bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome- and Transcriptome-wide association meta-analysis reveals new insights into genes affecting coronary and peripheral artery disease
Authors: Rode Michael , Rosolowski Maciej , Horn Katrin , Henger Sylvia , Teren Andrej , Wirkner Kerstin , Thiery Joachim , Loeffler Markus , Pott Janne , Kirsten Holger , Scholz Markus 
Published: January 2025

ABSTRACTBackgroundA low ankle-brachial Index (ABI) is an established condition for peripheral artery disease (PAD) and cardiovascular disease risk. The search for genetic determinants of the ankle-brachial index (ABI) is important to better understand molecular patho-mechanisms of PAD and its commonalities with cardiovascular diseases (CVD), supporting development of new drug targets and tailored preventive or therapeutic measures.MethodsTo search for genetic factors contributing to ankle-brachial index, we integrated genome-wide (GWAMA) and transcriptome-wide association analysis (TWAMA) of two German cohorts, the population-based LIFE-Adult cohort and LIFE-Heart, a cohort of patients with suspected or confirmed coronary artery disease. Pathway analysis of identified genes was used to explore biological mechanisms potentially involved in ABI pathophysiology. Finally, we analysed co-associations of known CAD or carotid plaque associations with ABI to detect possible genetic commonalities.ResultsBy our GWAMA, we identified four new gene loci associated with ABI that are also linked with coronary artery diseases (CAD) (6q26:LPAand 11q14.1:DLG2) or cholesterol levels (12q21.31:TMTC2and Xp21.1:DMD). Furthermore, we replicated a known ABI locus on cytoband 9p21.3 (CDKN2B) and four loci associated with PAD. In our TWAMA, we identified 145 blood transcripts associated with ABI at FDR 5% level. Gene set enrichment analysis of all TWAMA results revealed the inflammation-related pathwaysinterferon gamma response,neutrophil degranulation, andinterferon alpha responseas the top three upregulated pathways in patients with lower ABI. Among overlapping genes between blood TWAMA and tissue-specific genetically regulated gene-expression association analysis, 24 genes showed consistent effect directions at nominal significance, with lower ABI-associated genes relating to stress response and vascular integrity, while higher ABI-associated genes linked to cellular homeostasis and metabolism.ConclusionsIn our integrated genome- and transcriptome-wide meta-analysis, we identified novel and confirmed known candidate genes and pathways associated with ABI. Association signals partly overlap with those of other cardiovascular traits such as CAD and carotid plaque formation. The integration of gene-expression data, validated known and added new molecular insight how inflammatory signaling can contribute to atherosclerosis and vascular dysfunction. These findings pave the way for improved understanding of the molecular underpinnings of PAD and inform future strategies for targeted prevention and therapy.
Projected Cost-beneficial Impact of the Selective Cytopheretic Device in Pediatric Acute Kidney Injury Requiring Kidney Replacement Therapy
Authors: Kleinman Nathan , Kammerer Jennifer , Iyer Sai Prasad N. , Goldstein Stuart L. , Kleinman Alec , Chung Kevin K. , Thakar Charuhas V. 
Published: January 2025

AbstractRationale & ObjectiveThe Selective Cytopheretic Device for Pediatrics (SCD-PED) is a cell-directed extracorporeal therapy approved by US FDA for pediatric patients with acute kidney injury (AKI) due to sepsis or a septic condition, requiring antibiotics and continuous renal replacement therapy (CRRT). This study aimed to estimate hospitalization costs and outcomes of SCD-PED therapy by leveraging the Kids’ Inpatient Database (KID) and SCD-PED studies.Study DesignPublicly available hospitalization cost data were combined with clinical metrics from prior SCD-PED studies to assess the impact of SCD-PED on inpatient hospital costs among pediatric patients receiving CRRT.Setting & PopulationThe SCD-PED was evaluated in two multicenter pediatric studies, involving 16 and 6 patients, respectively. Pediatric patients with AKI and multi-organ dysfunction receiving CRRT as part of standard care were included. The KID subset comprised hospitalizations with CRRT, a length of stay (LOS) up to 60 days, mortality and severity level 4, an AKI diagnosis, and total parenteral nutrition (TPN) procedures.InterventionsPatients received SCD-PED therapy for up to 7 or 10 days or until CRRT termination.OutcomesOutcomes analyzed included hospital LOS, mortality, vasopressor use, mechanical ventilation, sepsis diagnosis, number of SCD-PED devices used, and hospitalization cost estimates.Model, Perspective, & TimeframeA regression-based economic cost model compared costs between SCD-PED therapy and theoretical controls, adjusted to 2024 US dollars.ResultsModeled hospitalization costs were $457,092 in the KID cohort and $389,451 in the ppCRRT cohort. Median hospital LOS was lower in the SCD-PED group (28 days vs. 31 days), resulting in lower estimated costs ($320,304) and an estimated savings of $69,146 per hospitalization.LimitationsSmall sample sizes and single-arm design with no prospective control arm. Reported costs are estimates based on models.ConclusionsThe SCD-PED shows potential for survival benefit and cost-benefit in critically ill children with AKI requiring CRRT, including those with sepsis.
Kinetic mechanism for fidelity of CRISPR-Cas9 variants
Authors: Hecht Andrew D. , Igoshin Oleg A. 
Published: January 2025

