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PubMed1998

Hypervariable digital DNA codes for human paternal lineages: MVR-PCR at the Y-specific minisatellite, MSY1 (DYF155S1).

We describe the first haploid minisatellite, the human Y chromosome-specific locus, MSY1. It consists of an array of 48-114 AT-rich 25 bp repeats of at least five different variant types. A minisatellite variant repeat PCR (MVR-PCR) system gives Y-specific DNA codes, with a virtual heterozygosity of 99.9%, making MSY1 by far the single most variable locus on the Y. African populations contain the most diverged MSY1 structures. MSY1 is the only Y-chromosomal system where the characteristics of large numbers of mutations can be studied in detail: it provides a uniquely powerful tool both for the investigation of mutation in a haploid system, and for the dating of paternal lineages.

Africa↗
PubMed2003

Norepinephrine transporter splice variants and their interaction with substrates and blockers.

Norepinephrine transporter (NET), a member of the Na+/Cl--dependent neurotransmitter transporter family, displays species-specific isoforms produced by alternative RNA splicing. This occurs at 3'-flanking coding and noncoding regions, resulting in different carboxy-terminals. When these NET splice variants were expressed in cultured cell lines, the characteristics of substrate transport and the sensitivity to uptake inhibitors differed between isoforms. The different functional expression suggests the physiological importance of the action and interaction of NET splice variants in synaptic transmission.

Alternative Splicing↗
PubMed1999

Allelic variants in the interleukin-6 gene and essential hypertension in Japanese women.

Genes that can be implicated in hypertension in experimental animals are plausible candidates in the pathogenesis of human hypertension. A recent genome-wide search for quantitative-trait loci (QTL) in hypertensive rats revealed a strong correlation between the interleukin-6 (IL-6) locus on rat chromosome 4 and systolic, diastolic, and mean arterial pressure in this mammalian species. To investigate a possible association between genetic variations of the IL-6 gene and hypertension in humans, we identified two novel single-nucleotide sequence variations, a C/G substitution at -634 in the promoter region and a G/A substitution at 4391 in a 3' non-coding portion of exon 5, and a previous reported sequence variant, an A/T variation in the composition of the AnTn tract around -447 in the promoter region (Fishman D et al. J Clin Invest 1998; 102: 1369-1376), within a test population of 96 Japanese subjects. Allelic associations involving these variations were analyzed in 150 hypertensive and 143 normotensive Japanese women. The distribution of alleles of the three polymorphisms, as well as a dinucleotide repeat present at the IL-6 locus, was similar in the two groups. Therefore, the IL-6 gene appears to play a minimal role in the genetic etiology of essential hypertension in Japanese women.

Aged↗
PubMed2001

Molecular determinants of virulence, cell tropism, and pathogenic phenotype of infectious bursal disease virus.

Infectious bursal disease viruses (IBDVs), belonging to the family Birnaviridae, exhibit a wide range of immunosuppressive potential, pathogenicity, and virulence for chickens. The genomic segment A encodes all the structural (VP2, VP4, and VP3) and nonstructural proteins, whereas segment B encodes the viral RNA-dependent RNA polymerase (VP1). To identify the molecular determinants for the virulence, pathogenic phenotype, and cell tropism of IBDV, we prepared full-length cDNA clones of a virulent strain, Irwin Moulthrop (IM), and constructed several chimeric cDNA clones of segments A and B between the attenuated vaccine strain (D78) and the virulent IM or GLS variant strain. Using the cRNA-based reverse-genetics system developed for IBDV, we generated five chimeric viruses after transfection by electroporation procedures in Vero or chicken embryo fibroblast (CEF) cells, one of which was recovered after propagation in embryonated eggs. To evaluate the characteristics of the recovered viruses in vivo, we inoculated 3-week-old chickens with D78, IM, GLS, or chimeric viruses and analyzed their bursae for pathological lesions 3 days postinfection. Viruses in which VP4, VP4-VP3, and VP1 coding sequences of the virulent strain IM were substituted for the corresponding region in the vaccine strain failed to induce hemorrhagic lesions in the bursa. In contrast, viruses in which the VP2 coding region of the vaccine strain was replaced with the variant GLS or virulent IM strain caused rapid bursal atrophy or hemorrhagic lesions in the bursa, as seen with the variant or classical virulent strain, respectively. These results show that the virulence and pathogenic-phenotype markers of IBDV reside in VP2. Moreover, one of the chimeric viruses containing VP2 sequences of the virulent strain could not be recovered in Vero or CEF cells but was recovered in embryonated eggs, suggesting that VP2 contains the determinants for cell tropism. Similarly, one of the chimeric viruses containing the VP1 segment of the virulent strain could not be recovered in Vero cells but was recovered in CEF cells, suggesting that VP1 contains the determinants for cell-specific replication in Vero cells. By comparing the deduced amino acid sequences of the D78 and IM strains and their reactivities with monoclonal antibody 21, which binds specifically to virulent IBDV, the putative amino acids involved in virulence and cell tropism were identified. Our results indicate that residues Gln at position 253 (Gln253), Asp279, and Ala284 of VP2 are involved in the virulence, cell tropism, and pathogenic phenotype of virulent IBDV.

