Pcal_0768, a hyperactive 4-α-glucanotransferase from <Emphasis Type="Italic">Pyrobacculum calidifontis</Emphasis>

Genome sequence of hyperthermophilic archaeon Pyrobaculum calidifontis revealed the presence of an open reading frame, Pcal_0768, corresponding to a putative 4-α-glucanotranferase belonging to glycoside hydrolases (GH) family 77. We have produced, in Escherichia coli, and purified recombinant Pcal_0768 which exhibited high disproportionation (690 U mg^?1) activity. To the best of our knowledge, this is the highest ever reported activity for any member of family GH77. Maltooligosaccharides, when used as sole substrates, were disproportionated into linear maltooligohomologues. The analysis of the reaction end products revealed no evidence for the production of cycloamyloses. Catalytic activity of the enzyme remained unchanged in the presence or the absence of ionic and nonionic detergents. γ-cyclodextrin, an inhibitor of 4-α-glucanotransferases, did not show any inhibitory effect on Pcal_0768 activity. These properties make Pcal_0768 a potential candidate for starch processing industry.     

CLUSTOM-CLOUD: In-Memory Data Grid-Based Software for Clustering 16S rRNA Sequence Data in the Cloud Environment

High-throughput sequencing can produce hundreds of thousands of 16S rRNA sequence reads corresponding to different organisms present in the environmental samples. Typically, analysis of microbial diversity in bioinformatics starts from pre-processing followed by clustering 16S rRNA reads into relatively fewer operational taxonomic units (OTUs). The OTUs are reliable indicators of microbial diversity and greatly accelerate the downstream analysis time. However, existing hierarchical clustering algorithms that are generally more accurate than greedy heuristic algorithms struggle with large sequence datasets. To keep pace with the rapid rise in sequencing data, we present CLUSTOM-CLOUD, which is the first distributed sequence clustering program based on In-Memory Data Grid (IMDG) technology–a distributed data structure to store all data in the main memory of multiple computing nodes. The IMDG technology helps CLUSTOM-CLOUD to enhance both its capability of handling larger datasets and its computational scalability better than its ancestor, CLUSTOM, while maintaining high accuracy. Clustering speed of CLUSTOM-CLOUD was evaluated on published 16S rRNA human microbiome sequence datasets using the small laboratory cluster (10 nodes) and under the Amazon EC2 cloud-computing environments. Under the laboratory environment, it required only ~3 hours to process dataset of size 200 K reads regardless of the complexity of the human microbiome data. In turn, one million reads were processed in approximately 20, 14, and 11 hours when utilizing 20, 30, and 40 nodes on the Amazon EC2 cloud-computing environment. The running time evaluation indicates that CLUSTOM-CLOUD can handle much larger sequence datasets than CLUSTOM and is also a scalable distributed processing system. The comparative accuracy test using 16S rRNA pyrosequences of a mock community shows that CLUSTOM-CLOUD achieves higher accuracy than DOTUR, mothur, ESPRIT-Tree, UCLUST and Swarm. CLUSTOM-CLOUD is written in JAVA and is freely available at http://clustomcloud.kopri.re.kr.     

Senescence in Detached Oat Leaves II. Identification and Changes in the Activity Levels of Aminopeptidases

Five aminopeptidases have been identified in the leaves of 7-dayold oat seedlings. Three aminopeptidases were able to hydrolyseL-Met ßNA, and two were active towards L-Arg ßNA.Only one of the enzymes (AP1) could cleave a variety of aminoacid residues. The enzymes active toward L-Met ßNA,L-Arg ßNA and L-Ala ßNA had pH optima 7.6,8.2 and 8.3 respectively. All the enzymes were fully activein the presence of various catalytic inhibitors tested, except1,10-phenanthroline which inhibited the activity of all theaminopeptidases, but only at a very high concentration (10mM).The activity levels of three types of aminopeptidases testedin the crude leaf extract decreased during the senescence ofoat leaves. ¹Present address: C. F. Kettering Research Laboratory, 150 EastSouth College Street, Yellow Springs, Ohio 45387, U.S.A. (Received November 4, 1982; Accepted June 1, 1983)     

A simple enzymeimmunoassay of milk progesterone for monitoring fertility in dairy buffaloes

