Characterization of Upstream Sequences of the <Emphasis Type="Italic">LOJ</Emphasis> Gene Leads to Identification of a Novel Enhancer Element Conferring Lateral Organ Junction-Specific Expression in <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>

Isolation and characterization of promoters are important in understanding gene regulation and genetic engineering of crop plants. Earlier, a pentatricopeptide repeat protein (PPR) encoding gene (At2g39230), designated as Lateral Organ Junction (LOJ) gene, was identified through T-DNA promoter trapping in Arabidopsis thaliana. The upstream sequence of the LOJ gene conferred on the reporter gene a novel LOJ-specific expression. The present study was aimed at identifying and characterizing the cis-regulatory motifs responsible for tissue-specific expression in the −673 and +90 bases upstream of the LOJ gene recognized as LOJ promoter. In silico analysis of the LOJ promoter revealed the presence of a few relevant regulatory motifs and a unique feature like AT-rich inverted repeat. Deletion analysis of the LOJ promoter confirmed the presence of an enhancer-like element in the distal region (−673/−214), which stimulates a minimal promoter-like sequence in the −424/−214 region in a position and orientation autonomous manner. The −136/+90 region of the LOJ promoter was efficient in driving reporter gene expression in tissues like developing anthers and seeds of Arabidopsis. A positive regulation for the seed- and anther-specific expression module was contemplated within the 5′ untranslated region of the LOJ gene. However, this function was repressed in the native context by the lateral organ junction-specific expression. The present study has led to the identification of a novel lateral organ junction-specific element and an enhancer sequence in Arabidopsis with potential applications in plant genetic engineering.     

A Mass Spectrometric Study for Comparative Analysis and Evaluation of Metabolite Recovery from Plasma by Various Solvent Systems

A solvent system that extracts a maximum number of metabolites belonging to diverse chemical classes from complex biofluids, such as plasma, may offer useful inputs to understand the metabolic and physiological state of an individual. The present study compared seven solvent systems for extraction of metabolites from plasma. The extracts were analyzed by mass spectrometry (MS) and MS/MS (MS2) using a quadrupole time-of-flight liquid chromatography/MS system in positive and negative modes of ionization. Metabolites with molecular mass below 400 were identified using Human Metabolome Database MS2 and MS search interfaces. The acetone/isopropanol (2:1) system yielded promising results in positive ionization mode, as the maximum number of MS and MS2 features was detected in the extract. It was found to be superior in extraction of various classes of metabolites, especially organic acids, nucleosides and nucleoside derivatives, and heterocyclic molecules. Glycerophosphocholines in the mass range of 400–700 were found to be efficiently extracted by the methanol/chloroform/water (8:1:1) system. In negative mode as well, the maximum number of MS2 features was detected in methanol/chloroform/water and acetone/isopropanol extracts. The fingerprints of molecular features obtained in the negative and positive modes differed from each other to a significant extent.     

Reducing acetylated tau is neuroprotective in brain injury

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Improved photosynthetic characteristics correlated with enhanced biomass in a heterotic F1 hybrid of maize (Zea mays L.)

Photosynthesis Research - Heterosis is a phenomenon wherein F1 hybrid often displays phenotypic superiority and surpasses its parents in terms of growth and agronomic traits. Investigations on the...     

How good are comparative models in the understanding of protein dynamics?

The 3D structure of a protein is essential to understand protein dynamics. If experimentally determined structure is unavailable, comparative models could be used to infer dynamics. However, the effectiveness of comparative models, compared to experimental structures, in inferring dynamics is not clear. To address this, we compared dynamics features of ~800 comparative models with their crystal structures using normal mode analysis. Average similarity in magnitude, direction, and correlation of residue motions is >0.8 (where value 1 is identical) indicating that the dynamics of models and crystal structures are highly similar. Accuracy of 3D structure and dynamics is significantly higher for models built on multiple and/or high sequence identity templates (>40%). Three-dimensional (3D) structure and residue fluctuations of models are closer to that of crystal structures than to templates (TM score 0.9 vs 0.7 and square inner product 0.92 vs 0.88). Furthermore, long-range molecular dynamics simulations on comparative models of RNase 1 and Angiogenin showed significant differences in the conformational sampling of conserved active-site residues that characterize differences in their activity levels. Similar analyses on two EGFR kinase variant models highlight the effect of mutations on the functional state-specific αC helix motions and these results corroborate with the previous experimental observations. Thus, our study adds confidence to the use of comparative models in understanding protein dynamics.     

Efficiency of RAPD,ISSR and ITS markers in detecting genetic variability among Salacia species sampled from the Western Ghats of Karnataka

Diversity and phylogenetic relationship between four closely related Salacia species, i.e., Salacia chinensis, Salacia macrosperma, Salacia fruticosa and Salacia oblonga, collected from the Western Ghats of Karnataka, India, was assessed. Ten each of RAPD and ISSR primers generated a total of 76 and 68 loci, generating polymorphisms of 92.21 and 89.71%, respectively. Maximum likelihood analysis of the ITS sequences revealed three clades. Dendrogram analyses of RAPD and ISSR revealed two and four clusters, respectively. Overall polymorphism revealed by RAPD was 41.45?±?10%, ISSR was 33.58?±?6.52%, and ITS was 25.50?±?17.25%. Molecular variance revealed significant variance within and among the Salacia species. Tajima’s D neutrality test and Fu’s Fs were negative for all four species, implying presences of rare alleles and population expansion. Comparative study of RAPD, ISSR and ITS for Salacia species has given an insight into the efficiency of each technique in detecting diversity within and among the population sampled in the Western Ghats of Karnataka.

