bluuebunny/crossref_metadata_2025_split huggingface dataset:
Database Chemistry for Genomics-Based Safety and Quality Evaluation of Biologics
Authors: Ogata Norichika , Matsuda Tomoko , Hosaka Aoi , Shina Akihisa , Hashiba Noriko , Uchida Kazuhisa , Kawabe Yoshinori , Kamihira Masamichi , Yamaoka Takanori , Kurita Hiromu , Yamano-Adachi Noriko , Omasa Takeshi 
Published: February 2025

AbstractGenomics-based safety and quality evaluation studies are advancing the bioindustry by enhancing various aspects, including viral safety, host cell protein (HCP) control, product heterogeneity control, cellular heterogeneity control, and process reproducibility. High-throughput instruments and genome-scale databases are essential in genomics, with the reference genome sequence being the most critical database. The completeness and accuracy of these genome sequences depend on DNA quality, sequencing instruments, read coverage, and assembly strategies. Significant efforts are being made to perfect genome assembly and continuously improve it. However, the quantitative impact of reference genome sequence accuracy on the safety of biologics is not yet fully understood. In this study, we compared and benchmarked six Chinese hamster genomes, including four newly sequenced genomes derived from Chinese hamster cell lines, from an industrial perspective. We also developed database assembly techniques to enhance the safety of biologics. We recommend using two or more independent reference genomes for viral safety studies. For HCP control, we suggest using protein sequences in which trypsin degradation peptides that overlap with high-risk proteins should be masked and unified. Additionally, we can predict microenvironments using single-cell transcriptome data. In bioengineering processes, any nucleotide samples have potential commercial benefits.
Near 100% efficient homology-dependent genome engineering in the human fungal pathogenCryptococcus neoformans
Authors: Nalley Matthew J. , Banerjee Sanjita , Huang Manning Y. , Madhani Hiten D. 
Published: February 2025

ABSTRACTWe recently described CRISPR/Cas9-based short homology-dependent genome engineering in the human fungal pathogenCryptococcus neoformans, a haploid budding yeast that is the most common cause of fungal meningitis and an emerging model organism. This was achieved by electroporation of strains stably expressing a codon-optimized Cas9 with two separate DNA molecules, one encoding a selectable marker flanked by short homology arms and a second encoding a sgRNA under the control of the U6 snRNA promoter. However, the efficiency of desired homology-dependent repair relative to undesired non-homologous end-joining (NHEJ) events can be low and variable. Here, we describe methods and strains enabling extremely efficient (∼99%) homology-dependent genome editing inC. neoformans. This high-efficiency method requires two manipulations. First, we placed the sgRNA-expressing segment into the marker-containing DNA flanked by targeting homology; thus, only a single DNA molecule is introduced into cells. Second, we used a strain mutant for the non-homologous end-joining factor Ku80 (encoded byYKU80). We also report the engineering of ayku80::amdSmutant strain harboring an insertion mutation that can be removed scarlessly via recombination between direct repeats. This enables the functional restoration ofYKU80after homology- dependent genome editing via selection against theamdSmarker using fluoroacetamide. This approach minimizes documented drawbacks of using Ku-defective strains in downstream experiments. Finally, we describe a plasmid series that enables rapid cloning of sgRNA-marker constructs for genomic manipulation ofC. neoformans, including gene deletion and C-terminal tagging. These methods, strains, and plasmids accelerate the genomic manipulation ofC. neoformans.
The Role of Microglia and Complement C5/C5a in the Pathogenesis of Rhegmatogenous Retinal Detachment with Choroidal Detachment
Authors: Xu Huiyan , Wang Qiuhong , Chen Xuan , Huang Qingyu , Xu Shasha , Wu Zhifeng 
Published: February 2025

