ZIAUDDIN UNIVERSITY MULTIDSCIPLINARY RESEARCH LAB FACILITY

INTRODUCTION

Research excellence in all fields of study is central to the mission of Ziauddin University and a pinnacle priority, as the key element to success of the University’s academic profile that need to be preserved. ZU community is in continued pursuit of ever greater accomplishments in research through our commitment to innovation, excellence and quality. We share new knowledge for educating and inspiring tomorrow’s leaders as University is all about generation of new knowledge through research. The ZU faculty maintains active research laboratories that are exploring existing questions, spanning from the most basic to the most translational aspects of health sciences research. Everybody should feel free to communicate directly with faculty to explore the availability of research opportunities and specific areas of investigation

 

CORE FACILITY SERVICES

Ziauddin University is offering core lab services to the researchers at national level at an affordable cost such as RNA isolation, DNA isolation, reverse transcription, primer designing, PCR, RFLP, gel electrophoresis, gel imaging, nucleic acid sequence analysis, ELISA, HPLC, routine and specialized histological techniques along with high resolution microscopy and advanced imaging technology.

Multidisciplinary Research Laboratories

Multidisciplinary Research Laboratory 1 (MDRL 1)

Welcome to MDRL 1. Through support from the Faculty of Health Sciences, we foster excellence in investigator-led genomics studies. The core provides genomics service to investigators at the Ziauddin University access to high content cutting edge technologies, education and technical expertise.

Core personnel continue to stay abreast of technological advances that will impact the research efforts of faculty, staff, fellows and students. We encourage to contact our research scientists to arrange for consultation or to provide feedback. Our staff is available to share their experience and expertise to help with development of projects of all caliber, standard or custom assay design, and any other specialized application needs.

MDRL 1 is a University Core Research Facility with shared resources that operate high-content and high-throughput technologies for basic and translational genomic research.

Our laboratory offer DNA and RNA extraction services for blood, tissue, frozen tissues cultured cells and other biological samples. Quality and quantity assessment of nucleic acid samples, and gene amplification are also available.

DNA Analysis

Genomics Research Core Staff will work with you to provide solutions for your sequencing and genotyping needs. The choice of assay platforms is based on project goals and throughput needs.

 

DNA Extraction

DNA extraction is available for whole blood, tissue, cultured cells, buccal cells, and saliva. Standard quantification is by spectrophotometer 260nm/280nm ratio.

 

PCR Services

Custom PCR and RT-PCR services for human, bacterial, viral, animal, and plant tissues.
PCR assays are available to detect bacterial, viral and protozoal pathogens in human and animal tissues. Some of the common uses of PCR or RT-PCR include, as follows:

  • Presence of a gene RNA or DNA sequence in human samples which may be, for example, either homozygous (two identical genes) or heterozygous (having inherited different forms of a particular gene from each parent)
  • Quantitation of an expressed RNA, e.g. RNA expression in response to a drug dosed into a cell

 

Sanger Sequencing

Sanger sequencing samples can be submitted for full service sequencing.

 

SNP Genotyping

There are numerous custom, user defined and fixed content SNP genotyping technologies. Our knowledgeable staff can help you to determine the best application for your research needs.

 

DNA Methylation

Technologies using genome-wide assays or targeting specific sites are available to examine DNA methylation.  We can assist you in finding the appropriate platform for your research aims.

 

Genomic Sequencing

Genomics Research Core DNA sequencing services include genome wide and targeted applications with both fixed panel and custom options.

Wide variety of next generation DNA sequencing services are available for applications that range from whole exome sequencing to gene sequencing.  The technology can be applied to human and complex model species as well as to microbial and viral research studies. Multiple types of genomic alterations can be detected including germline and somatic single nucleotide variants, copy number variants, small insertions and deletions and chromosomal rearrangements.

Projects can be directed to Ion Torrent or Illumina sequencing platforms based on which technology is most suitable for the study.

