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PubMed1995

On the biological role of the nuclear polymerizing NAD+: protein(ADP-ribosyl) transferase (ADPRT): ADPRT from Dictyostelium discoideum and inactivation of the ADPRT gene in the mouse.

Two approaches have been used to elucidate the role of the nuclear polymerizing NAD+:protein(ADP-ribosyl)-transferase (ADPRT): i) comparison of the primary structure of Dictyostelium discoideum ADPRT derived from a 2 kb, partial cDNA sequence with the mammalian, fish, amphibian and insect counterparts revealed an overall homology of 25%. Whereas the automodification domain was not conserved at all, the NAD+ binding domain (aa 859-908) showed more than 70% identical amino acids in all species. Together with the similar enzymatic properties of the ADPRTs the genetic conservation underlined the notion that ADPRT plays a major role in various cellular processes; and ii) inactivation of the ADPRT gene in murine embryonic stem cells by homologous recombination led to mouse strains with a complete lack of nuclear poly(ADP-ribosyl)ation. These ADPRT mutant mice were viable and fertile indicating that ADPRT is dispensable in mouse development. Moreover, repair of UV and MNNG induced DNA damage was not affected in ADPRT/3T3 like fibroblasts, as measured by reactivation of in vitro damaged reporter plasmids and unscheduled DNA synthesis. However, about 30% of the ADPRT mutant mice developed pathological skin aberrations on a mixed 129/Sv x C57B1/6 genetic background. These mice will be extremely useful to define the precise biological role of poly(ADP-ribosyl)ation.

ADP Ribose Transferases↗

PubMed1971

Genetic restriction of energy conservation in Schizophyllum.

A genetically determined malfunction of energy conservation reduces assimilation of substrate to half or less its normal level while leaving oxidative processes apparently unchanged. This metabolic defect, which differs in many ways from any previously described, is related to the function of the B incompatibility factor and occurs both in the common A heterokaryon (A = B not equal)-in which two compatible, wild B factors interact-and in mutant-B homokaryons.

Basidiomycota↗

PubMed2003

Allozyme variation and population genetic structure of Betula alnoides from Guangxi, China.

Allozyme variation and population genetic structure of Betula alnoides Buch Ham. ex D. Don in 11 natural populations from Guangxi Zhuang Autonomous Region, China, were investigated by starch gel electrophoresis. Variation at 15 loci from 10 enzyme systems was analyzed. Allozyme analysis revealed a high level of genetic variation in this species, with percentage of polymorphic loci (P(p)), the average number of alleles per locus (A(p)), and the expected heterozygosity (H(ep)) being 55.2%, 2.0, and 0.204, respectively, which exceeds the average level among out-crossing wind-pollinated woody species at the population level. At the species level, P(s), A(s), and H(es) were 60.0%, 2.67, and 0.206, respectively. The observed heterozygosity (H(op)) was higher than H(ep), indicating the existence of natural selection against homozygotes. The negative fixation index (F = -0.216) implied a significant excess of heterozygosity at the population level Among-population differentiation (F(ST)) accounted for 4.0% of the total variation. No significant correlation was detected between the genetic distance and geographic distance among populations. Extensive gene flow was inferred, based on the allozyme data (N(m) = 6.000 from F(ST), N(m) = 5.605 from the "private allele" method). The results demonstrated that the fragmentation status of B. alnoides had no remarkable effects on the population genetic structure of this species. Some populations are recommended for both in situ genetic conservation and germplasm collection for breeding programs.

Betula↗

PubMed1990

Vascular smooth muscle biglycan represents a highly conserved proteoglycan within the arterial wall.

Two overlapping cDNA clones containing sequences homologous to human bone biglycan were isolated from a rat vascular smooth muscle (VSM) cell cDNA library. Nucleotide sequence analysis demonstrated that these clones encoded the rat VSM biglycan complete core protein sequence. A high degree of genetic conservation was observed for biglycan since nucleotide sequence homology comparisons revealed an 88% homology occurring between rat and human biglycan cDNA coding regions. The deduced core protein for the secreted form of VSM biglycan was found to be composed of ten leucine-rich repeating units whose consensus sequence was similar to that present in human bone and bovine cartilage biglycans. Protein homology comparisons revealed that the mature rat VSM biglycan core protein was 97% homologous to both human bone and bovine cartilage biglycan core proteins. Most of the amino acid substitutions in the secreted form of rat VSM biglycan are of the conservative type thereby maintaining the hydrophobic property of this proteoglycan within the arterial wall. The highest frequency of amino acid substitutions occurring between rat, bovine and human biglycan core proteins was found to reside within a small hypervariable region located near the N-terminus of these proteoglycans. Rat VSM biglycan was found to contain dinucleotide repeat elements located in the 3' untranslated region of its mRNA which may influence the expression of this transcript. Biglycan mRNA levels were not found to vary significantly as a function of VSM cell density. However, biglycan transcript levels did vary significantly as a function of VSM cell growth state. Similar studies revealed that collagen, fibronectin, and laminin were able to influence biglycan mRNA levels in quiescent VSM cells.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗

