Conventional Genetic Approaches Research Articles

Severe hemophilia A caused by an unbalanced chromosomal rearrangement identified using nanopore sequencing

Unlabelled Box BackgroundNo F8 genetic abnormality is detected in about 2% of severe hemophilia A patients using conventional genetic approaches. In these patients, deep intronic variation or F8 disrupting genomic rearrangement could be causal. ObjectiveTo characterize, in a genetically unresolved severe hemophilia A patient, a new Xq28 rearrangement disrupting F8 using comprehensive molecular techniques including nanopore sequencing. ResultsLong‐range polymerase chain reaction (PCR) performed throughout F8 identified a nonamplifiable region in intron 25 indicating the presence of a genomic rearrangement. F8messanger ribonucleic acid (mRNA) analysis including 3′rapid amplification of complementary deoxyribonucleic acid (cDNA) ends and nanopore sequencing found the presence of a F8 fusion transcript in which F8 exon 26 was replaced by a 742‐bp pseudoexon corresponding to a noncoding region located at the beginning of the long arm of chromosome X (Xq12; chrX: 66 310 352‐66 311 093, GRCh37/hg19). Cytogenetic microarray analysis found the presence of a Xq11.1q12 gain of 3.8 Mb. The PCR amplification of junction fragments and fluorescent in situ hybridization (FISH) analysis found that the Xq11q12 duplicated region was inserted in the F8 intron 25 genomic region. ConclusionWe characterized a novel genomic rearrangement in which a 3.8‐Mb Xq11.1q12 gain inserted in the F8 intron 25 led to an aberrant fusion transcript in a patient with severe hemophilia A (HA), using comprehensive molecular techniques. This study highlights the value of single‐molecule long‐read sequencing technologies for molecular diagnosis of HA especially when conventional genetic approaches have failed.

Concurrent Proteomic Fingerprinting and Molecular Analysis of Cyathostomins.

Rapid, cost-effective, efficient, and reliable helminth species identification is of considerable importance to understand host-parasite interactions, clinical disease, and drug resistance. Cyathostomins (Nematoda: Strongylidae) are considered to be the most important equine parasites, yet research on this group is hampered by the large number of 50 morphologically differentiated species, their occurrence in mixed infections with often more than 10 species and the difficulties associated with conventional identification methods. Here, MALDI-TOF MS, previously successfully applied to identify numerous organisms, is evaluated and compared with conventional and molecular genetic approaches. A simple and robust protocol for protein extraction and subsequent DNA isolation allowing molecular confirmation of proteomic findings is developed, showing that MALDI-TOF MS can discriminate adult stages of the two closely related cyathostomin species Cylicostephanus longibursatus and Cylicostephanus minutus. Intraspecific variability of proteomic profiles within morphospecies demonstrated an identification of morphospecies with an accuracy of close to 100%. In contrast, three genospecies within C. minutus and sex-specific profiles within both morphospecies could not be reliably discriminated using MALDI-TOF MS. In conclusion, MALDI-TOF MS complemented by the molecular protocol is a reliable and efficient approach for cyathostomin species identification.

A chemical approach for global protein knockdown from mice to non-human primates

Although conventional genetic modification approaches for protein knockdown work very successfully due to the increasing use of CRISPR/Cas9, effective techniques for achieving protein depletion in adult animals, especially in large animals such as non-human primates, are lacking. Here, we report a chemical approach based on PROTACs technology that efficiently and quickly knocks down FKBP12 (12-kDa FK506-binding) protein globally in vivo. Both intraperitoneal and oral administration led to rapid, robust, and reversible FKBP12 degradation in mice. The efficiency and practicality of this method were successfully demonstrated in both large and small animals (mice, rats, Bama pigs, and rhesus monkeys). Furthermore, we showed this approach can also be applied to effectively knockdown other target proteins such as Bruton's tyrosine kinase (BTK). This chemical protein knockdown strategy provides a powerful research tool for gene function studies in animals, particularly in large animals, for which gene-targeted knockout strategies may remain unfeasible.

