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A combination of bioinformatics, steady-state kinetics, and NMR spectroscopy has revealed the catalytic functions of YcjQ, YcjS and YcjR from the ycj gene cluster in Escherichia coli K-12. YcjS was determined to be a 3-keto-d-glucoside dehydrogenase with a k(cat) = 22 s(−1), and k(cat)/K(m) = 2.3 × 10(4) M(−1) s(−1) for the reduction of methyl α-3-keto-d-glucopyranoside at pH 7.0 with NADH. YcjS also exhibited catalytic activity for the NAD(+)-dependent oxidation of d-glucose, methyl β-d-glucopyranoside, and 1,5-anhydro-d-glucitol. YcjQ was determined to be a 3-keto-d-guloside dehydrogenase with k(cat) = 18 s(−1), and k(cat)/K(m) = 2.0 × 10(3) M(−1) s(−1) for the reduction of methyl α-3-keto-gulopyranoside. This is first reported dehydrogenase for the oxidation of d-gulose. YcjQ also exhibited catalytic activity with d-gulose and methyl β-d-gulopyranoside. The 3-keto products from both dehydrogenases were found to be extremely labile under alkaline conditions. The function of YcjR was demonstrated to be a C-4 epimerase that interconverts 3-keto-d-gulopyranosides to 3-keto-d-glucopyranosides. These three enzymes, YcjQ, YcjR, and YcjS, thus constitute a previously unrecognized metabolic pathway for the transformation of d-gulosides to d-glucosides via the intermediate formation of 3-keto-d-guloside and 3-keto-d-glucoside.

YcjR from Escherichia coli K-12 MG1655 catalyzes the manganese-dependent reversible epimerization of 3-keto-α-D-gulosides to the corresponding 3-keto-α-D-glucosides as a part of a proposed catabolic pathway for the transformation of D-gulosides to D-glucosides. The three-dimensional structure of the manganese-bound enzyme was determined by X-ray crystallography. The divalent manganese ion is coordinated to the enzyme by ligation to Glu-146, Asp-179, His-205, and Glu-240. When either of the two active site glutamate residues are mutated to glutamine the enzyme loses all catalytic activity for the epimerization of α-methyl-3-keto-D-glucoside at C4. However, the E240Q mutant is able to catalyze hydrogen/deuterium exchange of the proton at C4 of α-methyl-3-keto-D-glucoside in solvent D(2)O. The E146Q mutant does not catalyze this exchange reaction. These results indicate that YcjR catalyzes the isomerization of 3-keto-D-glucosides via proton abstraction at C4 by Glu-146 to form a cis-enediolate intermediate that is subsequently protonated on the opposite face by Glu-240 to generate the corresponding 3-keto-D-guloside. This conclusion is supported by docking of the cis-enediolate intermediate into the active site of YcjR based on the known binding orientation of D-fructose and D-psicose in the active site of D-psicose-3-epimerase. It is proposed that YcjR be named 3-keto-D-glucoside-4-epimerase.

The substrate profiles for three uncharacterized enzymes (YcjM, YcjT, and YcjU) that are expressed from a cluster of twelve genes (ycjM-W and ompG) of unknown function in Escherichia coli K-12 have been determined. Through a comprehensive bioinformatic and steady-state kinetic analysis, the catalytic function of YcjT was determined to be kojibiose phosphorylase. In the presence of saturating phosphate and kojibiose (α-(1,2)-D-glucose-D-glucose) this enzyme catalyzes the formation of D-glucose and β-D-glucose-1-phosphate (k(cat) = 1.1 s(−1), K(m) = 1.05 mM, and k(cat)/K(m) = 1.12 x 10(3) M(−1) s(−1)). Additionally, it was also shown that in the presence of β-D-glucose-1-phosphate, YcjT can catalyze the formation of other disaccharides using 1,5-anhydro-D-glucitol, L-sorbose, D-sorbitol or L-iditol as a substitute for D-glucose. Kojibiose is a component of cell wall lipoteichoic acids in Gram-positive bacteria and is of interest as a potential low-calorie sweetener and prebiotic. YcjU was determined to be a β-phosphoglucomutase that catalyzes the isomerization of β-D-glucose-1-phosphate (k(cat) = 21 s(−1), K(m) = 18 μM, and k(cat)/K(m) = 1.1 x 10(6) M(−1) s(−1)) to D-glucose-6-phosphate. YcjU was also shown to exhibit catalytic activity with β-D-allose-1-phosphate, β-D-mannose-1-phosphate, and β-D-galactose-1-phosphate. YcjM catalyzes the phosphorolysis of α-(1,2)-D-glucose-D-glycerate with a k(cat) = 2.1 s(−1), K(m) = 69 μM, and k(cat)/K(m) = 3.1 x 10(4) M(−1) s(−1).

