Scaling read aligners to hundreds of threads on general-purpose processors

Unveiling gut microbiota and metabolic functions contributed to polyvinyl chloride degradation in Spodoptera frugiperda larvae

The accumulation of synthetic plastic waste, particularly polyvinyl chloride (PVC), threatens ecosystems globally. While microbial biodegradation represents a sustainable solution, limited effective PVC-degrading microbial bioresources have been identified. Here, we investigated the gut microbiota of Spodoptera frugiperda larvae, revealing a consistent microbial profile dominated by Enterococcus in both gut contents and tissues. PVC film feeding induced significant microbiota shifts, with functional parallels to PVC powder-fed Tenebrio molitor larvae despite taxonomic divergence. Through enzyme-centric analysis, we found an Enterococcus casseliflavus strain from the gut of S. frugiperda larvae could encode a NAD-dependent oxidoreductase that directly dechlorinates additive-free PVC, representing the first case of enzymatic polymer dechlorination. This enzyme reduced PVC molecular weight (Mn: 12.02 %; Mw: 14.07 %) and notably liberated chloride ions (6.48 mg/L with NADH as a co-factor). Our findings demonstrate the PVC-degrading capacity of S. frugiperda gut microbiota and reveal its dechlorination mechanism, offering an enzymatic candidate for developing novel biocatalysts and engineered microbial strains for enhanced biodegradation. By unravelling insect-associated microbes and enzymes, this work lays a theoretical foundation for their application potentials in sustainable PVC wastes upcycling and microplastic remediation.

Defining three dimensional chromatin structures of pediatric and adolescent B cells using primary B cell and EBV-immortalized B cell reference genomes

BACKGROUND/PURPOSE

Knowledge of the 3D genome is essential to elucidate genetic mechanisms driving autoimmune diseases. The 3D genome is distinct for each cell type, and it is uncertain whether cell lines faithfully recapitulate the 3D architecture of primary human cells or whether developmental aspects of the pediatric immune system require use of pediatric samples. We undertook a systematic analysis of B cells and B cell lines to compare 3D genomic features encompassing risk loci for juvenile idiopathic arthritis (JIA), systemic lupus (SLE), and type 1 diabetes (T1D).

METHODS

We isolated B cells from four healthy individuals, ages 9-17. HiChIP was performed using a CTCF antibody, and CTCF peaks were called within each sample separately. Peaks observed in all four samples were identified. CTCF loops were called within the pediatric samples using three CTCF peak datasets: 1) self-called CTCF consensus peaks called within the pediatric samples, 2) ENCODE's publicly available GM12878 CTCF ChIP-seq peaks, and 3) ENCODE's primary B cell CTCF ChIP-seq peaks from two adult females. Differential looping was assessed within the pediatric samples and each of the three peak datasets.

RESULTS

The number of consensus peaks called in the pediatric samples was similar to that identified in ENCODE's GM12878 and primary B cell datasets. We observed < 1% of loops that demonstrated significantly differential looping between peaks called within the pediatric samples themselves and when called using ENCODE GM12878 peaks. Significant looping differences were even fewer when comparing loops of the pediatric called peaks to those of the ENCODE primary B cell peaks. When querying loops found in juvenile idiopathic arthritis, type 1 diabetes, or systemic lupus erythematosus risk haplotypes, we observed significant differences in only 2.2%, 1.0%, and 1.3% loops, respectively, when comparing peaks called within the pediatric samples and ENCODE GM12878 dataset. The differences were even less apparent when comparing loops called with the pediatric vs ENCODE adult primary B cell peak datasets.

CONCLUSION

The 3D chromatin architecture in B cells is similar across pediatric, adult, and EBV-transformed cell lines. This conservation of 3D structure includes regions encompassing autoimmune risk haplotypes. Thus, even for pediatric autoimmune diseases, publicly available adult B cell and cell line datasets may be sufficient for assessing effects exerted in the 3D genomic space.

Model of metabolism and gene expression predicts proteome allocation in Pseudomonas putida

The genome-scale model of metabolism and gene expression (ME-model) for Pseudomonas putida KT2440, iPpu1676-ME, provides a comprehensive representation of biosynthetic costs and proteome allocation. Compared to a metabolic-only model, iPpu1676-ME significantly expands on gene expression, macromolecular assembly, and cofactor utilization, enabling accurate growth predictions without additional constraints. Multi-omics analysis using RNA sequencing and ribosomal profiling data revealed translational prioritization in P. putida, with core pathways, such as nicotinamide biosynthesis and queuosine metabolism, exhibiting higher translational efficiency, while secondary pathways displayed lower priority. Notably, the ME-model significantly outperformed the M-model in alignment with multi-omics data, thereby validating its predictive capacity. Thus, iPpu1676-ME offers valuable insights into P. putida's proteome allocation and presents a powerful tool for understanding resource allocation in this industrially relevant microorganism.

A standardized framework for robust fragmentomic feature extraction from cell-free DNA sequencing data

Fragmentomics features of cell-free DNA represent promising non-invasive biomarkers for cancer diagnosis. A lack of systematic evaluation of biases in feature quantification hinders the adoption of such applications. We compare features derived from whole-genome sequencing of ten healthy donors using nine library kits and ten data-processing routes and validated in 1182 plasma samples from published studies. Our results clarify the variations from library preparation and feature quantification methods. We design the Trim Align Pipeline and cfDNAPro R package as unified interfaces for data pre-processing, feature extraction, and visualization to standardize multi-modal feature engineering and integration for machine learning.

Fusobacterium nucleatum is enriched in invasive biofilms in colorectal cancer

Fusobacterium nucleatum is an oral bacterium known to colonize colorectal tumors, where it is thought to play an important role in cancer progression. Recent advances in sequencing and phenotyping of F. nucleatum have revealed important differences at the subspecies level, but whether these differences impact the overall tumor ecology, and tumorigenesis itself, remain poorly understood. In this study, we sought to characterize Fusobacteria in the tumor microbiome of a cohort of individuals with CRC through a combination of molecular, spatial, and microbiologic analyses. We assessed for relative abundance of F. nucleatum in tumors compared to paired normal tissue, and correlated abundance with clinical and pathological features. We demonstrate striking enrichment of F. nucleatum and the recently discovered subspecies animalis clade 2 (Fna C2) specifically in colon tumors that have biofilms, highlighting the importance of complex community partnerships in the pathogenesis of this important organism.

Genome-Wide Analysis of DtxR and HrrA Regulons Reveals Novel Targets and a High Level of Interconnectivity Between Iron and Heme Regulatory Networks in Corynebacterium glutamicum

Iron is vital for most organisms, serving as a cofactor in enzymes, regulatory proteins, and respiratory cytochromes. In Corynebacterium glutamicum, iron and heme homeostasis are tightly interconnected and controlled by the global regulators DtxR and HrrA. While DtxR senses intracellular Fe2+, HrrSA is activated by heme. This study provides the first genome-wide analysis of DtxR and HrrA binding dynamics under varying iron and heme conditions using chromatin affinity purification and sequencing (ChAP-Seq). We revealed 25 novel DtxR targets and 210 previously unrecognized HrrA targets. Among these, metH, encoding homocysteine methyltransferase, and xerC, encoding a tyrosine recombinase, were bound by DtxR exclusively under heme conditions, underscoring condition-dependent variation. Activation of metH by DtxR links iron metabolism to methionine synthesis, potentially relevant for the mitigation of oxidative stress. Beyond novel targets, 16 shared targets between DtxR and HrrA, some with overlapping operator sequences, highlight their interconnected regulons. Strikingly, we demonstrate the significance of weak ChAP-Seq peaks that are often disregarded in global approaches, but feature an impact of the regulator on differential gene expression. These findings emphasize the importance of genome-wide profiling under different conditions to uncover novel targets and shed light on the complexity and dynamic nature of bacterial regulatory networks.

Mapping chromatin interactions at melanoma susceptibility loci uncovers distant cis-regulatory gene targets

Genome-wide association studies (GWASs) of melanoma risk have identified 68 independent signals at 54 loci. For most loci, specific functional variants and their respective target genes remain to be established. Capture-HiC is an assay that links fine-mapped risk variants to candidate target genes by comprehensively mapping chromatin interactions. We performed a melanoma GWAS region-focused capture-HiC assay in human primary melanocytes to identify physical interactions between fine-mapped risk variants and potential causal melanoma-susceptibility genes. Overall, chromatin-interaction data alone nominated potential causal genes for 61 of the 68 melanoma risk signals, identifying many candidates beyond those reported by previous studies. We further integrated these data with epigenomic (chromatin state, accessibility), gene expression (expression quantitative trait locus [eQTL]/transcriptome-wide association study [TWAS]), DNA methylation (methylation QTL [meQTL]/methylome-wide association study [MWAS]), and massively parallel reporter assay (MPRA) data generated from melanoma-relevant cell types to prioritize potentially cis-regulatory variants and their respective candidate gene targets. From the set of fine-mapped variants across these loci, we identified 140 prioritized credible causal variants linked to 195 candidate genes at 42 risk signals. In addition, we developed an integrative scoring system to facilitate candidate gene prioritization, integrating melanocyte and melanoma datasets. Notably, at several GWAS risk signals, we observed long-range chromatin connections (500 kb to >1 Mb) with distant candidate target genes. We validated several such cis-regulatory interactions using CRISPR inhibition, providing evidence for known cancer driver genes MDM4 and CBL, as well as the SRY-box transcription factor SOX4, as likely melanoma risk genes.

