bluuebunny/crossref_metadata_2025_split huggingface dataset:
Generation and Characterization of a Knockout Mouse of an Enhancer ofEBF3
Authors: Hurtado Emily Cordova , Wotton Janine M. , Gulka Alexander , Burke Crystal , Ng Jeffrey K. , Bah Ibrahim , Manuel Juana , Heins Hillary , Murray Stephen A. , Gorkin David U. , White Jacqueline K. , Peterson Kevin A. , Turner Tychele N. 
Published: January 2025

ABSTRACTGenomic studies of autism and other neurodevelopmental disorders have identified several relevant protein-coding and noncoding variants. One gene with an excess of protein-codingde novovariants isEBF3that also is the gene underlying the Hypotonia, Ataxia, and Delayed Development Syndrome (HADDS). In previous work, we have identified noncodingde novovariants in an enhancer ofEBF3called hs737 and further showed that there was an enrichment of deletions of this enhancer in individuals with neurodevelopmental disorders. In this present study, we generated a novel mouse line that deletes the highly conserved, orthologous mouse region of hs737 within the Rr169617 regulatory region, and characterized the molecular and phenotypic aspects of this mouse model. This line contains a 1,160 bp deletion within Rr169617 and through heterozygous crosses we found a deviation from Mendelian expectation (p = 0.02) with a significant depletion of the deletion allele (p = 5.8 × 10-4).Rr169617+/-mice had a reduction ofEbf3expression by 10% andRr169617-/-mice had a reduction ofEbf3expression by 20%. Differential expression analyses in E12.5 forebrain, midbrain, and hindbrain inRr169617+/+versusRr169617-/-mice identified dysregulated genes including histone genes(i.e.,Hist1h1e,Hist1h2bk,Hist1h3i,Hist1h2ao)and other brain development related genes (e.g.,Chd5,Ntng1).A prioriphenotyping analysis (open field, hole board and light/dark transition) identified sex-specific differences in behavioral traits when comparingRr169617-/-males versus females; whereby, males were observed to be less mobile, move slower, and spend more time in the dark. Furthermore, both sexes when homozygous for the enhancer deletion displayed body composition differences when compared to wild-type mice. Overall, we show that deletion within Rr169617 reduces the expression ofEbf3and results in phenotypic outcomes consistent with potential sex specific behavioral differences. This enhancer deletion line provides a valuable resource for others interested in noncoding regions in neurodevelopmental disorders and/or those interested in the gene regulatory network downstream ofEbf3.
Genomic and metagenomic survey of microbial carbonic anhydrase genes reveals novel clades, high diversity, and biome-specificity
Authors: Franco Mario E.E. , Singer Esther , Roux Simon , Meredith Laura K. , U’Ren Jana M. 
Published: January 2025

AbstractCarbonic anhydrase (CA) enzymes catalyze the interconversion of carbon dioxide and bicarbonate with an efficiency exceeded only by superoxide dismutase. CA enzymes have convergently evolved multiple times from phylogenetically distant organisms into structurally unrelated classes (α, β, γ,δ,ζ,η, θ, ι) with conserved physiological functions involved in photosynthesis, respiration, pH homeostasis, CO2transport, and carbonyl sulfide hydrolysis that play central roles in medicine and the environment. Here, we leverage the recent surge in publicly available genomes and metagenomes to re-examine our understanding of the abundance, diversity, and phylogenetic relationships of the three major CA classes in Bacteria/Archaea and microbial Eukaryotes (Fungi, algae). We recovered a total of 57,218 α-, β-, and γ-CA sequences from 24,184 metagenomes and genomes, including the first detection of α-CA from an Archaeal species. CA sequences formed 3,859 protein clusters (1,188 with ≥ 3 sequences) that were taxonomically conserved at higher levels (i.e., Superkingdom, Phylum, Class). When viewed within a phylogenetic framework, the majority of subclades contained CAs representing multiple Superkingdoms, although numerous novel β-CA clades appear unique to Fungi. Queries of CA Hidden Markov models (HMMs) against all public meta-genome and -transcriptome datasets revealed that CA is a ubiquitous enzyme present in virtually all sampled environments. However, CA clusters that were taxonomically conserved also appeared environment-specific, generating high CA diversity. This work represents an important contribution to the evolution, diversity, and environmental distribution of an enzyme that is key for life and has broad environmental and industrial applications.
Plasma-driven biocatalysis using the cytochrome P450 enzyme CYP152BSβ
Authors: Dirks Tim , Klopsch Sabrina , Stoesser Davina , Trenkle Sophie Desdemona , Yayci Abdulkadir , Schüttler Steffen , Golda Judith , Bandow Julia Elisabeth 
Published: January 2025