  • Whole exome sequencing allows examination of the coding sequences to find disease or phenotype variants.
  • Custom targeted DNA sequencing increases the power of your data by focusing on the genomic regions of interest. PCR and hybridization capture options are available.
  • Pathogen detection and typing using multi locus sequence typing or 16S variable region sequencing of microbes has facilitated microbiome, metagenomics, disease epidemiology and etiology studies.

 

FOR INFORMATION CONTACT:

Multi-Disciplinary Research Lab 1 (MDRL 1)

3rd Floor, Main University Building,

Ziauddin University, Clifton Campus.

4/B, Saharah-e-Ghalib, Block 6, Clifton Karachi – 7500 Sindh, Pakistan.

Telephone: 0213-5862937-9 Ext.: 2366, 2367| Email: [email protected]

 

RNA EXTRACTION

ZU offers total RNA isolation from blood, tissues (fresh or RNAlater preserved), cultured cells and plasma samples by methods appropriate to your project. RNA is extracted from client samples by appropriate methods, either TRIzol or column-based extraction, depending on sample type, client choice and end use. RNA is suitable for many downstream applications including cDNA synthesis, qPCR, Northern blots and library construction.

 

RNA QUANTIFICATION

Initial assessment of RNA purity and concentration is performed by by MultiScan Sky Spectrophotometer. The instrument for UV quantification consumes only 2-3 ul of material, and provides a measure of RNA purity (260/280 and 260/230 ratios).

Note: All RNA extraction service include quantification

GUIDELINES FOR SAMPLE SUBMISSION

General Notes

For best results, freshly drawn blood should be stored at 4°C for less than 4 days, or should be frozen at   -80°C on the day of collection if possible.  Samples should be submitted to the core within 1 – 4 days after collection for optimal results.  Samples at can be also storage at -20°C but for no more than 3-6 months.

Sample tissues must be submitted in the corresponding collection microtubes and caps. Tissue submitted for extraction must be in the appropriate weight range of 30-50mg, and can be either fresh or lyophilized.  Samples can be dropped off and are stored in the -80°C freezer until processed. All sample tubes should be labeled with a unique sample identifier, the PI name, and the date collected.

For RNA samples, please make sure samples are submitted directly to research staff member so that the samples are stored appropriately.

 

Whole Blood & Buffy Coat

Blood samples should be collected in PLASTIC TUBES, preferably EDTA (e.g. BD Vacutainer #366643 purple cap tubes). Collection in ACD (citrate, yellow cap tubes) is also acceptable. Please DO NOT USE GREEN CAP (Heparin) Tubes. Other plastic blood collection tubes are acceptable provided they meet the guidelines above

 

Tissue & Cell Pellets

Tissue samples and cell pellets should be snap frozen on dry ice and stored at -80°C.  Samples should never be stored at -20°C as they quickly degrade. Samples stored for more than 1 year or at less than -80°C may result in lower yield and quality of RNA.  Multiple freeze/thaws will also affect RNA yield and quality

 

REVERSE TRANSCRIPTION

cDNA synthesis is carried out following recommended protocols using customer supplied total RNA or RNA isolated by ZU.

RNA Requirements

  • RNA should be free of PCR inhibitors
  • Has a A260/230 ratio between 2.0 and 2.4
  • Has a A260/280 ratio between 1.8 and 2.1

The recommended amount of total RNA for preparing cDNA for Gene Expression Taqman Arrays is 10µl at 200ng/µl (2µg).

 

PRIMER DESIGNING

ZU offers a one-stop custom PCR & qPCR primer design service, aiming to save time, effort, and money from preventing complications or even failures in the experiments. A pair of well-designed primers is one of the key requirements for a successful PCR. With years of expertise in PCR/qPCR research and formulation, scientists at ZU are able to design primers with high specificity and minimizing the chance of primer dimer formation. This can be achieved with the use of developed software to run through simulations and predictions to select and ensure good primer designs.

 

FOR INFORMATION CONTACT:

Multi-Disciplinary Research Lab 1 (MDRL 1)

3rd Floor, Main University Building,

Ziauddin University, Clifton Campus.

