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PubMed2004

Independent origins of Indian caste and tribal paternal lineages.

The origins of the nearly one billion people inhabiting the Indian subcontinent and following the customs of the Hindu caste system are controversial: are they largely derived from Indian local populations (i.e. tribal groups) or from recent immigrants to India? Archaeological and linguistic evidence support the latter hypothesis, whereas recent genetic data seem to favor the former hypothesis. Here, we analyze the most extensive dataset of Indian caste and tribal Y chromosomes to date. We find that caste and tribal groups differ significantly in their haplogroup frequency distributions; caste groups are homogeneous for Y chromosome variation and more closely related to each other and to central Asian groups than to Indian tribal or any other Eurasian groups. We conclude that paternal lineages of Indian caste groups are primarily descended from Indo-European speakers who migrated from central Asia approximately 3,500 years ago. Conversely, paternal lineages of tribal groups are predominantly derived from the original Indian gene pool. We also provide evidence for bidirectional male gene flow between caste and tribal groups. In comparison, caste and tribal groups are homogeneous with respect to mitochondrial DNA variation, which may reflect the sociocultural characteristics of the Indian caste society.

Analysis of Variance↗
PubMed2003

Linkage of erm(B) and aadE-sat4-aphA-3 in multiple-resistant Enterococcus faecium isolates of different ecological origins.

Enterococcus faecium shares its antibiotic resistance gene pool with various Gram-positive bacteria. A gene cluster aadE-sat4-aphA-3, which was first described in staphylococci, has been recently identified also in E. faecium. In staphylococci, this gene cluster was mostly integrated into the transposable element, Tn5405. We identified five different cluster types of Tn5405-like elements that were linked to erm(B) in 47 of 67 aadE-sat4-aphA-3 and erm(B) positive isolates (70.1%). Clusters differed by insertion of additional DNA between the IS1182 transposase gene and the left inverted repeat of IS1182, an integration of IS1216 between erm(B) and ORF X deleting IS1182 and the 5' end of ORF X, or a loss of the left end of Tn5405 including IS1182, ORF X, and the 5' end of ORF Y. Twenty isolates (29.8%) possessed neither a link between erm(B) and aadE-sat4-aphA-3 nor an arrangement of aadE-sat4-aphA-3 in a Tn5405-like element. A 17-kb composite cluster was identified in a single hospital isolate linking determinants for glycopeptide (vanA), macrolide-lincosamide-streptogramin B [erm(B)], and aminoglycoside-streptothricin (aadE-sat4-aphA-3) resistances.

Aminoglycosides↗
PubMed2002

Isolation of Shigella dysenteriae type 1 and S. flexneri strains from surface waters in Bangladesh: comparative molecular analysis of environmental Shigella isolates versus clinical strains.

Bacillary dysentery caused by Shigella species is a public health problem in developing countries including Bangladesh. Although, shigellae-contaminated food and drinks are often the source of the epidemic's spread, the possible presence of the pathogen and transmission of it through environmental waters have not been adequately examined. We analyzed surface waters collected in Dhaka, Bangladesh, for the presence of shigellae by a combination of PCR assays followed by concentration and culturing of PCR-positive samples. Analysis of 128 water samples by PCR assays for Shigella-specific virulence genes including ipaBCD, ipaH, and stx1 identified 14 (10.9%) samples which were positive for one or more of these virulence genes. Concentration of the PCR-positive samples by filtration followed by culturing identified live Shigella species in 11 of the 14 PCR-positive samples. Analysis of rRNA gene restriction patterns (ribotype) showed that the environmental isolates shared ribotypes with a collection of clinical isolates, but in contrast to the clinical isolates, 10 of the 11 environmental isolates were either negative or carried deletions in the plasmid-encoded invasion-associated genes ipaB, ipaC, and ipaD. However, all environmental Shigella isolates were positive for the chromosomal multicopy invasion-associated gene ipaH and all Shigella dysenteriae type 1 isolates were positive for the stx1 gene in addition to ipaH. This study demonstrated the presence of Shigella in the aquatic environment and dispersion of different virulence genes among these isolates which appear to constitute an environmental reservoir of Shigella-specific virulence genes. Since critical virulence genes in Shigella are carried by plasmids or mobile genetic elements, the environmental gene pool may contribute to an optimum combination of genes, causing the emergence of virulent Shigella strains which is facilitated in particular by close contact of the population with surface waters in Bangladesh.

