Equipments & Facilities

• Gene quantification
--> Absolute quantification
--> Relative quantification
• Genetic variation analysis/Genotyping
(Genotyping based on endpoint analysis/melting curve analysis; Mutation scanning & SNP analysis through High resolution melting (HRM) analysis)
• Gene expression analysis

Contact Us: Director, ICAR-NIVEDI, PB No. 6450, Yelahanka, Bengaluru-560064

Phone: 080-23093111 Fax: 080-23093222

Email: [email protected]

Real-Time PCR
Real-Time PCR
Roche Diagnostics, Germany
Light Cycler® 480 II System with analytical Software
• Dimension:
W 60 cm x D 60 cm x H 54.5 cm <br>
W 24 in x D 24 in x H 21.5 in<br>
• Weight: 55 kg (121 lbs)<br>
• Temperature control<br>
->Peltier-based heating/cooling from 40°C - 95°C<br>
->Heated lid, PCR without any overlay (e.g., wax or oil)<br>
->Passive post-run cooling to &lt; 40°C<br>
• 5 excitation filters, high-intensity broad-spectrum xenon lamp<br>
• Run time: <br>
->60 minutes (96-well plate)<br>
40 minutes (384-well plate)<br>

• Gene Scanning or Methylation analysis with High Resolution Melting (HRM)
• User has to enter data “only” into blue colored boxes.
• Use the plate configuration box to determine sample number, row A1-12 is used for duplicate samples of standards and a no template control (NTC).
• Unknowns should either be run as duplicates or triplicates.
• After dispensing the reaction volume, seal plate with optical adhesive cover using manufacturer’s instructions.
• Briefly spin down plate at 1,000 rpm and now plate is ready to run.
• At end of run, analyze PCR products by electrophoresis to confirm the absence of non-specific products.

Usage charges : charges per hour excluding GST and consumables
Sl. No. University National Laboratories/R&D organization Industry
1 Rs.1000/- Rs.2500/- Rs.2500/-

Progress of DNA amplification during a Polymerase Chain Reaction (PCR) can be monitored in "real time" (RT-PCR) by measuring the release of fluorescent "flashes" during amplification. Reaction rates can be measured continuously, or determined at a fixed time-point during the exponential amplification phase. It aids the Melt-curve genotyping with HybProbe- or SimpleProbe probes and Endpoint genotyping with hydrolysis probes.

Gene Expression analysis, Genotyping/HRM capability, mRNA quantification, NGS quantification: library prep, result validation, Nucleic acid monitoring, Rare allele detection

Director, ICAR-NIVEDI, PB No. 6450, Yelahanka, Bengaluru-560064
Phone: 080-23093111 Fax: 080-23093222
Email: [email protected]

Ariamx Real Time PCR system
The AriaMx Real-time PCR System is a fully integrated quantitative PCR amplification, detection, and data analysis system. The instrument has five optics modules.
Leica Microsystems, Germany
Light Cycler® 480 II System with analytical Software
The facility does not have a technical support in terms of trained manpower at the moment. Any person who intends use the machine should obtain prior consent of the Director, ICAR-NIVEDI. , Further, the intended user should bring in his own plates (suitable for use in Ariamx machine), reagents and any other accessories required running real time PCR, For details user can visit https://www.genomics.agilent.com/en/AriaMx-qPCR-Instruments-Software/AriaMx-Real-time-PCR-System/?cid=AG-PT-169&tabId=prod2470021

The system design combines a state-of-the-art thermal cycler, an advanced optical system with an LED excitation source, and complete data analysis software. The instrument has five optics modules and the scanning optics design delivers optimal separation between the dyes and between samples. The instrument provides a closed-tube PCR detection format that can be used with a variety of fluorescence detection chemistries .

