Molecular Docking Analysis of 120 Potential HPV Therapeutic Epitopes Using a New Analytical Method

International Journal of Peptide Research and Therapeutics - The accurate modelling and scoring of protein–peptide (Pr–Pe) complexes are determining factors in the drug discovery...     

Association mapping and meta-analysis: two complementary approaches for the detection of reliable Septoria tritici blotch quantitative resistance in bread wheat (Triticum aestivum L.)

Septoria tritici blotch (STB), caused by the ascomycete Mycosphaerella graminicola, is one of the most ubiquitous and important diseases of bread wheat worldwide. The aim of this study was to identify markers linked to loci conferring resistance to STB from seven biparental populations. Linkage analysis, meta-analysis and association mapping were combined to identify robust quantitative trait loci (QTLs) for resistance. Linkage analysis led to the detection of 115 QTLs for resistance to STB and 66 QTLs linked to plant height and/or earliness. Meta-analysis clustered these 115 QTLs into 27 Meta-QTLs (MQTLs) of pathogen resistance, of which 14 were found to be linked to plant height and/or earliness. Both the relationship between dwarfing and susceptibility to STB and the significant negative correlation between earliness and STB symptoms were confirmed. Eleven loci were linked to STB resistance by association mapping using a general linear model and/or a mixed linear model, of which eight co-located with STB MQTLs and two co-located with individual QTLs. Associated markers located in MQTL regions enhanced the relevance of the results and validated the potential of an association mapping approach. With several biparental populations, meta-analysis is the most relevant form of genetic analysis study, but association mapping can be used as a validation method. Regions linked to resistance in both methods should be relevant for use in breeding programs for improving resistance to STB in wheat varieties. The main interest in comparing both approaches is to detect robust loci that will be functional in many genetic backgrounds rather than just in one or a few specific backgrounds.     

An analytical enrichment-based review of structural genetic studies on keratoconus

Keratoconus is a progressive bilateral corneal protrusion that leads to irregular astigmatism and impairment of vision. Keratoconus is an etiologically heterogeneous corneal dystrophy and both environmental and genetic factors play a role in its etiopathogenesis. In this analytical review, we have studied all the genes that are structurally associated with keratoconus and have tried to explain the function of each gene and its association with other eye disorders in a concise way. In addition, using gene set enrichment analysis, it was attempted to find the most important impaired metabolic pathways in keratoconus. Several genetic studies have been carried out on keratoconus and several genes have been identified as risk factors involved in the etiology of the disease. In the current study, 16 studies, including nine association studies, five genome-wide association studies, one linkage study, and one meta-analysis, were reviewed and based on the 19 genes found, enrichment was performed and the most important metabolic pathways involved in the disease were identified. The enrichment results indicated that the two pathways, interleukin 1 processing and assembly of collagen fibrils, are significantly associated with the disease. Obviously, the results of this study, in addition to providing information about the genes involved in the disease, can provide an integrated insight into the gene-based etiology of keratoconus and therapeutic opportunities thereof.     

Investigation on Mitochondrial tRNA<Superscript>Leu/Lys</Superscript>, NDI and ATPase 6/8 in Iranian Multiple Sclerosis Patients

As with chromosomal DNA, the mitochondrial DNA (mtDNA) can contain mutations that are highly pathogenic .In fact, many diseases of the central nervous system are known to be caused by mutations in mtDNA. Dysfunction of the mitochondrial Respiratory Chain (RC) has been shown in patients with neurological disease including Alzheimer’s disease (AD), Parkinson’s disease (PD) and Multiple sclerosis (MS). MS is a demyelinating disease of central nervous system characterized by morphological hallmarks of inflammation, demyelination and axonal loss. Considering this importance, we decided to investigate several highly mutative parts of mtDNA for point mutations as MT-LTI (tRNA^{Leucine1(UUA/G)}), MT-NDI (NADH Dehydrogenase subunit 1), MT-COII (Cytochrome c oxidase subunit II), MT-TK (tRNA^Lysine), MT-ATP8 (ATP synthase subunit F0 8) and MT-ATP6 (ATP synthase subunit F0 6) in 20 Iranian MS patients and 80 age-matched control subjects by PCR and automated DNA sequencing to evaluate any probable point mutations. Our results revealed that 15 (75%) out of 20 MS patients had point mutations. Some of point mutations were newly found in this study. This study suggested that point mutation occurred in mtDNA might be involved in pathogenesis of MS.     

