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PubMed2003

Gibbs Recursive Sampler: finding transcription factor binding sites.

The Gibbs Motif Sampler is a software package for locating common elements in collections of biopolymer sequences. In this paper we describe a new variation of the Gibbs Motif Sampler, the Gibbs Recursive Sampler, which has been developed specifically for locating multiple transcription factor binding sites for multiple transcription factors simultaneously in unaligned DNA sequences that may be heterogeneous in DNA composition. Here we describe the basic operation of the web-based version of this sampler. The sampler may be acces-sed at http://bayesweb.wadsworth.org/gibbs/gibbs.html and at http://www.bioinfo.rpi.edu/applications/bayesian/gibbs/gibbs.html. An online user guide is available at http://bayesweb.wadsworth.org/gibbs/bernoulli.html and at http://www.bioinfo.rpi.edu/applications/bayesian/gibbs/manual/bernoulli.html. Solaris, Solaris.x86 and Linux versions of the sampler are available as stand-alone programs for academic and not-for-profit users. Commercial licenses are also available. The Gibbs Recursive Sampler is distributed in accordance with the ISCB level 0 guidelines and a requirement for citation of use in scientific publications.

Algorithms↗
PubMed2004

Nested clade and phylogeographic analyses of the Chagas disease vector Triatoma brasiliensis in Northeast Brazil.

Triatoma brasiliensis (Hemiptera: Reduviidae: Triatominae) is the most important Chagas disease vector in the semiarid areas of Northeast Brazil. We analyzed mitochondrial cytochrome b sequence variation among 136 individuals representing 16 populations from across the species' distribution. Neighbor-joining and parsimony tree-building methods were used in conjunction with nested clade analysis to describe the systematics and phylogeography of this species. Our results indicate that T. brasiliensis is composed of four genetically distinct chromatic forms (referred to as brasiliensis, macromelasoma, juazeiro, and melanica) that present inter-population divergence values (0.027-0.119, corrected K2-p) and a pattern of haplotype geographic distribution compatible with the existence of a species complex. As a consequence, such forms can be treated as isolated targets in vector control programs. We were unable to infer what is shaping the population structure of the brasiliensis form as we obtained mutually exclusive causes of structure, namely a barrier to gene flow caused by past population fragmentation, and isolation by distance between populations (which would permit gene flow). We found indication of mitochondrial DNA introgression occurring among forms in putative hybrid zones.

Animals↗
PubMed1993

Correlation of the alpha-lactalbumin (+15) polymorphism to milk production and milk composition of Holsteins.

The alpha-lactalbumin (+15) polymorphism (a single base variation 15 basepairs 3' of the alpha-lactalbumin transcription start point) was examined for its usefulness as a genetic marker for Holsteins. The +15 polymorphism is located in a region of the gene that is potentially involved in the regulation of alpha-lactalbumin gene expression. Animals from two dairy herds and young sires from progeny-testing programs of four AI organizations were used in the analysis. A group of sons from a heterozygous sire were also evaluated. Each individual animal was genotyped at the alpha-lactalbumin (+15) locus, and differences of genotypes were investigated. Estimated differences among alleles were calculated for PTA for milk, kilograms of protein, protein percentage, protein dollars, kilograms of fat, fat percentage, and fat dollars. Animals having the alpha-lactalbumin (+15) AA (an adenine on both alleles at position +15) genotype had statistically higher PTA for milk, kilograms of protein, protein dollars, kilograms of fat, and fat dollars than did the alpha-lactalbumin (+15) BB (a cytosine, guanine, or thymine on both alleles at position +15) animals. The alpha-lactalbumin (+15) BB animals had higher protein and fat percentages than the alpha-lactalbumin (+15) AA animals. Animals that were heterozygous at this locus, alpha-lactalbumin (+15) AB, had intermediate values for all traits analyzed. These results indicate a potential marker or actual locus effect of the alpha-lactalbumin (+15) polymorphism in Holstein cattle.

Animals↗
PubMed2025

The CAP/ACMG CYCGH proficiency testing program: 10 years in review.

