Context-dependent encoding of fear and extinction memories in a large-scale network model of the basal amygdala

The basal nucleus of the amygdala (BA) is involved in the formation of context-dependent conditioned fear and extinction memories. To understand the underlying neural mechanisms we developed a large-scale neuron network model of the BA, composed of excitatory and inhibitory leaky-integrate-and-fire neurons. Excitatory BA neurons received conditioned stimulus (CS)-related input from the adjacent lateral nucleus (LA) and contextual input from the hippocampus or medial prefrontal cortex (mPFC). We implemented a plasticity mechanism according to which CS and contextual synapses were potentiated if CS and contextual inputs temporally coincided on the afferents of the excitatory neurons. Our simulations revealed a differential recruitment of two distinct subpopulations of BA neurons during conditioning and extinction, mimicking the activation of experimentally observed cell populations. We propose that these two subgroups encode contextual specificity of fear and extinction memories, respectively. Mutual competition between them, mediated by feedback inhibition and driven by contextual inputs, regulates the activity in the central amygdala (CEA) thereby controlling amygdala output and fear behavior. The model makes multiple testable predictions that may advance our understanding of fear and extinction memories.     

Complex recombination patterns arising during geminivirus coinfections preserve and demarcate biologically important intra-genome interaction networks

Genetic recombination is an important process during the evolution of many virus species and occurs particularly frequently amongst begomoviruses in the single stranded DNA virus family, Geminiviridae. As in many other recombining viruses it is apparent that non-random recombination breakpoint distributions observable within begomovirus genomes sampled from nature are the product of variations both in basal recombination rates across genomes and in the over-all viability of different recombinant genomes. Whereas factors influencing basal recombination rates might include local degrees of sequence similarity between recombining genomes, nucleic acid secondary structures and genomic sensitivity to nuclease attack or breakage, the viability of recombinant genomes could be influenced by the degree to which their co-evolved protein-protein and protein-nucleotide and nucleotide-nucleotide interactions are disreputable by recombination. Here we investigate patterns of recombination that occur over 120 day long experimental infections of tomato plants with the begomoviruses Tomato yellow leaf curl virus and Tomato leaf curl Comoros virus. We show that patterns of sequence exchange between these viruses can be extraordinarily complex and present clear evidence that factors such as local degrees of sequence similarity but not genomic secondary structure strongly influence where recombination breakpoints occur. It is also apparent from our experiment that over-all patterns of recombination are strongly influenced by selection against individual recombinants displaying disrupted intra-genomic interactions such as those required for proper protein and nucleic acid folding. Crucially, we find that selection favoring the preservation of co-evolved longer-range protein-protein and protein DNA interactions is so strong that its imprint can even be used to identify the exact sequence tracts involved in these interactions.     

Identification of hotspot regions of MurB oxidoreductase enzyme using homology modeling,molecular dynamics and molecular docking techniques

Despite the availability of effective chemotherapy and a moderately protective vaccine, new anti-tuberculosis agents are urgently needed to decrease the global incidence of tuberculosis (TB) disease. The MurB gene belongs to the bacterial cell wall biosynthesis pathway and is an essential drug target in Mycobacterium tuberculosis (Mtb) that has no mammalian counterparts. Here, we present an integrated approach involving homology modeling, molecular dynamics and molecular docking studies on Mtb-MurB oxidoreductase enzyme. A homology model of Mtb-MurB enzyme was built for the first time in order to carry out structure-based inhibitor design. The accuracy of the model was validated using different techniques. The molecular docking study on this enzyme was undertaken using different classes of well known MurB inhibitors. Estimation of binding free energy by docking analysis indicated the importance of Tyr155, Arg156, Ser237, Asn241 and His304 residues within the Mtb-MurB binding pocket. Our computational analysis is in good agreement with experimental results of site-directed mutagenesis. The present study should therefore play a guiding role in the experimental design of Mtb-MurB inhibitors for in vitro/in vivo analysis.     

EGFR and EphA2 are host factors for hepatitis C virus entry and possible targets for antiviral therapy

Hepatitis C virus (HCV) is a major cause of liver disease, but therapeutic options are limited and there are no prevention strategies. Viral entry is the first step of infection and requires the cooperative interaction of several host cell factors. Using a functional RNAi kinase screen, we identified epidermal growth factor receptor and ephrin receptor A2 as host cofactors for HCV entry. Blocking receptor kinase activity by approved inhibitors broadly impaired infection by all major HCV genotypes and viral escape variants in cell culture and in a human liver chimeric mouse model in vivo. The identified receptor tyrosine kinases (RTKs) mediate HCV entry by regulating CD81-claudin-1 co-receptor associations and viral glycoprotein-dependent membrane fusion. These results identify RTKs as previously unknown HCV entry cofactors and show that tyrosine kinase inhibitors have substantial antiviral activity. Inhibition of RTK function may constitute a new approach for prevention and treatment of HCV infection.     

