bluuebunny/crossref_metadata_2025_split huggingface dataset:
Utilizing full-length 16S rRNA sequencing to assess the impact of diet formulation and age on targeted gut microbiome colonization in laboratory and mass-reared Mediterranean fruit flies
Authors: Mason Charles J. , Nelson Rosalie C. , Weaver Mikinley , Simmonds Tyler , Geib Scott , Shikano Ikkei 
Published: December 2024

AbstractInsect gut microbiomes have important roles in overall host health and how hosts function in the environment. In laboratory and mass-reared insects, gut microbiomes can differ in composition and function compared to wild conspecifics. For fruit flies, like the Mediterranean fruit fly (medfly;Ceratitis capitata), these changes can influence male performance and behavior.Overall, understanding factors that influence the ability of bacteria to colonize hosts is an important for the establishment of lost or novel microbiota into mass-reared insects. The goal of this study was to evaluate how host age and diet inoculation method influenced bacterial establishment in laboratory and mass-reared medfly. We used anEnterobacterstrain with antibiotic resistance and coupled it with full-length PacBio 16S rRNA sequencing to track the establishment of a specific isolates under different adult dietary conditions. We also used two longstanding reared lines of medfly in our study. Our results identified that diet had a strong interaction with age. Host medfly fed a liquid diet with the target bacteria were able to be colonized regardless of age, but those fed a slurry-based diet and separate water source were more resilient. This was consistent for both fly rearing lines used in the study. 16S rRNA sequencing corroborated the establishment of the specific strain, but also revealed some species/strain-level variation ofEnterobactersequences associated with the flies. Additionally, our study illustrates that long-read 16S rRNA sequencing may afford improved characterization of species- and strain-level distribution of Enterobacteriaceae in insects.Importance:Insects form intimate relationships with gut microorganisms that can help facilitate several important roles. The goals of our study were to evaluate factors that influence microbial establishment in lines of the Mediterranean fruit fly (medfly), an important pest species throughout the world. Mass-reared insects for sterile insect technique often possess gut microbiomes that substantially differ from wild flies, which can impact their performance in pest control contexts. Here, we show that liquid-based formulations can be utilized to manipulate the gut microbiota of mass-reared medfly. Furthermore, using near full-length 16S rRNA metabarcoding sequencing, we uncovered strain-level diversity of that was not immediately obvious using other approaches. This is a notable finding, as it suggests that full-length 16S rRNA approaches can have marked improvements for some taxa compared to fewer hypervariable regions at approximately the same cost. Our results provide new avenues for exploring and interrogating medfly-microbiome interactions.
Morphometric Identification of Parvalbumin-Positive Interneurons: A Data-Driven Approach
Authors: Panday Maheshwar , Monteiro Leanne , Daudi Ahad , Murphy Kathryn M. 
Published: December 2024

AbstractTraditionally, anatomical studies of parvalbumin-positive (PV+) labelled interneurons describe them as a homogeneous population of neurons. In contrast, recent single-cell RNAseq studies have identified multiple transcriptomically distinct categories of PV+ cells. That difference between a single anatomical category of PV+ neurons and multiple transcriptomic categories presents a problem in understanding the role of these neurons in cortical function. One gap that might contribute to this discrepancy is that PV+ morphology is typically addressed using qualitative descriptions and simple quantifications, while single-cell RNAseq studies use big data and high dimensional analyses. PV+ neurons play critical roles in the experience-dependent development of the cortex and are often involved in disease-related changes associated with neurodegenerative and neuropsychiatric disorders. Here, we developed a modern data-driven analysis pipeline to quantify PV+ morphology. We quantified 97 morphometric features from 14274 PV+ neurons and applied unsupervised clustering that identified 13 different PV+ morphologies. We extended the analysis to compare PV+ dendritic arbour patterns and cell body morphologies. Finally, we compared the morphologies of PV+ neurons with the cell body morphologies of neurons expressing various genes associated with PV+ transcriptomic cell types. This approach identified a range of PV+ morphologies similar to the number of transcriptomic categories. It also found that the PV+ morphologies have cortical area, laminar, and transcriptomic biases that might contribute to cortical function.
Functional expression and sex dimorphism of the T-type Cav3.2 Calcium Channel in human DRG Neurons
Authors: Chemin Jean , Soubeyre Vanessa , Shiers Stephanie , François Amaury , Poulen Gaëtan , Lonjon Nicolas , Vachiery-Lahaye Florence , Bauchet Luc , Mery Pierre François , Price Theodore J , Bourinet Emmanuel 
Published: December 2024

