Diversity analysis of Indian tetraploid wheat using intersimple sequence repeat markers reveals their superiority over random amplified polymorphic DNA markers.
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DNA, Plant↗
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Immunoglobulin diversity: analysis of the germ-line VH gene repertoire of the murine anti-GAT response.
A cDNA clone was constructed from a mRNA encoding an anti-GAT (Glu60 Ala30 Tyr10) BALB/c monoclonal antibody heavy chain. Its sequence, covering codons -5 to 162 and therefore encompassing the complete V-D-J region, was determined. Surprisingly, the sequence of the VH gene-encoded region was almost identical with that of the BALB/c VH anti-HNP (4-hydroxy-3-nitrophenyl) acetyl VH region, suggesting that the same VH germ-line might be used to encode two heavy chains contributing to antibodies of discrete specificities. A specific VH probe was derived and annealed to Eco RI and Bg1 II restriction fragments of liver (unrearranged) DNA extracted from the BALB/c, DBA/2 and C57BL/6 mouse strains that differ in their H chain allotypes. Under stringent conditions, only a few bands were identified by Southern blotting. The different patterns observed suggest that the VH anti-GAT repertoire differs between these strains even though their various anti-GAT antibodies express the same public idiotypic specificities.
Amino Acid Sequence↗
Application of bovine microsatellite markers for genetic diversity analysis of Swiss yak (Poephagus grunniens).
In order to assess the applicability of bovine microsatellite markers for population genetic studies in Swiss yak, 131 bovine microsatellite markers were tested on a panel of 10 animals. Efficient amplification was observed for 124 markers (94.6%) with a total of 476 alleles, of which 117 markers (94.3%) were polymorphic. The number of alleles per locus among the polymorphic markers ranged from two to nine. Seven loci (ILSTS005, BMS424B, BMS1825, BMS672, BM1314, ETH123 and BM6017) failed to amplify yak genomic DNA. Two cattle Y-chromosome specific microsatellite markers (INRA126 and BM861) amplified genomic DNA from both male and female yaks. However, two additional markers on cattle Y-chromosome (INRA124 and INRA189) amplified DNA from only males. Of the polymorphic markers, 24 microsatellites proposed by CaDBase for within- and cross-species comparisons and two additional highly polymorphic markers (MHCII and TGLA73) were used to investigate the genetic variability and the population structure of a Swiss yak herd that included 51 additional animals. The polymorphic information content ranged from 0.355 to 0.752, while observed heterozygosity (HO) ranged from 0.348 to 0.823. Furthermore, a set of 13 markers, organized into three multiplex polymerase chain reactions, was evaluated for routine parentage testing. This set provided an exclusion probability in a family of four yaks (both parents and two offspring) of 0.995. These microsatellites serve as useful tools for genetic characterization of the yak, which continues to be an important domestic livestock species.
Animals↗
Application of bovine microsatellite markers for genetic diversity analysis of European bison (Bison bonasus).
In this study, the cross-amplification of a commercial multiplex set of 11 cattle (Bos taurus) microsatellites was tested on a panel of 35 European bison (Bison bonasus) individuals. After polymerase chain reaction optimization, all loci cross-amplified successfully in investigated bisons. Number of alleles and observed and expected heterozygosity per locus are in the range of 2-4, 0.086-0.629 and 0.288-0.621 respectively. The availability of a heterologous set of multiplexed microsatellite markers derived from cattle opens an avenue for collecting profound genetic data for efficient conservation management strategies of the European bison.
Animals↗
Phylogenetic diversity analysis of subterranean hot springs in Iceland.
Geothermal energy has been harnessed and used for domestic heating in Iceland. In wells that are typically drilled to a depth of 1,500 to 2,000 m, the temperature of the source water is 50 to 130 degrees C. The bottoms of the boreholes can therefore be regarded as subterranean hot springs and provide a unique opportunity to study the subterranean biosphere. Large volumes of geothermal fluid from five wells and a mixture of geothermal water from 50 geothermal wells (hot tap water) were sampled and concentrated through a 0.2-microm-pore-size filter. Cells were observed in wells RG-39 (91.4 degrees C) and MG-18 (71.8 degrees C) and in hot tap water (76 degrees C), but no cells were detected in wells SN-4, SN-5 (95 to 117 degrees C), and RV-5 (130 degrees C). Archaea and Bacteria were detected by whole-cell fluorescent in situ hybridization. DNAs were extracted from the biomass, and small-subunit rRNA genes (16S rDNAs) were amplified by PCR using primers specific for the Archaea and Bacteria domains. The PCR products were cloned and sequenced. The sequence analysis showed 11 new operational taxonomic units (OTUs) out of 14, 3 of which were affiliated with known surface OTUs. Samples from RG-39 and hot tap water were inoculated into enrichment media and incubated at 65 and 85 degrees C. Growth was observed only in media based on geothermal water. 16S rDNA analysis showed enrichments dominated with Desulfurococcales relatives. Two strains belonging to Desulfurococcus mobilis and to the Thermus/Deinococcus group were isolated from borehole RG-39. The results indicate that subsurface volcanic zones are an environment that provides a rich subsurface for novel thermophiles.