4/B, Saharah-e-Ghalib, Block 6, Clifton Karachi – 7500 Sindh, Pakistan.

Telephone: 0213-5862937-9 Ext.: 2366, 2367| Email: [email protected]

Cell Culture Facility

The Cell Culture Facility is located in Multidisciplinary Research Lab 1 at Ziauddin University, Clifton Campus supports research by providing space, equipments and expert’s consultation for researchers regarding cell culture needs, media, and experimental design. In addition, the facility trains users in cell culture techniques and provides sterile hood facilities for users.

Some of the services provided by the core are:

  • Isolation and propagation of stem cells from different sources
  • Morphological examination of the cells
  • Cell cytotoxicity analysis
  • Cell migration assay
  • Immunocytochemistry
  • Cell growth analysis
  • MTT assay/Cell proliferation assay
  • Cryopreservation & revival of cryopreserved cells
  • Media preparation

Following equipments are available in the cell culture facility of Ziauddin University

  1. Class II Biohazard Safety Cabinet
  2. CO2 Incubator
  3. Live Cell Imaging Microscope
  4. Centrifuge machine
  5. Automated Cell Counter
  6. Fridge
  7. Liquid Nitrogen Tank
  8. -80 Freezer
  9. Water Bath

FOR INFORMATION CONTACT:

Tissue and Cell Culture Lab, Multidisciplinary Research Lab 1 (MDRL 1)

3rd Floor, Main University Building,

Ziauddin University, Clifton Campus.

4/B, Saharah-e-Ghalib, Block 6, Clifton Karachi – 7500 Sindh, Pakistan.

Telephone: 0213-5862937-9 Ext.: 2364, 2367| Email: [email protected]

 

SPECTROPHOTOMETER SERVICES

ZU offers ELISA and nucleic acid estimation services to using state of the art Multiskan Sky Microplate Spectrophotometer, a UV/Visible microplate spectrophotometer. It can analyze upto 96-samples in a plate designed for any ELISA based research application. Endpoint, kinetic and spectral assays can be performed in 96-well plate format. The instrument is fully compatible with commercially available ELISA kits (direct, indirect and sandwich ELISAs). Optimization and result interpretation of ELISA assays can also be provided.

 

Nucleic Acid and Protein Estimation

With the help of μDrop Plate up to 16 samples can be analyzed simultaneously for nucleic and protein estimation. Furthermore, the samples can be analyzed individually in cuvettes also. Microliter quantity of sample is required to estimate the double stranded or single stranded DNA/RNA and protein in the sample provided by customer.

 

Specifications

  • Made: Thermo Fisher
  • Wavelength range: 200–1,000 nm
  • Plate format: 96- and 384-well plates
  • Incubation temperature range: + 2°C to 45°C
  • Plate shaking: Yes

 

Sample Guidelines for ELISA assay

Following samples can be submitted for ELISA assay in Eppendorf tube:

  • Cell culture supernatant, serum, plasma, milk, cell/tissue extract, urine, saliva, conditioned medium
  • Whole blood (vacutainer tube with or without anticoagulant)

 

Sample Guideline for nucleic acid estimation

  • Extracted DNA/RNA or purified protein in suitable buffer/solvent to be provided in Eppendorf tube on ice.

 

FOR INFORMATION CONTACT:

Multi-Disciplinary Research Lab 1 (MDRL 1)

3rd Floor, Main University Building,

Ziauddin University, Clifton Campus.

4/B, Saharah-e-Ghalib, Block 6, Clifton Karachi – 7500 Sindh, Pakistan.

Telephone: 0213-5862937-9 Ext.: 2367 | Email: [email protected]

Multidisciplinary Research Laboratory 2 (MDRL 2)

Histopathology & High Resolution Imaging Facility

Research Department of Ziauddin University (Clifton Campus) has established Histology section and High Resolution Imaging facilities in Cell Biology and Histology Lab of the Ziauddin University. High Resolution Imaging is performed by Ts2R-FL Inverted Research Microscope (Nikon, Japan) and Image Analysis is done by updated Nikon NIS Elements-D Software.

