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PubMed1992

[Molecular genetics of the human brain].

The review discusses the contribution of molecular genetic studies to the understanding of human brain performance and defines three genetic objectives: 1) to reveal structural or functional features of brain genes specific merely to man; 2) to outline the complete spectrum of genes involved in brain activity and their regulation; 3) to search for genes and genetic defects resulting in common mental disorders. The plasticity and great variety of brain functions are shown to be based on the unique diversity of genes actively transcribing in the brain and the molecular mechanisms of various genetic products of the same gene: alternative splicing, "antiparallel" coding, regulation of gene activity by signal DNA sequences. Gene search policies are described for common mental disorders such as schizophrenia, manic-depressive psychosis, Alzheimer's disease. The attempts to map defective genes by "reverse" genetics have proved that there is a genetic heterogeneity of these diseases. The novel directions in the study of the brain molecular genetic apparatus can be examinations of chromosomal behavior in the cells in various brain regions and genome imprinting.

Base Sequence↗

PubMed1992

Genetic linkage analysis in hypertension: principles and practice.

BACKGROUND: Primary hypertension is a hereditary disorder characterized by a complex etiological interplay of multiple genetic and environmental factors, until now defying attempts at identifying pathogenetically important genes. The marriage of classical genetics and molecular techniques is now offering a powerful set of tools to uncover such disease-relevant genes. SUMMARY: Based upon the availability of methods to directly examine chromosomal and genomic DNA structures, molecular genetics has at its disposal today an array of markers far more numerous and specific than the phenotype parameters used in classical genetics. In addition, use of DNA polymorphisms takes the process of genetic analysis immediately to that level of investigation--the genome--from which relevant data will ultimately come forth. The deployment of these tools in the pursuit of elucidating the pathogenesis of hereditary hypertension, and their use for two commonly applied strategies, candidate gene analysis and reverse genetics, are discussed. SIGNIFICANCE: Whilst still in its early stages, the application of molecular genetic methods to the study of hereditary hypertension now holds the realistic promise of identifying disease-relevant genes. This will provide the basis for advanced diagnostic, preventive and therapeutic approaches.

Animals↗

PubMed1992

Familial screening for genetic haemochromatosis by means of DNA markers.

Genetic haemochromatosis (HFE) is a frequent and potentially fatal disease. Early phlebotomies may prevent complications. The recessive gene for HFE is unknown but closely linked to the HLA-A locus. No direct test for homozygosity for HFE is currently available, apart from HLA typing within the family of a patient with confirmed HFE. During a reverse genetic approach to identify the gene, we found three anonymous genomic probes (P3, P5, and I.82) derived from previously cloned YACs and physically mapped in the HLA class I region. P3 and P5 probes recognise 3 loci (P3A, P3B, P5) and I.82 one locus about 100 kb from HLA-A. Using five biallelic polymorphisms (I.82/BglII, P3B/EcoRV, P3B/PstI, P5/HindIII, P3A/PstI), we tested 198 HLA typed subjects from the families of 22 haemochromatosis patients. The information from the five polymorphisms was sufficient to identify unequivocally extended restriction haplotypes in all families. The restriction haplotypes cosegregate with the HFE allele and enable identification of genotypically identical sibs in all families studied. The linked DNA markers described in this article avoid the disadvantages of HLA serological typing and can be used in genetic counselling of HFE families.

DNA↗

PubMed1992

Colocalization of the gene for nephrogenic diabetes insipidus (DIR) and the vasopressin type 2 receptor gene (AVPR2) in the Xq28 region.

The gene for nephrogenic diabetes insipidus (DIR) and the vasopressin type 2 receptor gene (AVPR2) have both been localized in the Xqter region by genetic mapping and functional expression studies, respectively. In this paper genetic evidence that the DIR locus is localized distal to the DXS305 locus and that the functional gene for the V2 receptor is localized between the markers DXS269 and F8 is presented. These further refinements in the localization of both genes strengthen the assumption that both genes are identical and provide a rationale for cloning the gene by reversed genetics strategies.

Animals↗

PubMed2025

Genetic crosses reveal genomic loci responsible for virulence in Cryptosporidium parvum infection.

