bluuebunny/crossref_metadata_2025_split huggingface dataset:
Worrisome Emergence of Pan-INSTI Resistance: A Systematic Scoping Review of Dolutegravir Resistance in INSTI-Naïve Patients Post-Therapy Failure
Authors: Arora Sumit , Raman Nishant , Anilkumar Anirudh , Ashta Kuldeep , Kisenjang N , Mohan Charu 
Published: February 2025

AbstractIntroductionDolutegravir (DTG), a second-generation integrase strand transfer inhibitor (INSTI), is widely used in HIV treatment, especially in low-resource settings. Despite its proven efficacy, concerns about DTG resistance mutations (DRMs) have emerged in patients failing dual NRTI + DTG-based ART regimens. This review examines the patterns and frequencies of these DRMs in INSTI-naïve patients.MethodsA systematic scoping review was conducted, synthesizing data from 21 studies (2013–2024) involving 59 INSTI-naïve persons living with HIV-1 (PLH) who experienced virological failure (VF) on dual NRTI + DTG-based ART. Data extraction was undertaken by two independent reviewers, and key information included ART history, DRM profiles, duration of DTG-based ART, and viral load at failure. A qualitative synthesis identified common resistance patterns, geographic distributions, and HIV subtype correlations.ResultsThe most prevalent DRMs were G118R (42.4%) and R263K (38.9%). G118R, when combined with T66I and E138K, was associated with high-level resistance and pan-INSTI resistance. R263K, frequently occurring alone or with minor mutations, also conferred modest resistance. Resistance patterns varied by HIV subtype, with non-B subtypes showing higher frequencies of G118R and Q148HRK mutations, while R263K predominated in subtype B.ConclusionEmerging DTG resistance in INSTI-naïve patients, particularly in resource-limited settings, is a cause for concern. G118R and R263K were the most prevalent mutations, with the former leading to pan-INSTI resistance. These findings stress the importance of monitoring resistance patterns, especially in non-HIV-B subtypes, to optimize ART strategies.
Class IV plant U-box proteins function redundantly to optimize protein accumulation of receptor-like cytoplasmic kinase BIK1
Authors: Dou Ruoqi , Miguel Virginia N. , Grubb Lauren E. , Rana Mansuba , Saltzman Brandon , Monaghan Jacqueline 
Published: February 2025

AbstractInArabidopsis thaliana, the receptor-like cytoplasmic kinase BOTRYTIS INDUCED KINASE 1 (BIK1) is a direct substrate of multiple transmembrane immune receptor kinases and plays a crucial role in immune signal transduction. Inactive BIK1 is poly-ubiquitinated and degraded by the 26S proteasome, which is thought to optimize BIK1 levels in naive cells and may protect against inappropriately high immune responses. Here, we provide biochemical and genetic evidence that supports redundant roles between related Plant U-Box (PUB) proteins PUB22, PUB23, PUB24, PUB25, and PUB26 in BIK1 turnover.
Neuronal endolysosomal acidification relies on interactions between transmembrane protein 184B (TMEM184B) and the vesicular proton pump
Authors: Wright Elizabeth B. , Larsen Erik G. , Padilla-Rodriguez Marco , Langlais Paul R. , Bhattacharya Martha R.C. 
Published: February 2025

