bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractUnscheduled 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

AbstractThe 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.
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

AbstractBackgroundIn 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.ResultsHere 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).ConclusionsOur 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

AbstractHepatitis 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 statementHepatitis 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

ABSTRACTThe 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

AbstractMultiple 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

AbstractProlonged 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

AbstractHuman 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

AbstractIL-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

AbstractCommander 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.
Satun province’s research-based learning initiative under Thailand’s “education sandbox” policy: design, implementation and outcomes
Authors: Khuvasanond Kirati , Chitradub Sompong 
Published: February 2025

PurposeThis study aims to enhance the quality of education in Thailand by exploring an educational innovation emphasizing community identities, available resources and needs. It describes the design and implementation of the Satun research-based learning (RBL) initiative under Thailand’s Education Innovation Area Act B.E. 2562, which allowed 10 pilot schools in Satun to develop curriculums for early childhood and primary school levels that incorporated localities’ contexts during the 2018–2019 academic year.Design/methodology/approachTo evaluate the innovation’s impacts, primary data were collected and verified through methodological triangulation and cross-validation, and then qualitatively analyzed using content analysis.FindingsStudents demonstrated improvements in reading and writing, analytical thinking, problem-solving, teamwork, public presentation and creativity. Teachers were more engaged in students’ learning development and felt closer to students. School administrators embraced collaboration with teachers, school committees, parents and communities. Parents recognized students’ eagerness to study and academic improvements. Quantitatively, a difference-in-differences analysis of all 6th-grade Satun students’ standardized test scores from 2016 to 2019 showed that improvements in the participating students’ Thai and English scores were statistically significant at the 0.05 level. These findings suggest that policymakers can improve educational quality by accounting for community contexts and constraints.Originality/valueThe originality of this study lies in the large-scale RBL initiative under investigation and its approach to evaluating the quantitative impacts of this initiative.
How does research and development intensity influence the performance of firms through different stages in product life cycle?
Authors: Li Dan 
Published: February 2025

PurposeIt is widely acknowledged that the ability of a firm to develop and exploit their innovative capabilities is a critical determinant that maintains their competitive advantage. The purpose is to evaluate the research and development (R&D) inputs and outcomes on the performance of firms in different stages.Design/methodology/approachDrawing on a sample of 30 firms over 8 years (2009–2016), the results from a three-stage Bayesian stochastic frontier analysis model support were used.FindingsSome interesting findings were discovered. First, the R&D intensity is positively associated with the number of patents granted, which is negatively associated with the number of new drug approvals (NDAs). Second, R&D inputs, including expenditures and human resources, are negatively related to the number of NDAs and firm performance. Third, state-owned firms perform better and have more patents granted than private-owned firms in China. Finally, the traditional Chinese medicine firms and non-coastal firms both gain fewer profits, but they generate more new drugs than chemical drug firms and coastal firms in terms of policy support.Originality/valueIt is revealed that there are no common factors among Chinese pharmaceutical firms except for ownership, and this heterogeneous behavior indicates that there is no common factor for enhancing the efficiency of all Chinese pharmaceutical firms.
Are lead independent directors greener? Evidence from climate change commitment and ESG performance
Authors: Owusu Andrews , Omoteso Kamil , Gyimah Daniel , Ejiogu Amanze 
Published: February 2025

PurposeThis paper sheds light on how appointing a lead independent director (LIDIR) affects a firm’s commitment to climate change and to what extent environmental, social and governance (ESG) performance is affected by a firm’s commitment to climate change in the presence of a LIDIR.Design/methodology/approachThe authors utilise ordinary least squares (OLS) and a sample of 12,236 firm-year observations in the United States of America (USA) over the 2002–2019 period to test the predictions. The authors also apply alternative research designs such as propensity score matching, Heckman two-step and instrumental variable techniques to address endogeneity concerns.FindingsThe authors find that a LIDIR representation on the board is positively associated with a firm’s commitment to climate change. The authors also find that the association between a LIDIR representation on the board and a firm’s commitment to climate change is more pronounced in firms with a combined chief executive officer (CEO) and board chair positions than firms with both positions separated. Additional analysis suggests that increased commitment to climate change in the presence of a LIDIR improves ESG performance.Originality/valueWhile the effect of a LIDIR on firm financial outcomes has received much attention, there is a lack of empirical evidence on whether lead independent directors are greener. The authors provide new and important contribution to the literature by investigating the relationship between an LIDIR representation on the board and non-financial outcomes from the perspective of climate change commitment and ESG performance. The findings may be informative to policymakers seeking to deal with climate change impacts on society to encourage the appointment of a LIDIR.