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PubMed2005

Integrative genetic analysis of transcription modules: towards filling the gap between genetic loci and inherited traits.

Genetic loci that regulate inherited traits are routinely identified using quantitative trait locus (QTL) mapping methods. However, the genotype-phenotype associations do not provide information on the gene expression program through which the genetic loci regulate the traits. Transcription modules are 'self-consistent regulatory units' and are closely related to the modular components of gene regulatory network [Ihmels, J., Friedlander, G., Bergmann, S., Sarig, O., Ziv, Y. and Barkai, N. (2002) Revealing modular organization in the yeast transcriptional network. Nat. Genet., 31, 370-377; Segal, E., Shapira, M., Regev, A., Pe'er, D., Botstein, D., Koller, D. and Friedman, N. (2003) Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat. Genet., 34, 166-176]. We used genome-wide genotype and gene expression data of a genetic reference population that consists of mice of 32 recombinant inbred strains to identify the transcription modules and the genetic loci regulating them. Twenty-nine transcription modules defined by genetic variations were identified. Statistically significant associations between the transcription modules and 18 classical physiological and behavioral traits were found. Genome-wide interval mapping showed that major QTLs regulating the transcription modules are often co-localized with the QTLs regulating the associated classical traits. The association and the possible co-regulation of the classical trait and transcription module indicate that the transcription module may be involved in the gene pathways connecting the QTL and the classical trait. Our results show that a transcription module may associate with multiple seemingly unrelated classical traits and a classical trait may associate with different modules. Literature mining results provided strong independent evidences for the relations among genes of the transcription modules, genes in the regions of the QTLs regulating the transcription modules and the keywords representing the classical traits.

Animals↗
PubMed2003

The identification of candidate genes for a reverse genetic analysis of development and function in the Arabidopsis gynoecium.

The screening for mutants and their subsequent molecular analysis has permitted the identification of a number of genes of Arabidopsis involved in the development and functions of the gynoecium. However, these processes remain far from completely understood. It is clear that in many cases, genetic redundancy and other factors can limit the efficiency of classical mutant screening. We have taken the alternative approach of a reverse genetic analysis of gene function in the Arabidopsis gynoecium. A high-throughput fluorescent differential display screen performed between two Arabidopsis floral homeotic mutants has permitted the identification of a number of genes that are specifically or preferentially expressed in the gynoecium. Here, we present the results of this screen and a detailed characterization of the expression profiles of the genes identified. Our expression analysis makes novel use of several Arabidopsis floral homeotic mutants to provide floral organ-specific gene expression profiles. The results of these studies permit the efficient targeting of effort into a functional analysis of gynoecium-expressed genes.

Arabidopsis↗
PubMed2025

Genetic analysis of four cases of Poirier Bienvenu neurodevelopmental syndrome associated with CSNK2B variant.

BACKGROUND: CSNK2B deficiency underlies the pathogenesis of Poirier-Bienvenu neurodevelopmental syndrome (POBINDS). In this study, we present four cases of pediatric seizures caused by de novo variants in CSNK2B, with the aim to reinforce the clinical and variant data pertaining to early genetic factors associated with epilepsy. METHODS: Trio whole exome sequencing were used to detect variants in the proband and her family members, and bioinformatics annotation was performed for the variant. Sanger sequencing and CSNK2B cDNA sequencing were employed to ascertain the carrier status of additional family members and evaluate the potential impact of variants on splicing. RESULTS: All four cases presented with epilepsy as the initial manifestation, accompanied by global developmental delay, particularly in language and motor developmental delay. Cases 1, 3 and 4 exhibited full-scale tonic-clonic seizures, while case 2 displayed myoclonic and typical absence seizures. Furthermore, case 2 demonstrated delayed growth and development compared to age-matched peers. No abnormality was detected in the head magnetic resonance imaging (MRI). Genetic analysis revealed novel heterozygous variants in the CSNK2B gene in all four cases, including c.175 + 1G > A, c.73-2A > G, c.291 + 1G > A and c.481delA. In case 2, reverse transcription analysis of CSNK2B mRNA revealed the retention of the 3' end sequence of Intron 2 and deletion of the 5' end sequence of Exon 3. In treatment, four case received a combination of one to three types of antiseizure medication and rehabilitation training individually. Case 1 continued to experience seizures to varying degrees, while cases 2-4 demonstrated effective seizure control. Overall motor and intellectual development improved in all four cases, however, there was slow recovery in language function. CONCLUSION: This study elucidates the molecular etiology of epilepsy in four cases with POBINDS and expands the mutational spectrum of pathogenic variants in the CSNK2B, highlighting their impact on splicing. The highly genetic heterogeneous phenotype of POBINDS relies on the detection of pathogenic variants in CSNK2B. Conventional antiseizure medication effectively control seizures, while rehabilitation treatment can significantly improve intelligence and motor function to varying degrees; however, language recovery tends to be relatively slow.

