In general, the P. falciparum infections include a complex mixture of biologically and genetically different popula- tions, as has been demonstrated by different techniques, including the Restriction Fragment Length Polymorphism (RFLP)  and the Polymerase Chain Reaction (PCR) . PCR has been used to study the existing polymorphisms in various markers, such as the Merozoite Surface Proteins 1 (MSP-1) and 2 (MSP-2), the circumsporozoite protein (CSP) and the glutamate-rich protein (GLURP) . Vari- ous studies indicate that the genetic diversity in a specific area is related to the level of transmission [5,6]. Therefore, a high prevalence of infection multiplicity has been detected in hyper- and holoendemic zones , compared to low transmission zones . Only a number of basal or identical genotypes has been found in low transmission areas, such as Brazil  and Honduras . The basis of the genetic diversity is the recombination that occurs in the sexual phase of the parasite within the mosquito. Accord- ing to this, the higher the transmission, the greater the recombination frequency . However, some authors indicate that the transmission level would not be the only cause for genotype variability .
Identification of existence of variability among the isolates of the pathogen would orient the breeding pro- cedures to create new cultivars with a broader spectrum of resistance against this pathogen. Although we tested only 16 isolates of R. areola, the results would serve as a basis for future studies in this area. More detailed infor- mation is required to comprehend the virulence fre- quency and the existance of the genetic lineages if any, using a wider range of cultivars and isolates originating from different cotton growing areas of Brazil. It is possi- ble that other molecular techniques may also show genetic differences among the isolates and assist in identification of distinct genetic lineages of R. areola in Brazil. This
HIV-1 entry into host cells requires cooperate engage- ments of both the viral envelope and host cell surface (CD4) receptor, in a process requiring the engagement of one or more of a group of seven-transmembrane che- mokine receptors (co-receptors), the CCR5 and CXCR4 being the most common [5, 6]. Viral tropism (co-recep- tor usage) has important consequences and relationships with infection and disease outcomes. Thus, viruses have been characterized phenotypically on the basis of trop- ism into syncytium inducing (SI) and non syncytium in- ducing (NSI) . CXCR4 (X4) tropic viruses are largely of SI phenotype. These T-Cell tropic viruses arise during late stages of disease progression or infection . CCR5 (R5) tropic viruses are of NSI phenotype of macrophage lineage and dominate the early stages of infection. HIV has demonstrated ability to switch tropism during the course of disease, a process that the virus uses adaptively to propagate in the presence of antiviral immune or therapeutic pressure . Viral tropism can be deter- mined either by using the more rigorous but expensive cell based phenotypic test or assigned on the basis of the relatively inexpensive genotyping sequence analysis that however, suffer from reduced sensitivity . To improve robustness of genotypic tropism assignments, a number of tools have been developed including T-Cup 2.0, WebPSSM x4r5 , WebPSSM sinsi and Geno2Pheno, as well
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Twenty six genotypes of Sesbania aculeata and Sesbania rostrata were examined for variability in seed characters and seedling growth under field conditions. Though the smaller seeds had faster seedling emergence, the relative growth rate and rate of increase in seedling height was higher for larger and heavier seeds. The larger seeds also showed faster leaf emergence, i.e. lower phyllochron. In contrast to the field germination, all the Sesbania rostrata genotypes failed to imbibe moisture at room temperature indicating physical dormancy due to seed coat impermeability. These seed attributes can be useful in maintaining uniform crop stand (by selection of genotypes and seed treatment) for achieving faster biomass production in Sesbania species for green manuring in rice-wheat cropping system.
In general, excess soil moisture treatment reduced the plant height, stem elongation rate (SER), leaf area and root length (Table 1) irrespective of the genotypes. However, there was a remarkable genetic variability with regards to all the growth parameters. Maximum reduction in plant height due to waterlogging was found in CM 500 (16.76%) and CM 600(16.4%), whereas the impact was negligible in case of CM 122(1.93%). Data on SER revealed that 7 days of the stress decreased the elongation rate in all the genotypes. Stress condition severely inhibited SER in CM 119(68.87%) and CM 104(64.19%). Inhibition in leaf area was highly significant in all the genotypes under stress condition. Under control condition, maximum leaf area was found in CM 500(1140.33 cm 2 /plant), whereas minimum was in
A collection of lactic acid bacteria isolates from fish viscera was studied and investigated regarding to their functional properties and safety aspects. From these, three isolates GM1, GM2 and GM3 were identified as Enterococcus feacium species using molecular methods. Partial Amplified rDNA Restriction Analysis (partial ARDRA) with restriction en- zyme HaeIII separated these isolates into distinctive group which suggest genotypic variability within enterococci strains isolated from fish viscera. The three strains GM1, GM2 and GM3 exhibited antimicrobial activity. Indeed strains have been shown to produce bacteriocins with inhibitory effect against food spoilage bacteria and pathogenic fish in- cluding Carnobacterium maltaromaticum. The molecular mass of bacteriocin, as calculated by tricine-SDS-PAGE, was found to be 4.5 kDa. All isolates were tested positive upon PCR amplification of enterocin A structural gene. Investiga- tions of antibiotic resistance show that the isolates were mostly sensitive to several antibiotics (ampicillin, penicillin, tetracycline, gentamycine) and resistance to rifampicin. All isolates grow in esculin azide agar as a selective medium for enumeration of probiotic enterococci. This study suggests that our strains can be employed as probiotic or to improve the safety of food products.
