Antioxidants are molecules which work to protect our cells from the damage of free radicals and other oxidative molecules. Free radicals/oxidants are the molecular by-products during conversion of food into energy in cells. The cells in our body continuously fighting against the threat of these free radicals which have the potential to damage our cells and genetic material. Two of the best-known antioxidants are vitamin C and vitamin E, which helps to slow down or stop the processes that damages the cells in our body. Many fruits which are rich in vitamin C and phenolic compounds, including stress-linked phytochemicals are recommended for consumption to fight against oxidants/ free radicals. Plant polyphenols, which are the products of plant secondary metabolism, thus as dietary antioxidants in human health and disease might protect against oxidative damage. It is well-known that normally consumed fresh and processed fruits along with some vegetables, for instance, apples, grapes, berries, pears, tomatoes and jams, are the main sources of phenolic compounds. Some of the major phenolic compounds isolated and identified from these fruits peels, flesh, skin and seeds are anthocyanins, chlorogenic acids, quercetin glycosides, flavan-3ols, gallaocatechin, (-)-epicatechin, (+)-catechin, rosmarinic acid, ellagic acid, resveratrol, coumaric acid, L-DOPA etc. These natural polyphenols with health benefits fight against many heart diseases, obesity, diabetes, cancers and aging-related diseases.
Since decades cancer therapy has made slow but continuous strides in fighting primary tumors, but progress in the suppression of metastasis remains elusive. The spread of cancer to distant locations in the body is the major cause of cancer morbidity and mortality, and accounts for about 90% of cancer deaths. Although cancer survival rate has been significantly improved over the years, the improvement is primarily due to early diagnosis and cancer growth inhibition (Guan X, 2015) [1].
Bacterial Panicle Blight (BPB) and Sheath Blight (SB) are major rice diseases in the southeastern United States, and only quantitative disease resistance is known for these diseases. We analyzed draft genome sequence data for three U.S. rice varieties showing differential disease resistance traits for BPB and SB; Trenasse (long-grain, susceptible to BPB and SB), Bengal (medium-grain, susceptible to BPB and SB), and Jupiter (medium-grain, partial resistance to BPB and SB). Comparative genome sequence analysis along with 50 rice accessions revealed that the three US varieties are genetically close and clustered together, separated from other 50 accessions. According to this analysis, the long-grain semi-dwarf variety Trenasse is a tropical japonica type carrying a fraction of indica genome, while the medium-grain varieties Bengal and Jupiter are admixtures of tropical and temperate japonica types. Consistent with the breeding history and the phenotypic trait in grain-shape (but not with the phenotype in disease resistance), more variations were found in the Jupiter/Trenasse and Bengal/ Trenasse pairs compared to the Jupiter/Bengal pair. The whole genome sequence information of these US rice varieties will be a useful resource for genetic studies of disease resistance to BPB and SB as well as development of new disease-resistant lines. Introduction Bacterial Panicle Blight (BPB) and Sheath Blight (SB) are important chronic diseases of rice in the southeastern United States, as well as other parts of rice-growing regions around the world [1-4]. BPB is caused by two bacterial pathogens, Burkholderia glumae and B. gladioli, and the phytotoxin toxoflavin is known as the major virulence factor of the pathogens [5]. Oxolinic acid is somewhat effective to control BPB, but this chemical is not registered to use for agricultural purpose in the U.S., and resistant strains of B. glumae have been reported indicating the limitation of this chemical as a reliable control measure [5]. SB is caused by the fungal pathogen, Rhizoctonia solani, and fungicide application is the primary way to control this disease. However, recent reports of R. solani isolates resistant to Strobilurin-type fungicides [6,7] indicate the urgent need of developing reliable alternative management measures for this disease, including the cultivation of disease-resistant varieties. Quantitative (or partial) disease resistance, which is usually conferred by multiple Quantitative Trait Loci (QTLs), is thought to be the primary disease resistance mechanism of rice to BPB and SB. Qualitative (or complete) disease