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PubMed2026

Genomic resources to advance seed coat color and patterning genetics and breeding in common bean (Phaseolus vulgaris L.).

Seed coat color and patterning are key quality traits in common bean (Phaseolus vulgaris L.) that define market classes and strongly influence consumer preference and market value. These traits are controlled by a complex network of major genes (sometimes with epistatic interactions), which complicates the recovery of desired market class phenotypes following inter-market class hybridization. Although many of the underlying loci have been genetically mapped, diagnostic, high-throughput molecular markers for efficient allele tracking across the Middle American and Andean gene pools remain limited. In this study, we developed and validated 24 gene-specific PCR Allele Competitive Extension (PACE) markers targeting seven major seed coat color genes (G, B, V, J, Rk, T, and Z) and two patterning genes (CPi and CSt), together with a previously reported marker associated with the postharvest seed coat darkening locus (Psd). An additional PACE marker targeting the Phaseolin (Phs) locus was developed to distinguish Middle American (S-type) and Andean (T-type) gene pools, providing a complementary tool for assessing genetic background alongside seed coat-specific loci. Marker performance was evaluated across three diverse panels, revealing high diagnostic accuracy for most loci (90%-100%). However, for loci such as J, V, Rk, T, and Z, allele-specific markers or marker combinations were required to capture full allelic diversity. Haplotype analysis further revealed substantial allelic diversity across market classes and identified background-specific interactions. Collectively, these results provide a comprehensive set of high-resolution, gene-anchored PACE markers for seed coat color, patterning, and gene pool classification in common bean. These markers enable rapid and precise allele tracking in breeding populations and germplasm collections, facilitating marker-assisted selection for market class-specific seed coat traits and accelerating genetic improvement.

Phaseolus↗
PubMed1993

Na/Ca exchanger isoforms expressed in kidney.

The cardiac (versus retinal rod) Na/Ca exchanger gene has been cloned, sequenced and shown by RNA analysis to be present in diverse tissues. Analysis of published sequences shows that a single isoform is found in heart tissue from many species (NACA1 isoform). We provide evidence here by ribonuclease (RNase) protection assays and by reverse transcriptase-polymerase chain reaction (PCR) amplification with sequence analysis that a new isoform encoding the Na/Ca exchanger is present in renal tissue. This isoform (NACA3) reveals a 7-amino acid deletion in the tested region compared with the NACA2 isoform described by Reilly and Shugrue [Am. J. Physiol. 262 (Renal Fluid Electrolyte Physiol. 31): F1105-F1109, 1992] and is the dominant exchanger transcript in kidney. Analysis of the sequence of all isoforms indicates that the differences in the isoforms reside in the large intracellular loop region of the protein. Alternative splicing of a single Na/Ca exchanger message may be responsible for these tissue-specific transcripts.

Animals↗
PubMed1999

Analysis of the genetic diversity of Helicobacter pylori: the tale of two genomes.

Infection with Helicobacter pylori has been linked to numerous severe gastroduodenal diseases including peptic ulcer and gastric cancer. Several techniques have been used to measure the genetic heterogeneity of H. pylori at several different levels and to determine whether there is any correlation with severity of disease. The availability of two completed genome sequences from unrelated strains (J99 and 26,695) has allowed an analysis of the level of diversity from a large-scale yet detailed perspective. Although the two chromosomes are organized differently in a limited number of discrete regions, the genome size and gene order of these two "high-virulence" (cagA+ and vacA+) H. pylori isolates was found to be highly similar. The regions of organizational difference are associated with insertion sequences, DNA restriction/modification genes, repeat sequences, or a combination of the above. A significant level of variation at the nucleotide level is seen across the genome, providing an explanation for why the nucleotide-based typing techniques have such high discriminatory power among independent H. pylori isolates. This nucleotide variation together with the organizational rearrangements appears to have provided an over-estimation of the gene order diversity of H. pylori as assessed by pulse-field gel electrophoresis. Functional assignments are assigned to approximately only 60% of the gene products in each strain, with one-half of the remaining gene products of unknown function having homologues in other bacteria, while the remainder appear to be H. pylori-specific. Between 6% and 7% of the coding capacity of each strain are genes that are absent from the other strain, with almost one-half of these strain-specific genes located in a single hypervariable region called the plasticity zone. The majority of the strain-specific genes in each strain are also H. pylori-specific, with no homologues being identified in the public databases. Significantly, over one-half of the functionally assigned strain-specific genes in both H. pylori J99 and 26695 encode DNA restriction/modification enzymes. Analysis of the level of conservation between orthologues from the two strains indicates that the H. pylori specific genes have a lower level of conservation than those orthologues to which a putative function can be assigned. The plasticity zone represents one of several regions across each genome that is comprised of lower (G+C)% content DNA, some of which has been detected in self-replicating plasmids, suggesting that both horizontal transfer from other species and plasmid integration are responsible for the strain-specific diversity at this locus. These analyses have yielded results with important implications for understanding the genetic diversity of H. pylori and its associated diseases, and imply a need to reassess the respective roles of bacterial and host factors in H. pylori associated diseases.