Vibrio cholerae persistence in aquatic environments and colonization of intestinal cells: involvement of a common adhesion mechanism

Forty-one Tnpho A mutants of Vibrio cholerae O1 classical strain CD81 were analyzed for their ability to interact with chitin particles, Tigriopus fulvus copepods and the Intestine 407 cell line compared to the parent strain. Thirteen mutants were less adhesive than CD81; in particular, T21, T33 and T87 were less adhesive towards all substrates and insensitive to inhibition by N-acetyl glucosamine (GlcNAc). By SDS-PAGE analysis of sarkosyl-insoluble membrane proteins (siMPs) isolated from mutants and parent, it was found that a 53 kDa siMP is missing in T21, T33 and T87 mutants. It is hypothesized that this protein might have the function to mediate adherence to GlcNAc-containing substrates both in the aquatic environment and in human intestine.     

Monoclonal antibody AP33 defines a broadly neutralizing epitope on the hepatitis C virus E2 envelope glycoprotein

Hepatitis C virus (HCV) remains a significant threat to the general health of the world's population, and there is a pressing need for the development of new treatments and preventative vaccines. Here, we describe the generation of retrovirus-based pseudoparticles (HCVpp) incorporating a panel of full-length E1E2 clones representative of the major genotypes 1 through 6, and their application to assess the reactivity and neutralizing capability of antisera and monoclonal antibodies raised against portions of the HCV E2 envelope protein. Rabbit antisera raised against either the first hypervariable region or ectodomain of E2 showed limited and strain specific neutralization. By contrast, the monoclonal antibody (MAb) AP33 demonstrated potent neutralization of infectivity against HCVpp carrying E1E2 representative of all genotypes tested. The concentration of AP33 required to achieve 50% inhibition of infection by HCVpp of diverse genotypes ranged from 0.6 to 32 mug/ml. The epitope recognized by MAb AP33 is linear and highly conserved across different genotypes of HCV. Thus, identification of a broadly neutralizing antibody that recognizes a linear epitope is likely to be of significant benefit to future vaccine and therapeutic antibody development.     

Anthropogenic disturbances and plant biodiversity in forests of Uttaranchal,central Himalaya

Eight forest types varying in disturbance frequencies were identified along an elevational gradient in Uttaranchal, central Himalaya. Low elevation forests were close to human habitation and had high disturbance frequency, while high elevation forests were situated far from the human habitation and had low disturbance. The dominant tree species at low elevation were Pinus roxburghii and Quercus leucotrichophora, while Q. floribunda and Q. semecarpifolia dominated the high elevation forests. Pyracantha crenulata was the shrub present in all the forests except in Q. semecarpifolia forest and Anaphalis contorta, a herb species, was present in all the forests. Disturbance decreased the dominance of single species and increased the plant biodiversity by mixing species of different successional status. Species richness and diversity for all the vegetation layers were higher in low elevation–high disturbance forests. Mean tree density decreased from high to moderate and increased in low disturbance. The shrub density decreased from high to low disturbance while the reverse occured for herbs. High proportion of early successional species in disturbed forests indicated that disturbance induces succession. The mean number of young individuals increasing from high to low disturbance indicates that disturbance adversely affects regeneration. But, however, the high number of young individuals of Coriaria nepalensis, a small non-leguminous nitrogen fixing tree, in disturbed forests shows that the forest is regenerating. This species could be helpful in the re-establishment of original vegetation through triggering the regeneration of these forests. High elevation–low disturbed forests separated from low elevation–high disturbed forests. Forest type and elevation may have more influence on tree richness while shrub and herb richness may be more sensitive to disturbance and forest types.     

Cytomorphologic and morphometric limitations of the assessment of atypia in fibroadenoma of the breast

OBJECTIVE: To investigate the relevance of nuclear morphometry in separating the categories of "fibroadenoma" and "fibroadenoma with atypia." STUDY DESIGN: Thirty consecutive breast lumps, on which a fine needle aspiration (FNA) diagnosis of fibroadenoma was followed by excision and histopathologic confirmation of the diagnosis, were included. Atypia on cytology was based on cell overlap, nuclear enlargement and cell dyscohesion. Nuclear morphometric comparison was carried out between the categories of fibroadenoma, fibroadenoma with atypia and grade 1 ductal carcinoma cases that formed part of an earlier study. The parameters employed were area, roundness, diameter, perimeter and grey level. RESULTS: Among the 30 cases of fibroadenoma reported on FNA, an additional component of atypia was noted in 5. On subsequent histopathology, atypia was not confirmed in any of the cases. On morphometric analysis, a significant difference was noted between fibroadenoma and fibroadenoma with atypia categories, as between fibroadenoma and grade 1 ductal carcinoma cases. However, no significant difference was noted between fibroadenoma with atypia and grade 1 ductal carcinoma cases. CONCLUSION: FNA assessment of atypia in cases of fibroadenoma is difficult. Even conventional nuclear morphometry, though supporting the initial impression of atypia, does not help with this assessment. Also, based on morphometry alone, there may be difficulty separating fibroadenomas with atypia and grade 1 ductal carcinomas. Larger studies, employing other morphometric parameters, such as chromatin texture and fractal dimension, may shed further light on the subject.