Humans↗
PubMed1986

Genetic analysis of cleft lip with or without cleft palate in Chinese kindreds.

Cleft lip with or without cleft palate (CL +/- P) affects 1 in 500-1,000 newborns worldwide; the cause remains unclear. For CL +/- P, Asians are at higher risk than Caucasians or Blacks. This report presents the results of a genetic analysis of 163 CL +/- P proband families ascertained in Shanghai, China. Based on statistical tests of several predictions from the classical multifactorial/threshold model, no evidence could be found to support it. Further, goodness-of-fit (PGOODFIT) tests of this model were also unsupportive, there being more families with two or more affected sibs than expected. Classical segregation analysis for Mendelian inheritance showed a maximum likelihood estimate of the segregation ratio of 0.187 +/- 0.068. This value was not significantly less than 0.25 (recessive inheritance) but was significantly less than 0.50 (dominant inheritance). Sex ratio data from these Chinese families suggest that manifestation of the putative single major gene is sex influenced. The apparent reduced penetrance is likewise to be expected if manifestation of CL +/- P also depends on in utero exposure to deleterious environmental agents, as demonstrated in a variety of human and animal model studies.

California↗
PubMed2006

Genetic analysis of 4 new mutants at the unstable k2 Mdh1-n y20 chromosomal region in soybean.

In soybean (Glycine max (L.) Merr.), a chromosomal region defined by 3 closely linked loci, k2 (tan-saddle seed coat), Mdh1-n (malate dehydrogenase 1 null), and y20 (yellow foliage), is highly mutable. A total of 31 mutants have been reported from this region. In this study, a mutation with tan-saddle seed coat was found from bulk-harvested seed of cultivar Kenwood. Genetic analysis established that this tan-saddle seed coat mutation is allelic to the k2 locus and inherited as a recessive gene. Simple sequence repeat analysis showed that this mutant is not a contaminant from other existing k2 mutants. The mutant was named Kenwood-k2. To test for genetic instability at the k2 Mdh1-n y20 chromosomal region, Kenwood-k2 was crossed reciprocally with cultivars Harosoy and Williams. No new mutants were found in F2 families. In the genetic instability tests of T239 (k2) with cultivar Williams, 3 new mutants with yellow foliage (y20) and malate dehydrogenase 1 null (Mdh1-n) were identified. In the genetic instability tests of T261 (k2 Mdh1-n) with cultivar Williams, no new mutants were found. The Kenwood-k2 and the 3 yellow-foliage, malate dehydrogenase 1-null mutants provide additional genetic materials to study chromosomal aberrations in this mutable/unstable chromosomal region.

Alleles↗
PubMed2006

A genetic analysis of opioid-induced hyperalgesia in mice.

BACKGROUND: Opioid-induced hyperalgesia (OIH) is a syndrome of increased sensitivity to noxious stimuli, seen after both the acute and chronic administration of opioids, that has been observed in humans and rodent models. This syndrome may reduce the clinical utility of opioids in treating acute and chronic pain. METHODS: In these studies, the authors measured the propensity of 15 strains of inbred mice to develop mechanical manifestations of OIH. These data were subjected to in silico genetic analysis, which resulted in the association of haplotypic blocks within or near several known genes. Both pharmacologic agents and transgenic mice were used to confirm the functional association of the most strongly linked gene with OIH. RESULTS: Both baseline mechanical nociceptive thresholds and the percentage changes in these thresholds after 4 days of morphine treatment were found to be highly strain dependent. The haplotypic blocks most strongly associated with the mechanical OIH data were located within the beta2 adrenergic receptor gene (beta2-AR). Using the selective beta2-AR antagonist butoxamine, the authors observed a dose-dependent reversal of OIH. Furthermore, deletion of the beta2-AR gene sharply reduced the mechanical allodynia present after morphine treatment in the wild-type mouse strain. Analysis of the associated beta2-AR haplotypic block identified single nucleotide polymorphisms potentially explaining in part the strain specific differences in OIH. CONCLUSIONS: Genetic variants of the beta2-AR gene seem to explain some part of the differences between various strains of mice to develop OIH. The association of this gene with OIH suggests specific pharmacologic strategies for reducing the impact of OIH on patients consuming opioids.

