Genomic insights into positive selection

The traditional way of identifying targets of adaptive evolution has been to study a few loci that one hypothesizes a priori to have been under selection. This approach is complicated because of the confounding effects that population demographic history and selection have on patterns of DNA sequence variation. In principle, multilocus analyses can facilitate robust inferences of selection at individual loci. The deluge of large-scale catalogs of genetic variation has stimulated many genome-wide scans for positive selection in several species. Here, we review some of the salient observations of these studies, identify important challenges ahead, consider the limitations of genome-wide scans for selection and discuss the potential significance of a comprehensive understanding of genomic patterns of selection for disease-related research.     

Development of NaCl-tolerant strain in Chrysanthemum morifolium Ramat. through in vitro mutagenesis

One NaCl-tolerant chrysanthemum (Chrysanthemum morifolium Ramat.) variant (E2) has been developed in a stable form through IN VITRO mutagenesis using ethylmethane sulfonate (EMS) as the chemical mutagen. Salt tolerance was evaluated by the capacity of the plant to maintain both flower quality and yield under stress conditions. Enhanced tolerance of the E2 variant has been attributed to the increased activity of superoxide dismutase (SOD), ascorbate peroxidase (APX), and dehydroascorbate reductase (DHAR), and, to a lesser extent of membrane damage than NaCl-treated control plants. Isoform analysis revealed that an increase in total SOD activity in the E2 variant was solely due to significant activation of the Cu/Zn isoform. Elevated levels of carotenoids and ascorbate in E2 leaves have been reflected in their higher free radical scavenging capacity (RSC) expressed in terms of DPPH (2,2-diphenyl-1-picrylhydrazyl) scavenging ability. Data reflect that a proper balance between enzymatic and non-enzymatic defence systems is required for combating salinity stress in chrysanthemum. Better performance of the E2 progeny under same salinity stress condition, even in the second year, confirms the genetic stability of the salt-tolerance character. On the whole, the E2 variant, developed through 0.025 % EMS treatment, might be considered as a NaCl-tolerant strain showing positive characters towards NaCl stress.     

Elevated mitogen-activated protein kinase signalling and increased macrophage activation in cells infected with a glycopeptidolipid-deficient Mycobacterium avium

Mycobacterium avium is a significant cause of morbidity and mortality in AIDS patients. M. avium can be isolated as three major morphotypes: smooth-transparent (SmT ), smooth-opaque (SmO) and rough (Rg). Studies indicate that many Rg isolates lack or have modified glycopeptidolipids (GPLs). GPLs are major surface constituents of the M. avium cell wall and heterogeneity in their carbohydrate moieties has been used to classify M. avium into different serotypes, with serotypes 1, 4 and 8 being isolated with high frequency from AIDS patients. However, it is unclear what role GPLs play in M. avium pathogenicity. To begin to address how the absence of GPLs affects M. avium-macrophage interaction, we used the well-characterized M. avium 2151 SmT and Rg isolates which differ in GPL expression. We found macrophages infected with the Rg compared with SmT M. avium 2151 showed prolonged activation of the mitogen-activated protein kinases (MAPKs) p38 and ERK1/2. Macrophages infected with the Rg 2151 also showed increased tumour necrosis factor-alpha (TNF-alpha) production. Interestingly, TNF-alpha secretion by macrophages infected with SmO or SmT 2151 was dependent on p38, ERK1/2 and NF-kappaB while TNF-alpha secretion by Rg 2151-infected macrophages was dependent on NF-kappaB but not the MAPKs. Rg 2151-infected macrophages also produced increased levels of IL-6, IL-12, MCP-1 and RANTES relative to macrophages infected with SmT 2151. These results indicate that M. avium 2151 deficient in GPLs promote increased macrophage activation. This disparity in cellular activation stems from a quantitative and qualitative difference in the macrophage signalling response to the Rg and SmT M. avium 2151.     

