Numerous Genes Research Articles

Endurance Effort Affected Expression of Actinin 3 and Klotho Different Isoforms Basing on the Arabian Horses Model

Background: Among numerous genes that have been a focus of equine genetic research, the KL (Klotho) and ACTN3 (Alpha-actinin-3) genes stand out due to their significant roles in muscle function and overall health, as well as performance ability. Previous studies on Arabian horses and other mammalians have shown that both KL and ACTN3 occur in different isoforms that seem to have different roles in metabolism. The main purpose of this present study was to describe different isoforms (ACTN3, ACTN3-201, ACTN3-202, KL, KL-202, KL-203) expression levels affected by the endurance effort in Arabian horses. Methods: Blood samples were taken from a group of n = 10 Arabian horses taking part in a long-distance 120 km endurance ride. After RNA isolation and reverse transcription, real-time PCR was performed. The expression levels (Relative Quantity, RQ) were calculated using the delta-delta CT method. The results showed surprisingly large differences between different isoforms expression levels which brought us to the conclusion that both KL and ACTN3 genes are suitable genetic markers to measure endurance performance. Moreover, the correlation network analyses showed that the MIOX (myo-inositol oxygenase), SH3RH2 (SH3 domain-containing ring finger 2) and TNNI2 (Troponin I2, fast skeletal type) genes are significantly involved in the endurance effort metabolism.

New complete genome insights into Enterobacter roggenkampii FACU2: a potential player in cadmium bio-removal.

Industrial workplaces, particularly those involved in ore processing or smelting, pose a high risk of exposure to cadmium, a highly toxic metal. This study isolated and identified eight cadmium-resistant strains from industrial wastewater for their ability to resist cadmium. Enterobacter roggenkampii FACU2 demonstrated exceptional cadmium removal capabilities during our analysis, successfully eliminating 62% of the cadmium. Additionally, transmission electron microscopy (TEM) was utilized to examine the morphological change between the most and least efficient strains that responded to cadmium stress at the cellular level. Compared to the control bacteria, the treated bacteria exhibited notably higher levels of cadmium adsorption and accumulation within their cells. A complete genome analysis revealed that E. roggenkampii FACU2 has one chromosome and one plasmid with a size of 4,856,454bp and 80,926bp, respectively, in addition to harboring numerous heavy metal-resistant genes related to cadmium and other heavy metals. Moreover, the gene expression of four cadmium-resistant genes (czcA, cadA, czcC and czcD) showed that the high cadmium concentration led to a significant increase in czcA and cadA mRNA levels, thus indicating the activation of cadmium-resistant genes in the E. roggenkampii FACU2 compared to Enterobacter sp. strain FACU. Due to its ability to remove cadmium and other heavy metals, this strain holds promise as a source of genes for biological treatment methods. This application could contribute to environmental purification, ultimately benefiting human health.

Single-cell analysis of a bi-clonal chronic lymphocytic leukemia reveals two clones with distinct gene expression pattern

Dual productive B-cell receptor (BCR) rearrangements have been repeatedly reported for chronic lymphocytic leukemia (CLL), but the standard population-based PCR analyses cannot distinguish whether these are bi-clonal CLL, or a monoclonal CLL with bi-allelic productive rearrangements. We investigated CLL cells by combined single-cell RNA and BCR sequencing. We identified two CLL clones using different immunoglobulin (Ig) heavy-chain V region genes (IGHV) genes and distinct Ig λ light chains. One clone is classified as Ig unmutated the other as mutated. The two CLL clones have distinct transcriptomes: Numerous genes were differentially expressed, with genes typical for unmutated or mutated CLL showing the expected representation in the two clones. Using PCR, cloning and Sanger sequencing of the IGHV rearrangements we detected both CLL clones over a period of three years without clinical progression of the CLL and thus giving insights into the disease biology of multi-clonal CLL.

Modulation of signature cancer-related genes in oral cancer cells (Ca9-22) by anethole treatment: Insights into therapeutic potential.

