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In JoVE (1)
- विकास और वयस्क स्टेज में स्थिर माध्यमिक मेटाबोलिक फ्लक्स के समस्थानिक रूपरेखा Caenorhabditis एलिगेंस
Other Publications (26)
- American Journal of Medical Genetics. Part A
- American Journal of Medical Genetics. Part A
- Primary Care
- Pediatric Neurology
- Current Biology : CB
- Molecular Genetics and Metabolism
- PLoS Genetics
- PloS One
- Current Treatment Options in Neurology
- Molecular Genetics and Metabolism
- Journal of Developmental and Behavioral Pediatrics : JDBP
- Developmental Disabilities Research Reviews
- Developmental Disabilities Research Reviews
- Current Opinion in Pediatrics
- EMBO Molecular Medicine
- Current Opinion in Ophthalmology
- BMC Bioinformatics
- Current Biology : CB
- Human Mutation
- Methods in Molecular Biology (Clifton, N.J.)
- Methods in Molecular Biology (Clifton, N.J.)
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Articles by Marni J. Falk in JoVE
विकास और वयस्क स्टेज में स्थिर माध्यमिक मेटाबोलिक फ्लक्स के समस्थानिक रूपरेखा Caenorhabditis एलिगेंस
Marni J. Falk1,2, Meera Rao*1, Julian Ostrovsky*1, Evgueni Daikhin1, Ilana Nissim1, Marc Yudkoff1,2
1Department of Pediatrics, The Children's Hospital of Philadelphia, 2Department of Pediatrics, University of Pennsylvania
मध्यस्थ चयापचय प्रवाह की गैस क्रोमैटोग्राफी जन spectrometric विश्लेषण से स्थिर समस्थानिक रूपरेखा निमेटोड में वर्णित है,
Other articles by Marni J. Falk on PubMed
Pediatrics. Mar, 2003 | Pubmed ID: 12612238
Several studies have reported beneficial effects of bisphosphonates in children with osteogenesis imperfecta (OI); however, these studies have differed in the protocols they used, and none has been independently replicated. We intended to confirm the efficacy of a specific intravenous bisphosphonate protocol in children with moderate to severe OI.
American Journal of Medical Genetics. Part A. Jul, 2003 | Pubmed ID: 12838558
A patient who refuses to notify their relatives of potential at-risk status brings a genetics provider to face conflicting ethical principles and ill-defined legal precedent. Genetics professionals' views on the disclosure of patient information to at-risk relatives have remained largely unexamined. Prior analyses have been limited to identifying factors contributing to genetics providers' self-predicted responses in hypothetical scenarios. Our group was the first to examine the clinical experience of genetic counselors with this issue [Dugan et al., 2003]. We report here results from our follow-up survey of medical geneticists who are members of either the American Society of Human Genetics and/or American College of Medical Genetics in an effort to identify their experiences in warning at-risk relatives and the factors driving their decision-making processes. Over two-thirds of medical geneticists surveyed (69%, 143/206) believe they do bear responsibility to warn their patients' relatives when found to be at-risk for genetic disease. One-quarter (25%, 31/123) of medical geneticists who faced the dilemma of a patient refusing to notify their at-risk relatives seriously considered disclosure to those at-risk relatives without patient consent. Only four respondents proceeded to warn at-risk relatives of their status. Whereas genetic counselors cited emotional issues as playing a primary role in their decision not to warn, medical geneticists identified patient confidentiality, eventual case resolution by other means, and legal liability as the major factors leading to non-disclosure in 76% of actual scenarios. Responsibilities of medical geneticists, genetic counselors, and non-genetics healthcare professionals facing this issue will need to be more clearly defined to provide optimal medical care within the bounds of acceptable practice.
