Genomic Analysis Research Articles

Genomic and transcriptomic analyses of chemical hepatocarcinogenesis aggravated by oncoprotein loss

Background and Aims: The chemical carcinogen diethylnitrosamine (DEN) is often used to induce hepatocellular carcinoma (HCC) in mice. Curiously, several labs have reported that removal of oncoproteins from hepatocytes exacerbated DEN-induced HCC, with mechanisms unknown. This study aimed at deciphering molecular mechanisms underlying the tumor suppressive effect of oncoproteins. Methods and Results: We generated mutant mouse lines with hepatocyte-specific deletions of Met, Ptpn11/Shp2, Ikk, or ctnnb1/-catenin, and assessed DEN-induced tumorigenesis in the wild type (WT) and mutant mice. To systematically examine genetic and molecular signaling alternations, we performed whole exome and RNA sequencing on liver samples collected at the pre-cancer and established cancer stages. Although the mutational profiles of DEN-induced tumors were barely different in WT and mutant mice, oncoprotein ablation increased DEN-induced mutational burdens, especially in Shp2-deficient tumors. RNA-sequencing revealed multiple changes in signaling pathways, in particular upregulated epithelial-mesenchymal transition (EMT), cell migration and tumor metastasis as well as downregulated small molecule metabolism that were affected by oncoprotein ablation. We identified key molecules and pathways that are associated with hepatic innate immunity and implicated in liver tumorigenesis. In addition, we unveiled markedly changed expression of a few miRNAs in human HCC database. Conclusion: The aggravation of DEN-induced HCC progression seen on oncoprotein ablation could be caused by common and distinct genomic and signaling alterations. This study reveals a new level of complexity in hepato-carcinogenesis and elucidates molecular mechanisms underlying tumor evolution and recurrence.

In vitro probiotic potential of lactic acid bacteria isolated from the intestines of Muscovy ducks.

The current study was conducted to isolate, test and characterize molecularly and physiologically lactic acid bacteria from the intestines of Muscovy ducks to evaluate their probiotic potential for poultry farming. Three hundred lactic acid bacteria from the gastrointestinal tract of Muscovy ducks were isolated. The strains were phenotypically characterized by observing cell morphology, performing Gram staining, catalase production, and testing their ability to grow in MRS broth at different temperatures, pH values, NaCl concentrations, bile concentration, and in compatibility tests between strains. Nine strains were selected based on their resilience. Eight strains were identified using molecular techniques. These strains exhibited significant tolerance to acidic pH, bile salts, and NaCl, essential for probiotic function. All isolates inhibited the growth of Salmonella enterica serotype Typhimurium (DT104) and Enteropathogenic Escherichia coli serotype O86:H34 (EPEC), showcasing their antimicrobial potential. Antibiotic susceptibility testing revealed 100% resistance to clindamycin and erythromycin but high susceptibility to ampicillin and vancomycin. Growth was observed at various temperatures, indicating mesophilic characteristics. Compatibility tests confirmed their suitability for probiotic formulations. Genomic analysis identified the strains primarily as Enterococcus. Conclusively, the study identified eight out of nine selected lactic acid bacteria strains from Muscovy ducks as autochthonous probiotics, showing resilience to treatments and compatibility for consortium formulation. These strains are suitable for in vivo testing for potential poultry farming applications. Further research on their molecular mechanisms and in vivo effects is needed.