To explore an alternative strategy to chemotherapy to combat oral cancer, natural products and their derivates constitute one promising approach. In the last previous study, we have demonstrated the potential anti-tumor properties of anethole; an aromatic compound abundantly present in nature that serves as a major active ingredient found in plants like anise and fennel. In the current study, we aimed to investigate how this molecule inhibits oral cancer cell proliferation and induces apoptosis. This will be carried out by a transcriptomic study of its effects on the expression profile of cell cycle and apoptosis regulation genes in gingival cancer cells. cell cycle. Ca9-22 cells were treated with 10 μM of anethole (IC50) and cell proliferation was evaluated by MTT assay. The percentage of cells in different stages of the cell cycle was measured by flow cytometry. Cytotoxicity was evaluated by LDH assay and apoptosis was investigated by Pi/Annexin V assay following 24-hour treatment. Furthermore, we employed PCR array analysis to investigate alterations in the expression levels of oncogenes and tumor suppressor genes associated with cell cycle regulation and apoptosis. Finally, Gene-gene interactions were examined using the Gene MANIA database. Our findings demonstrate that anethole significantly attenuated the proliferation of Ca9-22 cells, leading to disturbances in cell cycle progression and eliciting cellular toxicity and apoptosis. By a double normalizing with two housekeeping genes (Actin and GAPDH), we show that, treatment with 10 μM of anethole alters (more than two-fold) the expression of 13 genes involved in the control of the cell cycle (8 were up regulated and 5 were down regulated) and 7 genes involved in the regulation of apoptosis (4 were up regulated and 3 downregulated by anethole). Finally, each group of genes modulated by anethole forms a network of connections between them or with other genes. Our study suggests that anethole holds promise as a potential alternative treatment for oral cancer by its ability to modify numerous oncogenes and tumor suppressor genes implicated in the cell cycle regulation and induction of apoptosis in oral cancer cells. These findings underscore the significance of further research into the potential therapeutic application of anethole as an alternative drug for managing oral cancer.

Molecular Mechanisms of Rett Syndrome: Emphasizing the Roles of Monoamine, Immunity, and Mitochondrial Dysfunction

Rett syndrome (RTT), which predominantly affects females, arises in most cases from mutations in the Methyl-CpG-binding Protein-2 (MECP2) gene. When MeCP2 is impaired, it disrupts the regulation of numerous genes, causing the production of dysfunctional proteins associated with various multi-systemic issues in RTT. In this review, we explore the current insights into molecular signaling related to monoamines, immune response, and mitochondrial function, and their implications for the pathophysiology of RTT. Research has shown that monoamines—such as dopamine, norepinephrine, epinephrine, serotonin, and histamine—exhibit alterations in RTT, contributing to a range of neurological symptoms. Furthermore, the immune system in RTT individuals demonstrates dysfunction through the abnormal activity of microglia, macrophages, lymphocytes, and non-immune cells, leading to the atypical release of inflammatory mediators and disruptions in the NF-κB signaling pathway. Moreover, mitochondria, essential for energy production and calcium storage, also show dysfunction in this condition. The delicate balance of producing and scavenging reactive oxygen species—termed redox balance—is disrupted in RTT. Targeting these molecular pathways presents a promising avenue for developing effective therapies.

MiPEPs and cPEPs as tools to monitor plant gene expression and develop alternative strategies in agriculture.

In order to develop a sustainable agriculture respecting the environment and to reduce chemical inputs, a new strategy has emerged in recent years, based on the use of products targeting plants' natural defense and growth mechanisms. In this context, a few years ago we demonstrated the existence in plants of regulatory peptides called miPEPs for "microRNA-encoded peptides". MicroRNAs (miRNAs) are small RNAs that down-regulate the expression of numerous genes in eukaryotes. MiPEPs increase the amount of their cognate miRNA, resulting in an even greater decrease in the expression of genes targeted by these miRNAs. Thus, the application of an artificial miPEP to a plant causes a phenotype associated with a change in the genes targeted by the corresponding miRNA. More recently we also identified new regulatory peptides, namely cPEPs for "complementary peptides", capable of enhancing the activity of a given protein, independently of any increase in transcriptional activity. Moreover, as for the miPEPs, the external application of these new peptides makes it possible to regulate the phenotypes associated with the targeted proteins. This review highlights the most recent advances in the potential use of miPEPs and cPEPs in agronomy to improve plant development and stress tolerance.

