Frequency of MTHFR GENE C677T Polymorphism for Non-Syndromic Autism Spectrum Disorder Patients

Background: The folate metabolism is a pathway that may involve in the non-syndromic Autism Spectrum Disorder (ASD). Methylenetetrahydrofolate reductase enzyme has a key role in folate metabolism. The C677T polymorphism of MTHFR gene could reduce the effectiveness of the enzyme.Objectives: To evaluate the frequency of MTHFR geneC677T polymorphism for non-syndromic ASD patients.Method: Thirty-four DNA samples were taken from each group. PCR mixture was consisted of 1µL DNA, 2.5µL PCR buffer, 0.5µL dNTP, 1.5µL MgCL2, 0.125µLTaqenzyme, 0.5µLofforwardandreverseprimerandaquabidesttoreach a volume of 25 µL. The PCR profiles were initiation 95ºC for 5 min, denaturation 94ºC for 1min, annealing 55ºCfor 45 seconds, and elongation 72ºC for30 seconds. The cycles were done in 35 times an dfinal elongation was at 72ºC for 5min. The PCR product was 198bp, and then digested by the Hinfl enzyme for 16hours at 37°C, and visualized using2%agarosegeland then electrophoresed for 30 minutes at 100 volts.Result: Non-syndromic ASD samples showed none had homozygote mutant type (677TT), 3 (8.8%) samples had heterozygote (677CT)and 31 (91.2%) samples had wild type (677CC). Meanwhile, normal control showed only 1 (2.9%)sample had homozygote mutant type(677TT), 9 (26.5%) samples had heterozygote (677CT)and 24 (70.6%) samples had wild type (677CC).Conclusion: The frequency of MTHFR geneC677T polymorphism in patients with non-syndromic ASD and controls are not significantly different

Estimation of Na Gene Frequency on Native Chicken Population and Its Effect on Hatchability Performance

The objective of this research was to estimate the Na gene frequency of the native chickenpopulation and its effect on hatchability performance. The research used Native Chickens with Nakedneckphenotype and Normal-feathered Native Chicken, consisted of 16 cocks and 48 hens as the parent.They were put in 4 breeding groups : 1) Breeding group of Legund Cock with Legund Hen (LL); 2)Legund Cock with Normal-feathered Native Hen (LN); 3) Normal-feathered Native Cock with LegundHen (NL); 4) Normal-feathered Native Cock with Normal-feathered Native Hen (NN). Each groupconsisted of 4 replications and each replication consisted of 1 Cock with 3 Hens. CompletelyRandomized Design (CRD) were used to analysis the fertility, hatchability and embryo mortality.Hardy-Weinberg\u27s Law of Gene equilibrium method was used to find out the spreading estimation of Naand na gene in whole offspring population. Experimental result showed that the breeding groups had noinfluence (P>0.05) on egg fertility, hatchability and embryo mortality. The phenotypes of the offspringof the breeding groups were not deviate from the Mendel\u27s law. The estimation of the Na gene frequencywas 19.7%

Frequency-modulated nuclear localization bursts coordinate gene regulation

In yeast, the transcription factor Crz1 is dephosphorylated and translocates into the nucleus in response to extracellular calcium. Here we show, using time-lapse microscopy, that Crz1 exhibits short bursts of nuclear localization (typically lasting 2 min) that occur stochastically in individual cells and propagate to the expression of downstream genes. Strikingly, calcium concentration controls the frequency, but not the duration, of localization bursts. Using an analytic model, we also show that this frequency modulation of bursts ensures proportional expression of multiple target genes across a wide dynamic range of expression levels, independent of promoter characteristics. We experimentally confirm this theory with natural and synthetic Crz1 target promoters. Another stress-response transcription factor, Msn2, exhibits similar, but largely uncorrelated, localization bursts under calcium stress suggesting that frequency-modulation regulation of localization bursts may be a general control strategy used by the cell to coordinate multi-gene responses to external signals

The HSV-1 Latency-Associated Transcript Functions to Repress Latent Phase Lytic Gene Expression and Suppress Virus Reactivation from Latently Infected Neurons

open access articleHerpes simplex virus 1 (HSV-1) establishes life-long latent infection within sensory neurons, during which viral lytic gene expression is silenced. The only highly expressed viral gene product during latent infection is the latency-associated transcript (LAT), a non-protein coding RNA that has been strongly implicated in the epigenetic regulation of HSV-1 gene expression. We have investigated LAT-mediated control of latent gene expression using chromatin immunoprecipitation analyses and LAT-negative viruses engineered to express firefly luciferase or β-galactosidase from a heterologous lytic promoter. Whilst we were unable to determine a significant effect of LAT expression upon heterochromatin enrichment on latent HSV-1 genomes, we show that reporter gene expression from latent HSV-1 genomes occurs at a greater frequency in the absence of LAT. Furthermore, using luciferase reporter viruses we have observed that HSV-1 gene expression decreases during long-term latent infection, with a most marked effect during LAT-negative virus infection. Finally, using a fluorescent mouse model of infection to isolate and culture single latently infected neurons, we also show that reactivation occurs at a greater frequency from cultures harbouring LAT-negative HSV-1. Together, our data suggest that the HSV-1 LAT RNA represses HSV-1 gene expression in small populations of neurons within the mouse TG, a phenomenon that directly impacts upon the frequency of reactivation and the maintenance of the transcriptionally active latent reservoir

