Phage Displayed Short Peptides against Cells of Candida albicans Demonstrate Presence of Species, Morphology and Region Specific Carbohydrate Epitopes

Candida albicans is a commensal opportunistic pathogen, which can cause superficial infections as well as systemic infections in immuocompromised hosts. Among nosocomial fungal infections, infections by C. albicans are associated with highest mortality rates even though incidence of infections by other related species is on the rise world over. Since C. albicans and other Candida species differ in their susceptibility to antifungal drug treatment, it is crucial to accurately identify the species for effective drug treatment. Most diagnostic tests that differentiate between C. albicans and other Candida species are time consuming, as they necessarily involve laboratory culturing. Others, which employ highly sensitive PCR based technologies often, yield false positives which is equally dangerous since that leads to unnecessary antifungal treatment. This is the first report of phage display technology based identification of short peptide sequences that can distinguish C. albicans from other closely related species. The peptides also show high degree of specificity towards its different morphological forms. Using fluorescence microscopy, we show that the peptides bind on the surface of these cells and obtained clones that could even specifically bind to only specific regions of cells indicating restricted distribution of the epitopes. What was peculiar and interesting was that the epitopes were carbohydrate in nature. This gives insight into the complexity of the carbohydrate composition of fungal cell walls. In an ELISA format these peptides allow specific detection of relatively small numbers of C. albicans cells. Hence, if used in combination, such a test could help accurate diagnosis and allow physicians to initiate appropriate drug therapy on time.

Formation of a G-quadruplex at the BCL2 major breakpoint region of the t(14;18) translocation in follicular lymphoma

The t(14;18) translocation in follicular lymphoma is one of the most common chromosomal translocations. Most breaks on chromosome 18 are located at the 3'-UTR of the BCL2 gene and are mainly clustered in the major breakpoint region (MBR). Recently, we found that the BCL2 MBR has a non-B DNA character in genomic DNA. Here, we show that single-stranded DNA modeled from the template strand of the BCL2 MBR, forms secondary structures that migrate faster on native PAGE in the presence of potassium, due to the formation of intramolecular G-quadruplexes. Circular dichroism shows evidence for a parallel orientation for G-quadruplex structures in the template strand of the BCL2 MBR. Mutagenesis and the DMS modification assay confirm the presence of three guanine tetrads in the structure. 1H nuclear magnetic resonance studies further confirm the formation of an intramolecular G-quadruplex and a representative model has been built based on all of the experimental evidence. We also provide data consistent with the possible formation of a G-quadruplex structure at the BCL2 MBR within mammalian cells. In summary, these important features could contribute to the single-stranded character at the BCL2 MBR, thereby contributing to chromosomal fragility.

Formation of a G-quadruplex at the BCL2 major breakpoint region of the t(14;18) translocation in follicular lymphoma

The t(14;18) translocation in follicular lymphoma is one of the most common chromosomal translocations. Most breaks on chromosome 18 are located at the 3'-UTR of the BCL2 gene and are mainly clustered in the major breakpoint region (MBR). Recently, we found that the BCL2 MBR has a non-B DNA character in genomic DNA. Here, we show that single-stranded DNA modeled from the template strand of the BCL2 MBR, forms secondary structures that migrate faster on native PAGE in the presence of potassium, due to the formation of intramolecular G-quadruplexes. Circular dichroism shows evidence for a parallel orientation for G-quadruplex structures in the template strand of the BCL2 MBR. Mutagenesis and the DMS modification assay confirm the presence of three guanine tetrads in the structure. 1H nuclear magnetic resonance studies further confirm the formation of an intramolecular G-quadruplex and a representative model has been built based on all of the experimental evidence. We also provide data consistent with the possible formation of a G-quadruplex structure at the BCL2 MBR within mammalian cells. In summary, these important features could contribute to the single-stranded character at the BCL2 MBR, thereby contributing to chromosomal fragility.

