Silent Mutations Research Articles

No induced mutagenesis in human lymphoblast cell line and bacterial systems upon their prolonged sub-culturing in irradiated food blended media.

Profound apprehension towards safety of irradiated food has remained a major cause behind tardy acceptance of this technology although it has immense socio-economic potential. Generation of in-depth scientific evidence will help to refute these apprehensions. With this prospective, the present study was undertaken where safety of various irradiated (Dmin up to 25 kGy) foods was evaluated through long-term exposure studies in models including human lymphoblast TK6 cell line (100 generations) and Escherichia coli MG1655 cells (exclusive sub-culturing in irradiated food medium for 3000 generations). Additionally, the Ames test, micronucleus test, comet assay, DNA sequencing and restriction profiling of phagemid DNA from E. coli cells sub-cultured in irradiated food medium were also performed. No induced mutagenesis was observed in these cells during long-term sub-culturing in various irradiated food medium. Also no change was observed in profiles of comet, micronucleus, restriction digestion, random amplification of polymorphic DNA as well as DNA sequences. The latter also ruled out the possibility of any silent mutation. Findings of the current study thus provided credible molecular evidence supporting the safety of irradiated foods. This would be helpful in confidence building among consumers, entrepreneurs, and strengthening the overall food irradiation program to achieve 'food safety' and 'security'. © 2017 Society of Chemical Industry.

Lack of induced mutagenesis in E. coli or human lymphoblast cell line upon long-term sub-culturing in medium from irradiated meat

Purpose: Current study was aimed to enhance the confidence of consumers as well as entrepreneurs towards food irradiation program.Materials and methods: In this work, safety of high dose (25 kGy) irradiated meat samples (HDIMS) was ascertained by scoring mutation frequency through a long-term sub-culturing study in Escherichia coli MG1655 cells (ATCC 700926) up to 1500 generations (at 1%), 250 generations (at 5% and 10%) and human lymphoblast thymidine kinase heterozygote (TK6) cell line (ATCC CRL-8015) [at two gene loci, tk−/+ (thymidine kinase) and hprt+ (Hypoxanthine Phosphoribosyltransferase)] up to 156 generations using goat meat sample. Also these samples were assayed at further radiation doses of 10, 45 and 70 kGy at 2% concentration (in cell line), and 1% (in E. coli). Study was also performed with other meat samples such as chicken, fishes (pomfret and rohu) and shrimps by carrying out limited long-term sub-culturing trials in human lymphoblast cell line. Mutation analysis was also carried out using a novel DPAR (Differential loss of Plasmid Antibiotic Resistance) assay followed by sequencing of tcR (tetracycline resistance) gene of pBR322 plasmid isolated from E. coli cells grown for 1500 generations on HDIMS medium and RAPD (Random Amplified Polymorphic DNA) analysis of the genome.Results and conclusion: None of the assays exhibited any induced mutation when analyzed at regular time intervals. RAPD analysis also did not indicate any change in its nucleotide sequence, ruling out the occurrence of any silent mutation. Thus, the present findings report absence of mutagenic effect of high dose irradiated meat samples.

Genome scale analysis of Escherichia coli with a comprehensive prokaryotic sequence-based biophysical model of translation initiation and elongation.

Translation initiation in prokaryotes is affected by the mRNA folding and interaction of the ribosome binding site with the ribosomal RNA. The elongation rate is affected, among other factors, by the local biophysical properties of the coding regions, the decoding rates of different codons, and the interactions among ribosomes. Currently, there is no comprehensive biophysical model of translation that enables the prediction of mRNA translation dynamics based only on the transcript sequence and while considering all of these fundamental aspects of translation. In this study, we provide, for the first time, a computational simulative biophysical model of both translation initiation and elongation with all aspects mentioned above. We demonstrate our model performance and advantages focusing on Escherichia coli genes. We further show that the model enables prediction of translation rate, protein levels, and ribosome densities. In addition, our model enables quantifying the effect of silent mutations on translation rate in different parts of the transcript, the relative effect of mutations on translation initiation and elongation, and the effect of mutations on ribosome traffic jams. Thus, unlike previous models, the proposed one provides comprehensive information, facilitating future research in disciplines such as molecular evolution, synthetic biology, and functional genomics. A toolkit to estimate translation dynamics of transcripts is available at: https://www.cs.tau.ac.il/∼tamirtul/transim

