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External craniofacial features, body size, and renal morphology in prenatal brachyrrhine mice.

The Brachyrrhine (Br) semidominant mouse mutant provides a useful model for studying factors responsible for midfacial hypoplasia. In order to determine early morphogenetic events responsible for midfacial hypoplasia in these mice, prenatal mutants must be differentiated from nonaffected littermates. The purpose of this study was to determine whether prenatal offspring from Br matings could be separated morphologically into groups of normal or midfacially deficient embryos. Thirty embryos resulting from Br matings were collected between day 15 and birth (Theiler stages 23-27). Qualitative observations on craniofacial morphology as well as renal morphology and histology suggested that embryos segregated into two distinct groups. External craniofacial and body measurements, collected from the embryos, as well as renal volumes, determined from computerized reconstructions of the kidneys, were subjected to quantitative analyses. A discriminant function analysis segregated the sample into two groups based primarily on midfacial length and renal volume. Bivariate regression analysis showed that midfacial length and renal volume differed significantly, and cranial length marginally so, between the two groups. The results indicate that a proportion of prenatal offspring from Br matings exhibits midfacial and renal hypoplasia and that these animals segregate completely from nonaffected embryos.

Abnormalities, Radiation-Induced↗

A two-locus model for hereditary non-polyposis colorectal cancer in Modena, Italy.

Complex segregation analysis was conducted in a series of patients with hereditary non-polyposis colorectal cancer (HNPCC) ascertained through probands registered in the Cancer Registry of the Health Care District of Modena, Northern Italy. Altogether there were 125 nuclear families segregating for HNPCC, for a total of 672 individuals. The analysis favoured a two-locus model, with both susceptibility genes rare and dominant. The gene frequency of the deleterious allele at the major locus is estimated to be low qm = 0.004 and for the second locus the estimate is even lower q = 0.00003. Both genes defining the two-locus model seem to be highly penetrant. The lifetime penetrance of the abnormal gene at the major locus is estimated to be 0.73 for female, while the estimation for male is higher, 0.85.

Adult↗

Evidence for the segregation of a major gene for human plasma GABA levels.

Gamma-aminobutryic acid (GABA) is a major neurotransmitter in the central nervous system, and plasma levels of GABA may reflect brain GABA activity. In 35-40% of patients with mood disorders, plasma GABA levels are low compared to psychiatrically normal controls. Low plasma GABA in this subgroup of patients has characteristics of a biological trait marker for mood disorders. Low plasma GABA is also found in a subset of patients with alcohol dependence, but not in schizophrenia, anxiety, or eating disorders, suggesting some diagnostic specificity. Previous data from a small study of monozygotic twins are consistent with the hypothesis that plasma GABA levels are under genetic control. To better understand these mechanisms, we conducted a segregation analysis of plasma GABA levels in a sample of 157 individuals from 50 nuclear families. Analysis using the Class D regressive model indicated that the familial transmission of plasma GABA levels is compatible with the segregation of a recessive major gene. Our results suggest that plasma GABA levels are under single gene control. Future research should address the precise mechanisms which may account for the abnormality in GABA levels seen in a subset of patients with mood disorders.

Adolescent↗

Inheritance of nuclear DNA markers in gynogenetic haploid pink salmon.

We describe the inheritance of 460 PCR-based loci in the polyploid-derived pink salmon (Oncorhynchus gorbuscha) genome using gynogenetic haploid embryos. We detected a length polymorphism in a growth hormone gene (GH-2) intron that is caused by an 81 bp insertion homologous to the 3' end of the salmonid short interspersed repetitive element (SINE) SmaI. Such insertion polymorphisms within species bring into question the use of SINEs as phylogenetic markers. We confirmed that a microsatellite locus encodes a PCR-null allele that is responsible for an apparent deficit of heterozygotes in a population sample from Prince William Sound. Another set of microsatellite primers amplified alleles of the same molecular weight from both loci of a duplicated pair. In our analysis of several PCR-based multilocus techniques, we failed to detect evidence of comigrating fragments produced by duplicated loci. Segregation analysis of PCR-based markers using gynogenetic haploid embryos ensures that the interpretation of molecular variation is not complicated by heterozygosity, diploidy, or gene duplication. We urge investigators to test the inheritance of polymorphisms in salmonids prior to using them to measure genetic variation.

Animals↗

Mapping of avirulence genes in the rice blast fungus, Magnaporthe grisea, with RFLP and RAPD markers.

