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PubMed1993

Estimating locus heterogeneity in autosomal dominant polycystic kidney disease (ADPKD) in the Spanish population.

Although most mutations causing ADPKD in European populations have been mapped to the PKD1 locus on chromosome 16, some of them appear to be unlinked to this locus. To evaluate the incidence of unlinked mutations in Spain we have typed 31 Spanish families from different geographical sites for six closely linked DNA polymorphic marker loci flanking PKD1 detected by probes D16S85, D16S21, D16S259, D16S125, D16S246, and D16S80. Multilocus linkage analysis indicated that in 26 families the disease resulted from PKD1 mutations, whereas in three families it resulted from mutations in a locus other than PKD1. The two other families were not informative. Using the HOMOG test, the incidence of the PKD1 linked mutations in Spain is 85%. Multipoint linkage analysis in the 26 PKD1 families showed that the disease locus lies in the interval between D16S259(pGGG1) and D16S125(26.6).

Alleles↗

PubMed1989

Transposable elements and fitness in Drosophila melanogaster.

Transposable elements constitute a significant fraction of the Drosophila melanogaster genome. The five families of moderately repeated transposable elements identified to date occupy dispersed and variable genomic locations, but have relatively constant copy numbers per individual. What effect to these elements have on the fitness of the individuals harboring them? Experimental evidence relating to this question is reviewed. The relevant data fall into two broad categories. The first involves the determination of the distribution of transposable elements in natural populations, by restriction mapping or in situ hybridization, and the comparison of the observed distribution with different theoretical expectations. The second approach is to study directly the effects of new transposable element-induced mutations on fitness. The P family of transposable elements is a particularly efficient mutagen, and the results of experiments in which initially P-free chromosomes are contaminated with P elements are discussed with regard to P-induced fitness mutations.

Animals↗

PubMed1994

Occurrence and inheritance of microsatellites in Pinus radiata.

Microsatellites are an important class of DNA marker because of their abundance and length hypervariability. As part of a project mapping the Pinus radiata genome, we have characterized some of the microsatellites in this species. Southern blots were screened with oligonucleotide probes [(CA)10, (GA)10, (GAA)9, (CAA)8, (CAC)5, (GACA)4] to assess their abundance. CA and GA were the most abundant microsatellites, while GAA was least abundant. A genomic library in lambda ZAP, covering 9 x 10(4) kb, was screened with a combined poly(CA) + poly(GA) probe and yielded 120 positives, approximately one CA or GA microsatellite every 750 kb of the P. radiata genome. It was found that 25% of the positives were embedded within highly repetitive DNA. Four of the five subclones sequenced contained compound microsatellites, with TA predominating as the additional repeat. Segregation analysis of PCR products for two microsatellites, PR4.6 and PR9.3, in 96 progeny of a controlled outcross verified simple Mendelian inheritance. Both loci are highly polymorphic with Polymorphism Information Content values of 0.63 and 0.70 for PR4.6 and PR9.3, respectively. These results indicate that microsatellites are abundant in a conifer genome and can be valuable markers for pine mapping, fingerprinting, and population genetic studies.

Base Sequence↗

PubMed1999

Distribution of Fos immunoreactivity in rat brain after sodium consumption induced by peritoneal dialysis.

Fos immunoreactivity was used to map the neuronal population groups activated after sodium ingestion induced by peritoneal dialysis (PD) in rats. Oxytocin immunoreactivity in combination with Fos immunoreactivity was also analyzed to evaluate whether the oxytocinergic neurons of the paraventricular nucleus of the hypothalamus (PVN) are activated during the satiety process of sodium appetite. Sodium ingestion stimulated by PD produced Fos immunoreactivity within defined cells groups of the lamina terminalis and hindbrain areas such us the nucleus of the solitary tract, area postrema, and lateral parabrachial nucleus. On the other hand, particular parvocellular and magnocellular oxytocinergic subdivisions of the PVN and supraoptic nucleus were double labeled after PD-induced sodium consumption. Approximately 27 and 2.1%, respectively, of the activated dorsomedial cap and parvocellular posterior subnuclei of the PVN, which project to the hindbrain, were oxytocinergic. Our data indicate that specific neuronal groups are activated during the satiety process of sodium appetite, suggesting they may form a circuit subserving sodium balance regulation. They also support a functional role for the oxytocinergic neurons in this circuit.