AbstractBackgroundRhegmatogenous retinal detachment with choroidal detachment (RRDCD) is an uncommon and sight-threatening disorder marked by fast development and significant inflammation. This study aimed to identify cellular and molecular signatures distinguishing RRDCD from typical rhegmatogenous retinal detachment (RRD) and to investigate the roles of microglia and the complement C5/C5a pathway in disease pathogenesis.MethodsSingle-cell RNA sequencing (scRNA-seq) was employed to analyze vitreous samples from patients with RRD and RRDCD, indicating its involvement in blood-retina barrier impairment.ResultsOur findings revealed a distinct cellular landscape in RRDCD, characterized by enhanced connectivity between microglia and dendritic cells, alongside a significant upregulation of the complement C5-C5AR1 interaction. In vitro experiments indicated that treatment with complement C5 promoted microglial proliferation and activation, induced apoptosis in RF/6A endothelial cells, and disrupted tight junctions in ARPE-19 epithelial cells, suggesting a role in blood-retina barrier dysfunction.ConclusionThe findings substantiate the inflammatory hypothesis regarding the pathogenesis of RRDCD, emphasizing the critical functions of microglia and the complement C5/C5a pathway in intensifying retinal inflammation and undermining vascular integrity.
Age- and Virus-Specific Signatures ofIn VitroReconstituted Human Airway Epithelia in the Presence and Absence of Respiratory Viral Infections
Authors: Bellon Mathilde , Alvarez Catia , Buendia Gustavo Ruiz , Sattonnet-Roche Pascale , Dbeissi Damien , Sarmiento Yoann , Kaiser Laurent , Didierlaurent Arnaud , Eckerle Isabella , Essaidi-Laziosi Manel 
Published: February 2025

AbstractWhile Influenza Virus and Respiratory Syncytial Virus (RSV) are considered as a significant health burden in children, Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) causes milder diseases in this age group compared to adults. To investigate the involvement of the upper respiratory tract human airway epithelium (HAE) in this pattern, we established an in-house model of reconstituted HAE cultured in air-liquid interface from nasal swabs of children and adults and characterised it before and afterex vivorespiratory viral infections using focused and unbiased approaches. Fully differentiated paediatric HAE exhibited an increasing induction level of genes related to mucociliary clearance, while higher expression of innate immune pathways was found in the ones from adults. While similar viral replication kinetics in both age groups were shown for SARS-CoV-2, Influenza A Virus (IAV), RSV and Rhinovirus (RV) infection, transcriptomic analysis showed stronger and earlier induction of IFN-related pathways in SARS-CoV-2-infected HAE from children compared to IAV, RSV and RV. IAV and RSV had the weakest innate immune response increase in HAE from children versus adults. RV infection showed an intermediate pattern, resembling SARS-CoV-2 more than RSV or IAV. Our work demonstrates a distinct sensing of SARS-CoV-2 compared to other respiratory virusesex vivo, which may contribute to the milder course of disease in SARS-CoV-2 infected children and argues for a role of early virus-HAE interaction in shaping viral pathogenesis. Furthermore, we show that innate immune responses towards respiratory viruses are virus-specific and differ between age groups. Hence, findings on SARS-CoV-2 cannot be extrapolated to other respiratory viruses.
Adaptive time course of the skeletal muscle proteome during programmed resistance training in rats
Authors: Stead Connor A , Hesketh Stuart J , Thomas Aaron C.Q , Viggars Mark R , Sutherland Hazel , Jarvis Jonathan C , Burniston Jatin G 
Published: February 2025

AbstractResistance training (RT) promotes muscle protein accretion and myofiber hypertrophy, driven by dynamic processes of protein synthesis and degradation. While molecular studies have focused on acute signalling or long-term hypertrophy and strength gains, a critical gap remains in understanding the intermediate processes of muscle adaptation. Acute signalling does not always correlate directly with long-term outcomes, highlighting the need for a time-course analysis of protein abundance and turnover rates. To address this, we utilised deuterium oxide labelling and peptide mass spectrometry to quantify absolute protein content and synthesis rates in skeletal muscle. A daily programmed resistance training regimen was applied to the rat tibialis anterior (TA) via electrical stimulation of the left hind limb for 10, 20, and 30 days (5 sets of 10 repetitions daily). Muscle samples from stimulated (Stim) and contralateral control (Ctrl) limbs were analysed, quantifying 658 protein abundances and 215 protein synthesis rates. Unsupervised temporal clustering of protein responses revealed distinct phases of muscle adaptation, with early (0-10 days) and mid (10-20 days) responses driven by differential protein accretion rates in ribosomal and mitochondrial networks, respectively. These findings suggest that subsets of proteins exhibit distinct adaptation timelines due to variations in translation and/or degradation rates. A deeper understanding of these temporal shifts could improve strategies for optimising muscle growth and functional adaptation to resistance training.
Long-term offspring loss in lactating rats: Neurobiological and emotional consequences in a novel animal model
Authors: Demarchi Luisa , Sanson Alice , Boos Anna-Lena , Bosch Oliver J. 
Published: February 2025

