aims to describe the concordance between lean mass assessed by DXA and BIA across the adult population.

Methods

This study is based on data from the Copenhagen Sarcopenia Study, a cross-sectional study of 1127 healthy participants aged 22-92 years with complete measurements of lean mass from both DXA (iDXA, GE Lunar) and BIA (Inbody 770). Relative appendicular lean mass (ALM) was calculated by normalizing ALM to height2to account for allometric differences in body size.

Results

For the total cohort, linear regression models showed a strong correlation between BIA and DXA for ALM (R2= 0.92) and relative ALM (R2= 0.83). A small, yet consistent, bias of relative ALM values was observed where BIA measures were on average 0.25±0.50 kg/m2higher compared to measurements by DXA. The bias was consistent across age groups with a mean difference in relative ALM of 0.24±0.50 kg/m2, and 0.26±0.49 kg/m2for younger participants, and older participants, respectively.

Conclusion

BIA is a reliable alternative to DXA for assessing muscle mass, in both younger, and older adults. The findings indicate that with simple correction models for ALM and relative ALM, BIA can be a practical and accessible tool in clinical settings where DXA is unavailable. These models make BIA particularly useful for diagnosing sarcopenia, allowing for early detection and management regardless of age.

Key messages

Bioelectrical impedance analysis (BIA) is considered a portable alternative to Dual-energy X-ray absorptiometry (DXA) when assessing deficient muscle mass, a major concern for older adults and is associated with increased risks of falls, fractures, disability, and mortality. However, several studies have demonstrated that BIA overestimates muscle mass in the older population and estimates of muscle mass may depend on the BIA and DXA devices utilized. By applying the models of regression equations developed in this study, clinicians can improve the accuracy of BIA measurements, making BIA a practical alternative to DXA in clinical settings where DXA is not accessible. These findings are especially relevant for the early detection and management of sarcopenia in older adults, allowing for timely interventions to preserve muscle function and reduce the risk of adverse health outcomes.
Evolution of Pandemic Cholera at its Global Source
Authors: Barton Amber , Afrad Mokibul Hassan , Taylor-Brown Alyce , Singh Nisha , Thakur Chetan , Islam Taufiqul , Rahman Sadia Isfat Ara , Akhtar Marjahan , Begum Yasmin Ara , Bhuiyan Taufiqur Rahman , Khan Ashraful Islam , Taneja Neelam , Thomson Nicholas R. , Qadri Firdausi
Published: February 2025

The seventh pandemic of cholera, caused by the 7thPandemic El Tor Lineage (7PET)Vibrio cholerae, was previously shown to have emanated in three global waves from the Bay of Bengal, bordering Bangladesh and India. However, the respective roles of the Ganges delta and basin regions in seeding these global pandemic waves were not known. We find that while there are transmission events between Bangladesh and India,V. choleraewithin the two countries has largely evolved separately over the past 20 years, contained by national borders rather than following hydrological features such as the Ganges delta and basin. Evolution within Bangladesh was distinct from that seen in India, involving rapid gain and loss of genes and mobile genetic elements, particularly those involved in phage defence. The loss/gain of these anti-phage elements mirrored loss/gain of anti-defence systems in lytic phage ICP1. Importantly, the loss of these systems was associated with increased risk of severe disease and transmission outside of Bangladesh. Here we show that the Ganges basin, falling across Bangladesh and Northern India, rather than the Ganges delta, acts as a global launch pad for pandemic disease. This completely shifts our understanding of Bangladesh as the purported global source of cholera, and the role of phage in controlling spread of lineages within the current seventh pandemic.
Association of Pre-pregnancy Mental Health Disorders with Hypertensive Disorders of Pregnancy
Authors: Ncube Collette N. , Choi Minhyuk , Barnard-Mayers Ruby , Zimmerman Scott C. , Vodovozov Shelli , Glymour M. Maria , Parker Samantha E.
Published: February 2025

Background

Hypertensive disorders of pregnancy (HDP) affect nearly 10% of pregnancies in the U.S. and are known to increase risk of severe maternal morbidity and later life cardiovascular disease and stroke. Mental health disorders are common among pregnant individuals and have been linked to high blood pressure and adverse pregnancy outcomes. However, there is limited research investigating the association between history of mental health conditions and HDP.

