Gonococcal pilus: genetics and structure.
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Amino Acid Sequence↗
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Mating patterns in malaria parasite populations of Papua New Guinea.
Description of the genetic structure of malaria parasite populations is central to an understanding of the spread of multiple-locus drug and vaccine resistance. The Plasmodium falciparum mating patterns from madang, Papua New Guinea, where intense transmission of malaria occurs, are described here. A high degree of inbreeding occurs in the absence of detectable linkage disequilibrium. This contrasts with other studies, indicating that the genetic structure of malaria parasite populations is neither clonal nor panmictic but will vary according to the transmission characteristics of the region.
Alleles↗
[Comparative analysis of genetic heterogeneity of seed progenies in the isolated population of Pinus sylvestris var. cretacea Kalenicz. ex Kom. in Donbass].
The article provides the analysis of the maintenance stability of genetic structure of generatively young and middle-aged trees in seed progenies formed during two years in Donbass population of Pinus sylvestris var. cretacea Kalenicz. ex Kom. protected in Ukraine. The analysis has been carried out at 10 allozyme loci. Allele and genotype diversity of the trees is reproduced annually in seed progenies in spite of the low values of outcrossing coefficient (ts = 0,371-0,687; tm = 0,731-0,790) and significant excess of homozygotes in the embryos. Genetic structure fluctuations are observed in embryos and in the pool of paternal gametes in seed progenies of different years.
Alleles↗
Prey specialization may influence patterns of gene flow in wolves of the Canadian Northwest.
This study characterizes population genetic structure among grey wolves (Canis lupus) in northwestern Canada, and discusses potential physical and biological determinants of this structure. Four hundred and ninety-one grey wolves, from nine regions in the Yukon, Northwest Territories and British Columbia, were genotyped using nine microsatellite loci. Results indicate that wolf gene flow is reduced significantly across the Mackenzie River, most likely due to the north-south migration patterns of the barren-ground caribou herds that flank it. Furthermore, although Banks and Victoria Island wolves are genetically similar, they are distinct from mainland wolf populations across the Amundsen Gulf. However, low-level island-mainland wolf migration may occur in conjunction with the movements of the Dolphin-Union caribou herd. Whereas previous authors have examined isolation-by-distance in wolves, this study is the first to demonstrate correlations between genetic structure of wolf populations and the presence of topographical barriers between them. Perhaps most interesting is the possibility that these barriers reflect prey specialization by wolves in different regions.
Animals↗
Genetic and structural polymorphism of complement receptor 1 in normal Indian subjects.
The human complement receptor 1 (C3b/C4b receptor, CD35, CR1), a polymorphic membrane bound glycoprotein, is differentially expressed on erythrocytes, eosinophils, monocytes, B and T-lymphocytes, dendritic cells and kidney podocytes. It also occurs in the plasma as soluble CR1 (sCR1) and in urine as urinary CR1 (uCR1). Different population studies have suggested the functional and physiological significance of the structural (CR1-A/190, CR1-B/220, CR1-C/160 and CR1-D/250 kDa) and genomic (HH, high erythrocyte CR1 expression, HL, intermediate and LL, low expression) polymorphisms in health and disease. However, simultaneous study on the structural and genomic polymorphism in the same group of study subjects is lacking. This is the first study on both quantitative and structural polymorphism in 101 healthy volunteers from different parts of India by random sampling. In our study, AA phenotype was found to be expressed in 84.2% of individuals and 14.8% carried AB phenotype. One individual (0.9%) was found to possess BB phenotype. Homozygous BB pattern was identified for the first time in Indian subjects. The relative gene frequencies for A and B allele were found to be 0.916 and 0.084, respectively. Pertaining to quantitative polymorphism, percentage distribution for HH, HL and LL phenotypes was found to be 23.7, 54.45 and 21.79%, respectively and the gene frequencies were 0.51 and 0.49 for H and L allele, respectively. The observations for quantitative as well as structural polymorphism showed a good probability of fitness with Hardy-Weinberg equilibrium, thus proving that both the types of CR1 polymorphic forms are encoded by autosomal co-dominant alleles. We found a higher frequency of HL and AA phenotypes in the study subjects. Our findings are unique as we found that gene frequencies for structural and quantitative polymorphism in our study subjects were a combination of those found in Caucasian and Oriental populations.
Adult↗
Expression of tumor related gene NAG6 in gastric cancer and restriction fragment length polymorphism analysis.