     

Increased ethanol production by metabolic modulation of cellulose fermentation in Clostridium thermocellum

Significant quantitative differences in ethanol yields along with repression in acetic acid production were observed in Clostridium thermocellum strains SS21 and SS22 in the presence of H 2 , acetone and sodium azide. Exogenous H 2 addition (1.0 atm) increased the ethanol yields to 0.40 g/g and ethanol to acetate ratio to 5.75 in strain SS21 but was inhibitory in strain SS22. Addition of acetone reversed the inhibition caused by H 2 and increased the ethanol yields and ethanol to acetate ratio of strain SS22 up to 0.40 g/g and 7.9, respectively. Enhancement in ethanol yields up to 0.40 g/g and 0.41 g/g and ethanol to acetate ratio up to 3.63 and 8.1 were observed in the presence of 0.2 mM and 0.15 mM concentration of sodium azide by strains SS21 and SS22, respectively.     

Molecular cloning,characterization and three-dimensional structure prediction of Lipoxygenase from Finger millet [Eleusine coracana (L.) Gaertn.] germinating seedlings

Lipoxygenases (LOXs) are functionally diverse class of non-heme iron containing dioxygenases. They involve in multiple physiological processes in plants and animals. In current study a full length cDNA of LOX has been cloned from finger millet germinating seedlings using PCR and RACE PCR methods. The ORF (2661 bp) encodes 887 amino acid residues, with an approximate molecular weight of 100.8 kDa and an isoelectric point of 5.90. The sequence exhibited significant similarity to already known LOXs. It comprises of a putative PLAT domain and an iron-binding catalytic domain. Sequence analysis demonstrated that this LOX is most probably a type 9-LOX, and shared highest identity (85 %) with the Setaria italica 9-LOX. TargetP predicted EcLOX as a cytoplasmic protein. It has an optimum pH of about 6.4 and increased lipid peroxidation levels were observed on day 5 of germination. Semi-quantitative RT-PCR analysis showed that EcLOX gene expression was preferentially higher on day 4 after germination, and in growing leaf and root tissues. Its expression could be induced by Methyl Jasmonate (MeJA), but not by Salicylic acid (SA). The 3-dimensional structure of the EcLOX was modeled using in silico approach and Molecular dynamics (MD) simulations were performed. Further, to understand the protein active site, docking studies were performed with substrates and inhibitors. In summary, EcLOX protein was characterized using various molecular, biochemical and in silico methods which improves our understanding of these fascinating enzymes.     

Artabotrys manoranjanii sp. nov. (Annonaceae) from the Andaman Islands,India

Artabotrys manoranjanii M. V. Ramana, J. Swamy & K. C. Mohan (Annonaceae), a new species from the foot hills of Saddle Peak National Park, north Andaman Islands, is described and illustrated. Its fleshy petals and prominent stigmas, distinguish it from all previously known species. Its affinity with A. parkinsonii Chatterjee, a Myanmar species, and A. grandiflorus King, a species from Malayan peninsula, is deliberated.     

Exquisite specificity of mitogenic lectin from <Emphasis Type="Italic">Cephalosporium curvulum</Emphasis> to core fucosylated N-glycans

Lectins are carbohydrate binding proteins that are gaining attention as important tools for the identification of specific glycan markers expressed during different stages of the cancer. We earlier reported the purification of a mitogenic lectin from human pathogenic fungus Cephalosporium curvulum (CSL) that has complex sugar specificity when analysed by hapten inhibition assay. In the present study, we report the fine sugar specificity of CSL as determined by glycan array analysis. The results revealed that CSL has exquisite specificity towards core fucosylated N-glycans. Fucosylated trimannosyl core is the basic structure required for the binding of CSL. The presence of fucose in the side chain further enhances the avidity of CSL towards such glycans. The affinity of CSL is drastically reduced towards the non-core fucosylated glycans, in spite of their side chain fucosylation. CSL showed no binding to the tested O-glycans and monosaccharides. These observations suggest the unique specificity of CSL towards core fucosylated N-glycans, which was further validated by binding of CSL to human colon cancer epithelial and hepatocarcinoma cell lines namely HT29 and HepG2, respectively, that are known to express core fucosylated N-glycans, using AOL and LCA as positive controls. LCA and AOL are fucose specific lectins that are currently being used clinically for the diagnosis of hepatocellular carcinomas. Most of the gastrointestinal markers express core fucosylated N-glycans. The high affinity and exclusive specificity of CSL towards α1-6 linkage of core fucosylated glycans compared to other fucose specific lectins, makes it a promising molecule that needs to be further explored for its application in the diagnosis of gastrointestinal cancer.