AbstractT-type/Cav3 calcium channels are key in neuronal excitability and pain processing with Cav3.2 being the prominent isoform in primary sensory neurons of the dorsal root ganglion (DRG). Its pharmacological inhibition or gene silencing induces analgesia in several preclinical models of inflammatory and neuropathic pain. However, the presence of Cav3.2, encoded by theCACNA1Hgene, in human DRG neurons remains unresolved. Using RNA in-situ hybridization and electrophysiological recordings, we show that human DRGs express Cav3.2 in a subset of neurons positive for the neurotrophic factor receptor TrkB (NTRK2gene). The Cav3.2 current exhibits typical biophysical and pharmacological properties, including inhibition by a low concentration of nickel and by Z944, a specific T-type calcium channel blocker in advanced clinical development. Conversely, ABT-639, a T-type calcium channel inhibitor that failed in Phase 2 trials for pain relief, does not inhibit Cav3.2 currents in human DRG neurons. Importantly, Cav3.2 currents are prominent in neurons from female organ donors, supporting the presence of sex differences in pain mechanisms in humans. These findings underscore the potential of continued exploration of Cav3.2 as a therapeutic target for pain treatment and highlight a specific subset of human neurons that likely rely on this channel to modulate their excitability.
Dominant Formation of DNA:RNA Hybrid G-Quadruplexes in the Genomes of Living Human and Mouse Cells
Authors: Tan Zheng 
Published: December 2024

AbstractGuanine-rich nucleic acids can form four-stranded structures known as G-quadruplexes (G4s), which play critical roles in essential cellular activities. Putative G-quadruplex-forming sequences (PQSs) are abundant in the genomes of animal cells. To date, research on G4s has focused primarily on intramolecular G4s formed by four contiguous G-tracts from the same nucleic acid strand. However, our recent study indicates that a hybrid type of G4s, DNA:RNA hybrid G4s (hG4s), comprising G-tracts from both DNA and RNA, is, in fact, the most abundant G4 species found in the genomes of living yeast cells. Here, we demonstrate that hG4s also readily form and predominate in the genomes of living human and mouse cells, with an abundance several orders of magnitude greater than that of intramolecular DNA G4s (dG4s). Furthermore, each individual G-tract in a PQS tends to form an hG4 independent of adjacent G-tracts. This independence of DNA G-tracts is maintained even in PQSs containing four G-tracts, despite their potential to form intramolecular DNA G4s only by themselves. Collectively, our studies demonstrate that hG4s are the predominant physiological G4 structures in the genomes of eukaryotic organisms. Given that hG4s differ significantly from intramolecular dG4s in terms of structural form, formation mechanism, abundance, and association with transcription, there is a clear need for a comprehensive revision of our current understanding of genomic G4s and their functional roles. We hypothesize that hG4 formation may serve as a global sensing mechanism to monitor RNA levels in cells to maintain transcriptional homeostasis.Abstract Figure
Tapetum specific TA29 promoter is regulated bycis- elements binding to positive and negative regulators
Authors: Sharma Preeti Apurve , Soni Kamlesh Kumar , Minhajuddin Bm , Yadava Satish Kumar , Burma Pradeep Kumar 
Published: December 2024

