40 research outputs found
Identification of cis-suppression of human disease mutations by comparative genomics.
No full textPatterns of amino acid conservation have served as a tool for understanding protein evolution. The same principles have also found broad application in human genomics, driven by the need to interpret the pathogenic potential of variants in patients. Here we performed a systematic comparative genomics analysis of human disease-causing missense variants. We found that an appreciable fraction of disease-causing alleles are fixed in the genomes of other species, suggesting a role for genomic context. We developed a model of genetic interactions that predicts most of these to be simple pairwise compensations. Functional testing of this model on two known human disease genes revealed discrete cis amino acid residues that, although benign on their own, could rescue the human mutations in vivo. This approach was also applied to ab initio gene discovery to support the identification of a de novo disease driver in BTG2 that is subject to protective cis-modification in more than 50 species. Finally, on the basis of our data and models, we developed a computational tool to predict candidate residues subject to compensation. Taken together, our data highlight the importance of cis-genomic context as a contributor to protein evolution; they provide an insight into the complexity of allele effect on phenotype; and they are likely to assist methods for predicting allele pathogenicity
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Neonatal enteral feeding tube as loci for Enterobacteriaceae colonisation and risk to neonatal health
No full textThe incidence of neonatal infections caused by Enterobacteriaceae has been increasing in recent years, and they are now recognised as the predominant causative agents in neonatal intensive care unit (NICU) outbreaks. Klebsiella spp. and Serratia spp. are the most common causative pathogens, and E. coli is one of the leading causes of neonatal meningitis and sepsis. The infant intestinal flora is influenced by the feeding regime. This study focuses on assessing the risk to neonates from the ingestion of the Enterobacteriaceae such as; Enterobacter hormaechei, Enterobacter ludwigii, Enterobacter aerogenes, Enterobacter cloacae and Klebsiella oxytoca. The strains under study were isolated from two sources; human mastic breast milk (MBM) and neonatal nasogastric enteral feeding tubes (EFT). The overall aim was to evaluate the risk to neonates posed by the ingestion of these organisms either from contaminated breast milk or from infant formula. Due to the lack of adequate source information, it was necessary to first confirm the identity of the strains under investigation. This was achieved using standard biochemical profiles (phenotyping) and where necessary 16S rDNA sequence analysis. Secondly, it was necessary to determine whether all strains were unique or if any were multiple isolations of the same strain. This was achieved using Pulsed-Field Gel Electrophoresis (PFGE). To determine the potential exposure of neonates to these organisms, a range of physiological and virulence related assays were undertaken; heat tolerance to 55°C, biofilm formation, capsule formation and acidic pH survival (pH 3.5)
De Novo Pathogenic Variants in CACNA1E Cause Developmental and Epileptic Encephalopathy with Contractures, Macrocephaly, and Dyskinesias.
No full text(The American Journal of Human Genetics 103, 666–678; November 1, 2018) In the version of this article originally published online, Qinghe Xing's name was misspelled as Qinghe Xin. Also, Azita Sadeghpour, Erica E. Davis, and Nicholas Katsanis (all at Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27701, USA) and the Task Force for Neonatal Genomics were omitted from the author list. The members of the Task Force for Neonatal Genomics are as follows: Alexander Allori, Misha Angrist, Patricia Ashley, Margarita Bidegain, Brita Boyd, Eileen Chambers, Heidi Cope, C. Michael Cotten, Theresa Curington, Erica E. Davis, Sarah Ellestad, Kimberley Fisher, Amanda French, William Gallentine, Ronald Goldberg, Kevin Hill, Sujay Kansagra, Nicholas Katsanis, Sara Katsanis, Joanne Kurtzberg, Jeffrey Marcus, Marie McDonald, Mohammed Mikati, Stephen Miller, Amy Murtha, Yezmin Perilla, Carolyn Pizoli, Todd Purves, Sherry Ross, Azita Sadeghpour, Edward Smith, and John Wiener. The authors apologize for these omissions
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Conference-EC-US Task Force Joint US-EU Workshop on Metabolomics and Environmental Biotechnology