Amino Acid Sequence↗
PubMed2003

Does a deletion in a virus-like particle protein have pleiotropic effects on the reproductive biology of a parasitoid wasp?

Endoparasitoid insects have evolved mechanisms to counteract host immune defences. At oviposition, the endoparasitoid Venturia canescens injects virus-like particles (VLPs) together with the egg that interfere with the immune system of the host. These prevent encapsulation of the parasitoid egg. It has been shown that the gene coding for one of the VLP proteins exists in two variants (called Repeat-Plus (RP) and Repeat-Minus (RM)). Previous observations suggested that these variants induce pleiotropic effects on the reproductive biology of the female resulting, in an impeded transfer of eggs from the ovarioles to the oviducts in RM females, and in alterations in the egg laying sequence. We show that RM females from another geographical locality do not exhibit any phenotypic alteration of the reproductive biology. By showing a lack of association between VLP alleles and the reproductive phenotypic characteristics in a given strain, our results do not support the hypothesis of pleiotropic effects. Conversely, the results suggest that different genes code for the VLPs and for the reproductive biology characteristics. Different phenomena such as linkage, the action of pathogens, etc. could explain the association between characters that is observed in some strains.

Animals↗
PubMed1999

Tuning biphenyl dioxygenase for extended substrate specificity.

Highly substituted polychlorinated biphenyls (PCBs) are known to be very resistant to aerobic biodegradation, particularly the initial attack by biphenyl dioxygenase. Functional evolution of the substrate specificity of biphenyl dioxygenase was demonstrated by DNA shuffling and staggered extension process (StEP) of the bphA gene coding for the large subunit of biphenyl dioxygenase. Several variants with an extended substrate range for PCBs were selected. In contrast to the parental biphenyl dioxygenases from Burkholderia cepacia LB400 and Pseudomonas pseudoalcaligenes KF707, which preferentially recognize either ortho- (LB400) or para- (KF707) substituted PCBs, several variants degraded both congeners to about the same extent. These variants also exhibited superior degradation capabilities toward several tetra- and pentachlorinated PCBs as well as commercial PCB mixtures, such as Aroclor 1242 or Aroclor 1254. Sequence analysis confirmed that most variants contained at least four to six template switches. All desired variants contained the Thr335Ala and Phe336Ile substitutions confirming the importance of this critical region in substrate specificity. These results suggest that the block-exchange nature of gene shuffling between a diverse class of dioxygenases may be the most useful approach for breeding novel dioxygenases for PCB degradation in the desired direction.

Amino Acid Sequence↗
PubMed1996

Infrequent CDKN2 mutation in human differentiated thyroid cancers.

We examined the frequency of cyclin-dependent kinase (CDK) N2 alterations in differentiated and anaplastic thyroid cancers to assess the involvement of CDKN2 in the development of these cancers. The CDKN2 gene, which encodes the cell-cycle regulator p16, was recently shown to be mutated or deleted in many tumor cell lines. Its role in the genesis of primary tumors is uncertain, however. Tumor and corresponding normal DNAs were prepared by microdissection of paraffin-embedded tissue blocks or from frozen surgical specimens of 15 papillary, 15 follicular, and five anaplastic thyroid carcinomas. The entire CDKN2 coding region was screened by single-strand conformational variant analysis and direct sequencing of variants. The presence of homozygous deletions was evaluated by multiplex polymerase chain reaction (PCR) analysis. Loss of heterozygosity (LOH) in the CDKN2 region was assessed by using flanking polymorphic markers. Two somatic missense mutations were found among the 35 thyroid cancers, one in a follicular tumor and one in an anaplastic tumor. Multiplex PCR suggested the presence of homozygous deletion in one anaplastic tumor and hemizygous deletions in four tumors. LOH studies revealed loss of 9p sequences in four follicular (27%) and two anaplastic (50%) cancers. Our data suggest that alterations in CDKN2 played a role in a minority of thyroid cancers (three of 35). LOH in the region of CDKN2 is seen in a significant proportion of follicular and anaplastic but not papillary cancers. Loss of 9p sequences suggests a role for a tumor suppressor gene in the development of follicular and anaplastic thyroid cancers.