AbstractCRISPR-Cas9 is a nuclease creating DNA breaks at sites with sufficient complementarity to the RNA guide. Notably, Cas9 does not require exact RNA-DNA complementarity and can cleave off-target sequences. Various high-accuracy Cas9 variants have been developed, but the precise mechanism of how these variants achieve higher accuracy remains unclear. Here, we develop a kinetic model of Cas9 substrate selection and cleavage. We parameterize the model using datasets available in the literature, including both high-throughput substrate binding and cleavage data and Förster resonance energy transfer measurements of the Cas9 HNH domain transitions. Based on the observed transition statistics, we predict that the Cas9 substrate recognition and cleavage mechanism must allow for HNH domain transitions independent of substrate binding. Additionally, we show that the enhancement in Cas9 substrate specificity must be due to changes in kinetics rather than changes in substrate binding affinities. Furthermore, the fitted model produces quantitatively realistic cleavage error predictions for substrates with protospacer adjacent motif (PAM)-distal mismatches. Finally, we use our model to identify kinetic parameters for HNH domain transitions that can be perturbed to enable high-accuracy cleavage while maintaining cleavage speeds. Our results refine the biophysical mechanism of Cas9 cleavage to inform future routes for its engineering.
Improved transfection methods of primary cultured astrocytes for observation of cytoskeletal structures
Authors: Ikoma Chieko , Inoue Kodai , Kasai Kouta , Tsukuda Satoko , Tamura Akiko , Nakata Shihoko , Iwata Yuto , Tamagawa Takumi , Nakayama Ayako , Takano Kazunori , Shigetomi Eiji , Koizumi Shuichi , Nakagawa Hiroyuki , Terasaki Asako G 
Published: January 2025

AbstractAstrocytes are the predominant type of glia in the central nervous system and have long branched stem processes and peripheral astrocyte processes (PAPs) contacting neurons and other glial cells. In many cell types, cell morphology and motility depend on actin cytoskeleton. However, a common astrocyte culture method in serum-containing medium generated undesired fibroblast-like cells; thus, the roles of cytoskeletal proteins in astrocyte morphology and motility have not been well studied. Previously, we reported a culture method of chicken astrocytes forming structures similar to stem processes and PAPs. In the current study, we improved transfection methods retaining astrocyte morphology at low cell density, suitable for observing the behavior of proteins. Immunostaining and live imaging of plasma membrane-actin linking protein ezrin (a PAP marker) and another actin-binding protein lasp-2 (highly expressed in cultured astrocytes) demonstrated that our cultured astrocytes had microvillus protrusions, filopodia, lamellipodia, and focal adhesion-like elliptical structures, and the two proteins accumulated in different substructures. Our developed methods offer significant advantages for analyzing how astrocytes form stem processes and PAPs to access target cells.
Culicoidesallergens expressed in insect cells induce sulfidoleukotriene release in peripheral blood leukocytes from horses affected with insect bite hypersensitivity
Authors: Jonsdottir S , Stefansdottir SB , Mirkovitch J , Ziegler A , Torsteinsdottir S , Marti E 
Published: January 2025