A simple, sensitive, direct (without extraction) enzymeimmunoassay (EIA) was usec to determine progesterone levels in whole milk samples of 400 Nili-Ravi dairy buffaloes. The mean progesterone values 22 d after A.I. were significantly higher in pregnant (16.6 +/- 9.2 ng/ml) than nonpregnant (below 5 ng/ml) animals. The mean progesterone values were below 0.34 +/- 0.12 (the detection limit) both at estrus and in cases of clinically diagnosed inactive ovaries, 3.18 +/- 1.9 at proestrus, 2.25 +/- 1.2 postestrus and 13.22 +/- 6.74 at Day 10 of the estrous cycle. Twenty buffaloes confirmed pregnant for 2 to 3 mo, had a mean value of 20.3 +/- 4.5 ng/ml. The EIA test is very reliable in the selection of nonpregnant buffaloes (100 %) and the confirmation of inactive ovaries and of estrus. Differential diagnosis of inactive or active ovaries can be made by analyzing two milk samples at a 7-d interval.     

In vitro selection for Fusarium wilt resistance in Gladiolus

Cormels pieces of four Fusarium susceptible Gladiolus cultivara (Friendship, Peter Pears, Victor Borge and Novalux) formed friable calli when cultured in vitro on Murashige and Skoog basal medium containing various concentrations of auxin and cytokinin. The friable calli established cell suspensions. Plantlet regeneration was obtained from the control callus, control cell suspension derived callus and in vitro selected Fusarium oxysporum Schlecht. resistant cell-lines of Friendship. The in vitro cormlets showed 85-95% germination after breaking dormancy of 8weeks at 4℃. Cell suspensions of all four Gladiolus cultivara were found to be highly sensitive to fusaric acid. Gradual Increase in fusaric acid concentrations to the cell-suspension cultures decreased cell growth considerably. One albino plant was found from the second generation of the In vitro selected cell line of Friendship. The albino plant was found to be highly susceptible to F. oxysporum. The cormlets of all in vitro selected call lines of Friendship were inoculated with a conidial suspension of the F. oxysporum before planting and were also sprayed with the same spore suspension for further characterization when the height of plants was about 6cm. The four selected cell lines showed the same response whether or not they were Inoculated with conidia of the F. oxysporum. Plantlets of all of the selected call lines exhibited significant growth as compared with the control after application of conidia of the F.oxysporum.     

Computational simulations assessment of mutations impact on streptokinase (SK) from a group G streptococci with enhanced activity – insights into the functional roles of structural dynamics flexibility of SK and stabilization of SK–μplasmin catalytic complex

Streptokinase (SK), a plasminogen activator (PA) that converts inactive plasminogen (Pg) to plasmin (Pm), is a protein secreted by groups A, C, and G streptococci (GAS, GCS, and GGS, respectively), with high sequence divergence and functional heterogeneity. While roles of some residual changes in altered SK functionality are shown, the underlying structural mechanisms are less known. Herein, using computational approaches, we analyzed the conformational basis for the increased activity of SK from a GGS (SKG132) isolate with four natural residual substitutions (Ile33Phe, Arg45Gln, Asn228Lys, Phe287Ile) compared to the standard GCS (SKC). Using the crystal structure of SK.Pm catalytic complex as main template SKC.μPm catalytic complex was modeled through homology modeling process and validated by several online validation servers. Subsequently, SKG132.μPm structure was constructed by altering the corresponding residual substitutions. Results of three independent MD simulations showed increased RMSF values for SKG132.μPm, indicating the enhanced structural flexibility compared to SKC.μPm, specially in 170 and 250 loops and three regions: R1 (149–161), R2 (182–215) and R3 (224–229). In parallel, the average number of Hydrogen bonds in 170 loop, R2 and R3 (especially for Asn228Lys) of SKG132 compared to that of the SKC was decreased. Accordingly, residue interaction networks (RINs) analyses indicated that Asn228Lys might induce more level of structural flexibility by generation of free Lys256, while Phe287Ile and Ile33Phe enhanced the stabilization of the SKG132.μPm catalytic complex. These results denoted the potential role of the optimal dynamic state and stabilized catalytic complex for increased PA potencies of SK as a thrombolytic drug.