Adrenergic beta-Antagonists↗
PubMed2002

Anarchy in the UK: Detailed genetic analysis of worker reproduction in a naturally occurring British anarchistic honeybee, Apis mellifera, colony using DNA microsatellites.

Anarchistic behaviour is a very rare phenotype of honeybee colonies. In an anarchistic colony, many workers' sons are reared in the presence of the queen. Anarchy has previously been described in only two Australian colonies. Here we report on a first detailed genetic analysis of a British anarchistic colony. Male pupae were present in great abundance above the queen excluder, which was clearly indicative of extensive worker reproduction and is the hallmark of anarchy. Seventeen microsatellite loci were used to analyse these male pupae, allowing us to address whether all the males were indeed workers' sons, and how many worker patrilines and individual workers produced them. In the sample, 95 of 96 of the males were definitely workers' sons. Given that approximately 1% of workers' sons were genetically indistinguishable from queen's sons, this suggests that workers do not move any queen-laid eggs between the part of the colony where the queen is present to the area above the queen excluder which the queen cannot enter. The colony had 16 patrilines, with an effective number of patrilines of 9.85. The 75 males that could be assigned with certainty to a patriline came from 7 patrilines, with an effective number of 4.21. They were the offspring of at least 19 workers. This is in contrast to the two previously studied Australian naturally occurring anarchist colonies, in which most of the workers' sons were offspring of one patriline. The high number of patrilines producing males leads to a low mean relatedness between laying workers and males of the colony. We discuss the importance of studying such colonies in the understanding of worker policing and its evolution.

Animals↗
PubMed1990

Courtship behavior and control of reproductive isolation in Drosophila mojavensis: genetic analysis of population hybrids.

Drosophila mojavensis from the Sonora region and Baja California show asymmetrical sexual isolation in the laboratory: males from Sonora mate equally frequently with Sonora and Baja females, while the mating success of Baja males with Sonora females is reduced. This failure has been localized to three separate behavioral landmarks occurring during courtship. Genetic analysis was conducted using reciprocal F1 hybrids of Sonora and Baja strains to examine inheritance patterns of the responsible courtship behaviors. Mating success and propensity of F1 males were similar to Sonora males. F1 females mated with males of Sonora and Baja races equally, although mating propensity of F1 females was intermediate between that of Sonora and Baja females. Males of Baja strains presented with F1 females showed a relatively high level of failure at attempted intromission. Genes for mating behaviors are located in the autosomes, but different loci responsible for the sexual isolation appear to act in males and females.

Animals↗
PubMed1986

[Genetical analysis and characterization of a new mutant, black tremor appearing in the Syrian hamster].

A black coat-color mutant with tremor was discovered in babies of 61 generations of an inbred strain APG of Syrian hamster which had been maintained in the Nippon Institute for Biological Science, Laboratory Animal Research Station. The genetical analysis by matings between four inbred strains which had different genes in the E and B loci and four mutant strains which were introduced the mutant gene into the four inbred strains and characterization were carried out on the mutant. The results obtained are summarized as follows: 1) The mutation occurred in a different locus with E and B loci. 2) The mutant was controlled by an autosomal recessive gene designated as "bt", and it was thought that both tremor and black coat-color were the pleiotropic effect of bt gene. 3) At least one E gene in the E locus was necessary for the appearance of black coat color. Therefore, the coat-color remained cream in ee (cream) hamsters showing only trembling. 4) The degree of blackness of the coat-color of EE hamsters differed from Ee ones. The former was darker than the latter. 5) The mutant may be a useful animal model for studying abnormal myelogenesis and biosynthesis of melanin.