Mutational landscape of RNA-binding proteins in human cancers

ABSTRACTRNA Binding Proteins (RBPs) are a class of post-transcriptional regulatory molecules which are increasingly documented to be dysfunctional in cancer genomes. However, our current understanding of these alterations is limited. Here, we delineate the mutational landscape of ∼1300 RBPs in ∼6000 cancer genomes. Our analysis revealed that RBPs have an average of ∼3 mutations per Mb across 26 cancer types. We identified 281 RBPs to be enriched for mutations (GEMs) in at least one cancer type. GEM RBPs were found to undergo frequent frameshift and inframe deletions as well as missense, nonsense and silent mutations when compared to those that are not enriched for mutations. Functional analysis of these RBPs revealed the enrichment of pathways associated with apoptosis, splicing and translation. Using the OncodriveFM framework, we also identified more than 200 candidate driver RBPs that were found to accumulate functionally impactful mutations in at least one cancer. Expression levels of 15% of these driver RBPs exhibited significant difference, when transcriptome groups with and without deleterious mutations were compared. Functional interaction network of the driver RBPs revealed the enrichment of spliceosomal machinery, suggesting a plausible mechanism for tumorogenesis while network analysis of the protein interactions between RBPs unambiguously revealed the higher degree, betweenness and closeness centrality for driver RBPs compared to non-drivers. Analysis to reveal cancer-specific Ribonucleoprotein (RNP) mutational hotspots showed extensive rewiring even among common drivers between cancer types. Knockdown experiments on pan-cancer drivers such as SF3B1 and PRPF8 in breast cancer cell lines, revealed cancer subtype specific functions like selective stem cell features, indicating a plausible means for RBPs to mediate cancer-specific phenotypes. Hence, this study would form a foundation to uncover the contribution of the mutational spectrum of RBPs in dysregulating the post-transcriptional regulatory networks in different cancer types.

Optimization and application of a DNA-launched infectious clone of equine arteritis virus.

Reverse genetics is one of the most powerful tools in modern virology. Equine arteritis virus (EAV) is the prototype member of the Equartevirus. In this study, a new reverse genetics system for the recovery of equine arteritis virus from a cDNA plasmid, which contains viral cDNA sequence flanked by hammerhead ribozyme (HamRz) and hepatitis delta virus ribozyme (HdvRz) sequences in both terminals of the viral genome, was developed by optimization of the promoter and terminator regions. Cellular RNA polymerase II drove the transcription of the viral genome. The results showed that the rescued virus (ic-EAV) shared similar morphological and growth characteristics with the wild-type (WT) virus, and could be distinguished from the WT virus via an engineered BspEI restriction site in the nsp3 gene. By using the reverse genetics method established in this study, a G-to-C silent mutation at site 12642 resulted in a significant change in the plaque size of the rescued virus. Moreover, an eGFP-labeled EAV was constructed by introducing the eGFP gene into the infectious clone of EAV, which facilitated the observation of the infection of EAV in target cells. Hence, the newly reverse genetics method of EAV established in this study can be easily manipulated and would be helpful for studying the pathogenic mechanism of EAV.

Rod- versus cone-driven ERGs at different stimulus sizes in normal subjects and retinitis pigmentosa patients.