Reduced Expression of Oxidative Stress-Related lncRNAs LINC-PINT and SNHG5 in Schizophrenia: Implications for Biomarker Development.

Schizophrenia is a mental condition that impairs several aspects of brain function and behavior. Recent investigations highlighted abnormal function of numerous genes in this context. Notably, genes that affect oxidative stress and neuron damage were the focus of several studies. In an attempt to find a biomarker that can be quantified in the peripheral blood, we assessed blood expression of three lncRNAs that were associated with these processes in patients with schizophrenia and matched controls. We observed a statistically significant downregulation of SNHG5 in the patient group compared to healthy controls, with P-values of < 0.0001, 0.0008, and 0.003 in total, male, and female patients, respectively. LINC-PINT was also found to be down-regulated in all comparisons between patients and controls with P-values of < 0.0001, < 0.0001 and = 0.01, in total, male, and female patients, respectively. However, statistical analyses disclosed no notable difference in the expression of TP53TG1 between study subgroups. Most notably, LINC-PINT and SNHG5 could discriminate between patients and controls with acceptable AUC and specificity values. Cumulatively, the results of this study propose down-regulation of LINC-PINT and SNHG5 as a possible peripheral indicator of the presence of schizophrenia.

Skin as outermost immune organ of vertebrates that elicits robust early immune responses after immunization with glycoprotein of spring viraemia of carp virus.

As the outermost immune organ in vertebrates, the skin serves as the primary interface with the external environment and plays a crucial role in initiating the early immune response. The skin contains a variety of immune cells that induce mucosal and systemic immune responses, rendering it a prime target for vaccination strategies. Insight into the mechanisms through which vaccination triggers early immune responses is paramount for advancing animal and human health, yet our current understanding remains limited. Given its significance in vertebrate evolution, teleost fish emerges as an excellent model for investigating the early immune response of skin. In this study, we demonstrate that significant quantities of vaccine can be absorbed by the skin and transported to the body through dermis and muscle metabolism by immerses immune zebrafish with glycoprotein of spring viraemia of carp virus. Immersion immunization can elicit robust and enduring immune protection, with the skin triggering a potent immune response early in the immunization process. Analysis of the skin transcriptome revealed the involvement of numerous immune-related genes in the immersion immune response, with indications that HSP70 and MAPK signals might play pivotal roles in the immune process induced by glycoprotein. Co-immunoprecipitation and cell co-localization studies confirmed the interaction between glycoprotein and HSP70. Subsequent research demonstrated that overexpression or inhibition of HSP70 could respectively enhance or impede the expression of JNK and related proteins. However, the survival rate and immune response of HSP70 inhibited zebrafish with glycoprotein treatment were significantly reduced. These findings propose that the interaction between glycoprotein and HSP70 may activate JNK, thereby modulating mucosal and systemic immune responses induced by glycoprotein. This investigation offers novel insights and a foundational understanding of early skin immune reactions.

Mechanism of acclimation to chronic intermittent hypoxia in the gills of largemouth bass (Micropterus salmoides).

The acclimation response of fish gills to chronic intermittent hypoxia (CIH) is an important aspect to understand, as anthropogenically induced hypoxia in water bodies has been a stressor for fish for many years and is expected to persist in the future. In order to investigate the acclimation response of fish gills to CIH stress, we conducted a study using largemouth bass (Micropterus salmoides) exposed to intermittent hypoxia (dissolved oxygen level, 2.0mg·L-1) for either 1 or 3h per day, over a period of 8weeks. Our findings indicate that exposure to CIH induced remodeling of the gills and an increase in gill surface area. This remodeling of the gills may be attributed to changes in cell growth and proliferation, which are influenced by the activation of the MAPK signaling pathway. We also observed significant upregulation of genes related to glycolysis (fba, pgam1, pepck, atp-pfk, pfk-2, g6pi, gapd-1, and pk), while genes associated with cholesterol synthesis (3β-hsd, cyp51, dsdr- × 1, dsdr, and dhcr7) were downregulated following CIH exposure. Furthermore, we observed the presence of elongated megamitochondria in mitochondria-rich cells within the gills of fish exposed to hypoxia. Additionally, numerous genes involved in calcium signaling pathways were upregulated in the gills of largemouth bass, suggesting an enhanced sensitivity of gills to environmental cues in hypoxia conditions. However, the expression levels of certain genes related to innate and adaptive immune responses were inhibited following CIH exposure. Moreover, the number of mucous cells decreased after CIH exposure. This may have made the gills more susceptible to infection by pathogens, although it facilitated oxygen uptake. These findings highlight the potential vulnerability of gills to pathogenic organisms in the presence of CIH. Overall, our study contributes to a better understanding of how fish acclimate to CIH.