Adenocarcinoma, Follicular↗
PubMed2005

Mutation spectrum in Jewish cystic fibrosis patients in Israel: implication to carrier screening.

We have tested 144 unrelated Jewish patients suffering from the classical form of cystic fibrosis. The patients were screened for a panel of 12 mutations including the six Ashkenazi founder mutations (DeltaF508, W1282X, N1303K, G542X, 3849 + 10 kb C-->T, 1717-1G > A) and six mutations that were found in non-Ashkenazi Jewish patients (S549R (T-->G), G85E, 405 + 1G-->A, W1089X, Y1092, and D1152H). Patients of Georgian origin were tested also for the Q359K/T360K mutation. In addition, all the patients were tested for the IVS-8 variant (9T/7T/5T). Of all the cystic fibrosis (CF)-bearing chromosomes, 94% (264/281) were accounted for by one of the known mutations, and none of the patients had the 5T allele of the IVS-8 variant. Single strand conformation polymorphism (SSCP) analysis of the coding sequence of the CFTR gene followed by sequencing showed eight mutations on ten CF chromosomes, leaving seven chromosomes (2.5%) with unknown mutations. We identified three mutations in two or more CF chromosomes, 2571 + 1insT in Jews from Iraq, 3121-1G > A in patients from Kurdistan and I1234V in Yemenite Jewish patients. The other five mutations appeared on a single allele and are considered "private mutations." In this study we have identified 99% of CF alleles in Ashkenazi Jewish patients, 91% in Jews of North African origin and 75% in Jewish patients from Iraq. The significance of these findings to the population screening in Israel is discussed.

Cystic Fibrosis↗
PubMed2004

Genetic characterization and structural analysis of VHL Spanish families to define genotype-phenotype correlations.

Von Hippel-Lindau (VHL) disease is a hereditary cancer syndrome caused by germline mutations in the VHL gene. This gene, located in the 3p25-26 chromosome, is a tumor suppressor gene associated with the inhibition of angiogenesis and apoptosis, cell cycle exit, fibronectin matrix assembly, and proteolysis. To define the molecular basis of VHL in a Spanish population, we studied 33 patients suspected of suffering familial or de novo VHL disease and two familial pheochromocytoma cases. Sequence analysis of the coding regions of the VHL gene revealed germline sequence variants in 68.7% (24 out of 35) of the patients, and four of them presented with undescribed germline alterations: g.5429-5430insG, p.Leu128Arg, p.Tyr175Cys, and p.Tyr175Asn. For the remaining 11 patients who showed negative for point mutations, we performed Southern blot analysis and detected gross rearrangements in eight cases (22.8% of the index cases). Our results support the relevance of VHL gene analysis in familial pheochromocytoma cases and also in those with no familial history. In order to investigate the relevance of different amino acid changes in the VHL phenotype, we also analyzed the genotype-phenotype correlations using structural analysis to assess protein stability and complexes. The association of clear cell renal carcinoma (CCRC) development with a relatively high loss of structural stability in pVHL missense-mutants was consistent. Structural stability data in the genotype-phenotype correlations therefore provides us with a better understanding of VHL clinical implications. It is also a suitable approach to the evaluation of unknown significance changes.

Adenocarcinoma, Clear Cell↗
PubMed2004

Analysis of the allele-specific expression of the mismatch repair gene MLH1 using a simple DHPLC-Based Method.

Quantitative measures of allele-specific gene expression allow the indirect detection of mutations or sequence variants in regulatory elements or in other non-coding regions that may result in significant physiological or pathological changes of gene expression and may contribute to Mendelian or multifactorial disorders. We have devised a simple method, based on RT-PCR and single nucleotide primer extension (SNuPE) with unlabelled dideoxynucleotides, followed by DHPLC (denaturing high performance liquid chromatography). We established optimal conditions for separation of the extended products corresponding to the alleles of the c.655A>G (p.Ile219Val) SNP, which is the most frequent exonic polymorphism of MLH1. We then genotyped 99 unrelated control subjects and measured the allele-specific MLH1 expression in the 40 heterozygous controls found in this group. This method allowed us to define a narrow range of normal biallelic expression of MLH1, each allele contributing between 44.7% and 55.3% of the total expression. We then measured the allele-specific expression in hereditary nonpolyposis colorectal cancer (HNPCC) patients with MLH1 mRNAs bearing different stop-codon or frame-shift mutations, or in-frame deletions, in order to detect the effects of nonsense-mediated mRNA decay (NMD). Defects that induce mRNA instability were identified unambiguously and the data were consistent with current models of NMD. This study provides a sensitive tool to identify indirectly MLH1 defects that may escape detection in genomic DNA screenings but result in a quantitative change at the mRNA level.