To study how rod- and cone-driven responses depend on stimulus size in normal subjects and patients with retinitis pigmentosa (RP), and to show that comparisons between responses to full-field (FF) and smaller stimuli can be useful in diagnosing and monitoring disorders of the peripheral retina without the need for lengthy dark adaptation periods. The triple silent substitution technique was used to isolate L-cone-, M-cone- and rod-driven ERGs with 19, 18 and 33% photoreceptor contrasts, respectively, under identical mean luminance conditions. Experiments were conducted on five normal subjects and three RP patients. ERGs on control subjects were recorded at nine different temporal frequencies (between 2 and 60Hz) for five different stimulus sizes: FF, 70°, 60°, 50° and 40° diameter circular stimuli. Experiments on RP patients involved rod- and L-cone-driven ERG measurements with FF and 40° stimuli at 8 and 48Hz. Response amplitudes were defined as those of the first harmonic component after Fourier analysis. In normal subjects, rod-driven responses displayed a fundamentally different behavior than cone-driven responses, particularly at low temporal frequencies. At low and intermediate temporal frequencies (≤12Hz), rod-driven signals increased by a factor of about four when measured with smaller stimuli. In contrast, L- and M-cone-driven responses in this frequency region did not change substantially with stimulus size. At high temporal frequencies (≥24Hz), both rod- and cone-driven response amplitudes decreased with decreasing stimulus size. Signals obtained from rod-isolating stimuli under these conditions are likely artefactual. Interestingly, in RP patients, both rod-driven and L-cone-driven ERGs were similar using 40° and FF stimuli. The increased responses with smaller stimuli in normal subjects to rod-isolating stimuli indicate that a fundamentally different mechanism drives the ERGs in comparison with the cone-driven responses. We propose that the increased responses are caused by stray light stimulating the peripheral retina, thereby allowing peripheral rod-driven function to be studied using the triple silent substitution technique at photopic luminances. The method is effective in studying impaired peripheral rod- and cone- function in RP patients.

Association analysis of polymorphisms in six keratin genes with wool traits in sheep.

ObjectiveThe purpose of this study was to investigate the genetic effects of six keratin (KRT) genes on the wool traits of 418 Chinese Merino (Xinjiang type) (CMXT) individuals.MethodsTo explore the effects and association of six KRT genes on sheep wool traits, The polymerase chain reaction-based single-strand conformation polymorphism (PCR-SSCP), DNA sequencing, and the gene pyramiding effect methods were used.ResultsWe report 20 mutation sites (single-nucleotide polymorphisms) within the six KRT genes, in which twelve induced silent mutations; five induced missense mutations and resulted in Ile→Thr, Glu→Asp, Gly→Ala, Ala→Ser, Se→His; two were nonsense mutations and one was a same-sense mutation. Association analysis showed that two genotypes of the KRT31 gene were significantly associated with fiber diameter (p<0.05); three genotypes of the KRT36 gene were significantly associated with wool fineness score and fiber diameter (p<0.05), three genotypes of the KRT38 gene were significantly associated with the number of crimps (p< 0.05); and three genotypes of the KRT85 gene were significantly associated with wool crimps score, body size, and fiber diameter (p<0.05). Analysis of the gene pyramiding effect between the different genotypes of the gene loci KRT36, KRT38, and KRT85, each genotype in a gene locus was combined with all the genotypes of another two gene loci and formed the different three loci combinations, indicated a total of 26 types of possible combined genotypes in the analyzed population. Compared with the other combined genotypes, the combinations CC-GG-II, CC-HH-IJ, CC-HH-JJ, DD-HH-JJ, CC-GH-IJ, and CC-GH-JJ at gene loci KRT36, KRT38, and KRT85, respectively, had a greater effect on wool traits (p<0.05).ConclusionOur results indicate that the mutation loci of KRT31, KRT36, KRT38, and KRT85 genes, as well as the combinations at gene loci KRT36, KRT38, and KRT85 in CMXT have significant effects on wool traits, suggesting that these genes are important candidate genes for wool traits, which will contribute to sheep breeding and provide a molecular basis for improved wool quality in sheep.

KIT-negative gastrointestinal stromal tumor presenting as omental nodule with silent PDGFRA mutation identified by next generation sequencing (NGS)

KIT-negative gastrointestinal stromal tumor presenting as omental nodule with silent PDGFRA mutation identified by next generation sequencing (NGS)

Attenuation and protective efficacy of Rift Valley fever phlebovirus rMP12-GM50 strain.

Rift Valley fever (RVF) is a mosquito-borne zoonotic disease endemic to Africa and the Arabian Peninsula that affects sheep, cattle, goats, camels, and humans. Effective vaccination of susceptible ruminants is important for the prevention of RVF outbreaks. Live-attenuated RVF vaccines are in general highly immunogenic in ruminants, whereas residual virulence might be a concern for vulnerable populations. It is also important for live-attenuated strains to encode unique genetic markers for the differentiation from wild-type RVFV strains. In this study, we aimed to strengthen the attenuation profile of the MP-12 vaccine strain via the introduction of 584 silent mutations. To minimize the impact on protective efficacy, codon usage and codon pair bias were not de-optimized. The resulting rMP12-GM50 strain showed 100% protective efficacy with a single intramuscular dose, raising a 1:853 mean titer of plaque reduction neutralization test. Moreover, outbred mice infected with one of three pathogenic reassortant ZH501 strains, which encoded rMP12-GM50 L-, M-, or S-segments, showed 90%, 50%, or 30% survival, respectively. These results indicate that attenuation of the rMP12-GM50 strain is significantly attenuated via the L-, M-, and S-segments. Recombinant RVFV vaccine strains encoding similar silent mutations will be also useful for the surveillance of reassortant strains derived from vaccine strains in endemic countries.

