Genetic diversity and distribution of tomato-infecting begomoviruses in Iran

The incidence and severity of tomato leaf curl disease (TLCD) is increasing worldwide. Here we assess the diversity and distribution within tomato producing areas of Iran of begomoviruses that cause this disease. Tomato with typical TLCD symptoms and asymptomatic weeds were collected in 2005 and 2006 and tested for the presence of begomovirus DNA using polymerase chain reaction (PCR). Analysis of cloned and sequenced PCR products revealed that both mono- and bipartite begomoviruses are associated with TLCD in Iran. Furthermore, our results confirmed the symptomless infection with mono- and bipartite begomoviruses of two weed species, Chrozophora hierosolymitana Spreng (Euphobiaceae) and Herniaria sp. (Caryophyllaceae). Eighteen Iranian begomovirus isolates were classified into two major groups and two or three subgroups according to the 5′-proximal 200 nucleotides of the coat protein (CP) gene or the N-terminal 600 nucleotides of the Rep gene. Whereas most of the monopartite isolates showed closest similarity to tomato yellow leaf curl virus-Gezira (TYLCV-Ge), the three bipartite isolates were most similar to Tomato leaf curl New Delhi virus (ToLCNDV). Mixed mono- and a bipartite begomovirus infections were detected in both tomato and C. hierosolymitana. Our results indicate that the tomato producing areas in central, southern, and southeastern Iran are threatened by begomoviruses originating from both the Mediterranean basin and the Indian subcontinent.     

Molecular diversity of coronaviruses in bats

The existence of coronaviruses in bats is unknown until the recent discovery of bat-SARS-CoV in Chinese horseshoe bats and a novel group 1 coronavirus in other bat species. Among 309 bats of 13 species captured from 20 different locations in rural areas of Hong Kong over a 16-month period, coronaviruses were amplified from anal swabs of 37 (12%) bats by RT-PCR. Phylogenetic analysis of RNA-dependent-RNA-polymerase (pol) and helicase genes revealed six novel coronaviruses from six different bat species, in addition to the two previously described coronaviruses. Among the six novel coronaviruses, four were group 1 coronaviruses (bat-CoV HKU2 from Chinese horseshoe bat, bat-CoV HKU6 from rickett's big-footed bat, bat-CoV HKU7 from greater bent-winged bat and bat-CoV HKU8 from lesser bent-winged bat) and two were group 2 coronaviruses (bat-CoV HKU4 from lesser bamboo bats and bat-CoV HKU5 from Japanese pipistrelles). An astonishing diversity of coronaviruses was observed in bats.     

Molecular epidemiology of hepatitis B virus in Iran

Hepatitis B virus (HBV) infection is a major cause of liver disease worldwide. Eight genotypes and 24 subgenotypes of HBV have been identified. The aim of this study was to determine the distribution of HBV genotypes, subgenotypes and subtypes, and to understand HBV genetic variability in the HBV genome circulating in Iranian provinces. Two hundred and forty-nine sera from HBV-infected patients living in 25 provinces of Iran were collected (2004–2007). A part of the HBV S / pol and whole BCP / C genes were amplified, sequenced and then subjected to phylogenetic, recombination and genetic variability analysis. Results revealed genotype D of HBV in all samples and subgenotypes  D1 (98.52%), D2 (0.74%) and D3 (0.74%) among Iranian patients living in different provinces of Iran. Subtypes  ayw2 (94.4%), ayw1 (2.8%), ayw3 (2%) and ayw4 (0.4%) were deduced, on the basis of HBV small surface antigen (HBsAg) amino acid sequences. The mean percentage intra-genotypic distance of S plus core regions was 2.8%; the mean percentage inter-genotypic distance of this region between Iranian strains and genotype D isolates was 3.1%; and this rate for other genotypes was 5.2–11.4%. Various rates of point mutations have been found within different HBV genes, e.g. HBsAg (17.2%), precore-G1896A (59.5%) and Basal core promoter (BCP) double mutations (49.2%), whereas no recombination was found. In conclusion, these results indicate that the only genotype circulating in the provinces of Iran is genotype D. There exist high genetic variabilities in the S / pol and BCP / C regions among the Iranian HBV isolates.     

