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- Stability-mediated epistasis constrains the evolution of an influenza protein. [Journal Article]
- Elife 2013.:e00631.
JOHN MAYNARD SMITH COMPARED PROTEIN EVOLUTION TO THE GAME WHERE ONE WORD IS CONVERTED INTO ANOTHER A SINGLE LETTER AT A TIME, WITH THE CONSTRAINT THAT ALL INTERMEDIATES ARE WORDS: WORD→WORE→GORE→GONE→GENE. In this analogy, epistasis constrains evolution, with some mutations tolerated only after the occurrence of others. To test whether epistasis similarly constrains actual protein evolution, we created all intermediates along a 39-mutation evolutionary trajectory of influenza nucleoprotein, and also introduced each mutation individually into the parent. Several mutations were deleterious to the parent despite becoming fixed during evolution without negative impact. These mutations were destabilizing, and were preceded or accompanied by stabilizing mutations that alleviated their adverse effects. The constrained mutations occurred at sites enriched in T-cell epitopes, suggesting they promote viral immune escape. Our results paint a coherent portrait of epistasis during nucleoprotein evolution, with stabilizing mutations permitting otherwise inaccessible destabilizing mutations which are sometimes of adaptive value. DOI:http://dx.doi.org/10.7554/eLife.00631.001.
- A role for PVRL4-driven cell-cell interactions in tumorigenesis. [Journal Article]
- Elife 2013.:e00358.
During all stages of tumor progression, cancer cells are subjected to inappropriate extracellular matrix environments and must undergo adaptive changes in order to evade growth constraints associated with the loss of matrix attachment. A gain of function screen for genes that enable proliferation independently of matrix anchorage identified a cell adhesion molecule PVRL4 (poliovirus-receptor-like 4), also known as Nectin-4. PVRL4 promotes anchorage-independence by driving cell-to-cell attachment and matrix-independent integrin β4/SHP-2/c-Src activation. Solid tumors frequently have copy number gains of the PVRL4 locus and some have focal amplifications. We demonstrate that the transformation of breast cancer cells is dependent on PVRL4. Furthermore, growth of orthotopically implanted tumors in vivo is inhibited by blocking PVRL4-driven cell-to-cell attachment with monoclonal antibodies, demonstrating a novel strategy for targeted therapy of cancer. DOI:http://dx.doi.org/10.7554/eLife.00358.001.
- Cloning, Nucleotide Sequencing and Bioinformatics Study of NcSRS2 Gene, an Immunogen from Iranian Isolate of Neospora caninum. [Journal Article]
- Iran J Parasitol 2013 Jan; 8(1):114-27.
Neosporosis is caused by an obligate intracellular parasitic protozoa Neospora caninum which infect variety of hosts. NcSRS2 is an immuno-dominant antigen of N. caninum which is considered as one of the most promising targets for a recombinant or DNA vaccine against neosporosis. As no study has been carried out to identify the molecular structure of N. caninum in Iran, as first step, we prepared a scheme to identify this gene in this parasite in Iran.Tachyzoite total RNA was extracted and cDNA was synthesized and NcSRS2 gene was amplified using cDNA as template. Then the PCR product was cloned into pTZ57R/T vector and transformed into E. coli (DH5α strain). Finally, the recombinant plasmid was extracted from transformed E. coli and sequenced. Bioinformatics analysis also carried out.The PCR product of NcSRS2 gene was sequenced and recorded in GenBank. The deduced amino acid sequence of NcSRS2 in current study was compared with other N. caninum NcSRS2 and showed some identities and differences.NcSRS2 gene of N. caninum successfully cloned in pTZ57R/T. Recombinant plasmid was confirmed by sequencing, colony PCR and enzymatic digestion. It is ready to express recombinant protein for further studies.
- Brain Tissue Cysts in Infected Mice with RH-Strain of Toxoplasma gondii and Evaluation of BAG1 and SAG1 Genes Expression. [Journal Article]
- Iran J Parasitol 2013 Jan; 8(1):40-6.