The maternal bond is a vital social connection that supports the survival and well-being of both the caregiver and offspring. Disruption of this bond, particularly following offspring loss, can result in profound trauma with long-lasting consequences. While considerable research has focused on the impact of maternal separation on offspring development, the biological effects of offspring loss on the mother remain largely unexplored. In this study, we examined the long-term effects of offspring loss on neuroplasticity, the oxytocin (OXT) and corticotropin-releasing factor (CRF) systems, and stress-coping behaviors in Sprague-Dawley rat mothers. We compared mothers that experienced one day of motherhood followed by 19 days of offspring loss, mothers that were with their pups throughout the 20 days, and naive virgin rats.Our results reveal that mothers who lost their pups expressed increased oxytocin receptor binding and decreased dendritic spine density in limbic brain regions, with no changes in estrogen receptor α or calbindin cells. Additionally, separated mothers showed increased passive stress-coping behaviors in the forced swim test and elevated plasma corticosterone levels. Remarkably, the passive stress-coping behavior was rescued by central CRF receptor blockade but not by oxytocin treatment, suggesting that the CRF system plays a key role in the grieving process following offspring loss, and highlights the suitability of the rat model for studying maternal grief. This research provides insights into the complex neurobiology of grief, and suggests potential directions for future studies.
Candida albicansgenome adaptation in azole resistant isolates from autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED) patients
Authors: Alwathiqi Faten , Gago Sara , Novak-Frazer Lily , Richardson Riina , Bowyer Paul 
Published: February 2025

AbstractChronic mucocutaneous candidosis due toCandida albicansis frequent in patients with autoimmune polyendocrinopathy candidosis ectodermal dystrophy (APECED). These patients require lifelong antifungal treatment with azoles which might result in the emergence of azole-resistantC. albicansisolates. However, the molecular mechanisms that allowC. albicansto cause disease and adapt to antifungal treatment in these patients in vastly unknown. Here we comparatively analysed the genome sequences and antifungal susceptibility profile of 14C. albicansisolates from the oral cavities of five APECED patients. 14/13C. albicansisolates showed reduced-susceptibly or resistance to fluconazole. Phylogenetic analyses demonstrated that all APECED isolates from individual patients arose from patient-specific lineages. Single nucleotide variants in genes related to homologous DNA repair mechanisms such as meiosis were associated with APECED (p <0.0001). Altogether our data demonstrates that antifungal adaptation ofC. albicansin APECED patients might be associated with polymorphisms in proteins responsible for maintaining DNA repair mechanisms.ImportanceChronic mucocutaneous canididosis (CMC) caused byCandida albicansis common in patients with primary immunodeficiencies such as autoimmune polyendocrinopathy candidosis ectodermal dystrophy (APECED). These patients receive to long-term antifungal therapy thus promoting the emergence of antifungal resistance. Our knowledge about the mechanisms facilitating CMC in patients with APECED is very limited. Here we demonstrated that mostC. albicansisolates from patients with CMC are resistant to azoles and that polymorphisms in genes responsible for maintaining DNA repair mechanisms might facilitate infection.
Long-term innovative potential of genetic research and its suppression
Authors: Chae Junghun , Kim WooJoong , Jung Woochul , Jeong Dawoon , Lim Roktaek , Chamlagain Manoj , Jung Giju , Jang Juneil , Lee Jae Won , Kang Nam Kyu , Baek Kwangryul , Shin Jonghyeok , Lee Ye-Gi , Koh Hyun Gi , Kim Chanwoo , Yook Sangdo , Cheung Allen Ka Loon , Jin Yong-Su , Youn Hyejin , Kim Pan-Jun , Ghim Cheol-Min 
Published: February 2025

