Y-chromosome-specific haplotypes of Jews detected by probes 49f and 49a.

A sample of Ashkenazic and Sephardic Jews has been studied with respect to haplotypes at the 49f-49a Y-specific DNA probes. Only seven haplotypes were found in Jews, three of them (VII, VIII, and XI) being the most widespread. Haplotype distribution in the European non-Jewish population is different.     

Y chromosome probe p49a detects complex PvuII haplotypes and many new TaqI haplotypes in southern African populations.

Y-specific 49a/TaqI haplotypes were determined for 831 individuals drawn from 21 different southern African populations. A total of 31 new haplotypes were observed, some of which contained new alleles or allelic variants. Duplication, in addition to CpG mutation, is implicated in the generation of certain allelic variants. Cluster analysis of genetic distances between the populations, calculated using the 49a/TaqI haplotype frequencies, revealed a basic split between African and non-African populations. Hybrid groups cluster with the caucasoid groups, indicating that male gene flow has occurred from the latter into the former. Clustering of the negroid and Khoisan groups is not what might have been expected from the known linguistic affinities. It is suggested that the 49a/TaqI haplotype analysis of these populations is not sufficiently sensitive to distinguish between many of the populations. The Y-specific 49a/PvuII polymorphism was studied in 127 individuals from southern African populations, and 17 polymorphic fragments ranging in size from 3.6 kb to greater than 48 kb were identified. A total of 53 PvuII haplotypes were observed, corresponding to only 30 TaqI haplotypes. There appears to be poor correlation between the two polymorphisms.     

Mitochondrial haplotypes reveal a strong genetic structure for three Indian sheep breeds

This survey represents the first characterization of mitochondrial DNA diversity within three breeds of Indian sheep (two strains of the Deccani breed, as well as the Bannur and Garole breeds) from different geographic regions and with divergent phenotypic characteristics. A 1061-bp fragment of the mitochondrial genome spanning the control region, a portion of the 12S rRNA gene and the complete phenyl tRNA gene, was sequenced from 73 animals and compared with the corresponding published sequence from European and Asian breeds and the European Mouflon (Ovis musimon). Analysis of all 156 sequences revealed 73 haplotypes, 52 of which belonged to the Indian breeds. The three Indian breeds had no haplotypes in common, but one Indian haplotype was shared with European and other Asian breeds. The highest nucleotide and haplotype diversity was observed in the Bannur breed (0.00355 and 0.981 respectively), while the minimum was in the Sangamneri strain of the Deccani breed (0.00167 and 0.882 respectively). All 52 Indian haplotypes belonged to mitochondrial lineage A. Therefore, these Indian sheep are distinct from other Asian and European breeds studied so far. The relationships among the haplotypes showed strong breed structure and almost no introgression among these Indian breeds, consistent with Indian sheep husbandry, which discourages genetic exchange between breeds. These results have implications for the conservation of India's ovine biodiversity and suggest a common origin for the breeds investigated.     

Linkage disequilibrium between haplotypes and allelic incompatibilities detected with p49f,a probe located on the Y chromosome

We have analyzed linkage disequilibrium between haplotypes and allelic incompatibilities betweenTaqI RELPs concerning the probe 49f, located on the Y chromosome. For most (but one) observed haplotypes, discrepancies between observed and expected frequencies can be easily explained allowing a small number of incompatibilities beetween alleles.     

Beta-globin-gene haplotypes, mitochondrial DNA, the Y-chromosome: their impact on the genetic epidemiology of the major structural hemoglobinopathies.

The history of the discovery of the globin beta-like globin-gene haplotypes and their importance in the understanding of hemoglobinopathies has been reviewed recently. We will add in this review more recent findings and other molecular genetic tools that can help in the understanding of the genetic epidemiology of structural hemoglobinopathies, leaving the thalassemias for a later effort.     

Human plasma lipid peroxide levels show a strong transient increase after successful revascularization operations.

This study was performed to evaluate the hypothesis that oxygen radicals/lipid peroxidation are involved in reperfusion injury in humans. The study included 37 patients, who underwent surgical revascularization operations for kidney transplantation (9 subjects) or limb salvage (28 subjects). Peripheral venous blood samples were taken 30 min before starting reperfusion (baseline) and 1, 2, 3, 4, and occasionally 6 to 18 h after revascularization. The amount of plasma malonaldehyde formed in the reaction with thiobarbituric acid (MDA-TBA) was determined by high-performance liquid chromatography (HPLC). The baseline MDA-TBA values of the patients were very close to the value determined for 20 age-matched healthy subjects (i.e. mean +/- SD 0.689 +/- 0.294 nmol/mL plasma [range 0.2 to 1.37] vs. 0.700 +/- 0.209 nmol/mL plasma [range 0.385 to 1.29]). All patients responded to successful revascularization with significant increase of the plasma MDA-TBA within about 1 h after onset of reperfusion. Thereafter the values decreased nearly to the preoperative state. The mean increase of MDA-TBA was 107% in kidney transplantation and 54% in limb revascularization. In a few patients with severe arteriosclerosis, revascularization was not optimal and no increase in the MDA-TBA value occurred. The results of this study indicate that therapeutic intervention to prevent lipid-peroxidation-mediated reperfusion injury is confined to a rather narrow time window and must be undertaken either prior to or immediately after revascularization.     