Objectives

We aimed to assess the association of pre-pregnancy mental health disorders with HDP.

Methods

We used the NIHAll of UsResearch Program, which began enrollment in May 2018 and linked participants’ electronic health records (EHRs). First pregnancies with conception dates between October 2015 and September 2021 were identified from EHRs. Risk of HDP was examined among pregnancies of at least 20 weeks of gestation. We assessed the association between a pre-pregnancy mental health diagnosis and the risk of HDP using log-binomial regression models, estimating risk ratios (RR) and 95% confidence intervals, adjusted for racial and ethnic group and maternal age. We examined early pregnancy loss as a secondary outcome among all identified pregnancies. Results were stratified by the timing of pregnancy start relative to enrollment in theAll of Uscohort.

Results

Among 11,756 pregnancies that occurred prior to study enrollment, we observed a 20% increased risk of HDP associated with pre-pregnancy anxiety and depression (RR 1.20, 95% CI 1.05,1.36) and a 50% increased risk of early pregnancy loss associated with pre-pregnancy anxiety and depression (RR 1.49, 95% CI 1.36,1.64). Among 2,358 pregnancies occurring after enrollment, findings for HDP were generally similar, but associations with early pregnancy loss were attenuated, with imprecise estimates.

Conclusions

Prior mental health disorder diagnoses were associated with a modest increase in risk of HDP and early pregnancy loss.

SYNOPSIS

Study question

Do pre-pregnancy mental health disorders increase the risk of pregnancy loss or hypertensive disorders of pregnancy (HDP)?

What’s already known

Few studies have evaluated pre-pregnancy mental health disorders and pregnancy loss. Findings from prior studies of the association between mental health disorders and HDP are inconsistent, with mental health status often ascertained in early pregnancy thus masking the temporal relationship with HDP.

What this study adds

In this study, which leverages theAll of UsResearch Program cohort, we report an increased risk of HDP associated with pre-pregnancy mental health disorders. Additionally, we found an increased risk of early pregnancy loss associated with pre-pregnancy mental health disorders, suggesting our results may underestimate the risk associated with HDP having conditioned on later gestations.
A public resource of 15 genomically characterised representative strains ofShigella sonnei
Authors: Miles Sydney L. , Hawkey Jane , Vezina Ben , Torraca Vincenzo , Jenkins Claire , Weill François-Xavier , Baker Stephen , Baker Kate S. , Mostowy Serge , Holt Kathryn E.
Published: February 2025

Shigella sonneiis rapidly emerging as the dominant agent of shigellosis, an enteric disease responsible for a significant burden of morbidity and mortality worldwide. Whole-genome sequencing ofS. sonneiisolated over the last three decades has revealed phylogenomic diversity within the population and the emergence of multiple lineages associated with distinct epidemiological patterns such as resistance to critical antimicrobials and/or transmission within different groups. However most experimental work onS. sonneibiology and pathogenicity has focused on a single laboratory strain (53G), which is phylogenetically distant from currently circulating strains. Here we introduce a set of 15 phylogenetically diverse and epidemiologically relevantS. sonneiisolates made available through publicly accessible culture collections as a resource for laboratory science. We present their complete whole-genome sequences, including the pINV invasion plasmid (missing from a large proportion of public genome data due to loss during laboratory culture). Finally, the characterisation and comparison of these complete genome sequences highlight evidence for ongoing adaptive evolution inS. sonnei, featuring the accumulation of insertion sequences, gene pseudogenisation and structural variation.

Significance as a BioResource to the community

Genomic analysis ofShigellahas historically been challenging due to presence of hundreds of repetitive sequence elements (which can cause fragmented assemblies) and loss of the pINV invasion plasmid (essential to virulence) during laboratory culture. Furthermore, most experimental work onS. sonneipathogenicity uses a lab strain that is phylogenetically distant from circulating isolates. To supportS. sonneiexperimental andin silicoresearch and increase its relevance to current clinical problems, we report here the complete, high-quality genome sequences of 15S. sonneiisolates, each selected to represent distinct sub-clades of epidemiological interest. We also make the corresponding strains publicly available in national reference culture collections.