Meaning, concept and application of bioinformatics

Bioinformatics, originating from the term coined in 1979 by Paulien Hogeweg and Ben Hesper, is a burgeoning interdisciplinary field at the nexus of biology, computer science, and information technology. It encompasses the collection, classification, storage, and analysis of vast biological datasets using computational methods, aiming to unravel the complexities of biological systems. This abstract provides a comprehensive overview of bioinformatics, emphasizing its definition, scope, branches, aims, research areas, databases, and applications, particularly highlighting its role in drug discovery through structural bioinformatics. Bioinformatics integrates diverse branches such as computational biology, genomics, proteomics, structural biology, systems biology, pharmacogenomics, and bioprogramming. Each branch applies mathematical modeling, molecular interactions analysis, or genomic data interpretation to advance understanding in biology and medicine. Key aims include applying advanced computational technologies to biological problems, presenting complex data clearly, and providing robust statistical tools for genomic analysis. The field also fosters collaborations across academic, commercial, and government sectors to leverage resources and expertise. Research areas span computational evolutionary analysis, genome annotation, gene expression analysis, cancer mutation studies, and comparative genomics, illuminating disease mechanisms and evolutionary relationships. Bioinformatics databases play a crucial role by storing and organizing biological data. Primary repositories like GenBank and the Protein Data Bank (PDB), secondary databases such as SWISS-Prot, and specialized databases support research and clinical applications by providing access to genomic, proteomic, and structural information. In drug discovery, structural bioinformatics techniques like homology modeling, molecular docking, and simulations predict protein structures, analyze interactions, and aid in designing therapies. These computational methods accelerate drug development, optimize drug-target interactions, and reduce costs associated with bringing new drugs to market. Overall, bioinformatics drives innovation in biological sciences and healthcare by leveraging computational methods to interpret biological data. As technology advances, bioinformatics will continue to play a pivotal role in addressing global health challenges, advancing personalized medicine, and facilitating groundbreaking discoveries in biology and medicine. The evolving field of bioinformatics promises continued growth and impact, shaping the future of biological research and its applications in improving human health and understanding the natural world.

Quantifying allele-specific CRISPR editing activity with CRISPECTOR2.0.

Off-target effects present a significant impediment to the safe and efficient use of CRISPR-Casgenome editing. Since off-target activity is influenced by the genomic sequence, the presence of sequence variants leads to varying on- and off-target profiles among different alleles or individuals. However, a reliable tool that quantifies genome editing activity in an allelic context is not available. Here, we introduce CRISPECTOR2.0, an extended version of our previously published software tool CRISPECTOR, with an allele-specific editing activity quantification option. CRISPECTOR2.0 enables reference-free, allele-aware, precise quantification of on- and off-target activity, by using de novo sample-specific single nucleotide variant (SNV) detection and statistical-based allele-calling algorithms. We demonstrate CRISPECTOR2.0 efficacy in analyzing samples containing multiple alleles and quantifying allele-specific editing activity, using data from diverse cell types, including primary human cells, plants, and an original extensive human cell line database. We identified instances where an SNV induced changes in the protospacer adjacent motif sequence, resulting in allele-specific editing. Intriguingly, differential allelic editing was also observed in regions carrying distal SNVs, hinting at the involvement of additional epigenetic factors. Our findings highlight the importance of allele-specific editing measurement as a milestone in the adaptation of efficient, accurate, and safe personalized genome editing.

Metabolomic analysis reveals the positive effects of Rhizopus oryzae fermentation on the nutritional and functional constituents of adlay millet seeds

Adlay millet seeds are well known for excellent health benefits. However, using fungal fermentation to improve their nutritional and functional constituents and the underlying mechanisms has not been thoroughly investigated. Herein, we used Rhizopus oryzae as starter and applied metabolomics combining with quantitative verification to understand the changes of the nutritional and functional profiles of adlay millet seeds. Results showed that a total of 718 metabolites from 18 compound classes were identified. The fermentation with R. oryzae varied 203 differential metabolites, of which 184 became more abundant and 19 got less abundant, and many components such as amino acids, nucleotides, vitamins, flavonoids, terpenoids, and phenols significantly increased after the fermentation process. Interestingly, we found that R. oryzae synthesized high levels of two important beneficial compounds, S-adenosylmethionine (SAMe) and β-Nicotinamide mononucleotide (β-NMN), with their contents increased from 0.56 to 370.26 μg/g and 0.55 to 8.32 μg/g, respectively. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of enriched metabolites revealed the amino acid metabolic pathways were important for conversion of the primary and secondary metabolites. Specifically, aspartate can up-regulate the biosynthesis of SAMe and β-NMN. These findings improved our understanding into the effects of R. oryzae fermentation on enhancing the nutritional and functional values of cereal foods.

Whole genome sequencing and analysis of Bacillus sp. TTMP2, a tetramethylpyrazine-producing bacterium.