American Journal of Medical Genetics. Part A. Jul, 2004 | Pubmed ID: 15211651
We describe eight members from two large Amish kindreds who share a phenotype characterized by early-onset pigmentary retinopathy and myopia, global developmental delay and mental retardation, microcephaly, short stature, hypotonia, joint hyperextensibility, small hands and feet, common facial appearance, and friendly disposition. Several of the children had intermittent granulocytopenia. The phenotypic occurrence in three siblings coupled with the increased coefficient of inbreeding in the Amish suggested that this disorder is autosomal recessive and due to a single founder allele. Despite similarity to the clinical features of Cohen syndrome, experienced dysmorphologists attending the 23rd David W. Smith Workshop suggested the facial gestalt of the Amish children was inconsistent with this diagnosis. We mapped the locus responsible for these individuals' phenotype to chromosome 8q22-q23, which contains the recently discovered Cohen syndrome gene, COH1. Complete sequencing of the COH1 gene identified a likely disease-causing frameshift mutation and a missense mutation in the Amish patients. A comparison of features among different Cohen syndrome populations with shared linkage to the COH1 locus or known COH1 gene mutations may allow for the determination of improved clinical criteria on which to suspect the diagnosis of Cohen syndrome. We conclude that facial gestalt seems to be an unreliable indicator of Cohen syndrome between ethnic populations, although it is quite consistent among affected individuals within a particular ethnic group. Other features common to almost all individuals with proven COH1 mutations, such as retinal dystrophy, myopia, microcephaly, mental retardation, global developmental delay, hypotonia, and joint hyperextensibility appear to be better clinical indicators of this disorder.
Primary Care. Sep, 2004 | Pubmed ID: 15331250
Children with congenital anomalies often represent a special diagnostic and management challenge. To provide optimal care for these children, one must employ a systematic approach to identify the likely pathogenic mechanism leading to the birth defects present. Determining how distinct anomalies relate to one another may lead to elucidation of a specific genetic etiology for the patient's condition. Genetic testing is increasingly available to allow for diagnostic confirmation. Using this systematic approach to a child with congenital anomalies permits accurate prognostic and recurrence risk counseling, informed management decisions, and the appropriate allocation of social support and medical resources.
Pediatric Neurology. Feb, 2005 | Pubmed ID: 15664772
Uniparental disomy is a genetic cause of disease implicated in a wide variety of neurologic disorders. A recently identified condition is maternal uniparental disomy for chromosome 14 (mUPD14) syndrome. A child with hypotonia and developmental delay was found to have mUPD14 after identification of a balanced karyotypic rearrangement involving both chromosomes 14. We explore the genetic mechanisms by which uniparental disomy can cause clinical abnormalities and karyotypic findings that should raise suspicion for uniparental disomy, review the literature on the mUPD14, and discuss clinical indications on which to suspect this diagnosis. Although it is more difficult to establish a diagnosis in the absence of visible karyotypic abnormalities involving chromosome 14, a distinct phenotype exists in mUPD14 syndrome: in utero growth restriction, congenital hypotonia, gross motor delay, arrested hydrocephalus, mild to moderate mental retardation, joint hyperextensibility, short stature, and precocious puberty. Testing for mUPD14 should be considered in infants with generalized hypotonia who have a history of in utero growth restriction.
Current Biology : CB. Aug, 2006 | Pubmed ID: 16920626
Despite the widespread clinical use of volatile anesthetics, their mechanisms of action remain unknown [1-6]. An unbiased genetic screen in the nematode C. elegans for animals with altered volatile anesthetic sensitivity identified a mutant in a nuclear-encoded subunit of mitochondrial complex I [7,8]. This raised the question of whether mitochondrial dysfunction might be the primary mechanism by which volatile anesthetics act, rather than an untoward secondary effect [9,10]. We report here analysis of additional C. elegans mutations in orthologs of human genes that contribute to the formation of complex I, complex II, complex III, and coenzyme Q [11-14]. To further characterize the specific contribution of complex I, we generated four hypomorphic C. elegans mutants encoding different complex I subunits . Our main finding is the identification of a clear correlation between complex I-dependent oxidative phosphorylation capacity and volatile anesthetic sensitivity. These extended data link a physiologic determinant of anesthetic action in a tractable animal model to similar clinical observations in children with mitochondrial myopathies . This work is the first to specifically implicate complex I-dependent oxidative phosphorylation function as a primary mediator of volatile anesthetic effect.
