Search

The mitochondrial genome of Metazoa is predominantly maternally inherited, providing a valuable genetic marker in various fields such as phylogenetics and phylogeography. However, mitochondrial heteroplasmy, where multiple copies of mitochondrial DNA (mtDNA) coexist within an individual or even cell, presents a challenge to the use of mtDNA markers. This phenomenon may arise from replication errors, mutagenic processes, or paternal leakage. In this study, we investigated mitochondrial heteroplasmy in the freshwater bug Aphelocheirus aestivalis (Fabricius, 1794) using both Sanger and Illumina sequencing approaches. Our analyses confirmed the presence of diverse mtDNA variants within individual specimens collected from various locations across Europe. Signals of mitochondrial heteroplasmy were observed in chromatograms derived from both female and male individuals, indicating a prevalent phenomenon across A. aestivalis populations in general. Further comparative analyses of COI (partial cytochrome c oxidase subunit I) haplotypes indicated their high similarity and complex phylogenetic relationships. In turn, Illumina sequencing of a single male specimen revealed 102 heteroplasmic sites across the protein-coding sequences of mitogenome. Our results suggest the widespread and heritable nature of mitochondrial heteroplasmy in A. aestivalis, highlighting its importance for future phylogenetic and phylogeographic studies. [ABSTRACT FROM AUTHOR]

Converting crop residues into biochar and subsequently incorporating it into soils is a promising strategy to improve carbon sequestration in agroecosystems. However, differences in the potential mechanisms for soil organic carbon (SOC) accumulation between biochar and its feedstock materials remain unclear. This study performed a nine-year field experiment involving four treatments in a Mollisol: mineral fertilizers alone and combined with maize straw or its biochar, and control without fertilizers and amendments. The main objectives of this study were to assess how straw and biochar incorporation influence SOC content, SOC chemical composition, microbial necromass carbon (MNC) content, and microbial community characteristics. Compared with mineral fertilizers alone, straw and biochar significantly (P < 0.05) increased SOC content, while biochar (40.5% increase) had more pronounced effects than straw (23.7% increase). Similarly, both straw and biochar increased MNC content and boosted microbial biomass, but straw had a more pronounced impact than did biochar. Additionally, biochar markedly increased SOC aromaticity by 26.6% (P < 0.05), while straw reduced SOC aromaticity by 2.85% (P > 0.05). Fungi, rather than bacteria, played a more crucial role in increasing SOC content through their necromass inputs under both straw and biochar incorporation. Our results demonstrated that straw enhanced SOC accumulation primarily through entombing effect of microbial necromass, while biochar enhanced SOC accumulation primarily through biochemical protection from recalcitrant aromatic carbon. The present findings provide valuable insight into the potential mechanisms of field practices that lead to maximize soil carbon sequestration. Highlights: SOC accumulation mechanism was distinct in Mollisol with MS and MSB amendments. Entombing effect from microbial necromass devoted more to SOC accumulation in MS-amended soil. Biochemical protection via aromatic carbon contributed more to SOC accumulation in MSB-amended soil. SOC was mainly governed by fungal rather than bacterial necromass in MS- and MSB-amended soil. [ABSTRACT FROM AUTHOR]

Background: Aconitum is an important medicinal genus widely used in traditional Chinese medicine, which produces types of diterpenoid alkaloids (DA) among different species. We performed whole genome resequencing (WGS) research in Aconitum spp., and wish to find diterpenoid alkaloids related genetic variations. Results: In this study, we re-sequenced 150 Aconitum vilmorinianum (A. vilmorinianum) including 102 from the cultivation garden and 48 from the wild, as well as nine wild samples of Aconitum weixiense. The intra-population differentiation of A. vilmorinianum was detected by evolutionary tree and population structure inference. We identify 47 DA biosynthesis genes that might be highly associated with the specialization of DA based on whole-genome resequencing. Of 616 significant SNPs and 105 significant InDels among these genes could be developed as polymorphic molecular markers capable of effectively recognizing A. vilmorinianum from A. weixiense. Furthermore, the significant SNPs and InDels were almost homozygous alternates in A. weixiense, whereas they tended to be homozygous references in the A. vilmorinianum. Conclusions: Our results discussed the difference in genetic background in A. vilmorinianum compared to A. weixiense and these high-quality DA biosynthesis-associated polymorphic locus provided useful genetic information for discrimination of A. vilmorinianum and could serve as a vehicle to study the mechanism of DA differentiation in Aconitum. [ABSTRACT FROM AUTHOR]

Severe fever with thrombocytopenia syndrome (SFTS), a tick-borne emerging infectious disease caused by SFTS virus (SFTSV), is a growing public health threat due to its high mortality rate. To understand the genomic characteristics of SFTSV samples isolated in Huzhou, China, the full-length genomes of Huzhou SFTSV isolates obtained between February 1, 2019 and December 30, 2023 were sequenced, and the gene loci, evolution, and sequence identity of the genome sequences were analyzed using MEGA. The complete genome sequences of seven SFTSV samples were obtained successfully. The full-length genome of each isolate was 11 490 bp in length, composed of a large (L) segment of 6368 bp, medium (M) segment of 3378 bp, and small (S) segment of 1744 bp. The SFTSV samples isolated in Huzhou belonged to multiple genotypes, but were mainly of type D. Each subtype showed nucleotide sequence and amino acid sequence identities of more than 93.67% and 97.18%, respectively, with the syngeneic human host reference strain and more than 93.67% and 97.76%, respectively, with the syngeneic tick-derived host reference strain. Nucleotide sequence analysis of SFTSV isolates from Huzhou showed mutations in genes on all three segments, with those on the M segment showing the highest mutation rate. The nucleotide variations were mainly base transversions. Further studies of the distribution of SFTSV genotypes, sites of nucleotide mutations, and amino acid variations are required. [ABSTRACT FROM AUTHOR]

Species delimitation is essential to study and conserve biological diversity. It is traditionally based on morphological trait variation observed in one or a few specimens. Nevertheless, such assessments may not sufficiently take intraspecific trait variation into account, misidentifying morphotypes as separate species. The use of high-throughput sequencing data alongside morphological data in taxonomic studies may substantially improve the accuracy of taxonomic assessments. The Musa genus, commonly known for comprising the wild relatives of banana varieties, consists of about seventy described species. However, the taxonomic status of multiple Musa species is uncertain due to typification errors and the lack of high-quality specimens. The species M. splendida and M. viridis from northern Viet Nam only substantially differ from each other in the color of their male flower bracts, which is red to pinkish-red in M. splendida and pink in M. viridis. Consequently, their taxonomic status as separate species has been debated. Here, we studied the genetic relationships between 121 M. splendida and M. viridis plants using high-throughput sequencing data (DArTseq) in which we identified 51,188 single nucleotide polymorphisms. We found that individuals genetically clustered in a principal component analysis (6 clusters), fastStructure analysis (four groups), and ASTRAL-III consensus phylogenetic tree (nine clades) based on their population origin rather than by their taxon identity. In addition, a strong signal for an isolation-by-distance pattern between populations was observed. Plants identified as M. viridis were more closely related to M. splendida plants from the same region than to M. viridis plants from other regions. Hence, we propose to treat M. viridis as a synonym of M. splendida. [ABSTRACT FROM AUTHOR]

Copyright of Shipin Kexue/ Food Science is the property of Food Science Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Shipin Kexue/ Food Science is the property of Food Science Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Wiskott-Aldrich syndrome (WAS) (MIM #301000) is a rare X-linked primary immunodeficiency due to mutations in the WAS gene, characterized by thrombocytopenia with small platelets, eczema, recurrent infections, and an increased incidence of autoimmunity and malignancies. A wide spectrum of mutations has been identified in the WAS gene responsible for a broad variety of clinical phenotypes. By using targeted next-generation sequencing (t-NGS), we identified in a 2-month-old boy with thrombocytopenia and immunological alterations a 4-nucleotide deletion from position +3 to +6 of intron 8 (c.777 + 3_777 + 6delGAGT) of WAS , currently classified on ClinVar as a variant of uncertain significance. The in-vitro characterization of the variant revealed the complete retention of intron 8 in the mature transcript, suggesting a splicing defect due to the loss of a splice donor site at the 5′-end of intron 8. By sequencing the polymerase chain reaction product, we identified a premature stop at codon 269; thus, consequently, no Wiskott-Aldrich syndrome protein (WASp) was detectable in peripheral blood mononuclear cells from the patient. Due to the total absence of a full-length WASp, it is expected that the patient will develop the severe form of the disease, although further monitoring is needed to better define his phenotype. [ABSTRACT FROM AUTHOR]