AbstractDisruption of endolysosomal acidification is a hallmark of several neurodevelopmental and neurodegenerative disorders. Impaired acidification causes accumulation of toxic protein aggregates and disrupts neuronal homeostasis, yet the molecular mechanisms regulating endolysosomal pH in neurons remain poorly understood. A critical regulator of lumenal acidification is the vacuolar ATPase (V-ATPase), a proton pump whose activity depends on dynamic assembly of its V0 and V1 subdomains. In this study, we identify transmembrane protein 184B (TMEM184B) as a novel regulator of endolysosomal acidification in neurons. TMEM184B is an evolutionarily conserved 7-pass transmembrane protein required for synaptic structure and function, and sequence variation in TMEM184B causes neurodevelopmental disorders, but the mechanism for this effect is unknown. We performed proteomic analysis of TMEM184B-interacting proteins and identified enrichment of components involved in endosomal trafficking and function, including the V-ATPase. TMEM184B localizes to early and late endosomes, further supporting a role in the endosomal system. Loss of TMEM184B results in significant reductions in endolysosomal acidification within cultured mouse cortical neurons. This alteration in pH is associated with impaired assembly of the V-ATPase V0 and V1 subcomplexes in the TMEM184B mutant mouse brain, suggesting a mechanism by which TMEM184B promotes flux through the endosomal pathway. Overall, these findings identify a new contributor in maintaining endosomal function and provide a mechanistic basis for disrupted neuronal function in human TMEM184B-associated nervous system disorders.Significance StatementEndolysosomal acidification is essential for neuronal protein homeostasis, yet its regulation in neurons remains poorly understood. Here, we identify TMEM184B as a key regulator of this process, establishing its first known cellular role. We show that TMEM184B interacts with vacuolar ATPase (V-ATPase) components and promotes the assembly of its V0 and V1 subdomains, facilitating lumenal acidification. Loss of TMEM184B disrupts endolysosomal pH in neurons, potentially impairing proteostasis. These findings reveal a critical function for TMEM184B in neuronal maintenance and provide mechanistic insight into its link to neurological disorders. This work advances our understanding of endolysosomal regulation and suggests TMEM184B regulation could improve outcomes in diseases involving lysosomal dysfunction.
The dramatic impact of the PER-DBT interaction on circadian timekeeping and temperature compensation
Authors: Petersen E. Nicholas , Sullivan Camille , Ludewig Hannes , Kern Dorothee , Rosbash Michael 
Published: February 2025

AbstractCircadian timekeeping depends on protein-protein interactions as well as post-translational modiﬁcations, yet the structural details that underlie these events remain largely uncharacterized. We used AlphaFold 2.3 to predict the interaction region between theDrosophilaPERIOD (PER) protein and the kinase Doubletime (DBT). The structure identiﬁed two conserved helical domains of PER, SYQ and LT, as critical for the interaction. We made mutations within these domains and used mutantperiodrescue constructs to assess their effects on circadian period and temperature compensation in vivo. A charge-reversal mutation (E to K) in the SYQ domain caused severe period lengthening and temperature sensitivity, which was rescued by a compensatory charge-reversal mutation in a predicted interacting LT domain residue (K to E); this validated an AlphaFold predicted interaction between two charged residues in SYQ and LT. Three additional mutations in the SYQ domain showed varying effects on period length and temperature compensation, with one uniquely displaying period shortening at higher temperatures. Most strikingly, two mutations in the LT domain (L770A, L775A) resulted in the longest recorded periods for single point mutations inperiod, with free-running periods > 44 hours at 25C. These also showed extreme temperature sensitivity with a magnitude of change >20 hrs. over the physiological temperatures tested. RNA-sequencing analysis of the L775A mutant shows that these behavioral changes are paralleled by altered molecular cycling. Our ﬁndings underscore the power of AlphaFold in predicting a crucial protein-protein interaction even with a largely disordered protein partner and reveal that the PER-DBT binding interface plays a crucial role in maintaining proper timekeeping and temperature-compensated circadian rhythms.
Telomerase mRNA Reduces Radiation-induced DNA Damage of human skin
Authors: Chang David F. , Li Shuang , Court Pinto Karem , Nguyen Thi Kim Cuc , Shah Vrutant V. , Morales Elisa , Carrier Jack , Ludlow Andrew T. , Brannan Kristopher W. , Spiegel Aldona J. , Olmsted-Davis  , Godin Biana , Mojiri Anahita , Cooke John P. 
Published: February 2025

AbstractOver four million people undergo radiation therapy annually in the United States. Among these, more than 90% experience varying degrees of radiation-induced skin injury. Despite the enormity of the problem, there is currently no FDA-approved agent to prevent or treat skin damage caused by ionizing radiation. In the current study, ionizing radiation induced dose-dependent genomic and mitochondrial DNA damage, leading to apoptosis in primary cutaneous cells. Prior treatment with mRNA encoding telomerase reverse transcriptase (TERT) substantially reduced radiation-induced DNA damage in human primary skin cells and tissues. Mechanistically, TERT mRNA pretreatment enhances DNA repair, reduces mitochondrial ROS, and decreases apoptosis without extending telomere length during the experimental period, suggesting a non-canonical function of TERT to accelerate the cellular recovery from radiation. These findings highlight a potential therapeutic approach for preventing radiation-induced skin injury.Graphic abstract
Extended Modelling of Platelet Calcium Signaling by Combined Recurrent Neural Network and Partial Least Squares Analyses
Authors: Tantiwong Chukiat , Cheung Hilaire Yam Fung , Dunster Joanne L , Gibbins Jonathan M. , Heemskerk Johan W. M. , Cavill Rachel 
Published: February 2025

