DNA microarray technology is an extremely effective technique for studying gene expression patterns in cells, and the main challenge currently faced by this technology is how to analyze the large amount of gene expres...DNA microarray technology is an extremely effective technique for studying gene expression patterns in cells, and the main challenge currently faced by this technology is how to analyze the large amount of gene expression data generated. To address this, this paper employs a mixed-effects model to analyze gene expression data. In terms of data selection, 1176 genes from the white mouse gene expression dataset under two experimental conditions were chosen, setting up two conditions: pneumococcal infection and no infection, and constructing a mixed-effects model. After preprocessing the gene chip information, the data were imported into the model, preliminary results were calculated, and permutation tests were performed to biologically validate the preliminary results using GSEA. The final dataset consists of 20 groups of gene expression data from pneumococcal infection, which categorizes functionally related genes based on the similarity of their expression profiles, facilitating the study of genes with unknown functions.展开更多
目的分析副溶血弧菌O10:K4血清型O抗原基因簇的分子特征,并构建基于基因组的分子血清型预测数据库。方法从美国国家生物技术信息中心Assembly数据库获取副溶血弧菌O抗原基因簇序列,使用blastn、fastANI、Sourmash和p i x y工具分析序列...目的分析副溶血弧菌O10:K4血清型O抗原基因簇的分子特征,并构建基于基因组的分子血清型预测数据库。方法从美国国家生物技术信息中心Assembly数据库获取副溶血弧菌O抗原基因簇序列,使用blastn、fastANI、Sourmash和p i x y工具分析序列相似性和多态性,使用g u b b i n s进行重组分析,并构建了副溶血弧菌分子血清型预测数据库。结果O10:K4的O抗原基因簇(OL10V1)与传统O10血清型基因簇(OL10)序列差异显著,而与OL4最为相似。公共数据库中116个OL10V1全长序列仅存在1个单核苷酸突变。OL10V1携带的IS1634和ISVa2转座酶基因广泛分布于弧菌属,提示该变异体可能通过水平基因转移形成。结论本研究揭示了O10:K4血清型快速传播的潜在分子机制,构建的分子血清型数据库可为基因组监测和溯源提供关键技术支撑。展开更多
Helicobacter pylori infection represents a widespread chronic condition with varying prevalence influenced by race, ethnicity, and geography. The severity of H. pylori-associated diseases is determined by an array of ...Helicobacter pylori infection represents a widespread chronic condition with varying prevalence influenced by race, ethnicity, and geography. The severity of H. pylori-associated diseases is determined by an array of virulence factors. Although extensive studies have been conducted globally, data on the distribution of Helicobacter pylori virulence genes in Libya remain limited, constraining insights into the pathogenicity of local strains and hindering the development of targeted interventions. This study aimed to evaluate the prevalence of H. pylori infection, characterize essential virulence genes [vacA variants (s1/s2, m1/m2), cagA, and iceA1], and examine their association with gastroduodenal diseases among Libyan patients. Gastric biopsies from 144 participants were analyzed using polymerase chain reaction (PCR) assays, and risk factor data were collected via questionnaires. H. pylori was detected in 63.2% of samples by PCR. The vacA gene was present in 84.6% of cases, cagA in 58.2%, and iceA1 in 29.7%. Among vacA variants, s1 allele was most common (53.2%), followed by m1 (42.9%), m2 (37.7%), and s2 (13%) alleles. Significant associations were identified between specific virulence genes and the development of gastroduodenal diseases, highlighting their role in pathogenicity. This investigation is one of Libya’s first comprehensive assessments of H. pylori virulence factors, addressing a critical epidemiological gap. The high prevalence of virulence genes suggests their potential as disease biomarkers. These findings contribute to a deeper understanding of H. pylori pathogenicity within the Libyan population and establish a basis for future clinical interventions and public health strategies to manage and prevent H. pylori-associated diseases in Libya and comparable regions.展开更多
文摘DNA microarray technology is an extremely effective technique for studying gene expression patterns in cells, and the main challenge currently faced by this technology is how to analyze the large amount of gene expression data generated. To address this, this paper employs a mixed-effects model to analyze gene expression data. In terms of data selection, 1176 genes from the white mouse gene expression dataset under two experimental conditions were chosen, setting up two conditions: pneumococcal infection and no infection, and constructing a mixed-effects model. After preprocessing the gene chip information, the data were imported into the model, preliminary results were calculated, and permutation tests were performed to biologically validate the preliminary results using GSEA. The final dataset consists of 20 groups of gene expression data from pneumococcal infection, which categorizes functionally related genes based on the similarity of their expression profiles, facilitating the study of genes with unknown functions.
文摘目的分析副溶血弧菌O10:K4血清型O抗原基因簇的分子特征,并构建基于基因组的分子血清型预测数据库。方法从美国国家生物技术信息中心Assembly数据库获取副溶血弧菌O抗原基因簇序列,使用blastn、fastANI、Sourmash和p i x y工具分析序列相似性和多态性,使用g u b b i n s进行重组分析,并构建了副溶血弧菌分子血清型预测数据库。结果O10:K4的O抗原基因簇(OL10V1)与传统O10血清型基因簇(OL10)序列差异显著,而与OL4最为相似。公共数据库中116个OL10V1全长序列仅存在1个单核苷酸突变。OL10V1携带的IS1634和ISVa2转座酶基因广泛分布于弧菌属,提示该变异体可能通过水平基因转移形成。结论本研究揭示了O10:K4血清型快速传播的潜在分子机制,构建的分子血清型数据库可为基因组监测和溯源提供关键技术支撑。
文摘Helicobacter pylori infection represents a widespread chronic condition with varying prevalence influenced by race, ethnicity, and geography. The severity of H. pylori-associated diseases is determined by an array of virulence factors. Although extensive studies have been conducted globally, data on the distribution of Helicobacter pylori virulence genes in Libya remain limited, constraining insights into the pathogenicity of local strains and hindering the development of targeted interventions. This study aimed to evaluate the prevalence of H. pylori infection, characterize essential virulence genes [vacA variants (s1/s2, m1/m2), cagA, and iceA1], and examine their association with gastroduodenal diseases among Libyan patients. Gastric biopsies from 144 participants were analyzed using polymerase chain reaction (PCR) assays, and risk factor data were collected via questionnaires. H. pylori was detected in 63.2% of samples by PCR. The vacA gene was present in 84.6% of cases, cagA in 58.2%, and iceA1 in 29.7%. Among vacA variants, s1 allele was most common (53.2%), followed by m1 (42.9%), m2 (37.7%), and s2 (13%) alleles. Significant associations were identified between specific virulence genes and the development of gastroduodenal diseases, highlighting their role in pathogenicity. This investigation is one of Libya’s first comprehensive assessments of H. pylori virulence factors, addressing a critical epidemiological gap. The high prevalence of virulence genes suggests their potential as disease biomarkers. These findings contribute to a deeper understanding of H. pylori pathogenicity within the Libyan population and establish a basis for future clinical interventions and public health strategies to manage and prevent H. pylori-associated diseases in Libya and comparable regions.