A pilot study of interferon-induced helicase and glutamate decarboxylase gene polymorphism with autoimmune thyroid disease

ABSTRACT Background Numerous genes are involved in immune system modulation, and their polymorphisms may contribute to developing autoimmune disorders. Genetic variation contributes significantly to disease susceptibility to autoimmune thyroid disease (AITD). Objectives This work aims to investigate the role of single-nucleotide polymorphisms (SNPs) of interferon induced with helicase C domain 1 (IFIH1) rs1990760 and glutamate decarboxylase (GAD) rs769404 in AITD development. Methods The study had 330 participants, including 153 cases of Hashimoto’s thyroiditis (HT), 77 cases of Graves’ disease (GD), and 100 healthy controls. All subjects underwent medical history assessment and clinical evaluation. Tests were conducted using real-time PCR, including genotyping of IFIH1 (rs1990760) and GAD (rs769404) via an allele discrimination assay. Results Most patients with AITD were females. About 18.3% of HT cases and 15.6% of GD cases have a positive family history of thyroid disease. A significant statistical difference was observed between AITD cases and control regarding IFIH1 (rs1990760) and GAD (rs769404) gene polymorphism. Moreover, GD patients, HT patients, and the control group showed increased CT and TT alleles in patients compared to those in controls. Conclusion IFIH1 and GAD polymorphisms are involved in AITDs (HT and GD) development and are associated with some clinical presentations. HT and GD cases had a positive family history of thyroid disease. There was a significant statistical difference between AITD cases and control regarding IFIH1 (rs1990760) and GAD (rs769404) gene polymorphism.

Prevalence and virulence of Vibrio parahaemolyticus isolated from clinical and environmental samples in Huzhou, China

BackgroundVibrio parahaemolyticus has emerged as the leading cause of seafood-associated infections worldwide. Previous studies have shown that V. parahaemolyticus can be detected in both environmental and clinical samples. However, the molecular characteristics of V. parahaemolyticus isolated from these sources remain unknown.ResultsThis study examined 128 strains of V. parahaemolyticus isolated from clinical and environmental samples collected between 2020 and 2023 in Huzhou, China. We identified 73 serotypes; O10:K4, O3:K6, and O4:KUT were the dominant serotypes among clinical isolates. We examined the proliferation and motility of major epidemic strains from environmental and clinical samples. Genetic diversity and evolution were assessed by average nucleotide identity (ANI), phylogenetic tree construction, and multilocus sequence typing (MLST). Furthermore, we identified 13 novel sequence types (STs) among the environmental isolates, indicating that V. parahaemolyticus strains are widely distributed and evolve rapidly in the environment in Huzhou, China. We found 206 virulence genes among these isolates, indicating that environmental isolates possess numerous virulence genes. Additionally, we detected 4 strains carrying the tdh or trh gene, which may increase their pathogenicity. The prediction results of antibiotic resistance genes shown that environmental isolates may carry up to 104 resistance genes, compared to 30 in clinical isolates.ConclusionsWe observed that the environmental serotypes of V. parahaemolyticus exhibit greater diversity compared to clinical isolates, which are predominantly concentrated in three major serotypes. Furthermore, a considerable genetic distance was found between most clinical and environmental isolates. Notably, some clinical isolates show a closer genetic proximity to environmental isolates. Additionally, the distribution of virulence genes, specifically T3SS and tdh, significantly differs among isolates from these two distinct sources. The prediction results for antibiotic resistance genes suggest that environmental isolates may harbor a broader spectrum of resistance genes. The findings of this study provide new insights into the phylogenetic relationships between V. parahaemolyticus strains from clinical and environmental sources, and they enhance the MLST database.

Fetal hepatocytes protect the HSPC genome via fetuin-A.