AbstractPlatelets play critical roles in hemostasis and thrombosis. The platelet activation process is driven by agonist-induced rises in cytosolic [Ca2+]i, where the patterns of Ca2+responses are still incompletely understood. In this study, we developed a number of techniques to model the [Ca2+]icurves of platelets from a single blood donor. Using a fluorescence ratio probe, the platelets were stimulated with a panel of agonists, i.e. thrombin, collagen, or CRP under various conditions, preventing extracellular Ca2+entry, secondary mediator effects or Ca2+reuptake into intracellular stores. To analyze the data, we developed two non-linear models, a multilayer perceptron (MLP) network and an autoregressive network with exogenous inputs (NARX). The trained networks accurately predicted the platelet [Ca2+]icurves in the presence of combinations of agonists and inhibitors, with the NARX model achieving an R2up to 0.64 for trend prediction of unforeseen data. In addition, we used the same dataset for construction of a partial least square (PLS) linear regression model, which estimated the explained variance of each input. The NARX model demonstrated that good fits could be obtained for the calcium curves modelled, whereas the PLS model gave useful interpretable information on the importance of each variable. These modelling results can be used for the development of novel platelet [Ca2+]i-inhibiting drugs.
Mitophagy at the oocyte-to-zygote transition promotes species immortality
Authors: Balachandar Thendral Siddharthan , Bacot Sasha , Morton Katherine S. , Chi Qiuyi , Kenny-Ganzert Isabel W. , Meyer Joel N. , Sherwood David R. 
Published: February 2025

AbstractThe quality of inherited mitochondria determines embryonic viability1, metabolic health during adulthood and future generation endurance. The oocyte is the source of all zygotic mitochondria2, and mitochondrial health is under strict developmental regulation during early oogenesis3–5. Yet, fully developed oocytes exhibit the presence of deleterious mitochondrial DNA (mtDNA)6,7and mitochondrial dysfunction from high levels of endogenous reactive oxygen species8and exogenous toxicants9. How fully developed oocytes prevent transmission of damaged mitochondria to the zygotes is unknown. Here we discover that the onset of oocyte-to-zygote transition (OZT) developmentally triggers a robust and rapid mitophagy event that we term mitophagy at OZT (MOZT). We show that MOZT requires mitochondrial fragmentation, activation of the macroautophagy system and the mitophagy receptor FUNDC1, but not the prevalent mitophagy factors PINK1 and BNIP3. Oocytes upregulate expression of FUNDC1 in response to diverse mitochondrial insults, including mtDNA mutations and damage, uncoupling stress, and mitochondrial dysfunction, thereby promoting selection against damaged mitochondria. Loss of MOZT leads to increased inheritance of deleterious mtDNA and impaired bioenergetic health in the progeny, resulting in diminished embryonic viability and the extinction of descendent populations. Our findings reveal FUNDC1-mediated MOZT as a mechanism that preserves mitochondrial health during the mother-to-offspring transmission and promotes species continuity. These results may explain how mature oocytes from many species harboring mutant mtDNA give rise to healthy embryos with reduced deleterious mtDNA.
MOLECULAR AND MORPHOMETRIC APPROACHES IN RECENTLY RADIATED SPECIES:Inga subnudaSALZM. EX BENTH ANDInga veraWILLD. (LEGUMINOSAE, MIMOSOID CLADE)
Authors: Badia Clara da Cruz Vidart , Garcia Flávia Cristina Pinto , Muller Larissa Areal , Fregonezi Jèferson Nunes 
Published: February 2025