Background: Early diagnosis of pulmonary tuberculosis can greatly reduce the harm caused by the disease. However, traditional diagnostic methods have various shortcomings in diagnosing pulmonary tuberculosis. Currently, with the increasing popularity, iteration, and decreasing costs of Next-generation sequencing (NGS) testing technology, NGS is being more widely applied in the diagnosis of pulmonary tuberculosis. Case presentation: A 29-year-old male presented with "fever accompanied by cough for more than 20 days." Multiple chest CT scans revealed progressive enlargement of the right hilar lymph nodes and thickening of the interlobular septa in the right upper lobe. Routine testing of bronchoalveolar lavage fluid, search for tuberculosis bacilli, bacterial and fungal cultures, X-pert MTB/RIF, and multiplex PCR-based targeted Next-generation sequencing (mp-tNGS) results were all inconclusive. Finally, bronchoalveolar lavage fluid was sent for hybrid capture-based targeted Next-generation sequencing (hc-tNGS) testing, and special staining of the enlarged lymph nodes confirmed the diagnosis of pulmonary tuberculosis. Conclusion: The hc-tNGS has significant value in diagnosing pulmonary tuberculosis, especially in cases that are difficult to detect with other methods. In the future, this could gradually become a routine diagnostic method for pulmonary tuberculosis, enhancing the accuracy of early diagnosis. [ABSTRACT FROM AUTHOR]

Advances in high-throughput sequencing (HTS) have made it a powerful resource for the conservation of threatened species, providing information at both population and individual levels to inform management decisions. In South America, however, the application of HTS in conservation has been limited, primarily due to challenges in funding and access to advanced genomic equipment and analytical expertise. Darwin's fox (Lycalopex fulvipes), endemic to Chile's Valdivian Temperate Rainforest, is the most endangered canid in South America with a small and declining population estimated at less than 1000 mature individuals. Despite its endangered status, significant knowledge gaps remain. Here we highlight the potential of HTS to address these challenges, such as clarifying its taxonomy, demographic history, geographic distribution, population structure, genetic diversity, and pathogen exposure. Integrating molecular data into conservation planning will be pivotal in ensuring the long-term survival of Darwin's fox by identifying priorities for targeted management interventions, highlighting areas of critical habitat for conservation, and guiding genetic rescue efforts to enhance genetic diversity and resilience. [ABSTRACT FROM AUTHOR]

Background: The capability of mNGS in diagnosing suspected LRTIs and characterizing the respiratory microbiome in lung cancer patients requires further evaluation. Methods: This study evaluated mNGS diagnostic performance and utilized background microbial sequences to characterize LRT microbiome in these patients. GSVA was used to analyze the potential functions of identified genera. Results: Bacteria were the most common pathogens (n=74) in LRTIs of lung cancer patients, and polymicrobial infections predominated compared to monomicrobial infections (p<0.001). In diagnosing LRTIs in lung cancer patients, the pathogen detection rate of mNGS (83.3%, 70/84) was significantly higher than that of sputum culture (34.5%, 29/84) (p<0.001). This result was consistent with that of non-lung cancer patients (p<0.001). Furthermore, in the specific detection of bacteria (95.7% vs. 22.6%) and fungi (96.0% vs. 22.2%), the detection rate of mNGS was also significantly higher than that of CMTs mainly based on culture (p<0.001, p<0.001). However, in the detection of CMV/EBV viruses, there was no significant difference between the detection rate of mNGS and that of viral DNA quantification (p = 1.000 and 0.152). mNGS analysis revealed Prevotella , Streptococcus , Veillonella , Rothia , and Capnocytophaga as the most prevalent genera in the LRT of lung cancer patients. GSVA revealed significant correlations between these genera and tumor metabolic pathways as well as various signaling pathways including PI3K, Hippo, and p53. Conclusion: mNGS showed a higher pathogen detection rate than culture-based CMTs in lung cancer patients with LRTIs, and also characterizing LRT microbiome composition and revealing potential microbial functions linked to lung carcinogenesis. [ABSTRACT FROM AUTHOR]

Advances in single-cell sequencing technologies have provided novel insights into the dynamics of gene expression and cellular heterogeneity within tissues and have enabled the construction of transcriptomic cell atlases. However, linking anatomical information to transcriptomic data and positively identifying the cell types that correspond to gene expression clusters in singlecell sequencing data sets remains a challenge. We describe a straightforward genetic barcoding approach that takes advantage of the powerful genetic tools in Drosophila to allow in vivo tagging of defined cell populations. This method, called Targeted Genetically-Encoded Multiplexing (TaGEM), involves inserting a DNA barcode just upstream of the polyadenylation site in a Gal4-inducible UAS-GFP construct so that the barcode sequence can be read out during single-cell sequencing, labeling a cell population of interest. By creating many such independently barcoded fly strains, TaG-EM enables positive identification of cell types in cell atlas projects, identification of multiplet droplets, and barcoding of experimental timepoints, conditions, and replicates. Furthermore, we demonstrate that TaG-EM barcodes can be read out using next-generation sequencing to facilitate population-scale behavioral measurements. Thus, TaG-EM has the potential to enable large-scale behavioral screens in addition to improving the ability to multiplex and reliably annotate single-cell transcriptomic experiments. [ABSTRACT FROM AUTHOR]

Copy number alterations (CNAs) play a fundamental role in cancer development and constitute a potential tool for tailored treatments. The CNAs recognition in formalin fixed paraffin embedded (FFPE) material for diagnostic purposes has relied for years mainly on fluorescence in situ hybridization. The introduction of other procedures, such as Next-Generation Sequencing has dramatically improved CNAs discovery at genome-wide level. The detection of CNAs by NGS in FFPE material is, nonetheless, a complex issue, which still requires validation studies. Herein, the CNAs detection by a widely used NGS assay (Oncomine Comprehensive Assay plus®, OCA+) were evaluated in 14 FFPE samples mirroring diagnostic daily practice and compared to a whole-genome assay. OCA+, a targeted DNA panel, showed lower CNAs detection sensitivity and equal specificity for gains and losses. According to proprietary software pipeline, OCA+ accurately identified gains characterized by CN ≥ 5,2. No significant threshold maximizing the difference between true and false positive losses was found. Orthogonal FISH tests validated seven CNAs characterized by CN gain ≥ 6 or complete loss. Considering the CNAs growing significance in precision medicine, our findings further prompt towards a robust validation of NGS detection in FFPE materials. [ABSTRACT FROM AUTHOR]

Background: Cassava (Manihot esculenta, Crantz), is a staple food and the main source of calories for many populations in Africa, but the plant is beset by several damaging viruses. So far, eight families of virus infecting cassava have been identified; the Geminiviridae (ssDNA viruses responsible for cassava mosaic disease, CMD) and Potyviridae (ssRNA + viruses responsible for cassava brown streak disease, CBSD) families being the most damaging to cassava in Africa. In several cassava-growing regions, the co-existence of species and strains from these two families results in a complex epidemiological situation making it difficult to correctly identify the viruses in circulation and delaying the implementation of disease management schemes. Nevertheless, the development of next generation sequencing (NGS) methods has revolutionized plant virus detection and identification. One NGS method that has been successfully used in virus detection and identification is ribodepleted RNA sequencing. Unfortunately, the relatively high cost makes it difficult to upscale this method to large epidemiological surveys and limits its adoption as a diagnostic tool. Results: Here, we develop a high-throughput sequencing protocol, named Ribo-M-Seq, that combines plant rRNA ribodepletion, cDNA synthesis, tagging with a 96 multiplexing scheme and Illumina sequencing. We evaluated the protocol on a series of cassava samples with a known assemblage of viruses. After confirming that the protocol was suitable for ribodepletion, we demonstrated it was possible to detect RNA and DNA viruses via identification of near full-size genomes. Additional phylogenetic analyses confirmed the presence of begomoviruses and ipomoviruses responsible for CMD and CBSD, respectively. We also detected a recently described ampelovirus (Manihot esculenta-associated virus) that was not detected in previous analyses. Conclusions: The use of the Ribo-M-Seq protocol will pave the way for large-scale sample analyses of collections with potentially complex viromes, such as those collected in the West African cassava integrated pest management program. [ABSTRACT FROM AUTHOR]