The maintenance of genomic integrity in rapidly proliferating cells is a substantial challenge during embryonic development1-3. Although numerous cell-intrinsic mechanisms have been revealed4-7, little is known about genome-protective effects and influences of developmental tissue microenvironments on tissue-forming cells. Here we show that fetal liver hepatocytes provide protection to haematopoietic stem and progenitor cell (HSPC) genomes. Lineage tracing and depletion in mice demonstrated that delayed hepatocyte development in early fetal livers increased the chromosomal instability of newly colonizing HSPCs. In addition, HSPCs developed tolerance to genotoxins in hepatocyte-conditioned medium, suggesting that hepatocytes protect the HSPC genome in a paracrine manner. Proteomic analyses demonstrated the enrichment of fetuin-A in hepatocyte-conditioned medium but not in early fetal livers. Fetuin-A activates a Toll-like receptor pathway to prevent pathogenic R-loop accumulation in HSPCs undergoing DNA replication and gene transcription in the fetal liver. Numerous haematopoietic regulatory genes frequently involved in leukaemogenic mutations are associated with R-loop-enriched regions. In Fetua-knockout mice, HSPCs showed increased genome instability and susceptibility to malignancy induction. Moreover, low concentrations of fetuin-A correlated with the oncogenesis of childhood leukaemia. Therefore, we uncover a mechanism operating in developmental tissues that offers tissue-forming cell genome protection and is implicated in developmental-related diseases.

The calcium sensor AtCML8 contributes to Arabidopsis plant cell growth by modulating the brassinosteroid signaling pathway.

Calcium signaling plays an essential role in integrating plant responses to diverse stimuli and regulating growth and development. While some signaling components and their roles are well-established, such as the ubiquitous calmodulin (CaM) sensor, plants possess a broader repertoire of calcium sensors. Notably, CaM-like proteins (CMLs) represent a poorly characterized class for which interacting partners and biological functions remain largely elusive. Our work investigates the role of Arabidopsis thaliana CML8 that exhibits a unique expression profile in seedlings. A reverse genetic approach revealed a function of CML8 in regulating root growth and hypocotyl elongation. RNA-seq analyses highlighted CML8 association with the regulation of numerous genes involved in growth and brassinosteroid (BR) signaling. Using co-immunoprecipitation experiments, we demonstrated that CML8 interacts with the BR receptor, BRI1, in planta in a ligand-dependent manner. This finding suggests the existence of a novel regulatory step in the BR pathway, involving calcium signaling.

Investigation of polymorphism and expression of the tyrosinase (TYR) gene as a gene controlling coat color in Bali cattle

Cattle coat color is governed by numerous genes, notably the tyrosinase gene (TYR). This study analyzed coat color anomalies like albinism and white spotting in Bali cattle. It aims to discern the TYR gene's diversity, expression patterns, and correlation with coat color abnormalities. The research encompassed 189 cattle, including those with standard coat color (n=53), white-spotted (n=11), and albino (n=17) Bali cattle, as well as Simmental (n=37), Limousin (n=14), Madura (n=21), and Peran-akan Ongole (PO) cattle (n=36). Total DNA was extracted and the TYR gene in exon 1 was amplified using forward and reverse primers with a target amplicon length of 994 bp. Direct sequencing unveiled TYR gene diversity, analyzed using BioEdit and MEGA6 software to identify SNPs. PCR-RFLP was used for SNP genotyping, while qPCR analyzed TYR gene expression. Two mutations (SNP g. 939A&gt;G and SNP g. 887C&gt;T) were discovered in Bali cattle TYR exon 1. SNP g. 939A&gt;G exhibited polymorphism, with the highest GG genotype frequency in standard Bali cattle, indicating a high G allele frequency. Conversely, Madura, Simmental, Limousin, and PO cattle had the lowest allele fre-quency. Chi-square (χ² test) results showed non-significance across all cattle types. TYR gene expres-sion differed significantly between standard Bali cattle and albinos (p&lt;0.05).