Concluding, commercial cultivars that are sown traditionally for many years may contain (or devel- oped) exploitable internal variability which depict that a selection within the cultivars may be effective for improving the total yield and other quantitative or qualitative traits. Many of these cultivars may not be protected any more. The concept of continuous selection seems to be a tool for improving the cultivars and overcoming problems of deterioration, useful for the official seed foundations that may need to preserve the productivity. Also, incorporation of tol- erance to the biotic and abiotic stresses may be valu- able for the preservation of the yield’s performance, especially under common insect infections that may reduce productivity. Cultivar uniformity seems to be indispensable for high yields because of the lack of the unfavourable effects of the genetic heterogeneity and the unequal sharing of the resources. Uniform cultivars exhibit reduced competition resulting in the maximum plant yield per area. In our paper, cultivars B and D showed two of the greatest grain yield values, together with cultivar A. Cultivar F exhibited a rather unstable performance. The latest may indicate cultivar heterogeneity on one hand and buffering that boosts yield components on the other hand. This behaviour may be a result of the farmers’ practices that keep part of the wheat seed after harvesting to be used in sowing for the next period of cultivation.
and strains impact the protective efficacy of neutralizing antibod- ies is not understood. Several recent studies of DENV MAbs sug- gest that genotypic differences in neutralization exist (28, 37–41). In this study, we investigated the molecular basis for significant differences in the neutralization sensitivity among two closely re- lated DENV1 strains representing distinct genotypes. The DENV1 type-specific MAb E111 inhibits infection of the DENV1 strain 16007 at antibody concentrations markedly lower than the amount required to neutralize the WP-74 strain (23, 28). We iden- tified a single amino acid residue on the E protein (residue 204) capable of altering neutralization potency at a site distant from the crystallographically defined E111 epitope-paratope interface (Fig. 4) (23). The conservative lysine-to-arginine substitution im- pacted sensitivity to numerous DIII-reactive MAbs as well as the stability of the RVPs in solution. These patterns of neutralization sensitivity were further confirmed by neutralization assays per- formed using Vero cells that do not express the attachment factor DC-SIGNR and with K562 cells that express the Fc receptor CD32 (data not shown). Our data suggest that position 204 regulates epitope accessibility on E-DIII through changes in the ensemble of structures sampled through viral breathing. Our results provide a striking example in which minor sequence variation among DENV strains can result in unexpectedly broad consequences im- pacting both the biology of the virus and the antiviral immune response.
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Figure 2.—Median pro- portion (percentage) of ge- notypic variance explained by detected QTL (p˜) deter- mined from estimation (ES), cross validation (CV/E, CV/G, CV/GE), and valida- tion with independent sam- ples (VS1 and VS2) as well as the average number of QTL detected in estimation (see box, ascending order of k) for a varying number of genotypic subsamples (k) and the entire data set (DS) of Experiment 1 for grain yield, grain moisture, ker- nel weight, and plant height. (䊉) ES, (䊐) CV/E, (䉫) CV/G, (䉭) CV/GE, (䉱) V/VS1, (䉲) V/VS2.
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Correct and rapid diagnosis is essential in the management of multidrug-resistant tuberculosis (MDR-TB). In this population-based study of 61 patients with drug-resistant tuberculosis, we evaluated the frequency of mutations and compared the performance of genotypic (mutation analysis by dot blot hybridization) and phenotypic (indirect proportion method) drug resistance tests. Three selected codons (rpoB531, rpoB526, and katG315) allowed identification of 90% of MDR-TB cases. Ninety percent of rifampin, streptomycin, and ethambutol resistance and 75% of isoniazid resistance were detected by screening for six codons: rpoB531, rpoB526, rrs-513, rpsL43, embB306, and katG315. The performance (reproducibility, sensitivity, and specificity) of the genotypic method was superior to that of the routine phenotypic method, with the exception of sensitivity for isoniazid resistance. A commercialized molecular genetic test for a limited number of target loci might be a good alternative for a drug resistance screening test in the context of an MDR “DOTS-plus” strategy.
