bluuebunny/crossref_metadata_2025_split huggingface dataset:
ACAD10 and ACAD11 enable mammalian 4-hydroxy acid lipid catabolism
Authors: Rashan Edrees H. , Bartlett Abigail K. , Khana Daven B. , Zhang Jingying , Jain Raghav , Smith Andrew J. , Baker Zakery N. , Cook Taylor , Caldwell Alana , Chevalier Autumn R. , Pfleger Brian F. , Yuan Peng , Amador-Noguez Daniel , Simcox Judith A. , Pagliarini David J. 
Published: January 2024

AbstractFatty acid β-oxidation (FAO) is a central catabolic pathway with broad implications for organismal health. However, various fatty acids are largely incompatible with standard FAO machinery until they are modified by other enzymes. Included among these are the 4-hydroxy acids (4-HAs)—fatty acids hydroxylated at the 4 (γ) position—which can be provided from dietary intake, lipid peroxidation, and certain drugs of abuse. Here, we reveal that two atypical and poorly characterized acyl-CoA dehydrogenases (ACADs), ACAD10 and ACAD11, drive 4-HA catabolism in mice. Unlike other ACADs, ACAD10 and ACAD11 feature kinase domains N-terminal to their ACAD domains that phosphorylate the 4-OH position as a requisite step in the conversion of 4-hydroxyacyl-CoAs into 2-enoyl-CoAs—conventional FAO intermediates. Our ACAD11 cryo-EM structure and molecular modeling reveal a unique binding pocket capable of accommodating this phosphorylated intermediate. We further show that ACAD10 is mitochondrial and necessary for catabolizing shorter-chain 4-HAs, whereas ACAD11 is peroxisomal and enables longer-chain 4-HA catabolism. Mice lacking ACAD11 accumulate 4-HAs in their plasma while comparable 3- and 5-hydroxy acids remain unchanged. Collectively, this work defines ACAD10 and ACAD11 as the primary gatekeepers of mammalian 4-HA catabolism and sets the stage for broader investigations into the ramifications of aberrant 4-HA metabolism in human health and disease.
Chlamydia trachomatismodulates the expression of JAK-STAT signaling components to attenuate the Type II interferon response of epithelial cells
Authors: Fontanilla Francis L. , Carabeo Rey A. , Brinkworth Amanda J. 
Published: January 2024

AbstractChlamydia trachomatishas adapted to subvert signaling in epithelial cells to ensure successful intracellular development. Interferon-γ (IFNγ) produced by recruited lymphocytes signals through the JAK/STAT pathway to restrict chlamydial growth in the genital tract. However, duringChlamydiainfectionin vitro, addition of IFNγ does not fully induce nuclear localization of its transcription factor STAT1 and target gene, IDO1. We hypothesize that this altered interferon response is a result ofChlamydiatargeting components of the IFNγ-JAK/STAT pathway. To assess the ability of replicatingChlamydiato dampen interferon signaling, HEp2 human epithelial cells were infected withC. trachomatisserovar L2 for 24 hours prior to exposure to physiologically relevant levels of IFNγ (500 pg/mL). This novel approach enabled us to observe reduced phospho-activation of both STAT1 and its kinase Janus Kinase 2 (JAK2) in infected cells compared to mock-infected cells. Importantly, basal JAK2 and STAT1 transcript and protein levels were dampened by infection even in the absence of interferon, which could have implications for cytokine signaling beyond IFNγ. Additionally, target genes IRF1, GBP1, APOL3, IDO1, and SOCS1 were not fully induced in response to IFNγ exposure. Infection-dependent decreases in transcript, protein, and phosphoprotein were rescued whende novobacterial protein synthesis was inhibited with chloramphenicol, restoring expression of IFNγ-target genes. SimilarChlamydia-dependent dampening of STAT1 and JAK2 transcript levels were observed in infected END1 endocervical cells and in HEp2s infected withC. trachomatisserovar D, suggesting a conserved mechanism of dampening the interferon response by reducing the availability of key signaling components.ImportanceAs an obligate intracellular pathogen that has evolved to infect the genital epithelium,Chlamydiahas developed strategies to prevent detection and antimicrobial signaling in its host to ensure its survival and spread. A major player in clearingChlamydiainfections is the inflammatory cytokine interferon-γ (IFNγ), which is produced by immune cells that are recruited to the site of infection. Reports of IFNγ levels in vaginal and cervical swabs fromChlamydia-infected patients range from 1-350 pg/mL, while mostin vitrostudies of the effects of IFNγ on chlamydial growth have used 15-85 fold higher concentrations. By using physiologically-relevant concentrations of IFNγ we were able assessChlamydia’sability to modulate its signaling. We found thatChlamydiadecreases the expression of multiple components that are required for inducing gene expression by IFNγ, providing a possible mechanism by whichC. trachomatiscan attenuate the immune response in the female genital tract to cause long-term infections.
Characterization of Recombinant Human Lactoferrin Expressed inKomagataella Phaffii
Authors: Lu Xiaoning , Cummings Chad , Osuala Udodili A. , Yennawar Neela H. , Namitz Kevin E. W. , Hellner Brittney , Besada-Lombana Pamela B. , Peterson Ross D. , Clark Anthony J. 
Published: January 2024

