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.     

Antiplasmodial and Cytotoxic Activities of Extract and Compounds from Ozoroa obovata (Oliv.) R. & A. Fern. var. obovata

Ozoroa obovata (Oliv.) R. & A. Fern. var. obovata found in KwaZulu-Natal in South Africa was investigated for phytochemical constituents, and for antiplasmodial and cytotoxic effects. The plant leaves were collected from the University of KwaZulu-Natal (UKZN) arboretum on the Pietermaritzburg Campus, in March 2019. The inhibitory activity against 3D7 Plasmodium falciparum was determined using the parasite lactate dehydrogenase (pLDH) assay and cytotoxicity against HeLa cells was evaluated using the resazurin assay. The bioactive compounds were isolated by chromatographic purification and their structures were established with spectroscopic and spectrometric techniques. The plant leaf extract displayed significant antiplasmodial activity at 50 μg/mL and was also cytotoxic against HeLa cells. Chromatographic purification of the extract led to the isolation of two biflavonoids, four flavonoid glycosides, a steroid glycoside, and a megastigmene derivative. The compounds displayed antiplasmodial and antiproliferative activities at 50 μg/mL but the activity was substantially reduced at 10 μg/mL. The activities and compounds are being reported in O. obovata for the first time.     

Oncolytic adenovirus: A tool for cancer therapy in combination with other therapeutic approaches

Cancer therapy using oncolytic viruses is an emerging area, in which viruses are engineered to selectively propagate in tumor tissues without affecting healthy cells. Because of the advantages that adenoviruses (Ads) have over other viruses, they are more considered. To achieve tumor selectivity, two main modifications on Ads genome have been applied: small deletions and insertion of tissue- or tumor-specific promoters. Despite oncolytic adenoviruses ability in tumor cell lysis and immune responses stimulation, to further increase their antitumor effects, genomic modifications have been carried out including insertion of checkpoint inhibitors and antigenic or immunostimulatory molecules into the adenovirus genome and combination with dendritic cells and chemotherapeutic agents. This study reviews oncolytic adenoviruses structures, their antitumor efficacy in combination with other therapeutic strategies, and finally challenges around this treatment approach.     

Termites Improve the Horizontal Movement of Carbonized Particles: A Step towards Sustainable Utilization of Biochar

Soil amendments containing carbonized materials increase the soil carbon reservoir, influence plant productivity, and, ultimately, help to clean the environment. There is data on the effect of such additions on soil physicochemical properties or plant growth, but few studies have focused on how these carbonized materials are distributed by termite species in the soil ecosystem. It is the first comprehensive study of the transportation of biochar (BC) by termite species under tropical environmental conditions in Pakistan. The present study was carried out to test the hypothesis that if termite species I) were involved in the distribution of biochar particles II) if yes, then how far these particles were transported during the study period (10 days) and III) check their preference between the enriched BC (EBC) and non-enriched BC. BC was enriched with the cattle slurry after its pyrolysis in the study. The results showed that EBC particles were significantly more widely distributed than non-enriched BC particles, but both types of BC were transported more than 4 cm (ring 4) within 10 days (at the end of the experiment). The current study also revealed that EBC was easily attached to the setae, cuticle, and legs of termites, implying that it could potentially be transported over a greater distance. Furthermore, transportation of EBC over larger distances indicated a potential preference of termite species between the EBC and BC particles. During the study, however, the preference among the termite species was also observed. Under the prevailing study conditions, the Coptotermes heimi and Heteroterme indicola species transported the EBC further than Microtermes obesi and Odontotermes obesus. These findings revealed that transportation preferences were observed among the four termite species. In conclusion, the current study found that termites were involved in the distribution of BC particles, with a preference for EBC and that these have the potential to transport BC particles more than 4 cm within 10 days. Furthermore, two species Coptotermes heimi and Heteroterme indicola may be more suitable candidates for EBC transpiration in Pakistani soils. It was necessary to conduct additional research into the effect of temperature on the transportation process.     

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.     

Prevalence of Neospora caninum antibodies in sheep and goats in Pakistan

The purpose of the present study was to obtain seroepidemiological information on the Neospora caninum infection status of sheep and goats in different areas of Punjab Province and Azad Kashmir (Pakistan). A cross-sectional study, with the use of a competitive ELISA, showed an overall 27.7% (35 of 128) (95% confidence interval [CI] ± 7.7%) and 8.6% (13 of 142) (95% CI ± 4.6%) seroprevalence of N. caninum antibodies in sheep and goats, respectively. The difference in seroprevalence between sheep and goat populations was statistically significant (P < 0.05). The highest prevalence (37.4% ± 13.2%) was recorded in the tailless breed of sheep.     

Production of biogas from solid organic wastes through anaerobic digestion: a review

Anaerobic digestion treatments have often been used for biological stabilization of solid wastes. These treatment processes generate biogas which can be used as a renewable energy sources. Recently, anaerobic digestion of solid wastes has attracted more interest because of current environmental problems, most especially those concerned with global warming. Thus, laboratory-scale research on this area has increased significantly. In this review paper, the summary of the most recent research activities covering production of biogas from solid wastes according to its origin via various anaerobic technologies was presented.