Data summary

All sequencing reads and complete assemblies have been deposited into the National Center for Biotechnology Information (NCBI) database (accessions to be determined). Genome assemblies and Bakta annotations used in the analysis can be found in Figshare (https://doi.org/10.6084/m9.figshare.28302986) together with Mauve multiple-sequence alignments for the chromosome and pINV plasmid sequences, and genome-scale metabolic models produced for each strain.

Pure cultures of all strains were deposited in the publicly accessible National Collection of Type Cultures (NCTC, UK) or the “Collection de l’Institut Pasteur” (CIP, France) (accessions to be determined).
CDK9 interacts with a RanGTP-NEMP1-Importin β complex to regulate erythroid enucleation
Authors: Newton Lucas M. , Lim Krystle Y. B. , Abeid Donia Y. , Wölwer Christina B. , Johnson Chad J. , Russell Sarah M. , Hawkins Edwin D. , Humbert Patrick O.
Published: February 2025

Erythroid enucleation is the final stage of erythroid terminal differentiation and involves the separation of an orthochromatic erythroblast into two daughter cells; a pyrenocyte containing the extruded nucleus, and the other a reticulocyte that will become a red blood cell. Our previous work identified CDK9 as a regulator of erythroid enucleation that appears to act independently of its known role in regulating RNA polymerase II transcription, suggesting the potential for a new CDK9 role. Using a co-immunoprecipitation and mass spectrometry approach, we have identified the interactome of CDK9 in differentiating erythroblasts. We show that CDK9 interacts with a RanGTP-NEMP1-Importin β complex during erythroid terminal differentiation, and inhibition of importin β in erythroblasts blocks erythroid enucleation. Using imaging analysis and functional assays of enucleating erythroblasts, we show that CDK9 and importin β co-locate at a critical site of activity opposite to the nucleus before nuclear extrusion and we describe a novel finding that physically links CDK9 and importin β activity prior to CaM/Ca2+signalling and subsequent F-actin activity to achieve enucleation.

Key Points

Importin β physically interacts with CDK9 in erythroid cells and is a novel regulator of erythroid enucleation

Functional assays show that CDK9 and importin β act prior to calcium-dependent actin-mediated nuclear extrusion
A novel DNA repair-independent role for Gen nuclease in promoting unscheduled polyploidy cell proliferation
Authors: Budzyk Manon , Simon Anthony , Mace Anne-Sophie , Basto Renata
Published: February 2025

Unscheduled whole genome duplication (WGD), also described as unscheduled or non-physiological polyploidy, can lead to genetic instability and is commonly observed in human cancers. WGD generates DNA damage due to scaling defects between replication factors and DNA content. As a result, DNA damage repair mechanisms are thought to be critical for ensuring cell viability and proliferation under these conditions. In this study, we explored the role of homologous recombination and Holliday junction resolution in non-physiological polyploidyin vivo. UsingDrosophilagenetics and high-resolution imaging, we identified a key and surprising role for Gen/Gen1 nuclease. Our findings revealed that loss-of-function and overexpression of Gen have opposing effects, delaying or accelerating the proliferation of polyploid cells, respectively. These changes ultimately impact cell proliferation, nuclear asynchrony and mitotic DNA damage levels. Surprisingly, our findings show that this effect is unrelated with the expected Gen’s function in DNA damage repair. Instead, Gen seems to influence polyploid DNA replication rates. This work identifies a novel function for Gen nuclease and provides new insights into the cellular and molecular requirements of non-physiological polyploidy.
A transcriptional control model fordoublesex-dependent sex differentiation inNasoniawasps
Authors: Rougeot Julien , Guerra Filippo , Verhulst Eveline C.
Published: February 2025

The transcription factor Doublesex (DSX) orchestrates insect sex differentiation. DSX affectsDrosophila melanogastermale and female transcriptome, yet how DSX regulates gene expression in other species is poorly understood. We investigated sex-biased gene expression during the development of the parasitoid waspNasonia vitripennis, finding that more than three-quarters of its genes are sex-biased in at least one developmental point. Next, we transiently knocked downdsxexpression to infer its role in sex-specific transcriptome regulation, revealing thousands of affected genes in males and a more subtle effect in females. Finally, we performed anin vitroDNA-protein interaction assay to identify DSX binding sites on the genome and primary DSX target genes. By integrating these three datasets, we defined DSX’s regulatory function for all genes inN. vitripennis, revealing that DSX acts mainly in males as both an activator and a repressor. This male-centric model for DSX-mediated regulation is likely to apply to many other insect species.
Protocol for a minigene splice assay using the pET01 vector
Authors: Andreae Hannah , Curcio Marialessandra , Esmaeelpour Sahar , Jahnke Friederike , Benseler Fritz , Brose Nils , Vona Barbara
Published: February 2025