The relationship between parasite genotype and pathogenesis is largely unknown for Cryptosporidium, a leading cause of diarrheal disease in children. An array of parasites with similar genomes produces varied disease outcomes in different hosts. Here, we isolate and characterize Cryptosporidium parvum strains that show marked differences in virulence and persistence in mice. Taking advantage of the sexual life cycle of this eukaryotic pathogen, we use genetic crosses to discover the underlying chromosomal loci. Whole-genome sequencing and bulk segregant analysis of infection-selected progeny mapped three loci on chromosomes 2, 6, and 7 associated with the ability to colonize and persist in mice and the positions of drug resistance genes. The chromosome 6 locus encodes the hyper-polymorphic surface glycoprotein GP60. Reverse genetic studies in both parental strains demonstrate that GP60 controls parasite burden and virulence, but not persistence, and reveal the dominance of the less virulent allele, suggesting it restricts virulence.

Cryptosporidium parvum↗

PubMed1992

DNA sequences amplified in cancer cells: an interface between tumor biology and human genome analysis.

There is growing evidence that amplification of specific genes is associated with tumor progression. While several proto-oncogenes are known to be activated by amplification, it is clear that not all the genes involved in DNA amplification in human tumors have been discovered. Our approach to the identification of such genes is based on the 'reverse genetics' methodology. Anonymous amplified DNA fragments are cloned by virtue of their amplification in a given tumor. These sequences are mapped in the normal genome and hence define a new genetic locus. The amplified domain is isolated by long-range cloning and analyzed along three lines of investigation: new genes are sought that can explain the biological significance of the amplification; the structure of the domain is studied in normal cells and in the amplification unit in the cancer cell; attempts are made to identify molecular probes of diagnostic value within the amplified domain. This application of genome technology to cancer biology is demonstrated in our study of a new genomic domain at chromosome 10q26 which is amplified specifically in human gastric carcinomas.

Blotting, Southern↗

PubMed1992

Cloning and expression in Escherichia coli of a phoA gene encoding a phosphate-irrepressible alkaline phosphatase of Zymomonas mobilis.

The Zymomonas mobilis phoA gene, encoding a phosphate-irrepressible alkaline phosphatase (ZAPase), was cloned and its expression was studied in phoA mutants of Escherichia coli. The ZAPase was recovered in the soluble fraction of E. coli. The enzyme was synthesized constitutively and its synthesis not repressed by phosphate, unlike the phoA gene of E. coli. The phoA gene of Z. mobilis was mutagenized by Mini Mu PR13 and the mutated gene crossed into Z. mobilis in order to obtain phoA mutants by reverse genetics. Although Z. mobilis mutants with Mini Mu PR13 integrated in the chromosome were obtained, none had an allele replacement for none was defective in ZAPase.

Alkaline Phosphatase↗

PubMed1992

Prevalence of dystrophin-positive fibers in 85 Duchenne muscular dystrophy patients.

The prevalence of dystrophin-positive fibers in Duchenne muscular dystrophy (DMD) muscle was estimated by direct counting on immunostained sections in a series of biopsy specimens from 85 patients, 42 of which were also screened for intragenic deletions by cDNA probes. Dystrophin-positive fibres are normotrophic and occur in muscle sections at a frequency between 0.01 and 6.81%. Frequencies over 1% were found only in patients older than 6 yr. The prevalence of dystrophin-positive fibers is about the same in patients with detectable and with undetectable deletions. The occurrence of positive fibers in small clusters supports the hypothesis of their clonal origin, suggesting that they may result from genetic reversion. No clinical differences were noticed in DMD patients of similar age with respect to the occurrence of dystrophin-positive fibres in their muscle biopsies.

Aging↗

PubMed2026

Aphid symbiotic virus engineered for in vivo expression of insecticidal effectors.