Spatial Analytics, Mapping and Visualization, 3DGIS, Realtime GIS, Imageryand Remote Sensing, Datacollection and Management Integrated, ArcMap, ArcCatalog, ArcToolbox, ArcScene, ArcGlobe, ArcGIS Pro, Intelligenceand Defense, Earth Sciences, Elected and Appointed Officials, Land Administration, National Mapping and Charting, Official Statistics, Community Developmentand Public Works, Retail and Supply Chain,Manufacturing,Insurance and Banking,Media & Entertainment,Education,Health & Human Services,Sustainable Development,Utilities & Communication,Transportation, Agriculture, Climate, Weather, and Atmosphere, Conservation, Environmental Management,Forestry,Mining ,Oceans,Petroleum,Water Resources

Director, ICAR-NIVEDI, PB No. 6450, Yelahanka, Bengaluru-560064
Phone: 080-23093111 Fax: 080-23093222
Email: [email protected] 
[email protected]

 ArcGIS software
ArcGIS software
ESRI
ArcGIS Software 10.2
ArcGIS is a geographic information system (GIS) for working with maps and geographic information. ArcGIS provides contextual tools for mapping and spatial reasoning , Spatial Analytics: Spatial analytics is the heart and soul of ArcGIS and used to find the best location, plan for smarter communities, and prepare or respond faster in crucial situations. Useful for powerful spatial and temporal prediction modelling , Mapping & Visualization: Maps helps to spot spatial patterns in the data so as to make better decisions and take action. Maps also break down barriers and facilitate collaboration. ArcGIS gives you the ability to create, use, and share maps on any device., Imagery & Remote Sensing: ArcGIS powerful for spatial image management, process, analyse, and share imagery. Not only do we get access to the world's largest imagery collection, we also get tools like satellite, aerial, drone and full motion video. , ArcGIS SOA framework features an authoring tier of professional ArcGIS for Desktop users, a publishing tier of services, and a presentation tier of viewers with access to available published services.
.NET Framework 3.5 SP1 must be installed prior to installingArcGISfor Desktop., Internet Explorer requirement: Microsoft Internet Explorer (minimum IE 9) must be installed prior to installing ArcGISfor Desktop. Internet Explorer 9, 10 and 11 are supported., Python requirement for Geoprocessing, CPU Speed : 2.2 GHz minimum; Hyper-threading (HHT) or Multi-core recommended, Platform : x86 or x64 with SSE2 extensions, Memory/RAM : 2 GB minimum, Display properties : 24-bit color depth, Screen resolution: 1024x768 recommended minimum at normal size (96 dpi), Disk space : 2.4 GB. In addition, up to 50 MB of disk space may be needed in the Windows System directory (typically, C:\Windows\System32)., Video/Graphics adaptor : 64 MB RAM minimum; 256 MB RAM or higher recommended. NVIDIA, ATI, and Intel chipsets supported. Be sure to use the latest available drivers.

Developer(s):Esri

Initial release:December 27, 1999; 18 years ago

Stable release:10.5.1 / June 29, 2017; 6 months ago

Development status:Active

Written in:C++

Operating system:Desktop: Windows 7 SP1 and later, Windows Server 2008 SP2 and later; Server (x64 only) additionally supports: Windows Server 2003 SP2 and later; RHEL 5 Update 7 and later, SLES 11 SP1 and later.

Type:Geographic information system

License:Proprietary commercial software

Website:http://www.esri.com/software/arcgis

Identification of microbes based on rRNA gene sequence data

Director, ICAR-NIVEDI, PB No. 6450, Yelahanka, Bengaluru-560064
Phone: 080-23093111 Fax: 080-23093222
Email: [email protected]

Automated Microbial identification system
Automated Microbial identification system
Applied biosystems, ThermoFisher scientific, USA
3500 genetic analyzer with MicroSEQ® ID Microbial Identification Software
The MicroSEQ® system comprises
Bacterial libraries of 500 bp 16S rDNA sequences and over 2300 validated entries
A fungal library containing more than 1100 entries, Radio frequency identification (RFID) technology tracks key consumables data and records administrative information , Advanced multiplexing capabilities for DNA fragment analysis with up to six unique dyes , Provision of GeneMapper® software for fragment analysis, MicroSEQ® ID Microbial Identification Software
Operating System: Windows 7, Windows Vista, Windows XP
During analyzing the any project data, the library search report has to be evaluated to check the library matches against each specimen consensus sequence. Use the Library Search Report to:
Identify the unknown organism.
Assess the accuracy of the identification.
Examine results for all matches.
Determine if a match was made against a validated (proprietary) library or a custom library.
View phylogenetic relationships between the unknown and the top matches in a phylogenetic tree., To construct a phylogenetic tree, first search libraries to add sequences to tree and then search projects to add specimens to tree., Click ‘Compute Tree’. The Tree Computation dialog box opens, then click OK., Click the species name as desired in the tree, and then click the second species name as your second selection to view the Genetic Distance % for the selected species in the tree diagram, While viewing the tree, zoom the tree diagram as needed and select ‘File Print’ to print the tree diagram

MicroSEQ® ID Microbial Identification Software allows easily identifying and classifying unidentified bacterial or fungal sequences by comparing them to a validated microbial library. This bundled version includes the bacterial and fungal sequence libraries comprising of over 2300 microbial 16S rDNA sequences.

