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Results for “Genomic characterization”

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PubMed1995

Human genomic characterization of a novel locus-specific repetitive sequence.

A novel human chromosome locus-specific repetitive sequence was identified and characterized using arbitrary PCR. The repeat monomer consensus sequence is 100 bp long, and there are a minimum of 140 to 160 copies of the repetitive sequence per haploid human genome. The repetitive sequence is highly clustered on 20q12 within a 200- to 400-kb region. The highly polymorphic repeat array is inherited in a stable Mendelian fashion. Hybridization analysis revealed detectable conservation of the repeated element only among hominoids and Old World monkeys, where repeat arrangements are also polymorphic.

Animals↗

PubMed1998

Chromosomal localization and genomic characterization of the mouse melastatin gene (Mlsn1).

We recently described a novel gene, melastatin, whose expression is inversely correlated with melanoma aggressiveness. Chromosomal localization of this gene places it on mouse chromosome 7 and in the 15q13-q14 region of the human genome. Although expression patterns and chromosomal localization in the mouse are consistent with involvement of melastatin mutations in the mouse ruby-eye-2 defect, congenic analysis showed genetic segregation of the two loci. Cloning of the full-length human cDNA revealed a much larger transcript than we had previously identified, corresponding to a 1533-amino-acid protein product with homology to members of the transient receptor potential (Trp) family of calcium channels. The mouse melastatin gene contains 27 exons and spans at least 58 kb of genomic DNA. The promoter region of Mlsn1 contains four potential microphthalmia binding sites including an M box, a transcriptional regulatory element unique to genes with a restricted melanocytic expression pattern. A 1-kb PvuII fragment from this region was capable of driving high levels of luciferase expression in B16 melanoma cells.

Amino Acid Sequence↗

PubMed2026

Genomic characterization of aggressiveness in pituitary neuroendocrine tumors.

BACKGROUND: Aggressive evolution of PitNETs is rare; metastatic spread is even more. Defining aggressiveness and malignancy is challenging, subsequently hard to predict, and to understand. The aim was to provide a molecular definition of aggressiveness using genomic approaches. METHODS: PitNETs from 206 patients were included. Associations between 9 clinicopathological features of aggressiveness and PitNETs' omics were explored. Omics included transcriptome, DNA methylation, chromosomal alterations, and mutations. Clonal tumor evolution was monitored in 7 patients. RESULTS: Among the 9 clinicopathological features of aggressiveness, only rapid progression, progression after radiotherapy, Ki67/MIB1 proliferation index ≥10%, temozolomide treatment, metastases, and specific death were associated with specific omics signatures, while tumour maximal diameter ≥40 mm, cavernous, and sphenoid invasion were not. The omic signatures associated with these features of aggressiveness overlapped but remained distinct between corticotroph and mammo-somato-thyrotroph lineages. For each lineage, a common signature of aggressiveness was identified, associating a proliferative transcriptome signature and DNA hypermethylation. Alterations in specific genes were associated with aggressive features, including a novel PitNET gene, LRP1B, and known cancer genes (TP53, CDKN2A), while USP8 and GNAS alterations were not. Integration of gene alterations with methylome and transcriptome signatures isolated a subset of molecularly aggressive PitNETs. Molecular signatures were stable during the course of the disease, despite evolution toward aggressiveness and potential clonal divergence. CONCLUSION: This systematic analysis of clinicopathological features of aggressiveness using an integrated multiomic approach establishes a histomolecular definition of aggressiveness in PitNETs. Prospective cohort studies are needed to validate these molecular signatures and establish their prognostic value.

Humans↗

PubMed2003

Serologic and genomic characterization of a G12 human rotavirus in Thailand.

The G and P type specificity of the human rotavirus strain T-152 (G12P[9]) isolated in Thailand was serologically confirmed with G12-specific monoclonal antibodies prepared in this study by using a reference G12 strain, L26, as an immunizing antigen and a P[9]-specific monoclonal antibody, respectively. The genomic relationship of strain T-152 with representative human rotavirus strains was examined by means of Northern blot analysis. The results showed that T152 is closely related to strain AU-1 (G3P[9]). Gene 5 (NSP1 gene) of T152, which did not hybridize with those of any other strains examined, was characterized by sequence determination. The T152 NSP1 gene is 1,652 nucleotides in length, encodes 493 amino acids, and exhibits low identity to those of representative human and animal rotaviruses.

Animals↗

PubMed2026

Near Full-Length Genome Characterization of a Novel Second-Generation HIV-1 CRF01_AE/CRF07_BC Recombinant Identified in an MSM Individual in Guizhou, China.