Three genetically independent avirulence genes, AVR1-Irat7, AVRI-MedNoi; and AVR1-Ku86, were identified in a cross involving isolates Guy11 and 2/0/3 of the rice blast fungus, Magnaporthe grisea. Using 76 random progeny, we constructed a partial genetic map with restriction fragment length polymorphism (RFLP) markers revealed by probes such as the repeated sequences MGL/MGR583 and Pot3/MGR586, cosmids from the M. grisea genetic map, and a telomere sequence oligonucleotide. Avirulence genes AVR1-MedNoi and AVR1-Ku86 were closely linked to telomere RFLPs such as marker TelG (6 cM from AVR1-MedNoi) and TelF (4.5 cM from AVR1-Ku86). Avirulence gene AVR1-Irat7 was linked to a cosmid RFLP located on chromosome 1 and mapped at 20 cM from the avirulence gene AVR1-CO39. Using bulked segregant analysis, we identified 11 random amplified polymorphic DNA (RAPD) markers closely linked (0 to 10 cM) to the avirulence genes segregating in this cross. Most of these RAPD markers corresponded to junction fragments between known or new transposons and a single-copy sequence. Such junctions or the whole sequences of single-copy RAPD markers were frequently absent in one parental isolate. Single-copy sequences from RAPD markers tightly linked to avirulence genes will be used for positional cloning.

Amino Acid Sequence↗

Exploring the c.406 C > T variant in TNNI3 gene: pathogenic insights into restrictive cardiomyopathy.

BACKGROUND: Restrictive cardiomyopathy (RCM) is a rare cardiac disorder characterized by diastolic dysfunction and myocardial stiffness, frequently associated with genetic variants. We aimed to explore the genetic basis of RCM in a diagnosed patient through comprehensive genetic analysis. METHODS: Whole exome sequencing (WES) was conducted on the proband, followed by Sanger sequencing for variant confirmation and familial segregation analysis. In silico tools and structural protein modeling were employed to assess the functional impact of the identified variant. RESULTS: The c.406 C > T variant, classified as likely pathogenic, results in a truncated TNNI3 protein. Bioinformatics analysis highlighted significant structural disruptions, likely impairing sarcomere function. The patient presented with growth retardation, progressive dyspnea, and echocardiographic findings consistent with RCM. Both parents were heterozygous carriers, supporting an autosomal recessive inheritance pattern. The homozygosity of the novel variant identified in this study is a critical factor in the genotype-phenotype correlation observed in this case. CONCLUSION: This study identified the novel c.406 C > T variant in TNNI3 as a potential pathogenic driver of RCM, emphasizing the critical role of genetic evaluations in early diagnosis and management of inherited cardiomyopathies. Further studies are warranted to explore therapeutic interventions targeting TNNI3-related pathologies.

Humans↗

Generation of sequence signatures from DNA amplification fingerprints with mini-hairpin and microsatellite primers.

DNA amplification fingerprinting (DAF) with mini-hairpins harboring arbitrary "core" sequences at their 3' termini were used to fingerprint a variety of templates, including PCR products and whole genomes, to establish genetic relationships between plant tax at the interspecific and intraspecific level, and to identify closely related fungal isolates and plant accessions. No correlation was observed between the sequence of the arbitrary core, the stability of the mini-hairpin structure and DAF efficiency. Mini-hairpin primers with short arbitrary cores and primers complementary to simple sequence repeats present in microsatellites were also used to generate arbitrary signatures from amplification profiles (ASAP). The ASAP strategy is a dual-step amplification procedure that uses at least one primer in each fingerprinting stage. ASAP was able to reproducibly amplify DAF products (representing about 10-15 kb of sequence) following careful optimization of amplification parameters such as primer and template concentration. Avoidance of primer sequences partially complementary to DAF product termini was necessary in order to produce distinct fingerprints. This allowed the combinatorial use of oligomers in nucleic acid screening, with numerous ASAP fingerprinting reactions based on a limited number of primer sequences. Mini-hairpin primers and ASAP analysis significantly increased detection of polymorphic DNA, separating closely related bermudagrass (Cynodon) cultivars and detecting putatively linked markers in bulked segregant analysis of the soybean (Glycine max) supernodulation (nitrate-tolerant symbiosis) locus.

DNA Fingerprinting↗

Genetic analysis of hybrid strains trisomic for the chromosome containing a fatty acid synthetase gene complex (fas1) in yeast.

Evidence of spontaneous n+1 aneuploidy has been obtained by trisomic segregation analysis of four independently maintained stocks of Saccharomyces cerevisiae defective in saturated fatty acid synthesis (fas1). In all cases tested, only the chromosome bearing the mutant fatty acid locus was disomic. Tetrad analysis of trisomic hybrids enabled the identification of chromosome XI as the one bearing the fatty acid locus and the assignment of fragment 5 to chromosome XI. Statistical analysis of tetrad frequencies generated by markers in triplex configuration provided information on the meiotic configuration of pairing of the three homologous chromosomes. The possible relationship between defective nuclear membranes and the disjunction of chromosomes in fas1 strains is discussed.