Tetramethylpyrazine has been extensively studied as an anticancer substance and a flavor substance in the fields of medicine and food industry. A strain with high tetramethylpyrazine production was screened from the fermented grains of Danquan winery. Genome sequencing can reveal the potential roles of bacteria by thoroughly examining the connection between genes and phenotypes from a genomic perspective. In this study, whole genome of this strain was sequenced and analyzed. This paper summarized the genomic characteristics of strain TTMP2 and analyzed genes related to the synthesis of tetramethylpyrazine. Bacillus sp. TTMP2 has a complete metabolic pathway for acetoin and tetramethylpyrazine metabolism. Gene function was analyzed by COG annotation, GO annotation, KEGG annotation and functional annotations for lipoproteins, carbohydrate-active enzymes, and pathogen-host interactions. Phylogenetic analysis indicated that Bacillus velezensis had the high homology with Bacillus sp. TTMP2. Genomes of 16 Bacillus species cover all genes of Bacillus, suggesting that genus Bacillus has an open pan-genome and can survive in diverse environments. The analysis of genome sequencing data from Bacillus sp. TTMP2 showed that its metabolic characteristics could be deeply understood, indicating that this bacterium had a particular role in tetramethylpyrazine synthesis.

North–south pathways, emerging variants, and high climate suitability characterize the recent spread of dengue virus serotypes 2 and 3 in the Dominican Republic

BackgroundDengue fever remains a significant public health challenge in tropical and subtropical regions, with its transmission dynamics being influenced by both environmental factors and human mobility. The Dominican Republic, a biodiversity hotspot in the Caribbean, has experienced recurrent dengue outbreaks, yet detailed understanding of the virus's transmission pathways and the impact of climatic factors remains limited. This study aims to elucidate the recent transmission dynamics of the dengue virus (DENV) in the Dominican Republic, utilizing a combination of genomic sequencing and epidemiological data analysis, alongside an examination of historical climate patterns.MethodsWe conducted a comprehensive study involving the genomic sequencing of DENV samples collected from patients across different regions of the Dominican Republic over a two-year period. Phylogenetic analyses were performed to identify the circulation of DENV lineages and to trace transmission pathways. Epidemiological data were integrated to analyze trends in dengue incidence and distribution. Additionally, we integrated historical climate data spanning several decades to assess trends in temperature and their potential impact on DENV transmission potential.ResultsOur results highlight a previously unknown north–south transmission pathway within the country, with the co-circulation of multiple virus lineages. Additionally, we examine the historical climate data, revealing long-term trends towards higher theoretical potential for dengue transmission due to rising temperatures.ConclusionThis multidisciplinary study reveals intricate patterns of dengue virus transmission in the Dominican Republic, characterized by the co-circulation of multiple DENV lineages and a novel transmission pathway. The observed correlation between rising temperatures and increased dengue transmission potential emphasizes the need for integrated climate-informed strategies in dengue control efforts. Our findings offer critical insights for public health authorities in the Dominican Republic and similar settings, guiding resource allocation and the development of preparedness strategies to mitigate the impacts of climate change on dengue transmission.

Comparative analysis of microbial community under acclimation of linear alkylbenzene sulfonate (LAS) surfactants and degradation mechanisms of functional strains

Linear alkylbenzene sulfonate (LAS) is one of the most widely used anionic surfactants and a common toxic pollutant in wastewater. This study employed high throughput sequencing to explore the microbial community structure within activated sludge exposed to a high concentration of LAS. Genera such as Pseudomonas, Aeromonas, Thauera and Klebsiella exhibited a significant positive correlation with LAS concentrations. Furthermore, Comamonas and Klebsiella were significantly enriched under the stress of LAS. Moreover, bacterial strains with LAS-degrading capability were isolated and characterized to elucidate the degradation pathways. The Klebsiella pneumoniae isolate L1 could effectively transform more than 60 % of 25 mg/L of LAS within 72 h. Chemical analyses revealed that L1 utilized the LAS sulfonyl group as a sulfur source to support its growth. Genomic and transcriptomic analyses suggested that strain L1 may uptake LAS through the sulfate ABC transport system and remove sulfonate with sulfate and sulfite reductases.