Critical exponent of the electrical conductivity in the paracoherence region of a thin film of YBa2Cu3O7?x

Critical exponent of the electrical conductivity in the paracoherence region (gamma) of the high temperature superconductor YBa2Cu3O7-x (YBCO) has been estimated for high quality thin film on ZrO2 substrate prepared by high pressure oxygen sputtering. High energy ion irradiation was carried out using 100 MeV O-16(7+) ions at liquid nitrogen to see the effects of disorder on the value of the exponent. The critical exponent from a value of about 2 to 1.62 upon irradiation. Studies were also carried film to see the effect of ageing and annealing.

Characterization of aerosol black carbon over a tropical semi-arid region of Anantapur, India

Black carbon (BC) aerosol mass concentrations measured using an aethalometer at Anantapur, a semi-arid tropical station in the southern part of peninsular India, from August 2006 to July 2007 are analyzed. Seasonal and diurnal variations of BC in relation to changes in the regional meteorological conditions have been studied along with the mass fraction of BC to the total aerosol mass concentration (M-t) and fine particle mass (FPM) concentration in different months. The data collected during the study period shows that the annual average BC mass concentration at Anantapur is 1.97 +/- 0.12 mu g m(-3). Seasonal variations of BC aerosol mass concentration showed high during the dry (winter and summer) seasons and low during the post-monsoon followed by the monsoon seasons. Diurnal variations of BC aerosols attain a gradual build up in BC concentration from morning and a sharp peak occurs between 07:00 and 09:00 h almost an hour after local sunrise and a broad nocturnal peak from 19:00 to 21:00 h with a minimum in noon hours. The ratio of BC to the fine particle mass concentration was high during the dry season and low during the monsoon season. The regression analysis between BC mass concentration and wind speed indicates that, with increase in wind speeds the BC mass concentrations would decrease and vice-versa. Aerosol BC mass concentration shows a significant positive correlation with total mass concentration (M-t) and aerosol optical depth (ACID, tau(p)) at 500 nm. (C) 2010 Elsevier B.V. All rights reserved.

Mycobacterium tuberculosis Expresses ftsE Gene Through Multiple Transcripts

Bacterial FtsE gene codes for the ATP-binding protein, FtsE, which in complex with the transmembrane protein, FtsX, participates in diverse cellular processes. Therefore, regulated expression of FtsE and FtsX might be critical to the human pathogen, Mycobacterium tuberculosis, under stress conditions. Although ftsX gene of M. tuberculosis (MtftsX) is known to be transcribed from a promoter inside the upstream gene, ftsE, the transcriptional status of ftsE gene of M. tuberculosis (MtftsE) remains unknown. Therefore, the authors initiated transcriptional analyses of MtftsE, using total RNA from M. tuberculosis cells that were grown under stress conditions, which the pathogen is exposed to, in granuloma in tuberculosis patients. Primer extension experiments showed the presence of putative transcripts, T1, T2, T3, and T4. T1 originated from the intergenic region between the upstream gene, MRA_3135, and MtftsE. T2 and T3 were found initiated from within MRA_3135. T4 was transcribed from a region upstream of MRA_3135. RT-PCR confirmed co-transcription of MRA_3135 and MtftsE. The cloned putative promoter regions for T1, T2, and T3 elicited transcriptional activity in Mycobacterium smegmatis transformants. T1, T2, and T3, but no new transcript, were present in the M. tuberculosis cells that were grown under the stress conditions, which the pathogen is exposed to in granuloma in tuberculosis patients. It showed lack of modulation of MtftsE transcripts under the stress conditions tested, indicating that ftsE may not have a stress response-specific function in M. tuberculosis.

A novel method for mapping assembled epitopes in batches: Identification of three epitopes at the receptor binding region of human chorionic gonadotropin

Identification of conformation-specific epitopes of hCG beta has been done using a simple batch method, Chemically or enzymatically-modified hCG beta has been prepared in a batch and the effect of modifications on the integrity of different epitope regions has been investigated in a quantitative manner using monoclonal antibodies (MAbs) immobilized on plastic tubes from culture supernatants. Based on the extent of damage done to different regions by different modifications, three conformation-specific epitopes of hCG beta have been identified. The method has been shown to have important advantages over the existing methods on many considerations, Using this approach, these epitopes have been shown to be at/near the receptor-binding region.

