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PubMed2004

Genomic characterization of Alzheimer's disease and genotype-related phenotypic analysis of biological markers in dementia.

More than 180 genes distributed across the human genome are potentially involved in the pathogenesis of Alzheimer's disease (AD). The AD population shows a higher genetic variation rate than the control population. Significant differences in allelic distribution and frequency exist when AD-related polygenic clusters are compared with other forms of dementia, indicating that the genetic component in neurodegenerative dementia differs from that of other CNS disorders. The characterization of AD genotype-related phenotypic profiles reveals substantial differences in biological markers among AD clusters associated with different genes and/or allelic combinations. AD and dementia with vascular component (DVC) are the most prevalent forms of dementia. Both clinical entities share many similarities, but they differ in their major phenotypic and genotypic profiles, as revealed by structural and functional genomics studies. Comparative phenotypic studies have identified significant differences in 25% of more than 100 parametric variables, including anthropometric values, cardiovascular function, blood pressure, lipid metabolism, uric acid metabolism, peripheral calcium homeostasis, liver function, alkaline phosphatase, lactate dehydrogenase, red and white blood cells, regional brain atrophy, and brain blood flow velocity. Functional genomic studies incorporating apolipoprotein E (APOE)-related changes in biological markers extended the difference between AD and DVC by up to 57%. Structural genomic studies with AD-related genes, including APP, MAPT, APOE, PS1, PS2, A2M, ACE, AGT, cFOS, and PRNP, demonstrate different genetic profiles in AD and DVC, with an absolute genetic variation rate in the range of 30-80%, depending upon genes and genetic clusters. The relative polymorphic variation in genetic clusters integrated by two, three or four genes associated with AD ranges from 1 to 3%. The main phenotypic differences in AD are genotype dependent, indicating a powerful influence of polygenic factors on the AD phenotypic profile. All these genotypic and phenotypic variations bring about important consequences for the pharmacogenomics of AD.

Adolescent↗
PubMed1987

Genomic characterization of a poxvirus isolated from a child.

A poxvirus was isolated from a six-year-old girl. The comparative analyses of the genome of this isolate (H-CP-LSax) which were carried out using the restriction endonucleases BamHI, HindIII, KpnI, MluI, NcoI, SacI, and SmaI revealed that this isolate is a member of the genus orthopoxvirus. Since the girl had never been vaccinated against smallpox, and had close contact to domestic animals, including cats, rabbits and guinea pigs, the genome of H-CP-LSax virus was genetically analysed in comparison with other known orthopoxviruses. The analysis demonstrates clearly that the HindIII cleavage pattern of H-CP-LSax DNA is different from the HindIII DNA cleavage patterns of vaccinia virus, cowpox virus, rabbit poxvirus, cat poxvirus, ectromelia virus, and okapi poxvirus. Surprisingly, it was found that the HindIII and SmaI cleavage patterns of the DNA of one out of six elephant poxviruses which were analysed under the same conditions were virtually identical to the HindIII and SmaI cleavage patterns of H-CP-LSax DNA. Although SmaI and HindIII digestion of both virus genomes gave the same fragment patterns, the viral DNAs can be distinguished from each other by the restriction endonucleases SacI, BamHI, and KpnI, which also show high similarities in the fragmentation patterns of both viruses. The results obtained in this study indicate three possibilities concerning the origin of H-CP-LSax virus. Firstly that the H-CP-LSax virus originated from an unknown animal species. Secondly, that this virus is a variant of elephant poxvirus in which the HindIII and SmaI sites are extremely conserved, and finally that H-CP-LSax can be a recombinant virus of unknown origin.

Child↗
PubMed2003

Genomic characterization of a repetitive motif strongly associated with developmental genes in Drosophila.

BACKGROUND: Non-coding DNA represents a high proportion of all metazoan genomes. Although an undetermined fraction of this DNA may be considered devoid of any function, it also contains important information residing in specific cis-regulatory sequences. RESULTS: We report a 27 bp motif that is overrepresented within the fly genome. This motif does not show any significant similarity with transposon sequences and is strongly associated with genes involved in development and/or signal transduction. The 27 bp motif is preferentially located within introns, and has a tendency to be present in multiple copies around genes. Furthermore, it is often found embedded in known non-coding regulatory regions. The regulatory network defined by this motif is partially shared in D. pseudoobscura. CONCLUSION: We have identified a 27 bp cis-regulatory sequence widely distributed within the Drosophila genome in association with developmental genes. This motif may be very useful towards the annotation of functional regulatory regions within the Drosophila genome and the construction of regulatory networks of Drosophila development.