CRISPR-Cas9 induces point mutation in the mucormycosis fungus Rhizopus delemar

Rhizopus delemar causes devastating mucormycosis in immunodeficient individuals. Despite its medical importance, R. delemar remains understudied largely due to the lack of available genetic markers, the presence of multiple gene copies due to genome duplication, and mitotically unstable transformants resulting from conventional and limited genetic approaches. The clustered regularly interspaced short palindromic repeat (CRISPR)-associated nuclease 9 (Cas9) system induces efficient homologous and non-homologous break points and generates individual and multiple mutant alleles without requiring selective marker genes in a wide variety of organisms including fungi. Here, we have successfully adapted this technology for inducing gene-specific single nucleotide (nt) deletions in two clinical strains of R. delemar: FGSC-9543 and CDC-8219. For comparative reasons, we first screened for spontaneous uracil auxotrophic mutants resistant to 5-fluoroorotic acid (5-FOA) and obtained one substitution (f1) mutationin the FGSC-9543 strain and one deletion (f2) mutation in the CDC-8219 strain. The f2 mutant was then successfully complemented with a pyrF-dpl200 marker gene. We then introduced a vector pmCas9:tRNA-gRNA that expresses both Cas9 endonuclease and pyrF-specific gRNA into FGSC-9543 and CDC-8219 strains and obtained 34 and 42 5-FOA resistant isolates, respectively. Candidate transformants were successively transferred eight times by propagating hyphal tips prior to genotype characterization. Sequencing of the amplified pyrF allele in all transformants tested revealed a single nucleotide (nt) deletion at the 4th nucleotide before the protospacer adjacent motif (PAM) sequence, which is consistent with CRISPR-Cas9 induced gene mutation through non-homologous end joining (NHEJ). Our study provides a new research tool for investigating molecular pathogenesis mechanisms of R. delemar while also highlighting the utilization of CRISPR-Cas9 technology for generating specific mutants of Mucorales fungi.

CRISPR-Based Targeted Epigenetic Editing Enables Gene Expression Modulation of the Silenced Beta-Galactoside Alpha-2,6-Sialyltransferase 1 in CHO Cells.

Despite great efforts to control and modify gene expression of Chinese Hamster Ovary (CHO) cells by conventional genetic engineering approaches, i.e. overexpression or knockdown/-out, subclonal variation, induced unknown regulatory effects as well as overexpression stress are still a major hurdle for efficient cell line engineering and for unequivocal characterization of gene function. The use of epigenetic modulators - key players in CHO clonal heterogeneity - has only been marginally addressed so far. Here, we present the application of an alternative engineering strategy in CHO cells by utilizing targeted epigenetic editing tools that enable the turning-on or -off of genes without altering the genomic sequence. The present, but silent beta-galactoside alpha-2,6-sialyltransferase 1 (ST6GAL1) gene is activated by targeting the catalytic domain (CD) of Ten-Eleven Translocation methylcytosine dioxygenase 1 (TET1) via deactivated Cas9 (dCas9) to its methylated promoter. Stable upregulation in up to 60% of transfected cells is achieved over a time span of more than 80 days. No difference in growth and recombinant protein productivity is observed between activated and control cultures. Re-silencing by targeted methylation via DNA methyltransferase (DNMT) 3A-CD resulted in an up to 5.4-fold reduction of ST6GAL1 mRNA expression in ST6GAL1 expressing cells. This proof-of-concept demonstrates the feasibility of using epigenetic editing tools to efficiently modulate gene expression and provide a promising complement to conventional genetic engineering in CHO cells.

Temporal control of growth factor‐mediated signaling pathways during cell differentiation and Xenopus embryonic development

Growth factor‐mediated signaling pathways regulate a wide‐spectrum of cellular functions such as survival, proliferation, differentiation, and apoptosis. Different growth factors typically trigger the activation of the same set of downstream signaling pathways which includes the mitogen activated protein kinase (MAPK), phosphoinositide 3‐kinase (PI3K)‐AKT, and phospholipase C (PLC) pathways Evidence suggests that precise spatiotemporal regulation of these signaling pathways is involved in generating diverse cellular outcomes. Although conventional genetic and pharmacological approaches have helped us understand different aspects of signaling pathways, a quantitative delineation of their signaling kinetics is pending due to a lack of tools that allow for precise temporal control of these pathways. Non‐neuronal optogenetics, an emerging technique that utilizes light to control intracellular signaling pathways, is a remarkable tool to help achieve this goal. Here, we introduce a bicistronic optogenetic system which we recently developed in our laboratory to achieve temporal control of the MAPK pathway. This tool uses the photoactivatable protein cryptochrome 2 (CRY2) and the N‐terminal domain of cryptochrome‐interacting basic‐helix‐loop‐helix (CIBN) from Arabidopsis thaliana. This novel system allows reversible, light‐mediated activation of the MAPK signaling pathway in intact mammalian cells as well as in developing Xenopus laevis embryos. In PC12 neuronal cells, light‐controlled, intermittent MAPK activity reveals a memory effect in light‐induced neurite outgrowth. In Xenopus embryos, developmental stage‐specific MAPK activation further reveals that this pathway can reprogram cell fate after a crucial time window when germ layers are specified. Our strategy can be generalized to control other kinase pathways with a similar activation mechanism. Results from our research will help resolve intracellular mechanisms of growth factor‐mediated signal transduction during cell differentiation and embryonic development.Support or Funding InformationKai Zhang, Department of Biochemistry, University of Illinois Urbana‐ChampaignThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Virus resistance in potato: Current state and prospects