Metabolomic and Transcriptomic Analysis of Unique Floral Coloration in Osmanthus fragrans Cultivars

The floral color phenotypes of Osmanthus fragrans cultivars range from light yellow to orange yellow, with ‘Yanzhi Hong’ being the only reported cultivar with a red color. However, the underlying reason for this unique floral coloration remains unclear. The study conducted targeted metabolomics and transcriptomics analyses on the petals of ‘Yanzhi Hong’ at both initial and peak flowering stages. Candidate gene expression was validated, and expression levels of the petals of three cultivars were compared using RT-qPCR. The results revealed the presence of 27 components in the petals of ‘Yanzhi Hong’, including 5 carotenoids, 8 xanthophylls, and 14 xanthophyll esters. Notably, lycopene was detected in abundance for the first time in O. fragrans cultivars. Carotenes accounted for 78.82 ± 3.17% and 91.19 ± 1.69% of the total carotenoid content in petals during the initial and peak flowering stages, respectively, with all carotene contents increasing during the peak flowering period. β-carotene, lycopene, and γ-carotene were identified as the top three carotene components in petals during both initial and full flowering stages. The unique blush red color of ‘Yanzhi Hong’ petals could be attributed to the low content of α-carotene and the rich accumulation of lycopene. Furthermore, a total of 1550 differentially expressed genes (DEGs) were identified in petals at the peak flowering stage relative to the initial flowering stage, with 1003 genes being downregulated and 547 genes being upregulated during the full flowering stage. There are 926 differentially expressed genes (DEGs) annotated in the Gene Ontology (GO) database. Among these DEGs, those that were downregulated and upregulated during the peak flowering period showed significant enrichment in carbohydrate metabolism and oxidation–reduction processes, respectively. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified 14 structural genes associated with phenylpropanoid biosynthesis and 7 structural genes linked to carotenoid biosynthesis. Expression levels of candidate genes involved in carotenoid biosynthesis were examined in the petals of three cultivars (‘Yanzhi Hong’, ‘Liuye Jingui’, and ‘Gecheng Dangui’) at both the initial and peak flowering stages. The results indicated that the decreased expression of LYG009054 (LYCE) and LYG018651 (LYCB) in ‘Yanzhi Hong’ resulted in higher lycopene accumulation and lower α-carotene content in the petals. This study offers valuable insights into the mechanisms underlying the unique flower color phenotype of O. fragrans, proving a basis for further research on carotenoid metabolism pathways and the breeding of new cultivars with a variety of flower colors in O. fragrans.

Genomic differentiation and interoceanic population structure of two large pelagic scombrid species

Tunas of the family Scombridae are of paramount importance for fisheries and the international seafood trade. In order to ensure a sustainable use of these valuable resources, it is crucial that stock delineation and management plans are in accordance. Here, we examined the population genetic structure of the two data-poor scombrid species wahoo (Acanthocybium solandri) and bigeye tuna (Thunnus obesus), both of growing significance in tuna fisheries. Our study employed whole-genome sequencing methods to conduct the most extensive genomic analysis of wahoo and bigeye tuna samples to date, collected from the Atlantic, Indian and Pacific Oceans. For both species, we observe genome-wide differentiation between samples from the Atlantic and the Indo-Pacific regions with little or no genetic structure within each of the ocean basins, indicative of high gene flow. However, by applying a set of extreme outlier tests, genomic differentiation between locations was identified within the Pacific Ocean for both species, as well as for wahoo within the Atlantic Ocean. Additionally, for bigeye tuna, we uncovered a putative chromosomal inversion with patterns of highly linked loci and strong population divergence, that may be involved in adaptive divergence across the distributional range of the species. Taken together, despite considerable gene flow, the detected substructures – most likely driven by local adaptation – challenge previously held assumptions of panmixia in both species. Our findings show that future stock assessment should consider genetic differences at both neutral and divergent loci to develop sustainable conservation and management actions for these valuable marine resources.

Diet of Andean leaf-eared mice (Phyllotis) living at extreme elevations on Atacama volcanoes: insights from metagenomics, DNA metabarcoding, and stable isotopes.

On the flanks of >6000 m Andean volcanoes that tower over the Atacama Desert, leaf-eared mice (Phyllotis vaccarum) live at extreme elevations that surpass known vegetation limits. What the mice eat in these barren, hyperarid environments has been the subject of much speculation. According to the arthropod fallout hypothesis, sustenance is provided by windblown insects that accumulate in snowdrifts ('aolian deposits'). It is also possible that mice feed on saxicolous lichen or forms of cryptic vegetation that have yet to be discovered at such high elevations. We tested hypotheses about the diet of mice living at extreme elevations on Atacama volcanoes by combining metagenomic and DNA metabarcoding analyses of gut contents with stable-isotope analyses of mouse tissues. Genomic analyses of contents of the gastrointestinal tract of a live-captured mouse from the 6739 m summit of Volcán Llullaillaco revealed evidence for an opportunistic but purely herbivorous diet, including lichens. Although we found no evidence of animal DNA in gut contents of the summit mouse, stable isotope data indicate that mice native to elevations at or near vegetation limits (~5100 m) include a larger fraction of animal prey in their diet than mice from lower elevations. Some plant species detected in the gut contents of the summit mouse are known to exist at lower elevations at the base of the volcano and in the surrounding Altiplano, suggesting that such plants may occur at higher elevations beneath the snowpack or in other cryptic microhabitats.