AbstractCurrent technological revolutions, involving artificial intelligence, mRNA vaccines, and quantum computing, are largely driven by industry. Despite the existing perception that commercial motives promote cutting-edge innovation, concerns may arise about their risk of limiting scientific exploration from diverse perspectives, which nurtures long-term innovative potential. Here, we investigate the interplay between scientific exploration and industrial influence by analyzing about 20 million papers and US, Chinese, and European patents in genetic research, a domain of far-reaching societal importance. We observe that research on new genes has declined since the early 2000s, but the exploration of novel gene combinations still underpins biotechnology innovation. Fields of highly practical or commercial focus are less likely to adopt the innovative approaches, exhibiting lower research vitality. Additionally, continuous scientific research creates exploratory opportunities for innovation, while industry’s R&D efforts are typically short-lived. Alarmingly, up to 42.2–74.4% of these exploratory opportunities could be lost if scientific research is restrained by industry interests, highlighting the cost of over-reliance on commercially-driven research. Given the industry’s dominance in recent technologies, our work calls for a balanced approach with long-term scientific exploration to preserve innovation vitality, unlock the full potential of genetic research and biotechnology, and address complex global challenges.
The ParB-CTP Cycle Activates Phase Separation in Bacterial DNA Segregation
Authors: Delimi Linda , Revoil Perrine , Rech Jérôme , Bouet Jean-Yves , Walter Jean-Charles 
Published: February 2025

AbstractCell function relies on liquid-like organelles formed through phase transitions, yet the mechanisms ensuring their specificity and rapid assembly remain poorly understood. In bacterial chromosome segregation via the ParABS system, hundreds of ParB proteins are recruited around the centromere-likeparSsequence forming the partition complex. Recent studies have shown that ParB binds CTP and undergoes cycles of binding and unbinding nearparS, however, this accounts for the recruitment of only a small fraction of ParB molecules, leaving its role unclear. Separately, a lattice gas model with fixed interaction energy has been proposed to describe ParB phase separation, but it fails to explain key experimental observations, including the absence of droplets in ParB variants. We reconcile these two perspectives by proposing that the ParB-CTP cycle acts as a molecular switch that enhances ParB-ParB interactions, triggering phase transition from vapor to liquid-like condensates. Our hypothesis is supported by numerical simulations of droplet formation and experiments showing that ParB variants disrupting the CTP cycle fail to undergo phase separation. These findings establish a mechanistic framework for ParB-CTP-mediated phase transitions and may have broader implications for understanding the spatial control of intracellular condensate formation.
Machine Learning-Enhanced Extraction of Protein Signatures of Renal Cell Carcinoma from Proteomics Data
Authors: Liu Hongyi , Ma Zhuo , Lih T. Mamie , Chen Lijun , Hu Yingwei , Wang Yuefan , Sun Zhenyu , Huang Yuanyu , Xu Yuanwei , Zhang Hui 
Published: February 2025

AbstractIn this study, we generated label-free data-independent acquisition (DIA)-based liquid chromatography (LC)-mass spectrometry (MS) proteomics data from 261 renal cell carcinomas (RCC) and 195 normal adjacent tissues (NAT). The RCC tumors included 48 non-clear cell renal cell carcinomas (non-ccRCC) and 213 ccRCC. A total of 219,740 peptides and 11,943 protein groups were identified with 9,787 protein groups per sample on average. We adopted a comprehensive approach to select representative samples with different mutation sites, considering histopathological, immune, methylation, and non-negative matrix factorization (NMF)-based subtypes, along with clinical characteristics (gender, grade, and stage) to capture the complexity and diversity of ccRCC tumors. We used machine learning identified 55 protein signatures that distinguish RCC tumors from NATs. Furthermore, 39 protein signatures that differentiate different RCC tumor subtypes were also identified. Our findings offer an extensive perspective of the proteomic landscape in RCC, illuminating specific proteins that serve to distinguish RCC tumors from NATs and among various RCC tumor subtypes.
THE CORRELATION BETWEEN REDOX ACTIVITY AND ANTIMICROBIAL PROPERTIES OF PYOCYANIN FROMPseudomonas aeruginosa
Authors: Saini Mansi , Das Subrata K , Dharmesh  , Dutt Gaurav , Singh Kishlay Kant , Prakash Divya 
Published: February 2025