The potato (Solanum tuberosum), one of the world’s most important food crops, is infected by numerous viruses, nine of which are of major economic importance as they cause significant yield losses and reduce the quality of the crop. To mitigate the consequences of viral infections, countries with highly developed agriculture are improving and promoting sanitary measures, which include constantly monitoring viruses and certification of potato seed material based on virus diagnostics and improved potato cultivars. However, the development of virus-resistant potato cultivars seems to be a preferable choice in the long term. By employing conventional breeding techniques and genetic engineering approaches using natural virus resistance genes, normally obtained from the wild growing Solanum species, or virus-specific sequences, a number of potato cultivars/lines, which are resistant to the majority of known potato viruses, have already been obtained. However, the above-mentioned techniques have certain limitations, which are determined, in particular, by the high virus specificity of the acquired resistance (against certain viruses only), its short duration, and the ability of the virus to overcome it, as well as the regularly declared bans on the use of genetically modified plants. In the modern era, the novel technologies allowing us to edit genomes for the purposes of gene design have created the possibility to engineer a new generation of resistance genes. The most promising approaches are thought to be the directed mutagenesis of resistance genes, which allows broadening the spectrum of the effects of the gene and the use of nonhost resistance (NHR) (nonspecific resistance) genes, allowing engineering plants resistant to unrelated viruses and in certain cases, to other pathogens and even abiotic stresses. The identification of genes involved in the mechanisms of NHR has only just begun. The nucleus is now being considered as a new source of still unknown factors involved in diverse signal pathways controlling the plant’s defensive response against virus infection. The review describes the approaches which are used to generate virus-resistant potato plants and the challenges faced in this path.

Probing and manipulating intracellular membrane traffic by microinjection of artificial vesicles

There is still a large gap in our understanding between the functional complexity of cells and the reconstruction of partial cellular functions in vitro from purified or engineered parts. Here we have introduced artificial vesicles of defined composition into living cells to probe the capacity of the cellular cytoplasm in dealing with foreign material and to develop tools for the directed manipulation of cellular functions. Our data show that protein-free liposomes, after variable delay times, are captured by the Golgi apparatus that is reached either by random diffusion or, in the case of large unilamellar vesicles, by microtubule-dependent transport via a dynactin/dynein motor complex. However, insertion of early endosomal SNARE proteins suffices to convert liposomes into trafficking vesicles that dock and fuse with early endosomes, thus overriding the default pathway to the Golgi. Moreover, such liposomes can be directed to mitochondria expressing simple artificial affinity tags, which can also be employed to divert endogenous trafficking vesicles. In addition, fusion or subsequent acidification of liposomes can be monitored by incorporation of appropriate chemical sensors. This approach provides an opportunity for probing and manipulating cellular functions that cannot be addressed by conventional genetic approaches. We conclude that the cellular cytoplasm has a remarkable capacity for self-organization and that introduction of such macromolecular complexes may advance nanoengineering of eukaryotic cells.

Wholly Rickettsia! Reconstructed Metabolic Profile of the Quintessential Bacterial Parasite of Eukaryotic Cells.