Anti-Bacterial Agents↗
PubMed2006

Global changes in cellular gene expression during bacteriophage PRD1 infection.

Virus-induced changes in cellular gene expression and host physiology have been studied extensively. Still, there are only a few analyses covering the entire viral replication cycle and whole-host gene pool expression at the resolution of a single gene. Here we report changes in Escherichia coli gene expression during bacteriophage PRD1 infection using microarray technology. Relative mRNA levels were systematically measured for over 99% of the host open reading frames throughout the infection cycle. Although drastic modifications could be detected in the expression of individual genes, global changes at the whole-genome level were moderate. Notably, the majority of virus-induced changes took place only after the synthesis of virion components, indicating that there is no major reprogramming of the host during early infection. The most highly induced genes encoded chaparones and other stress-inducible proteins.

Bacteriophage PRD1↗
PubMed2006

Hypertension and counter-hypertension mechanisms in giraffes.

The giraffe is unique as its head is 2500-3000 millimeters above its heart, thus the giraffe's heart must pump hard enough to overcome the huge hydrostatic pressure generated by the tall column of blood in its neck in order to provide its head with sufficient nutrients and oxygen. Giraffes therefore have exceptionally high blood pressure (hypertension) by human standards. Interestingly, the "unnaturally" high blood pressure in giraffes does not culminate in severe vascular lesions, nor does it lead to heart and kidney failure, whereas in humans, the same blood pressure is exceedingly dangerous and will cause severe vascular damage. Intrinsically, natural selection likely has provided an important protective mechanism, because hypertension develops as soon as the giraffe stands up and erects its neck immediately after birth. Therefore, those individual giraffes who did not tolerate the burden of hypertension presumably developed acute heart failure and renal failure, not surviving to reproductive age. The genes and genotypes of animals that did not survive are thus predicted to have been gradually eliminated from the gene pool by natural selection. By the same process, genes that protect against hypertensive damage would be preserved and inherited from generation to generation. Some unique ingredients of the giraffe's diet may also provide an extrinsic mechanism for the prevention of hypertension and the prevention of fatal end-stage organ damage. The fascinating nature of the protective mechanisms in giraffes may provide a conceptual framework for further experimental investigations into mechanisms as well as prevention and treatment of human hypertension and cardiovascular disease.

Anatomy, Comparative↗
PubMed2004

Insights into the western Bantu dispersal: mtDNA lineage analysis in Angola.

Africa is the homeland of humankind and it is known to harbour the highest levels of human genetic diversity. However, many continental regions, especially in the sub-Saharan side, still remain largely uncharacterized (i.e. southwest and central Africa). Here, we examine the mitochondrial DNA (mtDNA) variation in a sample from Angola. The two mtDNA hypervariable segments as well as the 9-bp tandem repeat on the COII/tRNA(lys) intergenic region have allowed us to allocate mtDNAs to common African haplogroups. Angola lies in the southern end of the putative western branch of the Bantu expansion, where it met the local Khoisan populations. Angolan mtDNA lineages show basically a Bantu substrate with no traces of Khoisan lineages. Roughly, more than half of the southwestern mtDNA pool can be assigned to west Africa, approximately 25% to central Africa and a significant 16% to east Africa, which points to the western gene pool having contributed most to the mtDNA lineages in Angola. We have also detected signals of extensive gene flow from southeast Africa. Our results suggest that eastern and western Bantu expansion routes were not independent from each other, and were connected south of the rainforest and along the southern African savannah. In agreement with historical documentation, the analysis also showed that the Angola mtDNA genetic pool shows affinities with the African lineages from Brazil, the main American destination of the slaves from Angola, although not all lineages in Brazil can be accounted for by the Angolan mtDNA pool.