AbstractIntroductionInsect bite hypersensitivity (IBH) is an IgE mediated dermatitis in horses caused by bites ofCulicoidesspp. The allergens are salivary gland proteins from these insects and nine major allergens fromCulicoides obsoletushave been identified and expressed inE. coli. However, proteins expressed in procaryotic systems have limitations in cellular assays, particularly in functional assays assessing the allergen-induced release of mediatorsin vitro, such as sulfidoleukotrienes (sLT) from basophils. Aims of the study were to produce functionalCulicoidesallergens in insect cells, to assess their allergenicity using a sLT release assay and to relate the sLT release with IgE sensitization to the respective allergens using ELISA.MethodsEight majorCulicoides obsoletusallergens (Cul o 1P, Cul o 2P, Cul o 3, Cul o 5, Cul o 7, Cul o 8, Cul o 9 and Cul o 11) were expressed in insect cells and purified. sLT release from peripheral blood leukocytes (PBL) following stimulation with the eightCulicoidesallergens was measured in 28 IBH-affected and 24 healthy control horses. Allergen-specific serum IgE levels was determined by ELISA.ResultsThe eight major allergens were successfully expressed in insect cells and purified. All allergens induced a significantly higher sLT release from PBL of IBH-affected horses compared to healthy controls. There was a high correlation and substantial to excellent agreement between sLT release and serum IgE levels for sixCulicoidesallergens, while for two the agreement was moderate. Positivity rates in IBH horses were usually higher in IgE serology but more false positive results were obtained. The allergens performing best in both assays were Cul o 3, Cul o 8 and Cul o 9, with very high specificity and good sensitivity.DiscussionInsect cell expressedCulicoidesrecombinant allergens are functionally relevant and will open new opportunities for the study of Culicoides hypersensitivity not only in horses, but also potentially in human patients or other species. They will also greatly improve IBH diagnostics using cellular assays as well as IgE serology.
Disulfide bonds are required for cell division, cell envelope biogenesis and antibiotic resistance proteins in mycobacteria
Authors: Mejia-Santana Adrian , Collins Rebecca , Doud Emma H. , Landeta Cristina 
Published: January 2025

AbstractMycobacteria, includingMycobacterium tuberculosis—the etiological agent of tuberculosis—have a unique cell envelope critical for their survival and resistance. The cell envelope’s assembly and maintenance influence permeability, making it a key target against multidrug-resistant strains. Disulfide bond (DSB) formation is crucial for the folding of cell envelope proteins. The DSB pathway in mycobacteria includes two enzymes, DsbA and VKOR, required for survival. Using bioinformatics and cysteine profiling proteomics, we identified cell envelope proteins dependent on DSBs. We validated viain vivoalkylation that key proteins like LamA (MmpS3), PstP, LpqW, and EmbB rely on DSBs for stability. Furthermore, chemical inhibition of VKOR results in phenotypes similar to those of Δvkor. Thus, targeting DsbA-VKOR systems could compromise both cell division and mycomembrane integrity. These findings emphasize the potential of DSB inhibition as a novel strategy to combat mycobacterial infections.
Microfluidic Co-Culture for Modeling Human Joint Inflammation in Osteoarthritis Research
Authors: Mirazi Hosein , Wood Scott T. 
Published: January 2025

AbstractHere we present a microfluidic model that allows for co-culture of human osteoblasts, chondrocytes, fibroblasts, and macrophages of both quiescent (M0) and pro-inflammatory (M1) phenotypes, maintaining initial viability of each cell type at 24 h of co-culture. We established healthy (M0-based) and diseased (M1-based) joint models within this system. An established disease model based on supplementation of IFN-γ and LPS in cell culture media was used to induce an M1 phenotype in macrophages to recapitulate inflammatory conditions found in OA. Cell viability was assessed using NucBlue™ Live and NucGreen™ Dead fluorescent stains, with mean viability of 83.9% ± 14% and 83.3% ± 12% for healthy and diseased models, respectively, compared with 93.3% ± 4% for cell in standard monoculture conditions. Cytotoxicity was assessed via a lactate dehydrogenase (LDH) assay and showed no measurable increase in LDH release into the culture medium under co-culture conditions, indicating that neither model promotes a loss of cell membrane integrity due to cytotoxic effects. Cellular metabolic activity was assessed using a PrestoBlue™ assay and indicated increased cellular metabolic activity in co-culture, with levels 5.9 ± 3.2 times mean monolayer cell metabolic activity levels in the healthy joint model and 5.3 ± 3.4 times mean monolayer levels in the diseased model. Overall, these findings indicate that the multi-tissue nature ofin vivohuman joint conditions can be recapitulated by our microfluidic co-culture system at 24 h and thus this model serves as a promising tool for studying the pathophysiology of rheumatic diseases and testing potential therapeutics.
PICRUSt2-MPGA: an update to the reference database used for functional prediction within PICRUSt2
Authors: Wright Robyn J. , Langille Morgan. G.I. 
Published: January 2025