Administration, Oral↗

PubMed2007

Separation of base allele and sampling term effects gives new insights in variance component QTL analysis.

BACKGROUND: Variance component (VC) models are commonly used for Quantitative Trait Loci (QTL) mapping in outbred populations. Here, the QTL effect is given as a random effect and a critical part of the model is the relationship between the phenotypic values and the random effect. In the traditional VC model, each individual has a unique QTL effect and the relationship between these random effects is given as a covariance structure (known as the identity-by-descent (IBD) matrix). RESULTS: We present an alternative notation of the variance component model, where the elements of the random effect are independent base generation allele effects and sampling term effects. The relationship between the phenotypic vales and the random effect is given by an incidence matrix, which results in a novel, but statistically equivalent, version of the traditional VC model. A general algorithm to estimate this incidence matrix is presented. Since the model is given in terms of base generation allele effects and sampling term effects, these effects can be estimated separately using best linear unbiased prediction (BLUP). From simulated data, we showed that biallelic QTL effects could be accurately clustered using the BLUP obtained from our model notation when markers are fully informative, and that the accuracy increased with the size of the QTL effect. We also developed a measure indicating whether a base generation marker homozygote is a QTL heterozygote or not, by comparing the variances of the sampling term BLUP and the base generation allele BLUP. A ratio greater than one gives strong support for a QTL heterozygote. CONCLUSION: We developed a simple presentation of the VC QTL model for identification of base generation allele effects in QTL linkage analysis. The base generation allele effects and sampling term effects were separated in our model notation. This clarifies the assumptions of the model and should also enhance the development of genome scan methods.

Alleles↗

PubMed2006

Survey and analysis of microsatellites from transcript sequences in Phytophthora species: frequency, distribution, and potential as markers for the genus.

BACKGROUND: Members of the genus Phytophthora are notorious pathogens with world-wide distribution. The most devastating species include P. infestans, P. ramorum and P. sojae. In order to develop molecular methods for routinely characterizing their populations and to gain a better insight into the organization and evolution of their genomes, we used an in silico approach to survey and compare simple sequence repeats (SSRs) in transcript sequences from these three species. We compared the occurrence, relative abundance, relative density and cross-species transferability of the SSRs in these oomycetes. RESULTS: The number of SSRs in oomycetes transcribed sequences is low and long SSRs are rare. The in silico transferability of SSRs among the Phytophthora species was analyzed for all sets generated, and primers were selected on the basis of similarity as possible candidates for transferability to other Phytophthora species. Sequences encoding putative pathogenicity factors from all three Phytophthora species were also surveyed for presence of SSRs. However, no correlation between gene function and SSR abundance was observed. The SSR survey results, and the primer pairs designed for all SSRs from the three species, were deposited in a public database. CONCLUSION: In all cases the most common SSRs were trinucleotide repeat units with low repeat numbers. A proportion (7.5%) of primers could be transferred with 90% similarity between at least two species of Phytophthora. This information represents a valuable source of molecular markers for use in population genetics, genetic mapping and strain fingerprinting studies of oomycetes, and illustrates how genomic databases can be exploited to generate data-mining filters for SSRs before experimental validation.

Codon↗

PubMed2005

On the genetic involvement of apoptosis-related genes in Crohn's disease as revealed by an extended association screen using 245 markers: no evidence for new predisposing factors.

Crohn's disease (CD) presents as an inflammatory barrier disease with characteristic destructive processes in the intestinal wall. Although the pathomechanisms of CD are still not exactly understood, there is evidence that, in addition to e.g. bacterial colonisation, genetic predisposition contributes to the development of CD. In order to search for predisposing genetic factors we scrutinised 245 microsatellite markers in a population-based linkage mapping study. These microsatellites cover gene loci the encoded protein of which take part in the regulation of apoptosis and (innate) immune processes. Respective loci contribute to the activation/suppression of apoptosis, are involved in signal transduction and cell cycle regulators or they belong to the tumor necrosis factor superfamily, caspase related genes or the BCL2 family. Furthermore, several cytokines as well as chemokines were included. The approach is based on three steps: analyzing pooled DNAs of patients and controls, verification of significantly differing microsatellite markers by genotyping individual DNA samples and, finally, additional reinvestigation of the respective gene in the region covered by the associated microsatellite by analysing single-nucleotide polymorphisms (SNPs). Using this step-wise process we were unable to demonstrate evidence for genetic predisposition of the chosen apoptosis- and immunity-related genes with respect to susceptibility for CD.