Pediatrics. Dec, 2007 | Pubmed ID: 18055683
Notorious variability in the presentation of mitochondrial disease in the infant and young child complicates its clinical diagnosis. Mitochondrial disease is not a single entity but, rather, a heterogeneous group of disorders characterized by impaired energy production due to genetically based oxidative phosphorylation dysfunction. Together, these disorders constitute the most common neurometabolic disease of childhood with an estimated minimal risk of developing mitochondrial disease of 1 in 5000. Diagnostic difficulty results from not only the variable and often nonspecific presentation of these disorders but also from the absence of a reliable biomarker specific for the screening or diagnosis of mitochondrial disease. A simplified and standardized approach to facilitate the clinical recognition of mitochondrial disease by primary physicians is needed. With this article we aimed to improve the clinical recognition of mitochondrial disease by primary care providers and empower the generalist to initiate appropriate baseline diagnostic testing before determining the need for specialist referral. This is particularly important in light of the international shortage of metabolism specialists to comprehensively evaluate this large and complex disease population. It is hoped that greater familiarity among primary care physicians with the protean manifestations of mitochondrial disease will facilitate the proper diagnosis and management of this growing cohort of pediatric patients who present across all specialties.
Molecular Genetics and Metabolism. May, 2008 | Pubmed ID: 18243024
Mitochondrial disease confirmation and establishment of a specific molecular diagnosis requires extensive clinical and laboratory evaluation. Dual genome origins of mitochondrial disease, multi-organ system manifestations, and an ever increasing spectrum of recognized phenotypes represent the main diagnostic challenges. To overcome these obstacles, compiling information from a variety of diagnostic laboratory modalities can often provide sufficient evidence to establish an etiology. These include blood and tissue histochemical and analyte measurements, neuroimaging, provocative testing, enzymatic assays of tissue samples and cultured cells, as well as DNA analysis. As interpretation of results from these multifaceted investigations can become quite complex, the Diagnostic Committee of the Mitochondrial Medicine Society developed this review to provide an overview of currently available and emerging methodologies for the diagnosis of primary mitochondrial disease, with a focus on disorders characterized by impairment of oxidative phosphorylation. The aim of this work is to facilitate the diagnosis of mitochondrial disease by geneticists, neurologists, and other metabolic specialists who face the challenge of evaluating patients of all ages with suspected mitochondrial disease.
PLoS Genetics. Apr, 2008 | Pubmed ID: 18437205
Coenzyme Q (CoQ) is an essential electron carrier in the respiratory chain whose deficiency has been implicated in a wide variety of human mitochondrial disease manifestations. Its multi-step biosynthesis involves production of polyisoprenoid diphosphate in a reaction that requires the enzymes be encoded by PDSS1 and PDSS2. Homozygous mutations in either of these genes, in humans, lead to severe neuromuscular disease, with nephrotic syndrome seen in PDSS2 deficiency. We now show that a presumed autoimmune kidney disease in mice with the missense Pdss2(kd/kd) genotype can be attributed to a mitochondrial CoQ biosynthetic defect. Levels of CoQ9 and CoQ10 in kidney homogenates from B6.Pdss2(kd/kd) mutants were significantly lower than those in B6 control mice. Disease manifestations originate specifically in glomerular podocytes, as renal disease is seen in Podocin/cre,Pdss2(loxP/loxP) knockout mice but not in conditional knockouts targeted to renal tubular epithelium, monocytes, or hepatocytes. Liver-conditional B6.Alb/cre,Pdss2(loxP/loxP) knockout mice have no overt disease despite demonstration that their livers have undetectable CoQ9 levels, impaired respiratory capacity, and significantly altered intermediary metabolism as evidenced by transcriptional profiling and amino acid quantitation. These data suggest that disease manifestations of CoQ deficiency relate to tissue-specific respiratory capacity thresholds, with glomerular podocytes displaying the greatest sensitivity to Pdss2 impairment.