PubMed2004

ISSR variation in the endemic and endangered plant Cycas guizhouensis (Cycadaceae).

BACKGROUND AND AIMS: Cycas guizhouensis (Cycadaceae) is a rare and endangered species endemic to the southwest of China. An investigation was undertaken into the genetic variation of wild populations. METHODS: ISSR markers were used to determine the genetic variation within and between 12 extant populations of this species. KEY RESULTS: Low genetic diversity (at population level, P = 14.21 %, H(E) = 0.0597; at species level, P = 35.90 %, H(T) = 0.1082) and a high degree of differentiation among populations (G(ST) = 0.4321) were detected. CONCLUSIONS: This genetic structure is considered to be due to the combined effects of slow biochemical evolution, genetic drift, inbreeding and limited gene flow between populations. Based on these findings, strategies are proposed for the genetic conservation and management of the species.

Cycas↗

PubMed2006

Identification and characterization of CYP3A4*20, a novel rare CYP3A4 allele without functional activity.

BACKGROUND: The major drug-metabolizing enzyme cytochrome P450 (CYP) 3A4 is genetically conserved. One outlier of Brazilian descent was found in a clinical pharmacokinetic trial exhibiting a 6-fold higher exposure than expected to an investigational drug, shown to be a CYP3A4 substrate. We aimed to investigate the genetic background of this finding. METHODS: The allelic variant of the CYP3A4 gene present in the outlier was sequenced, and the corresponding complementary deoxyribonucleic acid was expressed in yeast and human embryonic kidney cells. The outlier was phenotyped by use of intravenous administration of 1 mg midazolam. Analysis of phenotype and genotype correlation was carried out. The prevalence of the new allele was screened for in a white population. RESULTS: We identified a subject who heterozygously carried a novel CYP3A4 allele, named CYP3A4*20, with a premature stop codon yielding a truncated protein. Heterologous expression revealed that the CYP3A4.20 enzyme does not incorporate heme and thus is devoid of catalytic activity. CYP3A phenotyping in vivo showed that CYP3A4*20 exhibits a clear genotype-phenotype correlation, demonstrated by the subject's low systemic midazolam clearance (2.99 mL x min(-1) x kg(-1)). Genotyping of a white German population (n = 428) and relatives of the subject, as well as a review of published CYP3A4 sequencing data, suggests that CYP3A4*20 is a rare variant allele (<0.06% in white subjects). CONCLUSIONS: CYP3A4*20 represents the first CYP3A4 allele to be identified that has been shown to be devoid of functional activity. It causes an intermediate CYP3A4 metabolizer phenotype in a heterozygous carrier. Subjects of this genotype might be susceptible to side effects during drug therapy with substrates or inhibitors of CYP3A4.

Adult↗

PubMed2005

Impact of human immunodeficiency virus type 1 (HIV-1) genetic diversity on performance of four commercial viral load assays: LCx HIV RNA Quantitative, AMPLICOR HIV-1 MONITOR v1.5, VERSANT HIV-1 RNA 3.0, and NucliSens HIV-1 QT.

Human immunodeficiency virus type 1 (HIV-1) evolution and changing strain distribution present a challenge to nucleic acid-based assays. Reliable patient monitoring of viral loads requires the detection and accurate quantification of genetically diverse HIV-1. A panel of 97 HIV-1-seropositive plasma samples collected from Cameroon, Brazil, and South Africa was used to compare the performance of four commercially available HIV RNA quantitative tests: Abbott LCx HIV RNA Quantitative assay (LCx), Bayer Versant HIV-1 RNA 3.0 (bDNA), Roche AMPLICOR HIV-1 MONITOR v1.5 (Monitor v1.5), and bioMérieux NucliSens HIV-1 QT (NucliSens). The panel included group M, group O, and recombinant viruses based on sequence analysis of gag p24, pol integrase, and env gp41. The LCx HIV assay quantified viral RNA in 97 (100%) of the samples. In comparison, bDNA, Monitor v1.5, and NucliSens quantified viral RNA in 96.9%, 94.8%, and 88.6% of the samples, respectively. The two group O specimens were quantified only by the LCx HIV assay. Analysis of nucleotide mismatches at the primer/probe binding sites for Monitor v1.5, NucliSens, and LCx assays revealed that performance characteristics reflected differences in the level of genetic conservation within the target regions.