Mesopic and Photopic Rod and Cone Photoreceptor-Driven Visual Processes in Mice With Long-Wavelength-Shifted Cone Pigments.

The clearer divergence in spectral sensitivity between native rod and human L-cone (L*-cone) opsins in the transgenic Opn1lwLIAIS mouse (LIAIS) allows normal visual processes mediated by these photoreceptor subtypes to be isolated effectively using the silent substitution technique. The objective of this study was to further characterize the influence of mean luminance and temporal frequency on the functional properties of signals originating in each photoreceptor separately and independently of adaptation state in LIAIS mice. Electroretinographic (ERG) recordings to sine-wave rod and L*-cone modulation at different mean luminances (0.1-130.0 cd/m2) and temporal frequencies (6-26 Hz) were examined in anesthetized LIAIS (N = 17) and C57Bl/6 mice (N = 8). We report maximum rod-driven response with 8-Hz modulation at 0.1 to 0.5 cd/m2, which was almost four times larger than maximum cone-driven response at 8 Hz, 21.5 to 130 cd/m2. Over these optimal luminances, both rod- and cone-driven response amplitudes exhibited low-pass functions with similar frequency resolution limits, albeit their distinct luminance sensitivities. There were, however, two distinguishing features: (1) the frequency-dependent amplitude decrease of rod-driven responses was more profound, and (2) linear relationships describing rod-driven response phases as a function of stimulus frequency were steeper. Employing the silent substitution method with stimuli of appropriate luminance on the LIAIS mouse (as on human observers) increases the specificity, robustness, and scope to which photoreceptor-driven responses can be reliably assayed compared to the standard photoreceptor isolation methods.

Characterization of the DNA mismatch repair proteins MutS and MutL in a hypermutator Acinetobacter baumannii

Mutations of mutS and mutL genes have been linked with the emergence of hypermutator (HPM) phenotype in several bacteria. Nevertheless, there is scarce evidence that these mutations occurred in HPM Acinetobacter baumannii, therefore, it remains unknown whether the mutations located in domains mediating the functions of MutS and MutL. To address this information gap, the nucleotide sequences of mutS and mutL were characterized and their mutations were identified. Additionally, we proposed in silico models of mutated proteins and analyzed the secondary and tertiary structures, and the interaction interfaces of MutL and MutS. The HPM A. baumannii and a wild-type strain were subjected to PCR amplification of full length mutS and mutL, cloning, and sequencing. Following several reads of both strands of each gene and sequence assembly, the mutations were identified. Thereafter, the three-dimensional (3-D) structure of A. baumannii ATCC 19606 was developed and utilized as a template for homology modeling of the mutated amino acid sequences using the Phyre2 and I-TASSER, VMD 1.9.3, LigPlus v.1.4.5, PyMOL v.0.99 software. Regardless of silent mutations (n = 43), 11 missense mutations were identified in the MutS domains of HPM strain such as A4T, T272S, D278N in N-terminus, connector, and core domains, respectively. Three mutations –I357T, A408S, N447S– and 16 silent mutations were observed in MutL. Secondary structure prediction of MutS revealed that the amount of alpha helices, beta sheets, and coils in HPM were 35, 29, and 63, respectively, while these values were 36, 28, and 63 for A. baumannii ATCC 19606 as non mutator. In the case of MutL, for both HPM and non-mutator, 20, 21, and 39 of complete protein were alpha helices, beta sheets, and coils, respectively. Superimposition of structures of MutS of HPM on non-mutator revealed that T272, D278, G457, S528, A533, Y715, and E747 are closely matched with S272, D278, A457, P528, V533, C715, and K747, respectively in non-mutator strain. When the structure of MutL model in HPM was superimposed on its counterpart in non-mutator, all but residues S447, S408, and T357 were identical. Many mutations along the mutS and mutL were noted, but most of the mutations were observed in the interaction interfaces of MutS and MutL. Other substitutions were predominantly detected in C-terminus of MutS that may lead to reduced ATP binding and hydrolysis. Three substitution mutations were adjacent to C-terminus of MutL and are raising the suggestion of reduction in MutL dimerization. It seems that a combination of these mutations is implicated in increased mutation frequency and accordingly emergence of HPM strain.