Cell Survival↗

Exclusion of SOX9 as the testis determining factor in Ellobius lutescens: evidence for another testis determining gene besides SRY and SOX9.

In mammals the initiation of testis determination usually depends on the Y-chromosomal gene SRY. A few species, however, escape from this rule with a testis determination that is independent of SRY. The mole vole Ellobius lutescens is one of these species. It is not known how testis determination is initiated in this species but it has been suggested that a gene from the sex determination cascade usually acting downstream of SRY is mutated and has taken over the testis-determining function. At present SOX9 is the only candidate gene for which a testis-determining function in the absence of SRY has been observed. To test the hypothesis that testis differentiation in E. lutescens is initiated by SOX9, segregation analysis of SOX9 alleles was performed in an E. lutescens family. As there is no marker data available in this species we screened both Ellobius SOX9 introns for polymorphisms suitable for segregation studies. A biallelic polymorphism was found in the second intron of the SOX9 gene and analysis of this marker in the Ellobius family revealed an inheritance pattern completely independent of the sex of the animals. Thus, SOX9 can be excluded from being the testis-determining factor in E. lutescens. These results provide evidence for another possibly yet unknown gene besides SRY and SOX9 able to exert testis-determining function.

Alleles↗

A genetic study of idiopathic focal dystonias.

A genetic study of idiopathic focal dystonias was undertaken by examining 153 first-degree relatives of 40 index patients with torticollis (14 patients), other focal cranial dystonias (16 patients), and writer's cramp (10 patients). Nine relatives with dystonia were identified in 6 families; 8 of these had symptoms such as clumsiness or tremor, but none were aware of any dystonia. A further 4 relatives, now decreased, were affected by history. Overall, 25% of index patients had relatives with dystonia. The results of segregation analysis suggested the presence of an autosomal dominant gene or genes with reduced penetrance as a common cause for focal dystonia. Segregation ratios were not significantly different from those ratios observed in generalized or segmental dystonia in the United Kingdom, and it is possible that a single autosomal dominant gene mutation is responsible for inherited dystonia in the majority of patients irrespective of distribution or severity.

Adult↗

The effects of genetics and age on expression of MHC class II and CD4 antigens on rat cardiac interstitial dendritic cells.

Interstitial dendritic cells (IDC) in normal hearts of inbred rat strains and congenic and congenic recombinant lines were identified and quantitated by immunohistologic methods, on the basis of cellular reactivity with MRC-OX6, a monoclonal antibody (MAb) directed against MHC class II determinants, and with W3/25, a MAb directed against a CD4 epitope. In all strains and lines examined, the W3/25+ IDC frequency was uniformly high with little interstrain variation. In contrast, all rat strains and lines examined showed either high or low OX6+ IDC frequency. Double staining by two color immunofluorescence indicated that strains with a low OX6+ IDC frequency were characterized by a high frequency of W3/25+ OX6- IDC and a low frequency of W3/25+ OX6+ IDC. In strains with high OX6+ IDC frequency, the majority of IDC coexpressed both markers. Comparative analysis of (i) MHC identical background disparate strains and lines, (ii) MHC disparate background identical strains and lines, and (iii) F2 segregation analysis of intercrosses and backcrosses derived from an original cross between high and low frequency OX6+ IDC strains, all indicated that OX6+ IDC frequency is dependent upon both MHC- and non-MHC-linked genetic factors. It is suggested that rat cardiac OX6+ IDC frequency is influenced by a minimum of two autosomal genes, one of which is MHC linked. The frequencies of both W3/25+ IDC frequency reached adult levels by 10 days of age; adult levels of OX6+ IDC were not attained until Day 21. It is postulated that in the rat heart, W3/25+ OX6- IDC are potential precursors of W3/25+ OX6+ IDC, and that the cellular frequency of coexpression in the adult is under genetic influence. Whether these genetic factors modify constitutive or physiologic levels of class II-inducing lymphokine activity, or influence cellular susceptibility of IDC to induced class II expression is unclear.

Age Factors↗

Identification and mapping of six microdissected genomic DNA probes to the proximal region of mouse chromosome 1.