ABSTRACTWe performed a thorough analysis and characterization of multiple batches of Helaina recombinant human lactoferrin (rhLF, Effera™) expressed at an industrial scale in a yeast system. Bottom-up LC-MS/MS-based proteomics analysis detected the full sequence of Helaina rhLF protein and confirmed that its amino acid sequence is identical to that of native human LF (Uniprot i.d. P02788). Helaina rhLF had a protein purity of 98% or higher as determined by three orthogonal methods; reversed-phase HPLC, SDS-PAGE, and LC-MS proteomics analysis. N-linked glycans were detected at three known glycosylation sites, namely, Asparagines-156, -497, and -642. The identified N-glycans of Helaina rhLF were predominantly oligomannose structures with five to nine mannoses (M5-M9), which we also report to be present in both the native human and bovine LF. human milk LF (hmLF) possessed lower levels of oligomannose structures and were mainly M5 and M6. Helaina rhLF protein secondary structure was nearly identical to that of hmLF, as revealed by microfluidic modulation spectroscopy. Results of small-angle X-ray scattering (SAXS) and analytical ultracentrifugation analyses confirmed that, like hmLF, Helaina rhLF displayed well-folded globular structures in solution. Reconstructed solvent envelopes of Helaina rhLF, obtained through the SAXS analysis, demonstrated a remarkable fit with the reported crystalline structure of iron-bound native hmLF. Differential scanning calorimetry investigations into the thermal stability of Helaina rhLF revealed two distinct denaturation temperatures at 68.7±0.9 °C and 91.9±0.5 °C, consistently mirroring denaturation temperatures observed for apo-and holo-hmLF. Overall, the characterization analysis results affirmed that Helaina rhLF was of high purity and exhibited globular structures closely akin to that of hmLF.
Stacking effects on mutation detection by T4 DNA ligation within dimeric DNA origami triangle barcodes for single-molecule nanopore analysis
Authors: Aboagye-Mensah Dorothy , Confederat Samuel , Alammar Fahad , Kailas Lekshmi , Adedeji-Olulana Abimbola F. , Stopar Alex , Nicholson Allen W. , Thomson Neil H. , Actis Paolo , Castronovo Matteo 
Published: January 2024

AbstractSolid-state nanopores represent an emerging technology for the highly sensitive detection of biomolecular markers, but the detection of DNA point mutations is challenged by the high noise levels associated with solid-state nanopore reading. In contrast, barcoded DNA origami nanostructures can provide unique single-molecule nanopore fingerprints. In this work, we have integrated nanopore-barcoded DNA nanostructures with enzymatic DNA ligation, the latter of which is routinely involved in clinical protocols for DNA mutation detection. We designed two triangular DNA origami variants containing three elongated staples that provide strands extensions on one side that are complementary to a target sequence. Addition of the latter in solution promotes the formation of a DNA triangle dimer. Since T4 DNA ligase repairs a nick in a dsDNA segment only if there is Watson-Crick base-pairing at the nick, the two DNA triangles can be covalently linked only if the DNA sequence bridging the two triangles carries the targeted mutation. We have found striking differences between ligation detection by gel electrophoresis, AFM, and quartz capillary-based nanopores. The stacking interaction between DNA triangles is enhanced by the formation of dimers, and promote the formation of higher order nanostructure, which serve as molecular weight amplification for DNA ligation in gels. The triangle-triangle stacking dynamics presumably involves a clam-like folding mechanism, which is detectable by quartz nanopore analysis, and which hinders ligation by T4 DNA ligase. The results provide the basis for development of rapid, highly sensitive, and affordable high-throughput approaches for profiling genetic variations in point-of-care settings.
WITHDRAWN: The relationship between antibiotic use in humans and poultry and antibiotic resistance prevalence in humans: an ecological regression study of Campylobacter in the UK
Authors: Emes Eve , Guitian Javier , Knight Gwenan , Naylor Nichola 
Published: January 2024