Tigecycline Resistant Klebsiella pneumoniae Isolated from Austrian River Water.

Antibiotic-resistant bacteria are spreading worldwide in medical settings but also in the environment. These resistant bacteria illustrate a major health problem in our times, and last-line antibiotics such as tigecycline represent an ultimate therapy option. Reports on tigecycline non-susceptible Enterobacteriaceae are presented with regard to medical settings but are rare with that for the environment. The aim of this study was to characterize two tigecycline non-susceptible Klebsiella pneumoniae isolates from the river Mur, and to question the resistance mechanism. The screening for chromosomal mutations revealed a deletion and a silent point mutation in one isolate and a point mutation in the other isolate all within the ramR allele. RamR acts as repressor and prevents overexpression of ramA. These mutations are likely to cause a resistant phenotype due to the overexpression of AcrAB-TolC. MLST revealed that the isolates belonged to two unrelated MLST types (ST2392 and ST2394). Both isolates only revealed resistance to tigecycline and tetracycline. This is one of the rare reports of tigecycline-resistant Klebsiella pneumoniae from surface water. The presence of two genetically different isolates suggests that the river water may bear substances that favor mutations that can lead to this efflux pump-driven resistance.

Variants of katG, inhA and nat genes are not associated with mutations in efflux pump genes (mmpL3 and mmpL7) in isoniazid-resistant clinical isolates of Mycobacterium tuberculosis from India

To understand the impact of efflux pump genes such as mmpL3 and mmpL7 on isoniazid (INH) resistance and to correlate with presence or absence of mutations in essential genes of INH resistance (katG, inhA, and nat) in clinical isolates of Mycobacterium tuberculosis (M. tuberculosis). One hundred (75 resistant and 25 sensitive) clinical isolates of M. tuberculosis from India were selected for the study. The presence of mutations in specific regions of katG, inhA, and nat, efflux pump genes (mmpL3 and mmpL7) associated with INH resistance were analyzed using multiplex allele-specific polymerase chain reaction (MAS-PCR) and DNA sequencing methods, respectively. Substitution mutation AGC-ACC at codon 315 of the katG gene was detected in 65% of resistant isolates. Mutation (C-T at nucleotide position 15) in the inhA promoter region was seen in 22% of resistant isolates. Silent mutation (GGA to GGG) at codon 207 in the nat gene was found in three resistant isolates. No mutations were found in either of the efflux genes (mmpL3 and mmpL7) in any of the isolates. Of the 75 resistant isolates analyzed, 74% had mutation in katG and inhA genes. Thus, this report suggests that the role of mmpL3, mmpL7 and nat genes in INH resistance should not be overestimated in comparison to the primary contribution by katG and inhA in clinical isolates of M. tuberculosis. Further, this concise report is the first of its kind to our knowledge, to show the influence of efflux genes on INH resistance in relation to katG and inhA in clinical isolates of M. tuberculosis.

A tabersonine 3-reductase Catharanthus roseus mutant accumulates vindoline pathway intermediates.