First Report of Northern Root-Knot Nematode,Meloidogyne hapla,Parasitic on Oaks,Quercus brantii and Q. infectoria in Iran

Root-knot nematodes (RKN) are the most serious plant parasitic nematodes having a broad host range exceeding 2,000 plant species. Quercus brantii Lindl. and Q. infectoria Oliv are the most important woody species of Zagros forests in west of Iran where favors sub-Mediterranean climate. National Botanical Garden of Iran (NBGI) is scheduled to be the basic center for research and education of botany in Iran. This garden, located in west of Tehran, was established in 1968 with an area of about 150 ha at altitude of 1,320 m. The Zagros collection has about 3-ha area and it has been designed for showing a small pattern of natural Zagros forests in west of Iran. Brant’s oak (Q. brantii) and oak manna tree (Q. infectoria) are the main woody species in Zagros collection, which have been planted in 1989. A nematological survey on Zagros forest collection in NBGI revealed heavily infection of 24-yr-old Q. brantii and Q. infectoria to RKN, Meloidogyne hapla. The roots contained prominent galls along with egg sac on the surface of each gall. The galls were relatively small and in some parts of root several galls were conjugated, and all galls contained large transparent egg masses. The identification of M. hapla was confirmed by morphological and morphometric characters and amplification of D2-D3 expansion segments of 28S rRNA gene. The obtained sequences of large-subunit rRNA gene from M. hapla was submitted to the GenBank database under the accession number {"type":"entrez-nucleotide","attrs":{"text":"KP319025","term_id":"852381377","term_text":"KP319025"}}KP319025. The sequence was compared with those of M. hapla deposited in GenBank using the BLAST homology search program and showed 99% similarity with those {"type":"entrez-nucleotide","attrs":{"text":"KJ755183","term_id":"667714404","term_text":"KJ755183"}}KJ755183, {"type":"entrez-nucleotide","attrs":{"text":"GQ130139","term_id":"239819330","term_text":"GQ130139"}}GQ130139, {"type":"entrez-nucleotide","attrs":{"text":"DQ328685","term_id":"84794916","term_text":"DQ328685"}}DQ328685, and {"type":"entrez-nucleotide","attrs":{"text":"KJ645428","term_id":"657709843","term_text":"KJ645428"}}KJ645428. The second stage juveniles of M. hapla isolated from Brant’s oak (Q. Brantii) showed the following morphometric characters: (n = 12), L = 394 ± 39.3 (348 to 450) µm; a = 30.9 ± 4 (24.4 to 37.6); b = 4.6 ± 0.44 (4 to 5.1); b΄ = 3.3 ± 0.3 (2.7 to 3.7), c = 8.0 ± 1 (6.2 to 10.3), ć = 5.3 ± 0.8 (3.5 to 6.3); Stylet = 12.1 ± 0.8 (11 to 13) µm; Tail = 50 ± 5.6 (42 to 57) µm; Hyaline 15 ± 1.8 (12 to 18) µm. Oak manna, Q. infectoria population of second stage juveniles clearly possessed short body length and consequently other morphometric features were less than those determined for Q. brantii population, and these features were: (n = 12), L = 359.0 ± 17.3 (319 to 372) µm; a = 28.6 ± 3 (22.8 to 31); b = 5.0 ± 0.3 (4.8 to 5.2); b΄ = 3.3 ± 0.2 (3 to 3.6), c = 8.1 ± 0.5 (7.4 to 8.8), ć = 4.7 ± 0.5 (3.9 to 5.2); Stylet = 11.4 ± 0.7 (10 to 12) µm; Tail = 44 ± 1.8 (42 to 47) µm; Hyaline 12 ± 1.7 (10 to 15) µm. To date two species of Meloidogyne, M. querciana Golden, 1979 and M. christiei Golden and Kaplan, 1986 have been reported to parasitize oaks (Quercus spp.) from the United States of America. M. querciana was found on pin oak Quercus palustris in Virginia. The oak RKN infected pine oak, red oak, and American chestnut heavily in greenhouse tests (Golden, 1979). The other species M. christiei was described from turkey oak and Q. laevis in Florida, which has monospecific host range (Golden and Kaplan, 1986). Both of these RKN species seem to be restricted to the United States of America and have not been reported from other place. According to our knowledge this is the first report of occurrence of M. hapla on Q. brantii and Q. infectoria in the world. This study includes these two oak species to the host range of RKN, M. hapla for the world and expands the information of RKN, M. hapla host ranges on oaks.     