AbstractPlasma-driven biocatalysis utilizesin situH2O2production by atmospheric pressure plasmas to drive H2O2-dependent enzymatic reactions. Having previously established plasma-driven biocatalysis using recombinant unspecific peroxygenase fromAgrocybe aegerita(rAaeUPO) to produce (R)-1-phenylethanol from ethylbenzene (ETBE), we here employed CYP152 fromBacillus subtilis(CYP152BSβ). CYP152BSβnaturally hydroxylates medium and long-chain carboxylic acids, and, with short-chain carboxylic acids as decoy molecules, also converts non-natural substrates such as ETBE. To produce active CYP152BSβoverexpression and heme loading were optimized. The conversion of the non-natural substrates guaiacol and ABTS with heptanoic acid as decoy molecule and H2O2from stock solution yielded 18.28 and 21.13 nmol product min-1, respectively. These reactions also served to assess compatibility of CYP152BSβwith plasma-driven biocatalysis regarding temperature and H2O2operating windows. To establish CYP152BSβ-based plasma-driven biocatalysis, immobilized enzyme in a rotating bed reactor (5 ml reaction volume) was then supplied with H2O2from a capillary plasma jet operated with 1280 ppm H2O in helium. After a 120 min run time a turnover number (TON) of 18.82 mol(R)-1-PhOlwas reached. We conclude that plasma-driven biocatalysis can be extended to other H2O2-dependent enzymes. Future efforts will be directed at increasing the TON and product range.
Temporal Dynamics of Transcriptional Responses to Repeated mRNA Vaccination: Insights from Third Dose Profiling
Authors: Rinchai Darawan , Deola Sara , Ahamed Kabeer Basirudeen Syed , Gentilcore Giusy , Toufiq Mohammed , Mathew Lisa , Liu Li , Vempalli Fazulur Rehaman , Mubarak Ghada , Lorenz Stephan , Augustine Tracy , Panhuys Nicholas Van , Bedognetti Davide , Grivel Jean-Charles , Chaussabel Damien 
Published: January 2025

ABSTRACTmRNA vaccines have played a crucial role in combating the COVID-19 pandemic, but the long-term dynamics of immune responses to repeated vaccination remain poorly understood. In this study, we extend our previous work on first and second dose responses by characterizing the immune signatures elicited by a third dose of COVID-19 mRNA vaccines using high-resolution temporal profiling of blood transcriptomes collected daily for 9 days post-vaccination. We observed distinct patterns of gene expression related to interferon responses, inflammation, erythroid cell signatures, and plasmablast activity across the three doses. While the first dose elicited a modest response primarily characterized by interferon signaling, the second dose induced a robust, polyfunctional response. The third dose, administered approximately nine months later, maintained this polyfunctional character and matched the second dose in magnitude, though with distinct temporal dynamics. The interferon component peaked on day 2 (similar to the first dose) rather than day 1 (as seen in the second dose), while the erythroid signature showed a markedly different trajectory, with sustained elevation rather than decrease over the following week. Notably, we observed a progressive amplification of the plasmablast response across the three doses, with an earlier peak (day 4) compared to other vaccines, potentially a unique feature of mRNA vaccines. These findings demonstrate that the heightened, polyfunctional responsiveness induced by the second dose is robustly maintained even after a prolonged interval, suggesting effective immune memory. Our results contribute to understanding mRNA vaccine-induced immunity, with implications for optimizing booster strategies and developing next-generation vaccines.
The N-terminal order-disorder transition is a critical determinant for a metamorphosis of IscU
Authors: Na Jongbum , Heo Joongyu , Jeong Minchan , Ji Sangho , Ko Young Ho , Shafiei Alaleh , Baldir Nilufer , DeMirci Hasan , Yu Wookyung , Kim Jin Hae 
Published: January 2025