PURPOSE: The College of American Pathologists has offered proficiency testing (PT) for the detection of copy-number variations (CNV) in the constitutional setting (CYCGH) since 2008. We review and summarize data from the CYCGH PT program, including participant performance over time, changes made to the program, and ungraded challenges. METHODS: The PT challenges from 2011 through 2021 (22 total mailings) and changes to the program over time were reviewed. Laboratory enrollment and performance were assessed. RESULTS: Overall participation has increased over time, and laboratories have maintained a high level of proficiency. The major changes to the program have occurred twice during the time span examined. Reasons for challenges not meeting consensus were varied. The use of ungraded challenges was also discussed. CONCLUSION: The CYCGH PT program is challenging because it assesses both analytical performance and interpretation as a single analyte. The program has evolved over time to address the changes in the field of CNV detection. During this time, additional technologies with the ability to detect CNVs have emerged, and the possibility of developing a platform-agnostic CNV PT program is being explored.

Humans↗
PubMedDate not supplied

Prospects of breeding small ruminants for resistance to internal parasites.

Resistance to nematode parasites can be improved by selection, but efforts to include appropriate traits in commercial livestock breeding programs are only a recent development. Procedures for including resistance in breeding programs are similar to those involving other traits. The steps are described with special reference to sheep, and areas are highlighted where particular considerations exist. Three approaches are described and contrasted: breeding for resistance (reduced parasite numbers, as determined by faecal worm egg count); resilience (production during parasitism); or number of treatments required during parasitism. It is necessary, but difficult, to assess the economic benefits of improving resistance relative to other traits. Disease costs vary widely depending on the prevalence of the disease and on the availability, effectiveness and sustainability of alternative control measures. Costs of treatment and control are relatively simple to estimate for a given situation, but production losses are more difficult. Methods of dealing with this problem are discussed. Breeding for disease resistance usually requires that either selection candidates, or their relatives, are exposed to the pathogen so that resistance levels can be compared. Parasitic diseases generally create no special ethical problems in a breeding program unless natural challenge levels are insufficient to enable discrimination between hosts in their susceptibility. In the longer term, it is desirable that selection criteria for all major diseases be developed that will be informative in healthy animals. Molecular genetic markers offer promise, but simple genetic markers have so far been as elusive as physiological traits to predict resistance in undiseased animals. In the longer term, useful genetic markers will be found and techniques for combining these with phenotypic information need to be developed. Commercial breeding programs for sheep which include resistance to gastrointestinal roundworms are now operating in Australia and New Zealand, and issues related to breeding in the tropics are discussed.

Animals↗
PubMed2002

Animal genetic resources in Brazil: result of five centuries of natural selection.

Brazil has various species of domestic animals, which developed from breeds brought by the Portuguese settlers soon after their discovery. For five centuries, these breeds have been subjected to natural selection in specific environments. Today, they present characteristics adapted to the specific Brazilian environmental conditions. These breeds developed in Brazil are known as "Crioulo," "local," or naturalized. From the beginning of the 20th century, some exotic breeds, selected in temperate regions, have begun to be imported. Although more productive, these breeds do not have adaptive traits, such as resistance to disease and parasites found in breeds considered to be "native." Even so, little by little, they replaced the native breeds, to such an extent that the latter are in danger of extinction. In 1983, to avoid the loss of this important genetic material, the National Research Center for Genetic Resources and Biotechnology (Cenargen) of the Brazilian Agricultural Research Corporation (Embrapa) decided to include conservation of animal genetic resources in its research program Conservation and Utilization of Genetic Resources. Until this time, they were only concerned with conservation of native plants. Conservation has been carried out by various research centers of Embrapa, universities, state research corporations, and private farmers, with a single coordinator at the national level, Cenargen. Specifically, conservation is being carried out by conservation nuclei, which are specific herds in which the animals are being conserved, situated in the habitats where the animals have been subjected to natural selection. This involves storage of semen and embryos from cattle, horses, buffaloes, donkeys, goats, sheep, and pigs. The Brazilian Animal Germplasm Bank is kept at Cenargen, which is responsible for the storage of semen and embryos of various breeds of domestic animals threatened with extinction, where almost 45,000 doses of semen and more than 200 embryos exist presently. An important challenge for this program is to make the different segments of society realize the importance of the conservation of animal genetic resources.

Adaptation, Physiological↗
PubMed2003

Which genetic loci have greater population assignment power?

SUMMARY: WHICHLOCI is a program that determines the relative discriminatory power of alternate genetic loci and loci combinations for population assignment of individuals. AVAILABILITY: http://www.oregonstate.edu/dept/comes/genetics/software.htm

Algorithms↗
PubMed2004

Genetic epidemiology of Sarcoptes scabiei (Acari: Sarcoptidae) in northern Australia.