A worldwide population study of the Ag-system haplotypes, a genetic polymorphism of human low-density lipoprotein.

The aim of this investigation is to examine the distribution of the Ag immunological polymorphism in human populations on a worldwide scale and to look for possible explanations of this distribution in the field of modern human peopling history and Ag-system evolution. Extensive Ag-antigene typings were carried out on 13 human population samples, including sub-Saharan African, European, west and east Asiatic, Melanesian, Australian aborigine, and Amerindian groups. Complete Ag-haplotype frequencies were estimated by maximum-likelihood-score procedures, and the data were analyzed by genetic distance computations and principal coordinate projections. With the exception of the Amerindian sample, the Ag polymorphism is shown to be highly polymorphic in all the populations tested. Their genetic relationships appear to be closely correlated to their geographical distribution. This suggests that the Ag system has evolved as a neutral or nearly neutral polymorphism and that it is highly informative for modern human peopling history studies. From the worldwide Ag haplotypic distributions, a model for the Ag molecular structure is derived. According to this model and to the most recent results obtained from molecular data, the establishment of the Ag polymorphism could be explained by several mutations and recombination events between the haplotypes most frequently found in human populations today. As a conclusion, genetic and paleontological data suggest that the genetic structure of caucasoid populations (located from North Africa to India) may be the least differentiated from an ancestral genetic stock. Worldwide genetic differentiations are properly explained as the results of westward and eastward human migrations from a Near East-centered but undefined geographical area where modern humans may have originated. The importance of Ag polymorphism analyses for the reconstruction of human settlement history and origins is discussed in the light of the main conclusions of the most recent genetic polymorphism studies.     

Human genetic diversity,a critical resource for man's future

The human gene pool displays exuberant genetic variation; this is normal for a sexual species. Even small isolated populations contain a large percentage of the total variability, emphasizing the basic genetic unity of our species. As modern man spread across the world from its African source, the genetic basis for man's unique mental acuity was retained everywhere. Nevertheless, some geographical genetic variation such as skin color, stature and physiognomy was established. These changes were biologically relatively insignificant. Most of the genetic load in the genome has been carried throughout the history of the species. There is little hope of purging all of these harmful genes; we must accept them and continue to treat their syndromes medically. All populations carry extensive genetic variation due to genes that encode variations in quantitative traits. Of greatest importance among these is ubiquitous polygenic variability in brain function and intelligence. Mental acuity is what sets us apart from the rest of the biological world. Throughout our history, genetic recombination among the many genes involved in brain function has occurred. This has provided a genetic basis for the action of natural selection that favors intelligence in meeting the demands of the environment. As environments change in the future, this type of genetic variability will continue to be a crucial resource.This article is based on a contribution at the Session on Genetic Load chaired by Dr. Henretta Trent Band and presented at a meeting of the International Society for the History, Philosophy and Social Studies of Biology, Northwestern University, Evanston, Illinois in July 1991. The author is indebted to Professor Antonio Brito daCunha of the University of São Paulo, Brazil for his encouragement and comments.     

Human papillomavirus type 49, a type isolated from flat warts of renal transplant patients.

The cloning and characterization of the genome of human papillomavirus type 49 (HPV-49) is described. The viral DNA, which is most closely related to the DNAs of HPVs seen in patients with epidermodysplasia verruciformis, was aligned to the HPV-5 genome by electron microscopic analysis of heteroduplexes between the cloned viral DNAs.     

Proteus mirabilis MR/P fimbrial operon: genetic organization, nucleotide sequence, and conditions for expression.