AIM: NAG6 gene is a novel tumor related gene identified recently. This study was designed to examine the expression of this gene in gastric cancer and corresponding normal tissues, and to investigate its role in the occurrence and development of gastric cancer, also to study if the genetic structure of NAG6 was altered in gastric cancer. METHODS: Reverse transcription-polymerase chain reaction (RT-PCR), Northern blot analysis and dot hybridization were used to compare the expression level of NAG6 gene in 42 cases of gastric cancer tissues with their corresponding normal tissues of the same patients respectively. In addition, restriction fragment length polymorphism (RFLP) analysis was adopted to study if the genetic structure of NAG6 was altered in gastric carcinomas. RESULTS: The expression of NAG6 in 57.1% gastric cancer tissues (25/42) was absent by RT-PCR analysis. The down-regulation rate of NAG6 in gastric cancer tissues was significantly higher than that in corresponding normal tissues (P<0.01). However no correlation between the down-regulation of NAG6 and lymph-node and/or distance metastasis was found in this study (P>0.05). Dot hybridization confirmed the results of RT-PCR. Furthermore, the results of EcoRI RFLP analysis of NAG6 gene demonstrated that 3 of 7 cases of gastric cancer showed loss of 5 kb fragment in comparison with their corresponding normal tissues. CONCLUSION: NAG6 gene is significantly down regulated in gastric cancer. The loss of genetic materials may be the cause of down-regulation of NAG6 expression. This seems to suggest that NAG6 may represent a candidate of putative tumor suppressor gene at 7q31-32 loci associated with gastric carcinoma. The down-regulation of this gene may play a role in occurrence and development of this disease, however it may not be associated with lymph node and/or distance metastasis.
Adult↗
[Genetic variability of colonies of noninbred Cubavet and CENIC laboratory mice from the Republic of Cuba].
Genetic structure of non-inbred Cubavet and CENIC mice colonies was investigated for three loci of hair colouring (A, B, D), for potential fertility and embryo mortality. Mice colonies are polymorphis in three hair colour determining loci. Alleles rates are: a -- 0.17--0.36; b -- 0.21--0.26; d -- 0.07--0.17. Both colonies reliably differ in colour genotype distribution (p less than 0.001). There are also some differences in the number of live embryos, yellow bodies and postimplantation mortality (p less than 0.05--0.001). The data obtained allow to control the stability of genetic structure of the population for a long time.
Alleles↗
Molecular genetic analysis of Wanggu remains, Inner Mongolia, China.
The Wanggu tribe, which contributed significantly to the foundation of the Yuan Dynasty, was one of the groups living on the Mongolian steppes during the Jin-Yuan period (AD 1127-1368) of Chinese history. However, there has been both archaeological and historical dispute regarding the origin of the ancient tribe. Recently, we discovered human remains of the Wanggu tribe in the Chengbozi cemetery in the Siziwang Banner of Inner Mongolia, China. To investigate the genetic structure of the Wanggu tribe and to trace the origins of the tribe at a molecular level, we analyzed the control-region sequences and coding regions of mitochondrial DNA (mtDNA) from the remains by direct sequencing and restriction-fragment length polymorphism analysis. In combination with mtDNA data of 15 extant Eurasian populations, we performed phylogenetic analysis and multidimensional scaling analysis. Our results show that the genetic structure of the Wanggu tribe in the Jin-Yuan period is a complex matriline, containing admixture from both Asian and European populations. In addition, we reveal that on the basis of mtDNA data, the ancient tribe may share a recent common ancestor with the Turkic-speaking Uzbeks and Uighurs.
Adolescent↗
Microbial community structure at different depths in disturbed and undisturbed semiarid Mediterranean forest soils.