Microbial pesticides are eco-friendly alternatives to chemical pesticides. However, few viral pesticides have been developed. Insects harbor diverse symbiotic viruses, which have the potential to be engineered for translational applications in pest control. Here, we engineered Acyrthosiphon pisum virus (APV), a symbiotic virus of the pea aphid, to deliver anti-aphid effectors using reverse genetics technology. A cytomegalovirus (CMV) promoter-driven APV infectious clone was successfully rescued in pea aphids with the assistance of nanocarrier star polymer (SPc). Based on this infectious clone, the protein coding sequence of chymotrypsin inhibitor variant 8 (Chy8) and the double-stranded RNA sequence targeting the aphid clip-domain serine protease (SPLP) were separately assembled into the APV genome to generate APV-Chy8 and APV-dsSPLP infectious clones, respectively. The recombinant APV clones reduced aphid relative survival rates by 34% and 17% by microinjection, respectively. To enhance the transcriptional efficiency, the APV-Chy8 and APV-dsSPLP clones were transcribed in vitro using the T7 promoter. The in vitro-synthesized APV-Chy8 and APV-dsSPLP clones reduced aphid relative survival rates by 48% and 45% by microinjection, respectively. These results demonstrate that engineered APV can deliver cargos and reduce aphid survival under injection-based experimental conditions, highlighting the potential of symbiotic virus-based vectors for delivering insecticidal effectors.

Animals↗

PubMed1992

High-efficiency clonal growth of bloodstream- and insect-form Trypanosoma brucei on agarose plates.

This report describes a method for growing both bloodstream- and procyclic-form Trypanosoma brucei as colonies on agarose plates. Procyclic colonies, which took 2 weeks to develop, grew with approximately 17% plating efficiency on SDM-79/0.65% agarose supplemented with 20% (vol/vol) conditioned medium. Bloodstream forms were adapted to in vitro growth in liquid HMI-9 medium and then spread on HMI-9/0.65% agarose plates, where they grew to visible colonies in 3-5 days. Plating efficiencies were from 3 to 80%, depending upon the trypanosome variant and experiment. Colonies were proven to be the result of growth from a single cell and contained approximately 10(6) cells at maturity. Colonies were transferred to filters and probed for multicopy and single-copy genes. Potential uses of this method in conjunction with classical and reverse genetic approaches to studying trypanosomes are discussed.

Animals↗

PubMed1992

Intrahypothalamic injection of a cell line secreting gonadotropin-releasing hormone results in cellular differentiation and reversal of hypogonadism in mutant mice.

GT1 is an immortalized cell line that synthesizes and secretes the neurohormone gonadotropin-releasing hormone (GnRH). We have placed these cells into the brains of adult mutant hypogonadal (hpg) mice, which lack a functional GnRH gene, to determine whether such cells could differentiate in situ and support gonadal development. Immunocytochemical detection of GnRH revealed that these cells migrated widely in the central nervous system and elaborated axonal processes which on rare occasion projected to the normal target, the median eminence. Using a battery of antibodies, we demonstrated that these cells could cleave the GnRH precursor and that the amidated decapeptide as well as other cleavage products were present. The presence of biologically active material and its appropriate secretion were further documented by gonadal growth in both males and females. The morphological differentiation of the GT1 cells correlated with the density of cells injected. Those remaining within the injection site and/or forming a tumor retained a simple, rounded or fibroblastic appearance. Those cells that migrated into the host away from such tumors assumed the simple fusiform shape of normal GnRH neurons with dendrites extending from one or both poles. When cell density was drastically reduced a much more complex dendritic arbor was elaborated. These data suggest that such cell lines can be useful in reversing genetic defects and in studying such processes as GnRH neuronal migration, axonal targeting, and cytological differentiation.

Animals↗

PubMed2001

Bunyamwera bunyavirus nonstructural protein NSs is a nonessential gene product that contributes to viral pathogenesis.

Bunyamwera virus (family Bunyaviridae, genus Bunyavirus) contains a tripartite negative-sense RNA genome. The smallest RNA segment, S, encodes the nucleocapsid protein N and a nonstructural protein, NSs, in overlapping reading frames. We have generated a mutant virus lacking NSs, called BUNdelNSs, by reverse genetics. Compared with the wild-type (wt) virus, BUNdelNSs exhibited a smaller plaque size and generated titers of virus approximately 1 log lower. In mammalian cells, the mutant expressed greatly increased levels of N protein; significantly, the marked inhibition of host cell protein synthesis shown by wt virus was considerably impaired by BUNdelNSs. When inoculated by the intracerebral route BUNdelNSs killed BALB/c mice with a slower time course than wt and exhibited a reduced cell-to-cell spread, and titers of virus in the brain were lower. In addition, the abrogation of NSs expression changed Bunyamwera virus from a noninducer to an inducer of an interferon-beta promoter. These results suggest that, although not essential for growth in tissue culture or in mice, the bunyavirus NSs protein has several functions in the virus life cycle and contributes to viral pathogenesis.

