Accurate identification of structural variations from cancer samples.

Structural variations (SVs) are commonly found in cancer genomes. They can cause gene amplification, deletion and fusion, among other functional consequences. With an average read length of hundreds of kilobases, nano-channel-based optical DNA mapping is powerful in detecting large SVs. However, existing SV calling methods are not tailored for cancer samples, which have special properties such as mixed cell types and sub-clones. Here we propose the Cancer Optical Mapping for detecting Structural Variations (COMSV) method that is specifically designed for cancer samples. It shows high sensitivity and specificity in benchmark comparisons. Applying to cancer cell lines and patient samples, COMSV identifies hundreds of novel SVs per sample.

Elucidating the ecophysiology of soybean pod-sucking stinkbug Riptortus pedestris (Hemiptera: Alydidae) based on de novo genome assembly and transcriptome analysis.

Food security is important for the ever-growing global population. Soybean, Glycine max (L.) Merr., is cultivated worldwide providing a key source of food, protein and oil. Hence, it is imperative to maintain or to increase its yield under different conditions including challenges caused by abiotic and biotic stresses. In recent years, the soybean pod-sucking stinkbug Riptortus pedestris has emerged as an important agricultural insect pest in East, South and Southeast Asia. Here, we present a genomics resource for R. pedestris including its genome assembly, messenger RNA (mRNA) and microRNA (miRNA) transcriptomes at different developmental stages and from different organs. As insect hormone biosynthesis genes (genes involved in metamorphosis) and their regulators such as miRNAs are potential targets for pest control, we analyzed the sesquiterpenoid (juvenile) and ecdysteroid (molting) hormone biosynthesis pathway genes including their miRNAs and relevant neuropeptides. Temporal gene expression changes of these insect hormone biosynthesis pathways were observed at different developmental stages. Similarly, a diet-specific response in gene expression was also observed in both head and salivary glands. Furthermore, we observed that microRNAs (bantam, miR-14, miR-316, and miR-263) of R. pedestris fed with different types of soybeans were differentially expressed in the salivary glands indicating a diet-specific response. Interestingly, the opposite arms of miR-281 (-5p and -3p), a miRNA involved in regulating development, were predicted to target Hmgs genes of R. pedestris and soybean, respectively. These observations among others highlight stinkbug's responses as a function of its interaction with soybean. In brief, the results of this study not only present salient findings that could be of potential use in pest management and mitigation but also provide an invaluable resource for R. pedestris as an insect model to facilitate studies on plant-pest interactions.

Terpenes and Terpenoids in Plants: Interactions with Environment and Insects.

The interactions of plants with environment and insects are bi-directional and dynamic. Consequently, a myriad of mechanisms has evolved to engage organisms in different types of interactions. These interactions can be mediated by allelochemicals known as volatile organic compounds (VOCs) which include volatile terpenes (VTs). The emission of VTs provides a way for plants to communicate with the environment, including neighboring plants, beneficiaries (e.g., pollinators, seed dispersers), predators, parasitoids, and herbivores, by sending enticing or deterring signals. Understanding terpenoid distribution, biogenesis, and function provides an opportunity for the design and implementation of effective and efficient environmental calamity and pest management strategies. This review provides an overview of plant-environment and plant-insect interactions in the context of terpenes and terpenoids as important chemical mediators of these abiotic and biotic interactions.

Machine learning prediction of hepatic steatosis using body composition parameters: A UK Biobank Study.

Non-alcoholic fatty liver disease (NAFLD) has emerged as the most prevalent chronic liver disease worldwide, yet detection has remained largely based on surrogate serum biomarkers, elastography or biopsy. In this study, we used a total of 2959 participants from the UK biobank cohort and established the association of dual-energy X-ray absorptiometry (DXA)-derived body composition parameters and leveraged machine learning models to predict NAFLD. Hepatic steatosis reference was based on MRI-PDFF which has been extensively validated previously. We found several significant associations with traditional measurements such as abdominal obesity, as defined by waist-to-hip ratio (OR = 2.50 (male), 3.35 (female)), android-gynoid ratio (OR = 3.35 (male), 6.39 (female)) and waist circumference (OR = 1.79 (male), 3.80 (female)) with hepatic steatosis. Similarly, A Body Shape Index (Quantile 4 OR = 1.89 (male), 5.81 (female)), and for fat mass index, both overweight (OR = 6.93 (male), 2.83 (female)) and obese (OR = 14.12 (male), 5.32 (female)) categories were likewise significantly associated with hepatic steatosis. DXA parameters were shown to be highly associated such as visceral adipose tissue mass (OR = 8.37 (male), 19.03 (female)), trunk fat mass (OR = 8.64 (male), 25.69 (female)) and android fat mass (OR = 7.93 (male), 21.77 (female)) with NAFLD. We trained machine learning classifiers with logistic regression and two histogram-based gradient boosting ensembles for the prediction of hepatic steatosis using traditional body composition indices and DXA parameters which achieved reasonable performance (AUC = 0.83-0.87). Based on SHapley Additive exPlanations (SHAP) analysis, DXA parameters that had the largest contribution to the classifiers were the features predicted with significant association with NAFLD. Overall, this study underscores the potential utility of DXA as a practical and potentially opportunistic method for the screening of hepatic steatosis.