Cell counting, cell sorting, biomarker detection

Director, ICAR-NIVEDI, PB No. 6450, Yelahanka, Bengaluru-560064
Phone: 080-23093111 Fax: 080-23093222
Email: [email protected]

Flow Cytometer
Flow Cytometer
BD BioSciences, Belgium
FACS Canto™ II system
Fluorescence Detector Design: Reflective optics with single transmission filter in front of each PMT, Blue Laser Dyes: FITC, PE, PerCP or PerCP-Cy™5.5, PE-Cy™7 (525, 575, 678 or 695, 785 nm) , Red Laser Dyes: APC, APC-Cy7 (660, 785 nm), Sample Injection: Direct into flow cell, Max Particle Size 50 μm , Sample Flow Rate, Min 10 μL/min, Sample Flow Rate, Max 120 μL/min, Sample Acquisition Rate: 10,000 events/second, 6 compensated fluorescence parameters and 2 scatter parameters , Sample Dead Volume: 30 μL (BD Falcon™ tubes 12 x 75-mm), Integrated fluidics cart and compressor , Provision of fixed optical alignment procedure, The BD FACS™ Sample Prep Assistant II
Users can follow either of the standardize protocols as per the requirement of the user i.e. Direct staining, Indirect staining, intracellular staining or cell-cycle staining., Direct staining: Live or fixed cells are incubated with directly labeled antibodies against cell surface antigens., Indirect staining: If there is not a directly labeled antibody available, or user wish to amplify their signal he/she can do indirect staining. This is where user stain a cell with a primary antibody against the antigen of interest and visualize using a labeled secondary antibody which recognizes the primary., Intracellular staining: In order to detect antigen not present on the cell surface, cells have to be fixed and permeabilized to disrupt the cell membrane and allow entry of the antibody. Antigens can be then directly or indirectly labeled. Various methods are optimal depending on the antigen and antibody used., Cell-cycle staining: Measuring DNA content for cell cycle analysis requires fixation and permeabilization of the nuclear membrane., Users can also follow the procedure for cell preparation, cell activation to determine immune competence, marker upregulation, cytokine release and proliferation by flow cytometry.

TCell components are fluorescently labelled and then excited by the laser to emit light at varying wavelengths. The fluorescence can then be measured to determine the amount and type of cells present in a sample.

The Leica CM1850 is a powerful cryostat for routine as well as research applications in biology, medicine and industry. The instrument has been designed for rapid freezing and sectioning of tissue samples. , For use in Haematoxylin and Eosin staining of frozen tissue sections for early diagnosis, For use in immunohistochemistry staining of specific proteins/virus/bacteria/etc. , For use in cancer tissue sections to determine the prognosis immediately

Ph:080-23093110, 23093140
email: [email protected], [email protected]

Cryostat
Cryostat
Leica Microsystems, Germany
Leica CM1850UV
Mechanism of cooling : Peltier cooling, Single compressor, Disinfection : Ultra violet, Cryobar temperature (specimen cooling area) : 0 to -60 ºC, Motorised coarse advance : 0.7mm/s, Section thickness adjustment : 1 to 10µm in1µm increment
10 to 20µm in 2 µm increments
20 to 60µm in 5µm increments, Cryochamber temperature (Section cutting area) : 0 to -35ºC, Low profile blades and high profile blades usage : One holder is available to hold both blades but the high
profile blades require pressure plate and it has to be fitted
and unscrewed whenever required, Time required for cooling to -35ºC temperature : 4 hours, Defrost cycle : Automated, Touch screen : Yes
Take care when handling microtome knives and disposable blades. The cutting edge is extremely sharp and can cause severe injury., Never leave knives and knife holders with a knife/blade mounted lying around, Do not place a knife on a table with the cutting edge facing upward, Always clamp the specimen before the knife, Prior to manipulating the knife and specimen, or changing the specimen or knife, and during breaks, always lock the hand wheel and cover the cutting edge with the knife guard, Avoid contact with cold parts of the instrument as this can cause frostbite, To make sure that the condensation water stemming from the defrost cycles drains into the waste container and to avoid the risk of possible contaminations, ensure that the tap of the waste container is open when operating the instrument. Only shut the tap when draining the waste container, It is not necessary to remove the microtome for routinely disinfecting the cryochamber, Only use the cleaning agents and disinfectants (alcohol or common disinfectants based on alcohol)