Molecular investigation and cultivation of camelpox virus in Iran

Camelpox virus (genus Orthopoxvirus, family Poxviridae) is the etiologic agent of camel pox. The clinical manifestations of this virus range from inapparent infection to mild, moderate and, less commonly, severe systemic infection and death. Following an outbreak of camelpox, samples that were collected from camel flocks suspected to have camelpox in Qom Province in central Iran and Khash city, Sistan and Baluchestan Province and South Khorasan Province in eastern Iran were sent to Razi Vaccine and Serum Research Institute in Mashhad. DNA extraction was performed primarily by the phenol-chloroform method, and PCR was carried out using a Bioneer kit. Using the primer pair 5′-AAT-ACA-AGG-AGG-ATC-T-3′ and 5′-CTT-AAC-TTT-TTC-TTT-CTC-3′, the gene sequence encoding the A-type inclusion protein (ATIP) was amplified. The size of the PCR product, specific for camelpox virus, was 881 bp. The PCR product was purified, and to confirm its sequence, it was sent to the reference laboratory. The sequence was subjected to a BLAST search and then phylogenetically analyzed using CLC software. The results showed that all samples were nearly 100 % identical to each other and to strains CMS and M-96. These isolates also had 99 % and 95 % similarity to the CP-1 strain and isolate FIN/T2000, respectively. In Vero cell culture, inoculation with this virus caused a cytopathic effect (CPE), which appeared 2-5 days post-inoculation. Characteristic CPE showing foci of rounded cells, ballooning, giant-cell formation and syncytia with degenerative changes appeared.     

Molecular analysis and phylogenetic characterization of HIV in Iran

The rate of human immunodeficiency virus type 1 (HIV-1) infection in Iran has increased dramatically in the last few years. While the earliest cases were found in hemophiliacs, intravenous drug users are now fueling the outbreak. In this study, both the 122 clones of HIV-1 gag p17 and the 131 clones of env V1-V5 region were obtained from 61 HIV-1 seropositives belonging to these two groups in Iran. HIV-1 subtyping and phylogenetic analysis was done by heteroduplex mobility assays (HMA) and multiple clone sequencing. The result indicated all hemophiliacs are infected with HIV-1 subtype B and all intravenous drug users are infected with HIV-1 subtype A. Since intravenous drug abuse is the major transmission route in Iran, HIV-1 subtype A is likely to be the dominant viral subtype circulating in the country. The analysis of genetic distances showed subtype B viruses in Iran to be twice as heterogeneous as the subtype A viruses. In conclusion, this first molecular study of HIV-1 genotypes in Iran suggests two parallel outbreaks in distinct high-risk populations and may offer clues to the origin and spread of infection in Iran.     

Molecular diversity of Bacillus anthracis in Italy

We used multiple-locus variable-number tandem repeat analysis (MLVA) to type 64 Bacillus anthracis isolates from outbreaks that have occurred during the past 40 years in Italy. MLVA of the 64 isolates revealed 10 unique genotypes; 9 of these genotypes and the majority of isolates (63/64) belonged to the previously described genetic cluster A1.a. Within the A1.a isolates, two previously described genotypes (G1 and G3), which differ by a single mutation in the pX01 locus, account for the majority of isolates in the country (53/63). The low diversity of B. anthracis genotypes in Italy suggests a single, dominant historical introduction, followed by limited localized differentiation.     

Molecular Basis of Autosomal Recessive Chronic Granulomatous Disease in Iran

Introduction  

Chronic granulomatous disease (CGD) is a rare inherited condition resulting from mutations in the genes that encode the proteins of the NADPH oxidase enzyme in phagocytes, rendering these cells incapable of killing invading pathogens.     