Subcomplex Ilambda Specifically Controls Integrated Mitochondrial Functions in Caenorhabditis Elegans
PloS One. 2009 | Pubmed ID: 19672299
Complex I dysfunction is a common, heterogeneous cause of human mitochondrial disease having poorly understood pathogenesis. The extensive conservation of complex I composition between humans and Caenorhabditis elegans permits analysis of individual subunit contribution to mitochondrial functions at both the whole animal and mitochondrial levels. We provide the first experimentally-verified compilation of complex I composition in C. elegans, demonstrating 84% conservation with human complex I. Individual subunit contribution to mitochondrial respiratory capacity, holocomplex I assembly, and animal anesthetic behavior was studied in C. elegans by RNA interference-generated knockdown of nuclear genes encoding 28 complex I structural subunits and 2 assembly factors. Not all complex I subunits directly impact respiratory capacity. Subcomplex Ilambda subunits along the electron transfer pathway specifically control whole animal anesthetic sensitivity and complex II upregulation, proportionate to their relative impairment of complex I-dependent oxidative capacity. Translational analysis of complex I dysfunction facilitates mechanistic understanding of individual gene contribution to mitochondrial disease. We demonstrate that functional consequences of complex I deficiency vary with the particular subunit that is defective.
Current Treatment Options in Neurology. Nov, 2009 | Pubmed ID: 19891905
The treatment of mitochondrial disease varies considerably. Most experts use a combination of vitamins, optimize patients' nutrition and general health, and prevent worsening of symptoms during times of illness and physiologic stress. We agree with this approach, and we agree that therapies using vitamins and cofactors have value, though there is debate about the choice of these agents and the doses prescribed. Despite the paucity of high-quality scientific evidence, these therapies are relatively harmless, may alleviate select clinical symptoms, and theoretically may offer a means of staving off disease progression. Like many other mitochondrial medicine physicians, we have observed significant (and at times life-altering) clinical responses to such pharmacologic interventions. However, it is not yet proven that these therapies truly alter the course of the disease, and some experts may choose not to use these medications at all. At present, the evidence of their effectiveness does not rise to the level required for universal use. Based on our clinical experience and judgment, however, we agree that a therapeutic trial of coenzyme Q10, along with other antioxidants, should be attempted. Although individual specialists differ as to the exact drug cocktail, a common approach involves combinations of antioxidants that may have a synergistic effect. Because almost all relevant therapies are classified as medical foods or over-the-counter supplements, most physicians also attempt to balance the apparent clinical benefit of mitochondrial cocktails with the cost burden that these supplements pose for the family.
Mitochondrial Respiratory Chain Dysfunction Variably Increases Oxidant Stress in Caenorhabditis Elegans
Mitochondrion. Mar, 2010 | Pubmed ID: 19900588
Mitochondrial dysfunction and associated oxidant stress have been linked with numerous complex diseases and aging largely by in vitro determination of mitochondria oxidant production and scavenging. We applied targeted in vivo fluorescence analyses of mitochondria-dense pharyngeal tissue in Caenorhabditis elegans to better understand relative mitochondrial effects, particularly on matrix oxidant burden, of respiratory chain complex, MnSOD, and insulin receptor mutants displaying variable longevity. The data demonstrate significantly elevated in vivo matrix oxidant burden in the short-lived complex I mutant, gas-1(fc21), which was associated with limited superoxide scavenging capacity despite robust MnSOD induction, as well as decreased mitochondria content and membrane potential. Significantly increased MnSOD activity was associated with in vivo matrix oxidant levels similar to wild-type in the long-lived respiratory chain complex III mutant, isp-1(qm150). Yet, despite greater superoxide scavenging capacity in the complex III mutant than in the significantly longer-lived insulin receptor mutant, daf-2(e1368), only the former showed modest oxidative stress sensitivity. Furthermore, increased longevity was seen in MnSOD knockout mutants (sod-2(ok1030) and sod-2(gk257)) that had decreased MnSOD scavenging capacity and increased in vivo matrix oxidant burden. Thus, factors beside oxidant stress must underlie RC mutant longevity in C. elegans. This work highlights the utility of the C. elegans model as a tractable means to non-invasively monitor multi-dimensional in vivo consequences of primary mitochondrial dysfunction.