Utilising three hypervariable microsatellite markers we have previously shown that scabies mites on people are genetically distinct from those on dogs in sympatric populations in northern Australia. This had important ramifications on the formulation of public health control policies. In contrast phylogenetic analyses using mitochondrial markers on scabies mites infecting multiple animal hosts elsewhere in the world could not differentiate any genetic variation between mite haplotype and host species. Here we further analyse the intra-specific relationship of Sarcoptes scabiei var. hominis with S. scabiei var. canis by using both mitochondrial DNA and an expanded nuclear microsatellite marker system. Phylogenetic studies using sequences from the mitochondrial genes coding for 16S rRNA and Cytochrome Oxidase subunit I demonstrated significant relationships between S. scabiei MtDNA haplotypes, host species and geographical location. Multi-locus genotyping using 15 microsatellite markers substantiated previous data that gene flow between scabies mite populations on human and dog hosts is extremely rare in northern Australia. These data clearly support our previous contention that control programs for human scabies in endemic areas with sympatric S. scabiei var. hominis and var. canis populations must focus on human-to-human transmission. The genetic division of dog and human derived scabies mites also has important implications in vaccine and diagnostic test development as well as the emergence and monitoring of drug resistance in S. scabiei in northern Australia.

Animals↗
PubMed2006

Variation of glucosinolates in vegetable crops of Brassica rapa.

Glucosinolate levels in leaves were determined in a collection of 113 varieties of turnip greens (Brassica rapa L.) from northwestern Spain grown at two sites. Sensorial attributes were also assessed by a consumer panel. The objectives were to determine the diversity among varieties in total glucosinolate content and glucosinolate profile and to evaluate their sensory attributes in relation to glucosinolate content for breeding purposes. Sixteen glucosinolates were identified, being the aliphatic glucosinolates, gluconapin and glucobrassicanapin the most abundant. Other aliphatic glucosinolates, such as progoitrin, glucoalyssin, and gluconapoleiferin were relatively abundant in varieties with a different glucosinolate profile. Indolic and aromatic glucosinolate concentrations were low and showed few differences among varieties. Differences in total glucosinolate content, glucosinolate profile and bitterness were found among varieties, with a total glucosinolate content ranging from 11.8 to 74.0micromolg(-1) dw at one site and from 7.5 to 56.9micromolg(-1) dw at the other site. Sensory analysis comparing bitterness with variation in glucosinolate, gluconapin and glucobrassicanapin concentrations suggested that these compounds and their breakdown products are not the only determinants of the characteristic flavour of this vegetable. Other phytochemicals are probably involved on the characteristic bitter flavour. The varieties MBG-BRS0132, MBG-BRS0082, MBG-BRS0173, and MBG-BRS0184 could be good candidates for future breeding programs since they had high total glucosinolate content and good agronomic performance. The presence of glucoraphanin in some varieties should be studied more extensively, because this aliphatic glucosinolate is the precursor of sulforaphane, a potent anti-cancer isothiocyanate.

Brassica napus↗
PubMed1998

Ethnic differences in expression of susceptibility marker(s) in rheumatic fever/rheumatic heart disease patients.

The ability of monoclonal antibodies (MAb) against a human B lymphocyte alloantigen has been suggested to discriminate between rheumatic fever "susceptible" individuals and persons with a lower risk of developing RF. However, while such MAb have been reported to identify a majority of RF/RHD patients in some populations, a reduced discriminatory ability has been observed in others. Antigenic variation in the RF marker(s) may exist among ethnic groups which reduce the discriminatory ability of these monoclonal antibodies. We developed MAb using B lymphocytes from RF patients of North Indian ethnic origin. In this same population we compared the new MAb (PGI/MN II) with a previously described MAb of Caucasian ethnic origin (D8/17). In three groups: acute rheumatic fever patients (no evidence of previous attacks of rheumatic fever), patients with chronic rheumatic heart disease and normal controls from the same population, we found a greater discriminating ability of PGI/MNII MAb to identify Indian RF/RHD patients than with the D8/17 MAb. Further, sixty percent of 142 siblings of the RF/RHD patients were "positive" when tested with PGI/MN II. The data from these studies suggest that before such MAb can be used for identification of RF "susceptibles" in public health programs, variation among ethnic populations must be assessed.