Roles and occurrences of microbiota in the osmoregulatory organs, gills and gut, in marine medaka upon hypotonic stress.

Gills and gut are the two primary osmoregulatory organs in fish. Recently, studies have expanded beyond the osmoregulatory mechanisms of these organs to explore the microbiota communities inhabiting them. It is now known that microbial communities in both organs shift in response to osmotic stress. However, there are limited studies identifying the major contributors and co-occurrence among these microbiota in both organs under seawater and freshwater transfer conditions. The current data mining report performed a bioinformatics analysis on two previous published datasets from our group, aiming to provide insights into host-bacteria relationships under osmotic stress. We divided the samples into four groups: control seawater gills (LSW); control seawater gut (TSW); freshwater transfer gills (LFW); and freshwater transfer gut (TFW). Our results showed that LSW had higher diversities, richness, and evenness compared to TSW. However, both the LFW and LSW did not show any significant differences after the freshwater transfer experiment. We further applied co-occurrence network analysis and, for the first time, reported on the interactions of taxa shaping the community structure in these two organs. Moreover, we identified enriched ectoine biosynthesis in seawater samples, suggesting its potential role in seawater environments. Increased mRNA expression levels of Na+/K+-atpase, and cftr, were observed in gills after 6 h of ectoine treatment. These findings provide a foundation for future studies on host-bacteria interactions under osmotic stress.

Insights from metabolomics and transcriptomics studies on Perfluorohexanesulfonic acid (PFHxS) exposed zebrafish embryos.

Perfluorohexanesulfonic acid (PFHxS) is a short-chain perfluoroalkyl substance widely used to replace the banned perfluorooctanesulfonic acid (PFOS) in various industrial and household products. It can be found in the environment and human bodies; however, its potential toxicities are not well studied. Zebrafish have been extensively used as a model for studying toxicants, and currently, two studies have reported on the toxicity of PFHxS in zebrafish from different approaches. Ulhaq and Tse (J Hazard Mater. 2023; 457: 131722) conducted general biological experiments and applied transcriptomics to demonstrate that PFHxS at a concentration of 5 µM could affect glucose and fatty acid metabolism, leading to oxidative stress, developmental defects, and cell cycle arrest. Xu et al. (Sci Total Environ. 2023; 887: 163770) employed metabolomics and showed that concentrations of various metabolites changed after exposure to 3 and 10 µM PFHxS. As we observed a match between the metabolomics data and our biochemistry experimental findings, we integrated the two studies, which enabled us to unfold the possible mechanism of the deregulated metabolites. We identified 22 differential expressed genes (DEGs) in the tricarboxylic acid (TCA) cycle, 17 DEGs in glcyolytic process, including the critical glucokinase under the carbon metabolism. Besides, genes likes aldehyde dehydrogenases, and histone-lysine N-methyltransferases that participate in lipid peroxidation and amino metabolism respectively were spotted. Lastly, we further strengthen our discoveries by undergoing the gene set enrichment analysis. This article could provide insights into the toxicity of PFHxS, as well as prospects for environmental studies.

Integrated Omics Approaches Revealed the Osmotic Stress-Responsive Genes and Microbiota in Gill of Marine Medaka.

Aquatic fishes face osmotic stress continuously, and the gill is the first tissue that senses and responds to the external osmotic challenges. However, the understandings of how the gill microbiota could respond to osmotic stress and their potential host-bacterium relationships are limited. The objectives of the current study are to identify the hypotonic responsive genes in the gill cells and profile the gill microbiota communities after fresh water transfer experiment via transcriptome sequencing and 16S rRNA gene sequencing. Transcriptome sequencing identified 1,034 differentially expressed genes (DEGs), such as aquaporin and sodium potassium chloride cotransporter, after the fresh water transfer. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis further highlighted the steroid biosynthesis and glycosaminoglycan biosynthesis pathways in the gill. Moreover, the 16S rRNA gene sequencing identified Vibrio as the dominant bacterium in the seawater, which changed to Pseudomonas and Cetobacterium after the fresh water transfer. The alpha diversity analysis suggested that the gill bacterial diversity was lower in the fresh water transferred group. The KEGG and MetaCyc analysis further predicted the alteration of the glycosaminoglycan and chitin metabolisms in the gill bacteria. Collectively, the common glycosaminoglycan and chitin pathways in both the gill cells and gill microbiota suggest the host-bacterium interaction in gill facilitates the fresh water acclimation. IMPORTANCE This is the first study using the transcriptome and 16S rRNA gene sequencing to report the hypotonic responsive genes in gill cells and the compositions of gill microbiota in marine medaka. The overlapped glycosaminoglycan- and chitin-related pathways suggest host-bacterium interaction in fish gill during osmotic stress.

Hypoxia-induced epigenetic transgenerational miRNAs dysregulation involved in reproductive impairment of ovary.