Monoterpenoid indole alkaloids (MIAs) have remarkable biological properties that have led to their medical uses for a variety of human diseases. Mutagenesis has been used to generate plants with new alkaloid profiles and a useful screen for rapid comparison of MIA profiles is described. The MIA mutants identified are useful for investigating MIA biosynthesis and for targeted production of these specialised metabolites. The Madagascar periwinkle (Catharanthus roseus) is the sole source of the dimeric anticancer monoterpenoid indole alkaloids (MIAs), 3',4'-anhydrovinblastine and derivatives, which are formed via the coupling of the MIAs, catharanthine and vindoline. While intense efforts to identify parts of the complex pathways involved in the assembly of these dimers have been successful, our understanding of MIA biochemistry in C. roseus remains limited. A simple thin layer chromatography screen of 4000 ethyl methanesulfonate-metagenized M2 plants is described to identify mutant lines with altered MIA profiles. One mutant (M2-1865) accumulated reduced levels of vindoline inside the leaves in favour of high levels of tabersonine-2,3-epoxide and 16-methoxytabersonine-2,3-epoxide on the leaf surface. This MIA profile suggested that changes in tabersonine 3-reductase (T3R) activity might be responsible for the observed phenotype. Molecular cloning of mutant and wild type T3R revealed two nucleotide substitutions at cytosine residues 565 (CAT to TAT) and 903 (ACC to ACA) in the mutant corresponding to substitution (H189Y) and silent (T305T) amino acid mutations, respectively, in the protein. The single amino acid substitution in the mutant T3R protein diminished the biochemical activity of T3R by 95% that explained the reason for the low vindoline phenotype of the mutant. This phenotype was recessive and exhibited standard Mendelian single-gene inheritance. The stable formation and accumulation of epoxides in the M2-1865 mutant provides a dependable biological source of these two MIAs.

P171 Description of a novel HLA-DPB1 allele with polymorphic sites in exon 1

We describe a new HLA-DPB1 allele, which was first identified in an ASHI PT sample (HT-202) from an African American donor, and recently identified again in a 22-year-old African-American woman undergoing HLA typing as a potential bone marrow donor for her father. High-resolution HLA genotyping was performed using sequence based typing and analyzed using SBTengine software (GenDX, Netherlands). Typing of the PT sample showed allele pair ambiguity of DPB1∗03:01, 105:01 vs DPB1∗124:01, 463:01. Consensus results for the PT sample were DPB1∗03:01, 105:01, however, exon 1 sequence revealed heterozygous peaks at positions 24 (R) and 47 (Y). Given that DPB1∗03:01 and 105:01 are identical in exon 1 and that DPB1∗124:01 does not have a known exon 1 sequence, our lab typed the sample as DPB1∗124:01, 463:01. However it is possible the sample is HLA-DPB1∗03:01 and the new allele which is identical to DPB1∗105:01 except for exon 1. Long range sequencing encompassing exon 2 and 3 would be needed to rule out these two possible allele pairs. At this time, this would only be possible using the PacBio system or a method that allows for chromosome separation and sequencing of DPB1 alleles separately. We encountered the same exon 1 sequence producing heterozygous peaks at positions 24 and 47 while performing HLA typing for a potential bone marrow donor. Exclusion of exon 1 yielded DPB1∗01:01, 105:01, but HLA-DPB1 typing did not match any known allele in the IMGT/HLA database when exon 1 was included in analysis. Family analysis confirms that one of the donor’s alleles is DPB1∗01:01, since this is also present in the donor’s father. Her second allele has identical sequence to DPB1∗105:01 in exons 2, 3, and 4. The new allele contains single nucleotide substitutions at positions 24 and 47 of exon 1. Position 24 contains a G > A substitution; both codons code for alanine, making this a silent mutation. Position 47 contains a C > T substitution, resulting in an amino acid substitution of methionine for threonine. These findings represent a new HLA-DPB1 allele. This polymorphic site has previously been described in HLA-DPB1∗107:01.

Designing Signal Peptides for Efficient Periplasmic Expression of Human Growth Hormone in Escherichia coli.

The secretion efficiency of a protein in a Sec-type secretion system is mainly determined by an N-terminal signal peptide and its combination with its cognate protein. Five signal peptides, namely, two synthetic Sec-type and three Bacillus licheniformis alpha-amylase-derived signal peptides, were compared for periplasmic expression of the human growth hormone (hGH) in E. coli. Based on in silico predictions on the signal peptides' cleavage efficiencies and their corresponding mRNA secondary structures, a number of amino acid substitutions and silent mutations were considered in the modified signal sequences. The two synthetic signal peptides, specifically designed for hGH secretion in E. coli, differ in their N-terminal positively charged residues and hydrophobic region lengths. According to the mRNA secondary structure predictions, combinations of the protein and each of the five signal sequences could lead to different outcomes, especially when accessibility of the initiator ATG and ribosome binding sites were considered. In the experimental stage, the two synthetic signal peptides displayed complete processing and resulted in efficient secretion of the mature hGH in periplasmic regions, as was demonstrated by protein analysis. The three alpha-amylase-derived signal peptides, however, were processed partially from their precursors. Therefore, to achieve efficient secretion of a protein in a heterologous system, designing a specific signal peptide by using a combined approach of optimizations of the mRNA secondary structure and the signal peptide H-domain and cleavage site is recommended.

