Genetic diversity among proso millet (Panicum miliaceum) biotypes assessed by AFLP technique

The Amplified Fragment Length Polymorphism (AFLP) technique was used to access genetic diversity between three domestic and nine wild proso millet biotypes from the United States and Canada. Eight primer combinations detected 39 polymorphic DNA fragments, with the genetic distance estimates among biotypes ranging from 0.02 to 0.04. Colorado-Weld County black seeded and Wyoming-Platte County were the most distinct biotypes according to the dissimilarity level. A UPGMA cluster analysis revealed two distinct groups of proso millet without any geographic association. Six weed biotypes exhibiting some characters of cultivated plants were grouped together with domesticated biotypes of proso millet while the three typical wild phenotypes were clearly clustered into another group according to AFLP markers.

Multivariate genetic divergence and hybrid performance of cacao (Theobroma cacao L.)

Genetic distances among cacao cultivars were calculated through multivariate analysis, using the D2 statistic, to examine racial group classification and to assess heterotic hybrids. A 5 x 5 complete diallel was evaluated. Over a five-year period (1986-1990), five cultivars of the S1 generation, pertaining to the Lower Amazon Forastero and Trinitario racial groups and 20 crosses between the corresponding S0 parents were analyzed, based upon five yield components - number of healthy and collected fruits per plant (NHFP and NCFP), wet seed weight per plant and per fruit (WSWP and WSWF), and percentage of diseased fruits per plant (PDFP). The diversity analysis suggested a close relationship between the Trinitario and Lower Amazon Forastero groups. A correlation coefficient (r) was calculated to determine the association between genetic diversity and heterosis. Genetic distance of parents by D2 was found to be linearly related to average performance of hybrids for WSWP and WSWF (r = 0.68, P < 0.05 and r = 0.76, P < 0.05, respectively). The heterotic performance for the same components was also correlated with D2, both with r = 0.66 (P < 0.05). A relationship between genetic divergence and combining ability effects was suggested because the most divergent cultivar exhibited a high general combining ability, generating the best performing hybrids. Results indicated that genetic diversity estimates can be useful in selecting parents for crosses and in assessing relationships among cacao racial groups.

Calculation of breed direct and maternal genetic fractions and breed specific direct and maternal heterozygosity for crossbreeding data

Teaching, research, and herd breeding applications may require calculation of breed additive contributions for direct and maternal genetic effects and fractions of heterozygosity associated with breed specific direct and maternal heterosis effects. These coefficients can be obtained from the first NB rows of a pseudo numerator relationship matrix where the first NB rows represent fractional contributions by breed to each animal or group representing a specific breed cross. The table begins with an NB x NB identity matrix representing pure breeds. Initial animals or representative crosses must be purebreds or two-breed crosses. Parents of initial purebreds are represented by the corresponding column and initial two-breed cross progeny by the two corresponding columns of the identity matrix. After that, usual rules are used to calculate the NB column entries corresponding to breeds for each animal. The NB entries are fractions of genes expected to be contributed by each of the pure breeds and correspond to the breed additive direct fractions. Entries in the column corresponding to the dam represent breed additive maternal fractions. Breed specific direct heterozygosity coefficients are entries of an NB x NB matrix formed by the outer product of the two NB by 1 columns associated with sire and dam of the animal. One minus sum of the diagonals represents total direct heterozygosity. Similarly, the NB x NB matrix formed by the outer product of columns associated with sire of dam and dam of dam contains breed specific maternal heterozygosity coefficients. These steps can be programmed to create covariates to merge with data. If X represents these coefficients for all unique breed crosses, then the reduced row echelon form function of MATLAB or SAS can be used on X to determine estimable functions of additive breed direct and maternal effects and breed specific direct and maternal heterosis effects

Comparison of voluntary ethanol intake by two pairs of rat lines used as genetic models of anxiety

