Department of Bioscience & Bioengineering

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A common feature in most neurodegenerative diseases and aging is the progressive accumulation of damaged proteins. Proteins are essential for all crucial biological functions. Under some notorious conditions, proteins loss their three dimensional native conformations and are converted into disordered aggregated structures. Such changes rise into pathological conditions and eventually cause serious protein conformation disorders. Protein aggregation and inclusion bodies formation mediated multifactorial proteotoxic stress has been reported in the progression of Parkinson's disease (PD), Huntington's disease (HD), Alzheimer's disease (AD), amyotrophic lateral sclerosis (ALS) and Prion disease. Ongoing studies have been remarkably informative in providing a systematic outlook for better understanding the concept and fundamentals of protein misfolding and aggregations. However, the precise role of protein quality control system and precursors of this mechanism remains elusive. In this review, we highlight recent insights and discuss emerging cytoprotective strategies of cellular protein quality control system implicated in protein deposition diseases. Our current review provides a clear, understandable framework of protein quality control system that may offer the more suitable therapeutic strategies for protein-associated diseases. © 2013 Springer Science+Business Media New York.

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Molecular Neurobiology

Protein quality control system in neurodegeneration: A healing company hard to beat but failure is fatal

The effects of elevated CO2 and O3, singly and in combination were investigated on various physiological, biochemical and yield parameters of two locally grown wheat (Triticum aestivum L.) cultivars (HUW-37 and K-9107) in open top chambers (OTCs). Elevated CO2 stimulated photosynthetic rate (Ps) and Fv/Fm ratio and reduced the stomatal conductance (gs). Reactive oxygen species, lipid peroxidation, anti-oxidative enzymes, ascorbic acid and total phenolics were higher, whereas Ps, gs, Fv/Fm, protein and photosynthetic pigments were reduced in elevated O3 exposure, as compared to their controls. Under elevated CO2 + O3, elevated levels of CO2 modified the plant performance against O3 in both the cultivars. Elevated CO2 caused significant increase in economic yield. Exposure to elevated O3 caused significant reduction in yield and the effect was cultivar-specific. The study concluded that elevated CO2 ameliorated the negative impact of elevated O3 and cultivar HUW-37 was more sensitive to elevated O3 than K-9107.

Indian Journal of Biochemistry and Biophysics

Individual and interactive effects of elevated carbon dioxide and ozone on tropical wheat (Triticum aestivum L.) cultivars with special emphasis on ROS generation and activation of antioxidant defence system

Non-coding RNAs from transposable elements of human genome are gaining prominence in modulating transcriptome dynamics. Alu elements, as exonized, edited and antisense components within same transcripts could create novel regulatory switches in response to different transcriptional cues. We provide the first evidence for cooccurrences of these events at transcriptome-wide scale through integrative analysis of data sets across diverse experimental platforms and tissues. This involved the following: (i) positional anchoring of Alu exonization events in the UTRs and CDS of 4663 transcript isoforms from RefSeq mRNAs and (ii) mapping on to them A→I editing events inferred from ∼7 million ESTs from dbEST and antisense transcripts identified from virtual serial analysis of gene expression tags represented in Cancer Genome Anatomy Project next-generation sequencing data sets across 20 tissues. We observed significant enrichment of these events in the 30UTR as well as positional preference within the embedded Alus. More than 300 genes had cooccurrence of all these events at the exon level and were significantly enriched in apoptosis and lysosomal processes. Further, we demonstrate functional evidence of such dynamic interactions between Alu-mediated events in a time series data from Integrated Personal Omics Profiling during recovery from a viral infection. Such 'single transcript-multiple fate' opportunity facilitated by Alu elements may modulate transcriptional response, especially during stress. © 2013 The Author(s).