Alleles↗

PubMed2025

Analysis of ferroptosis-related genes in cerebral ischemic stroke via immune infiltration and single-cell RNA-sequencing.

Ischemic stroke (IS) represents a harmful neurological disorder with limited treatment options. Ferroptosis accounts for the iron-dependent, nonapoptotic cell death pattern, which shows the feature of fatal lipid ROS accumulation. Nonetheless, ferroptosis-related biomarkers for identifying IS early are currently lacking. The present study focused on investigating the possible ferroptosis-related biomarkers for IS and analyzing their effects on immune infiltration. Altogether five hub differentially expressed ferroptosis-related genes (DEFRGs) were identified from the relevant databases. Additionally, single-cell RNA-sequencing (seq) analysis was conducted for the comprehensive mapping of cell populations based on the IS database. These five hub DEFRGs were analyzed using gene set enrichment analysis, miRNA prediction, and single-cell RNA-seq analysis. A transient middle cerebral artery occlusion mouse model was constructed. We also adopted bioinformatics methods combined with western blot, changes to mitochondria, hematoxylin & eosin staining, Nissl staining, ROS fluorescence staining, immunohistochemistry, and quantitative real-time polymerase chain reaction (qRT-PCR) to show the involvement of ferroptosis in IS progression. The results revealed that nuclear factor erythroid-derived 2-like 2 (Nfe2l2) was the potential candidate biomarker for IS diagnosis, and ferroptosis may be suppressed via the Nfe2l2/HO-1 pathway. Thus, drug targeting Nfe2l2 can shed novel lights on IS treatment.

Ferroptosis↗

PubMed2004

Biethnic comparisons of autosomal genomic scan for loci linked to plasma adiponectin in populations of Chinese and Japanese origin.

Adiponectin is secreted by adipocytes and is thought to have insulin-sensitizing and antiatherogenic effects. Two previous genome scans for plasma adiponectin have identified different regions for European and Pima Indian populations. We here present multipoint linkage analysis of adiponectin levels using a variance-components model for 1007 siblings (from 360 nuclear families) of Chinese origin and 352 siblings (from 147 nuclear families) of Japanese origin. We found heritability for adiponectin concentrations was 0.70 for Chinese and 0.48 for Japanese. Autosomal genome scan was performed using microsatellite markers span at an interval of approximately 10 cM. Suggestive linkage of adiponectin, after adjusting for age and sex, was found on chromosome 15 at 39 cM (maximal LOD score = 3.19, P = 6.3 x 10(-5)) for Chinese; and on chromosome 18 at 28 cM (maximal LOD score = 2.40, P = 4.4 x 10(-4)) for Japanese. There were tentative loci of weak linkage on chromosomes 3, 18, and 20 in Japanese. We provide novel loci on chromosomes 15, 18, and 20 and confirm a region on chromosome 3 as reported in Pima Indians, which may influence differentially on circulating adiponectin concentrations in Chinese and Japanese populations. Further fine mapping of these regions will help to identify the gene(s) that might affect adiponectin levels.

Adiponectin↗

PubMed2005

Meat quality traits were unaffected by a quantitative trait locus affecting leg composition traits in Texel sheep.