The relationship between anxiety-related behaviors and voluntary ethanol intake was examined in two pairs of rat lines by the oral ethanol self-administration procedure. Floripa high (H) and low (L) rats selectively bred for contrasting anxiety responses in the open-field test, and two inbred strains, spontaneously hypertensive rats (SHR) and Lewis rats which are known to differ significantly when submitted to several behavioral tests of anxiety/emotionality, were used (9-10 animals/line/sex). No differences in the choice of ethanol solutions (2%, days 1-4, and 4%, days 5-8, respectively) in a 2-bottle paradigm were detected between Floripa H and L rats (1.94 ± 0.37 vs 1.61 ± 0.37 g/kg for ethanol intake on day 8 by the Floripa H and L rat lines, respectively). Contrary to expectations, the less anxious SHR rats consumed significantly more ethanol than Lewis rats (respective intake of 2.30 ± 0.45 and 0.72 ± 0.33 g/kg on day 8) which are known to be both addiction-prone and highly anxious. Regardless of strain, female rats consumed more ethanol than males (approximately 46%). The results showed no relationship between high anxiety and voluntary intake of ethanol for Floripa H and L rats. A negative association between these two variables, however, was found for SHR and Lewis rat strains. Data from the literature regarding the association between anxiety and alcohol intake in animal models are not conclusive, but the present results indicate that factors other than increased inborn anxiety probably lead to the individual differences in ethanol drinking behavior.

Polymorphism in CYP17, GSTM1 and the progesterone receptor genes and its relationship with mammographic density

Radiologic breast density is one of the predictive factors for breast cancer and the extent of the density is directly related to postmenopause. However, some patients have dense breasts even during postmenopause. This condition may be explained by the genes that codify for the proteins involved in the biosynthesis, as well as the activity and metabolism of steroid hormones. They are polymorphic, which could explain the variations of individual hormones and, consequently, breast density. The constant need to find markers that may assist in the primary prevention of breast cancer as well as in selecting high risk patients motived this study. We determined the influence of genetic polymorphism of CYP17 (cytochrome P450c17, the gene involved in steroid hormone biosynthesis), GSTM1 (glutathione S-transferase M1, an enzyme involved in estrogen metabolism) and PROGINS (progesterone receptor), for association with high breast density. One hundred and twenty-three postmenopausal patients who were not on hormone therapy and had no clinical or mammographic breast alterations were included in the present study. The results of this study reveal that there was no association between dense breasts and CYP17 or GSTM1. There was a trend, which was not statistically significant (P = 0.084), towards the association between PROGINS polymorphism and dense breasts. However, multivariate logistic regression showed that wild-type PROGINS and mutated CYP17, taken together, resulted in a 4.87 times higher chance of having dense breasts (P = 0.030). In conclusion, in the present study, we were able to identify an association among polymorphisms, involved in estradiol biosyntheses as well as progesterone response, and radiological mammary density.

Genetic analysis of the porcine group B rotavirus NSP2 gene from wild-type Brazilian strains

Group B rotaviruses (RV-B) were first identified in piglet feces, being later associated with diarrhea in humans, cattle, lambs, and rats. In human beings, the virus was only described in China, India, and Bangladesh, especially infecting adults. Only a few studies concerning molecular analysis of the RV-B NSP2 gene have been conducted, and porcine RV-B has not been characterized. In the present study, three porcine wild-type RV-B strains from piglet stool samples collected from Brazilian pig herds were used for analysis. PAGE results were inconclusive for those samples, but specific amplicons of the RV-B NSP2 gene (segment 8) were obtained in a semi-nested PCR assay. The three porcine RV-B strains showed the highest nucleotide identity with the human WH1 strain and the alignments with other published sequences resulted in three groups of strains divided according to host species. The group of human strains showed 92.4 to 99.7% nucleotide identity while the porcine strains of the Brazilian RV-B group showed 90.4 to 91.8% identity to each other. The identity of the Brazilian porcine RV-B strains with outer sequences consisting of group A and C rotaviruses was only 35.3 to 38.8%. A dendrogram was also constructed to group the strains into clusters according to host species: human, rat, and a distinct third cluster consisting exclusively of the Brazilian porcine RV-B strains. This is the first study of the porcine RV-B NSP2 gene that contributes to the partial characterization of this virus and demonstrates the relationship among RV-B strains from different host species.