Aedes↗

PubMed1992

CMAP: contig mapping and analysis package, a relational database for chromosome reconstruction.

In the contig mapping and analysis package, CMAP, we provide a foundation for reverse genetics by organizing information about DNA fragments obtained from an organism's genome into a physical map. The user can store information about a particular segment of DNA. This information can be both descriptive, such as any genes contained in a particular DNA fragment, or experimental, such as hybridization profiles or restriction digest patterns for comparison with other fragments. The package can then be instructed to update the physical map or provide information on a DNA fragment within the map, such as its location. The user interface is designed to minimize the learning curve associated with database usage, while eliminating the possibility of entering data outside the ranges of fields through error-checking protocols. Queries are currently accomplished by the use of dynamic SQL (structured query language), which gives the user the ability to build queries based on any combination of the attributes contained within the database without requiring that all possible queries be permanently programmed within the query software. In order to eliminate the need for knowledge of SQL, an interface was designed to allow users to build queries by menu choices. Thus, CMAP is a software package supporting a database for both the production and storage of a physical map as well as being the first step toward the production of a physical mapping workstation.

Algorithms↗

PubMed1992

Sexual development genes of Neurospora crassa.

The filamentous fungus Neurospora crassa undergoes a complex program of sexual development to form a fruiting body composed of several kinds of specialized tissue. Subtractive hybridization was used to isolate genes that are expressed preferentially during this sexual phase. Many such sexual development (sdv) genes were identified in a cosmid library of Neurospora genomic DNA. Fourteen of the sdv genes were subcloned, and their expression in mutant strains and under crossing and vegetative growth conditions was examined. All of the regulated transcripts were less abundant (and in many cases not detectable) in strains grown under vegetative (high nitrogen) conditions, suggesting that nitrogen starvation is required for their synthesis. The expression of most of the sdv genes also required a functional A mating type product, even under crossing growth conditions, suggesting that this product functions as a master control in sexual development. To determine if the products of the sdv genes play essential roles in the sexual cycle, a reverse-genetic approach (based on RIP (repeat-induced point mutation)-mediated gene disruptions) was used to create mutations in the genes. A mutant strain (asd-1) with a recessive crossing defect (apparently caused by the RIP process) was isolated; in this strain, early development is normal and may asci are formed, but ascospores are never delineated. A second recessive mutant strain (asd-2) was apparently created by ectopic integration of the transforming DNA into a gene required for the sexual process; in this strain the sexual process was blocked at an early stage, and the ascogeneous tissue underwent little development.

Cell Differentiation↗

PubMed1992

Gene targeting for somatic cell manipulation: rapid analysis of reduced chromosome hybrids by Alu-PCR fingerprinting and chromosome painting.

The techniques of reverse genetics rely heavily on parasexual methods for manipulating the human genome. However, the application of somatic cell genetics is severely limited by the availability of suitable endogenous selectable markers in the genome. We have addressed this problem by targeting a universally selectable marker into a predetermined region of the genome, using a stringent selection for homologous recombination. Correct gene targeting to human chromosome 7q11 was screened for by Southern blotting and confirmed by fluorescent in situ hybridization. Reduced chromosome 7 hybrids were generated by chromosome mediated gene transfer and selection for the neo gene. The resultant transgenomes were characterized by a combination of L1 fingerprinting, locus specific marker analysis, Alu-PCR and chromosome 'painting'. Alu-PCR and L1 'fingerprints' are complementary and mutually consistent. Chromosome 'painting' reflects and extends the results obtained for specific marker co-transfer. Thus Alu-PCR 'fingerprinting' and 'painting' combine to rapidly provide an accurate picture of transgenome content and complexity. Gene targeting, chromosome tagging and subsequent isolation can be applied to any region of the genome for which a molecular probe is available.