AbstractIscU, a key scaffold protein mediating the biogenesis of iron-sulfur (Fe-S) clusters, exhibits metamorphic characteristics crucial for its versatile and efficient function. Previous studies have demonstrated that IscU has two interconverting conformations: the structured state (S-state) and the disordered state (D-state), each contributing to its distinct functionality and interaction network. Despite its physiological importance, the precise mechanism underpinning the maintenance of IscU’s unique structural heterogeneity has remained elusive. In this study, we used computational and experimental approaches to reveal that the N-terminal order-disorder plays a critical role in the metamorphic modulation of IscU. We found that the N-terminal region displays greater structural plasticity, which is linked to other regions of IscU through coevolutionary relationships. Moreover, we demonstrated that the degree of orderliness in the N-terminal region correlates positively with the stabilization of IscU’s S-state and negatively with its affinity for HscA. This indicates that the flexibility in the N-terminal region is finely tuned to optimize IscU’s physiological efficiency and efficacy. Finally, our data suggest that a peptide mimicking the N-terminal motif can modulate IscU’s metamorphic properties, suggesting a novel therapeutic potential for related pathogenic processes.
Aggregation of HAPLN2, a component of the perinodal extracellular matrix, is a hallmark of physiological brain aging in mice
Authors: Watanabe Ayaka , Hirayama Shoshiro , Kominato Itsuki , Marchese Sybille , Esposito Pietro , Metodieva Vanya , Kameda Hiroshi , Sano Terunori , Takatori Sho , Takao Masaki , Koike Masato , Varela Juan Alberto , Tomita Taisuke , Murata Shigeo 
Published: January 2025

AbstractProtein aggregation is a hallmark of neurodegenerative diseases and is also observed in the brains of elderly individuals without such conditions, suggesting that aging drives the accumulation of protein aggregates. However, the comprehensive understanding of age-dependent protein aggregates involved in brain aging remains unclear. Here, we investigated proteins that become sarkosyl-insoluble with age and identified hyaluronan and proteoglycan link protein 2 (HAPLN2), a hyaluronic acid-binding protein of the extracellular matrix at the nodes of Ranvier, as an age-dependent aggregating protein in mouse brains. Elevated hyaluronic acid levels and impaired microglial function reduced the clearance of HAPLN2, leading to its accumulation. HAPLN2 oligomers induced microglial inflammatory responses bothin vitroandin vivo. Furthermore, age-associated HAPLN2 aggregation was also observed in the human cerebellum. These findings suggest that HAPLN2 aggregation results from age-related decline in brain homeostasis and may exacerbate the brain environment by activating microglia. This study provides new insights into the mechanisms underlying cerebellar aging and highlights the role of HAPLN2 in age-associated changes in the brain.Author SummaryTo identify age-dependent protein aggregates unrelated to disease, we analyzed the sarkosyl-insoluble proteome of young and aged mouse brains. We discovered that hyaluronan and proteoglycan link protein 2 (HAPLN2), a hyaluronic acid-binding protein existing in the nodal extracellular matrix, accumulated with age. Age-dependently accumulated HAPLN2 formed large protein aggregates that cannot be solubilized by the anionic detergent sarkosyl or by hyaluronidase digestion. In addition, HAPLN2 formed irregularly shaped puncta that were mislocalized from the nodes of Ranvier in the cerebellar white matter of not only aged mice but also aged human brains. Oligomers of full-length HAPLN2 specifically induced microglial activationin vitroandin vivo. Our findings suggest that the accumulation of HAPLN2 aggregates is a new hallmark of brain aging and a possible factor contributing to brain inflammation.
Predictive acoustical processing in human cortical layers
Authors: Faes Lonike K. , Zulfiqar Isma , Vizioli Luca , Yu Zidan , Wu Yuan-Hao , Shin Jiyun , Cloos Martijn A. , Auksztulewicz Ryszard , Melloni Lucia , Uludag Kamil , Yacoub Essa , De Martino Federico 
Published: January 2025