Rapid and high-throughput identification of thermal-responsive genes based on cDNA-library in Upland Cotton

Severe high temperature (HT) climate significantly impacts cotton quality and yield. Consequently, it is essential to mine thermal-responsive genes and explore the underlying mechanisms of HT response in cotton. In this study, we employed a high-throughput cDNA-library method in conjunction with the ALRS system to screen thermotolerant genes in Upland cotton. As a result, a total of 16,120, 13,216 and 172 effective survival genes were filtered after HT stress exposure (42 °C, 220 rpm) for 48 h, 60 h and 72 h, respectively. Functional annotation and enrichment analysis revealed that 170 common genes were involved in regulatory processes associated with HT stress, and the relevant transcriptome data indicated that the majority of these genes responded to temperature fluctuations. Twenty-one genes were randomly selected for verification, and it was found that these genes could enhance yeast resistance to HT stress. Additionally, we selected mutants of homologous Arabidopsis genes for four candidate genes to validate plant thermotolerance during flowering; the thermotolerances of SALK_201915 and SALK_120540.1 were significantly worse. The results demonstrate that numerous candidate genes identified from the cDNA-library contribute to the highly complex molecular network that governs the response and resistance to HT stress in Upland cotton. The high-throughput heat-screening method utilized in this study was optimized for mining thermotolerant genes including improvement in yeast library construction, screening system, gradient reverse pressure, and sequencing library construction. We hope that this new method can be applied in future studies on stress in cotton and other species.

Hypoxia-Inducible Factor inhibition affects luteal function with no effect on fertility in mice.

Hypoxia-inducible factors (HIFs) are transcription factors responsible for sensing low oxygen levels and, in response, inducing the transcription of numerous genes. One of the main processes stimulated by HIFs is the formation of new vessels to increase oxygen supply to the tissue. Formation of the corpus luteum strongly depends on the vasculature and an active angiogenesis occurs during luteinization. In this study, we aimed to analyze the role of HIF in corpora lutea early formation and function, and in female fertility. To this aim, we superovulated mice by eCG and hCG, and administered the HIF inhibitor acriflavine (ACF) to the mice 3 h before hCG. We found a decrease in ovarian HIF1A and VEGFA, and in the vascular area in the animals treated with ACF. Moreover, we observed an increase in aberrant structures in the ovaries and in luteal cell apoptosis. Serum progesterone levels were decreased together with ovarian STAR expression. However, the animals treated with ACF during the early formation of the corpus luteum were completely fertile and no alterations were observed when the treated females were mated with fertile males. These results collectively suggest that HIF regulates gonadotropin-induced corpus luteum formation acting on luteal blood vessel formation, luteal cell survival, and progesterone synthesis. However, adequate HIF activity may not be essential to achieve and maintain pregnancy. These findings are significant to better understand the complex mechanisms of corpus luteum formation and identify potential abnormalities to allow better knowledge of ovarian physiology and pathologies in which this factor could be involved.

RNA-seq and Ribosome Profiling Reveal the Translational Landscape of Rice in Response to Rice Stripe Virus Infection

Rice is a crucial staple food for over half the global population, and viral infections pose significant threats to rice yields. This study focuses on the Rice Stripe Virus (RSV), which is known to drastically reduce rice productivity. We employed RNA-seq and ribosome profiling to analyze the transcriptional and translational responses of RSV-infected rice seedlings. Our results reveal that translational reprogramming is a critical aspect of the plant’s defense mechanism, operating independently of transcriptional changes. Notably, less than half of the differentially expressed genes showed concordance between transcription and translation. Furthermore, RSV infection led to significant alterations in translational efficiency for numerous genes, suggesting that the virus selectively manipulates translation to enhance its pathogenicity. Our findings underscore the necessity of examining both transcriptional and translational landscapes to fully understand plant responses to viral infections.

Long-read sequencing enables comprehensive molecular genetic diagnosis of Fabry disease