Six independent DNA probes, lambda Mm1C-150, lambda Mm1C-153, lambda Mm1C-156, lambda Mm1C-162, lambda Mm1C-163, and lambda Mm1C-165, have been isolated from a library of microdissected fragments from mouse chromosome 1, spanning cytogenetic bands C2 to C5. These DNA probes have been mapped by restriction fragment length polymorphism analysis with respect to 12 marker loci previously assigned to this portion of mouse chromosome 1, in a panel of 251 segregating Mus spretus x C57BL/6J interspecific backcross mice. The gene order and intergene distances were determined by segregation analysis to be centromere- lambda Mm1C-162-11.1 cM-Col3a1-8.8 cM-Len-2-2.6 cM-lambda Mm1C-163-1.6 cM-Fn-1-1.6 cM-Tp-1-0.8 cM-lambda Mm1C-165/Vil-0.4 cM-Inha-2.8 cM-lambda Mm1C-153-2.4 cM-lambda Mm1C-156-1.2 cM-Pax-3-5.6 cM-Akp-3-0.8 cM-Acrg-2.0 cM-Sag-0.5 cM-Col6a3-1.8 cM-lambda Mm1C-150-15.4 cM-Ren1,2. Four of these probes map within a chromosome 1 segment that is homologous to human chromosome 2q. Southern blotting analyses indicate that one of these anonymous probes, lambda Mm1C-165, detects DNA fragments highly conserved across species. These novel polymorphic probes should prove useful for linkage and physical mapping of this chromosomal region.

Animals↗

The rec8 gene of Schizosaccharomyces pombe is involved in linear element formation, chromosome pairing and sister-chromatid cohesion during meiosis.

The fission yeast Schizosaccharomyces pombe does not form tripartite synaptonemal complexes during meiotic prophase, but axial core-like structures (linear elements). To probe the relationship between meiotic recombination and the structure, pairing, and segregation of meiotic chromosomes, we genetically and cytologically characterized the rec8-110 mutant, which is partially deficient in meiotic recombination. The pattern of spore viability indicates that chromosome segregation is affected in the mutant. A detailed segregational analysis in the rec8-110 mutant revealed more spores disomic for chromosome III than in a wild-type strain. Aberrant segregations are caused by precocious segregation of sister chromatids at meiosis I, rather than by nondisjunction as a consequence of lack of crossovers. In situ hybridization further showed that the sister chromatids are separated prematurely during meiotic prophase. Moreover, the mutant forms aberrant linear elements and shows a shortened meiotic prophase. Meiotic chromosome pairing in interstitial and centromeric regions is strongly impaired in rec8-110, whereas the chromosome ends are less deficient in pairing. We propose that the rec8 gene encodes a protein required for linear element formation and that the different phenotypes of rec8-110 reflect direct and indirect consequences of the absence of regular linear elements.

Chromatids↗

Genetic variation in homothallic and hyphal swelling isolates of Pythium ultimum var. ultimum and P. utlimum var. sporangiferum.

Genetic variation in a collection of 22 Pythium ultimum isolates was analyzed using restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNA (RAPD), and sequence characterized amplified regions (SCARs) as genetic markers. Qualitative evidence for the occurrence of sexual outcrossing in the field, asexual mechanisms affecting variation, and differences in aggressiveness between isolates was found. Codominant SCAR and RFLP markers detected multiple alleles in several isolates. Genetic analysis of F1 progeny from a cross indicates that heterozygosity is one cause of multiple alleles and contributes to genetic variation. Segregation analysis of F2 progeny fit diploid expectations and supported the use of the molecular markers for phenetic analysis. One isolate contained three alleles at one locus suggesting that polyploidy, aneuploidy or heterokaryosis may also contribute to genetic variation. Phenetic analysis using UPGMA clustering of Nei's distance calculated from RFLP data, UPGMA clustering of similarity matrixes calculated from RAPD data, and principle component analysis of RAPD data revealed no clustering of the three morphological types of Pythium ultimum (var. ultimum, var. sporangiferum, and group HS). Our results suggest that the three morphological variants of this homothallic oomycete are not genetically distinct.

Base Sequence↗

Analysis of candidate genes for genotypic diagnosis in the long QT syndrome.

Patients with the long QT syndrome (LQTS) suffer from cardiac arrhythmias that can lead to abrupt loss of consciousness and sudden death, already in young individuals. Thus, an early diagnosis of LQTS is essential for patients and their family members. So far, six genes (KCNQ1, HERG, SCN5A, ANK2, KCNE1, KCNE2) have been demonstrated to be involved in the development of LQTS. Since this syndrome is genetically heterogeneous and large-sized families are often not available for linkage analysis, alternative tools are required for a genetic diagnosis. To investigate genes with numerous exons, like KCNQ1, HERG, SCN5A and ANK2, segregation analysis of a Polish Romano-Ward family with eight members was performed as a reliable method faster than linkage analysis or direct sequencing. To test these four LQT loci, an appropriate selection of microsatellite markers covering different chromosomal regions was applied. Furthermore, two small genes KCNE1 and KCNE2 (at the LQT5 and LQT6 loci), and the SGK1 gene (encoding a kinase regulating KCNE1 and SCN5A channels) were sequenced. All six LQT loci and the SGK1 gene were excluded by these analyses, thus a different pathogenic mechanism of LQT syndromes can be presumed.