The site frequency spectrum of dispensable genes

The differences between DNA-sequences within a population are the basis to infer the ancestral relationship of the individuals. Within the classical infinitely many sites model, it is possible to estimate the mutation rate based on the site frequency spectrum, which is comprised by the numbers $C_1,...,C_{n-1}$, where n is the sample size and $C_s$ is the number of site mutations (Single Nucleotide Polymorphisms, SNPs) which are seen in $s$ genomes. Classical results can be used to compare the observed site frequency spectrum with its neutral expectation, $E[C_s]= \theta_2/s$, where $\theta_2$ is the scaled site mutation rate. In this paper, we will relax the assumption of the infinitely many sites model that all individuals only carry homologous genetic material. Especially, it is today well-known that bacterial genomes have the ability to gain and lose genes, such that every single genome is a mosaic of genes, and genes are present and absent in a random fashion, giving rise to the dispensable genome. While this presence and absence has been modeled under neutral evolution within the infinitely many genes model in previous papers, we link presence and absence of genes with the numbers of site mutations seen within each gene. In this work we derive a formula for the expectation of the joint gene and site frequency spectrum, denotes $G_{k,s}$ the number of mutated sites occurring in exactly $s$ gene sequences, while the corresponding gene is present in exactly $k$ individuals. We show that standard estimators of $\theta_2$ for dispensable genes are biased and that the site frequency spectrum for dispensable genes differs from the classical result.Comment: 24 pages, 8 figure

Prevalence of Panton-valentine gene in Staphylococcus aureus isolated from clinical samples and healthy carriers in Gorgan city, north of Iran

Aim. Staphylococcus aureus (S. aureus) is a nosocomial and community acquired pathogen. S. aureus is a pathogen that causes several types of disease from skin infections to systemic diseases that is because of having several virulence factors such as enzymes, toxins, superantigens and Panton-Valentine leukocidin (pvl). pvl is a bi-component leukotoxin that destroy PMNs and monocytes and causes furunculosis, abscesses and necrotizing soft tissue infections in patients without any risk factors for such infections. The goal of this study was determine the prevalence of pvl gene in S. aureus isolated from patients and healthy carriers in Gorgan city, north of Iran. Methods. One hundred seventy isolates of S. aureus, 95 from patients and 75 healthy carriers, were collected during one year. After identification and purification, DNA extraction was done by phenol-chloroform method. Amplification of pvl gene was done by specific primer and polymerase chain reaction method. Results. Among the 170 isolates of S. aureus, 20 contained pvl gene. The frequency of isolates contained pvl gene in MRSA and MSSA isolates were 21.6, 19.3, which was not statistically significant. The frequency of these genes was not related to age, sex and source of isolation from patients. Conclusion. The frequency of pvl gene in this region were much higher than expected. © Copyright 2016 Edizioni Minerva Medica

Transcriptome Analysis of Targeted Mouse Mutations Reveals the Topography of Local Changes in Gene Expression.

The unintended consequences of gene targeting in mouse models have not been thoroughly studied and a more systematic analysis is needed to understand the frequency and characteristics of off-target effects. Using RNA-seq, we evaluated targeted and neighboring gene expression in tissues from 44 homozygous mutants compared with C57BL/6N control mice. Two allele types were evaluated: 15 targeted trap mutations (TRAP); and 29 deletion alleles (DEL), usually a deletion between the translational start and the 3' UTR. Both targeting strategies insert a bacterial beta-galactosidase reporter (LacZ) and a neomycin resistance selection cassette. Evaluating transcription of genes in +/- 500 kb of flanking DNA around the targeted gene, we found up-regulated genes more frequently around DEL compared with TRAP alleles, however the frequency of alleles with local down-regulated genes flanking DEL and TRAP targets was similar. Down-regulated genes around both DEL and TRAP targets were found at a higher frequency than expected from a genome-wide survey. However, only around DEL targets were up-regulated genes found with a significantly higher frequency compared with genome-wide sampling. Transcriptome analysis confirms targeting in 97% of DEL alleles, but in only 47% of TRAP alleles probably due to non-functional splice variants, and some splicing around the gene trap. Local effects on gene expression are likely due to a number of factors including compensatory regulation, loss or disruption of intragenic regulatory elements, the exogenous promoter in the neo selection cassette, removal of insulating DNA in the DEL mutants, and local silencing due to disruption of normal chromatin organization or presence of exogenous DNA. An understanding of local position effects is important for understanding and interpreting any phenotype attributed to targeted gene mutations, or to spontaneous indels

The diversity of a distributed genome in bacterial populations

The distributed genome hypothesis states that the set of genes in a population of bacteria is distributed over all individuals that belong to the specific taxon. It implies that certain genes can be gained and lost from generation to generation. We use the random genealogy given by a Kingman coalescent in order to superimpose events of gene gain and loss along ancestral lines. Gene gains occur at a constant rate along ancestral lines. We assume that gained genes have never been present in the population before. Gene losses occur at a rate proportional to the number of genes present along the ancestral line. In this infinitely many genes model we derive moments for several statistics within a sample: the average number of genes per individual, the average number of genes differing between individuals, the number of incongruent pairs of genes, the total number of different genes in the sample and the gene frequency spectrum. We demonstrate that the model gives a reasonable fit with gene frequency data from marine cyanobacteria.Comment: Published in at http://dx.doi.org/10.1214/09-AAP657 the Annals of Applied Probability (http://www.imstat.org/aap/) by the Institute of Mathematical Statistics (http://www.imstat.org