Translational Research

Identification of a biosynthetic gene cluster for the polyene macrolactam sceliphrolactam in a Streptomyces strain isolated from mangrove sediment

Published date : 25 Jan 2018

Streptomyces are a genus of Actinobacteria capable of producing structurally diverse natural products. Here we report the isolation and characterization of a biosynthetically talented Streptomyces (Streptomyces sp. SD85) from tropical mangrove sediments. Whole-genome sequencing revealed that Streptomyces sp. SD85 harbors at least 52 biosynthetic gene clusters (BGCs), which constitute 21.2% of the 8.6-Mb genome. When cultivated under lab conditions, Streptomyces sp. SD85 produces sceliphrolactam, a 26-membered polyene macrolactam with unknown biosynthetic origin.

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Journal Paper
journal
Scientific Reports 8, Article no. 1594 (2018), doi:10.1038/s41598-018-20018-8
Impact Factor
4.259

The effects of Antibody Engineering CH and CL in Trastuzumab and Pertuzumab recombinant models: Impact on antibody production and antigen-binding

Published date : 15 Jan 2018

Current therapeutic antibodies such as Trastuzumab, are typically of the blood circulatory IgG1 class (Cκ/ CHγ1). Due to the binding to Her2 also present on normal cell surfaces, side effects such as cardiac failure can sometimes be associated with such targeted therapy. Using antibody isotype swapping, it may be possible to reduce systemic circulation through increased tissue localization, thereby minimising unwanted side effects. However, the effects of such modifications have yet to be fully characterized, particularly with regards to their biophysical properties in antigen binding.

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Journal Paper
journal
Scientific Reports 8, Article no 718, 2018, doi:10.1038/s41598-017-18892-9
Impact Factor
4.259

Modeling the full length HIV-1 Gag polyprotein reveals the role of its p6 subunit in viral maturation and the effect of non-cleavage site mutations in protease drug resistance

Published date : 13 Dec 2017

HIV polyprotein Gag is increasingly found to contribute to protease inhibitor resistance. Despite its role in viral maturation and in developing drug resistance, there remain gaps in the knowledge of the role of certain Gag subunits (e.g. p6), and that of non-cleavage mutations in drug resistance. As p6 is flexible, it poses a problem for structural experiments, and is hence often omitted in experimental Gag structural studies.

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Journal Paper
journal
Journal of Biomolecular Structure and Dynamics, 2017, Pg 1-40, doi: 10.1080/07391102.2017.1417160

A yeast two-hybrid system for the screening and characterization of small-molecule inhibitors of protein–protein interactions identifies a novel putative Mdm2-binding site in p53

Published date : 09 Nov 2017

Background: Protein–protein interactions (PPIs) are fundamental to the growth and survival of cells and serve as excellent targets to develop inhibitors of biological processes such as host-pathogen interactions and cancer cell proliferation. However, isolation of PPI inhibitors is extremely challenging. While several in vitro assays to screen for PPI inhibitors are available, they are often expensive, cumbersome, and require large amounts of purified protein. In contrast, limited in vivo assays are available to screen for small-molecule inhibitors of PPI.

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Journal Paper
journal
BMC Biology 2017 15:108, doi: 10.1186/s12915-017-0446-7
Impact Factor
6.779

APD volumetric app: android app for the quantification of reagents

Published date : 03 Nov 2017

Quantifying reagents is a necessity in laboratory experiment planning but to do so with reasonable accuracy is a challenge when using unmarked containers. While there are volumetric measuring cylinders, the demand of sterility and purity in many experiments prevent their use in a feasible fashion. As a result, experienced estimation is usually relied upon, but this is fairly subjective, and may lead to large margins of error.

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Journal Paper
journal
Scientific Phone Apps and Mobile Devices (2017) 3:7, doi: 10.1186/s41070-017-0019-8

Thyroid-SPOT for mobile devices: personalised thyroid treatment management app

Published date : 30 Aug 2017

Thyroid-SPOT is a mobile application that allows users to be able to analyse thyroid function tests laboratory reports by computing the homeostatic euthyroid set point based on regressing thyroid function data according to a patented algorithm to define the parameters that maximize the goodness-of-fit to a negative exponential model for target-centric individualized treatment.

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Journal Paper
journal
Scientific Phone Apps and Mobile Devices 2017, 3:4 doi: 10.1186/s41070-017-0016-y

The role of Antibody Vκ Framework 3 region towards Antigen binding: Effects on recombinant production and Protein L binding

Published date : 19 Jun 2017

Antibody research has traditionally focused on heavy chains, often neglecting the important complementary role of light chains in antibody formation and secretion. In the light chain, the complementarity-determining region 3 (VL-CDR3) is specifically implicated in disease states. By modulating VL-CDR3 exposure on the scaffold through deletions in the framework region 3 (VL-FWR3), we further investigated the effects on secretion in recombinant production and antigen binding kinetics.

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Journal Paper
journal
Scientific Reports 7, Article no: 3766 (2017), doi:10.1038/s41598-017-02756-3
Impact Factor
4.259

APD SpectBT: Arduino-based mobile vis-Spectrophotometer

Published date : 14 Mar 2017

Quantification of samples is an integral step in numerous biological and chemical experiments. Spectrophotometers are often used together with colorimetric assays that react with the compound of interest in the samples. However, spectrophotometers are often costly, bulky and immobile. To increase the convenience and ease the process of spectrophotometry, the APD SpectBT was developed using the Arduino-based platform to create a smartphone dependent mobile spectrophotometer.

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Journal Paper
journal
Nature Methods Application Notes 2017

Discovery of a novel splice variant of Fcar (CD89) unravels sequence segments necessary for efficient secretion: a story of bad signal peptides and good ones that nevertheless do not make it

Published date : 19 Jan 2017

The IgA receptor, Fcar (CD89) consists of five sequence segments: two segments (S1, S2) forming the potential signal peptide, two extracellular EC domains that include the IgA binding site, and the transmembrane and cytoplasmic tail (TM/C) region. Numerous Fcar splice variants have been reported with various combinations of the sequence segments mentioned above. Here, we report a novel splice variant termed variant APD isolated from a healthy volunteer that lacks only the IgA-binding EC1 domain.

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Journal Paper
journal
Cell Cycle 2016, doi: 10.1080/15384101.2017.1281480
Impact Factor
3.952

Structural analyses of 2015-updated drugresistant mutations in HIV-1 protease: an implication of protease inhibitor crossresistance

Published date : 16 Dec 2016

Background: Strategies to control HIV for improving the quality of patient lives have been aided by the Highly Active Anti-Retroviral Therapy (HAART), which consists of a cocktail of inhibitors targeting key viral enzymes. Numerous new drugs have been developed over the past few decades but viral resistances to these drugs in the targeted viral enzymes are increasingly reported. Nonetheless the acquired mutations often reduce viral fitness and infectivity.

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Journal Paper
journal
BMC Bioinformatics 2016, 17(Suppl 19):500 doi: 10.1186/s12859-016-1372-3
Impact Factor
2.435