Role of Arabidopsis BBX proteins in light signaling

Journal of Plant Biochemistry and Biotechnology - Light regulates numerous aspects of plant growth and development like seed germination, seedling de-etiolation, pigment accumulation, cotyledon...     

Aspartase/fumarase superfamily: a common catalytic strategy involving general base-catalyzed formation of a highly stabilized aci-carboxylate intermediate

Members of the aspartase/fumarase superfamily share a common tertiary and quaternary fold, as well as a similar active site architecture; the superfamily includes aspartase, fumarase, argininosuccinate lyase, adenylosuccinate lyase, δ-crystallin, and 3-carboxy-cis,cis-muconate lactonizing enzyme (CMLE). These enzymes all process succinyl-containing substrates, leading to the formation of fumarate as the common product (except for the CMLE-catalyzed reaction, which results in the formation of a lactone). In the past few years, X-ray crystallographic analysis of several superfamily members in complex with substrate, product, or substrate analogues has provided detailed insights into their substrate binding modes and catalytic mechanisms. This structural work, combined with earlier mechanistic studies, revealed that members of the aspartase/fumarase superfamily use a common catalytic strategy, which involves general base-catalyzed formation of a stabilized aci-carboxylate (or enediolate) intermediate and the participation of a highly flexible loop, containing the signature sequence GSSxxPxKxN (named the SS loop), in substrate binding and catalysis.     

Protection of Shrimp Penaeus monodon from WSSV Infection Using Antisense Constructs

White spot syndrome caused by white spot syndrome virus (WSSV) is one of the most threatening diseases of shrimp culture industry. Previous studies have successfully demonstrated the use of DNA- and RNA-based vaccines to protect WSSV infection in shrimp. In the present study, we have explored the protective efficacy of antisense constructs directed against WSSV proteins, VP24, and VP28, thymidylate synthase (TS), and ribonucleotide reductase-2 (RR2) under the control of endogenous shrimp histone-3 (H3) or penaedin (Pn) promoter. Several antisense constructs were generated by inserting VP24 (pH3–VP24, pPn–VP24), VP28 (pH3–VP28, pPn–VP28), TS (pH3–TS, pPn–TS), and RR2 (pH3–RR2) in antisense orientation. These constructs were tested for their protective potential in WSSV infected cell cultures, and their effect on reduction of the viral load was assessed. A robust reduction in WSSV copy number was observed upon transfection of antisense constructs in hemocyte cultures derived from Penaeus monodon and Scylla serrata. When tested in vivo, antisense constructs offered a strong protection in WSSV challenged P. monodon. Constructs expressing antisense VP24 and VP28 provided the best protection (up to 90 % survivability) with a corresponding decrease in the viral load. Our work demonstrates that shrimp treated with antisense constructs present an efficient control strategy for combating WSSV infection in shrimp aquaculture.     

Polyhydroxyalkanoate biosynthesis in Bacillus cereus SPV under varied limiting conditions and an insight into the biosynthetic genes involved

Aims:  A new strain of Bacillus, Bacillus cereus SPV, was found to be capable of using a wide range of carbon sources for the production of polyhydroxyalkanoates (PHAs) ( Valappil et al. 2007b ). Limiting nutrient in the culture conditions is crucial for PHA production. In this study, B.   cereus SPV was grown in different culture conditions with limitation of potassium, nitrogen, sulphur and phosphorous to establish the impact of nutritional limitation on PHA production.
Methods and Results:  The PHA yields obtained were found to be 13·4, 38, 13·15 and 33·33% dcw for potassium, nitrogen, sulphur and phosphorus limitations, respectively. Gas chromatography–mass spectrometry analysis of the isolated polymers showed the presence of P(3HB) under nitrogen, sulphur and phosphate-limiting conditions and P(3HB-3HV) copolymer under potassium limiting conditions. This ability of B. cereus SPV to accumulate different PHA monomers from structurally unrelated carbon sources led to an interest in the molecular analysis of PHA biosynthesis in this organism. To achieve this, PCR was used to identify the polyhydroxyalkanoate biosynthetic genes in B. cereus SPV.
Conclusion:  Sequence analysis of the PCR products from B. cereus SPV revealed the sequence of the putative biosynthetic genes, and possible regions involved in substrate binding.
The nucleotide sequence reported in this paper is in the GenBank nucleotide sequence database under accession number DQ486135 .
Significance and Impact of the Study:  This is the first report comparing the capability of B. cereus SPV to produce PHAs under different culture conditions of potassium, nitrogen, sulfur and phosphate limitations. The results in this study suggest the unique ability of B. cereus SPV to supply both 3HB and 3HV monomers from a structurally unrelated carbon source, glucose.     