Animals↗
PubMed2026

Genomic Characterization of Aeromonas dhakensis Isolated From a Fatal Dolphin Case.

Aeromonas dhakensis has emerged as a significant pathogen affecting both aquatic animals and humans; however, genomic data for isolates from marine mammals remain scarce. In this study, we characterised the genome of A. dhakensis strain KDL-001, isolated from a fatal dolphin case, using whole-genome sequencing and comparative genomics. Taxonomic analyses, including MLST and average nucleotide identity (ANI), confirmed the isolate as A. dhakensis. Core-genome phylogeny further revealed that KDL-001 is closely related to strains derived from fish and aquatic environments. Notably, in silico screening of virulence-associated genes showed that the virulence-associated gene profile of the dolphin isolate was broadly comparable to those of other A. dhakensis strains, with no isolate-specific virulence-associated genes being identified within the limits of this analysis. These findings demonstrate that the dolphin-derived isolate is genomically comparable to previously described A. dhakensis strains and possesses conserved virulence-associated genes commonly found within the species.

Animals↗
PubMed2002

Integration of Cot analysis, DNA cloning, and high-throughput sequencing facilitates genome characterization and gene discovery.

Cot-based sequence discovery represents a powerful means by which both low-copy and repetitive sequences can be selectively and efficiently fractionated, cloned, and characterized. Based upon the results of a Cot analysis, hydroxyapatite chromatography was used to fractionate sorghum (Sorghum bicolor) genomic DNA into highly repetitive (HR), moderately repetitive (MR), and single/low-copy (SL) sequence components that were consequently cloned to produce HRCot, MRCot, and SLCot genomic libraries. Filter hybridization (blotting) and sequence analysis both show that the HRCot library is enriched in sequences traditionally found in high-copy number (e.g., retroelements, rDNA, centromeric repeats), the SLCot library is enriched in low-copy sequences (e.g., genes and "nonrepetitive ESTs"), and the MRCot library contains sequences of moderate redundancy. The Cot analysis suggests that the sorghum genome is approximately 700 Mb (in agreement with previous estimates) and that HR, MR, and SL components comprise 15%, 41%, and 24% of sorghum DNA, respectively. Unlike previously described techniques to sequence the low-copy components of genomes, sequencing of Cot components is independent of expression and methylation patterns that vary widely among DNA elements, developmental stages, and taxa. High-throughput sequencing of Cot clones may be a means of "capturing" the sequence complexity of eukaryotic genomes at unprecedented efficiency.

Base Composition↗
PubMed2006

Genomic characterization of the unclassified bovine enteric virus Newbury agent-1 (Newbury1) endorses a new genus in the family Caliciviridae.

The pathogenic bovine enteric virus, Newbury agent-1 (Bo//Newbury1/1976/UK), first identified in 1976, was characterized as a possible calicivirus by morphology, buoyant density in CsCl and the presence of a single capsid protein but genomic sequence could not be obtained. In the present study, the complete genome sequence of Newbury1 was determined and classified Newbury1 in a new genus of the Caliciviridae. The Newbury1 genome, of 7454 nucleotides, had two predicted open reading frames (ORFs). ORF1 encoded the non-structural and contiguous capsid proteins. ORF2 encoded a basic protein characteristic of the family Caliciviridae. Compared to the 4 recognized Caliciviridae genera, Norovirus, Sapovirus, Lagovirus and Vesivirus, Newbury1 had less than 39% amino acid (47% nucleotide) identity in the complete 2C-helicase, 3C-protease, 3D-polymerase and capsid regions but had 89% to 98% amino acid (78% to 92% nucleotide) identity to the recently characterized NB virus in these regions. By phylogenetic analyses, Newbury1 and NB viruses formed a distinct clade independent of the 4 recognized genera. However, amino acid identities showed that Newbury1 and the NB virus were distinct polymerase types (90% amino acid identity), but their complete capsid proteins were almost identical (98% amino acid identity). Analyses of contemporary viruses showed that the two polymerase genotypes, Newbury1 and NB, were circulating in UK cattle and antibody to Newbury1-like viruses was common in cattle sera. The present study defined the existence of a new genus in the Caliciviridae that we propose be named Becovirus or Nabovirus to distinguish the new clade from bovine noroviruses.

Amino Acid Sequence↗
PubMed2026

Genomic Characterization of Influenza B Victoria Lineage Viruses Circulating in Saudi Arabia During the 2024-2025 Season.