Animals↗
PubMed1989

Genetic analysis of temperature-sensitive lethal mutants of Salmonella typhimurium.

We have isolated 440 mutants of Salmonella typhimurium that show temperature-sensitive growth on complex medium at 44 degrees. Approximately 16% of the mutations in these strains have been mapped to 17 chromosomal locations; two of these chromosomal locations seem to include several essential genes. Genetic analysis of the mutations suggests that the collection saturates the genes readily mutable to a ts lethal phenotype in S. typhimurium. Physiological characteristics of the ts lethal mutants were tested: 6% of the mutants can grow at high temperature under anaerobic conditions, 17% can grow when the medium includes 0.5 M KCl, and 9% of the mutants die after a 2-hr incubation at the nonpermissive temperature. Most ts lethal mutations in this collection probably affect genes required for growth at all temperatures (not merely during high temperature growth) since Tn10 insertions that cause a temperature-sensitive lethal phenotype are rare.

Chromosome Mapping↗
PubMed1996

[Usefulness of PCR-SSCP using non-RI coloration method as a routine genetic analysis].

The polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) analysis is considered as one of useful routine genetic analyses. However, that PCR-SSCP has been analyzed using radioisotope (RI) such as [32P] labeled compounds. So that, it was difficult to use this method routinely at clinical laboratories. In this paper, we compared with an RI mediated and a non-RI coloration mediated PCR-SSCP analysis regarding to those of sensitivity, time and money cost, respectively. The coloration method had enough sensitivity to detect one of cholesteryl ester transfer protein gene mutations. The time and money cost of non-RI coloration mediated method were more advantageous than the RI mediated one. Therefore, it is shown that the non-RI coloration mediated PCR-SSCP analysis is very useful for the routine genetic analysis at clinical laboratories.

Carrier Proteins↗
PubMed2003

Genetic analysis of the ADGF multigene family by homologous recombination and gene conversion in Drosophila.

Many Drosophila genes exist as members of multigene families and within each family the members can be functionally redundant, making it difficult to identify them by classical mutagenesis techniques based on phenotypic screening. We have addressed this problem in a genetic analysis of a novel family of six adenosine deaminase-related growth factors (ADGFs). We used ends-in targeting to introduce mutations into five of the six ADGF genes, taking advantage of the fact that five of the family members are encoded by a three-gene cluster and a two-gene cluster. We used two targeting constructs to introduce loss-of-function mutations into all five genes, as well as to isolate different combinations of multiple mutations, independent of phenotypic consequences. The results show that (1) it is possible to use ends-in targeting to disrupt gene clusters; (2) gene conversion, which is usually considered a complication in gene targeting, can be used to help recover different mutant combinations in a single screening procedure; (3) the reduction of duplication to a single copy by induction of a double-strand break is better explained by the single-strand annealing mechanism than by simple crossing over between repeats; and (4) loss of function of the most abundantly expressed family member (ADGF-A) leads to disintegration of the fat body and the development of melanotic tumors in mutant larvae.

Animals↗
PubMed1980

[Genetic control of pathways of pyrimidine metabolism in Aspergillus nidulans. 1. Isolation and genetic analysis of 6-azauracil resistant mutants].

147 mutants exhibiting the resistance to toxic effect of 6 azauracil have been isolated by nitrosoguanidine treatment from the wild strain of Aspergillus nidulans. This mutants have been divided into 11 phenotypic groups according to its cross-resistance to 5-fluoroderivatives of uracil, uridine and deoxyuridine. The genetic analysis has shown that all mutations of resistance are of nuclear origin and dominant nature, and they are distributed on six loci of the chromosome VIII.

Aspergillus nidulans↗
PubMedDate not supplied

Mitochondrial encephalopathy with lactic acidosis and stroke-like episodes (MELAS) in a Donegal kindred--clinical features and molecular genetic analysis.