Genetic analysis of the ELOVL6 gene polymorphism associated with type 2 diabetes mellitus

Recent animal studies have indicated that overexpression of the elongation of long-chain fatty acids family member 6 (Elovl6) gene can cause insulin resistance and β-cell dysfunction. These are the major factors involved in the development of type 2 diabetes mellitus (T2DM). To identify the relationship between single nucleotide polymorphisms (SNP) ofELOVL6 and T2DM pathogenesis, we conducted a case-control study of 610 Han Chinese individuals (328 newly diagnosed T2DM and 282 healthy subjects). Insulin resistance and islet first-phase secretion function were evaluated by assessment of insulin resistance in a homeostasis model (HOMA-IR) and an arginine stimulation test. Three SNPs of the ELOVL6 gene were genotyped with polymerase chain reaction-restriction fragment length polymorphism, with DNA sequencing used to confirm the results. Only genotypes TT and CT of the ELOVL6 SNP rs12504538 were detected in the samples. Genotype CC was not observed. The T2DM group had a higher frequency of the C allele and the CT genotype than the control group. Subjects with the CT genotype had higher HOMA-IR values than those with the TT genotype. In addition, no statistical significance was observed between the genotype and allele frequencies of the control and T2DM groups for SNPs rs17041272 and rs6824447. The study indicated that the ELOVL6 gene polymorphism rs12504538 is associated with an increased risk of T2DM, because it causes an increase in insulin resistance.

Sediment genotoxicity and its relationship to the frequency of chironomid labial plate deformities

Sediment samples were taken from seven locations in the WeIland River in December 1986 and April 1987. The DMSO extracts of these sediment samples showed a significant (p

Automatic Structure Generation using Genetic Programming and Fractal Geometry

Three dimensional model design is a well-known and studied field, with numerous real-world applications. However, the manual construction of these models can often be time-consuming to the average user, despite the advantages o ffered through computational advances. This thesis presents an approach to the design of 3D structures using evolutionary computation and L-systems, which involves the automated production of such designs using a strict set of fitness functions. These functions focus on the geometric properties of the models produced, as well as their quantifiable aesthetic value - a topic which has not been widely investigated with respect to 3D models. New extensions to existing aesthetic measures are discussed and implemented in the presented system in order to produce designs which are visually pleasing. The system itself facilitates the construction of models requiring minimal user initialization and no user-based feedback throughout the evolutionary cycle. The genetic programming evolved models are shown to satisfy multiple criteria, conveying a relationship between their assigned aesthetic value and their perceived aesthetic value. Exploration into the applicability and e ffectiveness of a multi-objective approach to the problem is also presented, with a focus on both performance and visual results. Although subjective, these results o er insight into future applications and study in the fi eld of computational aesthetics and automated structure design.

Genetic Analysis of Taste in Homo Sapiens

There are many known taste receptors specific to each taste attribute. This thesis examines the relationship between single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) in known taste and taste pathway receptors TAS2R38, Gustin, and TRPM5 and for PROP (6-n-propylthiouracil) taster status (PTS), thermal taster status (TTS), and orosensory sensation intensity ratings. PTS is a proxy for general taste responsiveness, and the ability to taste PROP classifies individuals into three phenotypes: super (PST), medium (PMT), and non-tasters (PNT). Another taste phenotype, also serving as a proxy for general taste responsiveness, is TTS, classifying individuals as thermal tasters (TTs) or thermal non-tasters (TnTs). DNA extractions from buccal cells obtained from 60 individuals were performed and analysis of TAS2R38, Gustin, and TRPM5 variations were conducted through Polymerase Chain Reaction (PCR), sequencing for SNPs, and upQMPSF for CNV analysis of TRPM5. Among the SNPs and CNVs studied, only TAS2R38 was found to be significantly associated with PTS and intensity ratings for sweet, bitter, and sour taste as well as astringency. However, not all PROP phenotypic differences can be explained by the variations at these three SNP sites in TAS2R38, suggesting the involvement of additional genes. No association was found between TTS and TAS2R38 or Gustin, confirming that PTS and TTS are not genetically associated. The examined TRPM5 SNPs and CNVs did not correlate with TTS. Therefore, further research is necessary into other factors contributing to PTS and TTS.

Disease-Gene Association Using a Genetic Algorithm

Understanding the relationship between genetic diseases and the genes associated with them is an important problem regarding human health. The vast amount of data created from a large number of high-throughput experiments performed in the last few years has resulted in an unprecedented growth in computational methods to tackle the disease gene association problem. Nowadays, it is clear that a genetic disease is not a consequence of a defect in a single gene. Instead, the disease phenotype is a reflection of various genetic components interacting in a complex network. In fact, genetic diseases, like any other phenotype, occur as a result of various genes working in sync with each other in a single or several biological module(s). Using a genetic algorithm, our method tries to evolve communities containing the set of potential disease genes likely to be involved in a given genetic disease. Having a set of known disease genes, we first obtain a protein-protein interaction (PPI) network containing all the known disease genes. All the other genes inside the procured PPI network are then considered as candidate disease genes as they lie in the vicinity of the known disease genes in the network. Our method attempts to find communities of potential disease genes strongly working with one another and with the set of known disease genes. As a proof of concept, we tested our approach on 16 breast cancer genes and 15 Parkinson's Disease genes. We obtained comparable or better results than CIPHER, ENDEAVOUR and GPEC, three of the most reliable and frequently used disease-gene ranking frameworks.