Influenza B viruses contribute substantially to global morbidity and mortality, yet genomic data from the Middle East remain limited. We retrospectively performed whole-genome sequencing of six influenza B virus-positive residual nasopharyngeal specimens collected at King Abdulaziz Medical City, Riyadh, during the 2024-2025 season, including one fatal pediatric case, and described their genomic features alongside clinical outcomes. All six genomes belonged to the B/Victoria lineage and clustered within V1A.3a.2-derived subclades circulating globally during 2024-2025. Five genomes, including the fatal pediatric case, were assigned to subclade C.5.6, whereas one non-fatal case belonged to C.5.7. The Saudi sequences were interspersed among contemporaneous reference strains from Europe, Asia, and North America, without evidence of a distinct local lineage. The fatal isolate did not occupy a distinct phylogenetic position and contained none of the screened virulence-associated markers, including the neuraminidase N342K substitution. These genomes provide regional surveillance data from an underrepresented setting. Given the small sample size and inclusion of a single fatal case, the findings are descriptive and do not permit inference regarding genomic determinants of disease severity. Larger studies integrating viral genomic, clinical, and host data are needed.

Humans↗
PubMed2002

Cloning and genomic characterization of Felis domesticus papillomavirus type 1.

A novel papillomavirus was cloned from hyperkeratotic cutaneous lesions of a Persian domestic cat. The Felis domesticus papillomavirus (FdPV-1) genome counts 8300 bp and has a typical genome structure with an early region (E1, E2, E4, E6, E7), a late region (L1, L2), and a noncoding upstream regulatory region (URR or NCR1) between the end of L1 and the beginning of E6. The FdPV-1 also shows an unusual second noncoding region (NCR2) of 1.3 kb, situated between the end of E2 and the beginning of L2. This NCR2 is uniquely related to a similar region in the canine oral papillomavirus (COPV). Phylogenetic analysis places FdPV-1 together with COPV, the cottontail rabbit papillomavirus, human papillomavirus type 1 (HPV-1), and HPV-63 in the group of the benign cutaneous papillomaviruses. The position of FdPV-1 in the phylogenetic tree allows us to hypothesize that already in an early phase of the papillomavirus molecular evolution, a split occurred into viruses with a dual tropism primarily for cutaneous epithelia but also secondarily for mucosal surfaces, and viruses with a specific monotropism for mucosal surfaces. The close relationship between FdPV-1 and COPV, and between their Canidae and Felidae hosts, supports the hypothesis that papillomaviruses have speciated and coevolved together with their hosts throughout vertebrate evolution. A papillomavirus mutation rate of 0.73 to 0.96 x 10(-8) nucleotide substitutions per base per year was calculated.

Animals↗
PubMed1990

Amplification of genomic sequences flanking transposable elements in host and heterologous plants: a tool for transposon tagging and genome characterization.

The isolation of sequences flanking integrated transposable elements is an important step in gene tagging strategies. We have demonstrated that sequences flanking transposons integrated into complex genomes can be simply and rapidly obtained using the polymerase chain reaction. Amplification of such sequences was established in a model system, a transgenic tobacco plant carrying a single Ac element, and successfully applied to the cloning of a specific Spm element from a maize line carrying multiple Spm hybridizing sequences. The described utilization of methylation sensitive restriction enzymes (including those with degenerate recognition sequences) in the generation of templates for amplification will simplify the cloning and mapping of genomic sequences adjacent to transposable elements.

Base Sequence↗
PubMed1995

Immediate-early transcription from the channel catfish virus genome: characterization of two immediate-early transcripts.

With cDNA probes and by Northern (RNA) blot analysis, a region containing immediate-early (IE) genes in the channel catfish virus (CCV) genome was identified. IE transcription in CCV-infected cells appears to be restricted to the terminal repeat region, suggesting that CCV is most closely related to the alpha subfamily of herpesviruses. CCV DNA fragments from this region encoding IE transcripts were cloned. Northern analysis with one of these cloned fragments, a 3,927-bp EcoRI-XbaI fragment, indicates that it encodes two IE transcripts. Both transcripts (ie1 and ie2) were characterized by S1 nuclease analysis, primer extension analysis, and analysis of cDNAs. The ie2 transcript is a 1.3-kb bicistronic mRNA containing open reading frame (ORF) 8a and ORF 9. ORF 8a is a 5'-truncated version of ORF 8 which, along with ORF 9, was previously identified (A. J. Davison, Virology 186:9-14, 1992). The ie1 transcript is 0.6 kb in size, contains only ORF 9, and is expressed at a level approximately six times that of ie2 in cycloheximide-treated cells. The putative product of ORF 9 is predicted to have a basic pI and contains a potential zinc-binding domain, making it a probable transcription factor. ORF 8a encodes a putative product which is very hydrophobic, an unusual characteristic for an IE protein.

