Deletion studies for elucidating the role of Streptomyces griseus ChiC non-catalytic residues

The soil bacterium, Streptomyces griseus, produces an antifungal chitinase (SgChiC) which has a smaller catalytic domain (in addition to a chitin binding domain) when compared with its counterparts from plants. Here, we carried out rational deletion of residues distant from the active site residues in the catalytic domain from 205 to 49 amino acid residues. The truncated residues were reconstructed and its 3-dimendional model predicted by homology modeling. In an insilico binding study, tri-N-acetyl glucosamine ((GlCNAc)3) was observed to bind to the active site of the truncated model similarly as in the wild type catalytic domain. This suggests that the variant model of SgChiC with a truncated catalytic domain possibly retains its chitinolytic properties. Further analysis of the simulation results revealed an increase in conformational space and flexibility of the reconstructed model over the less dynamic structure of the wild-type model. This suggests that the deleted residues played a role in the compactness and rigidity of the domain. Experimental assays to investigate the hydrolytic and kinetic properties of this truncated variant are currently been carried out. Outcomes of this study will reveal the relationship between the architecture of the ChiC domain and its function. This will guide future design studies for the enhancement of its functional properties and consequently its efficiency as a biocontrol agent.

Early resumption of sexual intercourse and its determinants among postpartum Iban mothers

Introduction: Recurrent pregnancy with close child spacing can result from early resumption of sexual intercourse during the postpartum period. This would expose mothers to complications such as unsafe abortion, postpartum depression and premature birth. The aim of this study is to identify the factors associated with early resumption of sexual intercourse among postpartum Iban mothers.Methods: This is a cross sectional study conducted in Sri Aman Division, Sarawak between 1st July and 31st August 2006. A total of 265 Iban mothers agreed to participate in this study. They were interviewed face-to-face using structured questionnaire. Any postpartum sexual intercourse at 6 weeks or less is considered an early resumption of sexual intercourse.Results: Univariable analyses showed significant association between early sexual intercourse and use of contraceptive; mothers’ and husbands’ income; mothers who believed their husbands were sexually abstinent during their confinement period; mothers who stayed with their spouse after delivery; and those with high libido. Multivariable analysis showed only mothers’ and husbands’ income, use of contraceptive and those who believed their husbands practiced sexual abstinence during their confinement period were significantly associated with early resumption of sexual intercourse. Conclusions: Counselling on postpartum resumption of sexual intercourse among Iban mothers should focus on these determinants to ensure a more effective counselling outcome among Iban mothers

A benchmark of modeling for sentiment analysis of the Indonesian Presidential Election in 2019

Researching with a machine learning method approach, the truth is to try to solve a case by using various algorithmic approaches to obtain the most suitable model for a case. In this research, we want to know which process of modelling that has the best accuracy value for classifying emotions in the text. The algorithm used is using the LSTM algorithm, while the benchmarking that we tested is the Random Forest and Naive Bayes algorithm. This research takes public opinion about the 2019 Indonesian Presidential Election by classifying it into four types of emotions: happy, sad, angry, and afraid. The data we use contains more than 1200 Indonesian tweets. In this experiment, we achieved an accuracy of 68.25% using the Random Forest model, whereas, with the Multinomial Naïve Bayes model, the accuracy was 66%

Thermostable lipases and their dynamics of improved enzymatic properties

Thermal stability is one of the most desirable characteristics in the search for novel lipases. The search for thermophilic microorganisms for synthesising functional enzyme biocatalysts with the ability to withstand high temperature, and capacity to maintain their native state in extreme conditions opens up new opportunities for their biotechnological applications. Thermophilic organisms are one of the most favoured organisms, whose distinctive characteristics are extremely related to their cellular constituent particularly biologically active proteins. Modifications on the enzyme structure are critical in optimizing the stability of enzyme to thermophilic conditions. Thermostable lipases are one of the most favourable enzymes used in food industries, pharmaceutical field, and actively been studied as potential biocatalyst in biodiesel production and other biotechnology application. Particularly, there is a trade-off between the use of enzymes in high concentration of organic solvents and product generation. Enhancement of the enzyme stability needs to be achieved for them to maintain their enzymatic activity regardless the environment. Various approaches on protein modification applied since decades ago conveyed a better understanding on how to improve the enzymatic properties in thermophilic bacteria. In fact, preliminary approach using advanced computational analysis is practically conducted before any modification is being performed experimentally. Apart from that, isolation of novel extremozymes from various microorganisms are offering great frontier in explaining the crucial native interaction within the molecules which could help in protein engineering. In this review, the thermostability prospect of lipases and the utility of protein engineering insights into achieving functional industrial usefulness at their high temperature habitat are highlighted. Similarly, the underlying thermodynamic and structural basis that defines the forces that stabilize these thermostable lipase is discussed

Integrative structural and computational biology of phytases for the animal feed industry

Resistance to high temperature, acidic pH and proteolytic degradation during the pelleting process and in the digestive tract are important features of phytases as animal feed. The integration of insights from structural and in silico analyses into factors affecting thermostability, acid stability, proteolytic stability, catalytic efficiency and specific activity, as well as N-glycosylation, could improve the limitations of marginal stable biocatalysts with trade-offs between stability and activity. Synergistic mutations give additional benefits to single substitutions. Rigidifying the flexible loops or inter-molecular interactions by reinforcing non-bonded interactions or disulfide bonds, based on structural and roof mean square fluctuation (RMSF) analyses, are contributing factors to thermostability. Acid stability is normally achieved by targeting the vicinity residue at the active site or at the neighboring active site loop or the pocket edge adjacent to the active site. Extending the positively charged surface, altering protease cleavage sites and reducing the affinity of protease towards phytase are among the reported contributing factors to improving proteolytic stability. Remodeling the active site and removing steric hindrance could enhance phytase activity. N-glycosylation conferred improved thermostability, proteases degradation and pH activity. Hence, the integration of structural and computational biology paves the way to phytase tailoring to overcome the limitations of marginally stable phytases to be used in animal feeds

Orbital inflammation and colitis in pediatric IgG4-related disease: A case report and review of the literature.