Electron transfer reaction in the marcus inverted region: role of high frequency vibrational modes

A theoretical study of the dynamics of photo-electron transfer reactions in the Marcus inverted regime is presented. This study is motivated partly by the recent proposal of Barbara et al. (J. Phys. Chem. 96, 3728, 1991) that a minimal model of an electron transfer reaction should consist of a polar solvent mode (X), a low frequency vibrational mode (Q) and one high frequency mode (q). Interplay between these modes may be responsible for the crossover observed in the dynamics from a solvent controlled to a vibrational controlled electron transfer. The following results have been obtained. (i) In the case of slowly relaxing solvents, the proximity of the point of excitation to an effective sink on the excited surface is critical in determining the decay of the reactant population. This is because the Franck-Condon overlap between the reactant ground and the product excited states decreases rapidly with increase in the quantum number of the product vibrational state. (ii) Non-exponential solvation dynamics has an important effect in determining the rates of electron transfer. Especially, a biphasic solvation and a large coupling between the reactant and the product states both may be needed to explain the experimental results. ©1996 American Institute of Physics

Cloning And Characterization of Mycobacteriophage-13 Promoters

Restriction fragments of mycobacteriophage 13 DNA capable of initiating transcription have been cloned into a promoter selection vector of Escherichia coli, and selected on the basis of development of resistance to chloramphenicol. The growth pattern of these 'promoter clones' on a concentration gradient of chloramphenicol and the biochemical assays of the chloramphenicol acetyl transferase have permitted the assessment of their relative promoter strengths. DNA sequence analysis revealed significant homology of these promoters to the -35 regions of the mycobacterial- and E. coli promoter consensus, but less so to the - 10 region. Based on the sequence of phage 13 promoters identified here and the reported sequences of mycobacterial promoters, a promoter consensus for mycobacteria has been generated.

Quantum and non-Markovian effects in the electron transfer reaction dynamics in the Marcus inverted region

Electron transfer reactions in large molecules may often be coupled to both the polar solvent modes and the intramolecular vibrational modes of the molecule. This can give rise to a complex dynamics which may in some systems, like betaine, be controlled more by vibrational rather than by solvent effects. Additionally, a significant contribution from an ultrafast relaxation component in the solvation dynamics may enhance the complexity. To explain the wide range of behavior that has been observed experimentally, Barbara et al. recently proposed that a model of an electron transfer reaction should minimally consist of a low-frequency classical solvent mode (X), a low-frequency vibrational mode (Q), and a high-frequency quantum mode (q) (J. Phys. Chem. 1991, 96, 3728). In the present work, a theoretical study of this model is described. This study generalizes earlier work by including the biphasic solvent response and the dynamics of the low-frequency vibrational mode in the presence of a delocalized, extended reaction zone. A novel Green's function technique has been developed which allowed us to study the non-Markovian dynamics on a multidimensional surface. The contributions from the high-frequency vibrational mode and the ultrafast component in the non-Markovian solvent dynamics are found to be primarily responsible for the dramatic increase in charge transfer rate over the prediction of the classical theories that neglect both these factors. These, along with a large coupling between the reactant and the product states, may combine to render the electron transfer rate both very large and constant over a wide range of solvent relaxation rates. A study on the free energy gap dependence of the electron transfer rate reveals that the rates are sensitive to changes in the quantum frequency particularly when the free energy gap is very large.