resistance, which involves specific interactions between a resistance gene of the host and its cognate a virulence gene of the pathogen [8], has not been found in BPB or SB of rice. Major QTLs associated with the disease resistance to BPB have been identified from several rice varieties. qBPB3-1 was identified on the short arm of chromosome 3 from the resistant variety, Teqing [9]. Later, qRBS1 (renamed later as RBG1) was mapped on the short arm of chromosome 10 with the 393-kb interval from the resistance variety, Nona Bokra [10]; and RBG2 was identified on the long arm of chromosome 1 with the 502 kb interval from the resistant traditional lowland variety, Kele [11]. Genetics of SB resistance Citation: Shrestha B, Oh DH, Dassanayake M, Ham JH (2018) Analysis of Genome Sequence Variations Among Three U.S. Rice Varieties Showing Differential Quantitative Disease Resistance to Bacterial Panicle Blight and Sheath Blight. Int J Genom Data Min 02: 122. DOI: 10.29011/2577-0616.000122 2 Volume 02; Issue 03 Int J Genom Data Min, an open access journal ISSN: 2577-0616 has been studied more intensively and widely compared to that of BPB resistance. More than 50 QTLs for SB resistance have been identified, and candidate genes responsible for SB resistance have also been found within some QTL regions [12-19]. Among the QTLs identified, qSB9-2 on chromosome 9 and qSBR11-1 on chromosome 11 are known to be major QTLs identified from multiple rice varieties [17,20]. Nevertheless, our knowledge of rice disease resistance to BPB and SB is still fractional and rudimentary. Three U.S. rice varieties, Trenasse, Jupiter and Bengal, have been used for our genetic studies of the disease resistance to BPB and SB. These rice varieties cultivated in the southeastern United States show different phenotypes in terms of major agronomic traits, including grain shape and quantitative disease resistance to BPB and SB; in that Jupiter (a medium-grain variety) shows quantitative resistance to BPB and SB [21], while Bengal (a medium-grain variety) and Trenasse (a long-grain variety) are highly susceptible to both diseases [22,23]. Nevertheless, genetic studies of the disease resistance to BPB and SB with these materials have been hindered due to the lack of polymorphic markers to be used for linkage mapping of QTLs. Whole genome sequencing of rice accessions using a High-Throughput DNA Sequencing (HTS) platform provides excellent opportunities to determine genome-wide sequence variations associated with various traits of rice, such as disease resistance, and to develop more reliable molecular markers in a high-throughput and cost-efficient way [24-26]. Especially, HTS data are very useful for identification of DNA polymorphisms between genetically close genotypes and for fine mapping. For example, comparative analyses have been conducted for the identification of DNA polymorphisms within japonica or indica rice varieties [27-31], and the whole genomes of 13 rice inbred lines derived from US varieties were analyzed for the identification of candidate genes for sheath blight resistance [32]. In this study, we sequenced and analyzed the whole genome sequences of three US rice varieties, Trenasse, Jupiter and Bengal, which represents differential phenotypes in disease resistance/ susceptibility to BPB and SB, using an HTS platform (Illumina Hiseq1000) in an attempt to develop new sequence-based molecular markers and to find a genome information basis for future genomic and genetic studies of rice disease resistance. Materials and Methods Rice Plants and DNA Extraction One-week-old seedlings of the rice varieties, Jupiter (mediumgrain, and moderately resistant to BPB and SB), Trenasse (longgrain, and susceptible to BPB and SB) and Bengal (mediumgrain, susceptible to BPB and SB) were used to extract genomic DNA for whole genome sequencing. DNeasy Plant Mini Kit (Qiagen, Valencia, CA) was used for DNA extraction following manufacturer’s instructions. The genomic DNA library for sequencing was prepared using a Nextera DNA Library Preparation Kit (Illumina Inc., San Diego, CA), and 100-bp paired-end sequencing was processed using the Illumina HiSeq1000 platform (Illumina Inc., San Diego, CA) at Virginia Bioinformatics Institute (VBI) Genomics Lab at Virginia-Tech (Blacksburg, VA). Mapping and Identification of Variants in Genome Sequences The quality of the sequence reads were examined using Fast QC [33], and cleaned high quality reads were aligned to the rice reference genome version 7 released by the International Rice Genome Sequence Project (IRGSP) for the