Interferon-γ Induced by In Vitro Re-Stimulation of CD4+ T-Cells Correlates with In Vivo FMD Vaccine Induced Protection of Cattle against Disease and Persistent Infection

The immune defense against FMDV has been correlated to the antibody mediated component. However, there are occasions when some animals with high virus neutralising (VN) antibody are not protected following challenge and some with low neutralising antibody which do not succumb to disease. The importance of cell mediated immunity in clinical protection is less clear and so we investigated the source and production of interferon-gamma (IFN-γ) in re-stimulated whole blood of FMDV immunized cattle and its correlation to vaccine induced protection and FMDV persistence. We were able to show a positive correlation between IFN-γ response and vaccine induced protection as well as reduction of long term persistence of FMD virus. When combining this IFN-γ response in re-stimulated blood with virus neutralizing antibody titer in serum on the day of challenge, a better correlation of vaccine-induced protection with IFN-γ and VN antibody was predicted. Our investigations also showed that CD4+ T-cells are the major proliferating phenotype and IFN-γ producing cells.     

Diversity and Species Relationship in Pearl Millet (Pennisetum typhoides) and Related Species

Thirteen accessions of pearl millet (Pennisetum typhoides (L) Leeke) collected from different states of India and eight wild species of the genus Pennisetum across the world were analyzed for genetic diversity using AFLP markers. A combined analysis of eight primer combinations showed 35% polymorphism among P. typhoides accessions while analysis with five primer combinations showed 99% polymorphism among the wild species. The dendrogram constructed for the P. typhoides accessions based on the UPGMA method revealed two major clusters with samples from Gujarat forming a separate cluster from the rest of the samples. Principal component analysis of the same data set revealed similar results with the first principal component accounting for 65% of the total variation. The percentage of rare and common alleles contributing to the diversity in the sample was analyzed using the Shannon Weiner diversity index. The SW index revealed that the samples from Gujarat contributed significantly to the overall diversity among the accessions. Among accessions of each geographical region, considerable variation was revealed by SW index with samples from Tamil Nadu being most polymorphic. The genetic diversity in the accessions could be utilized for future breeding work. The dendrogram constructed for the wild species revealed the extent of genetic diversity among them. Analysis with one primer combination showed P. typhoides being closer to P. mollissimum than to the other analyzed species.     

An oxidative and salinity stress induced peroxisomal ascorbate peroxidase from Avicennia marina: Molecular and functional characterization

APX (EC, 1.11.1.11) has a key role in scavenging ROS and in protecting cells against their toxic effects in algae and higher plants. A cDNA encoding a peroxisomal ascorbate peroxidase, Am-pAPX1, was isolated from salt stressed leaves of Avicennia marina (Forsk.) Vierh. by EST library screening and its expression in the context of various environmental stresses was investigated. Am-pAPX1 contains an ORF of 286 amino acids coding for a 31.4kDa protein. The C-terminal region of the Am-pAPX1 ORF has a putative transmembrane domain and a peroxisomal targeting signal (RKKMK), suggesting peroxisomal localization. The peroxisomal localization of Am-pAPX1 was confirmed by stable transformation of the GFP-(Ala)(10)-Am-pAPX1 fusion in tobacco. RNA blot analysis revealed that Am-pAPX1 is expressed in response to salinity (NaCl) and oxidative stress (high intensity light, hydrogen peroxide application and excess iron). The isolated genomic clone of Am-pAPX1 was found to contain nine exons. A fragment of 1616bp corresponding to the 5' upstream region of Am-pAPX1 was isolated by TAIL-PCR. In silico analysis of this sequence reveals the presence of putative light and abiotic stress regulatory elements.     

Gene proximity analysis across whole genomes via PQ trees.