Fulltext

Nucleic Acids Research

Transcriptome-wide expansion of non-coding regulatory switches: Evidence from co-occurrence of Alu exonization, antisense and editing

A versatile method of dual chemical functionalization of graphene oxide (GO) with Tris-[nitrilotris(acetic acid)] (Tris-NTA) and biotin for cellular delivery of oligohistidine- and biotin-tagged biomolecules is reported. Orthogonally functionalized GO surfaces with Tris-NTA and biotin to obtain a dual-functionalized GO (DFGO) are prepared and characterized by various spectroscopic and microscopic techniques. Fluorescence microscopic images reveal that DFGO surfaces are capable of binding oligohistidine-tagged biomolecules/proteins and avidin/biotin-tagged biomolecules/proteins orthogonally. The DFGO nanoparticles are non-cytotoxic in nature and can deliver oligohistidine- and biotin-tagged biomolecules simultaneously into the cell. Dual chemical functionalization of graphene oxide (GO) with Tris- [nitrilotris(acetic acid)] and biotin for cellular delivery of oligohistidine- and biotin-tagged biomolecules is described. The resulting nanoparticles are non-cytotoxic and can simultaneously deliver oligohistidine- and biotin-tagged biomolecules into the cell. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Macromolecular Bioscience

Dual Functionalized Graphene Oxide Serves as a Carrier for Delivering Oligohistidine- and Biotin-Tagged Biomolecules into Cells

Stabilization of G-quadruplex inhibits the activity of the enzyme telomerase in cancer cells. We found LL37, a host defense human cathelicidin antimicrobial peptide, to be a potent binder of G-quadruplex structures. © The Royal Society of Chemistry 2013.

Molecular BioSystems

Human cathelicidin peptide LL37 binds telomeric G-quadruplex

In past few years, atmospheric concentrations of carbon dioxide (CO2) and tropospheric ozone (O3) have increased due to anthropogenic activities. CO2 enhances the plant growth and surface level of O3 is a well-known phyto-toxic pollutant. Present study was conducted to assess the impact of elevated levels of CO2 and O3, singly and in combination on two wheat cultivars HUW-37 and K-9107 on their growth, yield attributes and grain quality in open top chambers (OTCs). Wheat plants under elevated CO2 (EC) showed increment in growth parameters while exposure to elevated O3 (EO) showed an opposite trend than EC. In elevated CO2+O3 (ECO) exposure, elevated CO2 fully protected wheat cultivars against negative effects of O3. Yield parameters showed significant increase in EC followed by ECO and in EO, significant reductions in yield were noticed in both the cultivars. Protein and total free amino-acids decreased in grains of EC, ECO and EO in both the test cultivars. Total soluble sugars and starch contents in grains increased due to EC and ECO and decreased in EO, however reducing sugars showed an opposite trend in both the cultivars. The yield data obtained from the experiment showed cultivar specific response as cultivar HUW-37 proved to be sensitive as compared to K-9107 against ambient and elevated levels of O3. The study also concludes that elevated CO2 nullified the negative impact of elevated O3 in both the test cultivars of wheat. © 2013 Elsevier B.V.

Field Crops Research

Differential response of dwarf and tall tropical wheat cultivars to elevated ozone with and without carbon dioxide enrichment: Growth, yield and grain quality

Singlet oxygen is a very important reactive oxygen species (ROS) involved in peroxidation of olefins and polymers, as well as in clinical photodynamic therapy treatments of tumors. Previously, it was reported that singlet oxygen can be formed via sensitization by spherical metal nanoparticles upon photo-excitation of the surface plasmon resonance (SPR) bands. In this paper, we report that sensitization and formation of singlet O2 is strongly dependent on the morphologies of gold and silver nanostructures. For example, singlet O2 can be generated via photo-irradiation and sensitization of silver decahedrons and silver triangular nanoplates, but not by silver nanocubes and gold decahedrons. The sensitization patterns of silver and gold nanoparticles are the reverse of each other. In the case of gold nanorods, singlet O2 can be generated via photo-excitation at the longitudinal SPR band, but not by excitation at the transverse SPR band. The controlling factors for such a morphology dependent singlet O2 sensitization will be discussed. Furthermore, we also demonstrate in vitro morphology dependent sensitization behaviour of silver nanoparticles in the photodynamic cancer treatment. Our results indicate that metal nanoparticles with certain morphologies are potentially very promising dual functional nanomaterials with capabilities of simultaneously serving as near infrared (NIR) activatable photodynamic therapy and photothermal therapy reagents for cancer treatments. © The Royal Society of Chemistry 2013.