japonica rice variety Nipponbare, using Bowtie 2 [34]. Genome-wide variants including Single Nucleotide Polymorphisms (SNPs) and small insertions and deletions (indels) between the reference genome and three rice varieties were identified and processed using SAMtools [35], and annotated using SnpEff v3.5e [36]. Population Structure Analysis Genetic relatedness of the three rice varieties with 50 rice accessions, including temperate and tropical japonica, aromatic and indica types, were analyzed by using FRAPPE [37]. SNP data of the 50 rice accessions for comparison were from the study by Xu, et al. [38], and the three US varieties for this study were analyzed in terms of admixture proportions with increasing value of K (number of clusters) from 3 to 7. Pairwise Comparison Pairwise comparisons between two varieties (Jupiter vs. Trenasse, Jupiter vs. Bengal, and Bengal vs. Trenasse) were performed with the help of vcftools, using the vcf files obtained from SnpEff analysis [39]. The output file from each comparison was filtered for common variants present in the varieties, which were identified from the comparison with the Nipponbare reference genome. Those variants between the varieties were again annotated and classified based on their effect on various regions in the genome and their functional type, using SnpEff v3.5e [36]. Statement of Reagent and Data Availability All the rice DNA sequence data used for this study were deposited to the NCBI SRA (accession numbers: SRX4017380, SRX4017381, and SRX4017382). DNA samples of the rice varieties, Bengal, Jupiter and Trenasse, will be sent to the researchers upon request. Results and Discussion High-Throughput Sequencing (HTS) Data Obtained in This Study In this study, the genomes of three US rice varieties, Jupiter, Trenasse and Bengal, were sequenced for comparative analysis of genome sequence variations. Fifty to 84 million of 100-bp pairedCitation: Shrestha B, Oh DH, Dassanayake M, Ham JH (2018) Analysis of Genome Sequence Variations Among Three U.S. Rice Varieties Showing Differential Quantitative Disease Resistance to Bacterial Panicle Blight and Sheath Blight. Int J Genom Data Min 02: 122. DOI: 10.29011/2577-0616.000122 3 Volume 02; Issue 03 Int J Genom Data Min, an open access journal ISSN: 2577-0616 end reads were obtained from each variety, resulting in 12X to 18X coverage based on the reference genome of ‘Nipponbare’ (Table 1). Jupiter Trenasse Bengal Total reads (in millions) 79 84 50 Coverage 18X 19X 12X Mapped with chromosomal genome (%) 95.78 91.02 96.33 Mapped with organelle genome (%) 13.21 11.05 9.43 Table 1: Total sequence reads (100-bp paired end) obtained from the high-throughput sequencing in this study, and percentage of the sequence reads mapped to the reference genome
Brain stimulation therapies for the treatment of neuropsychiatric and neurodegenerative diseases [1] have become of major interest to various global communities. Neuropsychiatric and neurodegenerative diseases associated with insulin resistance are expected to affect millions of people by the year 2050 [2,3]. The treatment by brain stimulation therapies in the early stages of neuropsychiatric conditions may allow stabilization or reversal of various conditions such as depression, schizophrenia, bipolar disorders, behavioural, cognition and memory disorders. Brain stimulation therapies include Electroconvulsive Therapy (ECT), Vagus Nerve Stimulation (VNS), Deep Brain Stimulation (DBS), Transcranial Direct Current Stimulation (tDCS) and repetitive transcranial magnetic stimulation. Brain stimulation therapies such as ECT should be reassessed with relevance to dose and frequency for the treatment of psychiatric and behavioral disorders. The major concern with ECT is associated with excessive heat generation and inactivation of genes required for neuron survival [4]. In diabetes and neurodegenerative diseases drug therapy may not be effective for depression and schizophrenia with unsuccessful anti-depressant or anti-psychotic drug treatment. Brain stimulation therapies such as ECT, VNS, DBS, tDCS and rTMS that use direct electrical currents to stimulate specific parts of the brain may be therapeutic when drug treatment is ineffective. However, brain treatment by these different stimulation therapies need to be compared with relevance to excessive heat generation with compete heat shock gene inactivation that leads to accelerated neuron death [5]. In man the heat shock gene Sirtuin 1 is essential to maintain mitochondrial function and its inactivation is associated with neuron mitophagy [4,5].
