Showing 7 results for Nucleotide
, Amin Oujifard1, ,
Volume 4, Issue 2 (9-2015)
Abstract
The effects of dietary nucleotide at 5 levels of 0.0% (Control), 0.15%, 0.25%, 0.35% and 0.5% on the body composition and fatty acids of the grouper, Epinepheluscoioides, with initial weight of 10.70 ± 0.29 g was investigated for a period of 10 weeks. The results indicated improvedgrowth parameters uponadding nucleotide. The best value of growth parameters were observed at nucleotide level of 0.35% that statistically showed higher values for final weight, weight gain andcondition factor than other treatments (P<0.05).There was nosignificant differenceinsurvival(P>0.05). The 0.35% nucleotide level also resulted in a better fatty acids profile, including EPA, EPA+DHA and n-3 than the control. However, 0.5% nucleotide showed significantly higher saturated fatty acids, MUFA and n3/n6 than the control. No significant differences were observed in arachidonic acid and DHA among the treatments (P>0.05). Chemical analysis showed the highest muscle protein in 0.15% and the highest muscle fat in 0.15 and 0.25 treatments, which were significantly higher (P<0.05) than the control group. The results of this study showed that dietary nucleotide has positive effects on growth performance and fatty acid profile of the grouper and the 0.35% level had a better performance.
Volume 10, Issue 3 (9-2019)
Abstract
Aims: Due to their unique properties, functionalized GNPs provide a high potential for solving many problems, such as diagnosis and treatment of genetic diseases using nanotechnology. Depending on the purpose of each experiment, a particular interaction of DNA and nanoparticle is desirable that can be achieved by changing various parameters. The purpose of this study was to investigate the effect of gold nanoparticles surface charge on the conjugation process and the type of DNA interactions, as well as increasing the loading of DNA on the surface of gold nanoparticles.
Materials and Methods: Two types of 30nm gold nanoparticles with positive and negative charge were synthesized. Gold nanoparticles were functionalized with three different concentrations of DNA. Bioconjugation was investigated using UV-Vis and fluorescence spectroscopy. Quantification of the DNA loading on each nanoparticle surface was done using two methods by fluorescence assay.
Findings: The SPR spectrum of nanoparticles confirmed the binding of DNA to the surface of nanoparticles and also illustrates the level of DNA loading to the surface of the nanoparticle, as well as the effect of the surface charge of nanoparticles on the bioconjugation process. The fluorescence assay showed a higher loading of DNA in CTAB-stabilized nanoparticles and more non-specific than citrate-stabilized nanoparticles.
Conclusion: Depending on the surface charge of GNPs, DNA loading on the surface of GNPs occurs with different affinities. Based on the purpose of the study, citrate stabilized GNPs and high concentration of DNA was appropriate to achieve this goal.
Volume 10, Issue 4 (12-2019)
Abstract
Revealing DNA sequences is vital for all branches of biological sciences. Next-Generation Sequencing (NGS) is a different approach in this area so that it has created a great evolution in biology science and covers various aspects of genome, transcriptome, epigenome and metagenome-level studies. NGS is considered as a high-performance method for genomic and transcriptomic information analysis in comparison with traditional methods due to providing good genomic coverage, determining each single pairs of bases and eliminating the first generation sequencing disadvantages (Sanger sequencing). Use of NGS has begun since 2005 and 2006, after the commercialization of various apparatus companies such as ABI/SOLiD Illumina, Science Roch/454Life, and Solexa to study the transcriptome of the model and non-model organisms. Recently, RNA sequencing is used widely to identify genes associated with growth and development processes and their expression patterns in response to a variety of biological and non-biological stresses, in various organs and growth stages in different organisms. It helps scientists to determine the amounts of gene expression, differentiation of different isoforms of genes, detection of gene fusions and characterization of small RNA as well as alternative splicing events, duplicate elements, exon of genes, new transcripts, UTRs, SNPs, and somatic mutations. The RNA-seq method typically consists of providing suitable biological samples, isolation of total RNA, enrichment of non-ribosomal RNAs, conversion of RNA to cDNA, construction of a fragment library, selecting size and adding linkers and sequencing on high-throughput sequencing platform, alignment, and assembly of the reads and downstream analysis.
Volume 11, Issue 2 (7-2022)
Abstract
Beet curly top Iran virus (BCTIV) and Beet curly top virus (BCTV) are responsible for the curly top disease in sugar beet Beta vulgaris L. and many other plants. Mixed infection by BCTIV and BCTV in sugar beet plants results in a synergistic interaction, with more severe symptoms than plants infected by either virus, accompanied by an increase in BCTIV and a decrease in BCTV titers. Interaction of the Replication associated protein (Rep) with the nonanucleotide motif within the origin of replication is crucial for the replication of the geminivirus genome. Using an in silico approach, we investigated the possible contribution of the interaction between Rep and the nonanucleotide motifs in the interference between BCTIV and BCTV in mixed infections. The physicochemical characterization of both Reps was performed, and their secondary and tertiary structures were predicted by SOMPA tool and I-TASSER server, respectively. Then, the binding affinity of each Rep towards cognate and non-cognate viral nonanucleotide motifs was assessed using Docking simulations. Cluster analysis of HADDOCK revealed that the total binding energy of BCTV Rep toward its cognate nonanucleotide motif was lower than for the BCTIV complex, confirming a higher affinity of BCTV encoded Rep for its nonanucleotide motif. Interestingly, the BCTIV Rep showed the highest affinity for the nonanucleotide motif of the non-cognate BCTV nonanucleotide motif. Since the replication of geminiviruses relies on species-specific Rep interactions and activities, this result could be considered responsible for the competitive interference of BCTIV towards BCTV.