A QTL affecting leg muscle and fat traits has been identified within the New Zealand Texel population. The QTL maps to a region on OAR 2 with a two-marker haplotype test established at markers BULGE20 and BM81124. These markers encompass the likely position of Growth Differentiation Factor 8 (GDF8). The pleiotropic effects of this QTL on meat quality traits are tested. Objective measures of meat quality including pH, color (L*, a*, and b*), and tenderness (as assessed by Warner-Bratzler shear force measurements) were assessed on longissimus and semi-membranosus muscles of 540 progeny from six Texel sires. Four of these sires were subsequently identified as segregating for leg muscle and fat traits. For these segregating sires, comparison of progeny that had inherited the favorable haplotype from their sire with those that had received the alternate haplotype revealed no significant differences in the meat quality traits assessed. This finding suggests that the muscling QTL does not have pleiotropic effects on meat quality. A general scan for meat quality QTL was carried out using genotype data for eight markers from FCB128 to RM356 flanking 122cM of OAR 2 using Haley-Knott regression. This analysis revealed two QTL for a single sire. A QTL detected in the region of Marker INRA40 for color L* mapped to a site close to the muscling QTL, but there was evidence to suggest it is at a distinct locus. The QTL in the region of Marker RM356 might map distal to Marker RM356, as no peak was observed. This QTL, which seems to affect pH, color a*, color b*, and Warner-Bratzler shear measurements, requires further characterization.

Animals↗

PubMed2002

Modular response analysis of cellular regulatory networks.

The sheer complexity of intracellular regulatory networks, which involve signal transducing, metabolic, and genetic circuits, hampers our ability to carry out a quantitative analysis of their functions. Here, we describe an approach that greatly simplifies this type of analysis by capitalizing on the modular organization of such networks. Steady-state responses of the network as a whole are accounted for in terms of intermodular interactions between the modules alone; processes operating solely within modules need not be considered when analysing signal transfer through the entire network. The intermodular interactions are quantified through (local) response coefficients which populate an interaction map (matrix). This matrix can be derived from a biochemical or molecular biological analysis of (macro) molecular interactions that constitute the regulatory network. The approach is illustrated by two examples: (i) mitogenic signalling through the mitogen-activated protein kinase cascade in the epidermal growth factor receptor network and (ii) regulation of ammonium assimilation in Escherichia coli.

Animals↗

PubMed2002

[Bacteriological investigations about paratuberculosis in dairy herds in Switzerland].

In Switzerland clinical bovine paratuberculosis is registered sporadically with on average seven outbreaks per year. Our present studies are aimed to investigate the prevalence of Mycobacterium avium ssp. paratuberculosis (MAP)-infections in the Swiss cattle population and, therefore methods to culture MAP from bovine feces as well as a commercially available ELISA to detect MAP-specific antibodies are evaluated by using fecal samples and blood sera from herds with cases of clinical paratuberculosis. A series of molecular methods i.e. PCR-coupled RFLP analysis of the IS1311-insertion element of M. avium, PCR-coupled RFLP-analysis of the mycobacterial rpoB-gene, and DNA analysis of the mycobacterial 16S rRNA gene are used to identify mycobacterial isolates grown from bovine feces. Up to now, MAP was detected by culture in 12 of 155 (7.7%) animals from herds with paratuberculosis. A rather striking result is the finding of atypical mycobacteria in feces of 75 cattle (48.3%). Among these isolates, M. avium ssp. avium, M. thermoresistibile, and M. hassiacum/M. buckleii have been identified so far.

Animals↗

PubMedDate not supplied

[The genetic structure of the European goldfish Carassius auratus s. lato (Cyprinidae) in Ukrainian water bodies: an analysis of bisexual samples].

Biochemical gene mapping of goldfish populations in the middle Dnieper basin demonstrated that 8 out of 17 studied enzyme and protein systems are uncoded by duplicated loci and two of them represent isoloci. Noteworthily, the heterozygosity in the studied goldfish samples was significantly higher than the average for bony fish (Hexp = 0.128, 0.135). Cytometric analysis of the samples demonstrated that one of them includes about 20% of presumably triploid females that, nevertheless, did not demonstrate a common electrophoretic pattern of the polymorphic loci, which is typical for unisexual parthenogenetic forms. Moreover, no additional gene applications (constant heterozygotes), unique alleles (diagnostic patterns), or stable manifestation of a gene dose effect were revealed in the polyploid females. Several hypotheses were proposed to explain such unusual structure of triploid parthenogenetic individuals.

Animals↗

PubMed2006

[Evaluation of morphological traits on near-isogenic lines of cold tolerance and molecular validation at booting stage in Japonica rice].