The cocirculation of CRF01_AE and CRF07_BC among men who have sex with men (MSM) in China may facilitate the emergence of genetically complex HIV-1 recombinants. Here, we identified and characterized a novel second-generation HIV-1 CRF01_AE/CRF07_BC recombinant, designated GY0192, from a 25-year-old MSM individual in Guiyang, Guizhou Province, southwest China, using near full-length genome (NFLG) analysis. Recombination analyses identified four breakpoints at HXB2 positions 3,125, 5,687, 6,375, and 9,176, generating a distinct five-segment mosaic genome. Subregion phylogenetic analyses showed that the two CRF01_AE-derived fragments clustered with the CRF01_AE cluster 5 lineage, while all three CRF07_BC-derived fragments grouped with CRF07_BC lineages frequently circulating among MSM in China, indicating that both parental components of GY0192 were phylogenetically related to lineages frequently reported among MSM populations in China. The virus was also predicted to be CCR5-tropic, adding epidemiological relevance because CCR5-tropic viruses are commonly involved in transmission and early infection. Together, these findings identify GY0192 as a distinct CRF01_AE/CRF07_BC mosaic and suggest that cocirculating MSM-associated HIV-1 lineages may provide opportunities for interlineage recombination. This case expands the known spectrum of CRF01_AE/CRF07_BC recombinants in Guizhou and underscores the value of NFLG-based surveillance for detecting underrecognized HIV-1 genetic complexity in southwest China.

Humans↗

PubMed1993

Morphological and genomic characterization of two reoviruses (P and W2) pathogenic for marine crustaceans; do they constitute a novel genus of the Reoviridae family?

P and W2 viruses are pathogenic in two crustaceans of the Mediterranean Sea, Macropipus depurator and Carcinus mediterraneus, respectively. Investigation of virus, virus density and genome structure leads us to propose their classification in a genus similar to aquareovirus of the Reoviridae family. They differ from aquareoviruses by the number of dsRNA segments forming the genome (12 instead of 11), their electrophoretic pattern in PAGE (1/5/6 instead of 3/3/5), and the absence of virus replication in fish cell lines.

Animals↗

PubMed2001

Genomic characterization of Helicobacter hepaticus: ordered cosmid library and comparative sequence analysis.

Helicobacter hepaticus is an important pathogen in laboratory mice and induces the development of liver tumors and gastrointestinal disease in susceptible strains of mice. In this study, a miniset of 36 cosmid clones from a genomic library of H. hepaticus was ordered and grouped into four large contigs representing approximately 1 Mb of the H. hepaticus genome using PCR, DNA sequencing, Southern and dot-blot hybridization and pulsed-field gel electrophoresis. From the 200-300 terminal nucleotide sequences of 38 cosmid clones, 56 coding regions were predicted, of which 51 were found to have orthologs in the public databases and five appeared to be unique to H. hepaticus. Of these 51 genes, 36 have orthologs in Helicobacter pylori and 25 display the highest sequence similarity to H. pylori. However, chromosomal positions of these genes are not conserved between these two helicobacters. In addition, 10 H. hepaticus genes had the highest sequence similarity to orthologs in Campylobacter jejuni. The GC content in a randomly selected 21-kb H. hepaticus genomic sequence was 35.8%, which approximates the average between H. pylori (39%) and C. jejuni (30.6%). These results demonstrate that: (1) H. hepaticus is more closely related to H. pylori than C. jejuni; (2) significant genomic alterations exist between H. hepaticus and H. pylori, including gene organization, protein sequences and GC content, probably in part due to specific adaptation to distinct ecological niches.

Animals↗

PubMed1996

[Antigenic and genomic characterization of Herpes simplex virus isolated from double genital infections].

Two Herpes simplex viral serotypes, HSV type 1 and HSV type 2 may cause genital herpes. The aim of this study was to perform a genetical analysis and characterization of virus isolated from four patients with double genital herpetic infections. In eleven viral isolates, the cytopathic effect in Vero cells was studied, the antigenic type was determined using monoclonal antibodies and genomic analysis was performed with Eco RI, Hind III and Bgl II enzymes. Five viral isolates generated a diffuse and 6 a localized cytopathic effect. Monoclonal antibodies identified four HSV-1 and seven HSV-2. Genomic analysis had concordant results. Four HSV-1 were obtained, with different genomic patterns within them, three were different to the standard North American strain. The seven HSV-2 obtained had three different types of electrophoretic profiles, that were different to the standard North American strain. It is concluded that the genomic and antigenic analysis allowed the detection of herpetic genital infections caused by herpes virus type 1 and 2 in the same individual and the identification of herpes virus strains with distinct regional characteristics.