Immunoregulatory mechanisms and cross-kingdom bacteriostatic effects of microRNAs in crustacean

MicroRNAs (miRNAs) are crucial regulators of gene expression, which contribute to immune response regulation in various organisms, including crustaceans. To investigate the immunoregulatory roles of miRNAs in Portunus trituberculatus, a comparative miRNAomic analysis of Vibrio parahaemolyticus infection was carried out. Through comparative miRNAomic analysis, we identified 17 differentially expressed miRNAs (DE-miRNAs), of which 12 were upregulated. Subsequently, miRNA-mRNA regulatory network analysis revealed that the DE-miRNAs were enriched in immune-related signaling pathways. Within the miRNA-mRNA regulatory network, miRNA novel0045 was identified as a crucial regulator of the tumor necrosis factor (TNF) pathway via targeting the TNF receptor-associated factor 6 gene. This result was corroborated by our RNA interference assay, confirming the significance of miRNA novel0045 in resistance to V. parahaemolyticus infection. Moreover, miRNA novel0294 was noted to possess cross-kingdom regulatory potential, translocating into bacterial cells and directly inhibiting V. parahaemolyticus proliferation. We validated this finding through fluorescence labeling and confocal microscopy, confirming effective internalization and presence of miRNA within bacterial. These results expand the current understanding of miRNA-mediated immune responses in crustaceans, highlighting the roles of miRNAs in host immune defense and cross-kingdom regulatory function in bacterial infection suppression, and have potential implications in the development of RNA-based antimicrobial strategies.

Hydrochar relieved long chain fatty acids (LCFA) inhibition in continuous anaerobic reactor treating food waste

In the anaerobic digestion (AD) process, high concentration of long-chain fatty acids (LCFA) can inhibit the metabolic activities of microorganisms and even cause reactor collapse. The present study showed hydrochar enhanced the methane production from LCFA-inhibited food waste by 37.2 % in a semi-continuous flow anaerobic reactor. Hydrochar not only enhanced the degradation of LCFA, but also promoted the AD of food waste itself. Genome-centric metatranscriptomics showed that the reactor with the addition of hydrochar induced the enrichment of different LCFA-degrading bacteria, thus facilitating the degradation of LCFA. Hydrochar also promoted the enrichment of highly active acidification bacteria, butyrate-oxidizing bacteria and propionate-oxidizing bacteria, as well as acetoclastic methanogens and hydrogenotrophic methanogens. This study provided intrinsic insights into the mechanisms of how hydrochar promoted the AD of LCFA-inhibited food waste, which was of great practical importance for understanding the impact of hydrochar on the actual process of anaerobic treatment of food waste.

ChIP-seq Data Processing and Relative and Quantitative Signal Normalization for Saccharomyces cerevisiae

Chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) is a widely used technique for genome-wide analyses of protein-DNA interactions. This protocol provides a guide to ChIP-seq data processing in Saccharomyces cerevisiae, with a focus on signal normalization to address data biases and enable meaningful comparisons within and between samples. Designed for researchers with minimal bioinformatics experience, it includes practical overviews and refers to scripting examples for key tasks, such as configuring computational environments, trimming and aligning reads, processing alignments, and visualizing signals. This protocol employs the sans-spike-in method for quantitative ChIP-seq (siQ-ChIP) and normalized coverage for absolute and relative comparisons of ChIP-seq data, respectively. While spike-in normalization, which is semiquantitative, is addressed for context, siQ-ChIP and normalized coverage are recommended as mathematically rigorous and reliable alternatives. Key features • ChIP-seq data processing workflow for Linux and macOS integrating data acquisition, trimming, alignment, processing, and multiple forms of signal computation, with a focus on reproducibility. • ChIP-seq signal generation using siQ-ChIP to quantify absolute IP efficiency-providing a rigorous alternative to spike-in normalization-and normalized coverage for relative comparisons. • Broad applicability demonstrated with Saccharomyces cerevisiae (experimental) and Schizosaccharomyces pombe (spike-in) data but suitable for ChIP-seq in any species. • In-depth notes and troubleshooting guide users through setup challenges and key concepts in basic bioinformatics, data processing, and signal computation. Graphical overview Flowchart depicting ChIP-seq data processing steps covered in this protocol.

Genetic variants in the IFNGR2 locus associated with severe chronic Q fever

Q fever is a highly contagious zoonosis capable of causing large outbreaks of important health and economic consequences. Host genetic factors are believed to influence the development of severe chronic Q fever following the infection by the etiological agent, Coxiella burnetii. Targetted next generation sequencing (NGS) was performed in a case-control genetic association study on 53 confirmed Q fever cases, including 38 compatible with acute and 15 with chronic disease, and 29 samples from the general Portuguese population. Four SNPs in the IFNGR2 locus, rs78407108 G > A, rs17879956 C > T, rs7277167 C > T, and rs9974603 C > A, showed a statistically significant association to chronic Q fever, resisting the Bonferroni correction. These belonged to haplotypes significantly associated with chronic Q fever. The individual SNPs are referenced in the GTEx database as possible eQTLs. Given the direct bearing of IFNGR2 on IFN-γ signaling, the possible involvement of the associated variants with higher IFNGR2 expression could be in line with observations suggesting that IFN-γ production in chronic Q fever patients is significantly higher than in healthy controls. Further investigations are required to clarify the role of IFNGR2 signaling in association with chronic Q fever.

ProteoSeeker: A Feature-Rich Metagenomic Analysis Tool for Accessible and Comprehensive Metagenomic Exploration

The vast majority of microbial diversity remains unculturable, limiting access to novel biotechnological resources. Advances in metagenomics have expanded the understanding of microbial communities, yet targeted protein discovery remains challenging. This study introduces ProteoSeeker, a command-line tool for streamlined metagenomic protein identification and annotation. ProteoSeeker operates in two primary modes: i) Seek mode, which screens the proteins according to user-defined protein families, and ii) Taxonomy mode, which uncovers the taxonomy of the host organisms. By automating key steps, ProteoSeeker reduces computational complexity, enabling time-efficient and comprehensive metagenomic analysis for both specialized and nonspecialized users. The efficiency of ProteoSeeker to achieve targeted enzyme discovery is demonstrated by identifying extremophilic enzymes with desired biochemical features, such as amylases for starch hydrolysis and carbonic anhydrases for CO₂ capture applications. By democratizing functional metagenomics, ProteoSeeker is anticipated to accelerate biotechnology, synthetic biology, and biomedical research and innovation.

Effect of fieldwork-friendly coffee blender-based extraction methods and leaf tissue storage on the transcriptome of non-model plants

The adaptation of plants to environmental conditions involves a transcriptional response. "Field transcriptomics" is an emerging concept for studying plants in their natural habitat. However, this term includes studies in which cold storage was possible until further processing in a laboratory. Previous studies proposing onsite RNA extraction methods are limited to descriptions of RNA purity, quantity, and quality, and lack a thorough evaluation of transcriptome quality, and transcriptomic evaluations of RNA storage solutions in plants are, to our knowledge, only available for periods of less than a day. This issue is critical for studying plants in geographically difficult-to-access regions, where keeping the cold chain is unrealistic. In this study, the transcriptome of the non-model plant Helonias orientalis (order: Liliales) was evaluated before and after storage of the leaf tissue for one and fourteen days at 25 °C in RNAlater and TRIzol, respectively. Additionally, field-friendly protocols were similarly evaluated for onsite plant RNA extraction at ambient temperature with lightweight equipment that can run on a portable generator, including a guanidine isothiocyanate-free protocol that is compatible with the polyphenol-rich wild strawberry Fragaria vesca. The quality of the transcriptome assembly after 1-day storage and our optimized onsite methods had similar results to that of the state-of-the-art. However, in terms of differential expression analysis, onsite extraction methods performed better overall than the stored tissue samples. We expect that our onsite RNA extraction methods will provide valuable insights into the transcriptional regulation of plants in areas where research equipment is difficult to access.