Introduction: Cunninghamella elegans infections cause rare and severe mucormycosis. Bordetella bronchiseptica and Pneumocystis jirovecii relate to pneumonia. They are all clinically uncommon pathogens and no reports of co-infections have been reported. Case presentation: Here we present a case of a 67-year-old male patient who initially presented with fever, chills, and mild cough. B. bronchiseptica, P. jirovecii, Aspergillus fumigatus, and human alphaherpesvirus 1 (HSV1) were detected by clinical metagenomic next-generation sequencing (mNGS) of his bronchoalveolar lavage fluid (BLAF). Despite receiving anti-infective treatment, the patient rapidly developed respiratory failure and was transferred to the intensive care unit. Subsequent mNGS testing further revealed the presence of C. elegans, indicating that different pathogens played dominant roles at various stages of the disease progression. The routine culture also identified several of the above pathogens, but the results were reported much later than those of mNGS. Eventually, imaging findings and symptoms of the patient improved with comprehensive antibiotic coverage, and he was transferred to a lower-level hospital for rehabilitation treatment. Conclusions: This is the first detailed report of the combined infection of B. bronchiseptica, P. jirovecii, and C. elegans. During the treatment process, we also observed rare and unusual neurological side effects: visual and auditory hallucinations, restlessness, and aphasia. Also, the case indicates that traditional methods are insufficient for the etiological diagnosis needs of critical and severe patient populations, and timely use of mNGS should be recommended. [ABSTRACT FROM AUTHOR]

Background: Seedless grapes are in high demand for fresh and dry fruit consumption. Seedlessness in grapes (Vitis vinifera L.) is triggered by two different mechanisms: stenospermocarpy and parthenocarpy. However, the key regulators of seed development and their targets in grapes are not well characterized. The present study used the seeded grape hybrid ARI 516 and its seedless mutant to understand the molecular mechanisms controlling the seedless phenotype in grapes. Results: Gametogenesis studies demonstrated that the seedless mutant exhibits pollen sterility due to abnormal pollen morphology, significantly low viability, and a complete lack of germination ability. The macrogametophyte in the seedless mutant was significantly smaller than in ARI 516. Transcriptomic comparisons were performed during three developmental stages, including pre-flowering stage E-L 15, anthesis stage E-L 23, and berry formation E-L 31, to study altered developmental processes in the seedless mutant and ARI 516. Genes downregulated in the seedless mutant were enriched in the male gametophyte development-related pathways, which may cause pollen sterility. The RNAseq results were validated by qRT-PCR. Genome sequence data was also used to identify induced mutations in the seedless mutant, which revealed three homozygous and 25 heterozygous InDels in the genes related to male gametophyte development. RNAseq and genome sequencing data collectively indicate parthenocarpic seedless phenotype due to aberrant developmental and physiological processes involved in pollen formation, maturation and germination in the seedless mutant of ARI 516. Conclusion: The study showed the downregulation of transcription factors and their target genes involved in cell division, gibberellin biosynthesis and signalling, cell wall development, organization, and pollen germination. This study represents a comprehensive attempt to identify putative candidate genes associated with parthenocarpic pollen sterility in grapes using genomic approaches. [ABSTRACT FROM AUTHOR]

Background: This study was designed to characterize gut microbiota changes of the patients with gastric cancer before and after the gastrectomy during their hospital staying periods. Methods: 16S ribosomal RNA (rRNA) gene sequencing was used to evaluate differences in gut microbiota among patients with gastric cancer before and after the gastrectomy by comparing gut microbiota α diversity, β diversity, and structure composition at different taxonomic levels. Results: A total of 120 fecal specimens were collected from 60 patients. There was no significant difference in Chao1 index, Shannon index, and Simpson index before and after gastrectomy (all P > 0.05). At the phylum level, the gut microbiota in the gastrectomy group showed less abundance of Bacteroidota , Synergistota , and Verrucomicrobiota but with higher abundance of Campylobacter , Actinobacteria , and Bacillota. At the genus level, the gut microbiota in the gastrectomy group showed less abundance of flora Bacteroides , Faecalibacterium , Blautia , and Lachnospiraceae nk4a136 group but with higher abundance of Campylobacter , Porphyromona , Finegordia , Dialist , Anaerococcus , and Corynebacterium. Conclusions: There was no significant change in the diversity of intestinal flora before and after surgery. However, significant changes in the structure of intestinal flora before and after surgery were occurred. [ABSTRACT FROM AUTHOR]

Flavors and fragrances are essential for product quality, yet they are highly susceptible to contamination due to high moisture content and rich nutrients. This study investigates microbial growth, pH changes, volatile compound dynamics, and microbial community changes during the storage of flavors and fragrances. Results indicate that total viable counts (TVC) remained stable for the first three days but increased rapidly afterward, exceeding the acceptable limit of 5 log CFU/mL by day 7. The pH levels initially rose slightly, followed by a steady decline, which indicates spoilage progression. Gas chromatography–mass spectrometry (GC–MS) analysis revealed significant degradation of key aromatic compounds, such as 5-hydroxymethylfurfural (5-HMF), vanillin, and its derivative ethyl vanillin. Whole genome shotgun (WGS) sequencing demonstrated a marked increase in microbial community richness and diversity as storage progressed, with a notable shift in composition. Early storage stages were dominated by fungal species from the Ascomycota phylum, while later stages saw a rise in spoilage-associated bacteria, particularly from the Firmicutes and Proteobacteria phyla. Throughout the storage process, Zygosaccharomyces and its dominant species, Zygosaccharomyces bailii , remained prevalent, though their average relative abundance decreased from 81.26 to 32.29%. In addition, the bacterial species Oceanobacillus sojae and Niallia nealsonii showed significant increases in relative abundance, suggesting that bacteria were one of the key contributors to the spoilage of flavors and fragrances. Functional analysis based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database indicated a shift in metabolic pathways within the microbial community, with heightened metabolic activity correlating with spoilage. These findings provide valuable insights for improving storage methods and quality control of flavors and fragrances. [ABSTRACT FROM AUTHOR]

Myxobacteria are a special kind of Gram-negative bacteria that can slide and produce a variety of bioactive substances against bacteria, fungi, and viruses. It has great development and research value in medicine and agriculture. Although myxobacteria have become a research hotspot at home and abroad, there are few systematic studies on the relationship between its diversity, geographical location, and environment factors. In order to solve these problems, 133 soil samples were collected from the east to the west of Inner Mongolia Autonomous Region and divided into five groups. The water content, pH, organic matter, available phosphorus, hydrolytic nitrogen, and available potassium content of soil samples were determined by national standards and other methods. The quantitative assessment of the abundance of myxobacteria in the soil sample was performed by quantitative real-time PCR. The composition of myxobacteria in the soil was determined by 16S rRNA high-throughput sequencing technology to analyze the differences in the community structure of myxobacteria among different groups, explore the relationship between the diversity of myxobacteria resources and the distribution and physical and chemical properties of the soil, and predict and analyze its community function. The results showed that there were abundant myxobacteria resources in the soils of Inner Mongolia, and the average relative abundance of myxobacteria in the soil samples from the central part of Inner Mongolia was higher than that in the eastern and western parts, but the richness and diversity of samples from the central to eastern regions were significantly higher than those from the western regions. The myxobacteria resources in the whole region included 10 families and 22 genera, among which the dominant genera were Labilitrix , Sandaracinus , Archangium , and Haliangium. The analysis of the species composition of myxobacteria among different groups found that the distribution of soil and soil type had an impact on the species composition of the samples. The species with significant differences in relative abundance among the five groups of samples were Labilitrix , Archangium , Sandaracinus , Minicystis , Polyangium , and Myxococcus. In addition, the latitude and longitude of the sampling point and the soil pH, water content, available phosphorus content and organic matter content had a greater impact on the myxobacteria community structure of samples, while the altitude of the soil sample and the contents of available potassium and alkaline nitrogen had a relatively small impact. Our data suggest that the distribution, type and nutrient composition of soil samples have an impact on the relative abundance and species composition of myxobacteria community. The completion of this work can provide basic data for the in-depth study of myxobacteria in the soil. [ABSTRACT FROM AUTHOR]

Background: Fulminant myocarditis (FM), a critical cardiac disease, is characterised by atypical initial symptoms and rapid progression and tends to lead to cardiomyocyte degeneration or necrosis. Reliable biological markers for FM screening remain lacking. Circular RNAs (circRNAs) are highly stable in peripheral blood due to their special closed-loop structure, and reports have described their involvement in regulating inflammatory responses and cell injury in cardiomyocytes. This study attempted to identify the abnormal expression of circRNAs in the peripheral blood of patients with FM and to evaluate the potential diagnostic value. Methods: Peripheral blood was collected from 5 children with FM and 5 sex- and age-matched healthy controls; total RNA was extracted from each sample, and the extracted RNA from each group was pooled. After RNase R treatment, high-throughput sequencing was performed to screen for differentially expressed circRNAs in the peripheral blood of patients. Biological function classification and enrichment analysis were used to explore the main action pathways involving differentially expressed circRNAs. A lipopolysaccharide (LPS)-induced cardiomyocyte inflammation model was used to explore the effect of inflammation on the expression of these dysregulated circRNAs. Receiver operating characteristic (ROC) curves were used to evaluate the potential clinical value of FM-related circRNAs as biomarkers in a large sample of patients. Results: CircRNA expression profiling of peripheral blood samples from patients revealed 6,435 and 3,678 circRNAs with upregulated and downregulated expression, respectively, compared with healthy controls. The expression of 1,749 circRNAs did not significantly differ between the groups. GO and KEGG analysis revealed that the genes encoding the dysregulated circRNAs were associated with various biological functions related to the risk of FM development, including infectious diseases, the immune system, and signal transduction. The high expression of hsa_circ_0064338 (circ_PPARG) was confirmed in both the myocardial cell inflammation model and peripheral blood from a large sample of FM patients. ROC curve analysis showed that the level of circ_PPARG in peripheral blood had a good ability to distinguish patients with FM from healthy controls. Conclusions: Large numbers of abnormally regulated circRNAs were identified in peripheral blood from patients with FM; among these, the highly expressed circ_PPARG could distinguish patients from healthy controls to a certain extent. It is expected to become a potential clinical biomarker of FM in the future. [ABSTRACT FROM AUTHOR]

