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At least 1,009 records · Page 56Linked to original sources
PubMed1995

Genome analysis of North American small ruminant lentiviruses by polymerase chain reaction and restriction enzyme analysis.

The polymerase chain reaction (PCR) was used to amplify portions of the gag and env structural genes of 8 ovine and 1 caprine lentivirus isolates of North American origin. Three sets of primers were used to amplify p16, p25, and N'-gp40 gene fragments, and 1 set, annealing highly conserved portions of long terminal repeat (LTR) among small ruminant lentiviruses, was used as a positive control. Variable PCR amplification efficiency was observed. Different stringency conditions of hybridization with specific DNA probes were used to maximize detection of the PCR product. The p25 primers detected all strains, the gp40 primers detected 1 ovine and the caprine strain, and the p16 primers detected only 1 ovine isolate. All strains were detected by LTR primers. Restriction endonuclease analysis of 5 amplified p25 and 2 N'-gp40 gene fragments revealed extensive heterogeneity among these North American small ruminant lentiviruses.

Animals↗
PubMed2001

Genomic analysis of clinical samples with serologic ABO blood grouping discrepancies: identification of 15 novel A and B subgroup alleles.

Since the cloning in 1990 of complementary DNA corresponding to messenger RNA transcribed at the blood group ABO locus, polymorphisms and phenotype-genotype correlations have been reported by several investigators. Exons 6 and 7, constituting 77% of the gene, have been analyzed previously in samples with variant phenotypes but for many subgroups the molecular basis remains unknown. This study analyzed 324 blood samples involved in ABO grouping discrepancies and determined their ABO genotype. Samples from individuals found to have known subgroup alleles (n = 53), acquired ABO phenotypes associated with different medical conditions (n = 65), probable chimerism (n = 3), and common red blood cell phenotypes (n = 109) were evaluated by ABO genotype screening only. Other samples (n = 94) from apparently healthy donors with weak expression of A or B antigens were considered potential subgroup samples without known molecular background. The full coding region (exons 1-7) and 2 proposed regulatory regions of the ABO gene were sequenced in selected A (n = 22) or B (n = 12) subgroup samples. Fifteen novel ABO subgroup alleles were identified, 2 of which are the first examples of mutations outside exon 7 associated with weak subgroups. Each allele was characterized by a missense or nonsense mutation for which screening by allele-specific primer polymerase chain reaction was performed. The novel mutations were encountered in 28 of the remaining 60 A and B subgroup samples but not among normal donors. As a result of this study, the number of definable alleles associated with weak ABO subgroups has increased from the 14 previously published to 29.

ABO Blood-Group System↗
PubMed2002

Genomic analysis of neural crest induction.

The vertebrate neural crest is a migratory stem cell population that arises within the central nervous system. Here, we combine embryological techniques with array technology to describe 83 genes that provide the first gene expression profile of a newly induced neural crest cell. This profile contains numerous novel markers of neural crest precursors and reveals previously unrecognized similarities between neural crest cells and endothelial cells, another migratory cell population. We have performed a secondary screen using in situ hybridization that allows us to extract temporal information and reconstruct the progression of neural crest gene expression as these cells become different from their neighbors and migrate. Our results reveal a sequential 'migration activation' process that reflects stages in the transition to a migratory neural crest cell and suggests that migratory potential is established in a pool of cells from which a subset are activated to migrate.

Animals↗
PubMed2005

Biochemical and genomic analysis of substrate recognition by the double-stranded RNA binding domain of yeast RNase III.

Members of the RNase III family of double-stranded RNA (dsRNA) endonucleases are important enzymes of RNA metabolism in eukaryotic cells. Rnt1p is the only known member of the RNase III family of endonucleases in Saccharomyces cerevisiae. Previous studies have shown that Rnt1p cleaves dsRNA capped by a conserved AGNN tetraloop motif, which is a major determinant for Rnt1p binding and cleavage. The solution structure of the dsRNA-binding domain (dsRBD) of Rnt1p bound to a cognate RNA substrate revealed the structural basis for binding of the conserved tetraloop motif by alpha-helix 1 of the dsRBD. In this study, we have analyzed extensively the effects of mutations of helix 1 residues that contact the RNA. We show, using microarray analysis, that mutations of these amino acids induce substrate-specific processing defects in vivo. Cleavage kinetics and binding studies show that these mutations affect RNA cleavage and binding in vitro to different extents and suggest a function for some specific amino acids of the dsRBD in the catalytic positioning of the enzyme. Moreover, we show that 2'-hydroxyl groups of nucleotides of the tetraloop or adjacent base pairs predicted to interact with residues of alpha-helix 1 are important for Rnt1p cleavage in vitro. This study underscores the importance of a few amino acid contacts for positioning of a dsRBD onto its RNA target, and implicates the specific orientation of helix 1 on the RNA for proper positioning of the catalytic domain.