Molecular Genetics and Metabolism. Mar, 2010 | Pubmed ID: 19944634
Microarray expression profiling has become a valuable tool in the evaluation of the genetic consequences of metabolic disease. Although 3'-biased gene expression microarray platforms were the first generation to have widespread availability, newer platforms are gradually emerging that have more up-to-date content and/or higher cost efficiency. Deciphering the relative strengths and weaknesses of these various platforms for metabolic pathway-level analyses can be daunting. We sought to determine the practical strengths and weaknesses of four leading commercially available expression array platforms relative to biologic investigations, as well as assess the feasibility of cross-platform data integration for purposes of biochemical pathway analyses. Methods: Liver RNA from B6.Alb/cre,Pdss2(loxP/loxP) mice having primary coenzyme Q deficiency was extracted either at baseline or following treatment with an antioxidant/antihyperlipidemic agent, probucol. Target RNA samples were prepared and hybridized to Affymetrix 430 2.0, Affymetrix Gene 1.0 ST, Affymetrix Exon 1.0 ST, and Illumina Mouse WG-6 expression arrays. Probes on all platforms were re-mapped to coding sequences in the current version of the mouse genome. Data processing and statistical analysis were performed by R/Bioconductor functions, and pathway analyses were carried out by KEGG Atlas and GSEA. Results: Expression measurements were generally consistent across platforms. However, intensive probe-level comparison suggested that differences in probe locations were a major source of inter-platform variance. In addition, genes expressed at low or intermediate levels had lower inter-platform reproducibility than highly expressed genes. All platforms showed similar patterns of differential expression between sample groups, with 'steroid biosynthesis' consistently identified as the most down-regulated metabolic pathway by probucol treatment. Conclusions: This work offers a timely guide for metabolic disease investigators to enable informed end-user decisions regarding choice of expression microarray platform best-suited to specific research project goals. Successful cross-platform integration of biochemical pathway expression data is also demonstrated, especially for well-annotated and highly expressed genes. However, integration of gene-level expression data is limited by individual platform probe design and the expression level of target genes. Cross-platform analyses of biochemical pathway data will require additional data processing and novel computational bioinformatics tools to address unique statistical challenges.
Biochemistry. Sep, 2010 | Pubmed ID: 20677761
Mitochondrial function depends upon the coordinated expression of the mitochondrial and nuclear genomes. Although the basal factors that carry out the process of mitochondrial transcription are known, the regulation of this process is incompletely understood. To further our understanding of mitochondrial gene regulation, we identified proteins that bound to the previously described point of termination for the major mRNA-coding transcript H2. One was the leucine-rich pentatricopeptide-repeat containing protein (LRPPRC), which has been linked to the French-Canadian variant of Leigh syndrome. Cells with reduced expression of LRPPRC had a reduction in oxygen consumption. The expression of mitochondrial mRNA and tRNA was dependent upon LRPPRC levels, but reductions in LRPPRC did not affect the expression of mitochondrial rRNA. Reduction of LRPPRC levels interfered with mitochondrial transcription in vitro but did not affect the stability of mitochondrial mRNAs or alter the expression of nuclear genes responsible for mitochondrial transcription in vivo. These findings demonstrate the control of mitochondrial mRNA synthesis by a protein that has an established role in regulating nuclear transcription and a link to mitochondrial disease.
