Enzymatic production of glucose from different qualities of grain sorghum and application of ultrasound to enhance the yield

The objective of the present work was to add value to three different qualities of grain sorghum namely normal healthy, germinated, and blackened through production of glucose, and to intensify glucose production (yield) by means of ultrasound treatment. Liquefaction (using Bacillus licheniformis α-amylase) and saccharification (using amyloglucosidase) processes were optimized with use of normal sorghum flour as a starting material for the production of glucose. The effect of ultrasound treatment on the sorghum slurry prior to liquefaction was studied on the processes of liquefaction and saccharification under optimized conditions. Due to ultrasound treatment, liquefact DE increased by 10-25% depending upon sonication time and the intensity. Ultrasound treatment of 1 min at 100% amplitude was found to decrease the average particle size of the slurry from 302 μm to 115 μm, which resulted in an increased percentage of saccharification by about 8%. The reason for the increase in the percentage of saccharification was attributed to the availability of additional starch for hydrolysis due to ultrasound-assisted disruption of the protein matrix (surrounding starch granules) and the amylose-lipid complex. Integration of ultrasound treatment in the state of art of the production of glucose from dry-milled sorghum and its possible subsequent use in the bioethanol production may improve the overall economics of the process.     

Multifunctional grains for the future: genetic engineering for enhanced and novel cereal quality

Cereals provide more than half the world population’s calorific intake, and have a variety of other important uses as food and beverage ingredients, livestock feeds, and as sources of renewable energy and industrial components. The technology to genetically modify many important cereals is now well-established, thereby presenting new opportunities to produce cereals with enhanced quality and novel properties. In 2007, GM (genetically modified) maize with insect and herbicide resistance was grown on over 30 million hectares worldwide, yet to date, there are no GM cereals with enhanced or novel grain (end-use) qualities being grown in commercial farmers’ fields. This review will discuss some of the latest GM technology developments reported to enhance the quality of cereals for food and other uses. Developments and opportunities involving gene manipulation for starch and protein quality, as well as non-starch polysaccharides, phenolic compounds and micronutrients will also be discussed. The current paucity of GM cereals with enhanced grain quality is not related to the absence of technological progress, rather it is the regulatory and consumer acceptance issues that have slowed the release of these crops.     

TASSER_low‐zsc: An approach to improve structure prediction using low z‐score–ranked templates

In a variety of threading methods, often poorly ranked (low z‐score) templates have good alignments. Here, a new method, TASSER_low‐zsc that identifies these low z‐score–ranked templates to improve protein structure prediction accuracy, is described. The approach consists of clustering of threading templates by affinity propagation on the basis of structural similarity (thread_cluster) followed by TASSER modeling, with final models selected by using a TASSER_QA variant. To establish the generality of the approach, templates provided by two threading methods, SP³ and SPARKS², are examined. The SP³ and SPARKS² benchmark datasets consist of 351 and 357 medium/hard proteins (those with moderate to poor quality templates and/or alignments) of length ≤250 residues, respectively. For SP³ medium and hard targets, using thread_cluster, the TM‐scores of the best template improve by ～4 and 9% over the original set (without low z‐score templates) respectively; after TASSER modeling/refinement and ranking, the best model improves by ～7 and 9% over the best model generated with the original template set. Moreover, TASSER_low‐zsc generates 22% (43%) more foldable medium (hard) targets. Similar improvements are observed with low‐ranked templates from SPARKS². The template clustering approach could be applied to other modeling methods that utilize multiple templates to improve structure prediction. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

High-frequency<Emphasis Type="Italic">in vitro</Emphasis> flowering in six species of<Emphasis Type="Italic">ceropegia</Emphasis>

High-frequencyin vitro flowering is reported here fromin vitro regenerated shoots ofin vitro-raised seedlings of rare and endemicCeropegia lawii, Ceropegia maccannii, Ceropegia oculata, andCeropegia sahyadrica, as well as the widely distributedCeropegia bulbosa var.bulbosa andCeropegia hirsuta. In our first set of experiments, the MS medium contained 87 mM sucrose and was supplemented with varying concentrations of BAP (4.4 to 26.6 μM). For the second set of trials, varying concentrations of sucrose (87 to 233 mM) were tested in MS media containing a constant 4.4 p.M BAP. Sub-cultured apical as well as axillary buds flowered with similar frequencies after 30 d of incubation. For all six species, the highest percentage of flowering shoots was obtained with either 26.6 μM BAP or 175 mM sucrose. Although smaller in size, theirin vitro flowers were morphologically comparable within wVo-derived flowers. Variations among species were noted for the number of flower buds per shoot and the percentage of flower formation. Because all six species showed similar responses in both experiments, we can suggest that this protocol is applicable across the wide range ofCeropegia species.     

Mixed bilayer containing dipalmitoylphosphatidylcholine and dipalmitoylphosphatidylserine: lipid complexation, ion binding, and electrostatics

Two mixed bilayers containing dipalmitoylphosphatidylcholine and dipalmitoylphosphatidylserine at a ratio of 5:1 are simulated in NaCl electrolyte solutions of different concentration using the molecular dynamics technique. Direct NH.O and CH.O hydrogen bonding between lipids was observed to serve as the basis of interlipid complexation. It is deduced from our results and previous studies that dipalmitoylphosphatidylcholine alone is less likely to form interlipid complexes than in the presence of bound ions or other bilayer "impurities" such as dipalmitoylphosphatidylserine. The binding of counterions is observed and quantitated. Based upon the calculated ion binding constants, the Gouy-Chapman surface potential (theta) is calculated. In addition we calculated the electrostatic potential profile (Phi) by twice integrating the system charge distribution. A large discrepancy between and the value of Phi at the membrane surface is observed. However, at "larger" distance from the bilayer surface, a qualitative similarity in the z-profiles of Phi and psi(GC) is seen. The discrepancy between the two potential profiles near the bilayer surface is attributed to the discrete and nonbulk-like nature of water in the interfacial region and to the complex geometry of this region.     

Integration of related sequences with protein three-dimensional structural families in an updated version of PALI database

The database of Phylogeny and ALIgnment of homologous protein structures (PALI) contains three-dimensional (3-D) structure-dependent sequence alignments as well as structure-based phylogenetic trees of protein domains in various families. The latest updated version (Release 2.1) comprises of 844 families of homologous proteins involving 3863 protein domain structures with each of these families having at least two members. Each member in a family has been structurally aligned with every other member in the same family using two proteins at a time. In addition, an alignment of multiple structures has also been performed using all the members in a family. Every family with at least three members is associated with two dendrograms, one based on a structural dissimilarity metric and the other based on similarity of topologically equivalenced residues for every pairwise alignment. Apart from these multi-member families, there are 817 single member families in the updated version of PALI. A new feature in the current release of PALI is the integration, with 3-D structural families, of sequences of homologues from the sequence databases. Alignments between homologous proteins of known 3-D structure and those without an experimentally derived structure are also provided for every family in the enhanced version of PALI. The database with several web interfaced utilities can be accessed at: http://pauling.mbu.iisc.ernet.in/~pali.