Introduction: Immunoglobulin (Ig) refers to the nomenclature for all antibody proteins produced by B lymphocytes. The genetic locus encoding Ig is critical for vertebrate humoral immune responses and diverse antibody repertoires. Despite the critical role of buffaloes as livestock and their significance in disease transmission, the Ig loci of this species have not been thoroughly annotated. This study aimed to systematically characterize the Ig loci in buffaloes and their unique features, providing a foundation for understanding buffalo immune function. Methods: The genomic assembly of Murrah buffalo (NDDB_SH_1) was analyzed to annotate Ig loci. Annotation criteria included functional motifs, RSS sequences, and structural features of V, D, J, and C genes. The CDR3 repertoires were constructed using genomic DNA extracted from spleen samples of five healthy buffaloes. High-throughput sequencing of multiplex PCR products enabled repertoire analysis, and MiXCR software was used for alignment and CDR3 extraction. Repertoire diversity, gene usage, and clonal frequencies were analyzed using the Immunarch R package. Results: The IgH locus spans approximately 667 kb on chromosome 20, containing two D-J-C clusters, 54 VH genes, 10 DH genes, 8 JH genes, and 9 CH genes. The Igκ locus, located on chromosome 12, encompasses 24 Vκ genes, 5 Jκ genes, and 1 Cκ gene, while the Igλ locus on chromosome 17 includes 71 Vλ genes, 3 Jλ genes, and 3 Cλ genes. We also conducted a detailed examination of the buffalo IgH CDR3 repertoire, revealing the presence of ultra-long CDR3 sequences, a biased usage of certain V genes, and a high-frequency usage of IgHJ1-4 genes. Furthermore, we identified a set of shared clonotypes across the samples, highlighting commonalities in the buffalo antibody repertoire. Conclusion: These findings contribute to the understanding of buffalo immune function and provide insights into the evolution and diversity of ruminant immunoglobulin genes. [ABSTRACT FROM AUTHOR]

This case report presents a patient with metastatic adenocarcinoma of unclear primary focus at initial presentation and revealed lung adenocarcinoma in subsequent follow-up. The patient has been surviving for more than 10 years after pemetrexed-based treatment and local radiotherapy. Sequential gene tests showed kirsten rat sarcoma viral oncogene homolog (KRAS) G13D mutation and epidermal growth factor receptor (EGFR) 19ins. To further investigate the correlation between pemetrexed efficacy and genetic polymorphisms, genotyping tests on folate-metabolism-related genes [methylenetetrahydrofolate reductase (MTHFR) (C677T) and MTHFR (A1298C)] were performed, revealing that the patient exhibited the T/T genotype for MTHFR (C677T) and the A/A genotype for MTHFR (A1298C). The clinical data and gene analysis were discussed with literature review to explain the underlying explanation for the long survival. [ABSTRACT FROM AUTHOR]

Introduction: Little was known about the characteristics of low respiratory tract (LRT) microbiota of refractory M. pneumoniae pneumonia (RMPP) in children before and after the COVID-19 pandemic. Methods: Forty-two children diagnosed with RMPP in 2019 (Y2019 group) and 33 children diagnosed with RMPP in 2023 (Y2023 group), entered into the study. The characteristics of the clinical findings were examined, and the LRT microbiota was analyzed by metagenomic next generation sequencing. Results: The ratio of consolidate, atelectasis, lung necrosis, and erythema multiforme in Y2023 group was significantly higher than that in Y2019 (P <0.05). Mycoplasmoides pneumoniae was the top species of the LRT microbiota in both groups. The rate of macrolide resistance MP in Y2023 was significantly higher than that in Y2019 (P <0.05), and the mutant site was all 23S rRNA A2063G. There were no significant differences in α-diversity and β-diversity of LRT microbiota between Y2019 and Y2023 group. Trichoderma citrinoviride, Canine mastadenovirus A, Ralstonia pickettii, Lactococcus lactis, Pseudomonas aeruginosa were the biomarkers of LRT microbiota in children with RMPP of Y2023. The abundance of Mycoplasmoides pneumoniae positively correlated with the levels of D-dimer and LDH, negatively correlated with the counts of CD3+ T cells, CD8+ T cells, CD19+ B cells and CD16+CD56+ NK cells. Discussion: Our study showed that high abundance of MP was correlated with the severity of RMPP and decrease of immune cells. Trichoderma citrinoviride, Canine mastadenovirus A, Ralstonia pickettii, Lactococcus lactis, Pseudomonas aeruginosa were the biomarkers in microbiota of LRT in children with RMPP post COVID-19 era. [ABSTRACT FROM AUTHOR]

MODY, or maturity-onset diabetes of the young, is a group of monogenic diseases characterized by autosomal dominant inheritance of a non-insulin-dependent form of diabetes that classically manifests in adolescence or in young adults under 25 years of age. MODY is a rare cause of diabetes, accounting for 1% of all cases, and is often misdiagnosed as type 1 or type 2 diabetes. It is of great importance to accurately diagnose MODY, as this allows for the most appropriate treatment of patients and facilitates early diagnosis for them and their families. This disease has a high degree of phenotypic and genetic polymorphism. The most prevalent forms of the disease are attributed to mutations in three genes: GCK (MODY 2) and (HNF)1A/4A (MODY 3 and MODY 1). The remaining MODY subtypes, which are less prevalent, have been identified by next generation sequencing (NGS) in the last decade. Mutations in the GCK gene result in asymptomatic, stable fasting hyperglycemia, which does not require specific treatment. Mutations in the HNF1A and HNF4A genes result in pancreatic β-cell dysfunction, which in turn causes hyperglycemia. This often leads to diabetic angiopathy. The most commonly prescribed drugs for the treatment of hyperglycemia are sulfonylurea derivatives. Nevertheless, with advancing age, some patients may require insulin therapy due to the development of resistance to sulfonylurea drugs. The strategy of gene therapy for monogenic forms of MODY is still an experimental approach, and it is unlikely to be widely used in the clinic due to the peculiarities of MODY structure and the high genetic polymorphism and clinical variability even within the same form of the disease. Furthermore, there is a lack of clear gene-phenotypic correlations, and there is quite satisfactory curability in the majority of patients. This review presents the main clinical and genetic characteristics and mutation spectrum of common and rarer forms of MODY, with a detailed analysis of the field of application of AVV vectors in the correction of hyperglycemia and insulin resistance. [ABSTRACT FROM AUTHOR]

Structural variation (SV) typically refers to alterations in DNA fragments at least 50 base pairs long in the human genome. It can alter thousands of DNA nucleotides and thus significantly influence human health, disease, and clinical phenotypes. There is a shared and growing recognition that the emergence of effective computational tools and high-throughput technologies such as short-read sequencing and long-read sequencing offers novel insight into SV and, by extension, diseases affecting planetary health. However, numerous available SV tools exist with varying strengths and weaknesses. This is currently hampering the abilities of scholars to select the optimal tools to study SVs. Here, we reviewed 175 tools developed in the past two decades for SV detection, annotation, visualization, and downstream analysis of human genomics. In this expert review, we provide a comprehensive catalog of SV-related tools across different technology platforms and summarize their features, strengths, and limitations with an eye to accelerate systems science and planetary health innovations. [ABSTRACT FROM AUTHOR]