Metabolic abilities and micrfiobial community structure were investigated through three semiarid Mediterranean soils of SE Spain. The soils were (1) a Typic Calcixerept under an adult pine plantation (PP), growing on abandoned agricultural terraces; (2) a Typic Calcixeroll under a native pinewood (NP); and (3) a Typic Haploxerept covered with a grass steppe (GS). PP and NP were similar as regards their genesis, but the former used to be tilled. NP and GS were undisturbed and supported natural and seminatural vegetation, respectively. Seven samples in 10-cm depth increments were taken in triplicate along each soil profile. Community-level physiological profiles based on sole-C-source use were determined to characterize the metabolic abilities. A 16S rDNA polymerase chain reaction-denaturing gradient gel electrophoresis analysis was performed to investigate the microbial genetic structure. Plant cover and land-use history were major determinants of microbial community structure. Microbial communities residing in soils under a native pinewood, the most diverse and stable plant cover, were the most complex both metabolically and genetically. The microbial community structure distinctly changed with depth, related to the quantity and quality of total organic carbon. Both undisturbed soils showed falling gradients of metabolic and genetic complexity, which were invariably of a greater magnitude in the mature woodland than in the grass steppe. In the planted pinewood, however, the substrate-use diversity increased with depth, apparently a response to the depleted metabolic abilities within its upper layer (0-30 cm). Tilling and plant cover removal might be responsible for such a perturbation. In the same profile, molecular fingerprint patterns of the topsoil layer (0-10 cm) indicated a disturbed genetic structure that might underlie the loss of metabolic abilities. However, the genetic structure of the deeper layers of the planted and native pinewoods was not dissimilar, revealing that equivalent genetic resources perform different environmental functions under changing soil scenarios.
Bacteria↗
Arabidopsis thaliana centromere regions: genetic map positions and repetitive DNA structure.
The genetic positions of the five Arabidopsis thaliana centromere regions have been identified by mapping size polymorphisms in the centromeric 180-bp repeat arrays. Structural and genetic analysis indicates that 180-bp repeat arrays of up to 1000 kb are found in the centromere region of each chromosome. The genetic behavior of the centromeric arrays suggests that recombination within the arrays is suppressed. These results indicate that the centromere regions of A. thaliana resemble human centromeres in size and genomic organization.
Alleles↗
Phylogeography of the tailed frog (Ascaphus truei): implications for the biogeography of the Pacific Northwest.
Tailed frogs are distributed in high-gradient streams within the disjunct mesic forests of the Pacific Northwest and represent the basal lineage of the anurans. We sequenced 1,530 nucleotides of the mitochondrial cytochrome b and NADH dehydrogenase subunit two genes from 23 populations and used parsimony, maximum-likelihood, and nested-clade analyses to estimate relationships among populations and infer evolutionary processes. We found two divergent haplotype clades corresponding with inland Rocky Mountain populations and coastal populations and separated by up to 0.133 substitutions per site. Within the coastal assemblage, haplotypes formed clades by mountain range with 0.010-0.024 substitutions per site divergence among populations. Inland haplotypes exhibited minimal genetic structure, with the exception of 0.021 substitutions per site distance between populations from the East Fork of the South Fork of the Salmon River and all other inland haplotypes. The magnitude of divergence between inland and coastal populations, as well as the paleobotanical record, suggest isolation of these lineages occurred during the late Miocene to early Pliocene, probably in response to the rise of the Cascade Mountains. Genetic structure within coastal and inland populations is consistent with isolation in refugia during the late Pliocene and early Pleistocene. Closely related inland haplotypes reflect range expansion following glaciation. The depth of divergence between inland and coastal populations supports the persistence of mesic forests within the inland Pacific Northwest throughout the Pleistocene and is congruent with patterns found in several other mesic forest species. Based on mitochondrial divergence and previous allozyme and morphological data, we recommend recognition of inland populations as a distinct species, Ascaphus montanus.
Animals↗
Field and allozyme studies investigating optimal mating success in two sympatric spring-ephemeral plants, Trillium erectum and T. grandiflorum.
A combination of field experiments and allozyme studies was used to test whether two spring-ephemeral plants growing in eastern North America, Trillium erectum and T. grandiflorum (Liliaceae), exhibited an optimal outcrossing distance for fruit and seed production. Furthermore, the spatial genetic structure of the Trillium populations was examined in light of the outcrossing results. In field experiments, recipient plants were pollinated with either self pollen or with pollen from donors growing 1 m, 10 m, 100 m, and 1500 m away. These distances represented crosses between individuals growing within the same population (1 m, 10 m, and 100 m crosses) and between individuals growing in different populations (1500 m crosses). Self-pollinated T. erectum and T. grandiflorum produced 71% and 89% fewer seeds, respectively, than all other outcrossing treatments. However, there were no significant differences among outcrossing treatments for fruit or seed production. As neither T. erectum nor T. grandiflorum exhibited an optimal outcrossing distance for fruit or seed production, it was predicted that populations of the two would not demonstrate strong spatial genetic structure or isolation by distance. The allozyme results only partially supported the patterns revealed in the outcrossing treatments. Populations of T. erectum and T. grandiflorum showed moderate spatial genetic differentiation based on F-statistics, and only T. grandiflorum exhibited significant isolation by distance based on spatial autocorrelation analyses. The lack of optimal outcrossing distances and the patterns of allozyme variation in T. erectum and T. grandiflorum populations may be attributed to a number of factors, including active seed dispersal by ants, rare long-distance gene-flow events, post-pollination and post-fertilization selection, and/or the severity of inbreeding depression.