Identification of blacklist regions in cattle and pig genomes

Cattle and pigs are important farm animals and biomedical models for studying human development and diseases. Accurate annotation of their cis-regulatory elements is essential for advancing breeding strategies and biological research. Identifying these elements typically relies on ChIP-seq data, which profiles histone modifications and transcription factors. Although some large-scale ChIP-seq projects have decoded functional genomes in cattle and pigs, no comprehensive blacklist identification has been performed. In this study, we systematically identified and evaluated blacklist regions in cattle and pig genomes using the ENCODE pipeline. We annotated 126.8 Mb and 99.9 Mb of blacklist regions in cattle and pigs, respectively. We found that removing these blacklist regions is a critical quality control measure that can enhance the reliability of ChIP-seq analysis. Overall, our results provide a valuable resource for farm animal research, and we propose eliminating these problematic regions to reduce abnormally high signals and improve downstream analyses.

Advances in personalized medicine: translating genomic insights into targeted therapies for cancer treatment

Background

Personalized medicine has revolutionized cancer treatment by utilizing genomic insights to tailor therapies based on individual molecular profiles. This approach enhances therapeutic efficacy, minimizes adverse effects, and addresses tumor heterogeneity through precision-targeted interventions.

Methods

A scoping review was conducted through a comprehensive literature search in PubMed, using MeSH terms and keywords related to genomic profiling and targeted cancer therapies. Eligible studies included original research involving cancer patients who underwent genomic profiling and targeted therapies from January 1, 1950, to February 9, 2025.

Results

Advances in next-generation sequencing (NGS) and bioinformatics have accelerated the identification of clinically relevant mutations-such as epidermal growth factor receptor (EGFR) in non-small cell lung cancer (NSCLC) and BRAF V600E in melanoma-enabling the development of effective targeted therapies. Emerging technologies like clustered regularly interspaced short palindromic repeats (CRISPR) gene editing and artificial intelligence (AI) are further refining treatment selection by enabling more precise and adaptive therapeutic strategies. Despite these innovations, challenges persist regarding data interpretation, equitable access, costs, regulatory frameworks, and integration into routine clinical workflows.

Conclusions

Genomic profiling is central to the advancement of precision oncology. The convergence of genomics, gene editing, and AI is paving the way toward more personalized, efficient, and inclusive cancer care. Realizing the full potential of personalized medicine will require interdisciplinary collaboration, investment in infrastructure, and ethical oversight to ensure broad, equitable, and responsible implementation in clinical practice.

Candidate Genetic Markers of Schizophrenia Based on Exome Sequencing Data and Its Relation to Immunological, Clinical, and Morphometric Changes in the Russian Population

The aim of the study was to identify genetic markers of schizophrenia based on exome sequencing data, as well as to specify its potential relation to clinical manifestations of the disease, morphological changes in the brain and immune disorders.

Materials and Methods

The analyzed sample consisted of 48 patients (23 men and 25 women; average age - 31.5±7.7 years) having a confirmed diagnosis of paranoid schizophrenia.

Results

140 genes with differential polymorphisms and enriched categories that may be related to the pathogenesis of schizophrenia were identified. Analysis of genes with differential frequencies of functionally significant common single nucleotide polymorphisms (SNPs) by their major functions showed that the most common were genes involved in regulation of immune system functions and development of the nervous system, as well as genes being structural components of neurons and glia involved in the perception of sensory stimuli. The findings confirm the complexity of the genetic basis of schizophrenia. Analysis of the top 10 genes containing the most differential polymorphisms specifies such genes related to schizophrenia as MUC12 and SH3KBP1. The genes involved in regulation of the immune response include HLA-DQB2 which is one of the most significantly different SNPs between the group of patients and the general population; HLA-DQB2 SNP (rs9276572) in patients is related to the signs of dysfunction of the antiviral component of immune system, structural changes in the brain and cognitive challenges. Although most of the detected genes are unique to the sample studied, additional studies are required to confirm these genes' involvement in the pathogenesis of this disease as well as to identify the mechanisms of the disease onset and development. The rs9276572(C) polymorphism of HLA-DQB2 requires further study as a new potential marker of immunological disorders, morphometric changes in the brain and cognitive impairment in schizophrenia. The data obtained indicate the need for personalized medicine, because the majority of genetic prerequisites are patient-specific and highlight the importance of further research to understand the genetic aspects of schizophrenia and develop innovative approaches to its diagnosis and treatment.

Screening and transcriptomic analysis of anti-Sporothrix globosa targeting AbaA

Introduction

Sporotrichosis is a fungal disease caused by a complex of Sporothrix schenckii, leading to chronic infections of the epidermis and subcutaneous tissue in both humans and animals.

Methods

Through virtual screening targeting the key gene abaA to screen out the small-molecule drugs to treat Sporotrichosis. To further validate the antifungal activity of small-molecule drugs, growth curves, minimum bactericidal concentration (MBC), and minimum inhibitory concentration (MIC) for Sporothrix globosa (S. globosa) and Sporothrix schenckii (S. schenckii) were measured. In addition, we have done animal experiments to explore the function of the drugs. At the same time, qRT-PCR and transcriptome were used to verify the important role of abaA gene in Sporothrix.

Results

Azelastine and Mefloquine effectively inhibit S. globosa and S. schenckii. MBC, and MIC for S. globosa and S. schenckii confirmed that both Azelastine and Mefloquine inhibited the growth of S. globosa and S. schenckii. Additionally, animal experiments demonstrated that Azelastine and Mefloquine reduced skin lesions in mice; post-treatment observations revealed improvements in inflammatory infiltration and granuloma formation. Through transcriptome analysis and qRT-PCR for validation, our findings demonstrate that the abaA gene plays a crucial role in regulating the attachment of the Sporothrix cell wall to the host matrix and in melanin regulation. Notably, when the abaA gene was inhibited, there was a marked increase in the expression of repair genes. These results emphasize the significance of the abaA gene in the biology of Sporothrix.

Discussion

Two small-molecule drugs exhibit the ability to inhibit Sporothrix and treat sporotrichosis both in vitro and in murine models, suggesting their potential for development as therapeutic agents for sporotrichosis. And qRT-PCR and transcriptome results underscore the significance of the abaA gene in Sporothrix. Our results lay the foundation for the search for new treatments for other mycosis.

Optimization of Mapping Tools and Investigation of Ribosomal RNA Influence for Data-Driven Gene Expression Analysis in Complex Microbiomes

For gene expression analysis in complex microbiomes, utilizing both metagenomic and metatranscriptomic reads from the same sample enables advanced functional analysis. Due to their diversity, metagenomic contigs are often used as reference sequences instead of complete genomes. However, studies optimizing mapping strategies for both read types remain limited. In addition, although transcripts per million (TPM) is commonly used for normalization, few studies have evaluated the influence of ribosomal RNA (rRNA) in metatranscriptomic reads. This study compared Burrows-Wheeler Aligner-Maximal Exact Match (BWA-MEM) and Bowtie2 as mapping tools for metagenomic contigs. Even after optimizing Bowtie2 parameters, BWA-MEM showed higher efficiency in mapping both metagenomic and metatranscriptomic reads. Further analysis revealed that rRNA sequences contaminate predicted protein-coding regions in metagenomic contigs. When comparing TPM values across samples, contamination by rRNA led to an overestimation of TPM changes. This effect was more pronounced when the difference in rRNA content between samples was larger. These findings suggest that metatranscriptomic reads mapped to rRNA should be excluded before TPM calculations. This study highlights key factors influencing read mapping and quantification in gene expression analysis of complex microbiomes. The findings provide insights for improving analytical accuracy and advancing functional studies using both metagenomic and metatranscriptomic data.

Efficiently constructing complete genomes with CycloneSEQ to fill gaps in bacterial draft assemblies

Current microbial sequencing relies on short-read platforms like Illumina and DNBSEQ, which are cost-effective and accurate but often produce fragmented draft genomes. Here, we used CycloneSEQ for long-read sequencing of ATCC BAA-835, producing long-reads with an average length of 11.6 kbp and an average quality score of 14.4. Hybrid assembly with short-reads data resulted in an error rate of only 0.04 mismatches and 0.08 indels per 100 kbp compared to the reference genome. This method, validated across nine species, successfully assembled complete circular genomes. Hybrid assembly significantly enhances genome completeness by using long-reads to fill gaps and accurately assembling multi-copy rRNA genes, unlike short-reads alone. Data subsampling showed that combining over 500 Mbp of short-read data with 100 Mbp of long-read data yields high-quality circular assemblies. CycloneSEQ long-reads improves the assembly of circular complete genomes from mixed microbial communities; however, its base quality needs improving. Integrating DNBSEQ short-reads improved accuracy, resulting in complete and accurate assemblies.

