A Cellular Automata-Based Mathematical Model for Thymocyte Development

Intrathymic T cell development is an important process necessary for the normal formation of cell-mediated immune responses. Importantly, such a process depends on interactions of developing thymocytes with cellular and extracellular elements of the thymic microenvironment. Additionally, it includes a series of oriented and tunely regulated migration events, ultimately allowing mature cells to cross endothelial barriers and leave the organ. Herein we built a cellular automata-based mathematical model for thymocyte migration and development. The rules comprised in this model take into account the main stages of thymocyte development, two-dimensional sections of the normal thymic microenvironmental network, as well as the chemokines involved in intrathymic cell migration. Parameters of our computer simulations with further adjusted to results derived from previous experimental data using sub-lethally irradiated mice, in which thymus recovery can be evaluated. The model fitted with the increasing numbers of each CD4/CD8-defined thymocyte subset. It was further validated since it fitted with the times of permanence experimentally ascertained in each CD4/CD8-defined differentiation stage. Importantly, correlations using the whole mean volume of young normal adult mice revealed that the numbers of cells generated in silico with the mathematical model fall within the range of total thymocyte numbers seen in these animals. Furthermore, simulations made with a human thymic epithelial network using the same mathematical model generated similar profiles for temporal evolution of thymocyte developmental stages. Lastly, we provided in silico evidence that the thymus architecture is important in the thymocyte development, since changes in the epithelial network result in different theoretical profiles for T cell development/migration. This model likely can be used to predict thymocyte evolution following therapeutic strategies designed for recovery of the thymus in diseases coursing with thymus involution, such as some primary immunodeficiencies, acute infections, and malnutrition.     

Expression of recombinant Chrysanthemum virus B coat protein for raising polyclonal antisera

Chrysanthemum virus B (CVB genus Carlavirus, family Flexiviridae) is one of the major viral pathogens of chrysanthemum. This virus occurs worldwide, is a potential threat to the floriculture industry and hence is a quarantine pathogen. CVB has a positive sense single-stranded RNA (ssRNA) genome ~8.8 kb. The coat protein gene of CVB was amplified by RT-PCR, cloned and over expressed in E. coli BL21. The protein (CP) was expressed as a fusion protein with Glutathione S-Transferase (GST). Fused protein with GST was purified by GST tagged affinity chromatography and polyclonal (but monospecific) antibodies from rabbits immunized with the fusion protein was used for formulation of ELISA based diagnostic kit for CVB detection. The antisera produced showed specific reaction to CVB from infected chrysanthemums, Nicotiana glutinosa, Nicotiana clevelandii and Chenopodium quinoa at dilution of 1:1000 in ELISA. Results obtained were comparable (some times better) than commercial kit. The IgG against CVB performed favorably in specificity and sensitivity to the virus. Findings present a procedure for production of antibodies for CVB indexing of chrysanthemums propagative and mother stock materials to provide the disease free planting material.     

Molecular variability analyses of <Emphasis Type="Italic">Apple chlorotic leaf spot virus</Emphasis> capsid protein

The complete sequences of the coat protein (CP) gene of 26 isolates of Apple chlorotic leaf spot virus (ACLSV) from India were determined. The isolates were obtained from various pome (apple, pear and quince) and stone (plum, peach, apricot, almond and wild Himalayan cherry) fruit trees. Other previously characterized ACLSV isolates and Trichoviruses were used for comparative analysis. Indian ACLSV isolates among themselves and with isolates from elsewhere in the world shared 91–100% and 70–98% sequence identities at the amino acid and nucleotide levels, respectively. The highest degree of variability was observed in the middle portion with 9 amino acid substitutions in contrast to the N-terminal and C-terminal ends, which were maximally conserved with only 4 amino acid substitutions. In phylogenetic analysis no reasonable correlation between host species and/or geographic origin of the isolates was observed. Alignment with capsid protein genes of other Trichoviruses revealed the TaTao ACLSV peach isolate to be phylogenetically closest to Peach mosaic virus, Apricot pseudo chlorotic leaf spot virus and Cherry mottle leaf virus. Recombination analysis (RDP3 ver.2.6) done for all the available ACLSV complete CP sequences of the world and Indian isolates indicate no significant evidence of recombination. However, one recombination event among Indian ACLSV-CP isolates was detected. To the best of our knowledge, this is the first report of complete CP sequence variability study from India and also the first evidence of homologous recombination in ACLSV.     