Withdrawal StatementThe authors have withdrawn this manuscript because, upon running further robustness tests, some of the results presented in the preprint were determined not to be robust. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Proteomic Changes in the Human Cerebrovasculature in Alzheimer’s Disease and Related Tauopathies Linked to Peripheral Biomarkers in Plasma and Cerebrospinal Fluid
Authors: Wojtas Aleksandra M. , Dammer Eric B. , Guo Qi , Ping Lingyan , Shantaraman Ananth , Duong Duc M. , Yin Luming , Fox Edward J. , Seifar Fatemeh , Lee Edward B. , Johnson Erik C. B. , Lah James J. , Levey Allan I. , Levites Yona , Rangaraju Srikant , Golde Todd E. , Seyfried Nicholas T. 
Published: January 2024

AbstractDysfunction of the neurovascular unit stands as a significant pathological hallmark of Alzheimer’s disease (AD) and age-related neurodegenerative diseases. Nevertheless, detecting vascular changes in the brain within bulk tissues has proven challenging, limiting our ability to characterize proteomic alterations from less abundant cell types. To address this challenge, we conducted quantitative proteomic analyses on both bulk brain tissues and cerebrovascular-enriched fractions from the same individuals, encompassing cognitively unimpaired control, progressive supranuclear palsy (PSP), and AD cases. Protein co-expression network analysis identified modules unique to the cerebrovascular fractions, specifically enriched with pericytes, endothelial cells, and smooth muscle cells. Many of these modules also exhibited significant correlations with amyloid plaques, cerebral amyloid angiopathy (CAA), and/or tau pathology in the brain. Notably, the protein products within AD genetic risk loci were found concentrated within modules unique to the vascular fractions, consistent with a role of cerebrovascular deficits in the etiology of AD. To prioritize peripheral AD biomarkers associated with vascular dysfunction, we assessed the overlap between differentially abundant proteins in AD cerebrospinal fluid (CSF) and plasma with a vascular-enriched network modules in the brain. This analysis highlighted matrisome proteins, SMOC1 and SMOC2, as being increased in CSF, plasma, and brain. Immunohistochemical analysis revealed SMOC1 deposition in both parenchymal plaques and CAA in the AD brain, whereas SMOC2 was predominantly localized to CAA. Collectively, these findings significantly enhance our understanding of the involvement of cerebrovascular abnormalities in AD, shedding light on potential biomarkers and molecular pathways associated with CAA and vascular dysfunction in neurodegenerative diseases.
A Systematic Review and Meta-Analysis on the Effectiveness of Bivalent mRNA Booster Vaccines against Omicron Variants
Authors: Song Shangchen , Madewell Zachary J. , Liu Mingjin , Miao Yu , Xiang Shaolin , Huo Yanan , Sarkar Shoumi , Chowdhury Amily , Longini Ira M. , Yang Yang 
Published: January 2024

ABSTRACTBackgroundA global shift to bivalent mRNA vaccines is ongoing to counterbalance diminishing monovalent vaccine effectiveness (VE) due to the evolution of SARS-CoV-2 variants, yet substantial variation in the bivalent VE exists across studies and a complete picture is lacking.MethodsWe searched papers evaluating SARS-CoV-2 bivalent mRNA vaccines on PubMed, Web of Science, Cochrane Library, Google Scholar, Embase, Scopus, bioRxiv, and medRxiv published from September 1st, 2022, to November 8th, 2023. Pooled VE against Omicron-associated infection and severe events was estimated in reference to unvaccinated, ≥2 monovalent doses, and ≥3 monovalent doses.ResultsFrom 630 citations identified, 28 studies were included, involving 55,393,303 individuals. Bivalent boosters demonstrated superior protection against symptomatic or any infection compared to unvaccinated, ≥2 monovalent doses, and ≥3 monovalent doses, with corresponding relative VE estimated as 53.5% (95% CI: - 22.2-82.3%), 30.8% (95% CI: 22.5-38.2%), and 28.4% (95% CI: 10.2-42.9%) for all ages, and 22.5% (95% CI: 16.8-39.8%), 31.4% (95% CI: 27.7-35.0%), and 30.6% (95% CI: -13.2-57.5%) for adults ≥60 years old. Pooled bivalent VE estimates against severe events were higher, 72.9% (95% CI: 60.5-82.4%), 57.6% (95% CI: 42.4-68.8%), and 62.1% (95% CI: 54.6-68.3%) for all ages, and 72.0% (95% CI: 51.4-83.9%), 63.4% (95% CI: 41.0-77.3%), and 60.7% (95% CI: 52.4-67.6%) for adults ≥60 years old, compared to unvaccinated, ≥2 monovalent doses, and ≥3 monovalent doses, respectively.ConclusionsBivalent boosters demonstrated higher VE against severe outcomes than monovalent boosters across age groups, highlighting the critical need for improving vaccine coverage, especially among the vulnerable older subpopulation.
A randomized controlled trial of alpha phase-locked auditory stimulation to treat symptoms of sleep onset insomnia
Authors: Bressler Scott , Neely Ryan , Yost Ryan , Wang David 
Published: January 2024