The past decade has seen enormous progress in the genomics research in the abovementioned area, and the improvement in this area is very important as it directly or indirectly affects the human growth, development and sustainability. The plant genomic research has significant values and impact on agriculture, crop production, drug discovery/medicine and other plant natural products. The responsible genes for delivering important functions of plants, grouped together in biosynthetic gene clusters is hidden away in the dark matter of plant genomes. Current research involving genome sequencing, and now breakthroughs in sequencing technologies, i.e., the use of inexpensive Next-Generation Sequencing (NGS) technology will definitely accelerate the ability to find genes encoding enzymes and pathways for the biosynthesis of new natural products. Increased knowledge of the gene duplication event and plant metabolic gene clusters i.e., their architecture, regulation and assembly will help to understand the specialized metabolic events in plants and in expediting natural product discovery. For example, in soybean and sorghum species, significant depletions of whole-genome duplication-derived specialized metabolic genes were observed, but significant enrichment in local(tandem) duplication-derived specialized metabolic genes were seen. For, gene-clustering works, it has been documented that in rice one-fifth of the metabolic genes situated in clusters, and for Arabidopsis, soybean and sorghum one-third of the metabolic genes situated in clusters and clustered genes responsible for varying amount of phenylpropanoid and terpenoid metabolism. A gene-cluster of 10genes for potential anti-cancer drug noscapine from opium poppy (Papaver somniferum) encoding N-methyltransferase, and seven small clusters each of two to three genes encoding enzymes for anti-cancer vinblastine/vincristine biosynthetic pathway from Catharanthus roseus have also been documented. Knowing the vast chemical biodiversity of the plant world, and widespread applications of plant derived natural products, researchers should now focus on the poorly understood areas of plants such as genetic background, plant authentication through DNA-barcoding techniques, the agricultural traits, and the medicinal quality of the small medicinal herbs. [In the context of crop plant genome assembly, a recent work from King Abdulla Univ. must deserve mention who generated a genome assembly of the economically and nutritionally important tetraploid crop species quinoa].
In insects, metamorphosis is controlled by interaction of endocrine agents mainly by Juvenile hormone and ecdysone.Juvenile Hormone Epoxide Hydrolase (JHEH), one of the major enzymes is involved in degradation of Juvenile hormone pathway and could be applied to control insects due to its irreversible reaction.The present work is focused on cloning of partial gene sequence and Insilico analysis of JHEH gene in Diaphania pulverulentalis (Dp) that is a serious insect pest on mulberry.A cDNA (800bps) encoding the partial JHEH was cloned from the mulberry leaf webber, Diaphania pulverulentalis.Partial DpJHEH sequence contains an open reading frame encoding 244 amino acids with high degree of similarity to the reported insect JHEHs at NCBI.This is the kind of its first study on molecular cloning and sequence information of JHEH in Diaphania pulverulentalis.
1. Abstract Neurodegenerative diseases are irredeemable and incapacitating conditions that result in progressive degeneration. It is difficult to define the complexity of neuro-system quantitatively or meaningfully from a system standpoint. Thus, inclined towards the progress in developing new and effective therapeutic intervention, it is important to understand the underlying molecular mechanism and significance of neuro system and their complex molecular interaction. A biomarker discovery is an important need for early disease diagnosis, prognosis and monitoring of new therapy for neurological disorders. The emergence of system biology and network-based computational model approaches provides the underlying molecular mechanism and significance of disease and their complex molecular interaction. Thus, it becomes quite easy to understand the specific nature of neuro system as well as it plays a significant role in integrating the omics data at multiple levels that lead to key success in the development of more accurate and efficient biomarker for neurological disorders. The current review focused on significant contributions of system biology and network-based computational model approaches in biomarker discovery with special reference to neurological disorders. 2. Keywords: Biomarker discovery; Bioinformatics; System biology; Network-based computational model; Neurological disorders
Prorocentrum donghaiense is one of the most frequently occurred harmful algal blooms in the East China sea.In order to reveal the response mechanisms of P. donghaiense to different nutrient status, de novo transcriptome sequencing was used to examine transcriptomic differences in P. donghaiense that was grown under replete, nitrogen-limited or phosphorus-limited conditions.We noted that transcripts down-regulated by phosphate limitation included those encoding proteins involved in RNA transport, oxidative phosphorylation, photosynthesis, endocytosis, pyrimidine metabolism, glycolysis/gluconeogenesis, biosynthesis of amino acids, vitamin digestion and absorption, protein processing in endoplasmic reticulum, while the expression of genes involved in ribosomal protein metabolism were significantly up-regulated.The abundance of 896 transcripts were elevated or inhibited by nitrogen limitation and they were involved in metabolic processes similar to P depletion.Here, we presented the experimental procedures and analytical processes in detail.