No full textSince 1990, the EC-US Task Force on Biotechnology Research has been coordinating transatlantic efforts to guide and exploit the ongoing revolution in biotechnology and the life sciences. The Task Force was established in June 1990 by the European Commission and the White House Office of Science and Technology Policy. The Task Force has acted as an effective forum for discussion, coordination, and development of new ideas for the last 18 years. Task Force members are European Commission and US Government science and technology administrators who meet annually to enhance communication across the Atlantic, and to encourage collaborative research. Through sponsoring workshops, and other activities, the Task Force also brings together scientific leaders and early career researchers from both sides of the Atlantic to forecast research challenges and opportunities and to promote better links between researchers. Over the years, by keeping a focus on the future of science, the Task Force has played a key role in establishing a diverse range of emerging scientific fields, including biodiversity research, neuroinformatics, genomics, nanobiotechnology, neonatal immunology, transkingdom molecular biology, biologically-based fuels, and environmental biotechnology. The EC-US Task Force has sponsored a number of Working Groups on topics of mutual transatlantic interest. The idea to create a Working Group on Environmental Biotechnology research was discussed in the Task Force meeting of October 1993. The EC-US Working Group on Environmental Biotechnology set as its mission 'To train the next generation of leaders in environmental biotechnology in the United States and the European Union to work collaboratively across the Atlantic.' Since 1995, the Working Group supported three kinds of activities, all of which focus one early career scientists: (1) Workshops on the use of molecular methods and genomics in environmental biotechnology; (2) Short courses with theoretical, laboratory and field elements; and (3) Short term exchange fellowships. The short term exchange fellowships were created to enable young scientists to develop collaborations with colleagues across the Atlantic and to learn a new skill or expertise in the area of environmental biotechnology
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Diversity and virulence of the genus Cronobacter revealed by multilocus sequence typing (MLST) and comparative genomic analysis
No full textCronobacter spp. (previously known as Enterobacter sakazakii) is a diverse bacterial genus consisting of opportunistic food-borne pathogens affecting all age groups, with particularly severe clinical complications such as meningitis and necrotising enterocolitis in neonates and infants. In this study, a multilocus sequence typing (MLST) approach has been established to span the entire Cronobacter genus, by employing the alleles of 7 housekeeping genes (atpD, fusA, glnS, gltB, gyrB, infB and ppsA, total length 3036 bp). The 325 Cronobacter spp. strains used in the study included isolates from the highly publicised Cronobacter cases from USA in December 2011. The scheme identified 115 sequence types (ST) across the seven Cronobacter species. Multilocus sequence analysis (MLSA) revealed considerable diversity in the genus, with intraspecific variation ranging from low diversity in C. sakazakii to extensive diversity within some species such as C. muytjensii and C. dublinensis including evidence of recombination events between species. An evolutionary analysis revealed the Cronobacter genus to have evolved 45-68 million years ago, during the period of evolution of flowering plants. The MLSA was also used in a polyphasic study for the formal recognition of two new species – C. universalis and C. condimenti. The MLST scheme also revealed the high level of clonality in the species C. sakazakii and C. malonaticus. ST4 was found to be a highly stable clone of C. sakazakii, and a strong association was established between the C. sakazakii ST4 clonal complex with neonatal meningitis cases
CHROMOSOMAL ANALYSIS OF MENTALLY RETARDED CHILDREN WITH MICROCEPHALY
No full textBackground: Mental retardation is a common condition with the incidence of 1- 3% of the entire population; about 25% - 50% of them are genetic causes. Chromosomal causes account for up to 28%. Microcephaly and mental retardation
may occur together as a syndrome. Cytogenetic and molecular analysis has been approved to definitively diagnose those syndromes. This research is aimed to know the chromosomal characteristic of children with mental retardation and
microcephaly.
Method: This research is observational descriptive study with retrospective data taken start from 2007-2009. The data of head circumference and chromosome analysis from 39 children were processed. The data are then presented as a
descriptive statistic after being analyzed using Microsoft Excel 2007.
Results: Chromosomal analysis results shows 18 (46.15%) children with 46,XX karyotype, 11 (28.21%) children with 46, XY karyotype, 5 (12.82%) children with 47,XX+21 karyotype, and 4 (10.26%) children with 47,XY+21 karyotype. There is also one Robertsonian translocation with 46,XX,+21, t(14;21) karyotype.
Conclusion: Normal karyotype (46,XX and 46,XY) were found in 29 (74.36%) children. Visible chromosomal abnormalities detected includes 9 cases of Down syndrome trisomy 21 and one case of Robertsonian translocation with t(14;21)
karyotype.
Keyword: Mental retardation, microcephaly, chromosomal analysi
Genetic analysis of human absence epilepsy
No full textIdiopathic Mendelian epilepsies have been typically identified as channelopathies. Evidence suggests that mutations in genes encoding GABAA receptors, GABAB receptors or voltage-dependent calcium channels (VDCCs) may underlie childhood absence epilepsy (CAE), an idiopathic generalised epilepsy with complex inheritance.