Background and Objectives: Accurate screening of clinically significant tumor mutations is critical for precision medicine in oncology. This requires genotyping platforms with high accuracy and compatibility with varying DNA yields from challenging sample types. Here, we have validated a new, improved, compact, and self-contained pyrosequencing platform (Pyromark Q48 Autoprep; Q48) for screening N-, K- and H-RAS mutations in thyroid cancers. Methods: A set of 73 thyroid cancer and 16 non-thyroid cancer samples (fine needle aspirates and formalin-fixed paraffin-embedded) with known mutation status of RAS genes were tested using the Q48 platform. Performance parameters such as accuracy, precision, and limit-of-detection were established. Q48 workflow was compared to an older Q96 pyrosequencing platform to highlight the differences and advantages. RAS testing by pyrosequencing was also compared to a clinically validated next-generation sequencing platform using 56 thyroid cancer samples. Results: The Q48 Pyromark was found to be a very reliable platform suited for quick testing of RAS genes with complete accuracy, high precision, and high detection sensitivity. It had comparable accuracy, with higher sequencing success rates than NGS. The hands-on time, workflow ease, and efficiency were also significantly improved in comparison with the Q96 platform. Conclusions: Overall, the Q48 platform was found to be a well-suited and agile clinical sequencing platform to rapidly screen RAS mutations. [ABSTRACT FROM AUTHOR]

Background/Objectives: The accurate detection of EGFR mutations, particularly the rare S768I variant, is crucial for guiding treatment decisions in non-small cell lung cancer (NSCLC) patients. This study investigated the incidence of false positives in S768I mutation detection using the IdyllaTM qPCR system and compared results with next-generation sequencing (NGS). Methods: A prospective observational study was conducted at the Dr. Negrín University Hospital between July 2023 and July 2024. Six NSCLC patient samples with S768I variant detection by IdyllaTM were analyzed from all NSCLC cases tested during the study period. Initial testing was performed on tissue samples (Idylla1), followed by replicate analysis using extracted DNA (Idylla2). Results were compared with NGS as the reference method. Statistical analysis included the calculation of sensitivity, specificity, accuracy, and Kappa concordance index. Results: Initial Idylla testing showed an 80% false positive rate, with only one of five positive results confirmed by NGS. The first analysis demonstrated high sensitivity (100%) but low specificity (20%), with an accuracy of 0.333 and poor concordance with NGS (Kappa = 0.077). Repeat testing using extracted DNA showed improved performance, with increased accuracy (0.833) and better agreement with NGS (Kappa = 0.571). Analysis of amplification curves revealed that false positives typically showed normalized fluorescence values below 12 points, with no clear correlation between false positives and factors such as sample quantity or tumor content. Conclusions: While the IdyllaTM system shows high sensitivity for S768I detection, its initial specificity is problematic, leading to frequent false positives. These findings emphasize the importance of confirming positive S768I results through alternative methods like NGS, particularly when these results could influence therapeutic decisions. Results suggest the need to refine the system's interpretation algorithms to improve specificity. [ABSTRACT FROM AUTHOR]

Simple Summary: Equine atypical myopathy is a severe intoxication caused by protoxins synthesised by certain maple trees, notably sycamore maple (Acer pseudoplatanus). These protoxins are activated into harmful toxins that disrupt lipid metabolism by inhibiting specific steps of fatty acid β-oxidation, leading to the accumulation of acylcarnitines in the blood. This activation process is catalysed mainly by specific mitochondrial enzymes, which are also present in some bacteria. Horses grazing in close proximity to affected animals have shown differences in their faecal microbiota composition, suggesting that the role of gut microbiota in atypical myopathy could be more substantial than previously understood. Recently, blood analyses have demonstrated the existence of subclinical cases among these cograzers. The present study compares the faecal bacteria of horses affected by atypical myopathy, their cograzers, and a group of toxin-free horses serving as a control group. Results show significant differences in faecal bacterial diversity and composition between groups, particularly for certain bacterial genera. Additionally, blood levels of specific compounds appear to be associated with these bacterial changes. The theoretical presence of the enzymes involved in the protoxin activation process was also studied. These results highlight the importance of comprehensively studying intestinal microbiota to better understand its role in this generally fatal poisoning. Hypoglycin A and methylenecyclopropylglycine are protoxins responsible for atypical myopathy in equids. These protoxins are converted into toxins that inhibit fatty acid β-oxidation, leading to blood accumulation of acylcarnitines and toxin conjugates, such as methylenecyclopropylacetyl-carnitine. The enzymes involved in this activation are also present in some prokaryotic cells, raising questions about the potential role of intestinal microbiota in the development of intoxication. Differences have been noted between the faecal microbiota of cograzers and atypical myopathy-affected horses. However, recent blood acylcarnitines profiling revealed subclinical cases among cograzers, challenging their status as a control group. This study investigates the faecal microbiota of horses clinically affected by atypical myopathy, their cograzers, and a control group of toxin-free horses while analysing correlations between microbiota composition and blood parameters. Faecal samples were analysed using 16S amplicon sequencing, revealing significant differences in α-diversity, evenness, and β-diversity. Notable differences were found between several genera, especially Clostridia_ge, Bacteria_ge, Firmicutes_ge, Fibrobacter, and NK4A214_group. Blood levels of methylenecyclopropylacetyl-carnitine and C14:1 correlated with variations in faecal microbial composition. The theoretical presence of enzymes in bacterial populations was also investigated. These results underscore the critical need to investigate the potential role of intestinal microbiota in this poisoning and may provide insights for developing prevention and treatment strategies. [ABSTRACT FROM AUTHOR]

Tetrapedia diversipes is a Neotropical solitary bee commonly found in trap-nests, known for its morphological adaptations for floral oil collection and prepupal diapause during the cold and dry season. Here, we present the genome assembly of T. diversipes (332 Mbp), comprising 2,575 scaffolds, with 15,028 predicted protein-coding genes. Repetitive elements constitute 38.68% of the genome, notably Class II transposable elements. An investigation into lateral gene transfers identified a low frequency (0.037%) of nuclear copies of mitochondrial DNA and 18 candidate regions from bacterial origins. Furthermore, the annotation of 3 scaffolds reveals the presence of the Wolbachia endosymbiont genome, confirming the infection by 2 strains in T. diversipes populations. This genome contributes valuable insights into Neotropical bee genomics, offering a resource for comparative studies and enhancing our understanding of the molecular basis of solitary bee adaptations and interactions. [ABSTRACT FROM AUTHOR]

Background: To develop efficient selection strategies and improve the discovery of promising ligands, it is highly desirable to analyze the sequence composition of naïve phage display libraries and monitor the evolution of their peptide content during successive rounds of amplification. In the current study, we performed a comparative analysis of the compositional features in different lots of the same naïve phage display library and monitored alterations in their peptide compositions during three rounds of amplification. Methods: We conducted three rounds of duplicate serial amplification of two different lots of the Ph.D.™-12 phage display library. DNA from the samples was subjected to Next-Generation Sequencing (NGS) using an Illumina platform. The NGS datasets underwent a variety of bioinformatic analyses using Python and MATLAB scripts. Results: We observed substantial heterogeneity in the sequence composition of the two lots indicated by differences in the enhanced percentage of wildtype clones, reduced diversity (number of unique sequences), and increased enrichment factors (EFs) during amplification as well as by observing no common sequence between lots and decreased number of common sequences between the naïve library and the consecutive rounds of amplification for each lot. We also found potential propagation-related target-unrelated peptides (TUPs) with the highest EFs in the two lots, which were displayed by the fastest-propagating phage clones. Furthermore, motif analysis of the most enriched subpopulation of amplified libraries led to the identification of some motifs hypothesized to contribute to the increased amplification rates of the respective phage clones. Conclusion: Our results highlight tremendous heterogeneity in the peptide composition of different lots of the same type of naïve phage display library, and the divergent evolution of their compositional features during amplification rounds at the amino acid, peptide, and motif levels. Our findings can be instrumental for phage display researchers by bringing fundamental insights into the vast extent of non-uniformity between phage display libraries and by providing a clear picture of how these discrepancies can lead to different evolutionary fates for the peptide composition of phage pools, which can have profound impacts on the outcome of phage display selections through biopanning. [ABSTRACT FROM AUTHOR]

A recent trend in some wineries is the return to using spontaneous fermentation, but it is not clear whether winery flora or vineyard microorganisms drive fermentation. We compared fungal communities during the spontaneous fermentation of wine produced in a winery and in a laboratory with sterilized equipment using three grape cultivars (Chardonnay, Merlot, and Muscat Bailey A) obtained from the same harvest. High-throughput sequencing analysis based on the ITS1 region showed that Saccharomyces cerevisiae was the dominant species in winery batches at the end of fermentation, but it was not always dominant in laboratory batches. The number of laboratory batches where S. cerevisiae reached more than 50% at the end of fermentation was only 10 of 26. Consistent with this, in the grape juice/must before fermentation, S. cerevisiae accounted for 1.71% of fungal species identified in winery batches and 0.04% in laboratory batches. In addition, in laboratory-based winemaking, juice clarification of Chardonnay and cold maceration of Merlot influenced the microbial communities observed during fermentation. Our findings suggest that S. cerevisiae present in the winery environment participates at an early stage of fermentation, leading to its dominance at the end in wine produced by spontaneous fermentation in a winery. • Fungal community was compared between winery and laboratory spontaneous fermentation. • In winery fermentations, Saccharomyces cerevisiae ultimately became dominant. • In laboratory fermentations, S. cerevisiae was not always the dominant species. • S. cerevisiae present in the winery environment seems to participate in fermentation. • Conditions such as juice clarification affect microbial communities in fermentation. [ABSTRACT FROM AUTHOR]