Genetic Variation↗

PubMed1997

Limited diversity of Streptococcus pneumoniae psaA among pneumococcal vaccine serotypes.

The pneumococcal surface adhesin A (PsaA) is a surface-exposed protein of the gram-positive bacterium Streptococcus pneumoniae. It belongs to a group of proteins designated the lipoprotein receptor I antigen family. The gene encoding PsaA from an encapsulated strain of pneumococcal serotype 6B was cloned and sequenced. The peptide sequence was compared to that of homologs found in S. pneumoniae serotype 2, viridans streptococci, and Enterococcus faecalis. Identity values among the deduced peptides ranged from 57 to 98%. The polymorphism of psaA was examined among the 23 encapsulated vaccine serotypes by using PCR-restriction fragment length polymorphism analysis. Ten different enzymes were used to analyze 80 strains representing the 23 serotypes in a 23-valent polysaccharide vaccine. This analysis showed that restriction sites within the gene were highly conserved, with only a minor variation occurring in 10% of the strains, the result of an additional Tsp509I site. The lack of variation for the other restriction sites within the gene examined here indicates that psaA is genetically conserved, an important characteristic necessary for a candidate common protein vaccine.

Adhesins, Bacterial↗

PubMed2002

Pax6 is required for establishing naso-temporal and dorsal characteristics of the optic vesicle.

The establishment of polarity is an important step during organ development. We assign a function for the paired and homeodomain transcription factor Pax6 in axis formation in the retina. Pax6 is a key factor of the highly conserved genetic network implicated in directing the initial phases of eye development. We recently demonstrated that Pax6 is also essential for later aspects of eye development, such as lens formation and retinogenesis. In this study, we present evidence that a highly conserved intronic enhancer, alpha, in the Pax6 gene is essential for the establishment of a distal(high)-proximal(low) gradient of Pax6 activity in the retina. In the mature retina, the activity mediated by the alpha-enhancer defines a population of retinal ganglion cells that project to two sickle-shaped domains in the superior colliculus and lateral geniculate nucleus. Deletion of the alpha-enhancer in vivo revealed that retinal Pax6 expression is regulated in two complementary topographic domains. We found that Pax6 activity is required for the establishment, as well as the maintenance of dorsal and nasotemporal characteristics in the optic vesicle and, later, the optic cup.

Animals↗

PubMed1992

Cloning and sequence comparison of the mouse, human, and chicken engrailed genes reveal potential functional domains and regulatory regions.

We have isolated and characterized genomic DNA clones for the human and chicken homologues of the mouse En-1 and En-2 genes and determined the genomic structure and predicted protein sequences of both En genes in all three species. Comparison of these vertebrate En sequences with the Xenopus En-2 [Hemmati-Brivanlou et al., 1991) and invertebrate engrailed-like genes showed that the two previously identified highly conserved regions within the En protein ]reviewed in Joyner and Hanks, 1991] can be divided into five distinct subregions, designated EH1 to EH5. Sequences 5' and 3' to the predicted coding regions of the vertebrate En genes were also analyzed in an attempt to identify cis-acting DNA sequences important for the regulation of En gene expression. Considerable sequence similarity was found between the mouse and human homologues both within the putative 5' and 3' untranslated as well as 5' flanking regions. Between the mouse and Xenopus En-2 genes, shorter stretches of sequence similarity were found within the 3' untranslated region. The 5' untranslated regions of the mouse, chicken and Xenopus En-2 genes, however, showed no similarly conserved stretches. In a preliminary analysis of the expression pattern of the human En genes, En-2 protein and RNA were detected in the embryonic and adult cerebellum respectively and not in other tissues tested. These patterns are analogous to those seen in other vertebrates. Taken together these results further strengthen the suggestion that En gene function and regulation has been conserved throughout vertebrate evolution and, along with the five highly conserved regions within the En protein, raise an interesting question about the presence of conserved genetic pathways.

Amino Acid Sequence↗

PubMed2006

Genetic structure and phylogenetic relationships of the Polish Heavy horse.