Adaptor Proteins, Signal Transducing↗
PubMed1986

Protein kinase in nondiabetogenic coxsackievirus B4.

Alkali-dissociated, purified preparations of prototype coxsackievirus B4 release a protein kinase that catalyzes the incorporation of gamma-phosphate from 32P-labeled ATP into three virus capsid proteins (VP1, VP3, VP4), several additional proteins of the particle, and exogenous acceptor proteins. Using protamine sulfate as an acceptor protein, we detected nearly 20-fold more enzyme activity in membrane-bound virions (MBV) than in virions of the virus. The activity in the MBV is cyclic nucleotide-independent, divalent cation-dependent, and has a pH optimum of 8.0. Phosphoserine is labeled with 32P. The enzyme activity sediments at about 5S and is separated into at least two peaks of heterogeneous proteins by ion-exchange chromatography. The patterns of phosphorylation by these enzyme peaks are somewhat similar. Coxsackievirus-associated protein kinase appears to be located internally in the virus and may be host-cell-coded. The enzyme appears to be lacking in a variant of the virus that produced diabetes in mice.

Autoradiography↗
PubMed2005

Heterogeneous nature of HIV-1 recombinants spreading in Spain.

HIV-1 infections due to non-B subtypes are increasing rapidly in number and spreading across Europe. The genetic nature of HIV-1 non-B variants containing subtype G sequences at the protease (PR)-coding region are described from 48 unrelated subjects living in Spain. Phylogenetic analyses of the HIV-1 reverse transcriptase (RT) and envelope (env) genes (including the V3 loop) were performed. Up to 32 (66.6%) of samples carried inter-subtype recombinant viruses. Although double recombinants were found most frequently (G/A in 20; G/B in 8; G/K in 2), two individuals harbored triple recombinant viruses (GPR/BRT/Aenv and GPR/KRT/Aenv, respectively). Only 33 (68.7%) and 9 (18.7%) sequences clustered with clade G when examining the RT and env genes, respectively. Nearly 70% of samples with pol sequences (PR/RT) belonging to subtype G harbored env sequences ascribed to other clades: A (55.6%), B (11.1%), or K (3.7%). Of note, most recombinant viruses clustered with CRF02_AG, although CRF14_BG recombinants were also found. This study demonstrates that most viruses circulating in Spain with clade G sequences at the pol-coding region are in fact inter-subtype recombinants, with CRF02_AG being the most prevalent virus.

Adolescent↗
PubMed1990

Molecular genetics of alpha 2 plasmin inhibitor.

Analysis of the cDNA for alpha 2PI and its expression experiment indicated that the leader sequence is pre-pro peptide containing an N-terminal hydrophobic prepeptide (signal sequence) of 27 amino acids, followed by a hydrophilic propeptide of 12 amino acids. The alpha 2PI gene contains 10 exons and 9 introns distributed over approximately 16 kilobases of DNA. Two families of hereditary alpha 2PI deficiency were found to have changes of nucleotide sequence in an exon coding for plasma alpha 2PI, resulting in productions of variant proteins. These proteins are mostly retained within the cells, resulting in a deficiency of alpha 2PI in a circulating blood plasma.

Chromosome Deletion↗
PubMed1983

Alcohol dehydrogenase isozymes in the clawed frog, Xenopus laevis.

Alcohol dehydrogenase (ADH; EC 1.1.1.1) activity in Xenopus laevis was highest in liver tissue, with decreasing activities in kidney, heart, and gut tissues, respectively. Essentially no activity was found among other tissues screened, including lung, ovary, eye, and testes. Also, there was no apparent sexual dimorphism of ADH activity in either liver or kidney tissue. All ADH isozymes were inhibited by 10 mM pyrazole, and no eye-specific retinol dehydrogenase activity was detected on starch gel electropherograms. Isozyme patterns from 418 offspring from 11 different crosses could be explained genetically assuming the presence of two structural genes coding for ADH production: one carrying two electrophoretically separable variants and the other showing quantitative variation in its expression. The ADH system in X. laevis should be useful for studies concerning the molecular mechanisms governing the expression of ADH activity in vertebrate development.