Permutations on strings representing gene clusters on genomes have been studied earlier by Uno and Yagiura (2000), Heber and Stoye (2001), Bergeron et al. (2002), Eres et al. (2003), and Schmidt and Stoye (2004) and the idea of a maximal permutation pattern was introduced by Eres et al. (2003). In this paper, we present a new tool for representation and detection of gene clusters in multiple genomes, using PQ trees (Booth and Leuker, 1976): this describes the inner structure and the relations between clusters succinctly, aids in filtering meaningful from apparently meaningless clusters, and also gives a natural and meaningful way of visualizing complex clusters. We identify a minimal consensus PQ tree and prove that it is equivalent to a maximal pi pattern (Eres et al., 2003) and each subgraph of the PQ tree corresponds to a nonmaximal permutation pattern. We present a general scheme to handle multiplicity in permutations and also give a linear time algorithm to construct the minimal consensus PQ tree. Further, we demonstrate the results on whole genome datasets. In our analysis of the whole genomes of human and rat, we found about 1.5 million common gene clusters but only about 500 minimal consensus PQ trees, with E. Coli K-12 and B. Subtilis genomes, we found only about 450 minimal consensus PQ trees out of about 15,000 gene clusters, and when comparing eight different Chloroplast genomes, we found only 77 minimal consensus PQ trees out of about 6,700 gene clusters. Further, we show specific instances of functionally related genes in two of the cases.     

Microbial Dynamics and Diversity of Bacillus thuringiensis in Textile Effluent Polluted and Non-polluted Rice Field Soils of Orissa, India

Microbial diversity was assessed in the soils of non-polluted rice fields of Central Rice Research Institute and Choudwar, and textile effluent contaminated (about 30 years) rice fields of Choudwar about 4 years after cessation of pollution. The soils contained 0.62–1.01 % organic C and 0.07–0.12 % total N, and measured 6.18–8.24 pH and 0.6–2.68 mS/cm Eh which were more in the polluted Choudwar soil. The microbial populations (×10⁶ cfu/g soil) in the soils were: heterotrophs 1.21–10.9, spore formers 0.9–2.43, Gram (−)ve bacteria 4.11–8.0, nitrifiers 0.72–1.5, denitrifiers 0.72–2.43, phosphate solubilizers 0.14–0.9, asymbiotic nitrogen fixers 0.34–0.59, actinomycetes 0.07–0.11, fungi 0–0.5 and Bacillus thuringiensis (Bt) 0.4–0.61 which predominated in the polluted soil of Choudwar. The fungi were scarce in the polluted rice fields. The Bt isolates belonged to three motile and one non-motile group. Two motile Bt isolates were phenotyped as Bt subsp. sotto and israelensis, whereas, the non-motile isolate was Bt subsp. wahuensis. All Bt isolates produced extracellular protease, lipase and amylase enzymes. The microbial guilds had positive correlation among themselves, as well as, with soil physico-chemical characters but the fungi had negative relation and the nitrogen fixers were unrelated with the biotic and abiotic components.     

In situ observation of a cell adhesion and metabolism using surface infrared spectroscopy

In this study, we report on an in situ monitoring system of living cultured cells using infrared absorption spectroscopy in the geometry of multiple internal reflections (MIR-IRAS). In order to observe living cultured cells, the temperature in the sample chamber of a FT-IR spectrometer was maintained at 37 °C and a humidified gas mixture containing 5% CO₂ was introduced into the sample chamber. Human breast cell line MCF-7 cultured on Si MIR prisms were placed in the sample chamber and infrared spectra of MCF-7 cells were collected for 5 h. It was found that the adhesion and metabolism of MCF-7 cells could be monitored by the absorption intensity of amide-II protein band (1,545 cm⁻¹) and also by the absorption intensities of CH _x bands (2,700–3,100 cm⁻¹). These results suggest that our system is useful for a nondestructive and non-label monitoring of cell viability. Our method based on infrared absorption spectroscopy has a potential for bioscreening application.     

Effects of NaCl Stress on the Structure,Pigment Complex Composition,and Photosynthetic Activity of Mangrove Bruguiera parviflora Chloroplasts