AbstractSummaryPICRUSt2 is a bioinformatic tool that predicts microbial functions in amplicon sequencing data using a database of annotated reference genomes. We have constructed an updated database for PICRUSt2 that has substantially increased the number of bacterial (19,493 to 26,868) and archaeal (406 to 1,002) genomes as well as the number of functional annotations present. The previous PICRUSt2 database relied on many timely and computationally intensive manual processes that made it difficult to update. To make PICRUSt2 great again (MPGA), we constructed a new streamlined process to allow regular upgrades to the PICRUSt2 database on an ongoing basis. Additionally, we have shown that this updated database contains genomes that more closely match study sequences from a range of different environments. The genomes contained in the database therefore better represent these environments and this leads to an improvement in the predicted functional annotations obtained from PICRUSt2.AvailabilityPICRUSt2 source code is freely available athttps://github.com/picrust/picrust2and athttps://anaconda.org/bioconda/picrust2. The PICRUSt2-MPGA database comes pre-installed with PICRUSt2 from version 2.6.0 onwards. Step-by-step instructions for making the updated database are athttps://github.com/picrust/picrust2/wiki/Updating-the-PICRUSt2-database. All code used for the analyses and figures in this manuscript is athttps://github.com/R-Wright-1/picrust2_mpga_application_note.Funding and acknowledgementsThis work was supported by an NSERC Discovery Grant (2016-05039) and was enabled in part by the Digital Research Alliance of Canada (alliancecan.ca).We thank Dr. Gavin Douglas for invaluable insight and assistance with troubleshooting and several PICRUSt2 users for their time testing and giving feedback on an early version of the PICRUSt2 update.
Survival and Spread of EngineeredMycobacterium smegmatisand Associated Mycobacteriophage in Soil Microcosms
Authors: Fleeharty Megan S. , Carline Kate B.R. , Tchadi Bilalay V. , Shockey Bjorn B. , Holley Emma C. , Saha Margaret S. 
Published: January 2025

AbstractThe inoculation of microbes into soil environments has numerous applications for improving soil quality and crop health; however, the ability of exogenous and engineered microbes to survive and spread in soil remains uncertain. To address this challenge, we assayed the survival and spread ofMycobacterium smegmatis, engineered with either plasmid transformation or genome integration, as well as its mycobacteriophage Kampy, in both sterilized and non-sterilized soil microcosms over a period of 49 days. While engineeredM. smegmatisand Kampy persisted in all soil microcosms, there was minimal evidence of spread to 5 cm away from the inoculation site. There was a higher prevalence of Kampy observed in sterilized soil than non-sterilized soil, suggesting a detrimental effect of the native soil biotic and viral community on the ability of this phage to proliferate in the soil microcosm. Additionally, higher abundance of the genome-integrated bacteria relative to the plasmid-carrying bacteria as well as evidence for loss of plasmid over the duration of the experiment suggest a burden associated with bacteria harboring plasmids, although plasmids were still retained across 49 days. To our knowledge, this is the first study to simultaneously measure the persistence and spread of bacteria and their associated phage in both sterilized and non-sterilized soil microcosms, employing bacteria with plasmid-based and genome-integrated engineered circuits. As such, this study provides a novel understanding of challenges associated with the deployment of bioengineered microbes into soil environments.ImportanceHealthy soil is essential to sustain life, as it provides habitable land, enables food production, promotes biodiversity, sequesters and cycles nutrients, and filters water. Given the prevalence of soil degradation, treatment of soil with microbes that promote soil and crop health could improve global soil sustainability; furthermore, the application of bioengineering and synthetic biology to these microbes allows fine-tunable and robust control of gene-of-interest expression. These solutions require the successful deployment of bacteria into the soil, an environment in which abundant competition and often limited nutrients can result in bacterial death or dormancy. This study employsMycobacterium smegmatisas a chassis alongside its bacteriophage Kampy in soil microcosms to assess the ability of non-native microbes to survive and spread in soil. Insights from this experiment highlight important challenges which must be overcome for successful deployment of engineered microbes in the field.
Epidermal stem cell-derived extracellular vesicles induce fibroblasts mesenchymal-epidermal transition to alleviate hypertrophic scar via the miR-200s/ZEBs axis
Authors: Zhen Miao , Xie Juntao , Yang Rui , Liu Lijuan , Liu Hengdeng , He Xuefeng , Gao Suyue , Zhu Junyou , Li Jingting , Shu Bin , Wang Peng 
Published: January 2025