Journal of Materials Chemistry B

Morphology dependent photosensitization and formation of singlet oxygen (1Δg) by gold and silver nanoparticles and its application in cancer treatment

Fluorescent pseudomonads catabolize glucose simultaneously by two different pathways, namely, the oxidative pathway in periplasm and the phosphorylative pathway in cytoplasm. This study provides evidence for the role of glucose metabolism in the regulation of pyoverdine synthesis in Pseudomonas putida S11. We have characterized the influence of direct oxidation of glucose in periplasm on pyoverdine synthesis in P. putida S11. We identified a Tn5 transposon mutant of P. putida S11 showing increased pyoverdine production in minimal glucose medium (MGM). This mutant designated as IST1 had Tn5 insertion in glucose dehydrogenase (gcd) gene. To verify the role of periplasmic oxidation of glucose on pyoverdine synthesis, we constructed mutants S11 Gcd- and S11 PqqF- by antibiotic cassette mutagenesis. These mutants of P. putida S11 with loss of glucose dehydrogenase gene (gcd) or cofactor pyrroloquinoline quinone biosynthesis gene (pqqF) showed increased pyoverdine synthesis and impaired acid production in MGM. In minimal gluconate medium, the pyoverdine production of wild-type strain S11 and mutants S11 Gcd- and S11 PqqF- was higher than in MGM indicating that gluconate did not affect pyoverdine synthesis. In MGM containing PIPES-NaOH (pH 7.5) buffer which prevent pH changes due to gluconic acid production, strain S11 produced higher amount of pyoverdine similar to mutants S11 Gcd- and S11 PqqF -. Therefore, it is proposed that periplasmic oxidation of glucose to gluconic acid decreases the pH of MGM and thereby influences pyoverdine synthesis of strain S11. The increased pyoverdine synthesis enhanced biotic and abiotic surface colonization of the strain S11. © 2013 Springer-Verlag Berlin Heidelberg.

Applied Microbiology and Biotechnology

Influence of periplasmic oxidation of glucose on pyoverdine synthesis in Pseudomonas putida S11

The segregation of binary mixtures in a filled rotating double-walled drum is explored by simulations. Based on the characteristics of self-gravity and the centrifugal force, we argue that both percolation and buoyancy effects dominate the segregation process. The simulational results show that up to long enough times the segregation state is controlled by the rotational speed, the particle radius and density. At low rotational speeds, the smaller and heavier particles tend to accumulate towards the inner drum wall and the bigger and lighter ones towards the outer drum wall, while the segregation pattern reverses completely at higher rotational speeds. Two typical phase diagrams in the space of the density and radius ratio of bigger particles to smaller particles further confirm the predictions. © 2013 EDP Sciences, SIF, Springer-Verlag Berlin Heidelberg.

European Physical Journal E

Spin Brazil-nut effect and its reverse in a rotating double-walled drum

The microRNAs, also known as miRNAs, are the class of small noncoding RNAs. They repress the expression of a gene posttranscriptionally. In effect, they regulate expression of a gene or protein. It has been observed that they play an important role in various cellular processes and thus help in carrying out normal functioning of a cell. However, dysregulation of miRNAs is found to be a major cause of a disease. Various studies have also shown the role of miRNAs in cancer and the utility of miRNAs for the diagnosis of cancer and other diseases. Unlike with mRNAs, a modest number of miRNAs might be sufficient to classify human cancers. However, the absence of a robust method to identify differentially expressed miRNAs makes this an open problem. In this regard, this paper presents a novel approach for in silico identification of differentially expressed miRNAs from microarray expression data sets. It integrates judiciously the theory of rough sets and merit of the so-called B.632+ bootstrap error estimate. While rough sets select relevant and significant miRNAs from expression data, the B.632+ error rate minimizes the variability and bias of the derived results. The effectiveness of the proposed approach, along with a comparison with other related approaches, is demonstrated on several miRNA microarray expression data sets, using the support vector machine. © 2013 Paul and Maji, publisher and licensee Dove Medical Press Ltd.