The relationship between fructose consumption and risk of obesity in two Aboriginal populations

Résumé La prédominance de l'obésité qui touche les enfants et les adultes a augmenté dans le monde entier ces dernières décennies. Les différentes études épidémiologiques ont prouvé que l'obésité est devenue une préoccupation profonde de santé aux États-Unis et au Canada. Il a été montré que l'obésité a beaucoup d’effets sur la santé ainsi il serait important de trouver différentes causes pour le gain de poids. Il est clair que l'obésité soit la condition de multiples facteurs et implique des éléments génétiques et environnementaux. Nous nous concentrons sur les facteurs diététiques et particulièrement le fructose où sa consommation a parallèlement augmenté avec l'augmentation du taux d'obésité. La forme principale du fructose est le sirop de maïs à haute teneur en fructose (HFCS) qui est employé en tant qu'édulcorant primordial dans la plupart des boissons et nourritures en Amérique du Nord. Il a été suggéré que la prise du fructose serait probablement un facteur qui contribue à l’augmentation de la prédominance de l'obésité. L'objectif de cette étude était d'évaluer s'il y a un rapport entre la consommation du fructose et le risque d'obésité. Nous avons travaillé sur deux bases de données des nations Cree et Inuit. Nous avons eu un groupe de 522 adultes Cree, (263 femmes et 259 hommes) dans deux groupes d'âge : les personnes entre 20 et 40 ans, et les personnes de 40 à 60 ans. Nous les avons classés par catégorie en quatre groupes d'indice de masse corporelle (IMC). L'outil de collecte de données était un rappel de 24 heures. En revanche, pour la base de données d'Inuit nous avons eu 550 adultes (301 femmes et 249 hommes) dans deux groupes d'âge semblables à ceux du Cree et avec 3 catégories d’indice de masse corporelle. Les données dans la base d'Inuit ont été recueillies au moyen de deux rappels de 24 heures. Nous avons extrait la quantité de fructose par 100 grammes de nourriture consommés par ces deux populations et nous avons créé des données de composition en nourriture pour les deux. Nous avons pu également déterminer les sources principales du fructose pour ces populations. Aucun rapport entre la consommation du fructose et l’augmentation de l’indice de masse corporelle parmi les adultes de Cree et d'Inuit n’a été détecté. Nous avons considéré l’apport énergétique comme facteur confondant potentiel et après ajustement, nous avons constaté que l'indice de masse corporelle a été associé à l’apport énergétique total et non pas à la consommation du fructose. Puisque dans les études qui ont trouvé une association entre la consommation de fructose et l’obésité, le niveau de la consommation de fructose était supérieure à 50 grammes par jour et comme dans cette étude ce niveau était inférieur à cette limite (entre 20.6 et 45.4 g/jour), nous proposons que des effets negatifs du fructose sur la masse corporelle pourraient être testés dans des populations à plus haute consommation. Les essais cliniques randomisés et éventuelles études cohortes avec différents niveaux de consommation de fructose suivis à long terme pourraient aussi être utiles. Mots clés : fructose, sirop de maïs à haute teneur en fructose (HFCS), obésité et poids excessif