Endogenous MMTV proviruses induce susceptibility to both viral and bacterial pathogens

Most inbred mice carry germline proviruses of the retrovirus, mouse mammary tumor virus (MMTV) (called Mtvs), which have multiple replication defects. A BALB/c congenic mouse strain lacking all endogenous Mtvs (Mtv-null) was resistant to MMTV oral and intraperitoneal infection and tumorigenesis compared to wild-type BALB/c mice. Infection of Mtv-null mice with an MMTV-related retrovirus, type B leukemogenic virus, also resulted in severely reduced viral loads and failure to induce T-cell lymphomas, indicating that resistance is not dependent on expression of a superantigen (Sag) encoded by exogenous MMTV. Resistance to MMTV in Mtv-null animals was not due to neutralizing antibodies. Further, Mtv-null mice were resistant to rapid mortality induced by intragastric inoculation of the Gram-negative bacterium, Vibrio cholerae, but susceptibility to Salmonella typhimurium was not significantly different from BALB/c mice. Susceptibility to both MMTV and V. cholerae was reconstituted by the presence of any one of three endogenous Mtvs located on different chromosomes and was associated with increased pathogen load. One of these endogenous proviruses is known to encode only Sag. Therefore, Mtv-encoded Sag appears to provide a unique genetic susceptibility to specific viruses and bacteria. Since human endogenous retroviruses also encode Sags, these studies have broad implications for pathogen-induced responses in mice and humans.     

Enhancing blood-stage malaria subunit vaccine immunogenicity in rhesus macaques by combining adenovirus, poxvirus, and protein-in-adjuvant vaccines

Protein-in-adjuvant formulations and viral-vectored vaccines encoding blood-stage malaria Ags have shown efficacy in rodent malaria models and in vitro assays against Plasmodium falciparum. Abs and CD4(+) T cell responses are associated with protective efficacy against blood-stage malaria, whereas CD8(+) T cells against some classical blood-stage Ags can also have a protective effect against liver-stage parasites. No subunit vaccine strategy alone has generated demonstrable high-level efficacy against blood-stage infection in clinical trials. The induction of high-level Ab responses, as well as potent T and B cell effector and memory populations, is likely to be essential to achieve immediate and sustained protective efficacy in humans. This study describes in detail the immunogenicity of vaccines against P. falciparum apical membrane Ag 1 in rhesus macaques (Macaca mulatta), including the chimpanzee adenovirus 63 (AdCh63), the poxvirus modified vaccinia virus Ankara (MVA), and protein vaccines formulated in Alhydrogel or CoVaccine HT adjuvants. AdCh63-MVA heterologous prime-boost immunization induces strong and long-lasting multifunctional CD8(+) and CD4(+) T cell responses that exhibit a central memory-like phenotype. Three-shot (AdCh63-MVA-protein) or two-shot (AdCh63-protein) regimens induce memory B cells and high-titer functional IgG responses that inhibit the growth of two divergent strains of P. falciparum in vitro. Prior immunization with adenoviral vectors of alternative human or simian serotype does not affect the immunogenicity of the AdCh63 apical membrane Ag 1 vaccine. These data encourage the further clinical development and coadministration of protein and viral vector vaccine platforms in an attempt to induce broad cellular and humoral immune responses against blood-stage malaria Ags in humans.     

Development of mutants of <Emphasis Type="Italic">Melanocarpus albomyces</Emphasis> for hyperproduction of xylanase

The wild type filamentous fungus, Melanocarpus albomyces, produces many commercially valuable enzymes, including Xylanases and Xylan-debranching enzymes with low activity. In this paper, we report for the first time the development of M. albomyces mutants from vegetative spores. Profuse sporulation of M. albomyces was induced on Potato Carrot Agar medium. These spores, when subjected to chemical mutation, led to the isolation of the hyper-xylanase producing mutant, viz, M. albomyces IITD3A. Various parameters including number of spores, nitrogen source and C/N ratio of the medium were optimized for production of xylanase by the mutant in a shake flask culture. Under controlled pH at 7.8, the mutant produced highly active xylanase with 415 IU/mL after 36 h of growth on soluble alkaline lignocellulosic extract in a 14-L fermentor. The overall productivity of xylanase was 8-fold higher than the wild type culture with11, 530 IU/L/h. The enzyme can be easily stored at 37°C for 50 days by addition of a small amount of the preservative — thiomersal. Also, for long term storage, a lyophilized powder form of the enzyme can be used which retained 100% of its activity for > 50 days. When assayed at pH 7.5 and temperature 55°C, the xylanase retained 100% of its original activity, and also at pH 9.0, it retained > 50% of its activity for 2 h, which is promising for its application in the pulp and paper industry.     