Angola↗
PubMed1998

DNA sequence conservation and diversity in transposable element IS605 of Helicobacter pylori.

BACKGROUND: IS605, a transposable element-like sequence identified in the virulence-associated cag region of Helicobacter pylori reference strain NCTC11638, is unusual in containing two oppositely-oriented open reading frames whose products are homologues of the single transposases of the unrelated elements, IS200 and IS1341. METHODS: One hundred independent H. pylori isolates from different parts of the world were screened by PCR and dot blot hybridization to determine the presence of IS605. For some positive isolates, southern hybridizations and sequence analyses were done. RESULTS: Of the 100 isolates, 31 were found to contain sequences related to each ORF with orientation and spacing matching those in canonical IS605-hybridizing sequences. No isolate containing just one ORF and not the other was found. The frequencies of IS605 carriage were independent of geographical origin (U.S. vs. non-U.S.), and of the probable virulence of the isolate (cag status, toxin production or vacA alleles, patient symptoms). Southern blot hybridization of six IS605-containing strains revealed one to nine IS605 copies per genome. Two types of DNA sequence diversity were found: first, a specific 100 bp deletion in two isolates; second, base substitution divergence of 0.4% to 7.5% in pairwise comparisons among the eight isolates characterized, a level of divergence similar to that seen in other H. pylori chromosomal genes. CONCLUSIONS: Based on these findings, we speculate that IS605 is a relatively ancient component of the H. pylori gene pool that has proliferated in this species by horizontal gene transfer, homologous recombination, and transposition.

Base Sequence↗
PubMed2004

Chromatin turn ons and turn offs of ribosomal RNA genes.

Eukaryotes have hundreds (sometimes thousands) of ribosomal RNA (rRNA) genes whose transcription by RNA polymerase I helps establish the proliferative ability of cells by dictating the pace of ribosome production and protein synthesis. Interestingly, only a subset of the total rRNA gene pool is active at any one time, making rRNA genes attractive for understanding the dynamic balance between gene silencing and activation. However, the fact that rRNA genes are essentially identical in sequence in a pure species has been an obstacle to telling apart the active and inactive genes. Nature has provided one solution to this conundrum in the form of the epigenetic phenomenon, nucleolar dominance: the transcriptional silencing of one parental set of rRNA genes in a genetic hybrid. Parental genes in hybrids typically differ in sequence as well as expression, allowing a definition of the chromatin modifications of rRNA genes in the on and off states in vivo. By exploiting nucleolar dominance in plants, we recently showed that concerted changes in DNA methylation and histone methylation comprise an epigenetic switch that turns rRNA genes on and off. Independent studies using mouse and human cells have led to similar conclusions, implicating chromatin modifications as important components of the regulatory networks that control the effective dosage of active rRNA genes.

Animals↗
PubMed1996

mtDNA polymorphism in East Asian Populations, with special reference to the peopling of Japan.

Nucleotide sequences of the major noncoding (D-loop) region of human mtDNA from five East Asian populations including mainland Japanese, Ainu, Ryukyuans, Koreans, and Chinese were analyzed. On the basis of a comparison of 482-bp sequences in 293 East Asians, 207 different sequence types were observed. Of these, 189 were unique to their respective populations, whereas 18 were shared between two or three populations. Among the shared types, eight were found in common between the mainland Japanese and Koreans, which is the largest number in the comparison. The intergenic COII/tRNA(Lys) 9-bp deletion was observed in every East Asian population with varying frequencies. The D-loop sequence variation suggests that the deletion event occurred only once in the ancestry of East Asians. Phylogenetic analysis revealed that East Asian lineages were classified into at least 18 monophyletic clusters, though lineages from the five populations were completely intermingled in the phylogenetic tree. However, we assigned 14 of the 18 clusters for their specificity on the basis of the population from which the maximum number of individuals in each cluster was derived. Of note is the finding that 50% of the mainland Japanese had continental specificity in which Chinese or Koreans were dominant, while < 20% of either Ryukyuans or Ainu possessed continental specificity. Phylogenetic analysis of the entire human population revealed the closest genetic affinity between the mainland Japanese and Koreans. Thus, the results of this study are compatible with the hybridization model on the origin of modern Japanese. It is suggested that approximately 65% of the gene pool in mainland Japanese was derived from the continental gene flow after the Yayoi Age.