Hypophosphatemic rickets is a rare bone disease characterized by short stature, bone deformities, impaired bone mineralization, and dental problems. Most commonly, hypophosphatemic rickets is caused by pathogenic variants in the X-chromosomal PHEX gene, but autosomal dominant and recessive forms also exist. We investigated a Finnish family in which the son (index, 29 yr) and mother (56 yr) had hypophosphatemia since childhood. Both patients had typical clinical, radiographic, and biochemical features of hypophosphatemic rickets, including a pathological fracture in the son. Gene panels and whole-exome sequencing did not reveal any pathogenic variants in the known hypophosphatemia genes. Therefore, we performed whole genome sequencing and identified a deep intronic variant (c.2147 + 1197A > G) in PHEX. Both the affected individuals, but none of the unaffected family members, had the same variant, as confirmed by Sanger sequencing. According to RT-PCR, whole transcriptomic data, and in silico analyses, the variant led to a new splice donor site in intron 21 and an 84 basepair pseudoexon between exons 21 and 22, likely leading to the synthesis of abnormal PHEX protein. Our study underscores the importance of intronic PHEX variants in X-linked hypophosphatemia (XLH). In patients with features of XLH but negative gene panel or whole-exome sequencing results, the combination of whole-genome sequencing and whole transcriptomics should be considered to detect possible deep intronic variants. The methodologies presented have the potential to be used more widely in other rare diseases. [ABSTRACT FROM AUTHOR]

Copyright of Food Research & Development is the property of Food Research & Development Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Shipin Kexue/ Food Science is the property of Food Science Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

In this study, the complete mitochondrial genome of Pseudomphala latericea was sequenced by Illumina high-throughput sequencing and its characteristics were analyzed. The mitogenome of P. latericea is 16,635 bp long, and it encodes the standard set of 13 PCGs, 22 tRNA genes, and two rRNA genes. The mitogenome has a GC content of 29.3% and a very high AT content of 70.7%. The maximum-likelihood and Bayesian inference phylogenetic trees clearly demonstrated the relationships among the four genera (Pseudomphala, Assiminea, Sculptassiminea, and Optediceros) within the Assimineidae. [ABSTRACT FROM AUTHOR]

Breakthroughs in high-throughput sequencing and microscopic imaging technologies have revealed that chromatin structures vary considerably between cells of the same type. However, a thorough characterization of this heterogeneity remains elusive due to the labor-intensive and time-consuming nature of these experiments. To address these challenges, we introduce ChromoGen, a generative model based on state-of-the-art artificial intelligence techniques that efficiently predicts three-dimensional, single-cell chromatin conformations de novo with both region and cell type specificity. These generated conformations accurately reproduce experimental results at both the single-cell and population levels. Moreover, ChromoGen successfully transfers to cell types excluded from the training data using just DNA sequence and widely available DNase-seq data, thus providing access to chromatin structures in myriad cell types. These achievements come at a remarkably low computational cost. Therefore, ChromoGen enables the systematic investigation of single-cell chromatin organization, its heterogeneity, and its relationship to sequencing data, all while remaining economical. [ABSTRACT FROM AUTHOR]

Background: The air-curing process of cigar tobacco leaves is typically conducted in an open environment, involving the participation of various microorganisms. However, the effect of microbial communities during air-curing process on the formation of flavor components remains unclear. Therefore, this study aims to reveal the dynamics of flavor components and microbial community changes, and explore the potential role of microbial communities in flavor formation during the cigar tobacco air-curing process. Results: High-throughput sequencing analysis showed that Pantoea, Sphingomonas and Pseudomonas were the dominant bacterial genera during air-curing process, while Aspergillus was the dominant fungal genus. Subsequently, volatile flavor analysis shows that alkaloids were the most important volatile compounds in cigar leaves, followed by esters, alcohols and aldehydes. Furthermore, 38 characteristic volatile flavor compounds at different periods of air-curing were identified based on PLS-DA in different periods of air-curing. The correlation analysis between microorganisms and flavor components showed that Pantoea and Staphylococcus might promote the flavor formation from browning to post-air-curing and were positively correlated with specific flavor components like phenylacetaldehyde and acetophenone. Phoma, Mycosphaerella, Wallemia, and Cladosporium were identified as key fungal genera influencing flavor formation, as they showed positive correlations with multiple flavor components. These information enrich our understanding of the flavor formation of cigar tobacco during air curing. Conclusions: There is a complex correlation between the microbial community and the flavor components, which may have a great influence on the flavor formation during the air-curing process of cigar leaves. Bacterial communities have higher species diversity and richness during air-curing, and have more complex correlation characteristics with volatile flavor, which may play more roles in the flavor formation. This study revealed the potential role of microbial community on flavor formation in cigar tobacco air-curing process, and provided guidance for subsequent screening of specific functional microorganisms to improve and stabilize cigar tobacco flavor. [ABSTRACT FROM AUTHOR]

Background: The clinical presentations and prognostic indicators of C. psittaci pneumonia are inadequately investigated currently. The objective of the study was to assess the clinical presentation of C. psittaci pneumonia and the risk factors for severe pneumonia, within a systematic review and individual patient meta-analysis. Methods: We searched PubMed, CNKI, and Wanfang databases for case reports/series of proven/probable psittacosis published between 1st January 2000 and 28th February 2023, including all hospitalized individuals aged ≥ 18 years. Patient demographics, manifestations, diagnostic methods, and outcomes were summarized descriptively. Patients were divided into severe or non-severe pneumonia groups mainly according to the ATS/IDSA 2007 criteria. Prognostic predictors for severe C. psittaci pneumonia were identified using multivariate logistic regression. Results: 3062 articles of 196 (566 individual patient cases) were included in the final analysis. Patients with chronic cardiovascular disease face a significantly elevated risk of developing severe C. psittaci pneumonia (adjusted odds ratio (aOR) 2.63; 95% confidence interval (CI) 1.05–6.59; P = 0.039). Symptoms including dyspnea (aOR 4.88; 95% CI 3.19–7.46; P < 0.001), neuropsychiatric symptoms (aOR 3.58; 95% CI 2.05–6.28; P < 0.001), gastrointestinal symptoms (aOR 1.76; 95% CI 1.10–2.80; P = 0.018), or the presence of multilobar infiltrates on imaging (aOR 3.27; 95% CI 2.11–5.06; P < 0.001) upon admission frequently serve as indicators of severe pneumonia. Conclusions: Chronic cardiovascular disease increases susceptibility to severe C. psittaci pneumonia. The presence of dyspnea, neuropsychiatric symptoms, gastrointestinal symptoms, and multilobar infiltrates upon admission merits clinicians' attention, advocating for timely sample submission for metagenomic next-generation sequencing (mNGS) to ascertain the etiology. [ABSTRACT FROM AUTHOR]

Motivation: Genotyping of bi-parental populations can be performed with low-coverage next-generation sequencing (LC-NGS). This allows the creation of highly saturated genetic maps at reasonable cost, precisely localized recombination breakpoints (i.e., the crossovers), and minimized mapping intervals for quantitative-trait locus analysis. The main issues with these low-coverage genotyping methods are (1) poor performance at heterozygous loci, (2) high percentage of missing data, (3) local errors due to erroneous mapping of sequencing reads and reference genome mistakes, and (4) global, technical errors inherent to NGS itself. Recent methods like Tassel-FSFHap or LB-Impute are excellent at addressing issues 1 and 2, but nonetheless perform poorly when issues 3 and 4 are persistent in a dataset (i.e., "noisy" data). Here, we present a new algorithm for imputation of LC-NGS data that eliminates the need of complex pre-filtering of noisy data, accurately types heterozygous chromosomal regions, precisely estimates crossover positions, corrects erroneous data, and imputes missing data. The imputation of genotypes and recombination breakpoints is based on maximum-likelihood estimation. We compare its performance with Tassel-FSFHap and LB-Impute using simulated data and two real datasets. NOISYmputer is consistently more efficient than the two other software tested and reaches average breakpoint precision of 99.9% and average recall of 99.6% on illumina simulated dataset. NOISYmputer consistently provides precise map size estimations when applied to real datasets while alternative tools may exhibit errors ranging from 3 to 1845 times the real size of the chromosomes in centimorgans. Furthermore, the algorithm is not only highly effective in terms of precision and recall but is also particularly economical in its use of RAM and computation time, being much faster than Hidden Markov Model methods. Availability: NOISYmputer and its source code are available as a multiplatform (Linux, macOS, Windows) Java executable at the URL https://gitlab.cirad.fr/noisymputer/noisymputerstandalone/-/tree/1.0.0-RELEASE?reftype=tags. [ABSTRACT FROM AUTHOR]