Kotumsar Cave biodiversity: a review of cavernicoles and their troglobiotic traits

The evolutionary adaptations of the organisms which inhabit the unusual and fragile ecosystems within caves are of inherent interest to both biologists and laymen. Cave organisms generally develop a high degree of physiological and behavioural adaptation for survival in the subterranean environment. The Kotumsar Cave is biologically the best known cave in India and has attracted interest from researchers from all over the world. This paper assesses the ecological community and overall habitat of the cave. This is based on long-term field observations and the review of the extensive literature on Kotumsar. For each species, features indicative of evolutionary adaptation to the cave environment are noted and conclusions drawn regarding the status of the species as a cavernicole. Several species of this cave are yet to get a proper study for correct taxonomic position although they have apparent troglomorphic dispositions. Several species which are highly endemic to this cave are probably in verge of its extinction. A serious measure to conserve the whole biodiversity has been suggested.     

NaCl pretreatment alleviates salt stress by enhancement of antioxidant defense system and osmolyte accumulation in mungbean (Vigna radiata L. Wilczek)

Enhancement of salt (NaCl) tolerance by pretreatment with sublethal dose (50 mM) of NaCl was investigated in V. radiata seedlings. NaCl stress caused drastic effects on roots compared to shoots. Accompanying reductions in length, number of root hairs and branches, roots became stout, brittle and brown in color. Salt stress caused gradual reduction in chlorophyll, carotenoid pigment contents and chlorophyll fluorescence intensity also. Superoxide dismutase and catechol peroxidase activities increased under stress in both roots and leaves. But catalase activity showed an increase in roots and decrease in leaves. In these seedlings, the oxidative stress has been observed under salinity stress and the level of proline, H2O2 and malondialdehyde content were increased. But pretreatment with sublethal dose of NaCl was able to overcome the adverse effects of stress imposed by NaCl to variable extents by increasing growth and photosynthetic pigments of the seedlings, modifying the activities of antioxidant enzymes, reducing malondialdehyde and H2O2 content and increasing accumulation of osmolytes like proline. Thus, mungbean plants can acclimate to lethal level of salinity by pretreatment with sublethal level of NaCl, improving their health and production under saline condition.     

Analysis of microRNAs induced by Venezuelan equine encephalitis virus infection in mouse brain

MicroRNAs (miRNA) are small RNA (∼22nts) molecules that are expressed endogenously in cells and play an important role in regulating gene expression. Recent studies have shown that cellular miRNA plays a very important role in the pathogenesis of viral infection. Venezuelan equine encephalitis virus (VEEV) is an RNA virus and is a member of the genus Alphavirus in the family Togaviridae. VEEV is infectious in aerosol form and is a potential biothreat agent. In this study, we report for the first time that VEEV infection in mice brain causes modulation of miRNA expression. Pathway analyses showed that majority of these miRNAs are involved in the neuronal development and function. Target gene prediction of the modulated miRNAs correlates with our recently reported mRNA expression in VEEV infected mice brain.     

Rab7 mutants associated with Charcot-Marie-Tooth disease exhibit enhanced NGF-stimulated signaling

Missense mutants in the late endosomal Rab7 GTPase cause the autosomal dominant peripheral neuropathy Charcot-Marie-Tooth disease type 2B (CMT2B). As yet, the pathological mechanisms connecting mutant Rab7 protein expression to altered neuronal function are undefined. Here, we analyze the effects Rab7 CMT2B mutants on nerve growth factor (NGF) dependent intracellular signaling in PC12 cells. The nerve growth factor receptor TrkA interacted similarly with Rab7 wild-type and CMT2B mutant proteins, but the mutant proteins significantly enhanced TrkA phosphorylation in response to brief NGF stimulation. Two downstream signaling pathways (Erk1/2 and Akt) that are directly activated in response to phospho-TrkA were differentially affected. Akt signaling, arising in response to activated TrkA at the plasma membrane was unaffected. However Erk1/2 phosphorylation, triggered on signaling endosomes, was increased. Cytoplasmic phospho-Erk1/2 persisted at elevated levels relative to control samples for up to 24 h following NGF stimulation. Nuclear shuttling of phospho Erk1/2, which is required to induce MAPK phosphatase expression and down regulate signaling, was greatly reduced by the Rab7 CMT2B mutants and explains the previously reported inhibition in PC12 neurite outgrowth. In conclusion, the data demonstrate a mechanistic link between Rab7 CMT2B mutants and altered TrkA and Erk1/2 signaling from endosomes.