A possible role of poly-3-hydroxybuiyric acid in antibiotic production in<Emphasis Type="Italic">Streptomyces</Emphasis>

The occurrence of poly-3-hydroxybutyric acid (PHB) in 12 different strains of the genus Streptomyces was investigated. Gas chromatographic estimation indicated that all the strains produced PHB and the range of maximum PHB accumulation was between 1.5 and 11.8% dry cell weight. PHB was isolated from Streptomyces coelicolor A3(2) M145 and characterized using Fourier transform-infrared (FT-IR) spectroscopy. The correlation between PHB utilization and antibiotic production in S. coelicolor A3(2) M145, was studied; results indicated a possible role of PHB as a carbon reserve material used for antibiotic production.     

Fabrication and characterization of biodegradable poly(3-hydroxybutyrate) composite containing bioglass

Bacterially derived poly(3-hydroxybutyrate) (P(3HB)) has been used to produce composite films by incorporating Bioglass particles (<5 microm) in 5 and 20 wt % concentrations. P(3HB) was produced using a large scale fermentation technique. The polymer was extracted using the Soxhlet technique and was found to have similar thermal and structural properties to the commercially available P(3HB). The effects of adding Bioglass on the microstructure surface and thermal and mechanical properties were examined using differential scanning calorimetry, dynamic mechanical analysis (DMA), X-ray diffraction, surface interferometry, electron microscopy, and nanoindentation. The addition of increasing concentrations of Bioglass in the polymer matrix reduced the degree of crystallinity of the polymer as well as caused an increase in the glass transition temperature as determined by DMA. The presence of Bioglass particulates reduced the Young's modulus of the composite. The storage modulus and the loss modulus, however, increased with the addition of 20 wt % Bioglass. A short period (28 days) in vitro bioactivity study in simulated body fluid confirmed the bioactivity of the composites, demonstrated by the formation of hydroxyapatite crystals on the composites' surface.     

Planning adaptation to climate change in fast-warming marine regions with seafood-dependent coastal communities

Many coastal communities rely on living marine resources for livelihoods and food security. These resources are commonly under stress from overfishing, pollution, coastal development and habitat degradation. Climate change is an additional stressor beginning to impact coastal systems and communities, but may also lead to opportunities for some species and the people they sustain. We describe the research approach for a multi-country project, focused on the southern hemisphere, designed to contribute to improving fishing community adaptation efforts by characterizing, assessing and predicting the future of coastal-marine food resources, and co-developing adaptation options through the provision and sharing of knowledge across fast-warming marine regions (i.e. marine ‘hotspots’). These hotspots represent natural laboratories for observing change and concomitant human adaptive responses, and for developing adaptation options and management strategies. Focusing on adaptation options and strategies for enhancing coastal resilience at the local level will contribute to capacity building and local empowerment in order to minimise negative outcomes and take advantage of opportunities arising from climate change. However, developing comparative approaches across regions that differ in political institutions, socio-economic community demographics, resource dependency and research capacity is challenging. Here, we describe physical, biological, social and governance tools to allow hotspot comparisons, and several methods to evaluate and enhance interactions within a multi-nation research team. Strong partnerships within and between the focal regions are critical to scientific and political support for development of effective approaches to reduce future vulnerability. Comparing these hotspot regions will enhance local adaptation responses and generate outcomes applicable to other regions.     