AbstractIn our dynamic environments, predictive processing is vital for auditory perception and its associated behaviors. Predictive coding formalizes inferential processes by implementing them as information exchange across cortical layers and areas. With laminar-specific blood oxygenation level dependent we measured responses to a cascading oddball paradigm, to ground predictive auditory processes on the mesoscopic human cortical architecture. We show that the violation of predictions are potentially hierarchically organized and associated with responses in superficial layers of the planum polare and middle layers of the lateral temporal cortex. Moreover, we relate the updating of the brain’s internal model to changes in deep layers. Using a modeling approach, we derive putative changes in neural dynamics while accounting for draining effects. Our results support the role of temporal cortical architecture in the implementation of predictive coding and highlight the ability of laminar fMRI to investigate mesoscopic processes in a large extent of temporal areas.
Susceptibility of bovine respiratory and mammary epithelial cells to avian and mammalian derived clade 2.3.4.4b H5N1 highly pathogenic avian influenza viruses
Authors: Meliopoulos Victoria , Cherry Sean , Smith Maria , Sharp Bridgett , Brigleb Pamela H. , Roubidoux Ericka , Livingston Brandi , Morris Dorothea R. , Ripperger Tyler , Baker Pari , Gragg Sara , Dimitrov Kiril , Langel Stephanie , Schultz-Cherry Stacey 
Published: January 2025

AbstractZoonotic transmission of avian influenza viruses into mammals is relatively rare due to anatomical differences in the respiratory tract between species. Recently, clade 2.3.4.4b highly pathogenic H5N1 avian influenza viruses were detected circulating in North American cattle. Sporadic transmission between cattle, humans, and other animals proximal to cattle or after consuming products from infected cattle has occurred, but thus far there is no evidence of human-to-human transmission. However, the virus has the potential to adapt to the mammalian respiratory tract with every transmission event that occurs, making it crucial to understand cellular and species tropism of the H5N1 2.3.4.4b viruses. We compared viral kinetics of clade 2.3.4.4b viruses isolated from birds and mammals in respiratory epithelial cells derived from cattle, human, swine, and ferret. We found that avian derived viruses could replicate in swine cells only, yet mammalian derived strains could replicate efficiently in all tracheal and nasal epithelial cells tested. Interestingly, only bovine mammary epithelial cells (MEC) and swine respiratory epithelial cells were permissive to both avian and mammalian derived strains, possibly due to increased sialic acid expression on bovine MEC compared to bovine tracheal epithelial cells (TEC). However, sialic acid expression differed between dairy and beef cows: TEC derived from a dairy cow had increased expression of α2,3 sialic acid receptors compared to TEC from a beef-dairy cow cross. This study highlights the ability of clade 2.3.4.4b H5N1 viruses derived from mammals but not wild birds to infect the respiratory epithelium of other mammalian hosts.
CpgD is a phosphoglycerate cytidylyltransferase required for ceramide diphosphoglycerate synthesis
Authors: Dhakephalkar Tanisha , Guan Ziqiang , Klein Eric A. 
Published: January 2025

AbstractLipopolysaccharide (LPS) is essential in most Gram-negative bacteria, but mutants of several species have been isolated that can survive in its absence.Caulobacter crescentusviability in the absence of LPS is partially dependent on the anionic sphingolipid ceramide diphosphoglycerate (CPG2). Genetic analyses showed thatccna_01210, which encodes a nucleotidyltransferase, is required for CPG2 production. Using purified recombinant protein, we determined that CCNA_01210 (CpgD) is a phosphoglycerate cytidylyltransferase which uses CTP and 3-phosphoglycerate to produce CDP-glycerate, which we hypothesize is the phosphoglycerate donor for CPG2 synthesis. CpgD had optimum activity at pH 7.5-8 in the presence of magnesium. CpgD exhibited Michaelis-Menten kinetics with respect to 3-phosphoglycerate (Km,app = 10.9 ± 0.7 mM; Vmax,app = 0.72 ± 0.02 µmol/min/mg enzyme) and CTP (Km,app = 4.8 ± 0.9 mM; Vmax,app = 0.44 ± 0.03 µmol/min/mg enzyme). The characterization of this enzyme uncovers another piece of the pathway towards CPG2 synthesis.
Single-cell genomics of single soil aggregates: methodological assessment and potential implications with a focus on nitrogen metabolism
Authors: Matsumura Emi , Kato Hiromi , Hara Shintaro , Ohbayashi Tsubasa , Ito Koji , Shingubara Ryo , Kawakami Tomoya , Mitsunobu Satoshi , Saeki Tatsuya , Tsuda Soichiro , Minamisawa Kiwamu , Wagai Rota 
Published: January 2025