Genes, Bacterial↗
PubMed1975

Fate of 90 children with ileal conduit urinary diversion a decade later: analysis of complications, pyelography, renal function and bacteriology.

A study of the long-term results of ileal conduit urinary diversion for non-malignant disease in 90 children has shown that there were 75 survivors after 10 to 16 years. Stomal stenosis and ureteroileal or other intrinsic obstructions requiring ileal loop revisions occurred frequently and as late as 13 years postoperatively. Of 144 renal units 76 per cent improved or remained stable and 69.3 per cent of normal kidneys remained normal after more than a decade of urinary diversion. In order to obtain these results close lifetime followup and aggressive loop revisions have been required. Urine cultures were consistently negative in 70.5 per cent of all patients. Good results were obtained in terms of preservation of renal function in all categories. Creatinine clearance remained in the normal range after 10 years if the excretory urogram remained normal. Ileal conduit urinary diversion remains a major surgical undertaking but it also remains the standard of urinary diversion against which all other methods must be judged. The results in terms of renal preservation are impressive but so too are the significant number of long-term complications. Any other method of diversion (such as the sigmoid conduit) that can improve upon these results will be welcomed. All children with ileal conduit urinary diversion for reasons other than a neurogenic bladder must be considered candidates for urinary reconstruction.

Adolescent↗
PubMed2003

Comprehensive analysis of Alu-associated diversity on the human sex chromosomes.

A comprehensive analysis of the human sex chromosomes was undertaken to assess Alu-associated human genomic diversity and to identify novel Alu insertion polymorphisms for the study of human evolution. Three hundred forty-five recently integrated Alu elements from eight different Alu subfamilies were identified on the X and Y chromosomes, 225 of which were selected and analyzed by polymerase chain reaction (PCR). From a total of 225 elements analyzed, 16 were found to be polymorphic on the X chromosome and one on the Y chromosome. In line with previous research using other classes of genetic markers, our results indicate reduced Alu-associated insertion polymorphism on the human sex chromosomes, presumably reflective of the reduced recombination rates and lower effective population sizes on the sex chromosomes. The Alu insertion polymorphisms identified in this study should prove useful for the study of human population genetics.

Alu Elements↗
PubMed1993

PCR-based restriction fragment length polymorphism analysis of DNA sequence diversity of flagellin genes of Campylobacter jejuni and allied species.

Genotypes were analysed within 29 geographically diverse strains of Campylobacter jejuni mainly from human enteritis cases and four strains representing C. coli, C. lari and C. helveticus. A 1723 bp DNA fragment, amplified by the polymerase chain reaction (PCR) from the flagellin (fla) genes, was used to probe genomic Southern blots for restriction site variation at homologous loci. Internal Hin fl restriction fragment length polymorphisms (RFLP) of the fla gene PCR amplification product were also used to characterize isolates. Copy number and polymorphisms in and around the fla genes were detected, and strains were grouped into 10 genotypes on the basis of fla restriction site similarities. Campylobacter jejuni had a fla gene copy number of two and the majority (64%) of strains in the species had common internal fla gene sequences as indicated by Hin fl restriction analysis. A greater degree of diversity was detected around the fla loci in Hae III and Bgl II genomic Southern blots. The results showed that analysis of fla genes provided a novel and fundamental approach to grouping strains and offered a basis for defining a predominant clonal evolutionary line within C. jejuni.

Base Sequence↗
PubMedDate not supplied

Comparing various forms of morphological diversity by means of dispersion analysis (exemplified by studying measurable morphological traits variation in three rodent genera, Mammalia).

Dispersion analysis of variances (MANOVA) is shown to be of use in comparative analysis of different forms of morphological diversity expressed in measurable traits. This approach is exemplified by analysis of subgeneric, species, subspecies, sex, and individual forms of MD in rodent genera Allactaga, Alticola, and Spalax. Some conditions and limitations of the approach are discussed.

Analysis of Variance↗
PubMed1998

Phylogenetic diversity of mesophilic and thermophilic granular sludges determined by 16S rRNA gene analysis.