Faunistic analysis of fruit flies (Diptera: Tephritidae) in the Northern and Northwestern Regions of Rio de Janeiro State, Brazil

This study aimed to characterize the fruit fly populations in three municipalities of the Northern region and two municipalities of the Northwestern region of Rio de Janeiro State, Brazil, and to evaluate the similarity among their populations. A faunistic analysis was performed from the fruit fly specimens captured in plastic McPhail traps with an aqueous solution of hydrolyzed protein to 5% placed in orchards of guava (Psidium guajava L.) and/or other fruits during 26 months. The total of 3,952 females of 15 species of Anastrepha Schiner and 277 females of Ceratitis capitata (Wied.) was captured. The species richness differed among the municipalities, with the highest value in S?o Francisco do Itabapoana (S = 14), resulting on the highest Shannon-Wiener index (H = 1.27). The equitability was low in the five municipalities due to the dominance of one unique fruit fly species. The predominant species (more frequent, constant and dominant) were Anastrepha obliqua (Macquart) in Campos dos Goytacazes and S?o Francisco do Itabapoana, Anastrepha fraterculus (Wied.) in Cambuci and Itaocara, and Anastrepha sororcula Zucchi in S?o Jo?o da Barra. Fruit fly populations had low diversity index of Margalef (alpha = 0.58 to 1.82). Regarding to fruit fly species composition, the populations in S?o Jo?o da Barra and Cambuci were more similar between each other, composing a distinct group from the populations in Campos dos Goytacazes and Itaocara. These two groups differed quite a lot from the population in S?o Francisco do Itabapoana.     

EBV infection renders B cells resistant to growth inhibition via adenylyl cyclase

Cyclic AMP (cAMP) is an important physiological growth inhibitor of lymphoid cells, and the cAMP/protein kinase A (PKA) pathway is disrupted in several immunological disorders and cancers. Epstein Barr virus (EBV) infection of B lymphocytes is responsible for the development of lymphoproliferative disease as well as certain B-lymphoid malignancies. Here we hypothesized that EBV infection might render B lymphocytes resistant to cAMP/PKA-mediated growth inhibition. To test this, we assessed the growth-inhibitory response of cAMP-elevating compounds such as forskolin and isoproterenol, as well as the PKA activator 8-CPT-cAMP in normal B lymphocytes, EBV-infected B cells and in the EBV-negative B lymphoid cell line Reh. We could demonstrate that EBV infection indeed abolished cAMP-mediated growth inhibition of B cells. The defect was pinpointed to defective adenylyl cyclase (AC) activation by forskolin and isoproterenol, resulting in reduced formation of cAMP and lack of PKA activation and CREB phosphorylation. In contrast, 8-CPT-cAMP which directly activates PKA was able to inhibit EBV-infected B cell growth. The physiological implications of these results were underlined by the observation that the ability of forskolin to inhibit camptothecin-induced apoptosis was abolished in EBV-infected B cells. We conclude that EBV infection of B cells abrogates the activation of AC and thereby cAMP formation, and that this dysfunction renders the cells resistant to growth inhibition via the cAMP/PKA pathway.     