Isoenzymes↗
Identity by descent in island-mainland populations.
A new model is presented for the genetic structure among a collection of island populations, with fluctuating population sizes and continuous overlapping generations, using a stochastic birth, death and immigration (BDI) process. Immigrants enter each island from a large mainland population, with constant gene frequencies, according to a Poisson process. The average probability of identity by descent (IBD) for two haploid individuals randomly selected from an island population is f0 = (phi f1 + lambda)/(phi + lambda), where f1 is the probability of IBD for two randomly selected immigrants, lambda is the birth-rate for each individual, and phi is the arrival rate of immigrants into each island. The value of f0 is independent of the death process, time and N. The expected level of genetic differentiation among island populations is FST = (1 - 1/n)lambda/(phi + lambda), where n is the total number of islands receiving immigrants. Because f0 and FST are independent of the death process, for a BDI model, the population genetic structure for several general demographic situations may be examined using our equations. These include stochastic exponential, or logistic (regulated by death rate) growth within islands, or a ""source-sink" population structure. Because the expected values of both f0 and FST are independent of time, these are achieved immediately, for a BDI model, with no need to assume the island populations are at genetic equilibrium.
Demography↗
Does insecticide resistance alone account for the low genetic variability of asexually reproducing populations of the peach-potato aphid Myzus persicae?
The typical life cycle of aphids includes several parthenogenetic generations and a single sexual generation (cyclical parthenogenesis), but some species or populations are totally asexual (obligate parthenogenesis). Genetic variability is generally low in these asexually reproducing populations, that is, few genotypes are spread over large geographic areas. Both genetic drift and natural selection are often invoked to account for this low genetic variability. The peach-potato aphid, Myzus persicae, which encompasses both cyclical and obligate parthenogens, has developed several insecticide resistance mechanisms as a consequence of intense insecticide use since the 1950s. We collected asexually reproducing M. persicae from oilseed rape and examined genetic variability at eight microsatellite loci and three insecticide resistance genes to determine whether their genetic structure was driven by drift and/or selection. We identified only 16 multilocus microsatellite genotypes among 255 individuals. One clone, which combined two insecticide resistance mechanisms, was frequently detected in all populations whatever their location over a large geographical area (the northern half of France). These unexpected findings suggest that drift is not the unique cause of this low variability. Instead, the intensification of both insecticide treatments and oilseed rape cultivation may have favored a few genotypes. Thus, we propose that selective pressures resulting from human activities have considerably modified the genetic structure of M. persicae populations in northern France in a relatively short period of time.
Alleles↗
Coevolution of host and pathogen populations in the Hordeum vulgare-Rhynchosporium secalis pathosystem.
Isolates of Rhynchosporium secalis collected from two experimental barley populations were scored for putative isozyme, colony color, and virulence loci. Allelic frequencies, multilocus haplotype frequencies, and multilocus genetic structure differed in the two populations of R. secalis; haplotypes also differed widely from each other in virulence. The average virulence of isolates collected from the more resistant host population was greater than the average virulence of the isolates collected from the less resistant host population; also the least virulent haplotype, which made up 19% of the pathogen population collected from the less resistant host population, accounted for only 0.3% of the isolates collected from the more resistant host population. It was concluded that the genetic systems of the barley host and fungal pathogen interacted in a complementary fashion and that the genetic structures of both the host and pathogen populations were shaped by coevolutionary processes featuring interactions among loci affecting many different traits, including interactions among host resistance genes and pathogen virulence genes.
Biological Evolution↗
Polyclonal uses of T-cell receptor (TCR)alpha and beta genes for cytotoxic T lymphocytes in human metastatic melanoma: possible involvement of TCR alpha in tumor-cell recognition.