ABSTRACTReductive genome evolution has purged many metabolic pathways from obligate intracellular Rickettsia (Alphaproteobacteria; Rickettsiaceae). While some aspects of host-dependent rickettsial metabolism have been characterized, the array of host-acquired metabolites and their cognate transporters remains unknown. This dearth of information has thwarted efforts to obtain an axenic Rickettsia culture, a major impediment to conventional genetic approaches. Using phylogenomics and computational pathway analysis, we reconstructed the Rickettsia metabolic and transport network, identifying 51 host-acquired metabolites (only 21 previously characterized) needed to compensate for degraded biosynthesis pathways. In the absence of glycolysis and the pentose phosphate pathway, cell envelope glycoconjugates are synthesized from three imported host sugars, with a range of additional host-acquired metabolites fueling the tricarboxylic acid cycle. Fatty acid and glycerophospholipid pathways also initiate from host precursors, and import of both isoprenes and terpenoids is required for the synthesis of ubiquinone and the lipid carrier of lipid I and O-antigen. Unlike metabolite-provisioning bacterial symbionts of arthropods, rickettsiae cannot synthesize B vitamins or most other cofactors, accentuating their parasitic nature. Six biosynthesis pathways contain holes (missing enzymes); similar patterns in taxonomically diverse bacteria suggest alternative enzymes that await discovery. A paucity of characterized and predicted transporters emphasizes the knowledge gap concerning how rickettsiae import host metabolites, some of which are large and not known to be transported by bacteria. Collectively, our reconstructed metabolic network offers clues to how rickettsiae hijack host metabolic pathways. This blueprint for growth determinants is an important step toward the design of axenic media to rescue rickettsiae from the eukaryotic cell.

A Dual Function for Prickle in Regulating Frizzled Stability during Feedback-Dependent Amplification of Planar Polarity

SummaryThe core planar polarity pathway coordinates epithelial cell polarity during animal development, and loss of its activity gives rise to a range of defects, from aberrant morphogenetic cell movements to failure to correctly orient structures, such as hairs and cilia. The core pathway functions via a mechanism involving segregation of its protein components to opposite cells ends, where they form asymmetric intracellular complexes that couple cell-cell polarity. This segregation is a self-organizing process driven by feedback interactions between the core proteins themselves. Despite intense efforts, the molecular pathways underlying feedback have proven difficult to elucidate using conventional genetic approaches. Here we investigate core protein function during planar polarization of the Drosophila wing by combining quantitative measurements of protein dynamics with loss-of-function genetics, mosaic analysis, and temporal control of gene expression. Focusing on the key core protein Frizzled, we show that its stable junctional localization is promoted by the core proteins Strabismus, Dishevelled, Prickle, and Diego. In particular, we show that the stabilizing function of Prickle on Frizzled requires Prickle activity in neighboring cells. Conversely, Prickle in the same cell has a destabilizing effect on Frizzled. This destabilizing activity is dependent on the presence of Dishevelled and blocked in the absence of Dynamin and Rab5 activity, suggesting an endocytic mechanism. Overall, our approach reveals for the first time essential in vivo stabilizing and destabilizing interactions of the core proteins required for self-organization of planar polarity.

Deficiency of TYROBP, an adapter protein for TREM2 and CR3 receptors, is neuroprotective in a mouse model of early Alzheimer\u2019s pathology

Conventional genetic approaches and computational strategies have converged on immune-inflammatory pathways as key events in the pathogenesis of late onset sporadic Alzheimer’s disease (LOAD). Mutations and/or differential expression of microglial specific receptors such as TREM2, CD33, and CR3 have been associated with strong increased risk for developing Alzheimer’s disease (AD). DAP12 (DNAX-activating protein 12)/TYROBP, a molecule localized to microglia, is a direct partner/adapter for TREM2, CD33, and CR3. We and others have previously shown that TYROBP expression is increased in AD patients and in mouse models. Moreover, missense mutations in the coding region of TYROBP have recently been identified in some AD patients. These lines of evidence, along with computational analysis of LOAD brain gene expression, point to DAP12/TYROBP as a potential hub or driver protein in the pathogenesis of AD. Using a comprehensive panel of biochemical, physiological, behavioral, and transcriptomic assays, we evaluated in a mouse model the role of TYROBP in early stage AD. We crossed an Alzheimer’s model mutant APPKM670/671NL/PSEN1Δexon9(APP/PSEN1) mouse model with Tyrobp−/− mice to generate AD model mice deficient or null for TYROBP (APP/PSEN1; Tyrobp+/− or APP/PSEN1; Tyrobp−/−). While we observed relatively minor effects of TYROBP deficiency on steady-state levels of amyloid-β peptides, there was an effect of Tyrobp deficiency on the morphology of amyloid deposits resembling that reported by others for Trem2−/− mice. We identified modulatory effects of TYROBP deficiency on the level of phosphorylation of TAU that was accompanied by a reduction in the severity of neuritic dystrophy. TYROBP deficiency also altered the expression of several AD related genes, including Cd33. Electrophysiological abnormalities and learning behavior deficits associated with APP/PSEN1 transgenes were greatly attenuated on a Tyrobp-null background. Some modulatory effects of TYROBP on Alzheimer’s-related genes were only apparent on a background of mice with cerebral amyloidosis due to overexpression of mutant APP/PSEN1. These results suggest that reduction of TYROBP gene expression and/or protein levels could represent an immune-inflammatory therapeutic opportunity for modulating early stage LOAD, potentially leading to slowing or arresting the progression to full-blown clinical and pathological LOAD.