Base Sequence↗

The genetic origin of leucocytic mucopolysaccharides in cancer patients.

The presence or absence of lymphocytic mucopolysaccharides (MPS) is studied in 223 subjects: 100 normals (controls); 8 cancer patients cured for more than 6 years; 30 cancer patients at the start of their treatment; and 85 relatives of first degree consanguinity of these last patients. The data are studied by statistical and genetic analysis. The results confirm the findings reported earlier and show that the difference in the probability of a high frequency of leucocytic MPS between the relatives of cancer patients and the controls is highly significant. Furthermore, this probability in a relative of first degree of consanguinity of a cancer patient is more than three times greater than in an individual of the general population. Genetic segregation analysis shows that the high leucocytic MPS trait segregates in the families of cancer patients after a classic pattern of dominant autosomal inheritance. Applying Falconer's nomogram it is concluded that the whole of this phenotypic variation is of genetic origin. Its interrelationships with cancer are discussed and it is postulated that this disturbance of the lymphocytic MPS represents a subclinical variant, not known until now, of the clinical mucopolysaccaridoses.

Chromosome Aberrations↗

Analysis of the genetic basis of the endothelium-dependent impaired vasorelaxation in the stroke-prone spontaneously hypertensive rat: a candidate gene approach.

OBJECTIVE: To investigate the role of potential candidate genes in the pathogenesis of the endothelium-dependent impaired vasorelaxation that associates and co-segregates with stroke in the stroke-prone spontaneously hypertensive rat (SHRsp) compared with the stroke-resistant SHR (SHRsr). DESIGN AND METHODS: An SHRsp/SHRsr F2-intercross (n = 137; 64 males, 73 females) was obtained and, at the age of 6 weeks, it was placed under a stroke permissive Japanese-style diet for 4 weeks. At the end of the treatment the vascular function of each rat was characterized. The maximal vasorelaxation to acetylcholine after maximal vasoconstriction (delta ratio) was considered as the quantitative phenotype. The following candidate genes were related to the delta ratio: renin, angiotensinogen, angiotensin-converting enzyme, angiotensin II AT1b receptor, atrial natriuretic peptide, brain natriuretic peptide, atrial natriuretic peptide GC-A receptor, kallikrein, endothelial nitric oxide synthase. In addition, polymorphic markers located inside areas of the rat genome where other candidates (i.e. adrenomedullin, endothelin, Ang II AT1a receptor) are known to map were included. RESULTS: The endothelial vascular dysfunction of the SHRsp showed a variable distribution among SHRsp/SHRsr F2 descendants, independently from the blood pressure levels. A genotype/phenotype co-segregation analysis for each of the genes tested did not show any statistically significant co-segregation with the vascular phenotype. CONCLUSION: A candidate gene approach used to investigate the genetic basis of the endothelial-dependent vascular dysfunction of the SHRsp strain did not reveal any evidence to support the hypothesis that the genes tested play any role in the pathogenesis of the stroke-related vascular abnormality.

Animals↗

Cloning and characterization of Xenopus beta2-microglobulin.

cDNAs for Xenopus beta2-microglobulin (beta2m), the obligatory light chain of most vertebrate Major Histocompatibility Complex (MHC) class I molecules, were isolated and ESTs were identified. Alignment of the deduced amino acid sequence to other species' beta2m showed that the overall structure is evolutionarily conserved, and phylogenetic analysis showed that the Xenopus beta2m sequence is intermediate between fish and bird/mammal beta2m. The Xenopus beta2m mRNA is expressed ubiquitously with highest expression in intestine, spleen, and thymus, correlating well with classical class Ia expression. beta2m mRNA and protein were also detected in Xenopus thymic tumor and kidney cell lines. Segregation analysis on a tetraploid Xenopus laevis family revealed two independently segregating, non-MHC-linked loci. As expected, only one locus was found in the diploid Xenopus tropicalis, strongly suggesting that the two beta2m loci in the tetraploid species were generated by genome-wide duplication, and did not undergo diploidization unlike many other MHC genes.

Amino Acid Sequence↗