Antigens, Viral↗

PubMed2006

[Genomic characterization of tomato yellow leaf curl China virus and its associated satellite DNA infecting tobacco in Guangxi].

The virus isolates G102 and G103 were collected from tobacco showing leaf curl symptoms in Jingxi, Guangxi Province. A 0.5kb fragment was obtained by PCR using primers specific to geminivirus genome. The nucleotide sequence identity of the partial DNA-A sequence between the two isolates was over 99%. The complete DNA-A sequence of G102 was determined to be 2728 nucleotides. Comparisons showed that the DNA-A of G102 had the highest sequence identity (96.5%) with that of Tomato yellow leaf curl China virus (TYLCCNV). Further studies showed that both G102 and G103 were associated with satellite DNA molecules (DNAbeta). Sequence analysis revealed that DNAbeta of G102 and G103 contained 1342nt and they shared the highest sequence identities (92.9% and 93.4%, respectively) with that of TYLCCNV. This is the first report that TYLCCNV isolates in Guangxi were also associated with satellite DNA molecules. The previously results demonstrated that all 25 TYLCCNV isolates collected in Yunnan province were associated with DNA beta molecules. The finding that TYLCCNV isolates collected in Guangxi province were also associated with DNA beta molecules gives further evidence that TYLCCNV isolates are associated with DNA beta molecules in nature.

Begomovirus↗

PubMed2026

Genomic Characterization of Antimicrobial Resistance and Virulence in ST11 Carbapenem-Resistant Klebsiella Pneumoniae Colonizing the Intestinal Tract of Elderly Inpatients.

BACKGROUND: This study aimed to elucidate the molecular epidemiology and virulence characteristics of ST11 carbapenem-resistant Klebsiella pneumoniae (CRKP) colonizing the intestinal tract of elderly inpatients in the Chongzhou region, providing a basis for controlling the transmission of such resistant bacteria in high-risk populations. METHODS: CRKP strains isolated from the intestines of elderly inpatients in this region between January 2023 and June 2024 were collected. ST11 strains were identified via multilocus sequence typing (MLST). Whole-genome sequencing, antimicrobial susceptibility testing, and string test, serum killing, biofilm formation, capsular polysaccharide quantification were employed to characterize their resistance genes, virulence genes, and molecular typing profiles. RESULTS: Among 58 CRKP isolates, 17 (29.3%) were ST11. ST11-KL64 was the dominant clone (70.6%). All isolates carried the carbapenemase gene bla KPC-2 and exhibited extensive drug resistance, with tigecycline retaining the highest susceptibility (64.7%). The yersiniabactin system genes (ybtS, fyuA, entB) were universally present, whereas the aerobactin gene cluster (iucABCD-iutA) was detected in only 17.6% of isolates. The virulence regulator rmpA2 was incomplete in all carriers. The hypermucoviscosity phenotype was observed in 35.3% of isolates, which correlated with serum resistance in some strains. Biofilm formation was variable. The mortality rate among colonized patients was 35.3%. CONCLUSION: The ST11-KL64 clone is dominant among CRKP strains colonizing the intestinal tract of elderly patients in this region. This clone universally carries the bla KPC-2 gene conferring carbapenem resistance and exhibits a unique virulence gene profile characterized by a low carriage rate of classical hypervirulence markers and an incomplete rmpA2 regulator gene. This finding clarifies the local epidemic status of this clone and underscores the importance of implementing active surveillance and targeted prevention strategies for high-risk populations.

KL64 serotype↗

PubMed2004

Genomic characterization of thermophilic Geobacillus species isolated from the deepest sea mud of the Mariana Trench.

The thermophilic strains HTA426 and HTA462 isolated from the Mariana Trench were identified as Geobacillus kaustophilus and G. stearothermophilus, respectively, based on physiologic and phylogenetic analyses using 16S rDNA sequences and DNA-DNA relatedness. The genome size of HTA426 and HTA462 was estimated at 3.23-3.49 Mb and 3.7-4.49 Mb, respectively. The nucleotide sequences of three independent lambda-phage inserts of G. stearothermophilus HTA462 have been determined. The organization of protein coding sequences (CDSs) in the two lambda-phage inserts was found to differ from that in the contigs corresponding to each lambda insert assembled by the shotgun clones of the G. kaustophilus HTA426 genome, although the CDS organization in another lambda insert is identical to that in the HTA426 genome.

Bacillaceae↗

PubMed1997

A proposed rapid method for genomic characterization of GBV-C/hepatitis G virus (HGV).