Base Sequence↗
PubMed2006

Establishment of ovarian reconstruction system in culture for functional genomic analysis.

In a previous study, we reported a list of genes expressed differentially in primordial and primary follicles [Park et al., Fertil. Steril., 83, 410-418 (2005)]. An innovative experimental system is required to evaluate the functions of these genes in folliculogenesis, particularly primordial-primary follicle transition. In this study, ovarian tissues were dissociated, and isolated cells were transfected using small interfering RNAs (siRNAs) for disrupting a specific gene, followed by ovarian reconstruction via calcium alginate encapsulation. The effects of RNA interference (RNAi) on follicular development were evaluated by a histological observation of the reconstructed ovarian tissue. Interestingly, follicular formation and development showed differences between control and experimental groups. Thus, even though this system includes some problems that need to be solved, ovarian reconstruction following the modification of gene expression of individual ovarian component cells could lead the way to methods of studying molecular mechanisms of primordial-primary follicle transition.

Animals↗
PubMed2004

Hepatozoon sauritus: a polytopic hemogregarine of three genera and four species of snakes in north Florida, with specific identity verified from genome analysis.

Hemogregarines from Thamnophis s. sirtalis, Coluber constrictor priapus, Elaphe obsoleta quadrivittata, and E. g. guttara in northern Florida appeared to be conspecific on the basis of similar gamonts from all the hosts and sporogonic stages obtained from 3 hosts. The resemblance of gamonts to those of Hepatozoon sauritus, described from T. sauritus sackenii in southern Florida, justified comparison of DNA isolates from the type infection of H. sauritus with samples from each of the northern Florida hosts and with a morphologically distinct species, H. sirtalis, from northern Florida. A nucleotide sequence (530 bp) alignment of the 18S ribosomal RNA gene revealed 2 hemogregarine haplotypes that varied at 15 sites (p distance = 2.8%), which included 10 transitions and 5 transversions. Two well-supported clusters (100% bootstrap support) were revealed by a neighbor-joining tree topology. One cluster included the type infection of H. sauritus and all 4 of the other samples from the northern Florida hosts, with samples of H. sirtalis comprising a second cluster. Hepatozoon sauritus, therefore, is a polytopic species in contrast to the 8 other Hepatozoon species thus far described from snakes in Florida, each of which appears to parasitize a single host species.

Animals↗
PubMed2004

Ancient phylogenetic separation between Pacific and Atlantic cephalochordates as revealed by mitochondrial genome analysis.

The subphylum Cephalochordata (lancelets) is a relatively small taxonomic group in contrast to the subphyla Urochordata and Vertebrata. As an initial step to determine whether lancelets exhibit small genetic divergence in keeping with their conservative body organization or large genetic variation, four Branchiostoma species from the Pacific (B. belcheri and B. malayanum) and Atlantic (B. floridae and B. lanceolatum) Oceans were genetically compared using partial mitochondrial DNA sequences of the cytochrome oxidase c subunit I (COI) and 16S ribosomal RNA (16S rRNA) genes. In both genes, large genetic differences were revealed between the Pacific and Atlantic species, as well as within the former. Two maximum-likelihood trees from the COI and 16S rRNA genes showed that the Pacific and Atlantic lancelets were reciprocally clustered into different clades. Furthermore, both gene trees consistently exhibited deep phylogenetic separation between the two oceans. The estimated divergence time suggested that differentiation may have followed the migration of ancestral lancelets from the Pacific to the Atlantic Oceans via the Tethys Sea.

Animals↗
PubMed2002

Oral cancer research with an emphasis on genomic analysis.

Ablative surgery has been a standard procedure for many years, but during the past few years there has been a significant improvement in our understanding of invasion and metastasis in oral cancer. Each procedure has to be planned individually. Before surgery, every attempt must have been made to arrive at a proper diagnosis, including the exact nature and aggressiveness of the tumor and an analysis of the patient's genetic background. These procedures and the prognosis will be discussed.

Carcinoma, Squamous Cell↗
PubMed2006

Genomic analysis of the impact of fescue toxicosis on hepatic function.