Animals↗
PubMed2006

The ROP2 family of Toxoplasma gondii rhoptry proteins: proteomic and genomic characterization and molecular modeling.

Four rhoptry proteins (ROP) of Toxoplasma gondii previously identified with mAb have been affinity purified and analyzed by MS; the data obtained allowed the genomic sequences to be assigned to these proteins. As previously suggested for some of them by antibody crossreactivity, these proteins were shown to belong to a family, the prototype of which being ROP2. We describe here the proteins ROP2, 4, 5, and 7. These four proteins correspond to the most abundant products of a gene family that comprises several members which we have identified in genomic and EST libraries. Eight additional sequences were found and we have cloned four of them. All members of the ROP2 family contain a protein-kinase-like domain, but only some of them possess a bona fide kinase catalytic site. Molecular modeling of the kinase domain demonstrates the conservation of residues critical for the stabilization of the protein-kinase fold, especially within a hydrophobic segment described so far as transmembrane and which appears as an helix buried inside the protein. The concomitant synthesis of these ROPs by T. gondii tachyzoites suggests a specific role for each of these proteins, especially in the early interaction with the host cell upon invasion.

Amino Acid Sequence↗
PubMed1997

Genomic characterization of a testis-specific TFIIS (TCEA2) gene.

There is a family of genes encoding TFIIS-related proteins in human cells. We have focused upon the genomic organization of one family member expressed primarily in the testis. This gene encodes a transcription elongation factor similar to but distinct from that encoded by a previously reported TFIIS gene. Also in contrast to the previously reported TFIIS gene, the testis gene contains introns. All exon-intron junction sequences match the consensus GT/AG rule. The gene consists of seven exons and six introns with a total size of approximately 7 kb. The nucleotide sequence of the 5 flanking region of the testis TFIIS gene contains several potential regulatory factor-binding sites, not all of which are present in the TFIIS gene, whose expression is nearly ubiquitous. Elucidation of the full structure of the testis TFIIS gene should be useful for determining its chromosomal localization and its potential role in the regulation of gene expression in human tissues.

Animals↗
PubMed2006

Genomic characterization of POS5, the Saccharomyces cerevisiae mitochondrial NADH kinase.

Disruption of the Saccharomyces cerevisiae mitochondrial NADH kinase POS5 increases the mitochondrial mutation rate 50-fold. Whereas most multicellular eukaryotic genomes have one NADH kinase gene, the yeast genome contains three distinct genes encoding NAD/H kinase activity. To determine if all three genes are essential for viability we constructed combinations of gene knockouts. We show that only the pos5Deltautr1Delta combination is synthetically lethal, demonstrating an essential overlapping function, and showing that NAD/H kinase activity is essential for eukaryotic viability. The single human NAD/H kinase gene can rescue the lethality of the double knockout in yeast, demonstrating that the single human gene can fill the various functions provided by the three yeast genes. The human NAD/H kinase gene harbors very common sequence variants, but all of these equally complement the synthetic lethality in yeast, illustrating that each of these are functionally wild-type. To understand the molecular mechanism of the mitochondrial genome instability of pos5 mutation we performed gene expression analysis on the pos5Delta. The pos5Delta resulted in an increase in expression of most of the iron transport genes including key genes involved in iron-sulfur cluster assembly. Decreased expression occurred in many genes involved in the electron transport chain. We show that the pos5Delta expression pattern is similar to the frataxin homolog knockout (yfh1Delta), the yeast model for Friedreich's ataxia. These combined data show that the POS5 NAD/H kinase is an important protein required for a variety of essential cellular pathways and that deficient iron-sulfur cluster assembly may play a critical role in the mitochondrial mutator phenotype observed in the pos5Delta.

Fungal Proteins↗
PubMed1997

Genomic characterization of Brazilian hepatitis C virus genotypes 1a and 1b.