Molecular genetic profiling of functional genes of pearl oyster, Pinctada fucata

There are a number of genes involved in the regulation of functional process in marine bivalves. In the case of pearl oyster, some of these genes have major role in the immune/defence function and biomineralization process involved in the pearl formation in them. As secondary filter feeders, pearl oysters are exposed to various kinds of stressors like bacteria, viruses, pesticides, industrial wastes, toxic metals and petroleum derivatives, making susceptible to diseases. Environmental changes and ambient stress also affect non-specific immunity, making the organisms vulnerable to infections. These stressors can trigger various cellular responses in the animals in their efforts to counteract the ill effects of the stress on them. These include the expression of defence related genes which encode factors such as antioxidant genes, pattern recognition receptor proteins etc. One of the strategies to combat these problems is to get insight into the disease resistance genes, and use them for disease control and health management. Similarly, although it is known that formation of pearl in molluscs is mediated by specialized proteins which are in turn regulated by specific genes encoding them, there is a paucity of sufficient information on these genes.In view of the above facts, studies on the defence related and pearl forming genes of the pearl oyster assumes importance from the point of view of both sustainable fishery management and aquaculture. At present, there is total lack of sufficient knowledge on the functional genes and their expressions in the Indian pearl oyster Pinctada fucata. Hence this work was taken up to identify and characterize the defence related and pearl forming genes, and study their expression through molecular means, in the Indian pearl oyster Pinctada fucata which are economically important for aquaculture at the southeast coast of India. The present study has successfully carried out the molecular identification, characterization and expression analysis of defence related antioxidant enzyme genes and pattern recognition proteins genes which play vital role in the defence against biotic and abiotic stressors. Antioxidant enzyme genes viz., Cu/Zn superoxide dismutase (Cu/Zn SOD), glutathione peroxidise (GPX) and glutathione-S-transferase (GST) were studied. Concerted approaches using the various molecular tools like polymerase chain reaction (PCR), random amplification of cDNA ends (RACE), molecular cloning and sequencing have resulted in the identification and characterization of full length sequences (924 bp) of the Cu/Zn SOD, most important antioxidant enzyme gene. BLAST search in NCBI confirmed the identity of the gene as Cu/Zn SOD. The presence of the characteristic amino acid sequences such as copper/zinc binding residues, family signature sequences and signal peptides were found out. Multiple sequence alignment comparison and phylogenetic analysis of the nucleotide and amino acid sequences using bioinformatics tools like BioEdit,MEGA etc revealed that the sequences were found to contain regions of diversity as well as homogeneity. Close evolutionary relationship between P. fucata and other aquatic invertebrates was revealed from the phylogenetic tree constructed using SOD amino acid sequence of P. fucata and other invertebrates as well as vertebrates

Plasmodium vivax lineages: geographical distribution, tandem repeat polymorphism, and phylogenetic relationship

Background: Multi-drug resistance and severe/ complicated cases are the emerging phenotypes of vivax malaria, which may deteriorate current anti-malarial control measures. The emergence of these phenotypes could be associated with either of the two Plasmodium vivax lineages. The two lineages had been categorized as Old World and New World, based on geographical sub-division and genetic and phenotypical markers. This study revisited the lineage hypothesis of P. vivax by typing the distribution of lineages among global isolates and evaluated their genetic relatedness using a panel of new mini-satellite markers. Methods: 18S SSU rRNA S-type gene was amplified from 420 Plasmodium vivax field isolates collected from different geographical regions of India, Thailand and Colombia as well as four strains each of P. vivax originating from Nicaragua, Panama, Thailand (Pak Chang), and Vietnam (ONG). A mini-satellite marker panel was then developed to understand the population genetic parameters and tested on a sample subset of both lineages. Results: 18S SSU rRNA S-type gene typing revealed the distribution of both lineages (Old World and New World) in all geographical regions. However, distribution of Plasmodium vivax lineages was highly variable in every geographical region. The lack of geographical sub-division between lineages suggests that both lineages are globally distributed. Ten mini-satellites were scanned from the P. vivax genome sequence; these tandem repeats were located in eight of the chromosomes. Mini-satellites revealed substantial allelic diversity (7-21, AE = 14.6 +/- 2.0) and heterozygosity (He = 0.697-0.924, AE = 0.857 +/- 0.033) per locus. Mini-satellite comparison between the two lineages revealed high but similar pattern of genetic diversity, allele frequency, and high degree of allele sharing. A Neighbour-Joining phylogenetic tree derived from genetic distance data obtained from ten mini-satellites also placed both lineages together in every cluster. Conclusions: The global lineage distribution, lack of genetic distance, similar pattern of genetic diversity, and allele sharing strongly suggested that both lineages are a single species and thus new emerging phenotypes associated with vivax malaria could not be clearly classified as belonging to a particular lineage on basis of their geographical origin.

Genetic influences on hypoxic conditioning

This paper addresses the relationship between noise-induced hearing loss (NIHL) and hypoxic conditioning prior to noise exposure. The study begins the process of determining the number and characteristic of the gene(s) involved in the cochlear hypoxic conditioning response.