A 19 year old female with a background history of migraine, sensorineural deafness and recent personality change developed a parieto-occipital cerebral infarct. Investigations revealed altered lactate to pyruvate ratios, ragged red fibres in muscle and an A-G point mutation at position 3243 in mitochondrial DNA. Subsequent clinical and molecular genetic analysis of 14 family members in three generations identified 12 affected individuals, two of whom were asymptomatic. Maternal inheritance was confirmed. MEALS is an important but under recognised cause of stroke and seizures in the young. There is insufficient data available to determine if the treatment of asymptomatic individuals retards the onset or reduces the severity of stroke.

Adult↗
PubMed1995

Genetic analysis of kifafa, a complex familial seizure disorder.

Kifafa is the Swahili name for an epileptic seizure disorder, first reported in the early 1960s, that is prevalent in the Wapogoro tribe of the Mahenge region of Tanzania in eastern Africa. A 1990 epidemiological survey of seizure disorders in this region reported a prevalence in the range of 19/1,000-36/1,000, with a mean age at onset of 11.6 years; 80% of those affected had onset prior to 20 years of age. A team of investigators returned to Tanzania in 1992 and collected data on > 1,600 relatives of 26 probands in 20 kifafa families. We have undertaken a genetic analysis of these data in order to detect the presence of familial clustering and whether such aggregation could be attributed to genetic factors. Of the 127 affected individuals in these pedigrees, 23 are first-degree relatives (parent, full sibling, or offspring) of the 26 probands; 20 are second-degree relatives (half-sibling, grandparent, uncle, or aunt). When corrected for age, the risk to first-degree relatives is .15; the risk to second-degree relatives is .063. These risks are significantly higher than would be expected if there were no familial clustering. Segregation analysis, using PAP (rev.4.0), was undertaken to clarify the mode of inheritance. Among the Mendelian single-locus models, an additive model was favored over either a dominant, recessive, or codominant model. The single-locus model could be rejected when compared with the mixed Mendelian model (inclusion of a polygenic background), although the major-gene component tends to be recessive.(ABSTRACT TRUNCATED AT 250 WORDS)

Adolescent↗
PubMed2003

Intracranial plasma cell granuloma with genetic analysis.

BACKGROUND: Plasma cell granuloma of the central nervous system is rare and less than 30 cases have been reported in literature. METHOD/FINDINGS: A 64-year-old woman complained of headache, and computed tomography (CT) and magnetic resonance (MR) imaging of the brain revealed a tumour at the right anterior-third parasagittal region which led us to diagnose a parasagittal meningioma. We performed total resection of the tumour and the pathological diagnosis was plasma cell granuloma. Polymerase chain reaction (PCR) analysis of immunoglobulin heavy chain (IgH) gene rearrangements produced no monoclonal band. This patient underwent no supplementary treatment and no recurrent tumour was observed for 3 years. INTERPRETATION: A case of plasma cell granuloma which is diagnosed with genetic analysis is presented. An analysis of the clonality using the PCR procedure would play an important role in supporting the pathological and clinical diagnosis.

Brain Diseases↗
PubMed1991

Genetic analysis of B-Peru, a regulatory gene in maize.

The B locus in maize is required for the accumulation of anthocyanin pigments. Numerous B alleles have been described: each determines a particular pattern of pigment synthesis with respect to the tissues that are pigmented and the time during development that pigment synthesis begins. We report here a genetic analysis of one B allele, B-Peru, which regulates synthesis of pigments in both kernel and plant tissues. We used stocks with active Mutator transposable elements to produce eight mutations in B-Peru. All eight alter pigment synthesis in all the kernel and plant tissues pigmented by B-Peru, suggesting that each mutation has disrupted a region of the gene required for expression in all tissues. Six of the mutations cause a colorless phenotype, while two cause a reduction in pigment in both kernel and plant tissues. Four of the mutations are unstable, and four are stable upon self-pollination. Multiple independent revertants were isolated from each unstable allele. DNA blot analysis demonstrated that all eight mutants are the result of insertions within an approximately 5-kb region that encodes the B-Peru transcript. One of the four unstable alleles contains a Mu element, Mu1.7. Two others contain insertions related to the Spm family of transposable elements. Thus, our Mutator stocks also contained active transposable elements from the unrelated Spm family. Our experiments suggest that the B-Peru allele is not complex, but contains a single coding region that regulates pigment synthesis in multiple tissues.

Alleles↗