Background: Coccidia are among the primary pathogens causing diarrhea and even fatalities in lambs. With the increasing use of chemical drugs to treat coccidiosis, the problem of drug resistance is becoming more and more threatening. Therefore, there is an urgent need to identify novel alternative drugs for the treatment of the lamb coccidia. In this study, the effect of different doses and extraction methods of Artemisia annua (A. annua) on anticoccidial activity and growth performance was assessed by oocysts output (OPG), fecal index, average daily gain (ADG) and the new production value of experimental lambs. High-throughput sequencing technology was employed to investigate the effect of A. annua on the intestinal microbiota and metabolites of lambs afflicted with coccidiosis. Results: The results revealed that all A. annua treatment groups exhibited good anticoccidial effects. According to the soft stool index and ADG analysis, the Low-dose A. annua (AL) and A. annua alcohol extract (AA) groups demonstrated a better overall effect. The microbiota and metabolites of lambs changed after A. annua was administered. Unclassified_Muribaculaceae exhibited a significant positive correlation with ADG (P < 0.05) and a negative correlation with OPG, although the latter was not statistically significant (P > 0.05). Alistipes displayed a significant negative correlation with ADG (P < 0.05), and a positive correlation with OPG (P > 0.05). Additionally, UCG 005 exhibited a highly significant negative correlation with OPG (P < 0.01). Conclusion: The above results demonstrated that AL and AA groups had more effective anticoccidial action. Unclassified_Muribaculaceae could be employed as a suitable probiotic to enhance weight gain in lambs, while UCG-005 could inhibit intestinal Eimeria colonization in lambs. Alistipes may serve as a biomarker for predicting the risk of intestinal coccidia outbreaks in lambs. A. annua induced significant changes in gut microbiota, accompanied by corresponding changes in metabolites. These differences in gut microbiota and metabolites provide valuable insights for subsequent research on the mechanisms underlying anticoccidial action. [ABSTRACT FROM AUTHOR]

Background: Integrating germline genetic testing (GGT) recommendations from tumor testing into hereditary cancer clinics and precision oncology trials presents challenges that require multidisciplinary expertise and infrastructure. While there have been advancements in standardizing molecular tumor boards, the implementation of tumor profiling for germline-focused assessments has only recently gained momentum. However, this progress remains inconsistent across institutions, largely owing to a lack of systematic approaches for managing these findings. This study outlines the development of a clinical pathway for identifying potential germline variants from an institutional tumor-sequencing research program at Princess Margaret Cancer Centre. Methods: Between August 2022 and August 2023, a clinical pathway led by a germline Molecular Tumor Board (gMTB) was established to review tumor genetic variants (TGVs) flagged as potential germline findings in patients with advanced cancer via a multigene panel. Eligibility for hereditary cancer syndrome investigation ('germline criteria') followed Cancer Care Ontario's Hereditary Cancer Testing Criteria and clinical judgment. Germline-focused analysis of TGVs followed the European Society of Medical Oncology guidelines and similar published criteria ('tumor-only criteria'). Results: Of 243 tumor profiles, 83 (34.2%) had at least one TGV flagged by the genetic laboratory as potentially germline and were therefore referred to the gMTB for further review. Among these 83 cases, 47 (56.6%) met 'germline criteria' for GGT, regardless of the TGV assessment. A total of 127 TGVs were assessed in these 83 cases, of which 44 (34.6%) were considered germline relevant. Tier I TGVs, interpreted as pathogenic/likely pathogenic (P/LP) and found in most- or standard-actionable genes with high germline conversion rates (GCRs) in any context, were more likely to be considered germline relevant (p-value < 0.05). One confirmed germline variant was identified in nine patients meeting solely 'tumor-only criteria'. Overall, 27/44 germline relevant TGVs underwent germline testing. We found a germline P/LP variant in 9 cases of the entire cohort, with a GCR of 33% (9/27). Conclusions: Incorporating genetic counselors into gMTBs enhanced the integration of research findings into clinical care and improved the detection of disease-causing variants in patients outside traditional testing criteria. [ABSTRACT FROM AUTHOR]

With the development of next-generation sequencing (NGS) technologies it became possible to simultaneously analyze millions of variants. Despite the quality improvement, it is generally still required to confirm the variants before reporting. However, in recent years the dominant idea is that one could define the quality thresholds for "high quality" variants which do not require orthogonal validation. Despite that, no works to date report the concordance between variants from whole genome sequencing and their gold-standard Sanger validation. In this study we analyzed the concordance for 1756 WGS variants in order to establish the appropriate thresholds for high-quality variants filtering. Resulting thresholds allowed us to drastically reduce the number of variants which require validation, to 4.8% and 1.2% of the initial set for caller-agnostic (DP, AF) and caller-dependent (QUAL) thresholds, respectively. [ABSTRACT FROM AUTHOR]

The application of metagenomic next-generation sequencing (mNGS) in the diagnosis of cryptococcal meningitis is relatively under characterized. Here, we retrospectively evaluated data from cryptococcal meningitis patients who were tested using mNGS and/or routine testing, including fungal culture, India ink staining, and cryptococcal antigen (CrAg) testing. The performance of mNGS was then assessed. Initial cerebrospinal fluid (CSF) samples were collected from 65 patients with suspected central nervous system (CNS) infection and tested using conventional tests and/or mNGS. mNGS offers a culture-independent approach, facilitating a rapid and unbiased detection of a broad spectrum of pathogens. Patients with bacterial tuberculous or viral meningitis were used as mNGS-positive controls and one autoimmune encephalitis patient was used as an mNGS-negative control. In the 45 patients diagnosed with cryptococcal meningitis, the sensitivity, specificity, positive predictive value, negative predictive value, and concordance rate of mNGS were 92%, 100%, 100%, 90.9%, and 95.6%, respectively. Compared to conventional methods, the sensitivity of mNGS was slightly lower than CrAg tests (96.7%) but higher than India ink (79.5%) and culturing (63.4%). Of the two negative mNGS cases (2/25, 8.0%), one was positive by India ink staining, culture, and CrAg testing, while the other was positive only by CrAg testing. A combination of mNGS and conventional methods enhanced the detection rate to 100%. Our study demonstrates that both CrAg and mNGS offer excellent diagnostic accuracy for cryptococcal meningitis, and utilizing both tests can enhance clinical assessment and patient management. [ABSTRACT FROM AUTHOR]

Exophiala spinifera strain FM, a black yeast and melanized ascomycete, shows potential for oil biodesulfurization by utilizing dibenzothiophene (DBT) as its sole sulfur source. However, the specific pathway and enzymes involved in this process remain unclear due to limited genome sequencing and metabolic understanding of E. spinifera. In this study, we sequenced the complete genome of E. spinifera FM to construct the first genome-scale metabolic model (GSMM) for this organism. Through bioinformatics analysis, we identified genes potentially involved in DBT desulfurization and degradation pathways for hazardous pollutants. We focused on understanding the cost associated with metabolites in sulfur assimilation pathway to assess economic feasibility, optimize resource allocation, and guide metabolic engineering and process design. To overcome knowledge gaps, we developed a genome-scale model for E. spinifera, iEsp1694, enabling a comprehensive investigation into its metabolism. The model was rigorously validated against growth phenotypes and gene essentiality data. Through shadow price analysis, we identified costly metabolites such as 3'-phospho-5'-adenylyl sulfate, 5'-adenylyl sulfate, and choline sulfate when DBT was used as the sulfur source. iEsp1694 encompasses the degradation of aromatic compounds, which serves as a crucial first step in comprehending the pan metabolic capabilities of this strain. [ABSTRACT FROM AUTHOR]

The emergence of Next Generation Sequencing (NGS) technology has catalyzed a paradigm shift in clinical diagnostics and personalized medicine, enabling unprecedented access to high-throughput microbiome data. However, the inherent high dimensionality, noise, and variability of microbiome data present substantial obstacles to conventional statistical methods and machine learning techniques. Even the promising deep learning (DL) methods are not immune to these challenges. This paper introduces a novel feature engineering method that circumvents these limitations by amalgamating two feature sets derived from input data to generate a new dataset, which is then subjected to feature selection. This innovative approach markedly enhances the Area Under the Curve (AUC) performance of the Deep Neural Network (DNN) algorithm in colorectal cancer (CRC) detection using gut microbiome data, elevating it from 0.800 to 0.923. The proposed method constitutes a significant advancement in the field, providing a robust solution to the intricacies of microbiome data analysis and amplifying the potential of DL methods in disease detection. [ABSTRACT FROM AUTHOR]