The microbial diversity of two types of methanogenic granular sludge, mesophilic (35 degrees C) and thermophilic (55 degrees C), which had been treating sucrose/propionate/acetate-based artificial wastewater were compared. 16S rDNA clone libraries were constructed by PCR with a prokaryote-specific primer set, and partial sequencing of the clonal 16S rDNAs was conducted for phylogenetic analysis. Of 115 mesophilic granule and 110 thermophilic granule clones sequenced, 19 and 22%, respectively, were phylogenetically affiliated with the domain Archaea, and the remainder in each case were assigned to the domain Bacteria. Within the domain Archaea, the 16S rDNA clones in both libraries showed relatively close relationships with those of methanogens. Within the Bacteria, a major group represented in the mesophilic clone library was the delta subclass of the Proteobacteria (27%), in which high degrees of relatedness were observed between the clonal 16S rDNA sequences and those of previously identified syntrophic bacteria and sulfate-reducing bacteria. In contrast, in the thermophilic clone library, the Thermodesulfovibrio group (19%), the green non-sulfur bacteria (18%) and the low G + C subclass of the Gram-positive bacteria (18%) were predominant. A significant difference between the two libraries was that no clone affiliated with the Proteobacteria was detected in the thermophilic clone library, whereas the Proteobacteria was detected in the thermophilic clone library, whereas the Proteobacteria was the most predominant group in the mesophilic clones. Thirty-six and 24 different sequences were found in the mesophilic and thermophilic clones, respectively, suggesting that the microbial diversity of the thermophilic granule was lower than that of the mesophilic granule.

Archaea↗
PubMed2004

16S rDNA library-based analysis of ruminal bacterial diversity.

Bacterial 16S rDNA sequence data, incorporating sequences > 1 kb, were retrieved from published rumen library studies and public databases, then were combined and analysed to assess the diversity of the rumen microbial ecosystem as indicated by the pooled data. Low G+C Gram positive bacteria (54%) and the Cytophaga-Flexibacter-Bacteroides (40%) phyla were most abundantly represented. The diversity inferred by combining the datasets was much wider than inferred by individual studies, most likely due to different diets enriching for bacteria with different fermentative activities. A total of 341 operational taxonomic units (OTU) was predicted by the Chao1 non-parametric estimator approach. Phylogenetic and database analysis demonstrated that 89% of the diversity had greatest similarity to organisms which had not been cultivated, and that several sequences are likely to represent novel taxonomic groupings. Furthermore, of the 11% of the diversity represented by cultured isolates (> 95% 16S rDNA identity), not all of the bacteria were of ruminal origin. This study therefore reinforces the need to reconcile classical culture-based rumen microbiology with molecular ecological studies to determine the metabolic role of uncultivated species.

Animals↗
PubMed1997

Analysis of the sequence diversity of the P1, HC, P3, NIb and CP genomic regions of several yam mosaic potyvirus isolates: implications for the intraspecies molecular diversity of potyviruses.

Partial sequences from serologically characterized yam mosaic potyvirus (YMV) isolates were determined in conserved (helper-component proteinase, HC; nuclear inclusion b, NIb) and variable (first protein, P1; third protein, P3; and coat protein, CP) regions of the potyviral genome in order to investigate the intraspecies molecular diversity of YMV. Multiple sequence alignments and pairwise comparisons were used to quantify the sequence polymorphism in these regions. Two levels of diversity were observed among YMV isolates: above 90% nucleotide (nt) sequence identities were found between YMV isolates of the same group (intragroup) regardless of the region considered, whereas identities between isolates from different groups (intergroup) were lower and depended upon the protein chosen. For instance, the average intergroup nt sequence identity between YMV isolates was about 65% in the P1 protein and the N terminus of the CP while there was more than 80% nt identity in the HC, P3 and NIb proteins. Thus P3 appeared to be conserved between YMV isolates even though this region was variable between potyvirus species. Similar analysis of the intraspecies molecular diversity of other potyviruses (potato virus Y, zucchini yellow mosaic virus, plum pox virus, pea seed-borne mosaic virus) led to the same results: (i) two levels of intraspecies molecular diversity were found (intragroup and intergroup); (ii) intraspecies molecular diversity differed from interspecies molecular diversity in the P3, P1 and N-terminal regions.