Five parents and their near-isogenic lines (NILs) were grown in field experiments in Kunming (elevation 1916 m, two kinds of water temperatures at booting stage were 19.5 +/- 0.7 degrees C and 17.8 +/- 1.1 degrees C) and Aziying (elevation 2150 m, water temperature at booting stage was 18.2 +/- 0.22 degrees C), Yunnan, China, in 2004. Seventeen agronomic traits and SSR molecular markers were clustered by Statistica. The results showed that: (1) The morphological traits of NILs of cold tolerance and recurrent parents (Towada) at booting stage were similar, but the traits related cold tolerance, such as spike neck length, full grains, seed setting rate, anther length, anther volume, were different obviously; (2) using 7 markers had polymorphism between Towada and NILs were chosen from 78 SSR markers, the cold tolerance of NILs proved to be different to Towada. This demonstrates that these NILs were promising population for fine mapping and cloning genes for cold tolerance.

Breeding↗

PubMed1990

Head-direction cells recorded from the postsubiculum in freely moving rats. II. Effects of environmental manipulations.

The discharge characteristics of postsubicular head-direction cells in a fixed environment were described in the previous paper (Taube et al., 1990). This paper reports changes in the firing properties of head-direction cells following changes in the animal's environment. Head-direction cells were recorded from rats as they moved freely in a 76-cm-diameter gray cylinder. A white card, occupying 100 degrees of arc, was taped to the inside wall of the cylinder and served as the major orienting spatial cue in the animal's environment. Rotation of the cue card produced near-equal rotation in the preferred firing direction of head-direction cells, with minimal changes in peak firing rate, directional firing range, or asymmetry of the firing-rate/head-direction function. Card removal had no effect on peak firing rate or range of firing, but in 8/13 cells the preferred direction rotated by at least 24 degrees. Similarly, changing the shape of the environment to a rectangular or square enclosure caused the preferred firing direction to rotate by at least 48 degrees for 8/10 cells in the rectangle and 3/8 cells in the square, with minimal changes in the peak firing rate or directional firing range. Hand holding the animals and moving them around the cylinder had no effect on the preferred direction or firing range of the cell, but decreased the maximal firing rate in 7/9 cells. On 2 occasions, 2 head-direction cells were recorded simultaneously. The rotation of the preferred firing direction for one cell was the same as the rotation of the preferred direction for the second cell after each environmental manipulation. These results demonstrate that specific visual cues in the environment can exert control over the preferred firing direction and indicate that head-direction cell firing is not a simple sensory response to visual cues, but rather represents more abstract information concerning the animal's spatial relationship with its environment. The constancy of the angle between the preferred firing directions of pairs of simultaneously recorded head-direction cells suggests that there is a fixed mapping of the population onto direction within the environment. Thus, environmental manipulations appear to cause only a change in the reference direction, but leave all other discharge characteristics of directional cells unchanged. In the discussion, comparisons are drawn between the responses of head-direction cells and hippocampal place cells to similar environmental manipulations (Muller and Kubie, 1987), and ways in which these 2 spatial systems interact in navigation are discussed.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗

PubMed1984

Immunoglobulin light chain classes in a teleost fish.

Analysis of predominant, approximately 700,000 dalton serum antibody (Ab) of the channel catfish by SDS-PAGE revealed only one molecular mass species of heavy (H) chain (approximately 70,000 daltons), whereas a marked heterogeneity in the relative mobilities of the light (L) chains was evident. Three molecular mass L chain variants of approximately 26,000, approximately 24,000, and approximately 22,000 daltons were observed. The relationships between the L chain variants were not clear until mouse monoclonal Ab (mAb) reactive with catfish immunoglobulin (Ig) were developed. Two of these mAb, designated 3F12 and 1G7, were found to independently recognize different populations of catfish Ig. In addition, when these two mAb were used in combination they immunoprecipitated greater than 95% of specifically purified catfish anti-DNP or anti-fluorescein Ab. The L chains of catfish Ig recovered from immunoabsorbent affinity matrices conjugated with either mAb 3F12 or 1G7 were found to be clearly distinct. Monoclonal Ab 3F12 reacted with a subpopulation of catfish Ig that contained the approximately 24,000 and approximately 22,000 dalton L chain variants, whereas mAb 1G7 reacted with another subpopulation of catfish Ig that contained only the approximately 26,000 dalton L chain variant. Solid phase plate binding assays with the use of mildly reduced catfish Ig H and L chains showed that both of these mAb preferentially reacted with catfish L chains. Subsequent analysis of the two antigenically distinct L chain populations by peptide mapping procedures demonstrated that these L chains were structurally different. Furthermore, analysis of the serum from individual catfish showed the presence of both L chain types in each of 25 catfish examined. These studies strongly suggest that distinct L chain classes have evolved in fish.