Identification of genetic structure and diversity of T-cell receptor (TCR)alpha and beta genes for cytotoxic T lymphocytes (CTLs) infiltrating human cancers is important for the better understanding of molecular mechanisms of host defense at tumor sites. cDNAs of TCR alpha and beta genes of 22 different melanoma-specific CTL clones established from the tumor-infiltrating lymphocytes of 2 patients were sequenced for analysis of their genetic structure and diversity. V alpha 7.2-J alpha 10-C alpha was found in 4 of 22 clones, 2 of which also used the same beta-chain. The other 20 clones showed different combinations of alpha and beta use. At deduced amino-acid levels, 7 of 9 clones from one patient used a threonine residue at the 26th position in the complementarity-determining region (CDR)1 of TCR alpha. Eight of 13 clones used a threonine at the 99th or a serine residue at the 100th position in CDR3 of TCR alpha CTL clones with the same or different TCR alpha showed the same or different patterns of cytotoxicity, respectively. These results suggest that CTLs usually do not demonstrate clonal expansion at tumor sites of metastatic melanoma's but rather that polyclonal T cells capable of binding to multiple melanoma determinants through CDR3 of TCR alpha accumulate in the tumor.
Base Sequence↗
Genetic and structural organization of the aminophenol catabolic operon and its implication for evolutionary process.
The aminophenol (AP) catabolic operon in Pseudomonas putida HS12 mineralizing nitrobenzene was found to contain all the enzymes responsible for the conversion of AP to pyruvate and acetyl coenzyme A via extradiol meta cleavage of 2-aminophenol. The sequence and functional analyses of the corresponding genes of the operon revealed that the AP catabolic operon consists of one regulatory gene, nbzR, and the following nine structural genes, nbzJCaCbDGFEIH, which encode catabolic enzymes. The NbzR protein, which is divergently transcribed with respect to the structural genes, possesses a leucine zipper motif and a MarR homologous domain. It was also found that NbzR functions as a repressor for the AP catabolic operon through binding to the promoter region of the gene cluster in its dimeric form. A comparative study of the AP catabolic operon with other meta cleavage operons led us to suggest that the regulatory unit (nbzR) was derived from the MarR family and that the structural unit (nbzJCaCbDGFEIH) has evolved from the ancestral meta cleavage gene cluster. It is also proposed that these two functional units assembled through a modular type gene transfer and then have evolved divergently to acquire specialized substrate specificities (NbzCaCb and NbzD) and catalytic function (NbzE), resulting in the creation of the AP catabolic operon. The evolutionary process of the AP operon suggests how bacteria have efficiently acquired genetic diversity and expanded their metabolic capabilities by modular type gene transfer.
Amino Acid Sequence↗
Comparative allozyme analysis of Oriental migratory locust Locusta migratoria manilensis from two breeding areas in north China.
The allozyme analysis using horizontal starch gel electrophoresis was employed to compare the genetic structure in the population of oriental migratory locust Locusta migratoria manilensis from two breeding areas, Beidagang(Tianjin) and Huanghua(Hebei). The two areas are adjacent but with distinct ecological features, with the recorded locust outbreaks and migration. The zymograms showed that among nineteen loci four (Mdh-1, Pgm, Adk and G3pd) showed extremely low variability level with the frequency of the most common allele higher than 0.95 in the populations from both sites. The rest loci had 2 to 4 alleles but the allele frequencies between the two populations were all similar except Fbp and Got-2 loci. In the 27 chi 2-tests for the genotypes at polymorphic loci only two (Pgi and Got-1) of beidagang population did fit the Hardy-Weinberg's expectations. This is due to high frequencies of the most common homozygotes and the corresponding heterozygote deficiency. The allozyme data demonstrated that the locusts had remarkable genetic variability within each population, but little divergence between the populations. The genetic variability measurements were found similar: Percentage of polymorphic loci (P) was between 73.7% and 78.9%; The mean number of alleles per locus (A) was from 2.9 to 3.1; and the mean heterozygosity (Ho) was nearly identical (about 0.138). The F-statistics (FST = 0.053) also showed the genetic uniformity of the populations, corresponding to the high Nei's genetic identity (I = 0.938). These results of the allozyme analysis suggested that the two populations appeared to be a part of a large population. It is reasoned that the genetic polymorphism and differentiation at certain loci between the two populations may depend on at least two agnostic factors that are all related to migration. First, the unusual dispersal capability of L. m. manilensis tends to make a continuous genetic structure distribution. Second, the frequent migration also results in the individuals to be exposed to drastically various environments. Since the broad adaptability is crucial to survive the changing environments, the genetic variation at population level is necessarily required to offer the population resilience for successful survival and reproduction under those ecologically divergent abiotic and biotic conditions. Thus, the migration contributes to the maintenance of dynamic equilibrium of genetic polymorphism in this highly specialized subspecies.
Alleles↗