YBaCuFeO5 is a multiferroic compound, which has the magnetic and dielectric transition temperature above 200 K. The multiferroic properties of the compound can be tuned by increasing the distortion or changing chemical pressure in the system. The structure can be distorted via non-magnetic substitution at Ba site or by replacing Y with some other rare earth ions. The partial replacement of Ba with Sr shifts the magnetic transition towards higher temperature while dielectric transition shifts towards lower temperature. Here we have investigated the thermal conductivity of the layered perovskite materials YBa1-xSrxCuFeO5 (x = 0, 0.25, 0.5) in the temperature range of 2 K to 300 K. Our results indicates that the thermal conductivity of the compound decreases upon Sr doping. The decrease in the thermal conductivity is due to the increase in various defects in the crystals such as point defects in the system.

Online instruction is a growing field, but there are concerns about lack of student engagement with mastery of content. Researchers at a small, private, southern university were concerned about increasing student engagement with online course content. A synchronous interactive online tool (SIOT) was added to six sections of online graduate education courses. Data was collected and analyzed from the university administered end of the course survey questions asking students to rate their course learning. Student survey responses were compared from courses without a SIOT, courses where a SIOT was used for office hours, and courses where a SIOT was used for assignments. The differences in the question means from end of the course survey without the SIOT and those where the SIOT was used for office hours were not significant. However, when the SIOT was used to provide instruction related to student assignments, the data from the question responses were significantly more positive. Students 1) became more confident; 2) gained an excellent understanding of the concepts; 3) gained significant knowledge; 4) learned to analyze and critically evaluate; and 5) learned to apply course concepts to solve problems. Consequently it became evident that the implementation of the SIOT did not have a significant effect. The important component that impacted students’ perception of their content understanding was the way in which the SIOT was used within the online course.

Background Presence of Kunitz trypsin inhibitor (KTI) in soybean seeds necessitates pre-heat treatment of the soy-flour for its inactivation before using it in food and feed products. The heat treatment not only enhances processing costs of the soy-based foods and feeds but also affects seed-protein quality and solubility. Genetic elimination of KTI is an important and effective approach. Therefore, molecular marker-assisted backcross breeding (MABB) approach was adopted for genetic elimination of KTI from two popular soybean genotypes, DS9712 and DS9814. PI542044, an exotic germplasm line was used as donor of the kti allele which inhibits functional KTI peptide production. Results Foreground selection for the kti allele was performed with three closely linked SSR markers while background selection was done with 93 polymorphic SSR markers. Plants in the BC1F1 generation were found to recover 70.4–87.63 % and 60.26–73.78 % of the recurrent parent genome (RPG) of DS9712 and DS9814, respectively. Similarly, selected plants in the BC2F1 generation had 93.01–98.92 % and 83.3–91.67 % recovery of their respective RPGs. Recombinant selection was performed so as to identify plants with minimal linkage drag. Biochemical analysis of the seeds of the selected plants (ktikti) confirmed absence of KTI peptides in the seeds. Phenotypically, the selected plants were comparable to the respective recurrent parent in yield and other traits. Conclusions MABB approach helped in speedy development of 6 KTI free breeding lines of soybean. Such lines will be suitable for the farmers and the soybean industries to use in production of soy-based foods and feeds without pre-heat treatment of the soy-flour. It would contribute towards wider acceptability of soy-based foods and feeds. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0413-2) contains supplementary material, which is available to authorized users.