Mohamad Larijani, Roya Bakhtiar, Mehrnoush Norouzi, Raha Fadaei,
Volume 12, Issue 3 (9-2023)
Abstract
This study was performed to determine the identification (barcoding) using cytochrome oxidase gene of common carp, between three provinces of Golestan, Mazandaran and Gilan (respectively in Gomishan, Tajan and Kiashahr) in 2011. The results of sequencing showed that all samples from the three regions had a genetic distance less than 2%, so all samples were from the same species. The results of sequencing 30 tail samples of carp species on the southern shores of the Caspian Sea showed that all samples are of the same species and their genetic distance does not reach at least 2%. Therefore, all carp samples of the three provinces are of the same species and have the same type of barcode. In the study of nucleotide and haplotypic distance, Gomishan region was 10.75000, 1 and Kiashahr region were 3.200 and 0.9333, respectively. In the study of nucleotide diversity between the two regions, 0.01978 and the average nucleotide difference was 12.187. Haplotypic diversity in Gomishan region was 38.095 and in Kiashahr region was 23.809%. Out of 13 haplotypes, Gomishan region with 8 haplotypes (61.53%) and Kiashahr region with 5 haplotypes (38.46%) had the lowest haplotypes.The results of this study show that there is a significant difference between carp samples in Gomishan and Kiashahr regions in terms of nucleotide and haplotypic diversity (P <0.05).
Volume 23, Issue 2 (3-2021)
Abstract
Heat stress, or
hyperthermia, can have a serious effect on chicken performance in poultry industry in many parts of the world. Both genetics and environment play key role in the performance of a chicken and, therefore, it is important to consider both factors in addressing heat stress. On genetics level, genome-wide association studies have become a popular method for studying heat stress in recent years. A population of 202 F
2 chickens was reared for 84 days to find genes and genomic regions affecting growth traits and immune system. But, due to unexpected acute increase in temperature at day 83, 182 birds died (case) and 20 birds remained alive (control). At the age of 70 days, blood sample of all birds was collected to extract their DNA, using modified salting out method. All samples were genotyped by a 60 K Single Nucleotide Polymorphism (SNP) chip. Genome-wide association study was carried out by GCTA to identify gene and genomic regions associated with heat stress tolerance. Results indicated a close relationship between 28 SNPs, located on chromosomes 2, 3, 5, 6, 7, 12, 19, 20, and 21 and heat stress tolerance at the level of suggestive significance.
Two suggestively significant markers on chromosome 5, namely, GGaluGA273356 and Gga_rs16479429, were located within and 52 Kb downstream of two genes, including MAPKBP1and SPON1, respectively. Gene ontology analysis indicated that the resistance of chickens to acute increase of temperature might be linked to the function of MAPKBP1 and SPON1 genes and their biological pathways. These results will be useful for understanding the molecular mechanisms of SNPs and candidate genes for heat stress tolerance in chickens and provide a basis for increasing genetic resistance in breeding programs.
Volume 26, Issue 2 (3-2024)
Abstract
Larvae of numerous Noctuidae and Nolidae species have significant annual economic losses in agriculture. DNA-based diagnostics have been proposed as an effective way to accelerate the identification and discovery of new species. This study aimed to determine the utility of up to 642 bp Cytochrome c Oxidase subunit I (COI) barcodes for identifying 12 major Iranian Noctuidae and Nolidae crop pests and confirming morphological identifications based on classical taxonomy. We combined molecular and morphological analysis to identify 53 specimens collected from populations throughout Iran. The results indicated the presence of a distinct barcode gap for different pest species. The mean interspecific sequence divergence (Kimura 2-parameter) was an order of magnitude (10.0%) greater than the mean intraspecific sequence divergence (0.29%). This combination of DNA and morphological analyses identified 13 species, one of which was previously unknown and may represent a new previously overlooked Earias species. There were no, or very few, sequences from Iran in international databases for some of the test species. Here, we increase the number of specimens from Iran and aid in taxonomic interpretation. The current study will aid in the identification of the most common Noctuidae and Nolidae major pest species in Iran, regardless of the observer’s taxonomic skills, developmental stage of the vouchers, as well as sex, or insect preservation condition. Our data enables researchers and practitioners involved in the bio-surveillance of insect pests to identify taxa based on simple DNA sequence comparisons quickly. DNA barcoding in conjunction with morphological identifications can provide secondary evidence supporting morphological identifications and improve taxonomic resolution.