The aims of this project were:
i) Ascertainment of a patient resource
ii) Investigation of candidate genes by linkage analysis
iii) Mutation analysis by direct sequencing
iv) Construction of single nucleotide polymorphism (SNP) based haplotypes in candidate genes
v) Intra-familial association analysis using SNP based haplotypes
DNA and clinical data were obtained from: 53 nuclear CAE pedigrees; 29 families including individuals with CAE and a broader „absence‟ epilepsy phenotype; 217 parent-child trios; a North American family in which absence epilepsy segregates with episodic ataxia type 2 (EA2)
Sixteen calcium channel genes and seven GABAA and two GABAB receptor subunit genes were excluded by linkage analysis. Significant linkage was demonstrated for CACNG3 on chromosome 16p12-p13.1 for both CAE and the broader absence phenotype. Positive linkage was also obtained at the GABRA5, GABRB3, GABRG3 cluster on chromosome 15q11-q13. Non-parametric linkage analysis was significant at both the 16p and 15q loci. Two-locus analysis supported a digenic effect from these two loci. Sequencing of CACNG3 revealed 34 sequence variants, none clearly causal, although bioinformatic analysis provided supportive functional evidence. Association analysis showed significant transmission disequilibrium both for individual single nucleotide polymorphisms (SNPs) and SNP based haplotypes spanning CACNG3. This work has provided genetic evidence that CACNG3 and at least one of the three GABAA receptor genes are susceptibility loci for absence epilepsy.
Linkage analysis performed in the family with absence epilepsy and EA2 was suggestive that the VDCC CACNA1A was the causative gene. This was subsequently confirmed by sequence analysis in collaboration with the Institute of Neurology, UCL. This is the first reported family in which a CACNA1A mutation that impairs calcium channel function cosegregates with typical absence seizures and 3Hz spike-wave discharges on EEG
Mutations in NCAPG2 Cause a Severe Neurodevelopmental Syndrome that Expands the Phenotypic Spectrum of Condensinopathies.
No full textThe use of whole-exome and whole-genome sequencing has been a catalyst for a genotype-first approach to diagnostics. Under this paradigm, we have implemented systematic sequencing of neonates and young children with a suspected genetic disorder. Here, we report on two families with recessive mutations in NCAPG2 and overlapping clinical phenotypes that include severe neurodevelopmental defects, failure to thrive, ocular abnormalities, and defects in urogenital and limb morphogenesis. NCAPG2 encodes a member of the condensin II complex, necessary for the condensation of chromosomes prior to cell division. Consistent with a causal role for NCAPG2, we found abnormal chromosome condensation, augmented anaphase chromatin-bridge formation, and micronuclei in daughter cells of proband skin fibroblasts. To test the functional relevance of the discovered variants, we generated an ncapg2 zebrafish model. Morphants displayed clinically relevant phenotypes, such as renal anomalies, microcephaly, and concomitant increases in apoptosis and altered mitotic progression. These could be rescued by wild-type but not mutant human NCAPG2 mRNA and were recapitulated in CRISPR-Cas9 F0 mutants. Finally, we noted that the individual with a complex urogenital defect also harbored a heterozygous NPHP1 deletion, a common contributor to nephronophthisis. To test whether sensitization at the NPHP1 locus might contribute to a more severe renal phenotype, we co-suppressed nphp1 and ncapg2, which resulted in significantly more dysplastic renal tubules in zebrafish larvae. Together, our data suggest that impaired function of NCAPG2 results in a severe condensinopathy, and they highlight the potential utility of examining candidate pathogenic lesions beyond the primary disease locus
Molecular biology of hearing
No full textThe inner ear is our most sensitive sensory organ and can be subdivided into three functional units: organ of Corti, stria vascularis and spiral ganglion. The appropriate stimulus for the organ of hearing is sound, which travels through the external auditory canal to the middle ear where it is transmitted to the inner ear. The inner ear houses the hair cells, the sensory cells of hearing. The inner hair cells are capable of mechanotransduction, the transformation of mechanical force into an electrical signal, which is the basic principle of hearing. The stria vascularis generates the endocochlear potential and maintains the ionic homeostasis of the endolymph. The dendrites of the spiral ganglion form synaptic contacts with the hair cells. The spiral ganglion is composed of neurons that transmit the electrical signals from the cochlea to the central nervous system. In recent years there has been significant progress in research on the molecular basis of hearing. An increasing number of genes and proteins related to hearing are being identified and characterized. The growing knowledge of these genes contributes not only to greater appreciation of the mechanism of hearing but also to a deeper understanding of the molecular basis of hereditary hearing loss. This basic research is a prerequisite for the development of molecular diagnostics and novel therapies for hearing loss