Toxoplasma gondii is an obligate intracellular parasite that infects humans at high prevalence rates. The virulent RH strain of T. gondii is generally considered to have lost its cyst forming capacity. This study performed to obtain tissue cysts in mice infected with tachyzoites of RH strain treated with sulfadiazine (SDZ). It provides the opportunity to analyze the conversion of tachyzoite to bradyzoite stage of the RH strain, followed by stage-specific gene-expression analyzing.Two groups of Swiss-Webster and BALB/c mice were infected subcutaneously with 10(4) tachyzoites of T. gondii, RH strain and given SDZ (300 mg/l) with NaHCO3 (5 g(-1)) in drinking water from day1 to day 14 post infection (p.i). The infected mice were sacrificed on day 50 post infection. Their brains were removed and the numbers of tissue cysts were microscopically counted. Total RNA was extracted from brains and cDNA synthesis was carried out. Finally, RT-PCR (Reverse transcription PCR) was used to detect the expression of bradyzoite (BAG1) and tachyzoite (SAG1) specific genes during tachyzoite / bradyzoite stage conversion.Sixty five percent of all infected mice were survived. Cysts were detectable in mice brain (45%) on day 50 p.i. Also RT-PCR of the brain samples was positive for SAG1 and BAG1.It seems that conversion of tachyzoites to bradyzoites in brain of mice undergoing SDZ was not completed until 50 days after inoculation.
- Anthelmintics Resistance; How to Overcome it? [Journal Article]
- Iran J Parasitol 2013 Jan; 8(1):18-32.
Many parasitic helminthes of veterinary importance have genetic features that favor development of anthelmintic resistance, this becoming a major worldwide constrain in livestock production. The development of anthelmintic resistance poses a large threat to future production and welfare of grazing animals. Development of variable degrees of resistance among different species of gastrointestinal nematodes has been reported for all the major groups of anthelmintic drugs. It has been observed that frequent usage of the same group of anthelmintic; use of anthelmintics in sub-optimal doses, prophylactic mass treatment of domestic animals and frequent and continuous use of a single drug have contributed to the widespread development of anthelmintic resistance in helminthes. The degree and extent of this problem especially with respect to multidrug resistance in nematode populations is likely to increase. Maintaining parasites in refugia and not exposed to anthelmintics, seems to be a key point in controlling and delaying the development of resistance, because the susceptible genes are preserved. Targeted selective treatments attract the interest of scientists towards this direction. Additionally, adoption of strict quarantine measures and a combination drug strategy are two important methods of preventing of anthelmintic resistance. Experience from the development of anthelmintic resistance suggests that modern control schemes should not rely on sole use of anthelmintics, but employ other, more complex and sustainable recipes, including parasite resistant breeds, nutrition, pasture management, nematode-trapping fungi, antiparasitic vaccines and botanical dewormers. Most of them reduce reliance on the use of chemicals and are environmental friendly. Finally, if new anthelmintic products are released, an important question will be raised about how they should be used. It is suggested that slowing the development of resistance to a new class are likely to be gained by releasing it in combination with one or more of the older anthelmintic classes, especially where efficacy of the older active(s) remains high.
- A HIERARCHICAL FUNCTIONAL DATA ANALYTIC APPROACH FOR ANALYZING PHYSIOLOGICALLY BASED PHARMACOKINETIC MODELS. [JOURNAL ARTICLE]
- Environmetrics 2013 May 1; 24(3):172-179.
Ordinary differential equation (ODE) based models find application in a wide variety of biological and physiological phenomena. For instance, they arise in the description of gene regulatory networks, study of viral dynamics and other infectious diseases, etc. In the field of toxicology, they are used in physiologically based pharmacokinetic (PBPK) models for describing absorption, distribution, metabolism and excretion (ADME) of a chemical in-vivo. Knowledge about the model parameters is important for understanding the mechanism of action of a chemical and are often estimated using non-linear least squares methodology. However, there are several challenges associated with the usual methodology. Using functional data analytic methodology, in this article we develop a general framework for drawing inferences on parameters in models described by a system of differential equations. The proposed methodology takes into account variability between and within experimental units. The performance of the proposed methodology is evaluated using a simulation study and data obtained from a benzene inhalation study. We also describe a R-based software developed towards this purpose.
- Effects of regenerative radioelectric asymmetric conveyer treatment on human normal and osteoarthritic chondrocytes exposed to IL-1β. A biochemical and morphological study. [Journal Article]
- Clin Interv Aging 2013.:309-16.