Multi-point optimization of transonic airfoils using an enhanced genetic algorithm

In this study, two new techniques are proposed for accelerating the multi-point optimization of an airfoil shape by genetic algorithms. In such multi-point evolutionary optimization, the objective function has to be evaluated several times more than a single-point optimization. Thus, excessive computational time is crucial in these problems particularly, when computational fluid dynamics is used for fitness function evaluation. Two new techniques of preadaptive range operator and adaptive mutation rate are proposed. An unstructured grid Navier–Stokes flow solver with a two-equation [Formula: see text] turbulence model is used to evaluate the objective function. The new methods are applied for optimum design of a transonic airfoil at two speed conditions. The results show that using the new methods can increase the aerodynamic efficiency of optimum airfoil at each operating condition with about 30% less computational time in comparison with the conventional genetic algorithm approach.

Topological Design via a Rule Based Genetic Optimization Algorithm

A topological structural design approach is presented which is based upon the implementation of a two phase evolutionary optimization algorithm in conjunction with a finite element analysis code. The first phase utilizes a conventional genetic approach which performs a global search for the optimal design topology. Dual level material properties are specified within the genetic encoding and are applied to each individual element in the design mesh to represent either design material or a void. The second phase introduces a rule based refinement which allows for user design intent to accelerate the solution process and eliminate obvious design discrepancies resulting from the phase one search. A series of plate design problems are presented where the objective is to minimize the overall volume of the structure under predefined loading and constraint conditions. The constraints include both stress and deflection considerations where stress is calculated through the use of a commercial finite element package. The initial plate example incorporates a coarse mesh, but a gradual decrease in element size was employed for the remaining cases examined. Replacement of the phase one search with a set of randomly generated designs is demonstrated in order to form a greatly reduced design space which drastically increases the efficiency of the solution process. Comparison results are drawn between the conventional genetic algorithm and the two phase procedure.

Creating a customized intracellular niche: subversion of host cell signaling by Legionella type IV secretion system effectors.

The Gram-negative facultative intracellular pathogen Legionella pneumophila infects a wide range of different protozoa in the environment and also human alveolar macrophages upon inhalation of contaminated aerosols. Inside its hosts, it creates a defined and unique compartment, termed the Legionella-containing vacuole (LCV), for survival and replication. To establish the LCV, L. pneumophila uses its Dot/Icm type IV secretion system (T4SS) to translocate more than 300 effector proteins into the host cell. Although it has become apparent in the past years that these effectors subvert a multitude of cellular processes and allow Legionella to take control of host cell vesicle trafficking, transcription, and translation, the exact function of the vast majority of effectors still remains unknown. This is partly due to high functional redundancy among the effectors, which renders conventional genetic approaches to elucidate their role ineffective. Here, we review the current knowledge about Legionella T4SS effectors, highlight open questions, and discuss new methods that promise to facilitate the characterization of T4SS effector functions in the future.