Extrachromosomal DNA replication and maintenance couple with DNA damage pathway in tumors

Extrachromosomal DNA (ecDNA) drives the evolution of cancer cells. However, the functional significance of ecDNA and the molecular components involved in its replication and maintenance remain largely unknown. Here, using CRISPR-C technology, we generated ecDNA-carrying (ecDNA+) cell models. By leveraging these models alongside other well-established systems, we demonstrated that ecDNA can replicate and be maintained in ecDNA+ cells. The replication of ecDNA activates the ataxia telangiectasia mutated (ATM)-mediated DNA damage response (DDR) pathway. Topoisomerases, such as TOP1 and TOP2B, play a role in ecDNA replication-induced DNA double-strand breaks (DSBs). A subset of these elevated DSBs persists into the mitotic phase and is primarily repaired by the alternative non-homologous end joining (alt-NHEJ) pathway, which involves POLθ and LIG3. Correspondingly, ecDNA maintenance requires DDR, and inhibiting DDR impairs the circularization of ecDNA. In summary, we demonstrate reciprocal interactions between ecDNA maintenance and DDR, providing new insights into the detection and treatment of ecDNA+ tumors.

Exploring a Novel Metallophosphoesterase for Polycarbonate Degradation via Transcriptome Analysis

Polycarbonate (PC), a widely used thermoplastic, poses significant environmental challenges due to its persistence and the release of bisphenol A (BPA), a known xenoestrogen. Here, we report the isolation of Bacillus subtilis JNU01 (BsJNU01), capable of utilizing PC as its sole carbon source. Through transcriptomic analysis, we identified metallophosphoesterase from BsJNU01 (BsMPPE), the first reported metallophosphoesterase capable of degrading polycarbonate by catalyzing the hydrolysis of carbonate ester bonds. This enzyme operates under mild aqueous conditions (30 °C, pH 7), releasing 30 μmol of BPA as a monomer and demonstrating effective PC degradation under environmentally friendly conditions. PC biodegradation was confirmed by Fourier transform infrared spectroscopy (FT-IR), nuclear magnetic resonance (NMR), and gas chromatography-mass spectrometry (GC-MS). Furthermore, surface and mechanical analyses revealed significant degradation and structural changes in PC films following BsMPPE treatment, with toughness showing a 40-70 % decrease compared to untreated PC films. This study represents a breakthrough in microbial plastic degradation, establishing a sustainable biocatalytic platform for PC recycling and upcycling technologies.

The Small RNA Landscape in Azoospermia: Implications for Male Infertility and Sperm Retrieval-A Preliminary Study

MicroRNAs (miRNAs), a class of small noncoding RNAs, play a crucial role in spermatogenesis. However, their specific expression patterns in azoospermic patients, particularly in relation to sperm presence and pregnancy outcomes, remain underexplored. We performed small RNA sequencing on forty testicular tissue samples from idiopathic azoospermic and cryptozoospermic patients who underwent testicular sperm extraction (TESE). Differentially expressed (DE) miRNAs were identified across groups with high, rare, or no spermatozoa presence, as well as between individuals with successful and unsuccessful pregnancies following assisted reproduction. Functional enrichment analyses were conducted to assess the biological relevance of miRNA alterations. Our findings revealed distinct miRNA expression patterns linked to sperm presence and pregnancy outcomes. Samples with high sperm presence exhibited reduced miRNA expression, while those with impaired spermatogenesis demonstrated upregulated miRNAs associated with cell survival and differentiation pathways. Several regulatory pathways were also disrupted in samples leading to unsuccessful pregnancies, including the estrogen signaling receptor (ESR) pathway, interleukin-4 and interleukin-13 signaling, and transcription networks. This study highlights miRNA-mediated regulatory differences in azoospermic patients, identifying potential biomarkers for sperm retrieval success and fertility outcomes. Future validation and multi-omics approaches are needed to confirm these findings and enhance male infertility diagnostics.

Resolution of MALDI-TOF compared to whole genome sequencing for identification of Bacillus species isolated from cleanrooms at NASA Johnson Space Center

Introduction

Bacteria are frequently isolated from surfaces in cleanrooms, where astromaterials are curated, at NASA's Lyndon B. Johnson Space Center (JSC). Bacillus species are of particular interest because endospores can endure extreme conditions. Current monitoring programs at JSC rely on culturing microbes from swabs of surfaces followed by identification by 16S rRNA sequencing and the VITEK 2 Compact bacterial identification system. These methods have limited power to resolve Bacillus species. Whole genome sequencing (WGS) is the current standard for bacterial identification but is expensive and time-consuming. Matrix-assisted laser desorption - time of flight mass spectrometry (MALDI-TOF MS), provides a rapid, low-cost, method of identifying bacterial isolates and has a higher resolution than 16S rRNA sequencing, particularly for Bacillus species; however, few studies have compared this method to WGS for identification of Bacillus species isolated from cleanrooms.

Methods

To address this, we selected 15 isolates for analysis with WGS and MALDI-TOF MS. Hybrid next-generation (Illumina) and 3rd-generation (nanopore) sequencing were used to draft genomes. Mass spectra, generated with MALDI-TOF MS, were processed with custom scripts to identify clusters of closely related isolates.

Results

MALDI-TOF MS and WGS identified 13/15 and 9/14 at the species level, respectively, and clusters of species generated from MALDI-TOF MS showed good agreement, in terms of congruence of partitioning, with phylotypes generated with WGS. Pairs of strains that were > 94% similar to each other, in terms of average amino acid identity (AAI) predicted by WGS, consistently showed cosine similarities of mass spectra >0.8. The only discordance was for a pair of isolates that were classified as Paenibacillus species. This pair showed relatively high similarity (0.85) in terms of MALDI-TOF MS but only 85% similarity in terms of AAI. In addition, some strains isolated from cleanrooms at the JSC appeared closely related to strains isolated from spacecraft assembly cleanrooms.

Discussion

Since MALDI-TOF MS costs less than whole genome sequencing and offers a throughput of hundreds of isolates per hour, this approach appears to offer a cost-efficient option for identifying Bacillus species, and related microbes, isolated during routine monitoring of cleanrooms and similar built environments.

Size-dependent ecotoxicological impacts of tire wear particles on zebrafish physiology and gut microbiota: Implications for aquatic ecosystem health

The ecological impact of tire wear particles (TWP), a significant source of microplastics pollution, is increasingly concerning, especially given their potential effects on the health of aquatic ecosystems. This study investigates the size-dependent ecotoxicological responses of zebrafish (Danio rerio) to TWP exposure, focusing on physiological, metabolic, and microbial community impacts over a 15-day exposure period followed by a 15-day excretion period. Through integrated analysis of gut microbiome composition, liver transcriptomics, and host physiological markers, we found that smaller TWP particles (< 120 μm) induced oxidative stress, evidenced by increased SOD and MDA levels, and inhibited growth by reducing body mass and gut length. In contrast, larger TWP particles (250-380 μm) caused more substantial disruptions in lipid and xenobiotic metabolic pathways, as shown by significant downregulation of key metabolic genes (acads, cpt2_1, hadhaa), and alterations in the gut microbiome, including the enrichment of pathogenic genera, such as Enterococcus and Fusobacterium, while depleting beneficial microbes like Acinetobacter and Methyloversatilis. These microbiome shifts led to a more complex and potentially pathogenic gut microbiome. Notably, zebrafish displayed adaptive resilience during the excretion period, with significant recovery in body mass and microbial composition, emphasizing the adaptive capacity of aquatic organisms to pollutants. Our findings underscore the broader ecological risks posed by TWP, the pivotal role of gut microbiota in host resilience to pollutants, and the need for comprehensive management strategies addressing emerging contaminants in aquatic ecosystems.

Origin and stepwise evolution of vertebrate lungs

Lungs are essential respiratory organs in terrestrial vertebrates, present in most bony fishes but absent in cartilaginous fishes, making them an ideal model for studying organ evolution. Here we analysed single-cell RNA sequencing data from adult and developing lungs across vertebrate species, revealing significant similarities in cell composition, developmental trajectories and gene expression patterns. Surprisingly, a large proportion of lung-related genes, coexpression patterns and many lung enhancers are present in cartilaginous fishes despite their lack of lungs, suggesting that a substantial genetic foundation for lung development existed in the last common ancestor of jawed vertebrates. In addition, the 1,040 enhancers that emerged since the last common ancestor of bony fishes probably contain lung-specific elements that led to the development of lungs. We further identified alveolar type 1 cells as a mammal-specific alveolar cell type, along with several mammal-specific genes, including ager and sfta2, that are highly expressed in lungs. Functional validation showed that deletion of sfta2 in mice leads to severe respiratory defects, highlighting its critical role in mammalian lung features. Our study provides comprehensive insights into the evolution of vertebrate lungs, demonstrating how both regulatory network modifications and the emergence of new genes have shaped lung development and specialization across species.