GBV-C/Hepatitis G virus (HGV) has been identified as an infectious agent for humans although its potential involvement as a pathogenic virus is still controversial. Hitherto, 3 genotypes have been identified worldwide by c-DNA sequencing. This method allows genomic viral RNA clustering according to the geographical source of the strains, but its potential value in type- (or even strain-) specific pathogenesis has only started to be explored. Since this method requires highly specialized laboratories and is rather expensive, we propose a rapid method based on differential restriction fragment length polymorphism (RFLP) of 5' NCR amplicons. Using Hinf I, Dra I and Mae II endonucleases, it is possible to obtain different restriction patterns to discriminate among 1a, 1b, 2a, 2b and 3 subtypes/types. This methodology could be useful for large scale molecular epidemiology as well as for studies on viral pathogenesis.

Flaviviridae↗

PubMed1997

Genomic characterization of the mouse homolog of the Saccharomyces cerevisiae recombination and double-strand break repair gene RAD52.

The yeast Saccharomyces cerevisiae RAD52 gene is involved in recombination and DNA double-strand break repair. Recently, mouse and human homologs of the yeast RAD52 gene have been identified. Here we present the genomic organization of the mouse RAD52 gene. It consists of 12 exons ranging in size from 67 to 374 bp spread over a region of approximately 18 kb. The first ATG is located in exon 2. Analysis of the promoter region revealed no classical promoter elements such as CCAAT or TATA boxes. Transcriptional mapping analysis revealed one major transcription start point. Analogous to the situation in yeast, transcription of the RAD52 gene in human skin fibroblasts and mouse Ltk- cells was not induced by methyl methanesulfonate treatment. Furthermore, no specific alteration in human RAD52 expression levels throughout the cell cycle was observed.

Animals↗

PubMed2025

Complete genome sequence and genomic characterization of the probiotic Limosilactobacillus reuteri PSC102.

BACKGROUND: Gut microbiota are potential sources of probiotics and play an essential role in maintaining intestinal health. Limosilactobacillus reuteri PSC102 (L. reuteri PSC102), which was isolated from the feces of healthy pigs, exhibited health-beneficial properties. AIM: We aimed to conduct a whole-genome sequencing analysis of L. reuteri PSC102 to determine its molecular characteristics as a probiotic strain. METHODS: Limosilactobacillus reuteri PSC102 cells were cultured in De Man-Rogosa-Sharpe medium, followed by DNA extraction for genomic analysis using the PacBio-Illumina sequencing platform. The EzBioCloud software was used to perform gene assembly, and the genes were interpreted by the National Center for Biotechnology Information (NCBI) and the Glimmer program. Core and pan-genomic analyses were performed to assess the extent of functional conservation in the genomic sequence. Moreover, the NCBI database and the Basic Local Alignment Search Tool software were used to identify antimicrobial resistance genes and virulence factors. RESULTS: Limosilactobacillus reuteri PSC102 consists of a single circular chromosome with 2,048,626 bp, a guanine- cytosine of 38.9%, 18 rRNA genes, and 69 tRNA genes. Among the 1,846 protein-coding sequences, genes associated with probiotic characteristics were identified, including genes involved in host-microbe interactions, stress tolerance, biogenesis, and defense mechanisms. Furthermore, the genome of L. reuteri PSC102 comprises 2,446 pan-genome and 1,222 core-genome orthologous gene clusters. A total of 74 unique genes were identified in L. reuteri PSC102 genome. These genes mostly encode proteins potentially involved in the transport and metabolism of amino acids and carbohydrates. Moreover, antibacterial resistance genes and virulence factors were absent in L. reuteri PSC102. CONCLUSION: The results of the molecular insight into L. reuteri PSC102 corroborates its use as a probiotic in humans and other animals.

Limosilactobacillus reuteri↗

PubMed2005

Genomic characterization of MHC class I genes of the horse.

The availability of a contig of bacterial artificial chromosome (BAC) clones spanning the equine major histocompatibility complex (MHC) made possible a detailed analysis of horse MHC class I genes. Prior to this study, only a single horse MHC class I gene had been sequenced at the genomic level. Although many ( approximately 60) MHC class I cDNA sequences had been determined and published, from this information, it was not possible to determine how many class I loci are expressed in horses or to assign individual sequences to allelic series. In this study, 15 MHC class I genes were identified in BAC subclones and fully sequenced. Because the BAC library donor horse had been bred for homozygosity at the MHC, these 15 genomic clones represent distinct MHC class I genes and pseudogenes and not alleles at a smaller number of loci. For five of the genes, cDNA sequences from these loci had previously been identified. Two additional expressed class I genes were discovered, bringing the known total of different equine MHC class I genes (loci) expressed as mRNA to seven. Expression of all seven loci was detected by reverse transcriptase-polymerase chain reaction in adult, fetal, and placental tissues. The remaining eight genes were designated as pseudogenes. This work resulted in moderate expansion of the horse MHC BAC contig length, and the remaining gap was shortened. The information contained in these equine MHC class I sequences will permit comparison of MHC class I genes expressed across different horse MHC haplotypes and between horses and other mammalian species.