Whole-exome sequencing identifies novel homozygous mutation in NPAS2 in family with nonobstructive azoospermia

To investigate the genetic cause of nonobstructive azoospermia (NOA) in a consanguineous Turkish family through homozygosity mapping followed by targeted exon/whole-exome sequencing to identify genetic variations. Whole-exome sequencing (WES). Research laboratory. Two siblings in a consanguineous family with NOA. Validating all variants passing filter criteria with Sanger sequencing to confirm familial segregation and absence in the control population. Discovery of a mutation that could potentially cause NOA. A novel nonsynonymous mutation in the neuronal PAS-2 domain (NPAS2) was identified in a consanguineous family from Turkey. This mutation in exon 14 (chr2: 101592000 C>G) of NPAS2 is likely a disease-causing mutation as it is predicted to be damaging, it is a novel variant, and it segregates with the disease. Family segregation of the variants showed the presence of the homozygous mutation in the three brothers with NOA and a heterozygous mutation in the mother as well as one brother and one sister who were both fertile. The mutation is not found in the single-nucleotide polymorphism database, the 1000 Genomes Project, the Baylor College of Medicine cohort of 500 Turkish patients (not a population-specific polymorphism), or the matching 50 fertile controls. With the use of WES we identified a novel homozygous mutation in NPAS2 as a likely disease-causing variant in a Turkish family diagnosed with NOA. Our data reinforce the clinical role of WES in the molecular diagnosis of highly heterogeneous genetic diseases for which conventional genetic approaches have previously failed to find a molecular diagnosis.

MP76-06 WHOLE-EXOME SEQUENCING IDENTIFIES NOVEL HOMOZYGOUS MUTATION IN NPAS2 IN FAMILY WITH NONOBSTRUCTIVE AZOOSPERMIA

You have accessJournal of UrologyInfertility: Basic Research, Physiology, Pathophysiology1 Apr 2015MP76-06 WHOLE-EXOME SEQUENCING IDENTIFIES NOVEL HOMOZYGOUS MUTATION IN NPAS2 IN FAMILY WITH NONOBSTRUCTIVE AZOOSPERMIA Ranjith Ramasamy, Emre Bakircioglu, Cenk Cengiz, Ender Karaca, Jason Scovell, Matthew Bainbridge, James Lupski, and Dolores Lamb Ranjith RamasamyRanjith Ramasamy More articles by this author , Emre BakirciogluEmre Bakircioglu More articles by this author , Cenk CengizCenk Cengiz More articles by this author , Ender KaracaEnder Karaca More articles by this author , Jason ScovellJason Scovell More articles by this author , Matthew BainbridgeMatthew Bainbridge More articles by this author , James LupskiJames Lupski More articles by this author , and Dolores LambDolores Lamb More articles by this author View All Author Informationhttps://doi.org/10.1016/j.juro.2015.02.2791AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookTwitterLinked InEmail INTRODUCTION AND OBJECTIVES Nonobstructive azoospermia (NOA) is characterized by lack of sperm in the ejaculate due to severe testicular failure. Due to genetic and clinical heterogeneity, the diagnosis is not straightforward. Current clinical practices have focused on karyotype and microdeletions. In the present study, we investigated the genetic cause of NOA in a consanguineous Turkish family through homozygosity mapping followed by targeted exon/whole-exome sequencing to identify genetic variations. METHODS We designed a whole-exome sequencing (WES)-based approach using NimbleGen SeqCap EZ Exome V3 sample preparation kit and the Illumina HiSeq 2000 next-generation sequencing platform. We sequenced the exomes of two affected siblings. Exome analysis resulted in the identification of 442 variants in the index patients. All variants that passed filter criteria were validated with Sanger sequencing to confirm familial segregation and absence in the control population. RESULTS A novel non-synonymous mutation in neuronal PAS 2 domain (NPAS2) was identified in a consanguineous family from Turkey. This mutation in exon 14 (chr2: 101592000 C>G) of NPAS2 segregates with the disease. Family segregation of the variants showed the presence of homozygous mutation in the three brothers with NOA and heterozygous mutation in one brother, and one sister who were fertile. The mutation is not found in the single nucleotide polymorphism (SNP) database, the 1000 Genomes Project, Baylor College of Medicine cohort of 500 Turkish patients (not a founder mutation) or matching 50 fertile controls. The absence of homozygous mutations in NPAS2 in these databases suggests that such gene perturbations are not consistent with fertility, and therefore the observed NPAS2 mutation is considered likely to be pathogenic. CONCLUSIONS Using WES, we identified a novel homozygous mutation in NPAS2 as a likely disease-causing variant in three brothers with NOA. Our data reinforce the clinical role of WES in the molecular diagnosis of highly heterogeneous genetic diseases where conventional genetic approaches have previously failed in achieving a proper diagnosis. © 2015 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 193Issue 4SApril 2015Page: e985-e986 Advertisement Copyright & Permissions© 2015 by American Urological Association Education and Research, Inc.MetricsAuthor Information Ranjith Ramasamy More articles by this author Emre Bakircioglu More articles by this author Cenk Cengiz More articles by this author Ender Karaca More articles by this author Jason Scovell More articles by this author Matthew Bainbridge More articles by this author James Lupski More articles by this author Dolores Lamb More articles by this author Expand All Advertisement Advertisement PDF downloadLoading ...