Recovery of recurrent parent (DS9712) genome in BC1F1 generation. Table S2. Recovery of recurrent parent (DS9814) genome in BC1F1 generation. Table S3. Recovery of recurrent parent genome (RPG) in BC2F1 generation. Table S4. Recombinant selections in BC2F1 generation of DS9712 cross. Table S5. Mean performance of the BC2F2 families under field conditions. Table S6. Details of the SSR markers screened for parental polymorphism between the recurrent (DS9712) and donor parent (PI542044). Table S7. Details of the Simple Sequence Repeat markers screened for parental polymorphism between the recurrent (DS9814) and donor parent (PI542044). (DOC 605Â kb)

Recovery of recurrent parent (DS9712) genome in BC1F1 generation. Table S2. Recovery of recurrent parent (DS9814) genome in BC1F1 generation. Table S3. Recovery of recurrent parent genome (RPG) in BC2F1 generation. Table S4. Recombinant selections in BC2F1 generation of DS9712 cross. Table S5. Mean performance of the BC2F2 families under field conditions. Table S6. Details of the SSR markers screened for parental polymorphism between the recurrent (DS9712) and donor parent (PI542044). Table S7. Details of the Simple Sequence Repeat markers screened for parental polymorphism between the recurrent (DS9814) and donor parent (PI542044). (DOC 605Â kb)

Multiple sequence alignment (MSA) accuracy is important, but there is no widely accepted method of judging the accuracy that different alignment algorithms give. We present a simple approach to detecting two types of error, namely block shifts and the misplacement of residues within a gap. Given a MSA, subsets of very similar sequences are generated through the use of a redundancy filter, typically using a 70–90% sequence identity cut-off. Subsets thus produced are typically small and degenerate, and errors can be easily detected even by manual examination. The errors, albeit minor, are inevitably associated with gaps in the alignment, and so the procedure is particularly relevant to homology modelling of protein loop regions. The usefulness of the approach is illustrated in the context of the universal but little known [K/R]KLH motif that occurs in intracellular loop 1 of G protein coupled receptors (GPCR); other issues relevant to GPCR modelling are also discussed.

A decade since the availability of Mycobacterium tuberculosis (Mtb) genome sequence, no promising drug has seen the light of the day. This not only indicates the challenges in discovering new drugs but also suggests a gap in our current understanding of Mtb biology. We attempt to bridge this gap by carrying out extensive re-annotation and constructing a systems level protein interaction map of Mtb with an objective of finding novel drug target candidates. Towards this, we synergized crowd sourcing and social networking methods through an initiative `Connect to Decode' (C2D) to generate the first and largest manually curated interactome of Mtb termed `3interactome pathway' (IPW), encompassing a total of 1434 proteins connected through 2575 functional relationships. Interactions leading to gene regulation, signal transduction, metabolism, structural complex formation have been catalogued. In the process, we have functionally annotated 87% of the Mtb genome in context of gene products. We further combine IPW with STRING based network to report central proteins, which may be assessed as potential drug targets for development of drugs with least possible side effects. The fact that five of the 17 predicted drug targets are already experimentally validated either genetically or biochemically lends credence to our unique approach.

In this study, the null allele of Kunitz trypsin inhibitor i.e. kti was transferred from PI542044, a germplasm line free from KTI in to a popular Indian soybean variety DS9712 through marker assisted backcross breeding (MABB) approach. Following foreground selection with 3 SSR markers viz., Satt228, Satt429 and Satt409 that are linked to kti, and background selection with 93 polymorphic SSR markers in BC1F1 and BC2F1 generations, target plants were selected that had 96–98% recovery of the recurrent parent genome (RPG). In BC2F2 generation, plants homozygous the for target allele (kti kti) were identified and harvested individually. In BC2F3 generation, seed proteins of the selected lines were extracted and analyzed through native polyacrylamide gel electrophoresis (PAGE) and confirmed absence of the KTI peptides. Four lines were identified that were free from Kunitz trypsin inhibitor but retained nearly all of the phenotypic features of DS9712. This study exemplified successful elimination of KTI from soybean seeds through MABB approach.

Une etude experimentale examine l'effet, chez des apprenants en espagnol L2, d'activites permettant aux etudiants d'acquerir de maniere dynamique une conscience des strategies d'apprentissage de la langue

A novel rearrangement of 3, 4-dihydro-2, 2-dimethyl-2H, 5H-pyrano [2, 3-b] [1] benzopyran-5-ones (dihydropyranochromones) has been observed during the dehydrogenation with DDQ. The products obtained are found to be 2, 2-dimethyl-2H, 5H-pyrano [3, 2-c] [1] benzopyran-5-ones (pyranocoumarins).

Cinnamylation par le phenyl-3 propene-2 ol-1 de dihydroxy-2',4' et trihydroxy-2',3',4' acetophenones, de chloro-4 phenol ou de resorcinol en presence d'acide phosphorique a 75-80°C: obtention de flavanes