Phylogeny and antiquity of M macrohaplogroup inferred from complete mt DNA sequence of Indian specific lineages

Background  

Analysis of human complete mitochondrial DNA sequences has largely contributed to resolve phylogenies and antiquity of different lineages belonging to the majorhaplogroups L, N and M (East-Asian lineages). In the absence of whole mtDNA sequence information of M lineages reported in India that exhibits highest diversity within the sub-continent, the present study was undertaken to provide a detailed analysis of this macrohaplogroup to precisely characterize and unravel the intricate phylogeny of the lineages and to establish the antiquity of M lineages in India.     

Analysis of the coat protein gene and untranslated region of RNA3 of Cucumber Mosaic Virus isolates infecting various Lilium species and hybrids: association of the isolate infecting asiatic hybrid lily with subgroup II

The variability in the coat protein gene of Cucumber mosaic virus (CMV) isolates from various Lilium species and hybrids namely L. longiflorum, L. tigrinum, Asiatic hybrid and Oriental hybrid lilies was studied by sequence comparison of ～900 bp regions spanning the entire coat protein, intercistronic regions and 3′-UTR. CMV isolate characterised from Asiatic hybrid lily showed the highest homology with subgroup II isolates (94 – 97%), whereas 73 – 76% homology was observed with those belonging to subgroup I. Similarly, another three isolates showed 91 – 98% amino acid sequence homology with subgroup I and 74 – 76% sequence homology with subgroup II. Based on the criteria for classification of CMV isolates all the Indian isolates fall in subgroup I, except the one characterized from Asiatic Hybrid lily which falls into subgroup II. Other lily isolates from world were placed in subgroup II. This is the first case of Asiatic hybrid lily CMV isolate belonging to subgroup II.     

Complete nucleotide sequence analysis of <Emphasis Type="Italic">Cymbidium mosaic virus</Emphasis> Indian isolate: further evidence for natural recombination among potexviruses

The complete nucleotide sequence of an Indian strain of Cymbidium mosaic virus (CymMV) was determined and compared with other potexviruses. Phylogenetic analyses on the basis of RNA-dependent RNA polymerase (RdRp), triple gene block protein and coat protein (CP) amino acid sequences revealed that CymMV is closely related to the Narcissus mosaic virus (NMV), Scallion virus X (SVX), Pepino mosaic virus (PepMV) and Potato aucuba mosaic virus (PAMV). Different sets of primers were used for the amplification of different regions of the genome through RT-PCR and the amplified genes were cloned in a suitable vector. The full genome of the Indian isolate of CymMV from Phaius tankervilliae shares 96–97% similarity with isolates reported from other countries. It was found that the CP gene of CymMV shares a high similarity with each other and other potexviruses. One of the Indian isolates seems to be a recombinant formed by the intermolecular recombination of two other CymMV isolates. The phylogenetic analyses, Recombination Detection Program (RDP2) analyses and sequence alignment survey provided evidence for the occurrence of a recombination between an Indian isolate (AM055720) as the major parent, and a Korean type-2 isolate (AF016914) as the minor parent. Recombination was also observed between a Singapore isolate (U62963) as the major parent, and a Taiwan CymMV (AY571289) as the minor parent.     

Analysis of the Coat Protein Gene of Indian Strain of Apple Stem Grooving Virus

A survey was undertaken in the temperate fruit growing regions of Himachal Pradesh (HP) and Jammu & Kashmir (J&K). Apple stem grooving virus (ASGV), a Capillovirus, was detected in different cultivars of apple, nectarines, plum, cherry, quince and apricot by double antibody sandwich ELISA (DAS-ELISA). The coat protein (CP) gene sequence of an amplicon produced by RT-PCR, confirmed the association of ASGV in apple cultivar Starkrimson, collected from Himachal Pradesh. The CP of Indian ASGV isolate shared 100 % sequence identity with a Brazilian isolate (AF438409). Sequence analysis by Recombination Detection Program (RDP2) indicated no recombination event for the Indian isolate. However, recombination was detected in Chinese, Korean and Citrus tatter leaf virus-Taiwan (CTLV) strains of ASGV. The study describes first report of ASGV infection in India and characterization of its CP gene.