ABSTRACTPseudomonas aeruginosa, a metabolically versatile gram-negative bacterium, has garnered attention for its ability to thrive in diverse environments and its capacity to produce pyocyanin, a secondary metabolite with multifunctional properties. Pyocyanin, a redox-active phenazine compound, plays a critical role in mediating the ecological competitiveness ofP. aeruginosathrough its antimicrobial, biofilm-modulating, and reactive oxygen species (ROS)-generating activities. Beyond its contributions to bacterial virulence, pyocyanin demonstrates significant potential in various industrial and biomedical applications due to its redox properties and ability to function under diverse environmental conditions. This study investigates the electrochemical behaviour and pH-dependent antimicrobial activity of pyocyanin to evaluate its applicability in environmental and medical fields. Soil-derivedP. aeruginosaisolates were cultured for pyocyanin (PYO) production, and the pigment was characterized using UV-visible spectroscopy to get its spectral integrity. Electrochemical analysis through cyclic voltammetry revealed enhanced redox activity in acidic environments and stable functionality in alkaline conditions. Antimicrobial assays demonstrated that pyocyanin exhibited optimal activity at neutral to slightly alkaline pH, effectively inhibiting bacterial and fungal growth, while extreme acidic conditions reduced its efficacy.The findings highlight pyocyanin’s versatility as both a redox mediator and an antimicrobial agent. In medical contexts, its pH-sensitive activity aligns well with physiological conditions, offering promise for combating multidrug-resistant pathogens. Future optimization of pyocyanin biosynthesis, particularly through cost-effective and scalable methods, could unlock its full potential in biotechnological and therapeutic innovations.
Deep-learning-based interpolation of longitudinal microbiome data powers biologically informative discovery
Authors: Qu Yixiang , Lyu Ruiqi , Wang Duan , Dai Yifan , Turcan Alistair , Yu Shilin , Xie Jialiu , Roach Jeffrey , Butler Catherine , Yap Pew-Thian , Zhu Hongtu , Dashper Stuart , Ribeiro Apoena Aguiar , Li Didong , Divaris Kimon , Wu Di 
Published: February 2025

AbstractThe human microbiome is a foundational and dynamic foundation for several health-related functions and disease processes. Advances in microbiome sequencing have enabled the characterization of microbial communities in several niches. Longitudinal microbiome studies further strive to discover clinically informative microbial community trajectories. However, these data are fraught with dropout events, high noise, and irregular sampling that limit and prevent the use of many available longitudinal analysis tools. To address these challenges, we introduce Bidirectional GRU-ODE-Bayes (BGOB), a deep learning framework developed for longitudinal microbiome interpolation. BGOB combines bidirectional information flow and ODE-based continuous modeling to jointly interpolate and smoothen trends across individual participants, providing uniform, denoised time intervals across patients. BGOB enables vastly improved performance in differential abundance testing and time-to-event analysis, and makes possible longitudinal analyses requiring uniformity, such as lead-lag detection and temporal clustering. After interpolation, previously low-powered datasets are able to broadly recapitulate known microbiology and elucidate interacting microbial communities. We highlight several associations between microbial taxa and disease, including novel species associated with Early Childhood Caries and disruption of key healthy gut microbiota in Inflammatory Bowel Disease. The BGOB package is publicly available athttps://github.com/Rachel-Lyu/BGOB_n_test.
Macromolecular crystallography at SPring-8 and SACLA
Authors: Yamamoto Masaki , Kumasaka Takashi 
Published: February 2025

Since the groundbreaking determination of the first protein crystal structure by J. C. Kendrew in 1959, macromolecular crystallography (MX) has remained at the forefront of structural biology, driven by continuous technological advancements. The advent of synchrotron radiation in the 1990s revolutionized the field, enhancing data quality, introducing novel phasing methods, and broadening the scope of target samples to include membrane proteins and supramolecular complexes. In 1997, Japan inaugurated SPring-8, one of the world's largest third-generation synchrotron radiation facilities. With its high-brilliance radiation from insertion devices, SPring-8 has dramatically increased the capability of MX. This paper describes MX's evolution, current developments, and prospects at SPring-8 and SACLA.