AbstractThe TA29 gene fromNicotiana tabacumwas one of the first tapetum-specific genes identified in 1990. Its promoter has been successfully used to developbarnase/barstargene-based male sterility and restorer transgenic lines for hybrid seed production in crops such as mustard. Despite its biotechnological significance, no major studies have been conducted to delineate the regulatory mechanisms of its promoter. The presented work identifies criticalcis-elements of the promoter, starting within-silicoanalysis followed by functional validation through mutational studies and promoter activity analysis in transgenic tobacco lines. This work led to the identification ofcis-elements that are putative binding sites for the transcription factors NtMYB12, NtGT-1a, NtNAG1, and NtLZ-HD. The binding sites for NtMYB12, NtGT-1a, and NtNAG1 act as positive regulators, whereas the binding site for NtLZ-HD functions as a negative regulator.
Mathematical Programming and Graph Neural Networks illuminate functional heterogeneity of pathways in disease
Authors: Triantafyllidis Charalampos P. 
Published: December 2024

ABSTRACTWe employ a computationally intensive framework that integrates mathematical programming and graph neural networks to elucidate functional phenotypic heterogeneity in disease by classifying entire pathways under various conditions of interest. Our approach combines three distinct yet seamlessly integrated modelling schemes: i) we first leverage Prior-Knowledge Networks (PKNs) derived from comprehensive and established databases to reconstruct their topology using genomic and transcriptomic data via mathematical programming optimization, ii) we apply causal learning via Additive Noise Models (ANMs) to further prune the optimized networks, and iii) we apply tailored Graph Convolutional Networks (GCNs) to classify each network as a single data point atgraph-level, using Mode of Regulation (MoR) and gene activity profiles as node embeddings. These networks may vary in their biological or molecular annotations, which serves as a labelling scheme for their supervised classification. We demonstrate the framework in the DNA damage and repair pathway using theTP53regulon in a pancancer study, classifying Gene Regulatory Networks (GRNs) across differentTP53mutation types. This scalable approach enables the classification of diverse conditions while addressing the multifactorial nature of diseases. It disentangles their polygenic complexity and reveals new functional patterns through a causal representation.
Spatially informed phenotyping by cyclic-in-situ-hybridization identifies novel fibroblast populations and their pathogenic niches in systemic sclerosis
Authors: Li Yi-Nan , Filla Tim , Györfi Andrea-Hermina , Liang Minrui , Devakumar Veda , Micu Alexandru , Chai Hongtao , Bergmann Christina , Pecher Ann-Christin , Henes Jörg , Moinzadeh Pia , Krieg Thomas , Kreuter Alexander , Schett Georg , Homey Bernhard , Dietrich Sascha , Distler Jörg H.W. , Matei Alexandru-Emil 
Published: December 2024

AbstractSpatially non-resolved transcriptomic data identified functionally distinct populations of fibroblasts in health and disease. However, in-depth transcriptional profilingin situat single-cell resolution has not been possible so far. Here, we studied fibroblast populations in the skin of SSc patients and healthy individuals using cyclic in situ hybridization (cISH) as a novel approach for spatially-resolved transcriptional phenotyping with subcellular resolution. cISH deconvoluted the heterogeneity of 20,979 cells including 3,764 fibroblasts (FB). BANKSY-based spatially-informed clustering identified nine FB subpopulations, with SFRP2+ RetD FB and CCL19+ nonPV FB as novel subpopulations that reside in specific cellular niches and display unique gene expression profiles. SFRP2+ RetD FB and CCL19+ nonPV FB as well as COL8A1+ FB, display altered frequencies in SSc skin and play specific, disease-promoting roles for extracellular matrix release and leukocyte recruitment as revealed by their transcriptional profile, their cellular interactions and ligand-receptor analyses. The frequencies of COL8A1+ FB and their interactions with monocytic cells and B cells are associated with progression of skin fibrosis in SSc. In summary, our spatially-resolved transcriptomic approach identified novel fibroblast subpopulations deregulated in SSc skin with specific pathogenic roles, some of which may potentially serve as biomarkers for progression of skin fibrosis.
Different hydrological conditions after permafrost thaw result in distinct microbial community compositions
Authors: Waqas Muhammad , Liebmann Patrick , Vogel Cordula , Varsadiya Milan , Wang Haitao , Shibistova Olga , Novák Milan , Urich Tim , Guggenberger Georg , Bárta Jiří 
Published: December 2024