Adolescent↗
PubMed2006

Entrez Gene: gene-centered information at NCBI.

Entrez Gene (www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene) is NCBI's database for gene-specific information. Entrez Gene includes records from genomes that have been completely sequenced, that have an active research community to contribute gene-specific information or that are scheduled for intense sequence analysis. The content of Entrez Gene represents the result of both curation and automated integration of data from NCBI's Reference Sequence project (RefSeq), from collaborating model organism databases and from other databases within NCBI. Records in Entrez Gene are assigned unique, stable and tracked integers as identifiers. The content (nomenclature, map location, gene products and their attributes, markers, phenotypes and links to citations, sequences, variation details, maps, expression, homologs, protein domains and external databases) is provided via interactive browsing through NCBI's Entrez system, via NCBI's Entrez programing utilities (E-Utilities), and for bulk transfer by ftp.

Databases, Genetic↗
PubMed2002

Differential expression of glycosaminoglycans and proteoglycans in the migratory pathway of the primordial germ cells of the mouse.

Primordial germ cells are an embryonic cell line that give rise to gametes in vertebrates. They originate outside the embryo proper and migrate by a well-defined route to the genital ridges. Proteoglycans and glycosaminoglycans have distinctive properties that affect many of the characteristics of the extracellular microenvironment of migratory pathways in a variety of developmental systems. The purpose of this work was to identify the proteoglycans and glycosaminoglycans that are spatially and temporally expressed in the migratory pathway of primordial germ cells. We showed that the expression of proteoglycans and glycosaminoglycans in the primordial germ cells migratory pathway changes according to the different phases of the migratory process. Some molecules such as chondroitin-0-sulfate, decorin, and biglycan are present only in certain phases of the migratory process of primordial germ cells. Heparan sulfate, chondroitin-6-sulfate, versican, perlecan, and syndecan-4, although exhibiting some variation in expression were detected during all phases of the migratory process. Our results indicate that the successive steps of primordial germ cell migration require a coordinated expression of proteoglycans and glycosaminoglycans, that should be present in appropriate levels and in specific areas of the embryo, and that the sequential expression of these extracellular matrix molecules is under a genetic program that appears to be common to a variety of cell types during embryonic development.

Animals↗
PubMed1989

Development of molecular approaches to estimating germinal mutation rates. I. Detection of insertion/deletion/rearrangement variants in the human genome.

DNA from 130 individuals was studied with up to 18 (primarily cDNA) probes for the frequency of variants in this initial experiment to determine the feasibility of this approach to screening for germinal gene mutations. This approach, a modification of the usual restriction enzyme mapping strategy, focuses on the detection of insertion/deletion/rearrangement (I/D/R) variants, because the DNA is digested with only two restriction enzymes before transfer to membranes and hybridization with an extensive series of unrelated probes. Some 4000 noncontiguous, independent DNA fragments ("loci"), functional loci, pseudogenes or anonymous fragments, (a total of approximately 77,400 kb) were screened. 19 different classes and 31 copies of presumably I/D/R variants were detected while 4 different classes and 24 individuals exhibiting base substitution variants were observed. 18 of the 19 I/D/R classes were rare variants, that is, each were observed at a frequency, within this population, of less than 0.01; 3 of the base substitution classes existed at polymorphic frequencies and only 1 was a rare variant. 10 of the I/D/R classes, occurring in a total of 18 individuals, were detected with probes which are not known to be associated with repetitive elements. This is a variant frequency for I/D/R variants without known repetitive elements of 0.15 classes and 0.23 copies for each 1000 kb screened; this would extrapolate to 1600 such variant sites in the genome of each individual. Within the context of a mutation screening program, the rare variants, either with or without repetitive elements, would have a higher probability of being de novo mutations than would polymorphic variants; this former group would be the focus of family studies to test for the heritability of the allele (fragment pattern). Sufficient DNA probes are available to screen a significant portion of the human genome for genetic variation and de novo mutations of this type.

Blotting, Southern↗
PubMed2000

The impact of COPD on lung health worldwide: epidemiology and incidence.