Shallow learning model for diagnosing neuro muscular disorder from splicing variants

PurposeDiagnosing genetic neuromuscular disorder such as muscular dystrophy is complicated when the imperfection occurs while splicing. This paper aims in predicting the type of muscular dystrophy from the gene sequences by extracting the well-defined descriptors related to splicing mutations. An automatic model is built to classify the disease through pattern recognition techniques coded in python using scikit-learn framework.Design/methodology/approachIn this paper, the cloned gene sequences are synthesized based on the mutation position and its location on the chromosome by using the positional cloning approach. For instance, in the human gene mutational database (HGMD), the mutational information for splicing mutation is specified as IVS1-5 T > G indicates (IVS - intervening sequence or introns), first intron and five nucleotides before the consensus intron site AG, where the variant occurs in nucleotide G altered to T. IVS (+ve) denotes forward strand 3′– positive numbers from G of donor site invariant and IVS (−ve) denotes backward strand 5′ – negative numbers starting from G of acceptor site. The key idea in this paper is to spot out discriminative descriptors from diseased gene sequences based on splicing variants and to provide an effective machine learning solution for predicting the type of muscular dystrophy disease with the splicing mutations. Multi-class classification is worked out through data modeling of gene sequences. The synthetic mutational gene sequences are created, as the diseased gene sequences are not readily obtainable for this intricate disease. Positional cloning approach supports in generating disease gene sequences based on mutational information acquired from HGMD. SNP-, gene- and exon-based discriminative features are identified and used to train the model. An eminent muscular dystrophy disease prediction model is built using supervised learning techniques in scikit-learn environment. The data frame is built with the extracted features as numpy array. The data are normalized by transforming the feature values into the range between 0 and 1 aid in scaling the input attributes for a model. Naïve Bayes, decision tree, K-nearest neighbor and SVM learned models are developed using python library framework in scikit-learn.FindingsTo the best knowledge of authors, this is the foremost pattern recognition model, to classify muscular dystrophy disease pertaining to splicing mutations. Certain essential SNP-, gene- and exon-based descriptors related to splicing mutations are proposed and extracted from the cloned gene sequences. An eminent model is built using statistical learning technique through scikit-learn in the anaconda framework. This paper also deliberates the results of statistical learning carried out with the same set of gene sequences with synonymous and non-synonymous mutational descriptors.Research limitations/implicationsThe data frame is built with the Numpy array. Normalizing the data by transforming the feature values into the range between 0 and 1 aid in scaling the input attributes for a model. Naïve Bayes, decision tree, K-nearest neighbor and SVM learned models are developed using python library framework in scikit-learn. While learning the SVM model, the cost, gamma and kernel parameters are tuned to attain good results. Scoring parameters of the classifiers are evaluated using tenfold cross-validation using metric functions of scikit-learn library. Results of the disease identification model based on non-synonymous, synonymous and splicing mutations were analyzed.Practical implicationsCertain essential SNP-, gene- and exon-based descriptors related to splicing mutations are proposed and extracted from the cloned gene sequences. An eminent model is built using statistical learning technique through scikit-learn in the anaconda framework. The performance of the classifiers are increased by using different estimators from the scikit-learn library. Several types of mutations such as missense, non-sense and silent mutations are also considered to build models through statistical learning technique and their results are analyzed.Originality/valueTo the best knowledge of authors, this is the foremost pattern recognition model, to classify muscular dystrophy disease pertaining to splicing mutations.

Further Molecular Analysis of G6PD Deficiency Variants in Southern Vietnam and a Novel Variant Designated as G6PD Ho Chi Minh (173 A>G; 58 Asp>Gly): Frequency Distributions of Variants Compared with Those in Other Southeast Asian Countries.