AbstractThe species-rich genusInga(Leguminosae) presents ca. 300 species widespread throughout the Neotropics and is recognized by its recent and rapid diversification. Forty-eight species ofIngaare endemic of the Brazilian Atlantic Forest. Among them,Inga subnuda, with two subspecies: subsp.subnuda, which occurs from the state of Paraíba to Rio de Janeiro; and subsp.luschnathiana, which occurs from Espírito Santo to the state of Santa Catarina. Both subspecies occur in sympatry in the southeastern region and share floral and leaf characters, which hampers the morphological delimitation. The co-occurrence ofInga verasubsp.affinis. with bothI. subnudasubspecies results in intermediate morphologies betweenI. verasubsp.affinisandI. subnudasubsp.luschnathiana, making the distinction between the latter species even harder. We sampled 94 individuals from 8 natural populations and evaluated morphological characters previously described as distinctive among the subspecies ofI. subnudain addition to others not measured yet. We used 84 plastid (trnD-trnTspacer) and 58 nuclear (ITS 1 and 2) sequences to characterize the phylogenetic relationships between the taxa. The results obtained point outI. subnudasubsp.subnudaas a more structured taxon in relation to the other subspecies, whilstI. subnudasubsp.luschnathianaandI. verasubsp.affinisconstituted a cohesive group. The apportionment of haplotypes differed between the markers used, thus evincing a retention of ancestral polymorphism between the subspecies, given their recent diversification. This paper explores different lines of evidence, thus contributing to the delimitation of these species. Demographic and biogeographic scenarios are also discussed. A new status of for the taxon currently circumscribed asInga subnudasubsp.luschnathianais suggested.
Platelet endocytosis and α-granule cargo packaging are essential for normal skin wound healing
Authors: Coenen Daniëlle M. , Alfar Hammodah R. , Whiteheart Sidney W. 
Published: February 2025

AbstractThe high prevalence of chronic wounds,i.e.,2.5-3% of the US population, causes a large social and financial burden. Physiological wound healing is a multi-step process that involves different cell types and growth factors. Platelet-rich plasma or platelet-derived factors have been used to accelerate wound repair, but their use has been controversial with mixed results. Thus, a detailed functional understanding of platelet functions in wound healing beyond hemostasis is needed. This study investigated the importance of platelet α-granule cargo packaging and endocytosis in a dorsal full-thickness excisional skin wound model using mice with defects in α-granule cargo packaging (Nbeal2-/-mice) and endocytosis (platelet-specific Arf6-/-and VAMP2/3Δmice). We found that proper kinetic and morphological healing of dorsal skin wounds in mice requires bothde novoas well as endocytosed platelet α-granule cargo. Histological and morphometric analyses of cross-sectional wound sections illustrated that mice with defects in α-granule cargo packaging or platelet endocytosis had delayed (epi)dermal regeneration in both earlier and advanced healing. This was reflected by reductions in wound collagen and muscle/keratin content, delayed scab formation and/or resolution, re-epithelialization, and cell migration and proliferation. Molecular profiling analysis of wound extracts showed that the impact of platelet function extends beyond hemostasis to the inflammation, proliferation, and tissue remodeling phases via altered expression of several bioactive molecules, including IL-1β, VEGF, MMP-9, and TIMP-1. These findings provide a basis for advances in clinical wound care through a better understanding of key mechanistic processes and cellular interactions in (patho)physiological wound healing.Key pointsDe novoand endocytosed platelet α-granule cargo support physiological skin wound healingPlatelet function in wound healing extends to the inflammation, proliferation, and tissue remodeling phases
The Psychological Impact of the COVID-19 Pandemic, A Meta-Analysis and General Population Study
Authors: Korff-Korn Derek C. , Trauben Andrew , Rayfield Elliot J. 
Published: February 2025

AbstractThis study assessed the impact of the financial, social and health disruptions due to the pandemic on increased rates of depression, anxiety, obsessiveness and substance abuse tendencies. In the meta-analysis portion of the study, a systematic search was performed and resulted in twenty studies which met the appropriate relevance and quality. The degree of symptoms was assessed in comparison to certain variables such as sex, age and income. Given the diversity of countries in which these studies were sourced, a varying severity of pandemic and subsequent restrictions were observed which allowed for a more expansive comprehension of the correlation to mental health risks. The complementary aspect of the meta-analysis was a general population study performed in the later months of 2020, which surveyed New York City residents. The provided questionnaire included sociodemographic background, previous mental health issues as well as associated factors such as social isolation, financial burdens and health concerns. The investigated levels of depression, anxiety and traumatic stress exposed positive correlations between younger age and mental health symptoms, a greater impact on one’s mental health due to social isolation than health exposure, a significance of news exposure, a fluctuation in various issues of anxiety, depression and stress when assessing participants who had been infected, and a difference in time from change in lifestyle to expressed mental health symptoms.
Anionic polymers stabilize Cas9 ribonucleoprotein nanoparticles to improve direct protein delivery and genome editing efficiencies in plant protoplasts
Authors: Hubbard Joshua D. , Tomatz Sophia , Carll Nicole , Matos Juliana , Hassan Danya , Ly Tong , Landry Markita P. 
Published: February 2025