Identification of quantitative trait loci (QTLs) for key cheese making phenotypes in the blue-cheese mold Penicillium roqueforti

Elucidating the genomic architecture of quantitative traits is essential for our understanding of adaptation and for breeding in domesticated organisms. Penicillium roqueforti is the mold used worldwide for the blue cheese maturation, contributing to flavors through proteolytic and lipolytic activities. The two domesticated cheese populations display very little genetic diversity, but are differentiated and carry opposite mating types. We produced haploid F1 progenies from five crosses, using parents belonging to cheese and non-cheese populations. Analyses of high-quality genome assemblies of the parental strains revealed five large translocations, two having occurred via a circular intermediate, one with footprints of Starship giant mobile elements. Offspring genotyping with genotype-by-sequencing (GBS) revealed several genomic regions with segregation distortion, possibly linked to degeneration in cheese lineages. We found transgressions for several traits relevant for cheese making, with offspring having more extreme trait values than parental strains. We identified quantitative trait loci (QTLs) for colony color, lipolysis, proteolysis, extrolite production, including mycotoxins, but not for growth rates. Some genomic regions appeared rich in QTLs for both lipid and protein metabolism, and other regions for the production of multiple extrolites, indicating that QTLs have pleiotropic effects. Some QTLs corresponded to known biosynthetic gene clusters, e.g., for the production of melanin or extrolites. F1 hybrids constitute valuable strains for cheese producers, with new traits and new allelic combinations, and allowed identifying target genomic regions for traits important in cheese making, paving the way for strain improvement. The findings further contribute to our understanding of the genetic mechanisms underlying rapid adaptation, revealing convergent adaptation targeting major gene regulators.

Chromatin landscape in paired human visceral and subcutaneous adipose tissue and its impact on clinical variables in obesity

BACKGROUND

Obesity is a global health challenge and adipose tissue exhibits distinct depot-specific characteristics impacting differentially on the risk of metabolic comorbidities.

METHODS

Here, we integrate chromatin accessibility (ATAC-seq) and gene expression (RNA-seq) data from intra-individually paired human subcutaneous (SAT) and omental visceral adipose tissue (OVAT) samples to unveil depot-specific regulatory mechanisms.

FINDINGS

We identified twice as many depot-specific differentially accessible regions (DARs) in OVAT compared to SAT. SAT-specific regions showed enrichment for adipose tissue enhancers involving genes controlling extracellular matrix organization and metabolic processes. In contrast, OVAT-specific regions showed enrichment in promoters linked to genes associated with cardiomyopathies. Moreover, OVAT-specific regions were enriched for bivalent transcription start site and repressive chromatin states, suggesting a "lingering" regulatory state. Motif analysis identified CTCF and BACH1 as most significantly enriched motifs in SAT and OVAT-specific DARs, respectively. Distinct gene sets correlated with important clinical variables of obesity, fat distribution measures, as well as insulin, glucose, and lipid metabolism.

INTERPRETATION

We provide an integrated analysis of chromatin accessibility and transcriptional profiles in paired human SAT and OVAT samples, offering new insights into the regulatory landscape of adipose tissue and highlighting depot-specific mechanisms in obesity pathogenesis.

FUNDING

SS received EU-Scientia postdoctoral Fellowship and project funding from the European Union's Horizon 2020 Research and Innovation program under the Marie Skłodowska-Curie Grant, (agreement No. 801133). LlCP and TR were supported by Helse Sør-Øst grants to Y.B (ID 2017079, ID 278908). MB received funding from grants from the DFG (German Research Foundation)-Projekt number 209933838-SFB 1052 (project B1) and by Deutsches Zentrum für Diabetesforschung (DZD, Grant: 82DZD00601).

Photoheterotrophic extracellular reduction of ferrihydrite activates diverse intracellular metabolic pathways in Rhodopseudomonas palustris for enhanced antibiotic degradation

Anoxygenic photosynthetic bacteria (APB) have been frequently detected as a photoautotrophic Fe-carbon cycling drivers in photic and anoxic environment. However, the potential capacity of these bacteria for photoheterotrophic extracellular reduction of iron-containing minerals and their impact on the transformation of organic pollutants remain currently unknown. This study investigated the capacity of R. palustris, a purple non-sulfur anoxygenic photosynthetic bacterium, to reduce ferrihydrite (Fh) and its correlation with sulfamethazine (SDZ) degradation were firstly investigated. The results revealed that R. palustris could undergo photoheterotrophic extracellular reduction of Fh to form goethite through direct contact, facilitating the formation of conductive bands and enter the interior of cells with a maximum Fe(II)/Fe(T) ratio of up to 39 % within 8 days which led to 13 % increase in assimilation rate of acetate carbon and 53.2 % increase in SDZ degradation rates, as compared with those by R. palustris alone. Moreover, the intermediates generated during the degradation of SDZ by R. palustris-Fh exhibited relatively lower developmental toxicity compared with the original SDZ molecule. The extracellular reduction of Fh significantly up-regulated the expression of genes related to photosynthetic metabolic enzymes, extracellular electron transporters, and extracellular degrading enzymes in R. palustris. This enhancement promoted the photoheterotrophic metabolism and extracellular secretion of photosensitive active compounds in R. palustris, thereby enhancing both the biodegradation and photosensitive degradation of SDZ.

Clonal memory of colitis accumulates and promotes tumor growth

Chronic inflammation is a well-established risk factor for cancer, but the underlying molecular mechanisms remain unclear. Using a mouse model of colitis, we demonstrate that colonic stem cells retain an epigenetic memory of inflammation following disease resolution, characterized by a cumulative gain of activator protein 1 (AP-1) transcription factor activity. Further, we develop SHARE-TRACE, a method that enables simultaneous profiling of gene expression, chromatin accessibility and clonal history in single cells, enabling high resolution tracking of epigenomic memory. This reveals that inflammatory memory is propagated cell-intrinsically and inherited through stem cell lineages, with certain clones demonstrating dramatically stronger memory than others. Finally, we show that colitis primes stem cells for amplified expression of regenerative gene programs following oncogenic mutation that accelerate tumor growth. This includes a subpopulation of tumors that have exceptionally high AP-1 activity and the additional upregulation of pro-oncogenic programs. Together, our findings provide a mechanistic link between chronic inflammation and malignancy, revealing how long-lived epigenetic alterations in regenerative tissues may contribute to disease susceptibility and suggesting potential therapeutic strategies to mitigate cancer risk in patients with chronic inflammatory conditions.

Functional genomic profiling of O-GlcNAc reveals its context-specific interplay with RNA polymerase II

BACKGROUND

How reversible glycosylation of DNA-bound proteins acts on transcription remains scarcely understood. O-linked β-N-acetylglucosamine (O-GlcNAc) is the only known form of glycosylation modifying nuclear proteins, including RNA polymerase II (RNA Pol II) and many transcription factors. Yet, the regulatory function of the O-GlcNAc modification in mammalian chromatin remains unclear.

RESULTS

Here, we combine genome-wide profiling of O-GlcNAc-modified proteins with perturbations of intracellular glycosylation, RNA Pol II-degron, and super-resolution microscopy. Genomic profiling of O-GlcNAc-modified proteins shows a non-random distribution across the genome, with high densities in heterochromatin regions as well as on actively transcribed gene promoters. Large-scale intersection of the O-GlcNAc signal at promoters with public ChIP-seq datasets identifies a high overlap with RNA Pol II and specific cofactors. Knockdown of O-GlcNAc Transferase (Ogt) shows that most direct target genes are downregulated, supporting a global positive role of O-GlcNAc on the transcription of cellular genes. Rapid degradation of RNA Pol II results in the decrease of the O-GlcNAc levels at promoters encoding transcription factors and DNA modifying enzymes. RNA Pol II depletion also unexpectedly causes an increase of O-GlcNAc levels at a set of promoters encoding for the transcription machinery.

CONCLUSIONS

This study provides a deconvoluted genomic profiling of O-GlcNAc-modified proteins in murine and human cells. Perturbations of O-GlcNAc or RNA Pol II uncover a context-specific reciprocal functional interplay between the transcription machinery and the O-GlcNAc modification.