The cryostat works in the principal that at low temperatures the liquid or the embedding medium freezes and acts as embedding material, the tissue becomes hard and becomes ice block. The microtome knife is used to make tissue sections of desired thickness without processing the tissues and fresh tissues can be used.

For separation of
Virus/viral antigen/proteins
Lipoproteins
Nanoparticles
Nucleic Acids

Director, ICAR-NIVEDI, PB No. 6450, Yelahanka, Bengaluru-560064
Phone: 080-23093111 Fax: 080-23093222
Email: [email protected]
Dr.S.S. Patil, ICAR-NIVEDI, Bengaluru (080-23093137)

 Ultracentrifuge with accessories
Ultracentrifuge with accessories
Sorvall™ Japan
MTX 150 Micro-Ultracentrifuge
The Thermo Scientific Automatic Securing Micro-Ultracentrifuge Swinging Bucket and Vertical , Rotors are for use in the Sorvall Discovery M150 , Rotor Type: S 52 ST-0319 , Tubes/Buckets: 4 (5 ml capacity), Speed: With good acceleration rate of 1,50,000 rpm which reaches in a short period of time. The range of RCF of 1,048, 000xg supports any separation. This benchtop ultracentrifuge offers powerful separation technology in a quiet, compact, easy to use benchtop design.
Sample must be pure and free from all contaminants, Concentrated sample volume should be small quantity to layer over gradient, Presently sucrose gradient is being used

There are different techniques/methods used for separation of proteins/antigens/nucleic acids using different gradients. Continuous sucrose gradient is usually followed for separation of viral proteins/antigens. Different gradients of sucrose are prepared in tubes and concentrated viral proteins are layered over the gradient with good acceleration of RCF 1,048,000xg for 3 hrs. The separated proteins can be collected from particular specific gravity band.

Brightfield microscopy, Fluorescence photomicrography

Director, ICAR-NIVEDI, PB No. 6450, Yelahanka, Bengaluru-560064
Phone: 080-23093111 Fax: 080-23093222
Email: [email protected]

Trinocular microscope model Eclips 80i
Trinocular microscope model Eclips 80i
Nikon, Japan
Eclipse 80i
The 'fly-eye' optics: Features the uniform illumination, Plan Apo VC objectives: High-resolution images, The DS-2Mv-L2 digital camera: Ease of imaging through Provision of bright illumination system with a 12v-100w halogen lamp , Ergonomic tube:
The ergonomic binocular-eyepiece tube can be inclined at angles from 10° to 30° and the eyepieces can be extended up to 40mm.
This ensures an optimum eye point and comfortable viewing posture
Users has to handle the equipment with due care., Prior and after use of the microscope, clean the stage with due care., Users should not use any harsh chemicals during wiping the stage.

The Eclipse 80i delivers remarkably high signal to noise ratios, producing fluorescence images. The noise terminator directs stray light away from the light-collection path, which helps in high signal-to-noise ratios and ultimately high contrast and clarity of images.