AbstractSoil particles in plant rooting zone are largely clustered to form complex porous structural unit called aggregates where highly diverse microbes coexist and drive biogeochemical cycling. The complete extraction of microbial cells and DNA from soil is a substantial task as certain microbes exhibit strong adhesion to soil surfaces and/or inhabit deep within aggregates. Yet, the degree of aggregate dispersion and the efficacy of extraction have rarely been examined, and thus adequate cell extraction method from soil remain unclear. We aimed to develop an optimal method of cell extraction for single-cell genomics (SCG) analysis of single soil aggregates by focusing on water-stable macroaggregates (diameter: 5.6-8.2 mm) isolated from a topsoil of cultivated Acrisol. Using the same six individual aggregates, we performed both SCG sequencing and amplicon analysis. While both bead-vortexing and sonication dispersion methods improved the extractability of bacterial cells compared to previous studies, the latter yielded higher number and more diverse microbes compared to the former. The analyses of nitrogen-cycling and exopolysaccharides-related genes suggested that the sonication-assisted extraction led to greater recovery of microbes strongly attached to soil particles and/or inhabited the aggregate subunits that were more physically stable (e.g., aggregate core). Further SCG analysis revealed that all six aggregates held intact microbes having the genes (i.e., potentials) to convert nitrate into all possible nitrogen forms while some low-abundance genes showed inter-aggregate heterogeneity. In addition, all six aggregates studied showed overall similarity in pore characteristics, phylum-level composition, and the microbial functional redundancy. Together, these results suggest that water-stable macroaggregates may act as a functional unit in soil and show potential as a useful experimental unit in soil microbial ecology. Our study also suggest that conventional methods employed for the extraction of cell and DNA may not be optimal. The current findings underscore the necessity to advance extraction methodologies, thereby facilitating a more comprehensive understanding of the microbial diversity and functioning within soil environments.
Neural plate pre-patterning enables specification of intermediate neural progenitors in the spinal cord
Authors: Nandagopal Sandy , Cha Anna , Jia Bill Z. , Liao Hongyu , Comenho Caroline , Lahav Galit , Wagner Daniel E. , Tsai Tony Y-C , Megason Sean G. 
Published: January 2025

SummaryDorsal-ventral patterning of neural progenitors in the posterior neural tube, which gives rise to the spinal cord, has served as a model system to understand how extracellular signals organize developing tissues. While previous work has shown that signaling gradients diversify progenitor fates at the dorsal and ventral ends of the tissue, the basis of fate specification in intermediate regions has remained unclear. Here we use zebrafish to investigate the neural plate, which precedes neural tube formation, and show that its pre-patterning by a distinct signaling environment enables intermediate fate specification. Systematic spatial analysis of transcription factor (TF) expression and signaling activity using a reference-based mapping approach shows that the neural plate is partitioned into a striking complexity of TF co-expression states that, in part, correspond to the activity of gastrulation signals such as FGF and Wnt that persist through axis extension. Usingin totoanalysis of cellular movement combined with fate mapping, we find thatdbx1b-expressing intermediate progenitors (p0) originate from a neural-plate specific state characterized by transient co-expression of the TFspax3a,olig4andher3. Finally, we show that this state is defined by Wnt signaling in the posterior neural plate and that ectopic Wnt activation withinpax3a/olig4+ cells is sufficient to promotedbx1bexpression. Our data broadly support a model in which neural progenitor specification occurs through the sequential use of multiple signals to progressively diversify the neural tissue as it develops. This has implications forin vitrodifferentiation of spinal cord cell types and for understanding signal-based patterning in other developmental contexts.