In this study a wide range of genetic markers (12 microsatellites, 7 blood-group loci, 10 blood-protein loci) and mitochondrial DNA (mtDNA) were used to assess genetic diversity in Polish Heavy horses. Three random samples were sequenced for 421 bp of the mitochondrial D-loop region, but no clear phylogenetic patterns were seen in mtDNA variation. Both heterozygosity and diversity levels are fairly high in Polish Heavy horses. In phylogenetic analysis the draught horses form a distinct cluster that pairs with the true pony breeds. Within this 'cold-blooded' group, the Polish Heavy Horse clusters most closely with the Posavina breed from Croatia and the Breton breed from France. From the standpoint of genetic conservation, the Polish Heavy Horse does not appear to be in jeopardy.

Animals↗

PubMed2003

[D-loop sequence variation of mitochondrial DNA in captive Chinese alligator].

Chinese alligator, Alligator sinensis, is a critically endangered endemic species under legislative protection in China. Result of recent investigations revealed that number of the alligators was continuously declining in the past 50 years and less than 150 individuals were surviving in the wild until 2000 years. In order to prevent the extinguishing of this species, two breeding farms were set up in early 1980s at Xuanzhou county, Anhui Province and Changxing County, Zhejiang Province respectively. After twenty years of breeding efforts, the number of captive individuals has been brought up to more than 9,000 in total, forming two separate captive subpopulations, Xuanzhou subpopulation (XZSP) and Changxing subpopulation (CXSP). Because of lack of the information regarding genetic diversity of the captive populations, 42 captive individuals including 33 individuals from XZSP and 9 from CXSP were sampled randomly to investigate their genetic status for the strategy in the next protection action. PCR method was adopted for amplification of mitochodrial DNA control region using primers designed in this research. After purification of PCR products, all of amplicons were sequenced directly with ABI BigDye Terminator Cycle Sequencing Ready Reaction Kit and ABI 310 genetic analyzer. Consequently, 5' end of control region with length of 462 base pair was obtained from 39 samples. Sequence alignment shows there is no any variation site in this range of control region among the individuals assayed here, namely only one haplotype of the region shared by these alligators. This result strongly indicates that the population of captive Chinese alligator is in very poor genetic diversity status. Reasons for the losing of genetic diversity in the population are mainly attributed to population depression and number of individual decreasing sharply in the past 50 years. Another factor accounting for the phenomena is the limit of founder number of captive population. Finally, authors proposed three pieces of advice for the genetic conservation of Chinese alligator.

Alligators and Crocodiles↗

PubMed2004

[The analysis of genetic variability of mtDNA 12S rRNA genes in the allotetraploid, triploid crucian carp and their parents].

The complete 12S rRNA genes from the five F11 allotetraploids, two diploid gynogens, two triploid crucian carps, one red crucian carp, one xiangjiang common carp, and one Japanese crucian carp were successfully cloned and sequenced. Sequence compositions and variations were analyzed with MEGA 1.0 software. Five F11 allotetraploids shared two haplotypes, and two diploid gynogens, two triploid crucian carps, one red crucian carp, one xiangjiang common carp, one Japanese crucian carp shared one haplotype, respectively. The similarities among red crucian carp, xiangjiang common carp, allotetraploid, diploid gynogen, Japanese crucian carp, and triploid crucian carp varied from 95% to 99%. The similarities between allotetraploid, triploid crucian carp and their female parents (red crucian carp and Japanese crucian carp, respectively) were higher than those between allotetraploid, triploid crucian carp and their male parents (xiangjiang common carp and allotetraploid, respectively). Such result indicated that mitochondrial 12S rRNA genes of the allotetraploid and triploid crucian carp were inherited maternally. A phylogenetic tree was reconstructed using the neighbor joining method of the MEGA package. It was noticeable that after nine generations from F3 to F11 hybrids, the five F11 allotetraploids shared two haplotypes (AT-1 and AT-2), indicating the allotetraploid stock had the genetic diversity. The results provided some valuable information for the breeding, genetic conservation, and population rejuvenation of the tetraploid stock.

Animals↗

PubMed2003

Genetically linked C-type lectin-related ligands for the NKRP1 family of natural killer cell receptors.