Animals↗

PubMed1993

Principles, main goals and methods of the nationwide program: "investigations on iodine deficiency and model of iodine prophylaxis in Poland".

The main reasons to start investigations on IDD in Poland as a nationwide project of the Ministry of Health and Welfare sponsored by the State Committee For Scientific Research and Foundation for Polish Science were: cessation of iodizing of kitchen salt in Poland in 1980, increase of the incidence of goitre in the population and hyperthyrotropinemia in newborns, results of the survey undertaken after Chernobyl disaster indicating an increase of goiter incidence (Nauman et al.) and results of the pilot study (Gutekunst, Gembicki, Kinalska and Rybakowa) indicating an increase of thyroid volume and diminishing of iodine excretion in urine of children in Kraków, Białystok ad Poznań regions. Therefore the main goals of the project were as follows: to evaluate IDD in Poland on the population basis, to map goiter incidence and iodine deficiency in geographic areas, to evaluate a voluntary model of iodine prophylaxis in Poland (20 mg of KI/kg of salt). The investigations were carried out in 19330 children (48.7% of boys and 51.3% for girls) in age group 6-13 years, attending 111 coeducational randomly selected schools from all the country. This number represents 0.35% of children subpopulation in the above age-groups. For practical purposes local coordinating centers at the relevant Departments of Endocrinology and Board of Coordinators were set up. The programme of survey included: filling the questionnaire by children's parents, thyroid palpation and classification according to WHO and ICCIDD criteria, thyroid volume determination by means of ultrasonograph Kontron Sigma 1 L with linear transducer 7.5 MHz, determination of iodine in casual morning urine sample using Sandell and Kalthoff method. Determination of iodine concentration in urine was performed in each case of goiter and in the same number of children without goiter. The results were segregated according to coordinating centers and according to 6 geographical areas of the country. The results were calculated according to the descriptive statistics using Student's test, Chi-square test F-test and Leven's test. The results segregated according to geographic areas were tested by means of analysis of variance using the linear model. The final results of the programme are presented in the next papers.

Adolescent↗

PubMed1993

Molecular cloning of human prostaglandin endoperoxide synthase type II and demonstration of expression in response to cytokines.

Prostaglandin endoperoxide synthase (PHS) catalyzes the committed step in the biosynthesis of prostaglandins and thromboxane. We recently observed dissociation of PHS activity and enzyme mass measured in an immunoassay of endothelial cells exposed to tumor necrosis factor. These data and observations by others suggested that endothelial cells express an alternate PHS. We now report the molecular cloning of human PHS type II from an endothelial cell cDNA library. The protein encoded by this cDNA shares 61% identity with the human PHS I. Southern analysis demonstrated a single copy of PHS II and we found a polymorphism in approximately 5% of the population. PHS II mapped to chromosome 1, in contrast to PHS I, which is on chromosome 9. The PHS II cDNA hybridized strongly to a 4.3-kilobase (kb) message from endothelial cells. Stimulation of the cells with tumor necrosis factor, phorbol 12-myristate 13-acetate, lipopolysaccharide, or interleukin-1 increased mRNA levels for PHS II, and this change correlated well with increased prostacyclin biosynthesis. Cycloheximide induced PHS II mRNA without a corresponding activity increase demonstrating that translation of the 4.3-kb message is required for increased prostacyclin biosynthesis. We conclude that expression of PHS II may have important pathophysiological effects in the vasculature.

Amino Acid Sequence↗