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Genomic profiling of malignant melanoma using tiling-resolution arrayCGH.

Malignant melanoma is an aggressive, heterogeneous disease where new biomarkers for diagnosis and clinical outcome are needed. We searched for chromosomal aberrations that characterize its pathogenesis using 47 different melanoma cell lines and tiling-resolution bacterial artificial chromosome-arrays for comparative genomic hybridization. Major melanoma genes, including BRAF, NRAS, CDKN2A, TP53, CTNNB1, CDK4 and PTEN, were examined for mutations. Distinct copy number alterations were detected, including loss or gain of whole chromosomes but also minute amplifications and homozygous deletions.

Resequencing genomic DNA of patients with severe hypertriglyceridemia (MIM 144650).

OBJECTIVE: The genetic determinants of severe hypertriglyceridemia (HTG; MIM 144650) in adults are poorly defined. We therefore resequenced 3 candidate genes, namely LPL, APOC2, and APOA5, to search for accumulation of missense mutations in patients with severe HTG compared with normolipidemic subjects. METHODS AND RESULTS: We resequenced >2 million base pairs of genomic DNA from 110 nondiabetic patients with severe HTG and determined the prevalence of coding sequence variants compared with 472 age- and sex-matched normolipidemic controls. We found: (1) heterozygous mutations (LPL p.Q-12E >11

Production of pseudoinfectious yellow fever virus with a two-component genome.

Application of genetically modified, deficient-in-replication flaviviruses that are incapable of developing productive, spreading infection is a promising means of designing safe and effective vaccines. Here we describe a two-component genome yellow fever virus (YFV) replication system in which each of the genomes encodes complete sets of nonstructural proteins that form the replication complex but expresses either only capsid or prM/E instead of the entire structural polyprotein. Upon delivery to the same cell, these genomes produce together all of the viral structural proteins, and cells rel

Virulence potential of Ehrlichia chaffeensis strains of distinct genome sequences.

Human monocytic ehrlichiosis, one of the most frequent life-threatening tick-borne zoonoses, is caused by Ehrlichia chaffeensis that lacks endotoxin and peptidoglycan. While sequence polymorphisms in several genes in E. chaffeensis strains have been reported, global genomic divergence and biological differences among strains are unknown. The objectives of the present study were to compare the genome sequences of strains of E. chaffeensis and to examine the virulence potentials of the strains with defined genome sequences. Genomic DNA was extracted from purified E. chaffeensis strains Wakulla a

The inheritance of cognitive skills: does genomic imprinting play a role?

Genomic imprinting refers to the differential expression of a gene based on parental origin. Animal and clinical studies have suggested that genomic imprinting is influential in brain development, with the maternal genome playing a disproportionate role in the development of the cortex. The present study investigated this phenomenon in a nonclinical human population, using intrafamilial correlations. Broadly consistent with predictions, it was found that abilities mediated by frontal, parietal, and temporal lobes, but not occipital lobes, were more closely correlated between children and mothe

Genome-wide scan for visceral leishmaniasis susceptibility genes in Brazil.

A genome-wide scan was conducted for visceral leishmaniasis (VL) in Brazil. Initially, 405 markers were typed in 22 multicase pedigrees (28 nuclear families; 174 individuals; 66 affected). Non-parametric multipoint analysis detected nine chromosomal regions with provisional evidence (logarithm of the odds (LOD) scores 0.95-1.66; 0.003<P<0.018) for linkage. To confirm linkage, 132 individuals (43 affected) from 19 independently ascertained families were genotyped across these regions. Three regions (6q27, 7q11.22 and 17q11.2-q21.3) retained evidence (LOD scores 1.08, 1.34, 1.14; P=0.013, 0.007,

Viruses and Hodgkin lymphoma: no evidence of polyomavirus genomes in tumor biopsies.

The epidemiology of young adult Hodgkin lymphoma (HL) suggests that delayed exposure to a common childhood pathogen may be involved in disease pathogenesis. The Epstein-Barr virus (EBV) is associated with a proportion of cases but cases of young adult HL in westernized countries are less frequently EBV-associated than cases in other age groups and geographical locales. This study investigated the possibility that polyomaviruses might be involved in the etiology of HL by analysing a series of 35 cases of classical HL using both specific and degenerate PCR assays for polyomavirus genomes. No pos

Rapid non-genomic vasoconstrictor actions of aldosterone in the renal microcirculation.

There is increasing evidence for the pathophysiological importance of aldosterone in renal diseases. Studies have so far demonstrated that aldosterone exerts deleterious renal effects by inducing oxidative stress, endothelial dysfunction, inflammation and fibrosis through a mineralocorticoid receptor (MR)-dependent genomic mechanisms. On the other hand, a number of recent studies provided evidence that aldosterone can act through a rapid non-genomic mechanism in cardiovascular tissues including the kidney, though the relative importance of such actions in renal diseases remains to be determine

Genome-wide linkage analysis of allergic rhinoconjunctivitis in a Swedish population.

BACKGROUND: Allergic rhinoconjunctivitis is a common complex disorder characterized by itching and irritation in the nose, bouts of sneezing, watery rhinorrhoea, nasal congestion and itchy eyes with tears and swelling. Like other atopic disorders such as allergic asthma and atopic dermatitis, the development involves complex interactions of genes and environmental factors. OBJECTIVE: The purpose of this study was to identify susceptibility loci for allergic rhinoconjunctivitis. METHODS: We conducted a genome-wide linkage analysis using a non-parametric, affected-relative-pair method. The 250

Transgenerational transmission of radiation damage: genomic instability and congenital malformation.