Information on the prevalence of COPD was obtained from vital statistics, health interview surveys, hospital charge records, national publications, and the World Health Organization (WHO). These data indicate that COPD is a common disease with implications for global health. In the United States, morbidity caused by COPD is 4%, making COPD the fourth leading cause of death, exceeded only by heart attacks, cancer, and stroke. Internationally, there is substantial variation in death rates possibly reflecting smoking behavior, type and processing of tobacco, pollution, climate, respiratory management, and genetic factors. The Global Obstructive Lung Disease Initiative, initiated by the National Heart, Lung, and Blood Institute and the WHO, aims to raise awareness of the increasing burden of COPD, decrease morbidity and mortality, promote further study of the condition, and implement programs to prevent COPD.

Adult↗
PubMed1998

Activated calphostin C cytotoxicity is independent of p53 status and in vivo metastatic potential.

The development of novel therapeutic agents to modulate programmed cell death independent of genetic background or malignant potential is a primary goal of modern cancer therapy. In this report, the light activation- and concentration-dependent cytotoxicity of calphostin C, a photoactivatable perylenequinone, is carefully evaluated using a series of nine well-characterized human and rodent prostate cancer cell lines representing the spectrum of disease progression (e.g., variations in metastatic ability, ploidy, and tumor suppressor gene status). Treatment of these cancer cell lines with nanomolar concentrations of calphostin C in combination with increasing amounts of light exposure established a relationship between light and dose dependence of calphostin C cytotoxicity. The induction of apoptosis is rapid, as evidenced by the fact that immediately after treatment, cells exposed to calphostin C with light activation exhibit both morphological and biochemical changes consistent with apoptosis (cellular and nuclear shrinkage and chromatin condensation). For example, 78% of cells treated with 100 nM calphostin C in combination with 2 h of light activation underwent apoptosis within 24 h of treatment. DNA ladder formation could be detected within 12 h of treatment. In the absence of light activation, treatment with calphostin C at all concentrations tested had no acute or durable cytotoxic effects in any of the cell lines. Our findings demonstrate that calphostin C cytotoxicity is strictly light dependent. Furthermore, its efficacy is independent of the genetic background, p53 status, or in vivo malignant potential of a cell, making it a suitable candidate for the treatment of heterogeneous tumor cell populations.

Animals↗
PubMed1997

Inferring the conformation of RNA base pairs and triples from patterns of sequence variation.

The success of comparative analysis in resolving RNA secondary structure and numerous tertiary interactions relies on the presence of base covariations. Although the majority of base covariations in aligned sequences is associated to Watson-Crick base pairs, many involve non-canonical or restricted base pair exchanges (e.g. only G:C/A:U), reflecting more specific structural constraints. We have developed a computer program that determines potential base pairing conformations for a given set of paired nucleotides in a sequence alignment. This program (ISOPAIR) assumes that the base pair conformation is maintained through sequence variation without significantly affecting the path of the sugar-phosphate backbone. ISOPAIR identifies such 'isomorphic' structures for any set of input base pair or base triple sequences. The program was applied to base pairs and triples with known structures and sequence exchanges. In several instances, isomorphic structures were correctly identified with ISOPAIR. Thus, ISOPAIR is useful when assessing non-canonical base pair conformations in comparative analysis. ISOPAIR applications are limited to those cases where unusual base pair exchanges indeed reflect a non-canonical conformation.

Base Composition↗
PubMed1993

A biochemical marker for differentiation is present in an in vitro aging cell system.

In this study it is shown that in an in vitro aging cell system of human diploid fibroblasts the ratio of the histone variants H2A.1/H2A.2 decreases in a linear manner as a function of cumulative population doublings This ratio is known to decrease during differentiation. This finding reinforces the theory that cellular aging is a result of differentiation and programmed cell death rather than degeneration.

Biomarkers↗
PubMed2006

Computation of individual latent variable scores from data with multiple missingness patterns.

Latent variable models are used in biological and social sciences to investigate characteristics that are not directly measurable. The generation of individual scores of latent variables can simplify subsequent analyses. However, missing measurements in real data complicate the calculation of scores. Missing observations also result in different latent variable scores having different degrees of accuracy which should be taken into account in subsequent analyses. This manuscript presents a publicly available software tool that addresses both these problems, using as an example a dataset consisting of multiple ratings for ADHD symptomatology in children. The program computes latent variable scores with accompanying accuracy indices, under a 'user-specified' structural equation model, in data with missing data patterns. Since structural equation models encompass factor models, it can also be used for calculating factor scores. The program, documentation and a tutorial, containing worked examples and specimen input and output files, is available at http://statgen.iop.kcl.ac.uk/lsc .

Attention Deficit Disorder with Hyperactivity↗