We conducted a survey of glucose-6-phosphate dehydrogenase (G6PD) deficiency among newborn babies at Tu Du Hospital, Ho Chi Minh, southern Vietnam. A total of 90 deficient babies were detected, including 85 in the Kinh ethnic group, 4 Chinese, and 1 in the K'Ho minority group. In the Kinh ethnic group, G6PD variants such as G6PD Viangchan (n=32), Kaiping (n=11), Canton (n=8), Chinese-5 (n=7), Union (n=5) and Quing Yuan (n=4) were detected. A variant with silent mutations at 1311 C>T and IVS11 nt 93 T>C was also detected in 17 cases. A novel mutation (173 A>G) in exon 4 with a predicted amino acid change of 58 Asp>Gly was also found in a Kinh newborn girl and her father, and it was designated as G6PD Ho Chi Minh. These findings demonstrated that the Kinh ethnic group in southern Vietnam has 8 different G6PD variants, indicating that the members of this group have many ancestors in terms of G6PD variants from Southeast Asia, China, and Oceania. We compared the frequency distribution of G6PD variants in the Kinh population with those of other Southeast Asian populations, and the Kinh population's distribution was quite similar to that in the Thai population, but differed from it by the absence of G6PD Mahidol.

Nusinersen: The First Option Beyond Supportive Care for Spinal Muscular Atrophy.

Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder characterized by degeneration of spinal motor neurons and poses significant adverse outcome in affected population. Survival motor neuron 1 (SMN1) protein encoded by SMN1 gene located on 5q13 is critical for survival and functioning of motor neurons. Almost identical gene SMN2, present on the same chromosome, produces a small truncated protein (SMN2) because of skipping of exon 7 from translation due to translation silent C6U substitution in exon 7 of SMN2 pre-mRNA transcript. Only 10% of the SMN2 mRNAs produce full length SMN2 protein by including exon 7 in healthy individuals. A large deletion or sometimes a point mutation in SMN1 gene is responsible for SMA. In this case the number of copies of SMN2 genes in an individual determines the severity of disease (the more the number of copies the less severe the disease). Nusinersen (ISIS 396443) binds to intron splicing silencer-N1 (ISS-N1; a site present ten nucleotides down to the junction of exon 7 and intron 7), modulating the splicing of SMN2 pre-mRNA transcript to increase the inclusion of exon 7, thereby increasing the production of full length SMN2 protein. Major evidence of its efficacy came from a sham controlled phase 3 clinical study ENDEAR. The study was stopped early based on significantly favorable results in interim analysis and all the patients were transitioned to receive nusinersen in an ongoing open-label, phase 3 study, SHINE, which will evaluate the long-term efficacy, safety and tolerability of the drug. Nusinersen is globally the first drug approved (by the US FDA) for treatment of SMA in children and adults.

Genetic polymorphism of scrA gene of Streptococcus mutans isolates is not associated with biofilm formation in severe early childhood caries

BackgroundTo explore and analyse the association between biofilm and the genetic polymorphisms of scrA gene of EnzymeIIscr found in clinical isolates of Streptococcus mutans (S. mutans) from severe early childhood caries (S-ECC) in 3 years old children.MethodsClinical strains of S. mutans were conserved from a previous study. Thirty strains of S. mutans from the S-ECC group and 30 strains of S. mutans from the caries free (CF) group were selected. Biomass and viability of biofilm formed by the strains were evaluated by crystal violet and alamar blue assay. Genomic DNA was extracted from the S. mutans isolates. PCR was conducted to amplify scrA gene. After purified and sequenced the PCR products, BioEdit sofeware was used to analyse the sequence results. A chi-square test was used to compare the results.ResultsCompared to the CF group, the biomass of S-ECC group was higher (P = 0.0424). However, the viability of the two groups showed no significant difference. All 60 clinically isolated S. mutans strains had a 1995 base pair (bp) scrA gene. Forty-nine point mutations were identified in scrA from the 60 clinical isolates. There were 17 missense point mutations at the 10, 65, 103, 284, 289, 925, 1444, 1487, 1494, 1508, 1553, 1576, 1786, 1822, 1863, 1886, and 1925 bp positions. The other 32 mutations were silent point mutations. No positions were found at active sites of ScrA. The statistic analyse showed no significant missense mutation rates between the two groups.ConclusionsThere was no association between biofilm and genetic polymorphisms of scrA from S. mutans with S-ECC in 3 years old children.