Similar finding were reported by Venkataramana et al. (2001). Nath and Alam (2002) Injeti (2008) also resulted low Genotypic co-efficient of variation for days to maturity. Phenotypic coefficient variation (PCV) which measures total relative variation was high for plant height (33.28) followed by kernel yield (30.01), seed yield per plant (30.00), pod yield per plant (29.21), pod per plant (28.09), field emergence (27.95) and pod yield (26.05). The moderate estimate of Phenotypic coefficient of variation value was observed in number of primary/ plant (10.36) and low Phenotypic coefficient variation of observed by seed index (8.09), days to 50% flowering (7.56), kernel uniformity (7.20), sound matured kernel (5.59), shelling % (2.43), days to maturity (1.34), (Table 2) Similar finding were observed for days to maturity by John et al. (2008). Sr.
One limit of the study was the small number of X4 viruses in our patients (4/26). However, R5 viruses with an X4 genotype using current algorithms were very informative and analysis of our dataset enabled us to propose a new interpretation rule for HIV-1 subtype D tropism. This new rule was subsequently validated by examination of a GenBank set of 67 subtype D V3 sequences belonging to viruses whose phenotype was known. The best concordance with the phenotype was obtained with the subtype D combined rule (sensitivity 68%, specificity 95%), giving a good agreement with the phenotypic assay (kappa coefficient of 0.63). This speci- fic genotypic algorithm predicted HIV-1 tropism better than did the MT2 or Trofile phenotypic assays (data not shown). The specificity of the V3 genotype is important for not excluding patients eligible for antiretroviral treatment based on a CCR5 antagonist and for epide- miological and pathophysiological studies. The specifi- city of the V3 genotype is also crucial for accurate characterization of HIV-1 quasispecies by ultra-deep
Development of an effective breeding program depends on the existence of genetic variability for various economic characters in the gene pool. Selection is effective only when there is enough magnitude of variability in the breeding population. An understanding of precise magnitude of variability present in a population is important in formulating the most appropriate breeding technique for improvement of various characters. The estimation of character associations helps to identify the relative importance of independent characters contributing to dependent ones and suggest upon the character(s) that may be useful as indicator for one or more of other characters. On the other hands, character associations between yield components can be used as the best guide for successful yield improvement by indirect selection.
Intrapatient sequence variability. In order to assess the longitudinal biological stability of HIV PR and RT se- quences, 168 sequences from 22 patients were analyzed (range, 4 to 18 sequences per patient). The mean duration of the follow-up analysis period for each patient was 29 months (range, 6 to 55 months). The overall full and partial intrapatient nucleotide discordances ranged from 0 to 3.5% (median, 1.1%) when sequential HIV PR or RT sequences were compared to the initial sequence for each patient. By definition, there were no mutations detected at key resis- tance-associated sites in any sequence, but a total of 389 mutations (231 in PR and 158 in RT) were identified at secondary or accessory sites. No sample had ⬎ 4 mutations at these sites. The mutations tended to remain constant in sequential samples from the same patient.
Rotavirus diarrhoea remains a public health problem in Côte d’Ivoire hence the reason for sentinel sur- veillance. This study highlight the genotypic variabil- ity of circulating rotavirus strains before the introduction of rotavirus vaccines in the expanded immunization program. Continuous surveillance will be necessary to monitor prevalent and newly evolv- ing rotavirus stains within the Ivorian community post vaccine introduction.
ABSTRACT DNA-assisted selection can be applied to vegetal species in the seed stage; however, little is known about the effect of seed fractionation on the physiological quality and viability of the seedlings or the effectiveness of DNA extraction from seed pieces. We evaluated the efficiency of pre-germinative genotypic screening by DNA markers from manually cut partial seeds of rice, beans and maize. Tests to evaluate PCR amplification and physiological quality were performed. We observed that the Sarkosyl method was efficient to extract DNA from a ½ fraction of the rice seeds and ¼ of the bean and maize seeds, generating good quality SSR- PCR products. The physiological quality of the rice seeds cut in half and the bean and maize seeds remaining fraction of ¾ of the original seed provided a high germination percentage. The method is effective for simultaneously genotyping and germinating plants from a single seed, since DNA extracted from these fractions of seeds can be used for studies with DNA markers, while the remaining portions can be used for seedling production.