AbstractSleep onset insomnia is a pervasive problem that contributes significantly to the poor health outcomes associated with insufficient sleep. Auditory stimuli phase-locked to slow-wave sleep oscillations have been shown to augment deep sleep, but it is unknown whether a similar approach can be used to accelerate sleep onset. The present randomized controlled crossover trial enrolled adults with objectively verified sleep onset latencies (SOLs) greater than 30 minutes to test the effect of auditory stimuli delivered at specific phases of participants’ alpha oscillations prior to sleep onset. During the intervention week, participants wore an electroencephalogram (EEG)-enabled headband that delivered acoustic pulses timed to arrive anti-phase with alpha for 30 minutes (Stimulation). During the Sham week, the headband silently recorded EEG. The primary outcome was SOL determined by blinded scoring of EEG records. For the 21 subjects included in the analyses, stimulation had a significant effect on SOL according to a linear mixed effects model (p = 0.0019), and weekly average SOL decreased by 10.5 ± 15.9 minutes (29.3 ± 44.4%). These data suggest that phase-locked acoustic stimulation can be a viable alternative to pharmaceuticals to accelerate sleep onset in individuals with prolonged sleep onset latencies.
Using gene complementation to identify a SulP-family bicarbonate transporter in an N2-fixing cyanobacterial endosymbiont of an open ocean diatom
Authors: Nieves-Morión Mercedes , Romero-García Rubén , Bardi Sepehr , López-Maury Luis , Hagemann Martin , Flores Enrique , Foster Rachel A. 
Published: January 2024

ABSTRACTDiatom-Diazotrophic Associations (DDAs) contribute significantly to new and primary production in the world’s oceans, yet the understanding of how production is sustained is poorly resolved. These symbioses involve diatoms and N2-fixing, heterocyst-forming cyanobacteria of the genusRichelia, both partners being photosynthetic.Richelia euintracellularisresides in the cytoplasm ofHemiaulus hauckii, whereasRichelia intracellularisis periplasmic inRhizosolenia clevei. In the ocean, bicarbonate is taken up by phytoplankton to provide CO2for photosynthesis. The genomes of bothRicheliaendobionts (ReuHH01 and RintRC01, respectively) contain genes encoding SulP-family proteins, which are oxyanion transporters. To study the possible involvement of these transporters in bicarbonate uptake, we used complementation of aSynechocystissp. PCC 6803 mutant with its five CO2uptake systems inactivated, which is unable to grow in air levels of CO2. Three genes from RintRC01 and one gene and a DNA fragment containing four partial gene sequences from ReuHH01 were chemically synthesized, cloned under the control of a strong gene promoter and incorporated in the chromosome of theSynechocystismutant. One gene from RintRC01, RintRC_3892, complemented theSynechocystismutant to grow with air levels of CO2or with low bicarbonate concentrations. The complemented strain showed strong sodium-dependent, low affinity bicarbonate uptake, which, together with phylogenetic analyses, identified RintRC_3892 as a BicA protein. Additionally, RintRC_3892 transcripts were consistently detected in environmental samples from three ocean basins. No evidence for a bicarbonate transporter was found, however, for ReuHH01, suggesting different strategies for inorganic carbon uptake in the periplasmic and cytoplasmic endobionts.
Comparative genomic analysis ofBradyrhizobiumstrains with natural variability in the efficiency of nitrogen fixation, competitiveness, and adaptation to stressful edaphoclimatic conditions
Authors: Klepa Milena Serenato , diCenzo George Colin , Hungria Mariangela 
Published: January 2024

