The Multidimensional Imaging Center (MDIC) is an imaging service facility and one of the three Technology Incubation Core Facilities (TICF), specializing in viewing biological samples and characterizing various materials. As part of the TICF, the MDIC aims to serve scientists and researchers in the respective research thrusts and endeavours by providing their technical needs in accurate imaging of both biological and non- biological samples.
Currently, the facility houses a wide array of light-based microscopes and other laboratory equipment, as well as an atomic force microscope. Technical assistance and consultation is also available to assist researchers in acquiring the best and clearest images for their needs.
Available services:
Other available equipment:
Molecular Biology & Biotechnology Studies Centre is an ISO accredited facility and benefits from an isolated containment level 3 facility for processing highly contagious pathogens.
Disease Molecular Biology and Epigenetics Laboratory (DMBEL)
The Laboratory Services arm of the Disease Molecular Biology and Epigenetics Laboratory (DMBEL) offers a suite of mostly cell-based assays to serve the needs of DOST-funded drug discovery projects as well as third-party clients.Bioactive hits from primary screens can be tested for drug-induced hepato-, nephro- and cardiotoxicity, which are responsible for high attrition rates in early-stage drug discovery. Confirmatory orthogonal and secondary assays are also available to eliminate artefactual drug bioactivities from primary screens due to pan-assay interference compounds and color effects. Most assays are in 96- or 384-well format and some are pathway-specific,thus providing clues on mechanism of action or the signaling cascade in which an extract/compound impinges. High-content imaging (using GE Healthcare’s IN Cell Analyzer 6000) is used in many of the assays, allowing more physiologically relevant readouts that are able to visualize subcellular and organelle phenomena.The medium-to-high throughput nature of HCI also affords multi-parametric information from each sample and even from individual cells, delivering different insights on a compound’s mode of action and/or non-specific effects early on.
The 16S rRNA gene has been a mainstay of sequence-based bacterial analysis for decades. However, high-throughput sequencing of the full gene has only recently become a realistic prospect. Here, we use in silico and sequence-based experiments to critically re-evaluate the potential of the 16S gene to provide taxonomic resolution at species and strain level. We demonstrate that targeting of 16S variable regions with short-read sequencing platforms cannot achieve the taxonomic resolution afforded by sequencing the entire (~1500 bp) gene. We further demonstrate that full-length sequencing platforms are sufficiently accurate to resolve subtle nucleotide substitutions (but not insertions/deletions) that exist between intragenomic copies of the 16S gene. In consequence, we argue that modern analysis approaches must necessarily account for intragenomic variation between 16S gene copies. In particular, we demonstrate that appropriate treatment of full-length 16S intragenomic copy variants has the potential to provide taxonomic resolution of bacterial communities at species and strain level.
Since the advent of high-throughput sequencing, PCR-amplified 16S sequences have typically been clustered based on similarity to generate operational taxonomic units (OTUs) and representative OTU sequences compared with reference databases to infer likely taxonomy. Although convenient and powerful, such usage of 16S has necessitated certain assumptions, e.g., the now historic assumption that sequences of > 95% identity represent the same genus, whereas sequences of > 97% identity represent the same species.
The ~1500 bp 16S rRNA gene comprises nine variable regions interspersed throughout the highly conserved 16S sequence. Sequencing the entire gene was originally accomplished by Sanger sequencing. This required cloning genes, generating, and assembling two to three reads per clone, and producing limited sampling depth at high cost and effort. Currently, however, the vast majority of studies sequence only part of the gene, because the widely used Illumina sequencing platform (higher throughput, lower cost, reduced effort compared with Sanger) produces short sequences ( ≤ 300 bases). Different sub-regions of the gene are therefore targeted, ranging from single variable regions, such as V4 or V6, to three variable regions, such as V1–V3 or V3–V5 (used in the Human Microbiome Project in conjunction with the 454 sequencing platform)