Animals↗

PubMed2025

Orthobunyavirus neurovirulence is a complex trait involving all three genome segments.

La Crosse orthobunyavirus (LACV) is a tri-segmented negative sense RNA virus and is the leading cause of pediatric arboviral encephalitis in the USA. The viral factors that mediate LACV's ability to replicate and cause damage and disease in the brain (neurovirulence) are not fully understood. We previously characterized the neurovirulence of LACV and closely related Inkoo virus (INKV) and discovered they have opposing neurovirulence phenotypes in mice and human neuronal cells: LACV has high neurovirulence and INKV has low neurovirulence. We therefore generated reassortant viruses between LACV and INKV to map the genome segments that mediate LACV's high neurovirulence phenotype. We recovered all six possible reassortant viruses of the L, M, and S genome segments using coinfection and reverse genetics approaches. We evaluated the neurovirulence of these reassortant viruses in mice in vivo and in human neuronal cells in vitro. Our results show that no single LACV genome segment alone was sufficient to cause wildtype LACV-like neurological disease in mice, and in fact all six reassortant viruses were attenuated from wildtype LACV. We found that the LACV M and S segments together were the primary drivers of neurological disease in mice, whereas the LACV L segment played a minor role. Our in vitro results indicate that the LACV M segment is crucial for efficient replication in neurons, but the LACV L segment appears to mediate slightly more efficient neuronal replication than the INKV L segment. The LACV M and S segments together induced wildtype LACV-like levels of neuronal death, indicating the LACV M and S are the primary mediators of neuronal death, and the L segment is not required. Together, these results indicate that LACV neurovirulence is a complex trait mediated by viral proteins on all three genome segments.

Journal Article↗

PubMed2026

A sequence-based classifier distinguishes phenotype-associated genes from other gene models in plants.

Only a small fraction of annotated plant genes possess experimentally validated associations with specific phenotypes. Phenotype-associated genes have distinct structural, molecular, and evolutionary characteristics compared with nonvalidated gene models. Here, we develop a simple classifier that uses sequence and evolutionary features, which can be generated for any species with an annotated reference genome assembly, to accurately distinguish phenotype-associated genes from both the overall population of annotated gene models and a specific set of genes identified as being tolerant of premature stop mutations. A model trained solely on genes from maize (Zea mays) identifies and prioritizes rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana) genes that are highly enriched in genes with experimentally validated links to phenotypes in both of these evolutionarily distant species. Gene models predicted to have a higher probability of being linked to phenotypes display patterns consistent with known biological properties of phenotype-associated genes. Notably, the sets of genes predicted to have a high probability of being linked to phenotype variation do not consist exclusively of well-characterized gene families but included many uncharacterized gene families carrying domains of unknown function. The quantitative scores generated by this model offer a valuable resource for prioritizing and exploring the vast number of uncharacterized gene models in plants, reducing the risk of failure in future reverse genetic efforts and potentially accelerating gene discovery and functional annotation in crops.

Phenotype↗

PubMed1992

The Trk family of tyrosine kinases: receptors for NGF-related neurotrophins.

Neurotrophins are known to have important functions in the survival of embryonic and adult subpopulations of neurons. The identification of Trk family RTKs as receptors for NGF-related neurotrophins indicates phosphotyrosine-mediated signal transduction as a principal mechanism for neurotrophin signaling. Previous trk and trkB expression studies (Klein et al. 1989, 1990b; Martin-Zanca et al. 1990) and more recent studies with trkC (L. Tessarollo et al., in prep.) provide important clues about function. Thus, trkB and trkC expression in motor neurons and in many nonneuronal cells suggests that these cells are targets for neurotrophin action in vivo, even though this has not been demonstrated in the classic in vitro survival assays. Expression of trkB and trkC in nonneuronal cells implies that these receptors may act in additional aspects of organogenesis and development. Current approaches to assay Trk receptor and neurotrophin function will be complemented by further studies in the living organism. Transgenic approaches aimed at ectopic expression and at interfering with normal receptor function should provide additional insights. Finally, reverse genetic approaches using targeted mutation of Trk receptors in embryonic stem cells (Stanton et al. 1992) will allow assessment of critical receptor requirements and provide powerful reagents for studying nervous system development and function.

Animals↗