The natural killer (NK) gene complex (NKC) encodes orphan lectin-like NK cell receptors that may explain uncharacterized NK cell specificities. Unlike other NKC-encoded receptors that recognize molecules with major histocompatibility complex (MHC) class I folds, here we show that mouse Nkrp1d and Nkrp1f bind specific C-type lectin-related (Clr) molecules. Nkrp1d mediated inhibition when recognizing Clrb, a molecule expressed in dendritic cells and macrophages. Nkrp1 (official gene name, Klrb1) and Clr are intertwined in a genetically conserved NKC region showing recombination suppression, reminiscent of plant self-incompatibility loci. Thus, these findings broaden the 'missing-self' hypothesis from solely involving MHC class I to including related NK cell receptors for lectin-like ligands, and reflect genetic strategies for biological self-recognition processes in other species.

Animals↗

PubMed2002

Assessment of hemagglutinin sequence heterogeneity during influenza virus transmission in families.

To examine the molecular epidemiology of influenza virus transmission, the nucleotide sequences of the HA1 domain of the hemagglutinin (HA) gene of 57 influenza A and 24 influenza B viruses recovered in a single season were analyzed. No nucleotide sequence differences were found among the 10 viruses that were recovered twice from the same patient. The nucleotide sequences of influenza A viruses were identical within each family but varied among the 14 families included in the study. The sequences of influenza A viruses recovered from 18 residents of the same community showed that 83% of the viruses differed from the others by at least 1 nucleotide residue. These findings indicate that most cases of influenza in households in which 1 family member has been infected are the result of secondary transmission from the index patient and not of acquisition from other community sources. Substantial genetic conservation during virus transmission within households is indicated.

Adolescent↗

PubMed2001

Selective recovery of founder genetic diversity in aquacultural broodstocks and captive, endangered fish populations.

Hatchery broodstocks used for genetic conservation or aquaculture may represent their ancestral gene pools rather poorly. This is especially likely when the fish that found a broodstock are close relatives of each other. We re-analysed microsatellite data from a breeding experiment on red sea bream to demonstrate how lost genetic variation might be recovered when gene frequencies have been distorted by consanguineous founders in a hatchery. A minimal-kinship criterion based on a relatedness estimator was used to select subsets of breeders which represented the maximum number of founder lineages (i.e., carried the fewest identical copies of ancestral genes). UPGMA clustering of Nei's genetic distances grouped these selected subsets with the parental gene pool, rather than with the entire, highly 'drifted' offspring generation. The selected subsets also captured much of the expected heterozygosity and allelic diversity of the parental gene pool. Independent pedigree data on the same fish showed that the selected subsets had more contributing parents and more founder equivalents than random subsets of the same size. The estimated mean coancestry was lower in the selected subsets, meaning that inbreeding in subsequent generations would be lower if they were used as breeders. The procedure appears suitable for reducing the genetic distortion due to consanguineous and over-represented founders of a hatchery gene pool.

Alleles↗

PubMed2000

Inbreeding depression and genetic load in laboratory metapopulations of the butterfly Bicyclus anynana.

We investigated the effects of inbreeding on various fitness components and their genetic load in laboratory metapopulations of the butterfly Bicyclus anynana. Six metapopulations each consisted of four subpopulations with breeding population sizes of N = 6 or N = 12 and migration rate of m = 0 or m = 0.33. Metapopulations were maintained for seven generations during which coancestries and pedigrees were established. Individual inbreeding coefficients at the F7 were calculated and ranged between 0.01 and 0.51. Even though considerable purging had occurred during inbreeding, the genetic load remained higher than that of many outbreeding species: approximately two lethal equivalents were detected for egg sterility, one for zygote survival, one for juvenile survival, and one for longevity. Severe inbreeding depression occurred after seven generations of inbreeding, which jeopardized the metapopulation survival. This finding suggests that the purging of genetic load by intentional inbreeding cannot be recommended for the genetic conservation of species with a high number of lethal equivalents.

Animals↗

PubMed2002

Genetic network of the eye in Platyhelminthes: expression and functional analysis of some players during planarian regeneration.

Planarians are the free-living members (order Tricladida) of the phylum Platyhelminthes. They are triploblastic, acoelomate, unsegmented and located at the base of the Lophotrochozoa clade. Besides their huge regenerative capacity, planarians have simple eyes, considered similar to the prototypic eye suggested by Charles Darwin in his book 'On the Origin of Species'. The conserved genetic network that determines the initial steps of eye development across metazoans supports a monophyletic origin of the various eye types present in the animal kingdom. Here we summarise the pattern of expression of certain genes involved in the eye network that have been isolated in planarians, such as Otx, Pax-6, Six, Rax and opsin. We describe the effects of RNA interference-mediated loss of function on eye regeneration. Finally, we discuss the relevance of these findings for the evolution of the eye gene network.

Amino Acid Sequence↗