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(Table 5). Modelling genotypic AMR can be more com- plicated as many genes can be linked to a specific anti- biotic, and the relationship between gene abundance and antibiotic use seems to be more complex than first antic- ipated . Modelling genotypic AMR requires the rele- vant genes for the modelled AMR to be represented, as well as circumstances allowing for the genetic AMR to be expressed as phenotypic AMR, leading to a spread of the resistant pathogen within the population. Published models of genotypic AMR do not link this AMR type to the development of phenotypic AMR and the subse- quent spread of the resistant pathogen between individ- uals . This is perhaps due to a lack of information on the necessary circumstances for the phenotypic ex- pression of genetic resistance determinants, thus empha- sising the need for more research to better understand this process. Understanding the process is essential in the prevention of AMR development and spread.
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Genotypic correlation was also analyzed among AFIS-measured properties and other traits including lint yield and fiber properties measured by single-instruments, i.e., stelometer, fibrograph, micronaire, etc. (Table 4). Lint yield was negatively (favorably) correlated with nep count (r=-0.47) and SCN count (r=-0.31) although correlations were moderate or low. These results implied simultane- ous improvement between lint yield and neppi- ness was possible or at least there would be little compensation between the traits in selection. A low, but significant positive correlation was identified between nep count and elongation (r=0.32) (Table 4). Fiber bundle strength was positively (unfavor- ably) correlated with SCN count (r=0.60). A similar unfavorable correlation between strength and SCN (r=0.31) was also observed in 38 cotton cultivars in a report by Boykin (2008). Nep count was unfa- vorably correlated to 2.5% span length (r=56), but not correlated to 50% span length (r=0.10). In our previous study, it was reported that 50% length was negatively (favorably) correlated to short fiber content (r=-0.40) and 2.5% length positively (unfa- vorably) correlated to short fiber content (r=0.34) (Zeng and Meredith, 2009). Close association between 50% length and short fiber content may contribute to the greater contribution of 50% length to fiber bundle strength than that of 2.5% length.
Abstract: Information on the extent and pattern of genetic variability, heritability, and genetic advance under selection are essential to design breeding strategies in the available germplasm of soybean and helps to identify elite genotypes that will be incorporated in to soybean crop improvement programs to address the growing demand of the crop in Ethiopia. Forty-nine soybean (Glycine max (L.) Merrill) genotypes were evaluated in a field study in 7x7 simple lattice design with two replications at Jimma Agricultural Research Center (JARC) with the objective of estimating genetic variability, heritability, expected genetic advance, and to estimate genetic divergence, thereby, to cluster the test genotypes in to genetically divergent classes. The result indicated substantial variations for all the traits evaluated. Analysis of variance revealed that there was statistically significant difference among the forty-nine genotypes for most of the traits studied except root volume and root dry weight. The highest heritability value was recorded for total nodules per plant followed by effective nodules per plant and plant height. Significant wide range of mean values was observed in all the characters evaluated. This indicates that the characters can be improved through selection. The Divergence analysis grouped the 49 soybean genotypes into five which shows crossing between genotypes which fall in to different classes would result in hybrid vigour. The principal component analysis revealed that 6 components have accounted for 79.90% of the total variation among the genotypes.
Sixty-one isolates and collection strains of Aspergillus fumigatus were compared for their phenotypic (mor- phological features and isoenzyme profiles) and genotypic (restriction enzyme-generated mitochondrial DNA and ribosomal DNA profiles and random amplified polymorphic DNA patterns) features. The examined strains exhibited highly variable colony morphologies and growth rates at different temperatures, but their micro- morphologies and conidial diameters were characteristic of the species. Of the isoenzymes studied, the b -arylesterase and phosphatase patterns were the most divergent, and the 61 strains could be classified into seven groups. The glucose 6-phosphate dehydrogenase and catalase isoenzyme patterns displayed only a limited variability, while the profiles of superoxide dismutase, lactate dehydrogenase, and glutamate dehydro- genase were highly conserved. The HaeIII-generated mitochondrial DNA patterns and SmaI-digested repetitive DNA and ribosomal DNA hybridization patterns of almost all strains were also invariable. The level of variation was much higher when random amplified polymorphic DNA analysis was applied. Although the patterns of the strains were very similar with most of the primers, the application of some primers made it possible to cluster the A. fumigatus isolates into several groups. The results indicate that the random amplified polymorphic DNA technique could be used more efficiently than isoenzyme analysis for typing A. fumigatus isolates. A good correlation was found between the dendrograms obtained from the isoenzyme and random amplified polymorphic DNA data, but the isoenzyme and amplified DNA patterns did not correlate with the pathogenicity, pigment production, or geographical origin of the strains. One ‘‘A. fumigatus’’ strain (strain FRR 1266) exhibited unique isoenzyme, mitochondrial DNA, ribosomal DNA, and random amplified polymorphic DNA patterns; it is proposed that this strain represents a new species of the section Fumigati.