Molecular analysis of microbial diversity in advanced caries

Real-time PCR analysis of the total bacterial load in advanced carious lesions has shown that the total load exceeds the number of cultivable bacteria. This suggests that an unresolved complexity exists in bacteria associated with advanced caries. In this report, the profile of the microflora of carious dentine was explored by using DNA extracted from 10 lesions selected on the basis of comparable total microbial load and on the relative abundance of Prevotella spp. Using universal primers for the 16S rRNA gene, PCR amplicons were cloned, and approximately 100 transformants were processed for each lesion. Phylogenetic analysis of 942 edited sequences demonstrated the presence of 75 species or phylotypes in the 10 carious lesions. Up to 31 taxa were represented in each sample. A diverse array of lactobacilli were found to comprise 50% of the species, with prevotellae also abundant, comprising 15% of the species. Other taxa present in a number of lesions or occurring with high abundance included Selenomonas spp., Dialister spp., Fusobacterium nucleatum, Eubacterium spp., members of the Lachnospiraceae family, Olsenella spp., Bifidobacterium spp., Propionibacterium sp., and Pseudoramibacter alactolyticus. The mechanisms by which such diverse patterns of bacteria extend carious lesions, including the aspect of infection of the vital dental pulp, remain unclear.     

Molecular diversity of neocortical GABAergic interneurones

In addition to being the main source of inhibition in the adult brain, GABAergic interneurones are instrumental in pacing the activity of large ensembles of principal cells. GABAergic interneurones have unique features that enable them to contribute to the generation of synchronized network activity thereby shaping principal cell behaviour. Whereas the anatomical and physiological characteristics of certain interneuronal types have been studied extensively over the last decades, the molecular diversity of interneurones is a more recent focus of investigation in this field. Molecular cloning and expression analysis of many receptor families often revealed differential expression in GABAergic interneurones and pyramidal cells. Here we review recent findings regarding the molecular diversity of GABAergic interneurones in the neocortex. Better knowledge about differential gene expression in GABAergic interneurones is the basis for further investigations aimed at understanding the contribution of specific proteins in interneurones to network function.     

Molecular typing of Staphylococcus aureus isolated from food samples in Iran

Staphylococcus aureus is the third most common cause of confirmed food poisoning in the world and is the predominant species involved in staphylococcal food poisoning outbreaks. Considerable genetic heterogeneity has been shown in natural populations of S. aureus isolates. Coagulase gene typing is one of the numerous molecular techniques to identify and compare S. aureus genotypes. The present study was conducted to type the coagulase gene in 25 S. aureus isolates isolated from food samples. All isolates were identified by routine biochemical tests and then confirmed by species-specific PCR and yielded products with the expected molecular size of 1.3 kb. PCR amplification of DNA with the primers COAG2 and COAG3 yielded single-banded PCR products in 24 isolates with the molecular size of approximately 500 bp (n?=?2, 8 %), 750 bp (n?=?1, 4 %), 850 bp (n?=?12, 48 %), and 950 bp (n?=?9, 36 %), while one isolate produced no band in PCR amplification of coagulase gene. Since human and bovine reservoirs of S. aureus represent two subpopulations that rarely cross-infect, detection of single bands by coagulase PCR in S. aureus isolates suggests that these isolates may be of bovine origin not human one, and contamination of food samples may initiate from the animal source not the food handlers. Digestion of coagulase PCR products with restriction endonuclease enzymes AluI and Hin6I yielded four different restriction profiles that indicate presence of heterogeneity in the coagulase gene of the isolates. This work showed that restriction analysis of the coagulase gene can be considered as a reliable and fast method for determining the origin of S. aureus in food samples.     

Molecular diversity at the plant-pathogen interface

Plants have evolved a robust innate immune system that exhibits striking similarities as well as significant differences with various metazoan innate immune systems. For example, plants are capable of perceiving pathogen-associated molecular patterns through pattern recognition receptors that bear structural similarities to animal Toll-like receptors. In addition, plants have evolved a second surveillance system based on cytoplasmic "NB-LRR" proteins (nucleotide-binding, leucine-rich repeat) that are structurally similar to animal nucleotide-binding and oligomerization domain (NOD)-like receptors. Plant NB-LRR proteins do not detect PAMPs; rather, they perceive effector proteins that pathogens secrete into plant cells to promote virulence. This review summarizes the current state of knowledge about the molecular functionality and evolution of these immune surveillance genes.     