Genomic analysis of enterococci carrying optrA, poxtA, and vanA resistance genes from wild boars, Italy.

To investigate enterococci carrying linezolid and vancomycin resistance genes from fecal samples recovered from wild boars. Florfenicol- and vancomycin-resistant enterococci, isolated on selective agar plates, were screened by PCR for the presence of linezolid and vancomycin resistance genes. Five isolates carried optrA or poxtA linezolid resistance genes; one strain was resistant to vancomycin for the presence of vanA gene. All isolates were tested for their antibiotic susceptibility and subjected to Whole Genome Sequencing (WGS) analysis. In Enterococcus faecalis (E. faecalis) V1344 and V1676, the optrA was located on the new pV1344-optrA and pV1676-optrA plasmids, respectively, whereas in Enterococcus faecium (E. faecium) V1339 this gene was on a 22 354-bp chromosomal genetic context identical to the one detected in a human E. faecium isolate. In both E. faecium V1682 and E. durans V1343, poxtA was on the p1818-c plasmid previously found in a human E. faecium isolate. In E. faecium V1328, the vanA gene was on the Tn1546 transposon in turn located on a new pV1328-vanA plasmid. Only E. faecium V1682 successfully transferred the poxtA gene to an enterococcal recipient in filter mating assays. The occurrence of genetic elements carrying linezolid and vancomycin resistance genes in enterococci from wild boars is a matter of concern, moreover, the sharing of plasmids and transposons between isolates from wild animals, human, and environment indicates an exchange of genetic material between these settings.

Genome and Transcriptome Analysis of NF-Y Transcription Factors in Sweet Potato under Salt Stress

Nuclear factor Y (NF-Y) is a heterotrimeric complex composed of three unique subunits: NF-YA, NF-YB, and NF-YC. This transcription factor complex binds to the CCAAT box of eukaryotic promoters, playing a crucial role in various biological processes in plants. Despite its importance, the NF-Y gene family has not been reported in the sweet potato (Ipomoea batatas) genome, an important food and energy crop. Understanding the role and function of NF-Y in sweet potatoes could provide valuable insights for genetic improvement and yield enhancement. To address this gap, our research aimed to comprehensively catalog and characterize the NF-Y genes in sweet potatoes, which we refer to as ‘IbNF-Y’, where ‘Ib’ denotes Ipomoea batatas. A total of 37 NF-Ys were identified, including 11 NF-YA, 21 NF-YB, and 5 NF-YC members, and their phylogeny, gene structure, chromosomal distribution, and conserved motifs were analyzed. Additionally, we assessed their expression patterns under salt stress in both light and dark conditions using transcriptome sequencing. Notably, we discovered that certain IbNF-Y genes showed significant changes in expression under salt stress, suggesting their potential roles in sweet potato’s adaptation to saline environments. Furthermore, our work enriches the genomics and genetic research on sweet potatoes and contributes valuable knowledge to the broader scientific community of the Convolvulaceae family.

The dual role of a highly structured RNA (the S fragment) in the replication of foot-and-mouth disease virus.

Secondary and tertiary RNA structures play key roles in genome replication of single-stranded positive sense RNA viruses. Complex, functional structures are particularly abundant in the untranslated regions of picornaviruses, where they are involved in initiation of translation, priming of new strand synthesis and genome circularization. The 5' UTR of foot-and-mouth disease virus (FMDV) is predicted to include a c. 360 nucleotide-long stem-loop, termed the short (S) fragment. This structure is highly conserved and essential for viral replication, but the precise function(s) are unclear. Here, we used selective 2' hydroxyl acetylation analyzed by primer extension (SHAPE) to experimentally determine aspects of the structure, alongside comparative genomic analyses to confirm structure conservation from a wide range of field isolates. To examine its role in virus replication in cell culture, we introduced a series of deletions to the distal and proximal regions of the stem-loop. These truncations affected genome replication in a size-dependent and, in some cases, host cell-dependent manner. Furthermore, during the passage of viruses incorporating the largest tolerated deletion from the proximal region of the S fragment stem-loop, an additional mutation was selected in the viral RNA-dependent RNA polymerase, 3Dpol. These data suggest that the S fragment and 3Dpol interact in the formation of the FMDV replication complex.