AbstractPermafrost degradation leads to the formation of contrasting hydrological conditions such as water-saturated anoxic and dry oxic soils, which significantly influence the bacterial community structure and abundance. To investigate the bacterial abundance and diversity under these hydrological conditions, we collected soil samples from different horizons of both dry and wet degraded permafrost soils and non-degraded intact permafrost soil for comparison. The bacterial alpha diversity, measured by the Observed and Chao1 indices, was significantly greater in wet degraded permafrost soil (wet site) and intact permafrost soil (intact site) than in dry degraded permafrost soils (dry site). Notably, the wet and intact sites exhibited similar levels of alpha diversity as well as shared greater number of zOTUs. The relative proportion of most bacterial taxa was significantly differed among the sites. At the class level, dry site was dominated mainly by K-strategic bacteria like aliphatic degraders (Thermoleophilia), acidophilic and cellulolytic (Acidobacteriae), while wet site was dominated by mainly r-strategic bacteria from class Gammaproteobacteria and anoxygenic aerobic phototrophs (Gemmatimonadetes). According to Spearman correlation analysis, the relative proportion of bacterial taxa in dry and wet sites showed significant correlation with soil physicochemical parameters, whereas fewer correlations were found in intact site. The relative proportion of Pseudomonadota classes and Acidobacteriota were positively correlated with SOC, N, and C:N ratio, but were negatively correlated with pH in both dry and wet sites. In contrast, anaerobic methylotrophs (Methylomirabilota), anoxygenic photoheterotrops (Chloroflexota), Gemmatimonadota and filamentous Actinobacteriota were negatively correlated with SOC, N, and C:N. Additionally, strong correlations were observed between bacterial taxa and extracellular enzyme activities, where Alphaproteobacteria, Gammaproteobacteria, and Acidobacteriota showed positive correlations with both hydrolytic and oxidative enzymes in dry and wet sites, except for PerOx in wet site where they showed negative correlation. Conversely, Gemmatimonadota and Actinobacteriota displayed negative correlations with enzymes in dry and wet site, except for the PerOx in wet site, where they showed positive correlation.
Temporary suspension of mineral phosphorus reduces mobilizable bone zinc in adult laying hens irrespective of the dietary zinc supply
Authors: Lucke Annegret , Weller Agnes , Pokorny Julia , Puntigam Reinhard , Slama Julia , Schedle Karl , Windisch Wilhelm , Brugger Daniel 
Published: December 2024

AbstractThis study examined the effects of short-term dietary zinc (Zn) and phosphorus (P) variations on the mobilizable bone Zn pool and overall Zn status in adult laying hens. Forty-eight hens (50% Lohmann Brown Classic, 50% Lohmann LSL Classic) were housed in pairs (one hen per breed per pen) across 24 pens. The pens were randomly assigned to one of two dietary P levels (0.37% or 0.84% in DM) using a high-protein corn-soybean diet (11.4 MJ AME/kg, 21.5% CP) during a 14-day acclimatization period. Following acclimatization, pens from both P groups were further randomized into four dietary treatments in a 2 × 2 factorial design, varying in P levels (low vs. high) and Zn supplementation (28 vs. 131 mg/kg) over an 8-day experimental feeding phase. Performance metrics, egg production and quality, and tissue mineral concentrations (plasma, liver, bone, and eggs) were measured. Statistical analyses were performed using linear mixed models in SAS 9.4, incorporating random effects of pen nested within treatment group and fixed effects of dietary P, dietary Zn, breed, and their interactions. Tukey-corrected 95% confidence intervals were used to estimate effect differences, with significance set at P < 0.05. Performance metrics, including egg production and body weight, were unaffected by dietary treatments (P > 0.1), indicating no clinical symptoms of Zn deficiency. However, hens on low-Zn diets exhibited significant reductions in plasma Zn concentration (-0.83 mg/L; P = 0.0008) and liver Zn concentration (-6.78 mg/kg DM; P = 0.01), confirming subclinical Zn deficiency. Low-Zn diets also increased the femoral molar Ca:P ratio by 0.15 (P = 0.01), irrespective of dietary P supply. Interestingly, low-P diets led to a significant reduction in femur Zn content (-0.46 mg; P = 0.0009), regardless of Zn supplementation, following 21 days of reduced P feeding. These findings highlight the higher susceptibility of laying hens to phytate antagonism compared to broilers, as evidenced by measurable subclinical Zn deficiency under short-term Zn deprivation. Additionally, a temporary suspension of mineral P supply appeared to impair the mobilizable bone Zn pool. The underlying functional mechanisms driving these interactions remain unclear and warrant further investigation.
Pelagic ecosystem responses to changes in seawater conditions during the Middle Pleistocene Transition in the Eastern Mediterranean
Authors: Agiadi Konstantina , Vasiliev Iuliana , Vite Antoine , Zarkogiannis Stergios , Fuster-Alonso Alba , Mestre-Tomás Jorge , Koskeridou Efterpi , Quillévéré Frédéric 
Published: December 2024