EBAX-1/ZSWIM8 destabilizes miRNAs, resulting in transgenerational inheritance of a predatory trait

Environmental influences on traits and associated transgenerational epigenetic inheritance have widespread implications but remain controversial and underlying mechanisms poorly understood. We introduce long-term environmental induction experiments on alternative diets in Pristionchus pacificus, a nematode exhibiting mouth-form plasticity including predation, by propagating 110 isogenic lines for 101 generations with associated food-reversal experiments. We found dietary induction and subsequent transgenerational inheritance of the predatory morph and identified a role of ubiquitin ligase EBAX-1/ZSWIM8 in this process. Ppa-ebax-1 mutants are transgenerational inheritance defective, and Ppa-EBAX-1 destabilizes the clustered microRNA family miR-2235a/miR-35. Deletions of a cluster of 44 identical miR-2235a copies resulted in precocious and extended transgenerational inheritance of the predatory morph. These findings indicate that EBAX-1/ZSWIM8 destabilizes miRNAs, resulting in transgenerational inheritance, suggesting a role for target-directed miRNA degradation.

Heart rate variability, daily cortisol indices and their association with psychometric characteristics and gut microbiota composition in an Italian community sample

The microbiota-gut-brain axis is a complex communication system that plays a crucial role in influencing various aspects of our physical and mental health. The goal of this study was to determine the extent to which individual differences in resting measures of vagally-mediated heart rate variability (HRV) and cortisol levels were associated with psychometric and specific gut microbiota characteristics in seventy-five (38 females) healthy individuals. Participants were assessed for vagally-mediated HRV, daily salivary cortisol levels, psychometric characteristics, and gut microbiota composition. Using a categorical approach based on the median split of HRV and cortisol values, we identified an association between low vagally-mediated HRV, greater depressive symptomatology, and altered gut microbiota (e.g., a higher abundance of Prevotella and a smaller abundance of Faecalibacterium, Alistipes, and Gemmiger). This suggests that vagally-mediated HRV may be a useful biomarker of microbiota-gut brain axis function, and that low vagally-mediated HRV may play an important role in the bidirectional link between gut dysbiosis and depression. On the other hand, daily cortisol parameters (e.g., cortisol awakening response, diurnal cortisol slope) were associated either with higher anxiety and perceived stress, or with a specific gut microbiota profile. Therefore, their utility as biomarkers of microbiota-gut-brain axis function needs further scrutiny.

Differential Gene Expression and Unbalanced Homeolog Expression Bias in 4 Million-Year-Old Allopolyploids of Nicotiana Section Repandae

Allopolyploidy, a phenomenon prevalent in angiosperms involving hybridization and whole-genome duplication, results in species with multiple subgenomes, altering genome structure and gene expression, leading to novel phenotypes. Allopolyploids often experience unbalanced homeolog expression bias, the preferential expression of homeologs from one of the two progenitor genomes. To explore the consequences of allopolyploidy and unbalanced homeolog expression bias, we investigate global gene expression and the fate of homeologs in Nicotiana (Solanaceae). We focus on Nicotiana section Repandae, including three allotetraploid species, Nicotiana nudicaulis, N. repanda, and N. stocktonii, derived from diploid progenitors N. sylvestris and N. obtusifolia ∼4.3 Ma. We identify genes with differential expression and investigate expression of candidate genes for flower size variation. Our results show expression differences with the allopolyploids intermediate between the two progenitor species, with a slight bias toward N. obtusifolia. Moreover, we demonstrate unbalanced homeolog expression bias toward the N. obtusifolia subgenome across developmental stages in the allopolyploids, with a stronger bias in N. nudicaulis. In contrast, unbalanced homeolog expression bias shifts toward N. sylvestris for flower size genes in N. nudicaulis, showing that genes involved in particular phenotypes can display different patterns of unbalanced homeolog expression than the overall transcriptome. We also see differential expression of several known flower size genes across corolla developmental stages. Our results highlight the role of unbalanced homeolog expression bias in shaping the evolutionary trajectory of Nicotiana species and provide a foundation for future research into the ecological and evolutionary implications of allopolyploidy in flowering plants.

Loop Catalog: a comprehensive HiChIP database of human and mouse samples

HiChIP enables cost-effective and high-resolution profiling of chromatin loops. To leverage the increasing number of HiChIP datasets, we developed Loop Catalog (https://loopcatalog.lji.org), a web-based database featuring loop calls from 1000+ distinct human and mouse HiChIP samples from 152 studies plus 44 high-resolution Hi-C samples. We demonstrate its utility for interpreting GWAS and eQTL variants through SNP-to-gene linking, identifying enriched sequence motifs and motif pairs, and generating regulatory networks and 2D representations of chromatin structure. Our catalog spans over 4.19M unique loops, and with embedded analysis modules, constitutes an important resource for the field.

Embed-Search-Align: DNA sequence alignment using Transformer models

MOTIVATION

DNA sequence alignment, an important genomic task, involves assigning short DNA reads to the most probable locations on an extensive reference genome. Conventional methods tackle this challenge in two steps: genome indexing followed by efficient search to locate likely positions for given reads. Building on the success of Large Language Models in encoding text into embeddings, where the distance metric captures semantic similarity, recent efforts have encoded DNA sequences into vectors using Transformers and have shown promising results in tasks involving classification of short DNA sequences. Performance at sequence classification tasks does not, however, guarantee sequence alignment, where it is necessary to conduct a genome-wide search to align every read successfully, a significantly longer-range task by comparison.

RESULTS

We bridge this gap by developing a "Embed-Search-Align" (ESA) framework, where a novel Reference-Free DNA Embedding (RDE) Transformer model generates vector embeddings of reads and fragments of the reference in a shared vector space; read-fragment distance metric is then used as a surrogate for sequence similarity. ESA introduces: (i) Contrastive loss for self-supervised training of DNA sequence representations, facilitating rich reference-free, sequence-level embeddings, and (ii) a DNA vector store to enable search across fragments on a global scale. RDE is 99% accurate when aligning 250-length reads onto a human reference genome of 3 gigabases (single-haploid), rivaling conventional algorithmic sequence alignment methods such as Bowtie and BWA-Mem. RDE far exceeds the performance of six recent DNA-Transformer model baselines such as Nucleotide Transformer, Hyena-DNA, and shows task transfer across chromosomes and species.

AVAILABILITY AND IMPLEMENTATION

Please see https://anonymous.4open.science/r/dna2vec-7E4E/readme.md.

Transcriptomic changes across subregions of the primate cerebellum support the evolution of uniquely human behaviors

Background

Compared to other primates, humans display unique behaviors including language and complex tool use. These abilities are made possible in part by the cerebellum. This region of the hindbrain, comprising the flocculus, vermis, and lateral hemispheres, has expanded throughout primate evolution, particularly in great apes. Given the cerebellum's architecture-differing in connectivity, neuron content, and functions across subregions-examining subregional differences is crucial to understanding its evolutionary trajectory.

Results

We performed bulk RNA-seq across samples from six primate species, representing 40-50 million years of evolutionary history, across four subregions of the cerebellum (vermis, flocculus, right lateral hemisphere, left lateral hemisphere). We analyzed changes in gene expression with respect to evolutionary relationships via the Ornstein-Uhlenbeck model and found that, on average, 8.5% of orthologous genes are differentially expressed in humans relative to other non-human primates. Subregion-specific gene expression patterns reveal that the primate lateral hemispheres exhibit significant differences in synaptic activity and glucose metabolism, which in turn are highly implicated in neural processing.

Conclusions

This study provides a novel perspective on gene expression divergences across cerebellar subregions in multiple primate species, offering valuable insights into the evolution of this brain structure. Our findings reveal distinct subregional transcriptomic patterns, with the lateral hemispheres emerging as key sites of divergence across the six primate species. The enrichment of genes related to synaptic activity, glucose metabolism, locomotion, and vocalization highlights the cerebellum's crucial role in supporting the neural complexity underlying uniquely human and other species-specific primate behaviors.

Plasmid conjugation drives within-patient plasmid diversity

Plasmids are well-known vehicles of antimicrobial resistance (AMR) gene dissemination. Through conjugation, plasmid-encoded AMR genes are spread among neighbouring bacteria, irrespective of their strain or even their species. This process is very concerning from a public health perspective, as plasmid-borne AMR gene outbreaks are often not confined to single species or strains and are therefore more difficult to fully uncover. At the moment, the impact of plasmid conjugation on within-patient plasmid diversity is not well understood. In this work, we will tackle the role of conjugation on within-patient plasmid diversity using a dataset of carbapenemase-producing Enterobacterales. The dataset of 256 sequences originates from bacterial isolates cultured from 115 English patients over 30 months. Each patient has more than one sequence, with at least one sequence carrying an OXA-48 gene, a well-known plasmid-borne carbapenemase-encoding gene. If more than one sequence carries the OXA-48 gene, they are carried in different bacterial hosts. Using a hybrid de novo-on-reference assembly pipeline, we were able to reconstruct the full OXA-48 plasmid from short read sequencing data for 232 of the 256 sequences. Of the 115 patients, 83 (72%) patients had an identical OXA-48 plasmid in two or more sequences. Only two patients carried very different (>200 SNPs) alleles of the OXA-48 plasmid, probably from separate acquisitions. Our study shows that when more than one bacterial host carrying an OXA-48 plasmid is found in a patient, it is most likely that the same plasmid has been shared via conjugation. The event of separate acquisition of different plasmids in different bacterial hosts is highly unlikely in our dataset.