Beyond cyanogenesis: Temperature gradients drive environmental adaptation in North American white clover (Trifolium repens L.).

Species that repeatedly evolve phenotypic clines across environmental gradients have been highlighted as ideal systems for characterizing the genomic basis of local environmental adaptation. However, few studies have assessed the importance of observed phenotypic clines for local adaptation: conspicuous traits that vary clinally may not necessarily be the most critical in determining local fitness. The present study was designed to fill this gap, using a plant species characterized by repeatedly evolved adaptive phenotypic clines. White clover is naturally polymorphic for its chemical defence cyanogenesis (HCN release with tissue damage); climate-associated cyanogenesis clines have evolved throughout its native and introduced range worldwide. We performed landscape genomic analyses on 415 wild genotypes from 43 locations spanning much of the North American species range to assess the relative importance of cyanogenesis loci vs. other genomic factors in local climatic adaptation. We find clear evidence of local adaptation, with temperature-related climatic variables best describing genome-wide differentiation between sampling locations. The same climatic variables are also strongly correlated with cyanogenesis frequencies and gene copy number variations (CNVs) at cyanogenesis loci. However, landscape genomic analyses indicate no significant contribution of cyanogenesis loci to local adaptation. Instead, several genomic regions containing promising candidate genes for plant response to seasonal cues are identified - some of which are shared with previously identified QTLs for locally adaptive fitness traits in North American white clover. Our findings suggest that local adaptation in white clover is likely determined primarily by genes controlling the timing of growth and flowering in response to local seasonal cues. More generally, this work suggests that caution is warranted when considering the importance of conspicuous phenotypic clines as primary determinants of local adaptation.

The octapeptide-repeat surface protein of Entamoeba nuttalli is a novel virulence factor that promotes adherence to host cells

Entamoeba nuttalli is genetically the closest to Entamoeba histolytica, the causative agent of human amebiasis, and its natural host is Macaca species. A unique E. nuttalli specific surface protein (PTORS) containing 42 repeats of octapeptide was identified by comparative genomic analysis of Entamoeba species. We aimed to elucidate the function of this protein. When trophozoites from various E. nuttalli strains were examined by immunofluorescence microscopy and flow cytometry using a PTORS-specific monoclonal antibody, only a limited proportion of trophozoites were stained, indicating that the protein was not commonly expressed in all E. nuttalli trophozoite. The proportion of trophozoites expressing PTORS increased after passage in hamster livers, suggesting that the protein functions in the virulence of trophozoites in the liver tissue. Single-cell analysis revealed that in the cluster including trophozoites with PTORS gene expression, genes of virulence-related proteins were also upregulated. Trophozoites of E. histolytica transfected with PTORS showed enhanced adherence and subsequent phagocytic activity towards human Jurkat cells, independent of the lectin. E. histolytica trophozoites expressing PTORS formed larger liver abscesses in hamsters. These results demonstrate that PTORS is a novel virulence factor in Entamoeba species.

Evolutionary Dynamics of Satellite DNA Repeats across the Tettigoniidae Family: Insights from Genomic Analysis

Evolutionary Dynamics of Satellite DNA Repeats across the Tettigoniidae Family: Insights from Genomic Analysis