Amino Acid Sequence↗
PubMed1999

Analysis of the structural diversity of mycolic acids of Rhodococcus and Gordonia [correction of Gordonla] isolates from activated sludge foams by selective ion monitoring gas chromatography-mass spectrometry (SIM GC-MS)

A method using Selective Ion Monitoring (SIM) gas chromatography-mass spectrometry is described for analysis of mycolic acids which reveals a hitherto unrecognised chemical structural diversity among these in some members of the Mycolata. The structural interpretation of mass spectral data of mycolic acids from Rhodococcus spp and Gordonia [corrected] spp using SIM is discussed.

Actinomycetales↗
PubMed2006

Voice analysis of patients with diverse types of Reinke's edema and clinical use of electroglottographic measurements.

CONCLUSIONS: Reinke's edema shows a variety of clinical patterns and differences in voice analysis depending on its type. Electroglottographic measurements help to objectively assess the severity of edema and voice quality before and after surgery. OBJECTIVES: Reinke's edema manifests various clinical findings and different voice characteristics depending on the degree of swelling and the severity of voice impairment. The aim of this study was to compare the aerodynamic, acoustic and electroglottographic parameters for the different types of Reinke's edema according to its morphological, perceptual and histopathological classifications, and to assess voice quality in patients with Reinke's edema before and after laryngomicrosurgery. We also aimed to determine which parameter was most associated with the improvement in postoperative voice quality and to investigate the clinical usefulness of electroglottographic analysis in Reinke's edema. MATERIAL AND METHODS: The clinical and voice records of 61 patients with Reinke's edema were reviewed. All the patients were classified according to stroboscopic findings (Yonekawa's classification), perceptual grade and histopathological findings. Voice analysis of the perceptual, acoustic, aerodynamic and electroglottographic measurements was carried out using various classifications, and the voices of 23 patients who underwent laryngomicrosurgery were evaluated 2 months after surgery. Furthermore, the voices of 30 normal speakers (controls) were recorded and analyzed. RESULTS: The fundamental frequency (FxM) of Yonekawa Type III was significantly lower than those of the other types of Reinke's edema, and the SD of the FxM, the percentage irregularity of the FxM (CFx) and the percentage irregularity of the amplitude were larger than those of the other types of Reinke's edema. The closed quotient was significantly higher in Yonekawa Type III. In addition, the mean flow rate (MFR), maximum phonation time and harmonics:noise ratio (HNR) differed significantly among the different types of Reinke's edema. The postoperative results showed an increase in the FxM and an improvement in the MFR, subglottic pressure, shimmer and HNR. Correlation analysis showed that jitter, the HNR, the mean closed quotient and the irregularity of the frequency were the parameters that had the best correlation with improvement in postoperative voice quality.

Adolescent↗
PubMed2005

Quality of life after cystectomy and urinary diversion: an evidence based analysis.

PURPOSE: We critically examined the evidence supporting the widely accepted notion that patients undergoing continent urinary tract reconstruction after cystectomy experience superior quality of life outcomes than patients receiving a conduit. MATERIALS AND METHODS: Based on a comprehensive MEDLINE literature search we retrieved and evaluated all full-length articles published in the English, French, German, Italian and Spanish languages comparing conduit diversion with continent cutaneous diversion and/or orthotopic bladder substitution with respect to quality of life or similar concepts. All studies were rated according to the International Consultation on Urological Diseases modification of Oxford Center for Evidence-Based Medicine levels of evidence. RESULTS: The literature on quality of life after radical cystectomy for bladder cancer was rather extensive but generally of questionable quality. The main problems were flaws in the patient materials and methodologies used. To our knowledge not a single randomized, controlled study exists in the field. Because only few articles achieved a level of evidence better than III, the International Consultation on Urological Diseases rating system does not allow further differentiation among studies. Most studies showed that overall quality of life after cystectomy remained good in most patients irrespective of urinary diversion type. CONCLUSIONS: Existing studies are unable to prove that continent reconstruction after radical cystectomy is superior to conduit diversion. This review emphasizes the importance of performing well designed studies in the future.

Adaptation, Physiological↗
PubMed2007

Microarray-based analysis of changes in diversity of microbial genes involved in organic carbon decomposition following land use/cover changes.

To increase our understanding of the impact of land use/cover changes on soil microbial decomposition genes involved in organic carbon decomposition, we analyzed soil samples in four sites with different land cover/use histories in a subalpine region of western Sichuan. One site was in a primitive Abies faxoniana forest, the second and the third sites were spruce plantations established in 1960's and 1980's, respectively, and the fourth site was in a cropland dating back to 1960's. The genomic DNA from the microbial community was isolated and hybridized against a functional gene microarray containing 1,961 probes. There were 39, 62, 41, and 28 gene probes with statistically significant positive signals and the gene diversity index (H') values were 3.59, 4.04, 3.70 and 3.16 in primitive forest, spruce plantations established in 1960s and 1980s and cropland, respectively. The results suggested that the number of functional genes and the gene diversity index were correlated with increasing amounts of soil organic carbon, except in the primitive Abies faxoniana forest site. cluster analysis demonstrated that primitive forest soil was clustered more closely to soil from the spruce plantation established in 1960s.