Molecular diversity of Rice grassy stunt virus in Vietnam

Rice grassy stunt virus (RGSV, Tenuivirus) recently emerged on rice in Vietnam, causing high yield losses during 2006–2009. The genetic diversity of RGSV is poorly documented. In this study, the two genes encoded by each ambisense segment RNA3 and RNA5 of RGSV isolates from six provinces of South Vietnam were sequenced. P3 and Pc3 (RNA3) have unknown function, P5 (RNA5) encodes the putative silencing suppressor, and Pc5 (RNA5) encodes the nucleocapsid protein (N). The sequences of 17 Vietnamese isolates were compared with reference isolates from North and South Philippines. The average nucleotide diversity among the isolates was low. We confirmed a higher variability of RNA3 than RNA5 and Pc3 than P3. No relationships between the genetic diversity and the geographic distribution of RGSV isolates could be ascertained, likely because of the long-distance migration of the insect vector. This data will contribute to a better understanding on the RGSV epidemiology in South Vietnam, a prerequisite for further management of the disease and rice breeding for resistance.     

Molecular genotyping of Giardia duodenalis in children from Behbahan,southwestern Iran

Parasitology Research - Giardia duodenalis is an intestinal flagellated protozoan that infects humans and several animal species. Giardiasis causing more than 200 million symptomatic infections...     

Molecular epidemiology of hepatitis A virus in patients in the Ahwaz region of Iran

Hepatitis A virus (HAV) is one of the etiologic agents of acute viral hepatitis, an important public health problem worldwide. The aim of this study was to investigate the genetic diversity of HAV in Southwest Iran (Ahwaz). A total of 59 sera were collected from acutely ill patients with anti-HAV IgM antibodies during 2009 and 2010 were tested also by RT-PCR targeting the 5' NCR for molecular diagnosis and examined in the VP1-2A and VP3-VP1 regions for genotyping. Twelve (20%) patients were detected VP1-2A by RT-PCR and 10 patients had VP3-VP1. The resulting amplicons were sequenced for genotype identification. All HAV strains were identified as subgenotype IB. Phylogenetic analysis revealed an extensive genetic heterogeneity among the strains. Seven hundred sixty-five S→F and 788 K→R amino acid substitutions in IRI49 isolate were found. It is concluded that subgenotype 1b is the sole genotype HAV in this region.     

Molecular and genetic diversity in the metastatic process of melanoma

Diversity between metastatic melanoma tumours in individual patients is known; however, the molecular and genetic differences remain unclear. To examine the molecular and genetic differences between metastatic tumours, we performed gene‐expression profiling of 63 melanoma tumours obtained from 28 patients (two or three tumours/patient), followed by analysis of their mutational landscape, using targeted deep sequencing of 1697 cancer genes and DNA copy number analysis. Gene‐expression signatures revealed discordant phenotypes between tumour lesions within a patient in 50% of the cases. In 18 of 22 patients (where matched normal tissue was available), we found that the multiple lesions within a patient were genetically divergent, with one or more melanoma tumours harbouring 'private' somatic mutations. In one case, the distant subcutaneous metastasis of one patient occurring 3 months after an earlier regional lymph node metastasis had acquired 37 new coding sequence mutations, including mutations in PTEN and CDH1. However, BRAF and NRAS mutations, when present in the first metastasis, were always preserved in subsequent metastases. The patterns of nucleotide substitutions found in this study indicate an influence of UV radiation but possibly also DNA alkylating agents. Our results clearly demonstrate that metastatic melanoma is a molecularly highly heterogeneous disease that continues to progress throughout its clinical course. The private aberrations observed on a background of shared aberrations within a patient provide evidence of continued evolution of individual tumours following divergence from a common parental clone, and might have implications for personalized medicine strategies in melanoma treatment. Published by John Wiley & Sons, Ltd. www.pathsoc.org.uk     

Molecular diversity and regulation of renal potassium channels

K(+) channels are widely distributed in both plant and animal cells where they serve many distinct functions. K(+) channels set the membrane potential, generate electrical signals in excitable cells, and regulate cell volume and cell movement. In renal tubule epithelial cells, K(+) channels are not only involved in basic functions such as the generation of the cell-negative potential and the control of cell volume, but also play a uniquely important role in K(+) secretion. Moreover, K(+) channels participate in the regulation of vascular tone in the glomerular circulation, and they are involved in the mechanisms mediating tubuloglomerular feedback. Significant progress has been made in defining the properties of renal K(+) channels, including their location within tubule cells, their biophysical properties, regulation, and molecular structure. Such progress has been made possible by the application of single-channel analysis and the successful cloning of K(+) channels of renal origin.