ABSTRACTBradyrhizobiumis known for its ability to fix atmospheric nitrogen in symbiosis with agronomically important crops. This study focused on two groups of strains, each containing eight putative natural variants ofB. japonicumSEMIA 586 (=CNPSo 17) orB. diazoefficiensSEMIA 566 (=CNPSo 10), previously used as commercial inoculants for soybean crops in Brazil. We aimed to detect genetic variations that might be related to biological nitrogen fixation, competitiveness for nodule occupancy, and adaptation to the stressful conditions of the Brazilian Cerrado soils. High-quality genome assemblies were produced for all strains and used for comparative genomic analyses. The core genome phylogeny revealed that strains of each group are closely related, confirmed by high average nucleotide identity (ANI) values. However, variants accumulated divergences resulting from horizontal gene transfer (HGT), genomic rearrangements, and nucleotide polymorphisms. TheB. japonicumgroup presented a larger pangenome and a higher number of nucleotide polymorphisms than theB. diazoefficiensgroup, probably due to its longer adaptation time to the Cerrado soil. Interestingly, five strains of theB. japonicumgroup carry two plasmids. The genetic variability found in both groups is discussed in light of the observed differences in their nitrogen fixation capacity, competitiveness for nodule occupancy, and environmental adaptation.SIGNIFICANCEThe two main reference strains for soybean inoculation in Brazil,B. japonicumCPAC 15 (=SEMIA 5079) andB. diazoefficiensCPAC 7 (=SEMIA 5080), have been considered highly competitive and highly efficient in nitrogen fixation, respectively. In this study, we obtained and analyzed the genomes of the parental and variant strains. We detected two plasmids in five strains and several genetic differences that might be related to adaptation to the stressful conditions of the soils of the Brazilian Cerrado biome. We also detected genetic variations in specific regions that may impact symbiotic nitrogen fixation. Our analysis contributes to new insights into evolution ofBradyrhizobium, and some of the identified differences may be applied as genetic markers to assist strain selection programs.
Sequencing coverage analysis for combinatorial DNA-based storage systems
Authors: Preuss Inbal , Galili Ben , Yakhini Zohar , Anavy Leon 
Published: January 2024

AbstractThis study introduces a novel model for analyzing and determining the required sequencing coverage in DNA-based data storage, focusing on combinatorial DNA encoding. We explore the application of the coupon collector model for combinatorial-letter reconstruction, post-sequencing, which ensure efficient data retrieval and error reduction. We use a Markov Chain model to compute the probability of error-free reconstruction. We develop theoretical bounds on the decoding probability and use empirical simulations to validate these bounds. The work contributes to the understanding of sequencing coverage in DNA-based data storage, offering insights into decoding complexity, error correction, and sequence reconstruction. We provide a Python package that takes the code design and other message parameters as input, and then computes the required read coverage to guarantee reconstruction at a given desired confidence.
Effective assessment of CD4+T cell Immunodominance patterns: impact of antigen processing and HLA restriction
Authors: Álvaro-Benito Miguel , Abualrous Esam T , Lingel Holger , Meltendorf Stefan , Holzapfel Jakob , Sticht Jana , Kuropka Benno , Clementi Cecilia , Kuppler Frank , Brunner-Weinzierl Monika C , Freund Christian 
Published: January 2024

AbstractIdentifying T cell epitopes is essential for studying and potentially tuning immune responses to pathogens. The polymorphic nature of major histocompatibility complex of class II (MHCII)-genes, and the complexity of the antigen processing mechanisms hinders the effective prediction of immunodominant patterns in humans, specially at the population level. Here, we combined the output of a reconstituted antigen processing system and ofin silicoprediction tools for SARS-CoV-2 antigens considering a broad-population coverage DRB1* panel to gain insights on immunodominance patterns. The two methods complement each other, and the resulting model improves upon single positive predictive values (PPV) from each of them to explain known epitopes. This model was used to design a minimalistic peptide pool (59 peptides) matching the performance reported for large overlapping peptide pools (> 500 peptides). Furthermore, almost 70 % of the candidates (23 peptides) selected for a frequent HLA background (DRB1*03:01/*07:01) feature immunodominant responsesex vivo, validating our platform for accessing T cell epitopes at the population level. The analysis of the impact of processing constraints reveals distinct impact of proteolysis and solvent accessible surface area on epitope selection depending on the antigen. Thus, considering these properties for antigens in question should improve available epitope prediction tools.