Archaea↗
Development of microsatellite markers in Fragaria, their use in genetic diversity analysis, and their potential for genetic linkage mapping.
We have developed 21 new microsatellites in the model diploid perennial species Fragaria vesca from an enriched genomic library developed using F. vesca 'Ruegen'. The transferability of the primer pairs to other Fragaria species was high; all 31 primer pairs produced amplicons in 3 accessions of the octoploid strawberry Fragaria x ananassa, whereas 24 (77%) amplified a product in 7 other diploid Fragaria species. We analysed the allelic variation among 15 F. vesca accessions using the 21 microsatellites reported here and 10 F. vesca microsatellites described previously. The level of polymorphism detected at these microsatellite loci was high; five loci were monomorphic. Only two microsatellites were required to unambiguously discriminate among the 15 F. vesca accessions. A preliminary survey of segregation in an F2 progeny indicates that 20 of the 26 polymorphic loci (77%) could be mapped.
Base Sequence↗
Shannon entropy--a novel concept in molecular descriptor and diversity analysis.
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Chemistry↗
[Genetic diversity analysis of the S10 gene of field and vaccine strains of Bluetongue virus].
S10 gene sequences of 1 attenuated vaccine strain and 31 Chinese field isolates & 1 South Africa strain of BTV were determined. The results revealed that all 33 S10 gene segments have 822 nucleotides in length with two in-frame initiation codons (nucleotides 20 to 22 and 59 to 61) and a common termination codon (nucleotides 707 to 709), which encodes two proteins (NS3 and NS3A). Nucleotide difference in the sequence of all S10 gene were from zero to 107 bp (86.4% - 100% identity). NS3/NS3A protein showed a light difference from zero to 10 amino acid (95.6% - 100% identity). Phylogenetic analysis of the S10 gene of above strains sequenced and 9 other strains from GenBank, segregated the Chinese viruses into a monophyletic group distinct from US viruses; Nucleotide identity was 85% between China Group and US group. The various Chinese isolates segregated into two phyletic subgroups based on S10 gene sequences. The clustering of viruses was dependent of geographical origin, and independent of host species of isolation, serotype & year of isolation.
Animals↗
[HPLC determination and diversity analysis of thiopurine methyltransferase activity in human and pig].
OBJECTIVE: To develop an HPLC method for the determination of 6-methylmercaptopurine concentration and then numerate the thiopurine methyltransferase (TPMT) activity in erythrocyte via formula and analysis of the TPMT activity difference between human and pig. METHODS: The chromatographic apparatus SHIMADZU GC-2010C was used. The stationary phase was a Symmetry C18 reverse-phase column (150 mm x 3.9 mm, 5 microm). The mobile phase was 0.1% acetic acid-methanol and the flow rate 1.0 mL/min. The samples were extracted by ethyl acetate and injected automatically. They were measured at UV 280 nm. 2-amino-6-methyl-mercaptopurine was used as the internal standard. RESULTS: The retention times for 6-MP, AMMP and 6-MMP were 4.4 min, 7.7 min and 9.3 min respectively. The calibration curves were linear over the range of 6.25-100 nmol/mL. the methodology recovery was 98.08%-100.05%. The extraction recovery of 6-MMP was 88.1%-92.4%. The within-group RSD 1.0%-1.5% and inter-group RSD 1.0%-4.4%. The levels of TPMT activity of human, pig and Banna Minipig Inbred Line (BMI) were (17.45 +/- 3.62) U, (7.65 +/- 1.35) U and (8.73 +/- 1.55) U respectively. CONCLUSION: The method is suitable for determination of TPMT activity in erythrocyte of different patients and species in that of clinical medicine and scientific research. TPMT activity of pig and BMI is obviously lower than human's.