Aberrant splicing is recognized as a key contributor of hereditary disorders, yet characterizing the molecular effects of splice variants is an important task that poses several challenges. Here, we present a protocol for an in vitro splice assay using a minigene approach, which is especially useful when patient samples are not available for RNA analysis or when target genes or isoforms are not expressed in accessible tissues for direct analysis. We describe steps for assay design, including the cloning of minigene plasmids and subsequent transfection, followed by RNA isolation and cDNA synthesis. We also provide details on quantitative fragment analysis using capillary electrophoresis and optional subcloning to facilitate optimal sequencing of multiple splicing products.
TrACES of Time: Towards estimating time-of-day of bloodstain deposition by targeted RNA sequencing
Authors: Gosch Annica , Sendel Sebastian , Caliebe Amke , Courts Cornelius
Published: February 2025

Background

In forensic molecular biology, the main task consists of identifying individuals who contributed to biological traces recovered from (potential) crime scenes. However, to support evidence-based reconstruction of the course of activities having taken place at the scene, contextualising information regarding how and when a biological trace was deposited is oftentimes required.

Results

Here we present the development of a forensic molecular biological analysis procedure for the prediction of the time-of-day at which a bloodstain has been deposited by targeted quantification of selected mRNA markers. Time-of-day candidate prediction markers with diurnally rhythmic expression have previously been identified by whole transcriptome sequencing. Here, we build on our previous findings by establishing a targeted cDNA sequencing protocol on an Ion S5 massively parallel sequencing device for the targeted gene expression quantification of 74 time-of-day candidate prediction markers. Based on expression measurements of these markers in 408 blood samples (from 51 individuals deposited at eight time points over a day), we establish and compare different statistical methods to predict time of deposition. The most suitable model employing penalised regression achieved a root mean squared error of 3 hours and 44 minutes with 78 % of predictions being correct within +/- 4 h (evaluated by five-fold cross-validation).

Conclusions

Our study provides the first prediction model for time-of-day of bloodstain deposition based on targeted RNA sequencing and thus represents an important step towards forensic trace deposition timing. It thereby relevantly contributes to the growing knowledge onTranscriptomicAnalyses for theContextualisation ofEvidentialStains (TrACES).
The hepatitis E virus capsid protein ORF2 counteracts cell-intrinsic antiviral responses to enable persistence in hepatocytes
Authors: Mehnert Ann-Kathrin , Stegmaier Sebastian , Ramirez Carlos , Magalhães Vladimir Gonçalves , Siebenkotten Carla , Hu Jungen , Costa Ana Luisa , Kirrmaier Daniel , Knop Michael , Wu Xianfang , Tubiana Thibault , Herrmann Carl , Binder Marco , Thi Viet Loan Dao
Published: February 2025

Hepatitis E virus (HEV) is a significant human pathogen causing both acute and chronic infections worldwide. The cell-intrinsic antiviral response serves as the initial defense against viruses and has been shown to be activated upon HEV infection. HEV can replicate in the presence of this response, but the underlying mechanisms remain poorly understood.

Here, we investigated the role of HEV structural proteins ORF2 and ORF3 in immunocompetent cells. Mechanistically, we found that ectopic ORF2, but not ORF3, interfered with inflammatory signaling pathways as well as with antiviral signaling downstream of pattern recognition receptors. The latter was at least in part mediated through direct interaction with the central adaptor protein TANK binding kinase 1. In addition, we discovered a protective mechanism mediated by ORF2 that shielded viral replication from antiviral effectors. Using single-cell RNA-sequencing, we confirmed that the ORF2-mediated antagonism in infected cells resulted in dampened antiviral responses in both HEV-infected and bystander cells. As a consequence, we found that early in the infection process, the progression of authentic HEV infection relied on the presence of ORF2, facilitating a balance between viral replication and the antiviral response within immunocompetent cells. Altogether, our findings shed new light on the multifaceted role of ORF2 in the HEV life cycle and improve our understanding of the determinants that may contribute to HEV persistence.