Proteus mirabilis, an agent of urinary tract infection, expresses at least four fimbrial types. Among these are the MR/P (mannose-resistant/Proteus-like) fimbriae. MrpA, the structural subunit, is optimally expressed at 37 degrees C in Luria broth cultured statically for 48 h by each of seven strains examined. Genes encoding this fimbria were isolated, and the complete nucleotide sequence was determined. The mrp gene cluster encoded by 7,293 bp predicts eight polypeptides: MrpI (22,133 Da), MrpA (17,909 Da), MrpB (19,632 Da), MrpC (96,823 Da), MrpD (27,886 Da), MrpE (19,470 Da), MrpF (17,363 Da), and MrpG (13,169 Da). mrpI is upstream of the gene encoding the major structural subunit gene mrpA and is transcribed in the direction opposite to that of the rest of the operon. All predicted polypeptides share > or = 25% amino acid identity with at least one other enteric fimbrial gene product encoded by the pap, fim, smf, fan, or mrk gene clusters.     

Phyllobothrium discopygi n. sp. (Cestoda: Tetraphyllidea) from Chile,with a critical comparison of the affinities of P. auricula van Beneden, 1858 and P. foliatum Linton, 1890

Phyllobothrium discopygi n. sp. is described from the spiral valve of Discopyge tschudi Heckel, 1846 (Torpedinidae) taken in the Pacific Ocean off Coquimbo, San Antonio and Antofagasta, Chile, Specimens are described from whole-mounts, sections and SEM. Phyllobothrium discopygi is distinguished from other tetraphyllidean cestodes of the genus Phyllobothrium van Beneden, 1849 by a bifurcate scolex with bothridia joined in pairs, short neck, testes number and distribution, and morphology of the vitelline follicles and ovary. Phyllobothrium foliatum Linton, 1890 is considered a junior synonym of P. auricula van Beneden, 1858 following comparisons of P. auricula from D. pastinaca, Linton's holotype of P. foliatum from D. centroura and fresh specimens from D. centroura taken in waters near Woods Hole, Massachusetts. A meristic comparison of the adult worms is presented.     

African Herald snakes,Crotaphopeltis, show population structure for a widespread generalist but deep genetic divergence for forest specialists

The African colubrid snake genus Crotaphopeltis currently comprises six species and occurs throughout sub-Saharan Africa. The most widespread of these, Crotaphopeltis hotamboeia, inhabits most biomes, aside from rainforest and hyper-arid regions, and its catholic niche has presumably facilitated substantial gene flow. Despite this, the geographical range is large enough that ecological or physical barriers might exist, facilitating allopatric diversification. In contrast, most of the other species are habitat specialists with limited distributions (e.g., Crotaphopeltis tornieri) and would be expected to show strong genetic structure. We therefore examined species boundaries within Crotaphopeltis in a phylogenetic context using five markers (16S, cyt b, ND4, c-mos, and RAG-1) for four of the six species. Species delimitation methods included two coalescent-based and one barcoding approach. Widespread geographical sampling of C. hotamboeia allowed examination of genetic structuring across its range. The species status of Crotaphopeltis barotseensis, C. degeni, and C. hotamboeia was confirmed, whereas the Afromontane species C. tornieri comprised two candidate species. Crotaphopeltis hotamboeia did not show cryptic speciation, although its phylogeographic structure corresponded with the spatiotemporal pattern of the African savanna. Our results show how the heterogeneous African environment could influence genetic partitioning of habitat specialist and generalist species at broad geographical scales.     

Biochemical and genetic characterization of enterocin P, a novel sec-dependent bacteriocin from Enterococcus faecium P13 with a broad antimicrobial spectrum.

Enterocin P is a new bacteriocin produced by Enterococcus faecium P13 isolated from a Spanish dry-fermented sausage. Enterocin P inhibited most of tested spoilage and food-borne gram-positive pathogenic bacteria, such as Listeria monocytogenes, Staphylococcus aureus, Clostridium perfringens, and Clostridium botulinum. Enterocin P is produced during growth in MRS broth from 16 to 45 degrees C; it is heat resistant (60 min at 100 degrees C; 15 min at 121 degrees C) and can withstand exposure to pH between 2.0 and 11.0, freeze-thawing, lyophilization, and long-term storage at 4 and -20 degrees C. The bacteriocin was purified to homogeneity by ammonium sulfate precipitation, gel filtration, cation-exchange, hydrophobic-interaction, and reverse-phase liquid chromatography. The sequence of 43 amino acids of the N terminus was obtained by Edman degradation. DNA sequencing analysis of a 755-bp region revealed the presence of two consecutive open reading frames (ORFs). The first ORF encodes a 71-amino-acid protein containing a hydrophobic N-terminal sec-dependent leader sequence of 27 amino acids followed by the amino acid sequence corresponding to the purified and sequenced enterocin P. The bacteriocin is apparently synthesized as a prepeptide that is cleaved immediately after the Val-Asp-Ala residues (positions -3 to -1), resulting in the mature bacteriocin consisting of 44 amino acids, and with a theoretical molecular weight of 4,493. A second ORF, encoding a putative immunity protein composed of 88 amino acids with a calculated molecular weight of 9,886, was found immediately downstream of the enterocin P structural gene. Enterocin P shows a strong antilisterial activity and has the consensus sequence found in the pediocin-like bacteriocins; however, enterocin P is processed and secreted by the sec-dependent pathway.     