Animals↗
[Genetic diversity analysis of isolates belonging to Bordetella genus].
In this study, RandomAmplified Polymorphic DNA (RAPD) method was used to track differences among human and animals isolates of eight known species of Bordetella genus. One hundred representative strains of these species from international and Polish bacterial collections were genotyped according to RAPD protocols using primer 1254 or 1247. Problems with reproducibility and discriminatory power, frequently discussed in literature, have been overcome by precise optimization procedure, which allowed to achieve reliable conditions for Bordetella species analysed. This study proved high potential of RAPD method using primers 1247/1254 for intra-species differentiation of B. bronchiseptica and B. hinzii isolates. Additionally RAPD method has been found to be useful for confirming B. avium and B. holmesii identification.
Animals↗
[Genetic diversity analysis of isolates belonging to Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica species].
In this study, Amplified Fragment Length Polymorphism (AFLP) method was used to track differences among human and animal isolates of B. pertussis, B. parapertussis and B. bronchiseptica species. One hundred and sixty representative strains of these species orginated from international and Polish bacterial collections were genotyped according to AFLP involving EcoRI/Msel and SpeI/ApaI restriction/ligation/amplification procedures. This study has confirmed high potential AFLP SpeI/ApaI procedure for intra-species differentiation of B. pertussis and B. bronchiseptica strains. Both AFLP EcoRI/MseI and SpeI/ApaI procedures have been found to be useful for species-specific classification in case of B. pertussis strains. In case of B. bronchiseptica or B. parapertussis species-specific classification, SpeI/ApaI procedure has been found more precise than EcoRI/MseI one.
Bordetella bronchiseptica↗
[Screening of peafowl microsatellite primers and analysis of genetic diversity].
The applicability of chicken microsatellite primers to peafowl population was analyzed in the present paper, and the results showed 14 of 29 pairs of microsatellite primers from chicken could amplify peafowl DNA and produce specific allele patterns. A mean of 1.71 alleles was found for each locus. Seven pairs were highly polymorphic, and MCW0080 and MCW0098 were ideal markers for peafowl. Genetic diversity analysis within and between the green peafowl and the blue peafowl populations demonstrated that the expected heterozygosity of two peafowl populations were 0.2482 and 0.2744, respectively. The inbreeding index (FST), Reynolds' genetic distance and gene flow between the two populations were 0.078, 0.0603 and 3.896 respectively. These results indicate that the heterozygosity and the genetic diversity of these two peafowl populations were very low, and suggest a tendency towards intermixing.
Alleles↗
F-statistics and analysis of gene diversity in subdivided populations.
It is show that Wright's F-statistics can be defined as ratios of gene diversities of heterozygosities rather than as the correlations of uniting gametes. This definition is applicable irrespective of the number of alleles involved or whether there is selection or not. The relationship between F-statistics and Nei's gene diversity analysis is discussed.
Alleles↗
Quantitative twin analysis of radial and ulnar ridge counts and ridge count diversity.
Analysis of variance was performed on the radial and ulnar finger ridge counts and ridge count diversity index in 360 twin sets from which estimates of genetic variance were obtained. Findings for radial and ulnar counts paralleled those previously obtained for finger pattern type and ridge count (larger of radial and ulnar count). In contrast, ridge count diversity showed no indication of unequal total variances, as previously found for the total ridge count. One must be cautious not to exclude genetic influences on traits, such as the thumb variables in this study, where there are unequal total variances between monozygotic and dizygotic twins and the more conservative estimate of genetic variance is not significant.
Analysis of Variance↗
Healthy human T-cell receptor beta-chain repertoire. Quantitative analysis and evidence for J beta-related effects on CDR3 structure and diversity.