Significance statement

Hepatitis E virus (HEV) is an important yet often underestimated pathogen. Depending on the genotype, HEV infections can progress to chronicity, but the underlying mechanisms remain poorly understood. To gain insight into potential determinants, we investigated how HEV evades the body’s first line of defense, the cell-intrinsic antiviral response. We discovered that the HEV capsid protein ORF2 is crucial in limiting this response by interfering with antiviral signaling pathways and shielding viral replication from immune effectors. This balance between viral replication and the antiviral response contributes to persistent HEV infection in immunocompetent cells. Our findings reveal a new role for the HEV capsid protein in the viral life cycle and highlight it as an important target for novel therapeutic approaches.
Inhibition of lysine deacetylase activity impacts formation of the vitamin D receptor activation complex
Authors: Dwyer Shannon , Kemper Kevin , Manna Vincent J.
Published: February 2025

The vitamin D endocrine system is responsible for the regulation of many biological processes including bone metabolism, calcium homeostasis, cell proliferation and cell differentiation. Alterations to the vitamin D signaling pathway are associated with several diseases including bone diseases, diabetes, cardiovascular diseases, autoimmune diseases, and cancer. Vitamin D precursors are obtained through diet or synthesized in the skin and must be further chemically modified to become the biologically active hormone, calcitriol. Calcitriol binds to the vitamin D receptor (VDR), a member of the nuclear hormone receptor (NHR) superfamily. VDR forms a heterodimer with retinoid X receptor (RXR) and together they bind to promoters containing vitamin D response elements (VDREs) to activate transcription of target genes. Other NHRs have been shown to accept post-translational modifications that can either increase or decrease their transcriptional output through alterations in protein-protein or protein-DNA interactions. We have generated evidence that two lysines on VDR may be targets of post-translational modifications, and alterations to lysine deacetylase activity will impact VDR transcriptional output through changes in co-activator and co-repressor binding. Together, these data suggest a novel way for the cell to modulate the response of VDR to available vitamin D.
Upregulation of voltage-gated potassium channels in peripheral blood mononuclear cells: a new approach to multiple sclerosis treatment
Authors: Martínez-Almeida Marta Iglesias , Ríos Ana Campos , Martínez Luís Freiría , Baltanás Tania Rivera , Amorim Daniela Rodrigues , Sánchez Franco César Manuel , Tébar Ainhoa Rodríguez , Peleteiro Mercedes , Tuche María Comis , Suárez Inés González , Olivares José Manuel , Lamas José Antonio , Spuch Carlos
Published: February 2025

Multiple sclerosis (MS) involves immune dysregulation and abnormal ion channel function. This study investigated the expression and function of voltage-gated potassium (Kv) channel isoforms (Kv1.1, Kv1.2, Kv1.3, Kv1.6, Kv4.2, Kv4.3, Kv7.2) in peripheral blood mononuclear cells (PBMCs) and lymphocytes from MS patients (remittent-recurrent) compared to controls. We found an upregulation of in six out of seven Kv isoforms in PBMCs from MS patients, with sex-specific differences observed (female showing a more pronounced upregulation of specific isoforms). Electrophysiological analysis of CD3+ T lymphocytes showed no significant differences, while CD19+ B lymphocytes displayed a notable decrease in outward current density. These findings suggest potential variations in Kv channel function across immune cell types and highlight the need for further exploration of their roles in MS pathogenesis, particularly within B lymphocytes and considering sex-based considerations.
Inhibition of adenylyl cyclase 1 (AC1) and exchange protein directly activated by cAMP (EPAC) restores ATP-sensitive potassium (KATP) channel activity after chronic opioid exposure
Authors: Klein Amanda H. , Alam Sabbir , Johnson Kayla , Kriner Christian , Beck Brie , Nelson Bethany , Hill Cassidy , Meyer Belle , Mellang Jonas , Watts Val J.
Published: February 2025