AbstractThe application of CRISPR-based genome editing tools in plants is often challenged by low editing efficiencies, requiring most plant editing workflows to proceed through the delivery of pre-formed ribonucleoprotein (RNP) complexes to protoplasts. Here, we report increases in protoplast-based RNP delivery and genome editing efficiencies through the addition of anionic polymers to standard protoplast transfection protocols. We test addition of various polymers and peptides for their ability to increase genome editing efficiencies in bothNicotiana benthamianaandArabidopsis thalianaprotoplasts, by adding these components to standard PEG-based protoplast transfection protocols:i)non-covalent addition of charged polymers,ii)non-covalent addition of amphiphilic peptide A5K, andiii)tyrosinase-mediated covalent conjugation of various relevant peptide motifs directly to the RNP. Incorporation of the amphiphilic peptide A5K or covalent attachment of peptides to the RNP had no positive effect on editing efficiencies. However, we found that addition of anionic polymer polyglutamic acid to standard PEG transfection protocols significantly improved editing efficiencies in bothNicotiana benthamianaandArabidopsis thalianaprotoplasts relative to RNPs alone without negatively impacting protoplast viability. Our results suggest anionic polymers stabilize the RNP and increase the colloidal stability of the protoplast transfection workflow. This simple and straightforward method of stabilizing Cas9 RNPs can be easily adopted by others working on direct protein delivery to plant protoplasts to increase genome editing efficiencies.Key messageThe addition of anionic polymer polyglutamic acid to standard protoplast PEG transfection workflows enhance CRISPR-Cas9-mediated gene editing in plant protoplasts. Our results suggest the mechanism of increased transfection efficiency is due to colloidal stabilization of RNPs.Graphical Abstract
AKAP12 variant 1 knockout enhances vascular endothelial cell motility
Authors: Ali Ashrifa , Roy Bhaskar , Schott Micah B. , Grove Bryon D. 
Published: February 2025

AbstractIn this study, we examined the role of AKAP12, in endothelial cell motility, with a specific focus on AKAP12 variants AKAP12v1 and AKAP12v2. Previous work has shown that AKAP12, a multivalent A-kinase anchoring protein that binds to PKA and several other proteins regulating protein phosphorylation, is expressed at low levels in most endotheliain vivobut at higher levels in cellsin vitro. Here, we found that AKAP12 expression in endothelial cell (HUVEC) cultures was cell density-dependent, with the expression being highest in subconfluent cultures and lowest in confluent cultures. AKAP12 expression was also elevated in cells at the wound edge of wounded endothelial cell monolayers. Knockdown of variants 1 and 2 inhibited cell migration, whereas CRISPR/Cas9 knockout of AKAP12v1 enhanced migration, indicating that the absence of this variant and the presence of AKAP12v2 may shift the signaling pathways. Further analysis using bulk RNA sequencing revealed that the loss of AKAP12v1 affects genes associated with cell migration and intercellular junctions. We propose that AKAP12v1 and AKAP12v2 work together to modulate endothelial cell migration, providing insights into their distinct yet complementary roles in endothelial function and potential implications for cardiovascular health.
An Open-Source Image Analysis Method for Quantifying Reporter Fluorescence
Authors: Ball Kathryn F. , Perez Jacob A. , Cooper Allen M. , Pira Charmaine U. , Oberg Kerby C. , Wilson Christopher G. 
Published: February 2025

AbstractImage analysis is a rapidly developing field that provides unique opportunities to characterize and quantify spatial information in images. We studycis-regulatory modules (CRMs), non-coding DNA regions that regulate gene expression, during development using fluorescent reportersin vivo.Characterizing CRM activity during development presents challenges including image segmentation into biologically relevant regions of interest that are not easily distinguishable via common segmentation methods, fluorophore band passing, and variable transfection undermine standardized analysis. To quantify and compare CRM activity levels, we compiled an open-source computer vision tool stack in the form of aPython-basedJupyternotebook and tested four analysis methods to assess their efficacy in quantifying CRM expression in limb development. ThisJupyternotebook provides a reproducible, standardized workflow that can be adapted to numerous image analysis applications.