AbstractWe present a multiproxy, ecosystem-level assessment of paleoenvironmental change and its impacts on marine organisms in the Eastern Mediterranean during the Middle Pleistocene Transition, between 923 and 756 kyr B.P. (marine isotope stages MIS 23–18). This study combines analyses of organic biomarkers; organic matter content; carbon and oxygen stable isotopes on bulk sediment, surface-dwelling, deep-dwelling planktonic and benthic foraminifera, ostracods and fish otoliths; as well as foraminiferal, ostracod and sponge abundance estimates, with a statistical assessment of paleoenvironmental regime shifts and estimation of fish distribution depths in the past. Our results show that temperature and productivity played the most important role in driving ecosystem changes in the study area at different times: temperature was the primary driver during MIS 21 interglacial, whereas productivity became a dominant factor in MIS 19 interglacial. In addition, the responses of organisms throughout the water column varied. Both interglacials yielded relatively higher plankton and benthos biomasses. However, for fishes, the responses differed. The abrupt global warming that occurred in early MIS 21, which was also captured by our record, probably led to a reduction in diel vertical migration by mesopelagic fishes and consequently to the efficiency of the biological carbon pump. In contrast, increased productivity across trophic levels is attested for MIS 19 that subsequently dropped in MIS 18, affecting foraminifera, ostracod and sponge biomasses, but not inhibiting fish diel vertical migration. Therefore, we conclude that carbon sequestration during MIS 19 was likely enhanced.
Water-conducting roots responsible for nitrogen uptake in maize (Zea mays)
Authors: Jiang Yutong , Whalen Joann K. 
Published: December 2024

AbstractNitrate (NO3-) uptake is primarily driven by mass flow and varies among maize root types. The importance of embryonic and crown roots in acquiring NO3-was determined here in wet and dry soils. Maize was grown in a split-root pot that segregated the embryonic and crown roots. The soil was moistened to water potentials of either -5kPa or -30kPa. A partial N mass balance was made by destructively sampling shoots, roots, and soils after 0, 24, and 48 h following15N-KNO3injection at the V3 and V6 stages. Gross nitrification was assessed using a15N isotope dilution technique. At the V3 stage, crown roots had 202% more N uptake than embryonic roots in wet soil (-5 kPa). However, in dry soil (-30 kPa), N uptake was similar for embryonic and crown roots, possibly due to an 80% reduction of hydraulic conductance in crown roots. By the V6 stage, crown roots dominated N uptake, with embryonic roots supplying < 20% of N uptake. Soil gross nitrification rate was similar for root types. The present studies indicated that maize NO3-uptake depends primarily on the crown roots, due to their capacity to extract water and NO3-from soil, even under dry conditions.HighlightThis study reveals how different maize root types contribute to nitrate uptake under varying soil moisture conditions, suggesting that soil water management is important to ensure optimal nitrogen uptake.