Prolonged exposure to Gαi/o receptor agonists such as opioids can lead to a sensitization of adenylyl cyclases (ACs), resulting in heterologous sensitization or cyclic AMP (cAMP) overshoot. The molecular consequences of cAMP overshoot are not well understood, but this adaptive response is suggested to play a critical role in the development of opioid tolerance and withdrawal. We found that genetic reduction of AC1 and simultaneous upregulation of ATP-sensitive potassium (KATP) channel subunits, SUR1 or Kir6.2, significantly attenuated morphine tolerance and reduced naloxone-precipitated withdrawal.In vitromodels utilized an EPAC2-GFP-cAMP biosensor to investigate sensitization of adenylyl cyclase in SH-SY5Y neuroblastoma cells and HEKΔAC3/6 knockout cells. Acute application of DAMGO significantly decreased the cAMP signal from the EPAC2-GFP-cAMP biosensor, while chronic DAMGO administration resulted in enhanced cAMP production following AC stimulation. Inhibition of cAMP overshoot was observed with naloxone (NAL), pertussis toxin (PTX), and the neddylation inhibitor, MLN4924 (Pevonedistat), as well as co-expression of β-adrenergic receptor kinase C-terminus (βARK-CT). After establishment of the AC1-EPAC sensitization in thein vitromodels, we found that inhibition of AC1 or EPAC enhanced potassium channel activity after chronic morphine treatment, using a thallium-based assay in SH-SY5Y cells. Similar data were obtained in mouse dorsal root ganglia (DRG) after chronic morphine treatment. This study presents evidence for investigating further AC1 signaling as a target for opioid tolerance and withdrawal, by increasing EPAC activity and affecting potassium channels downstream of opioid receptors.Graphical Abstract
Endogenous antimicrobial peptides in human colostrum: a peptidomics study by liquid-chromatography high-resolution mass-spectrometry (LC-HRMS) and bioinformatics
Authors: Campanhon Isabele B. , da Silva Nicole Cavalcante , Nunes Rosane de Oliveira , Bezerra Flávia Fioruci , Torres Alexandre Guedes , Soares Márcia R.
Published: February 2025

Human colostrum is recognized as a source of bioactive compounds that impact on neonatal development, such as antimicrobial peptides. Antimicrobial peptides (AMPs) present some common characteristics, as they are relatively small (<10 kDa), most of them are positively charged and possess α-helical regions. These molecules can protect the newborn against infectious agents such as bacteria, fungi, and viruses. Using an MS- based proteomic approach combined with the application of bioinformatic tools, 29 peptide sequences from human colostrum were annotated in human colostrum. These peptides are potentially antifungal and were enriched in glutamic acid (E), phenylalanine (F), lysine (K) and tryptophan (W) residues. Among the precursor proteins, two have a known 3D structure and their fragments are located in the protein core. In addition,in silicoanalyses revealed that AMPs containing regions of α-helix and random structures, and high aliphatic index (mean of 85.29) tend to be thermostable. In this work with human colostrum, previously unreported peptides with potential antimicrobial activity were annotated and structurally characterized via bioinformatic tools.
A CD25-CCR7 complex initiates non-canonical IL-2 signaling
Authors: Kim Sarah Hyun Ji , Lee Hosup , Gingras Alexandre , Ley Klaus , Spangler Jamie B. , Ginsberg Mark H.
Published: February 2025

IL-2, a central regulator of immune function, binds to its receptor subunit CD25 (IL-2Rα), promoting IL-2 interaction with β and γ subunits to trigger the canonical IL-2 signaling pathway. An anti-mouse CD25 antibody, PC61, triggers alternative IL-2 signaling, leading to integrin activation. PC61 induces a complex formed by the IL-2-dependent association of CD25 with CCR7, suggesting that the formation of this complex initiates alternative IL-2 signaling. Here, we used structure-based design together with combinatorial screening to identify an IL-2 mutant (denoted IL-2(E52K)) that spares canonical IL-2 signaling but disrupts both PC61-induced complex formation and integrin activation while retaining the full CD25 affinity of the parent molecule. We also report that heparan sulfate (HS), a physiological ligand of IL-2 that triggers alternative signaling, induced IL-2-dependent CD25-CCR7 association, whereas IL-2(E52K) failed to support both HS-induced CD25-CCR7 complex formation and integrin activation. Thus, both anti-CD25 antibody and HS require common features of IL-2 needed for CD25-CCR7 complex assembly and resulting integrin activation. Collectively, these data show that IL-2 promotes CD25 interaction with CCR7, thereby forming the signal initiating complex. Furthermore, canonical and alternative IL-2 signaling can be decoupled by an IL-2 mutation, creating a tool to specify the biological role of alternative IL-2 signaling in immune responses.
Identification of a RAB32-LRMDA-Commander membrane trafficking complex reveals the molecular mechanism of human oculocutaneous albinism type 7
Authors: Butkovič Rebeka , Healy Michael D. , de Heus Cecilia , Walker Alexander P. , Beyers Wyatt , McNally Kerrie E. , Lewis Philip A. , Heesom Kate J. , Liv Nalan , Klumperman Judith , Pietro Santiago Di , Collins Brett M. , Cullen Peter J.
Published: February 2025