Osteoarthritis (OA) is a degenerative disease characterized by a progressive loss of articular cartilage extracellular matrix and is due to functional impairments occurring in chondrocytes. In previous works, we highlighted that Regenerative Tissue Optimization (TO-RGN) treatment with radioelectric asymmetric conveyer (REAC) technology influenced the gene expression profiles controlling stem cell differentiation and the pluripotency of human skin-derived fibroblasts in vitro. Since interleukin-1 beta signaling has been implicated in the induction and progression of this disease (through metalloproteinase-3 synthesis and nitric oxide production), we investigated whether REAC TO-RGN might influence the biochemical and morphological changes induced by interleukin-1 beta in normal and OA chondrocytes.The induction of metalloproteinase-3 and proteoglycan synthesis was evaluated by a solid-phase enzyme-amplified sensitivity immunoassay, and nitric oxide production was evaluated with the Griess method. Ultrastructural features were observed by transmission electron microscopy.REAC TO-RGN treatment decreased nitric oxide and metalloproteinase-3 production in normal and OA chondrocytes, while inducing an increase in proteoglycan synthesis. OA chondrocytes were more affected by REAC TO-RGN treatment than were normal chondrocytes. Ultrastructural changes confirmed that REAC TO-RGN may counteract the negative effects of interleukin-1 beta incubation.The results of this in vitro study suggest that REAC TO-RGN treatment may represent a new, promising approach for the management of OA.
- A divergent P-element and its associated MITE, BuT5, generate chromosomal inversions and are widespread within the Drosophila repleta species group. [JOURNAL ARTICLE]
- Genome Biol Evol 2013 May 16.
The transposon BuT5 caused two chromosomal inversions fixed in two Drosophila species of the repleta group, D. mojavensis and D. uniseta. BuT5 copies are ∼1-kb long, lack any coding capacity and do not resemble any other transposable element. Due to its elusive features, BuT5 has remained unclassified to date. In order to fully characterize BuT5, we carried out bioinformatic similarity searches in available sequenced genomes, including 21 Drosophila species. Significant hits were only recovered for D. mojavensis genome, where 48 copies were retrieved, 22 of them ∼1-kb long. PCR and dot blot analyses on 54 Drosophila species showed that BuT5 is homogeneous in size and has a widespread distribution within the repleta group. Thus BuT5 can be considered as a MITE. A detailed analysis of the BuT5 hits in D. mojavensis revealed three partial copies of a transposon with ends very similar to BuT5 and a P-element-like transposase-encoding region in between. A putatively autonomous copy of this P-element was isolated by PCR from D. buzzatii. This copy is 3386-bp long and possesses a seven-exon gene coding for an 822-aa transposase. Exon-intron boundaries were confirmed by RT-PCR experiments. A phylogenetic tree built with insect P superfamily transposases showed that the D. buzzatii P-element belongs to an early diverging lineage within the P-element family. This divergent P-element is likely the master transposon mobilizing BuT5. The BuT5/P-element partnership probably dates back ∼16 Mya and is the ultimate responsible for the generation of the two chromosomal inversions in the Drosophila repleta species group.
- Draft Genome Sequence of Pseudomonas veronii Strain 1YdBTEX2. [Journal Article]
- Genome Announc 2013; 1(3)
Pseudomonas veronii strain 1YdBTEX2 was isolated from a benzene-contaminated site. Here we report the draft genome sequence of 1YdBTEX2 and its genes associated with aromatic metabolism. The broad catabolic potential of this strain is consistent with the environment from which it was isolated.
- Complete Genome Sequence of a Novel Reassortant H3N6 Avian Influenza Virus Isolated from Domestic Green-Winged Teal. [Journal Article]
- Genome Announc 2013; 1(3)
An avian influenza virus strain, A/domestic green-winged teal/Hunan/2036/2007(H3N6) (DGW-T2036), was isolated from healthy domestic green-winged teals (Anas crecca) in Hunan Province, South China. All eight gene segments of the isolate were sequenced. Genomic analysis demonstrated that this H3N6 virus is a novel reassortant avian influenza virus with a gene constellation originating from multiple ancestors.