Exposure of two-month-old seedlings of Bruguiera parviflora to NaCl stress (0 to 400 mM) for 45 d under hydroponic culture caused notable disorganisation of the thylakoid structure of chloroplasts in NaCl-treated leaves as revealed from transmission electron microscopy. The absorption spectra of treated and control thylakoid samples were similar having a red peak at 680 nm and Soret peaks at 439 and 471 nm in the blue region of the spectrum. The spectra of treated samples differed from control samples by gradual decrease in absorbance of 100, 200, and 400 mM NaCl treated samples at 471 and 439 nm, which could be due to scattering of radiation in these samples. Thus, absorption characteristics of thylakoid membranes indicated no major alterations in the structural integrity of the photosynthetic membranes during salt stress in B. parviflora. Analysis of pigment protein complexes of thylakoids on non-denaturing gel showed that CP1 complex consisting of photosystem (PS) 1 reaction centre decreased marginally by 19% and the CP47 constituting the core antenna of PS2 declined significantly by 30% in 400 mM NaCl treated samples in respect to control. This decrease in structural core antenna might cause inefficient photon harvesting capacity. However, CP43 content did not alter. An increase in CP2/CP1 ratio from 3.2 in control to 4.0 in 400 mM NaCl treated samples indicated significant structural changes in the thylakoids of salt treated plants. Haem staining of thylakoids revealed significant losses in cytochrome (Cyt)f and Cyt b ₆ contents by NaCl stress. However, Cyt b ₅₅₉ content remained nearly constant in both control and NaCl treated samples. SDS-PAGE of thylakoid proteins showed that the intensity of many of Coomassie stained polypeptide bands ranging from 15–22 and 28–66 kDa regions decreased significantly in NaCl treated samples as compared to control. Electron transport activity of thylakoids, measured in terms of DCPIP photoreduction, was 22% lower in 400 mM NaCl treated plants than in the control ones. Hence, NaCl induces oxidative stress in chloroplasts causing structural alterations in thylakoids. These structural alterations might be responsible for declined efficiency of photosystems and reduced electron transport activity. This revised version was published online in August 2006 with corrections to the Cover Date.     

Wearable All‐Fabric‐Based Triboelectric Generator for Water Energy Harvesting

Realizing energy harvesting from water flow using triboelectric generators (TEGs) based on our daily wearable fabric or textile has practical significance. Challenges remain on methods to fabricate conformable TEGs that can be easily incorporated into waterproof textile, or directly harvest energy from water using hydrophobic textile. Herein, a wearable all‐fabric‐based TEG for water energy harvesting, with additional self‐cleaning and antifouling properties is reported for the first time. Hydrophobic cellulose oleoyl ester nanoparticles (HCOENPs) are prepared from microcrystalline cellulose, as a low‐cost and nontoxic coating material to achieve superhydrophobic coating on fabrics, including cotton, silk, flax, polyethylene terephthalate (PET), polyamide (nylon), and polyurethane. The resultant PET fabric‐based water‐TEG can generate an instantaneous output power density of 0.14 W m^?2 at a load resistance of 100 MΩ. An all‐fabric‐based dual‐mode TEG is further realized to harvest both the electrostatic energy and mechanical energy of water, achieving the maximum instantaneous output power density of 0.30 W m^?2. The HCOENPs‐coated fabric provides excellent breathability, washability, and environmentally friendly fabric‐based TEGs, making it a promising wearable self‐powered system.     

Genome-Wide Identification of Mitogen-Activated Protein Kinase Gene Family across Fungal Lineage Shows Presence of Novel and Diverse Activation Loop Motifs

The mitogen-activated protein kinase (MAPK) is characterized by the presence of the T-E-Y, T-D-Y, and T-G-Y motifs in its activation loop region and plays a significant role in regulating diverse cellular responses in eukaryotic organisms. Availability of large-scale genome data in the fungal kingdom encouraged us to identify and analyse the fungal MAPK gene family consisting of 173 fungal species. The analysis of the MAPK gene family resulted in the discovery of several novel activation loop motifs (T-T-Y, T-I-Y, T-N-Y, T-H-Y, T-S-Y, K-G-Y, T-Q-Y, S-E-Y and S-D-Y) in fungal MAPKs. The phylogenetic analysis suggests that fungal MAPKs are non-polymorphic, had evolved from their common ancestors around 1500 million years ago, and are distantly related to plant MAPKs. We are the first to report the presence of nine novel activation loop motifs in fungal MAPKs. The specificity of the activation loop motif plays a significant role in controlling different growth and stress related pathways in fungi. Hence, the presences of these nine novel activation loop motifs in fungi are of special interest.