Commander is an endosome associated sixteen protein assembly that associates with the sorting nexin 17 (SNX17) cargo adaptor to regulate cell surface recycling of internalised integral membrane proteins including integrins and lipoprotein receptors. Mutations in Commander are causative for Ritscher-Schinzel syndrome (RSS), a multiorgan developmental disease associated with a core triad of cerebellar-cardiac-craniofacial malformation. Here, using unbiased proteomics and computational modelling, we identify leucine rich melanocyte differentiation associated (LRMDA) as a novel Commander binding protein. Using recombinant protein reconstitution, we show that LRMDA simultaneously associates with Commander and active RAB32, and, by revealing that LRMDA and SNX17 share a common mechanism of Commander association, establish the mutually exclusive nature of RAB32-LRMDA-Commander and SNX17-Commander assemblies. From functional analysis in human melanocytes, we establish an essential role for RAB32-LRMDA-Commander in melanosome biogenesis and pigmentation and reveal a distinct functional role for SNX17-Commander in this organelle biogenesis pathway. We reveal how LRMDA mutations, causative for oculocutaneous albinism type 7 (OCA7), a hypopigmentation disorder accompanied by poor visual acuity, uncouple RAB32 and Commander binding thereby establishing the mechanistic basis of this disease. Our discovery and characterisation of this alternative Commander assembly establishes an unrecognised plasticity of Commander function within a highly complex organelle biogenesis pathway. This extends Commander function beyond the confines of SNX17-mediated cell surface recycling into RAB32-family mediated biogenesis of lysosome-related organelles and, potentially, other RAB32 regulated pathways including host-pathogen defence mechanisms. Our work also extends the breath of Commander pathway dysfunction for human disease.
Single-particle spectral function of fractional quantum anomalous Hall states
Authors: Pichler Fabian , Kadow Wilhelm , Kuhlenkamp Clemens , Knap Michael
Published: February 2025

Fractional quantum Hall states are the most prominent example of states with topological order, hosting excitations with fractionalized charge. Recent experiments in twisted MoTe2 and graphene-based heterostructures provided evidence of fractional quantum anomalous Hall (FQAH) states, which spontaneously break time-reversal symmetry and persist even without an external magnetic field. Understanding the unique properties of these states requires the characterization of their low-energy excitations. To that end, we construct a parton theory for the energy- and momentum-resolved single-particle spectral function of FQAH states. We explicitly consider several experimentally observed filling fractions as well as a composite Fermi liquid in the half-filled Chern band. Charge fractionalization manifests itself in nearly momentum-independent spectra with a characteristic series of peaks determined from the filling fraction. The parton description qualitatively captures our numerical exact diagonalization results. Additionally, we discuss how the finite bandwidth of the Chern band and the nonideal quantum geometry affect the fractionalized excitations. Our work demonstrates that the energy- and momentum-resolved electronic single-particle spectral function provides a valuable tool to characterize fractionalized excitations of FQAH states in moiré lattices.

Published by the American Physical Society
2025
Direct
CP
violation in the
B¯s→K+K−K+K−
decay process induced by interferences of the intermediate vector particles
Authors: Zhang Chang-Chang , Lü Gang
Published: February 2025

We investigate CP violation in the decay process B¯s→VV→K+K−K+K− within the framework of perturbative quantum chromodynamics, where V represents vector mesons ϕ, ρ, and ω. We analyze the mixing mechanism among ϕ−ρ0−ω and provide amplitudes for these decay processes. Moreover, we explore CP violation in the four-body decay process of B¯s0→K+K−K+K− involving intermediate vector mesons and their mixing. Notably, significant CP violation is observed for specific two-vector meson intermediate states. Additionally, a substantial amount of CP violation arises from vector mixing when the invariant mass of K+K− falls within a certain range. This study holds potential implications for future detection by the LHC experiment.