The congenital malformation gastroschisis has a genetic disposition in the inbred mouse strain HLG/Zte. It is increased after preconceptional irradiation of males or females. Radiation exposures during the meiotic stages are most efficient. This malformation can also be induced by ionising radiation when the exposure takes place during the preimplantation period especially during the zygote stage. This latter effect can be transmitted to the next mouse generation. Other macroscopically visible or skeletal malformations are not significantly induced under these experimental conditions. These la

[Diagnostic performance of specific IgM detection and genomic amplification in rubella].

Nowadays, most exanthematic diseases for which a vaccine is available affect young adults. A large percentage of these cases prove to be rubella. The aim of this study is to assess the performance of specific IgM and RT-PCR for the diagnosis of rubella infection. Fifty-nine patients with clinically suspected measles or rubella, and with available serum, whole blood, urine and pharyngeal exudate specimens were studied. RT-PCR in pharyngeal exudate was found to be the most effective marker at the start of the disease (mean, 2.5 days). IgM detection yielded a larger percentage of positive results

Genome-wide linkage scan of schizophrenia: a cross-isolate study.

Genetic isolates are exceptional resources for the detection of susceptibility genes for complex diseases because of the potential reduction in genetic and clinical heterogeneity. However, the outcome of these mapping efforts is dependent upon the demographic history of a given isolated population, with the most significant factors being a constant population size, the number of generations since founding, and the pathogenic loci and their allele frequencies among founders. Here we employed a cross-isolate genome-wide multipoint linkage study design using uniform genetic and clinical methods i

Techniques for multi-genome synteny analysis to overcome assembly limitations.

Genome scale synteny analysis, the analysis of relative gene-order conservation between species, can provide key insights into evolutionary chromosomal dynamics, rearrangement rates between species, and speciation analysis. With the rapid availability of multiple genomes, there is a need for efficient solutions to aid in comparative syntenic analysis. Current methods rely on homology assessment and multiple alignment based solutions to determine homologs of genetic markers between species and to infer syntenic relationships. One of the primary challenges facing multi-genome syntenic analysis i

Разнообразие геномной последовательности и подсказки эволюции вируса вариолы.

Сравнительная геномика 45 эпидемиологически разнообразных вирусов вариолы, изолированных за последние 30 лет эры оспы, указывает на низкое разнообразие последовательности, что указывает на то, что функциональные различия в геновом содержании изолирующих веществ, вероятно, невелики. Филогеозное кластерирование позволило сделать вывод о том, что три клана совпадают с их географическим происхождением и частотой рассмотрения дел; последнее было связано с предполагаемыми белками, которые способствуют различиям в вирусной вирулентности. Анализ вирусного линейного генома ДНК свидетельствует о том, чт

Совпадение в аннотации оригинала
Comparative genomics of 45 epidemiologically varied variola virus isolates from the past 30 years of the smallpox era indicate low sequence diversity, suggesting that there is probably little difference in the isolates' functional gene content. Phylogenetic clustering inferred three clades coincident with their geographical origin and case-fatality rate; the…

High efficiency site-specific genetic engineering of the mosquito genome.

Current techniques for the genetic engineering of insect genomes utilize transposable genetic elements, which are inefficient, have limited carrying capacity and give rise to position effects and insertional mutagenesis. As an alternative, we investigated two site-specific integration mechanisms in the yellow fever mosquito, Aedes aegypti. One was a modified CRE/lox system from phage P1 and the other a viral integrase system from Streptomyces phage phi C31. The modified CRE/lox system consistently failed to produce stable germline transformants but the phi C31 system was highly successful, inc

NMR structure of the viral peptide linked to the genome (VPg) of poliovirus.

VPgs are essential for replication of picornaviruses, which cause diseases such as poliomyelitis, foot and mouth disease, and the common cold. VPg in infected cells is covalently linked to the 5' end of the viral RNA, or, in a uridylylated form, free in the cytoplasm. We show here the first solution structure for a picornaviral VPg, that of the 22-residue peptide from poliovirus serotype 1. VPg in buffer is inherently flexible, but a single conformer was obtained by adding trimethylamine N-oxide (TMAO). TMAO had only minor effects on the TOCSY spectrum. However, it increased the amount of stru

Genome rearrangements, deletions, and amplifications in the natural population of Bartonella henselae.

Cats are the natural host for Bartonella henselae, an opportunistic human pathogen and the agent of cat scratch disease. Here, we have analyzed the natural variation in gene content and genome structure of 38 Bartonella henselae strains isolated from cats and humans by comparative genome hybridizations to microarrays and probe hybridizations to pulsed-field gel electrophoresis (PFGE) blots. The variation in gene content was modest and confined to the prophage and the genomic islands, whereas the PFGE analyses indicated extensive rearrangements across the terminus of replication with breakpoint

Interactions among multiple genomes: tsetse, its symbionts and trypanosomes.

Insect-borne diseases exact a high public health burden and have a devastating impact on livestock and agriculture. To date, control has proved to be exceedingly difficult. One such disease that has plagued sub-Saharan Africa is caused by the protozoan African trypanosomes (Trypanosoma species) and transmitted by tsetse flies (Diptera: Glossinidae). This presentation describes the biology of the tsetse fly and its interactions with trypanosomes as well as its symbionts. Tsetse can harbor up to three distinct microbial symbionts, including two enterics (Wigglesworthia glossinidia and Sodalis gl