Asian People↗
PubMed1996

[Geography of effective size in the rural population of northern Eurasia: effective size and the intensity of random genetic drift].

On the basis of 655 direct and indirect estimations of effective size (Ne) of rural populations, a map of the geographic distribution of Ne in northern Eurasia was constructed. A geographic cline of Ne was found, with its value decreasing by three orders of magnitude from the direction of southwest (the western Caucasus and Central Asia) to northeast (the coasts of the Sea of Okhotsk and the Bering Sea). The area of highest distribution density of mean Ne values was situated meridionally between the Ob and Yenisei rivers from the Arctic coast of Taimyr Peninsula to the eastern Sayany and the south Baikal regions. Another similar area covered the south Baltic region, Belarus, and northwestern Ukraine. The average effective population size in northern Eurasia was Ne = 211.6, the geometrical mean G = 176, the harmonic mean H = 147, and the modal value Mo = 102. These characteristics of effective population size indicate a considerable contribution of stochastic gene drift to the differentiation of the northern Eurasian gene pool and the geographic cline of the rate of gene drift in the subcontinent. By means of transformation of the Ne map, a map for the rate of stochastic gene drift (1/4Ne) in northern Eurasia was obtained.

Asia↗
PubMed2003

The efficiency of pooling mRNA in microarray experiments.

In a microarray experiment, messenger RNA samples are oftentimes pooled across subjects out of necessity, or in an effort to reduce the effect of biological variation. A basic problem in such experiments is to estimate the nominal expression levels of a large number of genes. Pooling samples will affect expression estimation, but the exact effects are not yet known as the approach has not been systematically studied in this context. We consider how mRNA pooling affects expression estimates by assessing the finite-sample performance of different estimators for designs with and without pooling. Conditions under which it is advantageous to pool mRNA are defined; and general properties of estimates from both pooled and non-pooled designs are derived under these conditions. A formula is given for the total number of subjects and arrays required in a pooled experiment to obtain gene expression estimates and confidence intervals comparable to those obtained from the no-pooling case. The formula demonstrates that by pooling a perhaps increased number of subjects, one can decrease the number of arrays required in an experiment without a loss of precision. The assumptions that facilitate derivation of this formula are considered using data from a quantitative real-time PCR experiment. The calculations are not specific to one particular method of quantifying gene expression as they assume only that a single, normalized, estimate of expression is obtained for each gene. As such, the results should be generally applicable to a number of technologies provided sufficient pre-processing and normalization methods are available and applied.

Animals↗
PubMed2003

Evidence that acetyl phosphate functions as a global signal during biofilm development.

We used DNA macroarray analysis to identify genes that respond to the status of the intracellular acetyl phosphate (acP) pool. Genes whose expression correlated negatively with the ability to synthesize acP (i.e. negatively regulated genes) function primarily in flagella biosynthesis, a result consistent with observations that we published previously (Prüss and Wolfe, 1994, Mol Microbiol 12: 973-984). In contrast, genes whose expression correlated positively with the ability to synthesize acP (i.e. positively regulated genes) include those for type 1 pilus assembly, colanic acid (capsule) biosynthesis and certain stress effectors. To our knowledge, this constitutes the first report that these genes may respond to the status of the intracellular acP pool. Previously, other researchers have implicated flagella, type 1 pili, capsule and diverse stress effectors in the formation of biofilms. We therefore tested whether cells altered in their ability to metabolize acP could construct normal biofilms, and found that they could not. Cells defective for the production of acP and cells defective for the degradation of acP could both form biofilms, but these biofilms exhibited characteristics substantially different from each other and from biofilms formed by their wild-type parent. We confirmed the role of individual cell surface structures, the expression of which appears to correlate with acP levels, in fim or fli mutants that cannot assemble type 1 pili or flagella respectively. Thus, the information gained by expression profiling of cells with altered acP metabolism indicates that acP may help to co-ordinate the expression of surface structures and cellular processes involved in the initial stages of wild-type biofilm development.