Cyberlindnera fabianii, an Uncommon Yeast Responsible for Gluten Bread Spoilage

A single strain of yeast was isolated from industrial gluten bread (GB) purchased from a local supermarket. This strain is responsible for spoilage consisting of white powdery and filamentous colonies due to the fragmentation of hyphae into short lengths (dust-type spots), similar to the spoilage produced by chalk yeasts such as Hyphopichia burtonii, Wickerhamomyces anomalus and Saccharomycopsis fibuligera. The isolated strains were identified initially by traditional methods as Wickerhamomyces anomalus, but with genomic analysis, they were definitively identified as Cyberlindnera fabianii, a rare ascomycetous opportunistic yeast species with low virulence attributes, uncommonly implicated in bread spoilage. However, these results demonstrate that this strain is phenotypically similar to Wi. anomalus. Cy. fabianii grew in GB because of its physicochemical characteristics which included pH 5.34, Aw 0.97 and a moisture of about 50.36. This spoilage was also confirmed by the presence of various compounds typical of yeasts, derived from sugar fermentation and amino acid degradation. These compounds included alcohols (ethanol, 1-propanol, isobutyl alcohol, isoamyl alcohol and n-amyl alcohol), organic acids (acetic and pentanoic acids) and esters (Ethylacetate, n-propil acetate, Ethylbutirrate, Isoamylacetate and Ethylpentanoate), identified in higher concentrations in the spoiled samples than in the unspoiled samples. The concentration of acetic acid was lower only in the spoiled samples, but this effect may be due to the consumption of this compound to produce acetate esters, which predominate in the spoiled samples.

RACGAP1 is a pivotal gene in lung adenocarcinoma-associated membranous nephropathy: Based on comprehensive bioinformatics analysis and machine learning

BackgroundThis study performs a detailed bioinformatics and machine learning analysis to investigate the genetic foundations of membranous nephropathy (MN) in lung adenocarcinoma (LUAD). MethodsIn this study, the gene expression profiles of MN microarray datasets (GSE99339) and LUAD dataset (GSE43767) were downloaded from the Gene Expression Omnibus database, common differentially expressed genes (DEGs) were obtained using the limma R package. The biological functions were analyzed with R Cluster Profiler package according to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Machine learning algorithms, including LASSO regression, support vector machine (SVM), Random Forest, and Boruta analysis, were applied to identify hubgenes linked to LUAD-associated MN. These genes’ prognostic values were evaluated in the TCGA-LUAD cohort and validated through immunohistochemistry on renal biopsy specimens. ResultsA total of 36 DEGs in common were identified for downstream analyses. Functional enrichment analysis highlighted the involvement of the Toll-like receptor 4 pathway and several immune recognition pathways in LUAD-associated MN. COL3A1, PSENEN, RACGAP1, and TNFRSF10B were identified as hub genes in LUAD-associated MN using machine learning algorithms. ROC analysis demonstrated their effective discrimination of MN with high accuracy. Survival analysis showed that lung adenocarcinoma patients with higher expression of these genes had significantly reduced overall survival. In patients with lung adenocarcinoma-associated MN, RACGAP1, COL3A1, PSENEN, and TNFRSF10B were higher expressed in the glomerular, especially RACGAP1, indicating an important role in the pathogenesis of LUAD-associated membranous nephropathy. ConclusionsOur study underscores the critical role of RACGAP1, COL3A1, PSENEN, and TNFRSF10B in the development of LUAD-associated MN, providing important insights for future research and the development of potential therapeutic strategies.

Genomic and Transcriptomic Insights into the Evolution of C4 Photosynthesis in Grasses.

C4 photosynthesis has independently evolved over 62 times within 19 angiosperm families. The recurrent evolution of C4 photosynthesis appears to contradict the complex anatomical and biochemical modifications required for the transition from C3 to C4 photosynthesis. In this study, we conducted an integrated analysis of genomics and transcriptomics to elucidate the molecular underpinnings of convergent C4 evolution in the grass family. Our genome-wide exploration of C4-related gene families suggests that the expansion of these gene families may have played an important role in facilitating C4 evolution in the grass family. A phylogenomic synteny network analysis uncovered the emergence of C4 genes in various C4 grass lineages from a common ancestral gene pool. Moreover, through a comparison between non-C4 and C4 PEPCs, we pinpointed 14 amino acid sites exhibiting parallel adaptations. These adaptations, occurring post the BEP-PACMAD divergence, shed light on why all C4 origins in grasses are confined to the PACMAD clade. Furthermore, our study revealed that the ancestor of Chloridoideae grasses possessed a more favorable molecular pre-adaptation for C4 functions compared to the ancestor of Panicoideae grasses. This molecular pre-adaptation potentially explains why C4 photosynthesis evolved earlier in Chloridoideae than in Panicoideae and why the C3-to-C4 transition occurred once in Chloridoideae but multiple times in Panicoideae. Additionally, we found that C4 genes share similar cis-elements across independent C4 lineages. Notably, NAD-ME subtype grasses may have retained the ancestral regulatory machinery of the C4 NADP-ME gene, while NADP-ME subtype grasses might have undergone unique cis-element modifications.