Journal of Developmental and Behavioral Pediatrics : JDBP. Sep, 2010 | Pubmed ID: 20814259
Mitochondrial disease is an increasingly recognized but widely heterogeneous group of multisystemic disorders that commonly involve severe neurodevelopmental manifestations in childhood. This review explores the presentation, genetic basis, and diagnostic evaluation of primary mitochondrial disease. Emphasis is placed on neurodevelopmental findings that may be encountered by a Developmental Pediatrician that should provoke consideration of a mitochondrial disorder. The inheritance patterns and mechanisms by which mutations in genes located in either the nuclear or mitochondrial genomes can cause mitochondrial diseases are discussed. A general overview of the current diagnostic evaluation that can be readily initiated by the Developmental Pediatrician is provided, along with a summary of currently available treatment options.
Developmental Disabilities Research Reviews. Jun, 2010 | Pubmed ID: 20818723
Bacteria, Yeast, Worms, and Flies: Exploiting Simple Model Organisms to Investigate Human Mitochondrial Diseases
Developmental Disabilities Research Reviews. Jun, 2010 | Pubmed ID: 20818735
The extensive conservation of mitochondrial structure, composition, and function across evolution offers a unique opportunity to expand our understanding of human mitochondrial biology and disease. By investigating the biology of much simpler model organisms, it is often possible to answer questions that are unreachable at the clinical level. Here, we review the relative utility of four different model organisms, namely the bacterium Escherichia coli, the yeast Saccharomyces cerevisiae, the nematode Caenorhabditis elegans, and the fruit fly Drosophila melanogaster, in studying the role of mitochondrial proteins relevant to human disease. E. coli are single cell, prokaryotic bacteria that have proven to be a useful model system in which to investigate mitochondrial respiratory chain protein structure and function. S. cerevisiae is a single-celled eukaryote that can grow equally well by mitochondrial-dependent respiration or by ethanol fermentation, a property that has proven to be a veritable boon for investigating mitochondrial functionality. C. elegans is a multicellular, microscopic worm that is organized into five major tissues and has proven to be a robust model animal for in vitro and in vivo studies of primary respiratory chain dysfunction and its potential therapies in humans. Studied for over a century, D. melanogaster is a classic metazoan model system offering an abundance of genetic tools and reagents that facilitates investigations of mitochondrial biology using both forward and reverse genetics. The respective strengths and limitations of each species relative to mitochondrial studies are explored. In addition, an overview is provided of major discoveries made in mitochondrial biology in each of these four model systems.
Current Opinion in Pediatrics. Dec, 2010 | Pubmed ID: 21045694
Mitochondrial diseases are individually uncommon, but collectively pose a significant burden on human health. Primary mitochondrial disease is caused by defects in the mitochondrial DNA-encoded genes or in nuclear genes whose products are imported into the mitochondrion. Great strides have been made in determining the cause of mitochondrial disorders, but the clinical ability to diagnose these conditions lags behind because of phenotypic overlap between distinct genetic entities and the complexity and invasiveness of standard diagnostic testing. In this review, we evaluate new findings in mitochondrial genetics, recent developments in mitochondrial disease diagnostic testing, and emerging ideas for mitochondrial disease therapies.
EMBO Molecular Medicine. Jul, 2011 | Pubmed ID: 21567994
Therapy of mitochondrial respiratory chain diseases is complicated by limited understanding of cellular mechanisms that cause the widely variable clinical findings. Here, we show that focal segmental glomerulopathy-like kidney disease in Pdss2 mutant animals with primary coenzyme Q (CoQ) deficiency is significantly ameliorated by oral treatment with probucol (1% w/w). Preventative effects in missense mutant mice are similar whether fed probucol from weaning or for 3 weeks prior to typical nephritis onset. Furthermore, treating symptomatic animals for 2 weeks with probucol significantly reduces albuminuria. Probucol has a more pronounced health benefit than high-dose CoQ(10) supplementation and uniquely restores CoQ(9) content in mutant kidney. Probucol substantially mitigates transcriptional alterations across many intermediary metabolic domains, including peroxisome proliferator-activated receptor (PPAR) pathway signaling. Probucol's beneficial effects on the renal and metabolic manifestations of Pdss2 disease occur despite modest induction of oxidant stress and appear independent of its hypolipidemic effects. Rather, decreased CoQ(9) content and altered PPAR pathway signaling appear, respectively, to orchestrate the glomerular and global metabolic consequences of primary CoQ deficiency, which are both preventable and treatable with oral probucol therapy.