Background: Neuropilin-1 (NRP1) is a transmembrane protein involved in surface receptor complexes for a variety of extracellular signals. NRP1 expression in human cancers is associated with prominent angiogenesis and advanced progression stage. However, the molecular mechanisms underlying NRP1 activity in the tumor microenvironment remain unclear. Notably, diffusible forms of NRP1 in the extracellular space have been reported, but their functional role is poorly understood. Methods: Extracellular vesicles (EV) were isolated from conditioned media of diverse cancer cells. The quality of exosome-enriched preparations was validated by the presence of specific markers in western blotting, as well as by light scattering and nanoparticle tracking analysis. Wound healing, transwell, and digital real-time migration assays were carried out to assess the activity of cancer cell-derived exosomes in the regulation of endothelial cells. RNA interference was applied to obtain NRP1 knock-down, and cDNA transfer to achieve its overexpression, in exosome-releasing cells. The micro-RNA profile carried by exosomes was investigated by Next Generation Sequencing. miRNA-Scope in situ hybridization was used to assess the transfer of miRNA exosome cargo to target cells, and immunofluorescence analysis revealed expression regulation of targeted proteins. miRNA activity was blocked by the use of specific antago-miRs. Results: In this study, we show that diverse human cancer cells release NRP1 embedded in exosome-like small extracellular vesicles, which mediate a previously unknown NRP1-dependent paracrine signaling mechanism regulating endothelial cell migration. By transcriptomic analysis of the cargo of NRP1-loaded exosomes, we found a significant enrichment of miR-210-3p, known to promote tumor angiogenesis. Gene knock-down and overexpression experiments demonstrated that the loading of miR-210-3p into exosomes is dependent on NRP1. Data furthermore indicate that the exosomes released through this NRP1-driven mechanism effectively transfer miR-210-3p to human endothelial cells, causing paracrine downregulation of the regulatory cue ephrin-A3 and promotion of cell migration. The mechanistic involvement of miR-210-3p in this pathway was confirmed by applying a specific antago-miR. Conclusions: In sum, we unveiled a previously unknown NRP1-dependent paracrine signaling mechanism, mediated by the loading of pro-angiogenic miR-210-3p in exosomes released by cancer cells, which underscores the relevance of NRP1 in controlling the tumor microenvironment. [ABSTRACT FROM AUTHOR]

Copy number variation (CNV) is an important part of human genetic variations, which is associated with various kinds of diseases. To tackle the limitations of traditional CNV detection methods, such as restricted detection types, high error rates, and challenges in precisely identifying the location of variant breakpoints, a new method called MSCNV (copy number variations detection method for multi-strategies integration based on a one-class support vector machine model) is proposed. MSCNV establishes a multi-signal channel that integrates three strategies: read depth, split read, and read pair. First, a one-class support vector machine algorithm is used to detect abnormal signals in read depth and mapping quality values to determine the rough CNV region. Then, the rough CNV region is filtered by using paired read signals to improve the precision of MSCNV method. Finally, MSCNV explores and recognizes tandem duplication regions, interspersed duplication regions, and loss regions. It uses split read signals to determine the precise location of mutation points and to determine the type of variation. Compared with Manta, FREEC, GROM-RD, Rsicnv, and CNVkit, MSCNV significantly improves the sensitivity, precision, F1-score, and overlap density score of CNV detection while reducing the boundary bias of the detection results. [ABSTRACT FROM AUTHOR]

This study aimed to evaluate the usefulness of amplicon-based real-time metagenomic sequencing applied to cerebrospinal fluid (CSF) for identifying the causative agents of bacterial meningitis. We conducted a 16S rRNA amplicon sequencing using a nanopore-based platform, alongside routine polymerase chain reaction (PCR) testing or bacterial culture, to compare its clinical performance in pathogen detection on CSF samples. Among 17 patients, nanopore-based sequencing, multiplex PCR, and bacterial culture detected potential bacterial pathogens in 47.1%, 0%, and 47.1% samples, respectively. Nanopore-based sequencing demonstrated a sensitivity of 50.0%, specificity of 55.6%, positive predictive value of 50.0%, negative predictive value of 55.6%, and overall accuracy of 47.1%, compared to the gold standard method for bacterial culture. In 44.4% (4/9) of culture-negative cases, nanopore-based sequencing detected potentially causative pathogens, whereas four (23.5%) patients were positive only in culture. Using nanopore-based sequencing alongside bacterial culture increased the positivity rate from 47.1 to 70.6%. However, these values may be overestimated due to challenges in distinguishing significant pathogens from background noise. Meanwhile, the bioinformatics module in EPI2ME reduced the turn-around time to 10 min. Nanopore-based metagenomic sequencing is expected to serve as a complementary tool for pathogen detection in CSF samples by facilitating rapid and accurate diagnosis. [ABSTRACT FROM AUTHOR]

Background: Human noroviruses are the major cause of acute gastroenteritis and exhibit considerable genetic diversity. Next generation sequencing (NGS) analysis based on environmental surveillance has been proved to be an effective method in norovirus surveillance. Methods: Between January 2019 and December 2021, 36 sewage samples were collected and analyzed using real-time quantitative PCR to detect noroviruses. Partial VP1 region was amplified and subjected to NGS analysis to assess the abundance and genetic characterization of various norovirus genotypes across different samples. Results: A total of 23 norovirus genotypes were identified, including 9 genotypes of GI, 13 genotypes of GII and 1 genotype of GIX. The most frequently detected genotypes were GI.5 (86.11%), GII.2 (86.11%), GII.4 (63.89%), GII.17 (58.33%), and GII.13 (55.56%). Additionally, some rare genotypes, such as GI.7, GII.5, GII.9, and GII.16, which had not been previously reported in Shandong, were identified. No significant differences were observed in genotypic diversity or viral copy numbers in sewage samples when comparing pre- and post-COVID-19 periods. A total of 379 partial VP1 sequences were obtained, with the means sequence identity within a genotype of Shandong sequences ranging from 92.69 to 98.37% and a coefficient of variation ranging from 1.46 to 6.73%. Phylogenetic analysis indicated that local noroviruses within each genotype comprised multiple co-circulating lineages. Conclusions: Our data demonstrate that sewage contains noroviruses with considerable high diversities. NGS based environmental surveillance greatly improves the understanding of norovirus circulation and should be encouraged. [ABSTRACT FROM AUTHOR]

Introduction: Pufferfish are valuable ingredients and important fishery resources in Asia. Among them, approximately 25 Takifugu species have undergone explosive speciation in the marine environments of East Asia. Specifically, T. rubripes, T. pseudommus , and T. chinensis are remarkably similar in appearance and genetics, and their classification remains controversial. Here, we provide comprehensive genetic and genomic evidence regarding their speciation and classification. Methods: Whole genome sequencing was performed on T. pseudommus , leading to the identification and development of 15 novel tandem simple sequence repeats (SSRs) from its genomic data. Genetic diversity, differentiation, and population structure among T. rubripes, T. pseudommus, T. chinensis , and T. xanthopterus were subsequently analyzed using a combination of these 15 SSR loci and mitochondrial cytochrome oxidase subunit I (CoI) and cytochrome b (CytB) gene sequences. Furthermore, genomic variations, including single nucleotide polymorphisms, insertions, and deletions, were identified by comparing the genome of T. pseudommus with the reference T. rubripes genome retrieved from the National Center for Biotechnology Information. These variations were screened using ENSEMBL annotation and gene ontology analysis, and their potential association with morphological differences, such as dorsal spot patterns, was evaluated using reference Takifugu specimens. Results and discussion: Population genetic analysis of T. rubripes, T. pseudommus , and T. chinensis using the CoI and CytB genes, combined with the 15 SSR loci, revealed clustering into a single genetic group characterized by remarkably low genetic diversity (four haplotypes, with diversity values ranging from 0.0000 to 0.00065) and minimal pairwise differentiation (microsatellite-based F ST values ranging from -0.0021 to 0.0075). Additionally, comparative genomic analysis between T. pseudommus and the reference T. rubripes genome did not identify genetic variations that could directly explain the observed morphological differences among the species. These findings strongly suggest that T. rubripes, T. pseudommus , and T. chinensis represent a single species sharing a common genetic pool. [ABSTRACT FROM AUTHOR]