Hypoxia is a potent endocrine disruptor that is posing serious problems to the fish reproductive systems. Our previous studies reported that hypoxia could cause a transgenerational impairment of ovarian development and interfere hatching success in F2 offspring of marine medaka fish (Oryzias melastigma) through epigenetic regulation. As part of the epigenetic regulation, we investigated the involvement of microRNAs (miRNAs) in hypoxia-induced transgenerational reproductive impairments. In the present study, we used comparative small RNA sequencing to reveal that hypoxia caused miRNA dysregulation in ovaries of F0 hypoxia group and F2 transgenerational group. We found 4 common dysregulated miRNA in the F0 and F2 generations. Furthermore, integrated miRNA-mRNA analysis, followed by gene ontology enrichment analysis on the hypoxia-dysregulated miRNA-target genes further highlighted the importance of these dysregulated miRNAs in biological processes related to reproduction. More importantly, we identified 3 miRNA-mRNA pairs (novel miRNA-525-DIAPH2, novel miRNA-525-MYOCD, and novel miRNA-525-RAI14) that might play epigenetic roles in hypoxia-induced reproductive impairment. For the first time, our findings suggested the involvement of miRNA in hypoxia-induced reproductive impairments may be inherited via a transgenerational manner.

Osmotic Gradient Is a Factor That Influences the Gill Microbiota Communities in Oryzias melastigma.

The fish gill is the first tissue that is exposed to the external media and undergoes continuous osmotic challenges. Recently, our group published an article entitled "Integrated Omics Approaches Revealed the Osmotic Stress-Responsive Genes and Microbiota in Gill of Marine Medaka" in the journal mSystems (e0004722, 2022), and suggested the possible host-bacterium interaction in the fish gill during osmotic stress. The previous study was performed by the progressive fresh water transfer (i.e., seawater to fresh water transfer via 50% seawater (FW)). Our group hypothesized that osmotic gradient could be a factor that determines the microbiota communities in the gill. The current 16S rRNA metagenomic sequencing study found that the direct transfer (i.e., seawater to fresh water (FWd)) could result in different gill microbiota communities in the same fresh water endpoints. Pseduomonas was the dominant bacteria (more than 55%) in the FWd gill. The Kyoto Encyclopedia of Genes and Genomes and MetaCyc analysis further suggested that the FWd group had enhanced osmosensing pathways, such as the ATP-binding cassette transporters, taurine degradation, and energy-related tricarboxylic acid metabolism compared to the FW group.

A CAZyme-Rich Genome of a Taxonomically Novel Rhodophyte-Associated Carrageenolytic Marine Bacterium.

Carbohydrate-active enzymes (CAZymes) have significant biotechnological potential as agents for degradation or modification of polysaccharides/glycans. As marine macroalgae are known to be rich in various types of polysaccharides, seaweed-associated bacteria are likely to be a good source of these CAZymes. A genomics approach can be used to explore CAZyme abundance and diversity, but it can also provide deep insights into the biology of CAZyme producers and, in particular, into molecular mechanisms that mediate their interaction with their hosts. In this study, a Gram-negative, aerobic, rod-shaped, carrageenolytic, and culturable marine bacterium designated as AOL6 was isolated from a diseased thallus of a carrageenan-producing farmed rhodophyte, Kappaphycus alvarezii (Gigartinales, Rhodophyta). The whole genome of this bacterium was sequenced and characterized. Sequence reads were assembled producing a high-quality genome assembly. The estimated genome size of the bacterium is 4.4 Mb and a G+C content of 52%. Molecular phylogenetic analysis based on a complete sequence of 16S rRNA, rpoB, and a set of 38 single-copy genes suggests that the bacterium is an unknown species and represents a novel genus in the family Cellvibrionaceae that is most closely related to the genera Teredinibacter and Saccharophagus. Genome comparison with T. turnerae T7901 and S. degradans 2-40 reveals several features shared by the three species, including a large number of CAZymes that comprised > 5% of the total number of protein-coding genes. The high proportion of CAZymes found in the AOL6 genome exceeds that of other known carbohydrate degraders, suggesting a significant capacity to degrade a range of polysaccharides including κ-carrageenan; 34% of these CAZymes have signal peptide sequences for secretion. Three putative κ-carrageenase-encoding genes were identified from the genome of the bacterium via in silico analysis, consistent with the results of the zymography assay (with κ-carrageenan as substrate). Genome analysis also indicated that AOL6 relies exclusively on type 2 secretion system (T2SS) for secreting proteins (possibly including glycoside hydrolases). In relation to T2SS, the product of the pilZ gene was predicted to be highly expressed, suggesting specialization for cell adhesion and secretion of virulence factors. The assignment of proteins to clusters of orthologous groups (COGs) revealed a pattern characteristic of r-strategists. Majority of two-component system proteins identified in the AOL6 genome were also predicted to be involved in chemotaxis and surface colonization. These genomic features suggest that AOL6 is an opportunistic pathogen, adapted to colonizing polysaccharide-rich hosts, including carrageenophytes.