Parts of 5' non-coding (5' NC) and of E1 envelope regions of the hepatitis C virus (HCV) genome were amplified from sera of 26 Brazilian anti-HCV antibody-positive patients using the reverse transcription-polymerase chain reaction (RT-PCR). Fourteen samples were PCR positive with primers from the 5' NC region and 8 of them were also positive with primers from the E1 region. A genomic segment of 176 bp from the E1 region of 7 isolates was directly sequenced from PCR products. The sequences were compared with those of HCV strains isolated in other countries and the Brazilian isolates were classified by phylogenetic analysis into genotypes 1a and 1b. This could have a clinical importance since it has been shown that individuals infected with type 1 viruses are less likely to respond to treatment with interferon than individuals infected with types 2 and 3 viruses. Two quasispecies isolated from the same patient with an interval of 13 months differed by two base substitutions (1.1%). The sequence of another isolate presented a three-nucleotide deletion at codon 329.

Adult↗
PubMed2000

Expression and genomic characterization of protein phosphatase inhibitor-1: a novel marker for mesothelium in the mouse.

Protein phosphatase inhibitor-1 (inhibitor-1 or I-1) is involved in signal transduction and is an endogenous inhibitor of protein phosphatase-1. The mouse I-1 protein sequence has been deduced from cDNA and is strongly homologous to the published rat sequence. A mouse genomic library was screened, and the I-1 gene was characterized and localized by fluorescent in situ hybridization (FISH) to chromosome 15F. Protein expression in a range of embryonic and adult tissue was analysed using confocal microscopy. Inhibitor-1 is expressed by: the coelomic epithelium; the epithelial bounding layer of cells of the kidney, lung, liver, heart, intestine and gonad; and the surface ectoderm. The blast cells of the kidney do not express I-1. We conclude that I-1 is a marker for mesothelium.

Amino Acid Sequence↗
PubMed2005

Genome characterization of a flexuous rod-shaped mycovirus, Botrytis virus X, reveals high amino acid identity to genes from plant 'potex-like' viruses.

This study reports the molecular characterization of a flexuous rod-shaped mycovirus, Botrytis virus X (BVX), infecting the plant-pathogenic fungus, Botrytis cinerea. BVX contains a ssRNA genome of 6966 nucleotides, and a poly(A) tract at or very near the 3' terminus. Computer analysis of the genomic cDNA sequence of BVX revealed five potential open reading frames (ORFs). ORF1 showed significant amino acid sequence identity to the replicase proteins of plant 'potex-like' viruses, including 73% identity to the RNA-dependent RNA polymerase (RdRp) region of the allexivirus, garlic virus A (GarV-A). The C-terminal region of ORF3 shared amino acid homology with plant 'potex-like' coat proteins. The remaining ORFs did not reveal significant homology with known protein sequences. BVX differs substantially from Botrytis virus F (BVF), another flexuous rod-shaped mycovirus characterized from the same B. Cinerea isolate. It is proposed that the mycovirus BVX belongs to a new, as yet unassigned genus in the plant 'potex-like' virus group, distinct from BVF.

Amino Acid Sequence↗
PubMed2026

Whole-genome characterization and phylogenetic placement of Fusarium oxysporum f. sp. vasinfectum isolates.

Fusarium wilt of cotton, caused by Fusarium oxysporum f. sp. vasinfectum (Fov), remains a persistent threat to cotton production worldwide. Among the known races, Fov race 4 and its extra-virulent variants cause particularly severe losses in Upland cotton. Although several Fov genome assemblies have been assigned to races, the genomic diversity and evolutionary relationships among pathogenic and non-pathogenic isolates associated with cotton outbreaks remain poorly understood at the whole-genome level. This study addressed these gaps by generating and comparing high-quality genome assemblies of four Fusarium isolates collected from Texas cotton fields: two pathogenic (TX17-24 and TX18-9) and two non-pathogenic (TX17-6 and TX18-6). Draft assemblies were generated using Oxford Nanopore long reads and polished with Illumina reads. Comparative genomic analyses showed that pathogenic isolates possessed larger genomes and more conserved orthologous families, whereas non-pathogenic isolates contained more unique genes. Analyses of predicted secreted effectors, transposable elements, and carbohydrate-active enzymes further distinguished pathogenic and non-pathogenic lineages, suggesting roles in virulence adaptation and genome plasticity. Phylogenomic analyses using k-mer-based, assembly- and alignment-free methods incorporated all available long-read Fov genomes and revealed substantial genetic diversity within races 1 and 4, clustering isolates into multiple sublineages. These findings show that Fov race diversification is underestimated when based on traditional classification schemes and may be shaped by host specialization, geographic separation, or horizontal gene transfer. This work advances our understanding of the genomic diversity and evolutionary dynamics of Fov and establishes a foundation for improved race identification and characterization of Fusarium wilt pathogenesis in cotton.

Fusarium oxysporum↗