Natural variation in promoters of F3'5'H and ANS correlates with catechins diversification in Thea species of genus Camellia

Catechins were diversely accumulated in Thea plants and were crucial for tea flavor, yet the mechanism underlying the diverse catechins distribution in Thea plants remained elusive. We herein collected a total of 19 Thea and 12 non-Thea plants to investigate their catechins distribution and the underlying mechanism. Results showed that the distribution pattern of catechins in cultivated tea plants significantly differs from that of wild relatives. (+)-Gallocatechin gallate (GCG) was detected in over 50% of wild tea plants but was almost undetectable in cultivated tea plants. Conversely, (-)-Epigallocatechin gallate (EGCG) was extensively distributed in tea cultivars but accumulated extremely low in a few wild relatives such as Camellia tetracocca and C. ptilophylla. Expression analysis found that the expression of flavonoid 3',5'-hydroxylase (F3'5'H) was highly correlated with EGCG accumulation in Thea plants. Yeast one-hybrid and luciferase assays showed that CsMYB1, a key catechins regulator, could bind to the promoter of F3'5'H and activate its expression to promote EGCG accumulation in cultivated tea plants; yet it was unable to bind to and activate the promoter of F3'5'H of C. tetracocca due to a 14-bp deletion in the promoter, leading to a low content of EGCG. Results also showed that silencing the expression of anthocyanidin synthase (ANS) enhanced the metabolic flux of catechins toward GCG but not EGCG in tea plants, consistent with the observation of high GCG content in C. ptilophylla with low ANS expression. Overall, the results illustrated the mechanism underlying catechins variation in Thea plants and would help to facilitate the utilization of wild tea plants toward future breeding.

Effect of broccoli sprout extract and baseline gut microbiota on fasting blood glucose in prediabetes: a randomized, placebo-controlled trial

More effective treatments are needed for impaired fasting glucose or glucose intolerance, known as prediabetes. Sulforaphane is an isothiocyanate that reduces hepatic gluconeogenesis in individuals with type 2 diabetes and is well tolerated when provided as a broccoli sprout extract (BSE). Here we report a randomized, double-blind, placebo-controlled trial in which drug-naive individuals with prediabetes were treated with BSE (n = 35) or placebo (n = 39) once daily for 12 weeks. The primary outcome was a 0.3 mmol l-1 reduction in fasting blood glucose compared with placebo from baseline to week 12. Gastro-intestinal side effects but no severe adverse events were observed in response to treatment. BSE did not meet the prespecified primary outcome, and the overall effect in individuals with prediabetes was a 0.2 mmol l-1 reduction in fasting blood glucose (95% confidence interval -0.44 to -0.01; P = 0.04). Exploratory analyses to identify subgroups revealed that individuals with mild obesity, low insulin resistance and reduced insulin secretion had a pronounced response (0.4 mmol l-1 reduction) and were consequently referred to as responders. Gut microbiota analysis further revealed an association between baseline gut microbiota and pathophysiology and that responders had a different gut microbiota composition. Genomic analyses confirmed that responders had a higher abundance of a Bacteroides-encoded transcriptional regulator required for the conversion of the inactive precursor to bioactive sulforaphane. The abundance of this gene operon correlated with sulforaphane serum concentration. These findings suggest a combined influence of host pathophysiology and gut microbiota on metabolic treatment response, and exploratory analyses need to be confirmed in future trials. ClinicalTrials.gov registration: NCT03763240 .

Unraveling phase-dependent variations of viral community, virus-host linkage, and functional potential during manure composting process

The temporal dynamics of bacterial and fungal communities significantly impact the manure composting process, yet viral communities are often underexplored. Bulk metagenomes, viromes, metatranscriptomes, and metabolomes were integrated to investigate dynamics of double-stranded DNA (dsDNA) virus and virus-host interactions throughout a 63-day composting process. A total of 473 viral operational taxonomic units (vOTUs), predominantly Caudoviricetes, showed distinct phase-dependent differentiation. In phase I (initial-mesophilic), viruses targeted Gammaproteobacteria and Firmicutes, utilizing restriction-modification (RM) systems. In phase II (thermophilic-maturing), viruses infected Alphaproteobacteria, Chloroflexi, and Planctomycetes, employing CRISPR-Cas systems. Lysogenic and lytic viruses exerting differential effects on bacterial pathogens across phases. Additionally, six types of auxiliary metabolic genes (AMGs) related to galactose and cysteine metabolisms were identified. The homologous lineages of AMGs with bacterial genes, along with the significant temporal correlation observed between virus-host-metabolite interactions, underscore the critical yet often overlooked role of viral communities in modulating microbial metabolisms and pathogenesis within composting ecosystems.

Estropausal gut microbiota transplant improves measures of ovarian function in adult mice

Decline in ovarian function with age not only affects fertility but is also linked to a higher risk of age-related diseases in women (e.g. osteoporosis, dementia). Intriguingly, earlier menopause is linked to shorter lifespan; however, the underlying molecular mechanisms of ovarian aging are not well understood. Recent evidence suggests the gut microbiota may influence ovarian health. In this study, we characterized ovarian aging associated microbial profiles in mice and investigated the effect of the gut microbiome from young and estropausal female mice on ovarian health through fecal microbiota transplantation. We demonstrate that the ovarian transcriptome can be broadly remodeled after heterochronic microbiota transplantation, with a reduction in inflammation-related gene expression and trends consistent with transcriptional rejuvenation. Consistently, these mice exhibited enhanced ovarian health and increased fertility. Using metagenomics-based causal mediation analyses and serum untargeted metabolomics, we identified candidate microbial species and metabolites that may contribute to the observed effects of fecal microbiota transplantation. Our findings reveal a direct link between the gut microbiota and ovarian health.

Genome-wide CRISPR guide RNA design and specificity analysis with GuideScan2

We present GuideScan2 for memory-efficient, parallelizable construction of high-specificity CRISPR guide RNA (gRNA) databases and user-friendly design and analysis of individual gRNAs and gRNA libraries for targeting coding and non-coding regions in custom genomes. GuideScan2 analysis identifies widespread confounding effects of low-specificity gRNAs in published CRISPR screens and enables construction of a gRNA library that reduces off-target effects in a gene essentiality screen. GuideScan2 also enables the design and experimental validation of allele-specific gRNAs in a hybrid mouse genome. GuideScan2 will facilitate CRISPR experiments across a wide range of applications.

Clonal memory of colitis accumulates and promotes tumor growth

Chronic inflammation is a well-established risk factor for cancer, but the underlying molecular mechanisms remain unclear. Using a mouse model of colitis, we demonstrate that colonic stem cells retain an epigenetic memory of inflammation following disease resolution, characterized by a cumulative gain of activator protein 1 (AP-1) transcription factor activity. Further, we develop SHARE-TRACE, a method that enables simultaneous profiling of gene expression, chromatin accessibility and clonal history in single cells, enabling high resolution tracking of epigenomic memory. This reveals that inflammatory memory is propagated cell-intrinsically and inherited through stem cell lineages, with certain clones demonstrating dramatically stronger memory than others. Finally, we show that colitis primes stem cells for amplified expression of regenerative gene programs following oncogenic mutation that accelerate tumor growth. This includes a subpopulation of tumors that have exceptionally high AP-1 activity and the additional upregulation of pro-oncogenic programs. Together, our findings provide a mechanistic link between chronic inflammation and malignancy, revealing how long-lived epigenetic alterations in regenerative tissues may contribute to disease susceptibility and suggesting potential therapeutic strategies to mitigate cancer risk in patients with chronic inflammatory conditions.