1. Abstract Pea ( Pisum sativum L.) is one of the earliest domesticated cool season annual legume crop produced worldwide, mainly in temperate regions. In common with other grain legumes, pea plays an important role in food and nutritional security of humans as well as livestock. Pea is an annual plant which exhibits mainly self-pollination, although cross pollination through insects also occurs in nature. The improvement of pea through plant breeding requires considerable genetic variations in the key quantitative traits and the expression of those polygenic traits also depends on the environmental interactions. Therefore, UV irradiations have been employed in the present study to assess the genotypic sensitivity of the pea cultivar for possible application in mutation breeding of pea. Seed germination and seedling growth at different duration of exposures were calculated for estimating the effect of UV irradiations stress on pea. The findings of the present study conclude that the UV irradiation can be useful as non-ionizing physical mutagen for induction of selectable macromutations in local pea cultivars and the exposure to the increasing UV stress in the nature will be detrimental for the crop productions.
To examine the effect of plant densities and sowing patterns on yield and agronomical characteristics of corn (hybrid S.C.704), a field experiment was conducted at agricultural research station of Gorgan. This experiment was laid out in a randomized complete block design arranged in a factorial with four replications. Forage corn experiment had four levels of plant densities (D1=65000, D2=75000, D3=85000, D4=95000) and with two planting arrangements (p1=single row and p2=double row 15 cm space apart). The results showed; there was significant difference between planting arrangement for total dry matter, number of kernel per ear, kernel per row, ear length and double row produced higher amount for all above characters. In addition, plant density had a significant effect on total dry weight, number of kernel per ear, number of row per year, total fresh weight, ear length at 0.01 probability level and with an increase in plant density amount of biomass increased. The highest forage yield was produced by 95000 plant density and 15-centimeter double row at 5% significant (93.31-ton ha-1). It might be concluded that by using double row planting pattern the inter plant competition could be decreased and higher yield might be produced.
Following 25 years of extensive research by many scientists worldwide, a panel of ten reward gene risk variants, called the Genetic Addiction Risk Score (GARS), has been developed. In unpublished work, when GARS was compared to the Addiction Severity Index (ASI), which has been used in many clinical settings, GARS significantly predicted the severity of both alcohol and drug dependency. In support of early testing for addiction and other RDS subtypes, parents caught up in the current demographic of 127 people, both young and old, dying daily from opiate/opioid overdose, need help. In the past, families would have never guessed that their loved ones would die or could be in real danger due to opiate addiction. Author, Bill Moyers, in Parade Magazine, reported that as he traveled around the United States, he found many children with ADHD and other spectrum disorders like Autism, and noted that many of these children had related conditions like substance abuse. He called for better ways to identify these children and treat them with approaches other than addictive pharmaceuticals. To our knowledge, GARS is the only panel of genes with established polymorphisms reflecting the Brain Reward Cascade (BRC), which has been correlated with the ASI-MV alcohol and drug risk severity score. While other studies are required to confirm and extend the GARS test to include other genes and polymorphisms that associate with an hypodopaminergic trait, these results provide clinicians with a non-invasive genetic test. Genomic testing, such as GARS, can improve clinical interactions and decision-making. Knowledge of precise polymorphic associations can help in the attenuation of guilt and denial, corroboration of family gene-o-grams; assistance in risk-severity-based decisions about appropriate therapies, including pain medications and risk for addiction; choice of the appropriate level of care placement (i.e., inpatient, outpatient, intensive outpatient, residential); determination of the length of stay in treatment; determination of genetic severity-based relapse and recovery liability and vulnerability; determination of pharmacogenetic medical monitoring for better clinical outcomes (e.g., the A1 allele of the DRD2 gene reduces the binding to opioid delta receptors in the brain, thus, reducing Naltrexone's clinical effectiveness); and supporting medical necessity for insurance scrutiny.