AbstractHypertrophic scar (HS) is a prevalent yet unresolved wound healing complication characterized by persistent hyperactive and proliferative fibroblasts, leading to excessive extracellular matrix (ECM) synthesis and collagen contraction. Our previous studies have identified epidermal stem cells (ESCs) as critical for wound healing and HS remodeling, with its extracellular vesicles (EVs) playing a vital role. However, the specific mechanisms remain unclear. In this study, we first discovered that ESC-EVs could effectively induce the mesenchymal-epidermal transition (MET) of HS fibroblasts (HSFs) and inhibit their biological activity. Furthermore, by next-generation sequencing and multiplexed CRISPR/Cas9 system, we elucidated that this therapeutic effect is mediated by the miR-200 family (miR-200s) encapsulated in ESC-EVs, which targeted and inhibited ZEB1 and ZEB2 in HSFs. This vital role and mechanism have been thoroughly validated in both in vitro cell experiments and in vivo rat tail HS (RHS) models. These findings not only shed light on a previously unidentified mechanism of ESC-EVs for HS, but also provide potential novel targets and strategies for its precise treatment.
The Swiss national program for the surveillance of influenza A viruses in pigs and humans: genetic variability and zoonotic transmissions from 2010 – 2022
Authors: Lechmann J. , Szelecsenyi A. , Bruhn S. , Harisberger M. , Wyler M. , Bachofen C. , Hadorn D. , Tobler K. , Krauer F. , Fraefel C. , Cabecinhas A. R. Gonçalves 
Published: January 2025

AbstractInfluenza A viruses (IAV) are likely candidates for pandemics. This report summarizes the results of the Swiss national program for surveillance of influenza viruses in pigs and transmissions to humans between 2010 and 2022. Challenges and optimization options in the program are discussed.Nasal swabs or lung tissue samples from pigs with influenza-like signs (e.g. fever, cough) were screened by real-time RT-PCR for swine influenza virus (SIV) genomes, including that of the 2009 pandemic strain A(H1N1)pdm09; positive samples were subtyped for H1, N1, H3 and N2 by RT-PCR and Sanger sequencing. In parallel, humans with influenza-like symptoms and recent contact with diseased pigs were asked to self-sample themselves with a nasal swab. Human swabs were tested for IAV, and positive swabs further subtyped to identify potential cross-species transmission between swine and humans.In the pigs, SIV was detected in 375 of 674 farm visits. H1N1 is the only subtype detected in Swiss pigs so far. The (H1N1)pdm09 strain (HA clade 1A) was only detected in seven out of 375 SIV positive farm visits. Phylogenetic analyses from partial hemagglutinin (HA) and neuraminidase (NA) genome sequences indicate that the remaining pigs were infected with the Eurasian avian lineage (HA clade 1C), which is predominant in swine in Europe. The Swiss H1N1 strains form distinct clusters within HA clades 1C.2.1 and 1C.2.2 and seem to evolve comparably slowly. Infection of humans with SIV was identified in five cases. Sequence analysis assigned the five viruses to the Eurasian avian lineage (C), clades 1C.2.1 and 1C.2.2. There was no evidence for sustained human-to-human transmission.Although no critical IAV variants seem to have emerged so far in Switzerland, further surveillance of influenza viruses at the swine-human interface is of major importance.