Hyaluronic acid with or without bone marrow derived-mesenchymal stem cells improves osteoarthritic knee changes in rat model: a preliminary report

Despite being a complex degenerative joint disease, studies on osteoarthritis (OA) suggest that its progression can be reduced by the use of hyaluronic acid (HA) or mesenchymal stem cells (MSC). The present study thus aims to examine the effects of MSC, HA and the combination of HA-MSC in treating OA in rat model. The histological observations using O'Driscoll score indicate that it is the use of HA and MSC independently and not their combination that delays the progression of OA. In conclusion, the preliminary study suggest that the use of either HA or MSCs effectively reduces OA progression better than their combined use.     

Investigation of tRNA<Superscript>Leu/Lys</Superscript> and ATPase 6 Genes Mutations in Huntington’s Disease

Huntington disease (HD) is a genetically dominant condition caused by expanded CAG repeats which code for glutamine in the HD gene product, huntingtin. Huntingtin is expressed in almost all tissues, so abnormalities outside the brain can also be expected. Involvement of nuclei and mitochondria in HD pathophysiology has been suggested. In fact mitochondrial dysfunction is reported in brains of patients suffering from HD. The tRNA gene mutations are one of hot spots that can cause mitochondrial disorders. In this study, possible mitochondrial DNA (mtDNA) damage was evaluated by screening for mutations in the tRNA^leu/lys and ATPase 6 genes of 20 patients with HD, using PCR and automated DNA sequencing. Mutations including an A8656G mutation in one patient were observed, which may be causal to the disease. Understanding the role of mitochondria in the pathogenesis of neurodegenerative diseases could potentially be important for the development of therapeutic strategies in HD.     

Lack of association between cyclooxygenase 2−765G/C gene polymorphism and breast cancer risk in Ahvaz, west-south Iran

Cyclooxygenases are key enzymes in conversion of arachidonic acid into prostaglandin H2. Cyclooxygenase-2 (COX-2) increases prostaglandins in neoplastic tissue. COX-2 has important roles in cell proliferation cancers, angiogenesis, and alzheimer. COX-2 is up-regulated in several types of cancer, and it is hypothesized that COX-2 expression may be genetically influenced. Our main objective was to evaluated the association of polymorphism COX-2 with risk of breast cancer in khouzestan province, and the second objective of the study was to evaluate the association with biochemistry parameters. This study consisting of 150 patients with breast cancer and 120 normal DNA was extracted from the white blood cells. Polymorphism cox2 gene was detected by polymerase chain reaction according to the standard methods. The profile lipids and estrogen were measured in two groups by standard methods. Chi square analysis showed that there was no association between breast cancer risk and COX-2 ?765G>C genotype and alleles. Also, no association were observed between ?765G>C polymorphism and biochemistry parameters. A multiple logistic regression model with cox2 genotypes and LDL and HDL as covariates revealed that there is no significant association between cox2 genotypes and risk of breast cancer, but higher values of LDL and HDL significantly increase risk of breast cancer.