A 16-year-old Polish male child was referred to confirm the diagnosis of myotonia congenita. For several years he had experienced cold-induced myotonia and muscle stiffness. DNA analysis of the SCN4Agene showed a C to T transition at nucleotide position 3938 in exon 22 of SCN4A (Thrl313Met) in patient but not in his parents. Based on his symptoms and results of DNA analysis, paramyotonia congenita was diagnosed, which prevalence is very low in Poland.
Prediction of bi-molecular protein associations or interactions has been the object of a gamut of computational studies, however extrapolation of these methodologies to compute the structure and function of multi-meric proteins faces several complications. One of them stems from the combinatorial aspect of the problem, since in many cases it requires the prediction of the dynamic order in which the subunits interact (the interaction path). A second, not less important, is the size of these molecules which account to the thousands of atoms, and thus require sophisticated computational platforms. Catering to the need of predicting protein multi-meric configurations and thereby their dynamic order of formation we present here a genuine approach that requires the sole information of the isolated monomers’ structures. The method is based on a protocol we have developed to recognize interaction sites on protein’s surfaces. Hitherto attempts to solve this relevant problem in protein function elucidation have been limited to three body dockings using conventional docking algorithms. Here the aim is to infer complex configurations and dynamic orders of formation from the monomers known to constitute a multimeric complex unveiling active regions on the surfaces of the proteins and intermediate complexes. We present three case studies and show that important insights into the formation mechanisms of this type of multimeric complexes can be gained from the analysis of the surface characteristics of the interacting monomers which can facilitate, in a further stage, the docking and energy calculations involved in the prediction of the configurations of these complexes.
Redundancy is the duplication of a system's components or functions in order to increase its reliability. This system is provided with a pack of duplications of the components for saving backups in case of sudden malfunctioning. A satellite, for instance, is provided with basic duplications before its launch such as inertial navigation system which depends on 5 duplicate computers on the satellite and 3 inertial measurement congruent units. This is the same in living organisms, where genes duplicate in a way that protects them from any sudden mutations or failures. Redundancy is a biological Safety system that destroys the effect of mutations. Redundant mechanisms' duty is to achieve the aims of growth in complete perfection. This mechanism is necessary; as there is no system with such complexity as that of living organisms unless it will need the redundancy in its different phases of Decoding. This Phenomenon imposes a giant challenge to the conception of beneficial mutations. In order to get a beneficial mutation with evident effect, this mutation should have the same semblance and technique in all the redundant copies which produce this effect in a genome. The more redundant the genes are, the more we need synchronizing effective mutations on the progressive change, and the more difficult it is to believe in the ability of this change to get a wholesome model. This article sheds light on the decisive difficulties which face the hope of inducing any beneficial mutations.
The presented study gives an additional meaning to the word ‘Genomics’. In contrary to its traditional meaning, this paper introduces a method which is able to map consumer minds similarly to genome sequencing methods in molecular biology. Mind Genomics is not a traditional genomic method; it is used as a metaphor, since it uses expressions, or short stories to uncover the subconscious thinking of consumers about certain topics. The obtained information is used to differentiate so-called mind-sets, or alleles, which consist of people having similar opinions about the given topic. The agreement of respondents within the mind-sets is high, although there are significant differences between them. Mind genomics is a universal tool, giving the opportunity to researchers, entrepreneurs, students, everyone to use and sequence the mind of people about a topic of interest.
Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, India *Corresponding author: Shabir H Wani, Mountain Research Centre for Field Crops, Khudwani Anantnag-192101, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Jammu & Kashmir, India. Tel: +919419035566; +919797001791; Email: shabirhussainwani@gmail.com
In this study, we have analyzed 50 people. 20 patients Moyamoya disease and 30 Persons control group.The genes RNF213 on chromosome 17q25, ACTA2 on chromosome 10q23.3,GUCY1A3 on chromosome 4q32, analyzed in terms of genetic mutations made. In this study, people who have genetic mutations were targeted, with nervous disorders, Moyamoya disease. In fact, of all people with Moyamoya disease. 20 patients Moyamoya disease had a genetic mutation in the genes RNF213 on chromosome 17q25,ACTA2 on chromosome 10q23.3,GUCY1A3 on chromosome 4q32 Moyamoya disease. Any genetic mutations in the target genes control group, did not show.