Current Opinion in Ophthalmology. Sep, 2011 | Pubmed ID: 21730846
Mitochondrial disease is a heterogeneous group of energy metabolism disorders that present across all ages with a wide range of ocular or multisystemic manifestations. This review focuses on recent progress made toward understanding the various ophthalmologic manifestations of primary mitochondrial diseases and discusses the implications of mitochondrial dysfunction, placing particular emphasis on recent investigations into the pathogenesis and emerging therapies for mitochondrial-based ophthalmologic disorders.
Parkinson's Disease-like Neuromuscular Defects Occur in Prenyl Diphosphate Synthase Subunit 2 (Pdss2) Mutant Mice
Mitochondrion. Oct, 2011 | Pubmed ID: 21983691
The Pdss2 gene product is needed for the isoprenylation of benzoquinone to generate coenzyme Q (CoQ). A fatal kidney disease occurs in mice that are homozygous for a missense mutation in Pdss2, which can be recapitulated in conditional Pdss2 knockouts targeted to glomerular podocytes. We now report that homozygous missense mutants also demonstrate significant neuromuscular deficits, as validated by behavioral and coordination assays, and these deficits are recapitulated in conditional Pdss2 knockouts targeted to dopaminergic neurons. Both conditional knockout and missense mutant mice demonstrate deficiencies in tyrosine hydroxylase-positive neurons in the substantia nigra, implicating a pathology similar to sporadic Parkinson's disease (PD).
Mitochondrial Genome Sequence Analysis: a Custom Bioinformatics Pipeline Substantially Improves Affymetrix MitoChip V2.0 Call Rate and Accuracy
BMC Bioinformatics. 2011 | Pubmed ID: 22011106
Mitochondrial genome sequence analysis is critical to the diagnostic evaluation of mitochondrial disease. Existing methodologies differ widely in throughput, complexity, cost efficiency, and sensitivity of heteroplasmy detection. Affymetrix MitoChip v2.0, which uses a sequencing-by-genotyping technology, allows potentially accurate and high-throughput sequencing of the entire human mitochondrial genome to be completed in a cost-effective fashion. However, the relatively low call rate achieved using existing software tools has limited the wide adoption of this platform for either clinical or research applications. Here, we report the design and development of a custom bioinformatics software pipeline that achieves a much improved call rate and accuracy for the Affymetrix MitoChip v2.0 platform. We used this custom pipeline to analyze MitoChip v2.0 data from 24 DNA samples representing a broad range of tissue types (18 whole blood, 3 skeletal muscle, 3 cell lines), mutations (a 5.8 kilobase pair deletion and 6 known heteroplasmic mutations), and haplogroup origins. All results were compared to those obtained by at least one other mitochondrial DNA sequence analysis method, including Sanger sequencing, denaturing HPLC-based heteroduplex analysis, and/or the Illumina Genome Analyzer II next generation sequencing platform.
Current Biology : CB. Dec, 2011 | Pubmed ID: 22137475
Volatile anesthetics (VAs) cause profound neurological effects, including reversible loss of consciousness and immobility. Despite their widespread use, the mechanism of action of VAs remains one of the unsolved puzzles of neuroscience [1, 2]. Genetic studies in Caenorhabditis elegans [3, 4], Drosophila [3, 5], and mice [6-9] indicate that ion channels controlling the neuronal resting membrane potential (RMP) also control anesthetic sensitivity. Leak channels selective for K(+) [10-13] or permeable to Na(+)  are critical for establishing RMP. We hypothesized that halothane, a VA, caused immobility by altering the neuronal RMP. In C. elegans, halothane-induced immobility is acutely and completely reversed by channelrhodopsin-2 based depolarization of the RMP when expressed specifically in cholinergic neurons. Furthermore, hyperpolarizing cholinergic neurons via halorhodopsin activation increases sensitivity to halothane. The sensitivity of C. elegans to halothane can be altered by 25-fold by either manipulation of membrane conductance with optogenetic methods or generation of mutations in leak channels that set the RMP. Immobility induced by another VA, isoflurane, is not affected by these treatments, thereby excluding the possibility of nonspecific hyperactivity. The sum of our data indicates that leak channels and the RMP are important determinants of halothane-induced general anesthesia.