Published by the American Physical Society
2025
Vortical effects and the critical end point in the linear sigma model coupled to quark
Authors: Hernández L. A. , Zamora R.
Published: February 2025

In this paper, we study the effects of vorticity on the QCD phase transition using the linear sigma model coupled to quarks. By going beyond the mean-field approximation and incorporating screening effects via ring diagrams, we explore the chiral symmetry restoration in extreme conditions, such as high temperatures, high densities, and large angular velocities. Our analysis reveals how the critical temperature decreases as the angular velocity increases, suggesting that vorticity catalyzes the symmetry restoration. Additionally, we observe a shift in the critical end point (CEP) in the effective QCD phase diagram, where higher angular velocities move the CEP to lower quark chemical potentials and higher temperatures. Moreover, we analyze the baryon number fluctuations through the normalized fourth moment κσ2=c4/c2 as a function of the collision energy in heavy-ion reactions sNN, which serves as a key observable to identify the CEP. Our study reveals that, for high collision energies, κσ2 remains nearly constant; however, as the system approaches the CEP, the ratio increases sharply, indicating the proximity of the critical region. This rise is influenced by the presence of vorticity, which causes the CEP to shift to higher collision energies. These findings provide insight into the role of vorticity in heavy-ion collisions.

Published by the American Physical Society
2025
Collective Deformation Modes Promote Fibrous Self-Assembly in Deformable Particles
Authors: Le Roy Hugo , Terzi M. Mert , Lenz Martin
Published: February 2025

The self-assembly of particles into organized structures is a key feature of living organisms and a major engineering challenge. While it may proceed through the binding of perfectly matched, puzzle-piece-like particles, many other instances involve ill-fitting particles that must deform to fit together. These include some pathological proteins, which have a known propensity to form fibrous aggregates. Despite this observation, the general relationship between the individual characteristics of the particles and the overall structure of the aggregate is not understood. To elucidate it, we analytically and numerically study the self-assembly of two-dimensional, deformable ill-fitting particles. We find that moderately sticky particles tend to form equilibrium self-limited aggregates whose size is set by an elastic boundary layer associated with collective deformations that may extend over many particles. Particles with a soft internal deformation mode thus give rise to large aggregates. In addition, when the particles are incompressible, their aggregates tend to be anisotropic and fiberlike. Our results are preserved in a more complex particle model with randomly chosen elastic properties. This indicates that generic proteinlike characteristics such as allostery and incompressibility could favor the formation of fibers in protein aggregation, and suggests design principles for artificial self-assembling structures.

Published by the American Physical Society
2025
Bacterial proliferation pattern formation
Authors: Chuang John S. , Rao Riccardo , Leibler Stanislas
Published: February 2025

Bacteria can form a great variety of spatially heterogeneous cell density patterns, ranging from simple concentric rings to dynamical spiral waves appearing in growing colonies. These pattern formation phenomena are important as they reflect how cellular processes such as metabolism operate in heterogeneous chemical environments. In the laboratory, they can be studied in simplified setups, where spatial gradients of oxygen and nutrients are externally imposed, and cells are immobilized in a gel matrix. An intriguing example, observed in such setups over 80 years ago, is the sequential formation of narrow bands of high cell density, taking place even for a clonal population. However, key aspects of the dynamics of band formation remained obscure. Using time-lapse imaging of replicate transparent columns in simplified growth media, we first quantify the precision of the positioning and timing of band formation. We also show that the appearance and position of different bands can be modulated independently. This “modularity” is suggested by the observation that different bands differ in their gene expression, and it is reproduced by a theoretical model based on the existence of internal metabolic states and the induction of a pH gradient. Finally, we can also modify the observed pattern formation by introducing genetic modifications that impair selected metabolic pathways. In our opinion, the possibility of precise measurements and controls, together with the simplicity and richness of the “proliferation pattern formation” phenomenon, can make it a model system to study the response of cellular processes to heterogeneous environments.

Published by the American Physical Society
2025