An MRPS12 mutation modifies aminoglycoside sensitivity caused by 12S rRNA mutations.

Several homoplasmic pathologic mutations in mitochondrial DNA, such as those causing Leber hereditary optic neuropathy or non-syndromic hearing loss, show incomplete penetrance. Therefore, other elements must modify their pathogenicity. Discovery of these modifying factors is not an easy task because in multifactorial diseases conventional genetic approaches may not always be informative. Here, we have taken an evolutionary approach to unmask putative modifying factors for a particular homoplasmic pathologic mutation causing aminoglycoside-induced and non-syndromic hearing loss, the m.1494C>T transition in the mitochondrial DNA. The mutation is located in the decoding site of the mitochondrial ribosomal RNA. We first looked at mammalian species that had fixed the human pathologic mutation. These mutations are called compensated pathogenic deviations because an organism carrying one must also have another that suppresses the deleterious effect of the first. We found that species from the primate family Cercopithecidae (old world monkeys) harbor the m.1494T allele even if their auditory function is normal. In humans the m.1494T allele increases the susceptibility to aminoglycosides. However, in primary fibroblasts from a Cercopithecidae species, aminoglycosides do not impair cell growth, respiratory complex IV activity and quantity or the mitochondrial protein synthesis. Interestingly, this species also carries a fixed mutation in the mitochondrial ribosomal protein S12. We show that the expression of this variant in a human m.1494T cell line reduces its susceptibility to aminoglycosides. Because several mutations in this human protein have been described, they may possibly explain the absence of pathologic phenotype in some pedigree members with the most frequent pathologic mutations in mitochondrial ribosomal RNA.

GYY4137, a novel water-soluble, H2S-releasing molecule.

Hydrogen sulfide (H2S) is now recognized as the so called "third gasotransmitter" taking its place alongside nitric oxide and carbon monoxide. In recent years, H2S has been reported to exhibit a diverse range of pharmacological effects in biological systems. Much of this evidence is derived from a combination of conventional pharmacological and genetic approaches coupled with the use of chemical compounds such as sodium hydrosulfide, a rapid H2S releasing donor. Developments in the design of new drug entities which attempt to take into account physicochemical properties, targeting to specific cellular organelles, triggering of H2S release upon specific chemical reactions in the cell, and controlling the release of H2S over extended periods of time have been described. For most of these molecules, little or no work has been conducted to determine their biological activity or possible therapeutic effects. It is therefore not clear whether such molecules have therapeutic potential which highlights the need for further in vivo studies. One exception to the general rule is GYY4137 (morpholin-4-ium 4-methoxyphenyl(morpholino) phosphinodithioate), a slow releasing H2S donor, which has been evaluated for activity in a range of pharmacological models both in vitro and in vivo. GYY4137 was first reported to release H2S and exhibit vasodilator activity over 5 years ago and, to date, GYY4137 is becoming increasingly employed as a pharmacological "tool" to explore the biological functions of H2S.

ChemInform Abstract: Diversity‐Oriented Asymmetric Synthesis

AbstractReview: [116 refs.

Next-Gen Sequencing-Based Mapping and Identification of Ethyl Methanesulfonate-Induced Mutations in Arabidopsis thaliana.

Forward genetic analysis using ethyl methanesulfonate (EMS) mutagenesis has proven to be a powerful tool in biological research, but identification and cloning of causal mutations by conventional genetic mapping approaches is a painstaking process. Recent advances in next-gen sequencing have greatly invigorated the process of identifying EMS-induced mutations corresponding to a specific phenotype in model genetic hosts, including the plant Arabidopsis thaliana and the nematode Caenorhabditis elegans. Next-gen sequencing of bulked F2 mutant recombinants produces a wealth of high-resolution genetic data, provides enhanced delimitation of the genomic location of mutations, and greatly reduces hands-on time while maintaining high accuracy and reproducibility. In this unit, a detailed procedure to simultaneously map and identify EMS mutations in Arabidopsis is described.