Post-electrophoresis documentation of separated nucleic acids in gel , Quantitative western blot imaging and analysis, Chemiluminescent imaging, Multiplex fluorescent imaging analysis of overlapping proteins in the same blot

Director, ICAR-NIVEDI, PB No. 6450, Yelahanka, Bengaluru-560064
Phone: 080-23093111 Fax: 080-23093222
Email: [email protected]

Molecular Imager Gel documentation system
Molecular Imager Gel documentation system
Alpha Innotech, Germany
FluorChem Q Image analysis system
4.2 Megapixel camera for publication of ready images, 6 position filter wheel for flexible fluorescent detection, Excitation at 475 nm, 534 nm and 632 nm and optional 365nm and 245 nm providing the ability to image CY3, CY2, CY5 or Q dots, UV transilluminator for fluorescent gels, White light table for colorimetric samples like Coomassie Blue and Silver Stained protein gels (not illustrated), Protocol driven interface that remembers the optimal setting required to imaging your assay, AlphaView™ Q software for analysis of blots and gels., Features the ability to save analysis protocols, quickly normalize for loading controls, and automatically calculate for background levels.
AlphaView software has four main control windows for all image acquisition, contrast adjustment, enhancement and analysis functions., During the acquiring the images, the users has to use either the saved protocols or can adjust as per the requirement. , The user can browse for other saved protocols by clicking on the down arrow button, a list of existing protocols will be displayed., Selecting the protocol will go to the preview screen for user to verify setting or acquire., Clicking the Camera Acquire Icon launches the Camera Setup & Preview window., This window provides camera exposure control, sensitivity/resolution control, lighting/filter wheel position control, contrast display options, and cabinet door status., Clicking the green Preview box allows user to preview what the final image would look like, while still allowing user to make small adjustments to the options selected in focus., Select ‘Acquire Image’ to capture the final image. User will then be able to save, print or analyze their image., Users has to handle the equipment with due care., Users should not use any harsh chemicals during wiping.

DAfter electrophoresis, fluorescent dye stained agarose gel is exposed to a UV light source. The fluorescent dye bound nucleic acid fluoresces and becomes visible.

Fast and high-resolution separations of DNA molecules ranging from 200 kb to >6 Mb, Top down and bottom up mapping, Electrophoretic karyotyping, Analysis of tumor cell DNA rearrangements, Mammalian DNA analysis, Testing for bacterial, yeast, and parasite strain homogeneity.

Director, ICAR-NIVEDI, PB No. 6450, Yelahanka, Bengaluru-560064
Phone: 080-23093111 Fax: 080-23093222
Email: [email protected]

Pulsefield Gel Electrophoresis
Pulsefield Gel Electrophoresis
Biorad Pacific Ltd , Hongkong
CHEF-DR® III Variable Angle System
Electrophoresis cell dimension: 11.4 x 44.2 x 50.3 cm, horizontal format, Power module dimension:
Construction: Aluminum chassis
Weight: 10 kg, Maximum amps: 0.5 amperes , Allowable voltage gradients: 0.6–9 V/cm, in 0.1 V/cm increments
User has to pre-run the instrument 15-20 minutes prior to actual run for calibration., User has to use the deionized distilled water for the electrophoresis., Due care has to be followed for constant supply of the current without any voltaze fluctuation. , When the parameters are set, start the program by pressing PAUSE/START RUN. When the program is in progress, the left panel display will show the time remaining (hours) in the current Block with RUN TIME lit, and the right panel display will show the actual current (milliamps) with ACTUAL CURRENT and PAUSE/START RUN lit. After the program is started, it is not possible to edit any of the run parameters., The program in progress may be manually terminated by holding down PAUSE/START RUN for 3– 4 seconds. A program can be terminated only while it is in the run mode; it cannot be terminated in PAUSE. When the program is terminated two beeps will sound, and the right display will show OFF. Pressing PAUSE/START RUN again will start the program from the beginning., When the program terminates under the timer control, the PAUSE/START RUN light will go off, it will sound two beeps per second for 5 seconds, and the right display will show OFF. The run timers will be reset and all parameters will be retained. The run parameters may be used again as is, or further modified, and the program may be started again by pressing PAUSE/START RUN.

DNA is pulled through a PFGE gel due to electric charge, similar to the standard electrophoresis run. In principle, the apparatus itself is essentially the same as a standard electrophoresis unit. Similar to standard electrophoresis, there are electrodes that allow the electric charge to pass through the chamber. In PFGE however, these electrodes surround the gel and are not all active at once. Activating only certain electrodes is what allows the electric current to be modulated at specific angles. While a standard gel is usually only active for a couple hours, PFGE runs can take days. To keep the buffer temperature down, it is run through tubing and through a cooler before being fed back into the chamber.