TIP49b, a new RuvB-like DNA helicase, is included in a complex together with another RuvB-like DNA helicase, TIP49a.

We previously reported that TIP49a is a novel mammalian DNA helicase showing structural similarity with the bacterial recombination factor RuvB. In this study, we isolated a new TIP49a-related gene, termed TIP49b, from human and yeast cells. TIP49b also resembled RuvB, thus suggesting that TIP49a and TIP49b are included in a gene family. Like TIP49a, TIP49b was abundantly expressed in the testis and thymus. Enzyme assays revealed that TIP49b was an single-stranded DNA-stimulated ATPase and ATP-dependent DNA helicase. Most of the enzymatic properties of TIP49b were the same as those of TIP49a, whereas the polarity of TIP49b DNA helicase activity (5' to 3') was the opposite to that of TIP49a. TIP49b and TIP49a bound to each other and were included in the same complex of approximately 700 kDa in a cell. We found that TIP49b was an essential gene for the growth of Saccharomyces cerevisiae, as is the TIP49a gene, suggesting that TIP49b does not complement the TIP49a function and vice versa. From these observations, we suggest that TIP49b plays an essential role in the cellular processes involved in DNA metabolism.     

Human osteocalcin: a strong promoter for nitric oxide synthase gene therapy, with specificity for hormone refractory prostate cancer

BACKGROUND: Gene therapy has been identified as a promising treatment strategy for hormone refractory prostate cancer (HRPC). We report, for the first time, the use of the human osteocalcin (hOC) promoter to control inducible nitric oxide synthase (iNOS) transgene expression in HRPC. METHODS: Human prostate carcinoma cells (PC3, DU145, LNCaP), colon cancer cells (HT29) and human microvascular endothelial cells (HMEC-1) were transfected in vitro with constitutively driven CMV/iNOS or hOC/iNOS plasmid DNA by cationic lipid vector. End points of these experiments were Western blotting, NO(.) generation using the Greiss test to measure accumulated nitrite, and clonogenic assay. RESULTS: Transfection of the hOC/iNOS plasmid increased iNOS protein and total nitrite levels in PC3 and DU145 cells, but not LNCaP or HT29. Transfection with CMV/iNOS or hOC/iNOS resulted in no additional cytotoxicity in androgen-dependent LNCaP cells or in the non-prostate cell lines. However, transfection with either construct resulted in a greatly reduced cell survival (to 10-20%) in the androgen-independent PC3 and DU145 cell lines. CONCLUSIONS: Utilising the tumour-type specific properties of the hOC promoter in tandem with the iNOS gene, we have demonstrated target cell specificity, and transgene activation, in the androgen-independent prostate cancer cell lines (PC3 and DU145), an effect absent in normal and androgen-dependent cells. Furthermore, the levels of NO(.) generated are comparable with those seen generated with constitutively (CMV)-driven iNOS. The data obtained from this study provide a basis for future development of hOC/iNOS gene therapy.     

Human P1-450 gene sequence and correlation of mRNA with genetic differences in benzo[a]pyrene metabolism.

The human P1-450 gene (6,311 base pairs), as well as the 5' (1,604 bases) and 3' (113 bases) flanking regions, have been completely sequenced. Four highly homologous boxes (61, 82, 56 and 97 base pairs) between the human and mouse P1-450 genes are found in the "TATA" box promoter region, -226, -338, and -450 upstream from the cap site, respectively. Nine genomic-DNA samples were digested with each of 23 restriction endonucleases and probed with human P1-450 cDNA fragments; restriction fragment length polymorphisms are detected, although it remains to be seen whether such a recombinant DNA test will be useful in determining individuals at increased risk for cigarette smoking-induced cancer and toxicity. We show in this report, however, that human inducible P1-450 mRNA concentrations are very highly correlated (r = 0.98; N = 6) with genetic differences in benzo[a]pyrene metabolism in mitogen-activated lymphocyte cultures.     