No detectable effect of urbanization on genetic drift or gene flow in specialist herbivorous insects of milkweed

Urbanization is hypothesized to isolate populations and restrict dispersal, leading to reduced genetic diversity and increased genetic differentiation. We tested this hypothesis in specialist herbivorous insects of milkweed, positing that higher dispersal ability would mitigate the negative effects of urbanization on genetic drift and gene flow, and that these effects would vary with city size. In this study, we collected 383 milkweed insects from urban and rural sites in Toronto, Canada, and five surrounding cities. Using ddRADseq, we generated 145,000 SPNs for monarchs, 10,000 SNPs for beetles, 6,000 SNPs for weevils to quantify genetic diversity, demographic history and population genetic structure. Contrary to our hypotheses, our results indicated no effect of urbanization or dispersal ability on diversity or genetic differentiation. Genetic diversity, measured as π, varied between 0.0013 and 0.0044 across species, with no urban vs. rural component, but with monarchs having >2 X higher diversity compared to beetles and weevils. Similarly, genetic differentiation was generally low, FST varying between 0.01 and 0.28, but there are no consistent trends among urban vs. rural samples for any of the three species. However, demographic analyses revealed a consistent decline in effective population size for all three sampled species, beginning around the last glacial maximum and intensifying over the past 1,000 years. Our findings suggest that both urbanization and dispersal ability have not been a major factor in reducing gene flow or increasing genetic drift among milkweed's herbivorous insect populations. Instead, historical events such as climatic change since the last glacial maximum, and large-scale anthropogenic disturbance in general, have had a more pronounced impact on demography. These results highlight the importance of considering the combined effects of natural and anthropogenic long-term historical processes when studying population genetics in the context of urbanization.

A fully phased octoploid strawberry genome reveals the evolutionary dynamism of centromeric satellites

We systematically examine the application of different phasing strategies to decrypt strawberry genome organization and produce a fully phased and accurate reference genome for Fragaria x ananassa cv. "EA78" (2n = 8x = 56). We identify 147 bp canonical centromeric repeats across 50 strawberry chromosomes and uncover the formation of six neocentromeres through centromere turnover. Our findings indicate strawberry genomes have diverged centromeric satellite arrays among chromosomes, particularly across homoeologs, while maintaining high sequence similarity between homologs. We trace the evolutionary dynamics of centromeric repeats and find substantial centromere size expansion in wild and cultivated octoploids compared to the diploid ancestor, F. vesca.

DNA methylation shapes the Polycomb landscape during the exit from naive pluripotency

In mammals, 5-methylcytosine (5mC) and Polycomb repressive complex 2 (PRC2)-deposited histone 3 lysine 27 trimethylation (H3K27me3) are generally mutually exclusive at CpG-rich regions. As mouse embryonic stem cells exit the naive pluripotent state, there is massive gain of 5mC concomitantly with restriction of broad H3K27me3 to 5mC-free, CpG-rich regions. To formally assess how 5mC shapes the H3K27me3 landscape, we profiled the epigenome of naive and differentiated cells in the presence and absence of the DNA methylation machinery. Surprisingly, we found that 5mC accumulation is not required to restrict most H3K27me3 domains. Instead, this 5mC-independent H3K27me3 restriction is mediated by aberrant expression of the PRC2 antagonist Ezhip (encoding EZH inhibitory protein). At the subset of regions where 5mC appears to genuinely supplant H3K27me3, we identified 163 candidate genes that appeared to require 5mC deposition and/or H3K27me3 depletion for their activation in differentiated cells. Using site-directed epigenome editing to directly modulate 5mC levels, we demonstrated that 5mC deposition is sufficient to antagonize H3K27me3 deposition and confer gene activation at individual candidates. Altogether, we systematically measured the antagonistic interplay between 5mC and H3K27me3 in a system that recapitulates early embryonic dynamics. Our results suggest that H3K27me3 restraint depends on 5mC, both directly and indirectly. Our study also implies a noncanonical role of 5mC in gene activation, which may be important not only for normal development but also for cancer progression, as oncogenic cells frequently exhibit dynamic replacement of 5mC for H3K27me3 and vice versa.

Assessing Hybridization-Dependent Off-Target Risk for Therapeutic Oligonucleotides: Updated Industry Recommendations

Hybridization-dependent off-target (OffT) effects, occurring when oligonucleotides bind via Watson-Crick-Franklin hybridization to unintended RNA transcripts, remain a critical safety concern for oligonucleotide therapeutics (ONTs). Despite the importance of OffT assessment of clinical trial ONT candidates, formal guidelines are lacking, with only brief mentions in Japanese regulatory documents (2020) and US Food and Drug Administration (FDA) recommendations for hepatitis B virus treatments (2022). This article presents updated industry recommendations for assessing OffTs of ONTs, building upon the 2012 Oligonucleotide Safety Working Group (OSWG) recommendations and accounting for recent technological advancements. A new OSWG subcommittee, comprising industry experts in RNase H-dependent and steric blocking antisense oligonucleotides and small interfering RNAs, has developed a comprehensive framework for OffT assessment. The proposed workflow encompasses five key steps: (1) OffT identification through in silico complementarity prediction and transcriptomics analysis, (2) focus on cell types with relevant ONT activity, (3) in vitro verification and margin assessment, (4) risk assessment based on the OffT biological role, and (5) management of unavoidable OffTs. The authors provide detailed considerations for various ONT classes, emphasizing the importance of ONT-specific factors such as chemistry, delivery systems, and tissue distribution in OffT evaluation. The article also explores the potential of machine learning models to enhance OffT prediction and discusses strategies for experimental verification and risk assessment. These updated recommendations aim to improve the safety profile of ONTs entering clinical trials and to manage unavoidable OffTs. The authors hope that these recommendations will serve as a valuable resource for ONT development and for the forthcoming finalization of the FDA draft guidance and the International Council for Harmonization S13 guidance on Nonclinical Safety Assessment of Oligonucleotide-Based Therapeutics.

Chromatin accessibility and differentially expressed genes profiling in large yellow croaker (Larimichthys crocea) head kidney cells following iridovirus infection

Introduction

The large yellow croaker iridovirus (LYCIV) poses a significant threat to the aquaculture industry of Larimichthys crocea. Understanding the host defense response to LYCIV infection is crucial for developing effective strategies to mitigate its impact.

Methods

In this study, an epigenetic approach was employed to investigate dynamic changes in chromatin accessibility using the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq). Additionally, RNA sequencing (RNA-seq) was used to analyze the expression pattern of immune response genes upon LYCIV infection.

Results

Substantial alterations in chromatin accessibility were observed, particularly in the regulatory regions of key immune-related genes. Significant changes in the expression of AP-1 transcription factors, including the Batf gene, were noted. CUT&Tag results revealed that AP-1 was significantly enriched in the open chromatin regions of cytokine genes, with Batf potentially regulating the cytokine genes LIF and CLCF1.

Discussion

These findings suggest that AP-1 may play a crucial role in the defense response against viral infection by modulating inflammatory cytokines and contributing to cellular inflammatory responses. This study provides a comprehensive analysis of the epigenomic landscape and gene expression regulation during iridovirus infection in L. crocea, offering valuable insights for breeding programs aimed at combating iridovirus infections.

Comprehensive analysis of the interaction microbiome and prostate cancer: an initial exploration from multi-cohort metagenome and GWAS studies

INTRODUCTION

Prostate cancer is one of the most common cancers in the United States with a high mortality rate. In recent years, the traditional opinion about prostate microbiome was challenged. Although there still are some arguments, an escalating number of researchers are shifting their focus toward the microbiome within the prostate tumor environment.

METHODS

We mined the data of the microbiome extracted from the metagenome, and it offers a broader taxonomic coverage and accurate functional profiling. We used Kraken2, a mapping tool, to mine the gut microbiota of prostate cancer patients. A two-sample Mendelian Randomization was conducted to reflect the association between gut microbiome and cancer.

RESULTS

In the study, we found the consistency of the special intratumor microbiome of both non-metastatic tumors and metastatic tumors. And we dig the gut microbiome in patients with different treatments. We found that some microbiotas may be associated with prostate cancer progression and a special microbiome in metastatic prostate cancer may exist. The anti-androgen therapy can significantly change both the intratumor and gut microbiome.

CONCLUSION

With the progression and metastasis of prostate cancer, some intratumor microbiome changes. And anti-androgen influences both the intratumor and gut microbiome. Our discovery may help researchers further understand the progression, metastasis, and resistance of prostate cancer from the perspective of microbiome level.

ZBTB24 is a conserved multifaceted transcription factor at genes and centromeres that governs the DNA methylation state and expression of satellite repeats

Since its discovery as a causative gene of the Immunodeficiency with Centromeric instability and Facial anomalies syndrome, ZBTB24 has emerged as a key player in DNA methylation, immunity and development. By extensively analyzing ZBTB24 genomic functions in ICF-relevant mouse and human cellular models, we document here its multiple facets as a transcription factor, with key roles in immune response-related genes expression and also in early embryonic development. Using a constitutive Zbtb24 ICF-like mutant and an auxin-inducible degron system in mouse embryonic stem cells, we showed that ZBTB24 is recruited to centromeric satellite DNA where it is required to establish and maintain the correct DNA methylation patterns through the recruitment of DNMT3B. The ability of ZBTB24 to occupy centromeric satellite DNA is conserved in human cells. Together, our results unveiled an essential and underappreciated role for ZBTB24 at mouse and human centromeric satellite repeat arrays by controlling their DNA methylation and transcription status.