Alleles↗

PubMedDate not supplied

Genomic characterization of adenovirus serotype 7 isolated in Brazil from acute respiratory disease patients during the period from 1980 to 1991.

Forty isolates of adenovirus type 7 were analized by restriction enzyme digestion with BamHI, SmaI, EcoRI and HindIII. These isolates were obtained from acute respiratory disease patients during the years 1980 to 1991. Only two genomic types were found: Ad7b and Ad7e, with Ad7b (87.5%) being more frequent than Ad7e (12.5%). The genomic type Ad7e appeared in the years 1980, 1981 and 1983. Ad7b appeared in 1982 and it was the only genomic type found from 1984 to 1991. Both genomic types were responsible for lower (LRTI) and upper (URTI) respiratory tract infection, but the proportion LRTI/URTI is higher for Ad7b (25/6) than for Ad7e (1/4).

Acute Disease↗

PubMed2026

First molecular detection and genomic characterization of West Nile virus associated with a naturally aborted sheep in Tunisia.

In September 2025, West Nile virus (WNV) RNA was detected for the first time in a sheep in Zaghouan Governorate, Tunisia. Following sheep abortions, fetal specimens were analyzed and one tested positive for WNV by RT-qPCR. The generated near-complete WNV genome sequence by Oxford Nanopore Technologies belonged to Lineage 1a, previously associated with locally reported human neuroinvasive cases in the same area. Amino acid analysis of the envelope (E) protein confirmed the presence of the conserved NYS glycosylation motif (E154-E156), a characteristic feature of Euro-Mediterranean Lineage 1 WNV strains. These findings further support the endemic circulation of WNV in Tunisia and underline its significance for both animal and public health.

Abortion↗

PubMed2026

Comparative genomic characterization and antimicrobial resistance of bacteremia-causing Enterococcus faecium and Enterococcus faecalis in a Chinese hospital.

Enterococci are common commensals of the human gut and important opportunistic pathogens, with Enterococcus faecium and Enterococcus faecalis being the most clinically prevalent species. A significant epidemiological shift has emerged with an increasing clinical burden of E. faecium. To compare genomic evolution of E. faecium and E. faecalis, we performed whole-genome sequencing on 93 E. faecium and 32 E. faecalis isolates causing bloodstream infections at a single hospital (2022-2024). Analysis of patient demographics revealed that E. faecium infections originated from fewer sources than E. faecalis, with a higher proportion deriving from intra-abdominal infections. Multilocus sequence typing identified ST78 and ST789 as the predominant sequence types for E. faecium, whereas ST16 and ST179 were most common for E. faecalis. E. faecium carried more antimicrobial resistance genes and putative virulence marker (PVM)-type virulence genes than E. faecalis, with vancomycin resistance predominantly mediated by vanHAX (33/93, 35.5%) and a single E. faecalis isolate also carrying vanHAX (1/32, 3.1%); the structurally incomplete vanHMX gene cluster was detected in 11 E. faecium isolates. Pan-genome analysis indicated a larger core genome in E. faecalis compared to E. faecium, consistent with greater plasmid replicon diversity in the latter. Intra-host comparisons showed that two E. faecalis pairs from the same patient were clonally related, with one isolate acquiring a vanHAX plasmid conferring vancomycin resistance. In contrast, E. faecium isolates exhibited marked genomic diversity even among clonally related pairs. These findings suggest that E. faecium possesses greater genomic plasticity and adaptive potential to the clinical environment.IMPORTANCEThis study provides a detailed comparison of clinical and genomic features between Enterococcus faecium and Enterococcus faecalis from the same hospital setting. We show that E. faecium isolates, mainly ST78/ST789, carry more antimicrobial resistance genes and a higher number of putative virulence marker (PVM) genes than E. faecalis, reflecting their hospital-adapted nature. E. faecium also exhibits a smaller core genome and greater diversity of plasmid replicon types, indicating higher genomic plasticity and capacity for horizontal gene transfer. By contrast, E. faecalis retains a larger core genome and a set of classical virulence factors, and its within-host isolates are clonally related. These distinct genomic profiles help to understand how the two species adapt to clinical environments and may inform more targeted infection control strategies and resistance surveillance.

Enterococcus faecium↗