Structural basis for the catalytic mechanism of aspartate ammonia lyase

Aspartate ammonia lyases (or aspartases) catalyze the reversible deamination of L-aspartate into fumarate and ammonia. The lack of crystal structures of complexes with substrate, product, or substrate analogues so far precluded determination of their precise mechanism of catalysis. Here, we report crystal structures of AspB, the aspartase from Bacillus sp. YM55-1, in an unliganded state and in complex with L-aspartate at 2.4 and 2.6 ? resolution, respectively. AspB forces the bound substrate to adopt a high-energy, enediolate-like conformation that is stabilized, in part, by an extensive network of hydrogen bonds between residues Thr101, Ser140, Thr141, and Ser319 and the substrate's β-carboxylate group. Furthermore, substrate binding induces a large conformational change in the SS loop (residues G(317)SSIMPGKVN(326)) from an open conformation to one that closes over the active site. In the closed conformation, the strictly conserved SS loop residue Ser318 is at a suitable position to act as a catalytic base, abstracting the Cβ proton of the substrate in the first step of the reaction mechanism. The catalytic importance of Ser318 was confirmed by site-directed mutagenesis. Site-directed mutagenesis of SS loop residues, combined with structural and kinetic analysis of a stable proteolytic AspB fragment, further suggests an important role for the small C-terminal domain of AspB in controlling the conformation of the SS loop and, hence, in regulating catalytic activity. Our results provide evidence supporting the notion that members of the aspartase/fumarase superfamily use a common catalytic mechanism involving general base-catalyzed formation of a stabilized enediolate intermediate.     

Comparative expression analysis of tRF-3001a and tRF-1003 with corresponding miRNAs (miR-1260a and miR-4521) and their network analysis with breast cancer biomarkers

Molecular Biology Reports - MicroRNAs and tRFs (tRNA-derived fragments) are small non-coding RNAs that are promising breast cancer (BC) biomarkers. miRNA sequences are found within tRFs. For...     

Large-scale production and efficient recovery of PHB with desirable material properties, from the newly characterised Bacillus cereus SPV

A newly characterised Bacillus strain, Bacillus cereus SPV was found to produce PHB at a concentration of 38% of its dry cell weight in shaken flask cultures, using glucose as the main carbon source. Polymer production was then scaled up to 20 L batch fermentations where 29% dry cell weight of PHB was obtained within 48 h. Following this, a simple glucose feeding strategy was developed and the cells accumulated 38% dry cell weight of PHB, an increase in the overall volumetric yield by 31% compared to the batch fermentation. Sporulation is the cause of low PHB productivity from the genus Bacillus [Wu, Q., Huang, H., Hu, G.H., Chen, J., Ho, K.P., Chen, G.Q., 2001. Production of poly-3-hydroxybutyrate by Bacillus sp. JMa5 cultivated in molasses media. Antonie van Leeuwenhoek 80, 111-118]. However, in this study, acidic pH conditions (4.5-5.8) completely suppress sporulation, in accordance with Kominek and Halvorson [Kominek, L.A., Halvorson, H.O., 1965. Metabolism of poly-beta-hydroxybutyrate and acetoin in Bacillus cereus. J. Bacteriol. 90, 1251-1259], and result in an increase in the yield of PHB production. This observation emphasises the potential of the use of Bacillus in the commercial production of PHB and other PHAs. The recovery of the PHB produced was optimised and the isolated polymer characterised to identify its material properties. The polymer extracted, was found to have similar molecular weight, polydispersity index and lower crystallinity index than others reported in literature. Also, the extracted polymer was found to have desirable material properties for potential tissue engineering applications.