Status Survey of the Malabar Pied Hornbill in the Dandeli Region, Northern Western Ghats, India

The Malabar Pied Hornbill, Anthracoceros coronatus, is a near threatened species, endemic to the tropical deciduous forests of central and southern India and Sri Lanka. The Dandeli region in Karnataka (India) is believed to be the last stronghold of this species in the Western Ghats biodiversity hotspot. Being a rapidly developing area with a growing human population, the threats to this species and their habitat are mounting, especially due to a large number of hydroelectric projects and habitat fragmentation caused by paper and plywood industries. This study evaluated the change in population status of the Malabar Pied Hornbill over a 23 year period and defined priorities for the long term conservation and monitoring of hornbills in Dandeli. Encounter rates of hornbills were also analysed in relation to the density and species richness of trees and fruiting trees, basal area, canopy cover and distance from river. Hornbill encounters were not significantly different compared to the earlier study carried out by Reddy in 1988, but were significantly different across the five sites in the current study. Higher numbers of hornbills were encountered closer to the river, but these results were only marginally significant. The mean numbers of hornbills recorded at the two roost sites identified in Dandeli were 26 +/- 4.47 (n=16 counts) and 31.78 +/- 3.53 (n=14 counts) respectively. The study also helped build local awareness about the species, train local Forest Department staff in monitoring hornbills and develop a management plan for its conservation.

Implications of the recent high statistics determination of the pion electromagnetic form factor in the timelike region

The recently evaluated two-pion contribution to the muon g - 2 and the phase of the pion electromagnetic form factor in the elastic region, known from pi pi scattering by Fermi-Watson theorem, are exploited by analytic techniques for finding correlations between the coefficients of the Taylor expansion at t = 0 and the values of the form factor at several points in the spacelike region. We do not use specific parametrizations, and the results are fully independent of the unknown phase in the inelastic region. Using for instance, from recent determinations, < r(pi)(2)> = (0.435 +/- 0.005) fm(2) and F(-1.6 GeV2) = 0.243(-0.014)(+0.022), we obtain the allowed ranges 3.75 GeV-4 less than or similar to c less than or similar to 3.98 GeV-4 and 9.91 GeV-6 less than or similar to d less than or similar to 10.46 GeV-6 for the curvature and the next Taylor coefficient, with a strong correlation between them. We also predict a large region in the complex plane where the form factor cannot have zeros.

Turbulent heat flux variation over the Monsoon-Trough region during MONTBLEX-90

Tower data collected during the Monsoon-Trough Boundary Layer Experiment (MONTBLEX-90) have been analysed to understand the observed structure of the surface layer over an arid region (Jodhpur) and a moist region (Kharagpur) during active and weak phases of the 1990 southwest monsoon. Turbulent heat and momentum fluxes are estimated by the eddy correlation method using sonic data. The turbulent momentum flux at both Jodhpur and Kharagpur was larger when the winds were stronger, reaching a maximum of the order of 0.5 N m(-2) on 5 and 6 August when a low pressure system was located over the region. The heat flux at Jodhpur is high during weak monsoon days, the maximum being 450 W m(-2), whereas during active days the flux never exceeds 200 W m(-2). At Kharagpur, the flux does not vary significantly between active and weak monsoon days, the maximum in either phase being 160 W m(-2) At Jodhpur, there is significant contrast in the near-surface air temperature, being higher during weak monsoon days as compared to active days. Cloud cover did not vary significantly in both the regions. The turbulent heat flux variation at both the sites appears to be correlated mainly with soil mixture, and less sensitive to cloud cover.

Isolation of an 800 kb contiguous DNA fragment encompassing a 3.5-cM region of chromosome 1 in Arabidopsis using YAC clones

The apetalal mutation of Arabidopsis affects floral meristem identity and the development of sepal and petal primordia of the flower. We mapped the available RFLP markers on chromosome 1 that are in the general vicinity of apetalal on a fine structure map and then chose the closest RFLP as a starting point for contiguous DNA (contig) generation. We report here a contig of about 800 kilobases (kb) that spans a 3.5 cM region of chromosome 1. We used genomic libraries of Arabidopsis prepared in yeast artificial chromosome (YAC) vectors and the detailed characterization of 19 YACs is reported. RFLPs displayed by the end fragments from the walk were mapped to align and correlate the genetic and physical maps for this region of chromosome 1. In this segment of the genome, 1 cM corresponds to a little over 200 kb of physical distance.