Analysis of TCR repertoire usage and clonality is of potential value in understanding the pathogenesis of a number of human immune-mediated diseases. In diseases that are likely to be dependent on antigen-driven T cells, it has been suggested that particular TCR junctional region or CDR3 sequences may be critical. Rigorous methods for TCR analysis which are both quantitative and qualitative are therefore required. Of those commonly available, only anchor and inverse PCR are capable of giving high-quality information on V, D, N, and J region usage, but it has not been established whether both methods are quantitatively or analytically equivalent. We show here that both methods detected considerable variability in the usage of V beta and J beta segments in the peripheral blood repertoire of a normal individual. No preferential V-J pairing could be demonstrated. An excess usage of J beta 2 family members was indicated by both methods, although the relative usage of different J beta 2 families differed between the two techniques. The predominantly used V beta usage showed that for some families, estimates of their frequency in the repertoire differed significantly between the anchor and inverse libraries. When sampling relatively few clones the variation between V beta families estimated using the two methods can be considerable. This is likely to be a result of sampling error from a large gene family. Large-scale screening of several thousand clones is recommended to confirm the absolute values obtained from sequencing. Variation in CDR3 length appeared to be normally distributed, suggesting that a statistically optimal junctional region length may have been selected for contact with antigen. CDR3 length distribution differs significantly between receptors, which have rearranged to J beta 1 versus J beta 2 families, with the J beta 2-associated CDR3 on average between 0.5 and 1.2 of an amino acid longer. Thus the TCR beta junctional region repertoire of humans is subject to structural constraints associated with J beta usage. It will be important to establish whether variation in CDR3 length and J beta usage exists between subsets of human T cells in order to interpret TCR repertoire data from disease and control tissues.
Adult↗
The impact of applied behavior analysis on diverse areas of research.
The impact of applied behavior analysis on various disciplines and areas of research was assessed through two major analyses. First, the relationship of applied behavior analysis to the general area of "behavior modification" was evaluated by examining the citation characteristics of journal articles in JABA and three other behavior-modification journals. Second, the penetration of applied behavior analysis into diverse areas and disciplines, including behavior modification, psychiatry, clinical psychology, education, special education, retardation, speech and hearing, counselling, and law enforcement and correction was assessed. Twenty-five journals representing diverse research areas were evaluated from 1968 to 1974 to assess the extent to which operant techniques were applied for therapeutic, rehabilitative, and educative purposes and the degree to which methodological desiderata of applied behavior analysis were met. The analyses revealed diverse publication outlets for applied behavior analysis in various disciplines.
Behavior Therapy↗
A second-site suppressor strategy for chemical genetic analysis of diverse protein kinases.
Chemical genetic analysis of protein kinases involves engineering kinases to be uniquely sensitive to inhibitors and ATP analogs that are not recognized by wild-type kinases. Despite the successful application of this approach to over two dozen kinases, several kinases do not tolerate the necessary modification to the ATP binding pocket, as they lose catalytic activity or cellular function upon mutation of the 'gatekeeper' residue that governs inhibitor and nucleotide substrate specificity. Here we describe the identification of second-site suppressor mutations to rescue the activity of 'intolerant' kinases. A bacterial genetic selection for second-site suppressors using an aminoglycoside kinase APH(3')-IIIa revealed several suppressor hotspots in the kinase domain. Informed by results from this selection, we focused on the beta sheet in the N-terminal subdomain and generated a structure-based sequence alignment of protein kinases in this region. From this alignment, we identified second-site suppressors for several divergent kinases including Cdc5, MEKK1, GRK2 and Pto. The ability to identify second-site suppressors to rescue the activity of intolerant kinases should facilitate chemical genetic analysis of the majority of protein kinases in the genome.
Amino Acid Substitution↗
Isolation of a new retrotransposon-like DNA sequence and its use in analysis of diversity within the Oryza officinalis complex.
To better understand the genetic diversity of the wild relatives of rice (Oryza sativa L.) in the O. officinalis species complex repetitive DNA markers were obtained from the diploid species of this complex. One cloned sequence from O. eichingeri gave intense hybridization signals with all species of the O. officinalis complex. This 242 bp clone, named pOe.49, has a copy number from 0.9 to 4.0 x 10(4) in diploid species of this complex. Analysis of the primary structure and database searches revealed homology of pOe.49 to a number of sequences representing part of the integrase coding domain of retroviruses and gypsy-like retrotransposons. Sequencing of specific PCR products confirmed that pOe.49 is part of a gypsy-like retrotransposon. RFLP analysis was used to study the genomic organisation of pOe.49 among 30 accessions of the O. officinalis complex using 10 restriction enzymes. Diversity analysis based on 120 polymorphic fragments obtained from the RFLP assay grouped the O. officinalis complex accessions by genome, species and eco-geographic groups. The results suggest that, with further characterization, this retrotransposon-like DNA sequence may be useful for phylogenetic analysis of species in the O. officinalis complex.
Amino Acid Sequence↗