Bacterial Adhesion↗
PubMed2007

Persistence problem in schizophrenia and mitochondrial DNA.

Schizophrenia, a major psychosis with a strong genetic component, persists over generations despite a clearly reduced reproductive fitness of the patients. This 'persistence' problem has puzzled scientists for long years. A hypothesis of 'balanced polymorphism' proposed by Huxley et al. that the incidence could be sustained by a higher fertility in the siblings of the patients has not been supported by most epidemiological studies. Multiple-genes model, which most geneticists today accept, explains that the loss of susceptibility alleles resulting from the lower fertility of the patients would have a negligible effect on the overall gene pool in the population. We carefully examined the multiple-genes model and proved it cannot account for the persistence problem without unrealistic assumptions and hence the contribution of multiple genes in the nuclear DNA to the heredity of schizophrenia should be considerably limited. We demonstrated a pathogenic gene with a low penetrance, if located in the mitochondrial DNA, could be sustained given a higher fertility of the 'female' siblings and/or a decreased male-female ratio in the offspring of the susceptible females. This hypothesis, coupled with the report which suggests mitochondrial dysfunction in schizophrenia, may encourage a new direction in genetic study of this puzzling disorder.

DNA, Mitochondrial↗
PubMed1985

Immunoglobulin allotypes in Jewish populations living in Israel and the United States.

The ongoing interest in the interrelationships of Jewish populations justifies inclusion of the immunoglobulin allotypes in an ethnohistorical analysis. A total of 2,184 serum specimens obtained from unrelated Israeli Jewish and self-identified Milwaukee, WI, Jewish blood donors were classified as Ashkenazi, Sephardi, Asiatic, or North African and tested for G1m (a, x, z, and f), G3m (b0, b1, b3, b5, g), A2m (1 and 2), and Km (1). Selected sera were also tested for G3m (s, t, c3, c5). The estimated maximum likelihood Gm-Am haplotype frequencies were used in a heterogeneity chi-square analysis. The results indicate that there is less heterogeneity within Jewish populations from Europe, Middle East, and North Africa than in corresponding non-Jewish populations representing the same geographical areas. In order to avoid the hazards of a univariate focus, previously published data were incorporated into two additional analyses: 15 populations with information on 16 genetic loci and 24 populations with information on five genetic loci. Both sets of data were analyzed using principal-components and cluster analysis. In both sets of analyses, with the exception of the Yemenite Jews, Jewish populations grouped together. These analyses support the belief that Jewish populations appear to be derived from a common gene pool, and there has been some genetic drift and minimal gene flow with surrounding populations.

Humans↗
PubMed1998

tRNA(2Gln) mutants that translate the CGA arginine codon as glutamine in Escherichia coli.

We present a novel missense suppression system for the selection of tRNA(2GIn) mutants that can efficiently translate the CGA (arginine) codon as glutamine. tRNA(2Gln) mutants were cloned from a partially randomized synthetic gene pool using a plasmid vector that simultaneously expresses the tRNA gene and, to ensure efficient aminoacylation, the glutamine aminoacyl-tRNA synthetase gene (glnS). tRNA mutants that insert glutamine at CGA were selected as missense suppressors of a lacZ mutant (lacZ625(CGA)) that contains CGA substituted for an essential glutamine codon. Preliminary characterizations of four suppressors is presented. All of them contain two anticodon mutations: C-->U at position 34 and U-->C at position 35, which allow for cognate translation of CGA. U35 was previously shown to be an important determinant for glutaminylation of tRNA(2Gln) in vitro; suppression in vivo requires overexpression of the glutaminyl-tRNA synthetase gene (glnS). One tRNA variant contains no further mutations and has the highest missense suppression activity (8%). Three other isolates each contain an additional point mutation that alters suppression efficiency. This system will be useful for further studies of tRNA structure and function. In addition, because relatively efficient translation of the rare CGA codon as glutamine is not toxic for Escherichia coli, it may be possible to translate this sense codon with other alternate meanings, a property which could greatly facilitate protein engineering.