SERVICES OFFERED

  1. Histological Sample Processing and Staining

            – Tissue Fixation (NBF / Bouin’s)

            – Tissue Processing

            – Thin Tissue Sectioning & Slide Preparation

            – Hematoxylin and Eosin (H&E) Staining

            – Periodic Acid Schiff (PAS) Staining

            – Masson Trichrome Staining

  1. Reporting and preparation of Histological Slides (Animal & Human Tissues)
  2. Immunohistochemistry / Immunocytochemistry (IHC/ICC)

            – DAB based IHC/ICC

– Fluorophore based IHC/ICC (Red, Green Fluorescence) with DAPI Nuclear Staining (Blue Fluorescence)

  1. Results Interpretation of IHC/ICC Slides
  2. High Resolution Microscopy and Imaging

            – Bright Field Microscopy

            – 3D Differential Interference Contrast (DIC) Microscopy

            – Multichannel Fluorescence Microscopy (DAPI, FITC, Texas Red and Dual Channel)

  1. Histomorphometric Analysis (Quantitative measurements of the shape or form of tissue structures) by Nikon NIS Elements-D Software
  2. Image Processing and Graphic Designing of Figures by Adobe Photoshop Software (For publication purpose)

 

FOR INFORMATION CONTACT:

Cell Biology and Histology Lab (MDRL 2)

3rd Floor, Main University Building,

Ziauddin University, Clifton Campus.

4/B, Saharah-e-Ghalib, Block 6, Clifton Karachi – 7500 Sindh, Pakistan.

Telephone: 0213-5862937-9 Ext.: 2363 | Email: [email protected]

 

Bioinformatics Analysis

We provides statistical and bioinformatics data analysis services that help our customers to explain large amounts of data generated by sequencing, and genotyping.

Genomics Research Lab has expert staff offering comprehensive bioinformatics solutions in all aspects of sequencing. We provide data analysis services for data generated by a wide range of sequencing platforms i.e., Sanger’s & NGS. We use the cutting-edge bioinformatics algorithms and pipeline, and provide you with high-quality and ready-for-publication figures.

To initiate a study please contact us to schedule a consultation.

 

FOR INFORMATION CONTACT:

Bioinformatics Lab, Multi-Disciplinary Research Lab 2 (MDRL 2)

3rd Floor, Main University Building,

Ziauddin University, Clifton Campus.

4/B, Saharah-e-Ghalib, Block 6, Clifton Karachi – 7500 Sindh, Pakistan.

Telephone: 0213-5862937-9 Ext.: 2363, 2366 | Email: [email protected]

High Performance Liquid Chromatography (HPLC) Facility

The ZU Core Facility offers its expertise in chromatographic separation and purification by High performance liquid Chromatography (HPLC). The facility provides research lab training and assistance so POSTGRADUATE STUDENTS can operate any instruments necessary to successfully accomplish their research projects.

The Schimadzu LC model provides users accurate results. The system is equipped with gradient pump and offers excellent accuracy for separation and qualitative analysis. High Performance Liquid Chromatography (HPLC) is established in a various range of fields, including food production, medicine and environmental sciences.

Model:                                               Shimadzu LC-20AT
Make:                                                  Japan
Available Detector:                            UV Detector
Lamps:                                                Deuterium lamp
Wavelength range:                              180 nm to 1000 nm
Columns available:                             C18 columns

FOR INFORMATION CONTACT:

Multi-Disciplinary Research Lab 2 (MDRL 2)

3rd Floor, Main University Building,

Ziauddin University, Clifton Campus.

4/B, Saharah-e-Ghalib, Block 6, Clifton Karachi – 7500 Sindh, Pakistan.

Telephone: 0213-5862937-9 Ext.: 2363, 2367 | Email: [email protected]

 

ACKNOWLEDGING THE CORE:

Please acknowledge the Core in manuscripts as well as posters and talks.

Suggested language: “This work was supported by the MultiDisciplinary Research Lab at Ziauddin University.”