A chloroplast DNA phylogeny of lilacs (Syringa, Oleaceae): plastome groups show a strong correlation with crossing groups

Phylogenetic relationships and genomic compatibility were compared for 60 accessions of Syringa using chloroplast DNA (cpDNA) and nuclear ribosomal DNA (rDNA) markers. A total of 669 cpDNA variants, 653 of which were potentially phylogenetically informative, was detected using 22 restriction enzymes. Phylogenetic analyses reveal four strongly supported plastome groups that correspond to four genetically incompatible crossing groups. Relationships of the four plastome groups (I(II(III,IV))) correlate well with the infrageneric classification except for ser. Syringa and Pinnatifoliae. Group I, which includes subg. Ligustrina, forms a basal lineage within Syringa. Group II includes ser. Syringa and Pinnatifoliae and the two series have high compatibility and low sequence divergence. Group III consists of three well-defined species groups of ser. Pubescentes. Group IV comprises all members of ser. Villosae and has the lowest interspecific cpDNA sequence divergences. Comparison of cpDNA sequence divergence with crossability data indicates that hybrids have not been successfully generated between species with divergence greater than 0.7%. Hybrid barriers are strong among the four major plastome groups, which have sequence divergence estimates ranging from 1.096 to 1.962%. In contrast, fully fertile hybrids occur between species pairs with sequence divergence below 0.4%. Three regions of the plastome have length variants of greater than 100 bp, and these indels identify 12 different plastome types that correlate with phylogenetic trees produced from cpDNA restriction site data. Biparentally inherited nuclear rDNA and maternally inherited cpDNA length variants enable the identification of the specific parentage of several lilac hybrids.     

Population genetic evidence for speciation pattern and gene flow between Picea wilsonii,P. morrisonicola and P. neoveitchii

Background and Aims

Genetic drift due to geographical isolation, gene flow and mutation rates together make it difficult to determine the evolutionary relationships of present-day species. In this study, population genetic data were used to model and decipher interspecific relationships, speciation patterns and gene flow between three species of spruce with similar morphology, Picea wilsonii, P. neoveitchii and P. morrisonicola. Picea wilsonii and P. neoveitchii occur from central to north-west China, where they have overlapping distributions. Picea morrisonicola, however, is restricted solely to the island of Taiwan and is isolated from the other two species by a long distance.

Methods

Sequence variations were examined in 18 DNA fragments for 22 populations, including three fragments from the chloroplast (cp) genome, two from the mitochondrial (mt) genome and 13 from the nuclear genome.

Key Results

In both the cpDNA and the mtDNA, P. morrisonicola accumulated more species-specific mutations than the other two species. However, most nuclear haplotypes of P. morrisonicola were shared by P. wilsonii, or derived from the dominant haplotypes found in that species. Modelling of population genetic data supported the hypothesis that P. morrisonicola derived from P. wilsonii within the more recent past, most probably indicating progenitor–derivative speciation with a distinct bottleneck, although further gene flow from the progenitor to the derivative continued. In addition, the occurrence was detected of an obvious mtDNA introgression from P. neoveitchii to P. wilsonii despite their early divergence.

Conclusions

The extent of mutation, introgression and lineage sorting taking place during interspecific divergence and demographic changes in the three species had varied greatly between the three genomes. The findings highlight the complex evolutionary histories of these three Asian spruce species.     

Human serum amyloid P component, a circulating lectin with specificity for the cyclic 4,6-pyruvate acetal of galactose. Interactions with various bacteria.

Serum amyloid P component (SAP), a normal plasma glycoprotein, has recently been shown to have Ca2+-dependent binding specificity for methyl 4,6-O-(1-carboxyethylidene)-beta-D-galactopyranoside (MO beta DG) [Hind, Collins, Renn, Cook, Caspi, Baltz & Pepys (1984) J. Exp. Med. 159, 1058-1069]. SAP was found to bind in vitro to Klebsiella rhinoscleromatis, the cell wall of which is known to contain this particular cyclic pyruvate acetal of galactose. SAP also bound in similar amounts (approx. 6000 molecules per organism) to group A Streptococcus pyogenes, but very much less was taken up on Xanthomonas campestris, which contains the 4,6-cyclic pyruvate acetal of mannose. No SAP bound to Escherichia coli, which contains the 4,6-cyclic pyruvate acetal of glucose, or to Streptococcus pneumoniae type 4, which contains the 2,3-cyclic pyruvate acetal of alpha- rather than beta-galactopyranoside, or to other organisms (Streptococcus agalactiae, Staphylococcus aureus and Staphylococcus epidermidis), the carbohydrate structures of which are less well characterized. Binding of SAP to those organisms which it did recognize was completely inhibited or reversed by millimolar concentrations of free MO beta DG. SAP, a human plasma protein, thus behaves as a lectin and may be a useful probe for its particular specific ligand in the cell walls of bacteria and other organisms.