BackgroundThe clinical diagnosis of Fabry Disease (FD) can be challenging due to the clinical heterogeneity, especially in females. Patients with FD often experience a prolonged interval between the onset of symptoms and receiving a diagnosis. Genetic testing is the gold standard for precise diagnosis of FD, however conventional genetic testing could miss deep intronic variants and large deletions or duplications. Although next-generation sequencing, which analyzes numerous genes, has been successfully used for FD diagnosis and can detect complex variants, an effective and rapid tool for identifying a wide range of variants is imminent, contributing to decrease the diagnostic delay.MethodsThe comprehensive Analysis of FD (CAFD) assay was developed for FD genetic diagnosis, employing long-range PCR coupled with long-read sequencing to target the full-length GLA gene and its flanking regions. Its clinical performance was assessed through a comparative analysis with Sanger sequencing.ResultsGenetic testing was performed on 82 individuals, including 48 probands and 34 relatives. The CAFD assay additionally identified variants in two probands: one had a novel and de novo pathogenic variant with a 1715 bp insertion in intron 4, and the other carried two deep intronic VUS variants in cis-configuration also in intron 4. In total, CAFD identified 47 different variants among 48 probands. Of these, 42 (89.36%, 42/47) were pathogenic, while 5 (10.64%, 5/47) were VUS. Sixteen (34.04%, 16/47) of the variants were novel, including 15 SNV/Indels and one large intronic insertion. Pedigree analysis of 21 probands identified four de novo disease-causing variants. Hence, FD exhibits not only variable clinical presentations but also a wide spectrum of variants. Utilizing a comprehensive testing algorithm for diagnosing FD, which includes enzyme activity, clinical features, and genetic testing, the diagnostic yield of CAFD is 97.92% (47/48), which is higher than that of conventional Sanger sequencing, at 95.83% (46/48).ConclusionThe duration between initial clinical presentation and diagnosis remains long and winding. CAFD provides precise diagnosis for a wide spectrum of GLA variants, promoting timely diagnosis and appropriate treatment for FD patients.

The global regulator SpoVG is involved in biofilm formation and stress response in foodborne Staphylococcus aureus

Staphylococcus aureus (S. aureus) is a primary culprit of food poisoning. As a highly adaptable pathogen, S. aureus demonstrates formidable biofilm-forming and stress tolerance capabilities, inducing significant challenges to eradicate food contamination caused by this organism. SpoVG, a regulatory protein in S. aureus, controls the expression of numerous genes. However, its role in biofilm formation and stress response in foodborne S. aureus remains to be elucidated. In this study, we investigated the functions of SpoVG involved in food-related stress responses and biofilm formation in S. aureus RMSA50. The results demonstrated that SpoVG deletion enhanced biofilm formation and resistance to heat and desiccation, while decreased tolerance to oxidative stress. Further analysis revealed that cell aggregation and the accumulation of extracellular DNA (eDNA) may contribute to the enhanced biofilm formation. Real-time quantitative reverse transcription-PCR (RT-qPCR) revealed that the expression levels of nuc and sasC, which are related to cell aggregation and eDNA concentration, were significantly altered in the spoVG mutant. Electrophoretic mobility shift assays (EMSA) confirmed that SpoVG directly binds to the promoter region of nuc and sasC to regulate their expression. These findings suggest that SpoVG may serve as a target to decrease biofilm formation and control S. aureus contamination in the food industry.

Multi-biome analysis identifies distinct gut microbial signatures and their crosstalk in ulcerative colitis and Crohn’s disease

The integrative multi-kingdom interaction of the gut microbiome in ulcerative colitis (UC) and Crohn’s disease (CD) remains underinvestigated. Here, we perform shotgun metagenomic sequencing of feces from patients with UC and CD, and healthy controls in the Japanese 4D cohort, profiling bacterial taxa, gene functions, and antibacterial genes, bacteriophages, and fungi. External metagenomic datasets from the US, Spain, the Netherlands, and China were analyzed to validate our multi-biome findings. We found that Enterococcus faecium and Bifidobacterium spp. were enriched in both diseases. Enriched Escherichia coli was characteristic of CD and was linked to numerous antibiotic resistance genes involved in efflux pumps and adherent-invasive Escherichia coli virulence factors. Virome changes correlated with shifts in the bacteriome, including increased abundances of phages encoding pathogenic genes. Saccharomyces paradoxus and Saccharomyces cerevisiae were enriched in UC and CD, respectively. Saccharomyces cerevisiae and Escherichia coli had negative associations with short-chain fatty acid (SCFA)-producing bacteria in CD. Multi-biome signatures and their interactions in UC and CD showed high similarities between Japan and other countries. Since bacteria, phages, and fungi formed multiple hubs of intra- or trans-kingdom networks with SCFA producers and pathobionts in UC and CD, an approach targeting the interaction network may hold therapeutic promise.