Biodiversity↗
PubMedDate not supplied

Bariatric Analysis and Reporting Outcome System (BAROS) following biliopancreatic diversion.

BACKGROUND: The Bariatric Analysis and Reporting Outcome System (BAROS) has been recently introduced to assess the modifications of weight, comorbidities and quality of life (QOL) after bariatric surgery, in order to achieve a standard for comparison in the treatment of obesity. This study reports the Authors' experience, analyzing with BAROS a consecutive series of morbidly obese patients. METHODS: From November 1998 to February 2001, 30 patients with morbid obesity underwent biliopancreatic diversion (BPD) in our Department. Patients were followed-up after 1, 3, 6, 9, 12 months and than yearly. Modifications of the Body Mass Index (BMI), percentage of the initial excess weight loss (IEW%L), comorbidities and type and incidence of complications were measured. The course and QOL were assessed using BAROS after a minimum follow-up of 18 months, or in absence of IEW%L modification at two consecutive scheduled visits. RESULTS: According to the BAROS, the outcome was classified as Excellent in 10% of cases, Very Good in 63.3%, Good in 20%, Fair in 6.7%; no patients had Failure course. Ninety-three percent of patients had resolution of at least one of their major comorbidities, and an improvement of the medical conditions was registered in all the cases. The QOL was greatly improved in 55%, improved in 35% and did not change in 10% of the patients. CONCLUSION: BPD provides effective weight loss, improvement or resolution of major co-morbidities and increases the QOL of morbidly obese patients. BAROS is an useful tool to assess the outcome after bariatric surgery.

Adult↗
PubMed2004

DIVAA: analysis of amino acid diversity in multiple aligned protein sequences.

MOTIVATION: Multiple alignments of proteins are an effective way of identifying conserved amino acids that provide clues to functional relationships among proteins. Quantitation of the abundances of amino acids found at each position in a sequence motif can provide a basis for understanding the structural and functional constraints at each point. Distribution of information across a motif has been used previously, but the non-intuitive nature of the analysis has limited its impact. RESULTS: Here, we introduce a quantitative measure of amino acid sequence diversity (DIVAA) that has a simple, intuitive meaning. Diversity, as a measure of sequence conservation or variation, is inextricably linked to the probability of selecting identical pairs from a distribution. We demonstrate its utility through the analysis of four populations: ATP-binding P-loops, hypervariable domains of kappa light chains, signal sequences, and the N- and C- termini of proteins. DIVAA provides a simple means to generate hypotheses concerning the contribution of individual residues to the functional and evolutionary relationships among proteins. AVAILABILITY: Access to DIVAA software is available at RELIC (http://relic.bio.anl.gov).

Algorithms↗
PubMed1998

Genetic diversity in porcine Oesophagostomum dentatum and O. quadrispinulatum and their delineation by isoenzyme analysis.

The genetic diversity in eight strains of Oesophagostomum dentatum and O. quadrispinulatum was investigated by the electrophoresis study of ten enzyme systems. The loci Idh-2, Fbp, Sdh, and Pgm were found to be diagnostic between the species examined. Both the proportion of fixed allelic differences (26.3%) and the genetic distance coefficient (D = 0.54) are well above the range for differentiation of valid species. Isoenzyme patterns of susceptible and resistant lines of O. dentatum showed at polymorphic loci a reduced genetic heterogeneity in the latter group. No qualitative difference in terms of the presence/absence of alleles was observed among susceptible and resistant isolates with the enzymes studied. The detection of one possible hybrid indicates that introgression in O. dentatum and O. quadrispinuatum may occur.

Alleles↗
PubMed2002

Variations of plant life form diversity along the Northeast China Transect and its direct gradient analysis.

Plant life form diversity and its direct gradient analysis on a larger scale climate change gradient were tested, based on the data from Northeast China Transect platform. The results showed that the species numbers, life form richness and life form diversity were relative higher at the eastern forests and the ecotone between typical vegetation, while those on the meadow grasslands and typical steppes were lower. Although plant life forms can reflect the climate variations, life form diversity is not consistent with the major global gradient along the NECT.

China↗