Fescue toxicosis is caused by consumption of toxins produced by an endophytic fungus, Neotyphodium coenophialum, in tall fescue [Lolium arundinaceum (Schreb.) Darbysh]. Microarray analysis was used to identify shifts in genetic expression associated with the affected physiological processes to identify potential targets for future pharmacological/toxicological intervention. Male rats (n = 24) were implanted with temperature transmitters, which measure core temperature every 5 min. After an 8-d recovery, the rats were fed an endophyte-free diet for 5 d. During the following 5-d treatment period, rats were fed either an endophyte-free or an endophyte-infected (91.5 microg of ergovaline.kg of BW(-1).d(-1)) diet. At the end of treatment, rats were euthanized and a sample of the liver was obtained. Feed conversion efficiency was calculated for both treatment groups. Serum prolactin concentrations were measured using ELISA. Liver tissue RNA was reverse transcribed and hybridized to an oligonucleotide microarray chip. Microarray data were analyzed using a 2-step ANOVA model and validated by quantitative real-time PCR. Significant reductions in mean core temperature, feed intake, feed conversion efficiency, BW, liver weight per unit of BW, and serum prolactin concentrations were observed in endophyte-infected rats. There was downregulation (P < 0.05) of various genes associated with energy metabolism, growth and development, and antioxidant protection, as well as an upregulation of genes associated with gluconeogenesis, detoxification, and biotransformation. This study demonstrated that even short-term exposure of rats to tall fescue endophytic toxins under thermoneutral conditions can result in physiological responses associated with altered gene expression within the liver.

Animals↗
PubMed2001

Full-length genomic analysis of hepatitis B virus isolates in a patient progressing from hepatitis to hepatocellular carcinoma.

In hepatitis B virus (HBV)-endemic countries, the majority of hepatocellular carcinoma (HCC) arises in HBV carriers. High frequency of mutations at nucleotides 1762(A-->T) and 1764(G-->A) in the core promoter region have been described in HCC. Due to the differences in genetic backgrounds, environmental risk factors and random cellular insertion sites, it is difficult to analyze the possible roles of HBV variants detected in different HCC patients. In a follow-up cohort study, an HBsAg-positive asymptomatic carrier was diagnosed HCC within 4 years. Eleven full-length HBV isolates, three from the first serum sample obtained 4 years pre-HCC, and eight from serum sample, peri-tumor and tumor tissue post-HCC of this individual were sequenced and used to transfect HepG2 cells. When sequences were compared between pre- and post-HCC isolates, no single mutation common to all post-HCC isolates that differed from pre-HCC isolates was found. Among all 11 isolates, there were 20 predicted amino acid substitutions shared by two or more post-HCC isolates. These were located in the S(5), X(4), core(4), polymerase(4), pre-S1(2) and pre-S2(1) proteins. Possible roles of amino acid substitutions and enhanced replication efficiency in cells transfected by post-HCC isolates are discussed.

Amino Acid Substitution↗
PubMed2003

Functional genomic analysis of remyelination reveals importance of inflammation in oligodendrocyte regeneration.

Tumor necrosis factor alpha (TNFalpha), a proinflammatory cytokine, was shown previously to promote remyelination and oligodendrocyte precursor proliferation in a murine model for demyelination and remyelination. We used Affymetrix microarrays in this study to identify (1) changes in gene expression that accompany demyelination versus remyelination and (2) changes in gene expression during the successful remyelination of wild-type mice versus the unsuccessful attempts in mice lacking TNFalpha. Alterations in inflammatory genes represented the most prominent changes, with major histocompatibility complex (MHC) genes dramatically enhanced in microglia and astrocytes during demyelination, remyelination, and as a consequence of TNFalpha stimulation. Studies to examine the roles of these genes in remyelination were then performed using mice lacking specific genes identified by the microarray. Analysis of MHC-II-null mice showed delayed remyelination and regeneration of oligodendrocytes, whereas removal of MHC-I had little effect. These data point to the induction of MHC-II by TNFalpha as an important regulatory event in remyelination and emphasize the active inflammatory response in regeneration after pathology in the brain.

Animals↗
PubMed1989

[Genome analysis].

So far, about 1% of human genes have been molecularly cloned and chromosomally mapped. Thus only a small proportion of the hereditary disorders of man are accessible to molecular genetic analysis. Such an analysis, however, is a prerequisite for the development of diagnostic and therapeutic measures.

Animals↗
PubMedDate not supplied

[Multiple hybridization in genome analysis. 1. Reaction of diamine and bisulfite with cytosine for the introduction of nonradioactive markers into DNA].

A two-step chemical method has been developed for the introduction of biotin and other low-molecular derivatives into DNA. The method is based on the interaction of aliphatic diamines with cytosine residues of the polynucleotide chain in the presence of sodium bisulfite with subsequent addition of biotin. DNA modified this way may be used as an effective probe for non-isotopic hybridization which can be used simultaneously with 32P-labelled probes.

Animals↗