IgG4-related disease (IgG4-RD) is an inflammatory disorder characterized by tumor-like swelling in one or more organs, elevated serum IgG4 levels, and histological alterations with infiltration of IgG4-positive plasma cells. IgG4-RD is rare and likely underdiagnosed in children. We report a case of a 16-year-old girl with IgG4-positive colitis that developed weeks after IgG4-related ophthalmic disease and discuss diagnosis and treatment in the context of the literature available. Since the pathophysiology of IgG4-RD is unknown, treatment options are empiric and, for the most part, untargeted. Systemic corticosteroid treatment is the basis of anti-inflammatory treatment in IgG4-RD and induced early remission in our patient. During corticosteroid taper, the patient developed weight loss and intestinal inflammation. Histopathological assessment of the intestinal walls confirmed IgG4-positive colitis. Immune-modulating treatment with non-biologic (e.g., methotrexate (MTX) and mycophenolate mofetil) or biologic (rituximab) disease-modifying antirheumatic drugs has been reported in treatment refractory or corticosteroid-dependent patients. The patient responded to treatment with anti-inflammatory therapy with food rich in TGF-β2 (modulen) and MTX. This is one of the first pediatric patients reported with IgG4-related colitis extending the phenotype of pediatric IgG4-RD. International collaboration to prospectively document clinical presentation and treatment responses may help to further establish the phenotype and treatment options and to raise awareness for IgG4-RD

Trapping of Intermediates with Substrate Analog HBOCaA in the Polymerizations Catalyzer by Class III Polyhydroxybutyrate (PHB) Synthase from Allochromatium Vinosum

Polyhydroxybutyrate (PHB) synthases (PhaCs) catalyze the formation of biodegradable PHB polymers that are considered as an ideal alternative to petroleum-based plastics. To provide strong evidence for the preferred mechanistic model involving covalent and noncovalent intermediates, a substrate analog HBOCoA was synthesized chemoenzymatically. Substitution of sulfur in the native substrate HBCoA with an oxygen in HBOCoA enabled detection of (HB)nOCoA (n = 2–6) intermediates when the polymerization was catalyzed by wild-type (wt-)PhaECAv at 5.84 hr−1. This extremely slow rate is due to thermodynamically unfavorable steps that involve formation of enzyme-bound PHB species (thioesters) from corresponding CoA oxoesters. Synthesized standards (HB)nOCoA (n = 2–3) were found to undergo both reacylation and hydrolysis catalyzed by the synthase. Distribution of the hydrolysis products highlights the importance of the penultimate ester group as previously suggested. Importantly, the reaction between primed synthase [3H]-sT-PhaECAv and HBOCoA yielded [3H]-sTet-O-CoA at a rate constant faster than 17.4 s−1, which represents the first example that a substrate analog undergoes PHB chain elongation at a rate close to that of the native substrate (65.0 s−1). Therefore, for the first time with a wt-synthase, strong evidence was obtained to support our favored PHB chain elongation model

Ability of T1 lipase to degrade amorphous P(3HB): structural and functional study

An enzyme with broad substrate specificity would be an asset for industrial application. T1 lipase apparently has the same active site residues as polyhydroxyalkanoates (PHA) depolymerase. Sequences of both enzymes were studied and compared, and a conserved lipase box pentapeptide region around the nucleophilic serine was detected. The alignment of 3-D structures for both enzymes showed their active site residues were well aligned with an RMSD value of 1.981 Å despite their sequence similarity of only 53.8%. Docking of T1 lipase with P(3HB) gave forth high binding energy of 5.4 kcal/mol, with the distance of 4.05 Å between serine hydroxyl (OH) group of TI lipase to the carbonyl carbon of the substrate, similar to the native PhaZ7 Pl . This suggests the possible ability of T1 lipase to bind P(3HB) in its active site. The ability of T1 lipase in degrading amorphous P(3HB) was investigated on 0.2% (w/v) P(3HB) plate. Halo zone was observed around the colony containing the enzyme which confirms that T1 lipase is indeed able to degrade amorphous P(3HB). Results obtained in this study highlight the fact that T1 lipase is a versatile hydrolase enzyme which does not only record triglyceride degradation activity but amorphous P(3HB) degradation activity as well

A virtual screening approach for identifying plants with anti H5N1 neuraminidase activity

Recent outbreaks of highly pathogenic and occasional drug-resistant influenza strains have highlighted the need to develop novel anti-influenza therapeutics. Here, we report computational and experimental efforts to identify influenza neuraminidase inhibitors from among the 3000 natural compounds in the Malaysian-Plants Natural-Product (NADI) database. These 3000 compounds were first docked into the neuraminidase active site. The five plants with the largest number of top predicted ligands were selected for experimental evaluation. Twelve specific compounds isolated from these five plants were shown to inhibit neuraminidase, including two compounds with IC50 values less than 92 μM. Furthermore, four of the 12 isolated compounds had also been identified in the top 100 compounds from the virtual screen. Together, these results suggest an effective new approach for identifying bioactive plant species that will further the identification of new pharmacologically active compounds from diverse natural-product resources