Human Mutation. Mar, 2012 | Pubmed ID: 22213154
Renal coloboma syndrome, also known as papillorenal syndrome is an autosomal-dominant disorder characterized by ocular and renal malformations. Mutations in the paired-box gene, PAX2, have been identified in approximately half of individuals with classic findings of renal hypoplasia/dysplasia and abnormalities of the optic nerve. Prior to 2011, there was no actively maintained locus-specific database (LSDB) cataloguing the extent of genetic variation in the PAX2 gene and phenotypic variation in individuals with renal coloboma syndrome. Review of published cases and the collective diagnostic experience of three laboratories in the United States, France, and New Zealand identified 55 unique mutations in 173 individuals from 86 families. The three clinical laboratories participating in this collaboration contributed 28 novel variations in 68 individuals in 33 families, which represent a 50% increase in the number of variations, patients, and families published in the medical literature. An LSDB was created using the Leiden Open Variation Database platform: www.lovd.nl/PAX2. The most common findings reported in this series were abnormal renal structure or function (92% of individuals), ophthalmological abnormalities (77% of individuals), and hearing loss (7% of individuals). Additional clinical findings and genetic counseling implications are discussed. Hum Mutat 33:457-466, 2012. © 2011 Wiley Periodicals, Inc.
Fluorescence-activated Cell Sorting Analysis of Mitochondrial Content, Membrane Potential, and Matrix Oxidant Burden in Human Lymphoblastoid Cell Lines
Methods in Molecular Biology (Clifton, N.J.). 2012 | Pubmed ID: 22215552
Fluorescence-activated cell sorting (FACS) permits specific biologic parameters of cellular populations to be quantified in a high-throughput fashion based on their unique fluorescent properties. Relative quantitation of mitochondrial-localized dyes in human cells using FACS analysis allows sensitive analysis of a variety of mitochondrial parameters including mitochondrial content, mitochondrial membrane potential, and matrix oxidant burden. Here, we describe protocols that utilize FACS analysis of human lymphoblastoid cell lines (LCL) for relative quantitation of mitochondrial-localized fluorescent dye intensity. The specific dyes described include MitoTracker Green FM to assess mitochondrial content, tetramethylrhodamine ethyl ester (TMRE) to assess mitochondrial membrane potential, and MitoSOX Red to assess mitochondrial matrix oxidant burden. Representative results of FACS-based mitochondrial analyses demonstrate the variability of these three basic mitochondrial parameters in LCLs from healthy individuals, as well as the sensitivity of applying FACS analysis of LCLs to study the effects of pharmacologic induction and scavenging of oxidant stress.
Methods in Molecular Biology (Clifton, N.J.). 2012 | Pubmed ID: 22215553
Cellular effects of primary mitochondrial dysfunction, as well as potential mitochondrial disease therapies, can be modeled in living animals such as the microscopic nematode, Caenorhabditis elegans. In particular, molecular analyses can provide substantial insight into the mechanism by which genetic and/or pharmacologic manipulations alter mitochondrial function. The relative expression of individual genes across both nuclear and mitochondrial genomes, as well as relative quantitation of mitochondrial DNA content, can be readily performed by quantitative real-time PCR (qRT-PCR) analysis of C. elegans. Additionally, microarray expression profiling offers a powerful tool by which to survey the global genetic consequences of various causes of primary mitochondrial dysfunction and potential therapeutic interventions at both the single gene and integrated pathway level. Here, we describe detailed protocols for RNA and DNA isolation from whole animal populations in C. elegans, qRT-PCR analysis of both nuclear and mitochondrial genes, and global nuclear genome expression profiling using the Affymetrix GeneChip C. elegans Genome Array.