Alcohol Dehydrogenase↗
PubMed1982

Genetic variants of the Bombyx mori silkworn encoding sericin proteins of different lengths.

A variant sericin polypeptide originally found by acid gel electrophoresis in the Nd-s mutant strain of the silkworm, Bombyx mori, has been analyzed genetically. The variant polypeptide (called S-2v) is encoded by a gene which behaves as a codominant allele of the gene encoding the standard S-2 sericin polypeptide. Linkage analysis locates these alleles at 0.0 map unit on chromosome 11. SDS-polyacrylamide gel electrophoresis shows that the molecular weight of the S-2v variant polypeptide is lower by approximately 62,500 than that of the S-2 polypeptide. Amino acid analysis indicates that the two sericin polypeptides have similar compositions. These results are consistent with the idea that the variant allele arose by deletion within the S-2 coding sequence in the Src-2 gene locus as the result of unequal recombination.

Amino Acids↗
PubMed2002

TYRP1 and MC1R genotypes and their effects on coat color in dogs.

We used PCR amplification of cDNA prepared from skin biopsies to determine the nearly full-length, protein-coding sequence of dog TYRP1, and to define sequence variants potentially responsible for the B locus. One common variant contained a premature stop codon in exon 5 (Q331ter), and the other deleted a proline residue in exon 5 (345delP). A third variant in exon 2 (S41C) occurred less frequently. We genotyped 43 brown (including brown and white) and 34 black (including tricolor, black-and-tan, and black and white) dogs. All 43 of the brown group carried two or more of these sequence variants likely to interfere with TYRP1 function, whereas 0 of 34 in the black group carried two or more of these variants (10 carried one variant). We also genotyped 13 black-nosed and 10 brown-nosed dogs whose coat color was described as red, yellow, gold, apricot, or orange (including various degrees of white). All these dogs were homozygous for a R306X MC1R variant shown to be associated with these coat color phenotypes. The black or brown nose correlated perfectly with the absence or presence of the same three TYRP1 variants described above. TYRP1 was linkage mapped to dog chromosome 11, with a SNP in exon 7.

Amino Acid Sequence↗
PubMed1988

Evidence for gene conversion between the phosphoglycerate kinase genes of Trypanosoma brucei.

Trypanosoma brucei contains a tandem array of three genes for phosphoglycerate kinase (PGKase), genes A, B and C, each coding for a different protein. We have compared allelic variants of this gene array and find evidence for gene conversion between the three genes. Near the 3' end, the different alleles and gene B contain a variable sequence that is similar to the corresponding sequence in either gene A or gene C. This sequence is flanked by glycine triplets that are conserved in all PGKases from bacteria to mammals. The triplets are encoded by (GGT)n, resulting in sequences that resemble the recombination-promoting chi-sites of Escherichia coli. Upstream of the variable sequence, there is an area of 800 base-pairs in which genes A, B and C are highly homologous; in all three genes this region ends with a sharp boundary at which gene B again shows segmental homology with both genes A and C. These results suggest that repeated gene conversion events partially erase the differences between genes A, B and C that arise in evolution and suggest that chi-like sequences may act as recombinational hotspots in protozoa such as T. brucei.

Amino Acid Sequence↗
PubMed1994

Identification of an amino acid on VP2 that affects neutralization of bluetongue virus serotype 10.

Genome segment 2, coding for the VP2 protein, of a neutralization resistant variant was compared to segment 2 of the bluetongue virus (BTV) serotype 10 parent from which the variant was derived. Full-length double-stranded cDNA of BTV segment 2 RNA, which was prepared by reverse transcription, was used as template to prepare overlapping subgenomic cDNA products by PCR. Purified PCR cDNA fragments were sequenced by the dideoxy chain termination reaction. Each base was determined an average of 3.7 times. Comparison of the sequence of segment 2 of the neutralization resistant variant with segment 2 of the parental virus showed two base changes, one of which resulted in a changed amino acid. This change was in a different region of VP2 than those previously reported in other neutralization resistant variants of BTV. In addition to this change, both the parental virus and the variant virus differed in two amino acids from the previously published sequence of VP2 of BTV serotype 10.

Amino Acid Sequence↗