Alleles↗
PubMed1990

Test for linkage between the eumelanin dilution blue (B1), the extended black (E) allele at the E-locus and the linked pea comb (P) and eumelanin extension (M1) genes in the domestic fowl.

1. A mating was made between a Blue Andalusian bantam male and a pea comb striped necked bantam female to produce a quadruple heterozygote of the linked pea comb (P) and eumelanin extension (Ml) genes and of the eunmelanin dilution blue (Bl) gene and the extended black (E) allele at the E-locus. 2. Two pea comb blue females so produced were mated to a single comb striped necked bantam male, thus providing a backcross to the quadruple recessive. 3. Bl segregated independently with each of the other three genes whilst 25 crossovers occurred amongst the 55 progeny assessed for linkage between P and Ml, confirming loose linkage between P and Ml which had previously been shown to be approximately 46 units. Linkage of 0.3% had been previously reported (Crawford, 1986) between P and a "melanotic" gene isolated from a segregating gene pool. Evidence is presented to demonstrate that two different "melanotic" genes were being considered, thus explaining the apparently contradictory reports. Charcoal (cha) is suggested for the recessive gene linked with P by 0.3%. 4. Thirty-four crossovers occurred among the 97 progeny between P and E suggesting linkage of approximately 35 units. A further mating was made from among segregants in the backcross which confirmed P-E linkage with 17 crossovers in 55 gametes. Combining the tests produced a linkage value of approximately 34 units.

Alleles↗
PubMed2006

The maintenance of sex in bacteria is ensured by its potential to reload genes.

Why sex is maintained in nature is a fundamental question in biology. Natural genetic transformation (NGT) is a sexual process by which bacteria actively take up exogenous DNA and use it to replace homologous chromosomal sequences. As it has been demonstrated, the role of NGT in repairing deleterious mutations under constant selection is insufficient for its survival, and the lack of other viable explanations have left no alternative except that DNA uptake provides nucleotides for food. Here we develop a novel simulation approach for the long-term dynamics of genome organization (involving the loss and acquisition of genes) in a bacterial species consisting of a large number of spatially distinct populations subject to independently fluctuating ecological conditions. Our results show that in the presence of weak interpopulation migration NGT is able to subsist as a mechanism to reload locally lost, intermittently selected genes from the collective gene pool of the species through DNA uptake from migrants. Reloading genes and combining them with those in locally adapted genomes allow individual cells to readapt faster to environmental changes. The machinery of transformation survives under a wide range of model parameters readily encompassing real-world biological conditions. These findings imply that the primary role of NGT is not to serve the cell with food, but to provide homologous sequences for restoring genes that have disappeared from or become degraded in the local population.

Bacteria↗
PubMed1986

Genetic similarity and variability between natural populations and laboratory colonies of North American Boophilus (Acari: Ixodidae).

Four natural populations and 4 laboratory colonies of Boophilus microplus (Canestrini) and a laboratory colony of Boophilus annulatus (Say) were subjected to electrophoretic analysis to determine levels of genetic similarity and genetic variability. Populations of B. microplus exhibited high genetic similarity (I = 0.984 +/- 0.012) indicating that all populations share a relatively undifferentiated gene pool. Host vagility is proposed as an important mechanism promoting gene flow in ectoparasites. Levels of genetic variability for B. microplus (h = 0.092 +/- 0.008; P = 0.330 +/- 0.050) were within levels reported for other arthropods. The average genetic identity of 0.716 +/- 0.013 between B. microplus and B. annulatus is of a level characteristic of sibling species. Diagnostic isozymes between laboratory colonies will facilitate identification of these morphologically similar species.

Alleles↗