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Lab Facilities

Major equipment:

  • Applied Biosystems VeritiPro Thermal Cycler: It delivers proven reliability with advanced temperature control technology and connectivity. Take advantage of next-level PCR optimization with the precision offered by VeriFlex Block technology (96-well, 0.2 mL; 6-zone VeriFlex Block; 6.0°C/sec; 96 reactions; USB port and 16 GB onboard memory; onboard capacity >1,000 protocols). Connect to the cloud-enabled VeritiPro Thermal Cycler remotely. Conveniently design and securely upload your methods, monitor runs, and check instrument availability from any mobile device or desktop computer with Connect.

  • BluePippin, DNA Size Selection for Next-Gen Sequencing, with Pulsed-Field (100bp – 50kb): The BluePippin has the DNA capabilities of the Pippin Prep, plus the extra benefit of pulsed-field electrophoresis for resolving and collecting high molecular weight DNA.  For long-range genomic applications, high-pass filtering allows users to collect all fragments above a size threshold set by the user. Target sizes or ranges of sizes are entered into the software, and fractions are collected in the buffer. Up to 5 samples/gel cassettes may be run, with no possibility of cross-contamination. Gel cassettes for DNA selections are available in four agarose concentrations to provide a full range of size selection options between 100bp and 50kb.  Internal standards may be used for higher accuracy and increased sample capacity (from 4 to 5 samples/cassette) for smaller fragment sizes.  Higher molecular weight fragments require a dedicated lane to run a calibration marker.  Run times are as little as 30 minutes. This can be used for mRNA isolation, DNA sequencing, RNA-seq, genotyping, ChIP-seq, and Long-read sequencing (PacBio, Oxford Nanopore). 

  • Nanopore Sequencing (MinION Mk1C): Up to 50 Gb per MinION Flow Cell / 2.8 Gb per Flongle Flow Cell: Theoretical max output when the system is run for 72 hours (or 16 hours for Flongle) at 420 bases/second. Outputs may vary according to library type, run conditions, etc. Nanopores read the length of DNA or RNA presented to them — from short to ultra-long (longest >4 Mb); Nanopores read the length of DNA or RNA presented to them — from short to ultra-long (longest >4 Mb) 

  • Portable Chlorophyll meter: Fastest & most accurate mobile system for simultaneous leaf gas exchange & chlorophyll fluorescence measurement. This is an ideal setup for plant-stress-interaction-related experiments. It measures broader photosynthesis-related parameters which can predict the effects of environmental changes. 

  • Isotemp Digital Dry Baths

  • Gel electrophoresis system: The lab is equipped with a horizontal gel electrophoresis system that analyzes 24 samples in one go in 30 min time. This can be used for both RNA and DNA analysis. This is an important basic system for any metagenomics, genomics, and transcriptomics workflow. 

  • Thermo Scientific Invitrogen Qubit 4 Fluorometer: The Qubit 4 Fluorometer is the latest version of the popular Qubit fluorometer designed to measure DNA, RNA, and protein quantity accurately, and now also RNA integrity and quality, using the highly sensitive Qubit assays. The Qubit 4 Fluorometer was re-engineered to run the Qubit RNA IQ (integrity & quality) assay.

  • Incubator shaker: This ideally suits microbes subculturing and growing optimally. This can accommodate 10 liters of microbial medial. The changing stub helps adjust the flask and volume required for growing microbes. 

  • Eppendorf™ Centrifuge 5920 R: Centrifuge 5920 R has a superior capacity of up to 4 × 1,000mL; thus, making it the ideal instrument for high-throughput applications. It features a powerful state-of-the-art refrigeration system with advanced temperature management to keep your samples safe. It has swing-bucket rotors and adapters that accommodate tubes and bottles from 0.2mL to 1,000mL. Plate rotor options for centrifugation of all MTP, PCR, or Deep well Plates types. Fixed-angle rotors for high-speed molecular biology applications in tubes from 0.2 mL to 50 mL. High centrifugation speed of up to 25,062 × g (13,700 rpm). 

  • High-Performance Liquid Chromatography: We have an HPLC system (Thermo Scientific™ UltiMate™ 3000) for metabolite quantification and analysis. It has all the necessary columns and accessories to analyze the exudating root phenolics, flavonoids, and diterpenes.

  • Applied Biosystems QuantStudio™ 7 Flex Real-Time PCR System: This system has increased application versatility by accommodating 4 different block types.Compatible with over 8 million TaqMan® assays for gene expression, genetic variation, gene regulation, or protein expression experiments. The intelligent design of the QuantStudio™ platform combined with Applied Biosystems® instrument reliability and accuracy.

  • ELISA microplate reader: The lab has Tecan Spark 10M that is used for spectroscopic analysis of microbial growth, antioxidant activities, soil enzyme activities, and enzyme inhibition kinetic assays. The instrument includes UV/VIS spectra top & bottom with Time-resolved fluorescence (TRF), NanoQuant plate, Temperature control (RT+3°C – 42°C), Liquid dispensers with reagent heater and stirrer, DNA/RNA quantification etc.

  • Rotary evaporator: The lab is equipped with a rotary evaporator to prepare samples for metabolomics. It can handle several different kinds of solvent systems. The Rotavapor® R-300 meets the highest expectations of convenience and versatility in rotary evaporation.

 Other equipment available:

  • Shakers (open)

  • Plate spinner Fisherbrand

  • Vertex table top Fisherbrand

  • portable soil moisture

  • Potable pH/EC/Salinity meter Hanna

  • Portable Balance (3 decimal places; higher capacity)

  • Magnetic Sterir

  • Heating plate Fisher

  • Waring industrial blender (microbial isolations from soils)

  • GHGs sensors

  • Hirayama Autoclave, a medical autoclave, uses steam to sterilize equipment and other objects.

  • Several refrigerators and freezers are available to store the samples at 4oC, -20oC.

  • -80-degree C deep freezer to store antibodies, and purified enzymes for a long period.

 

Core-lab instrumentations:

  • Applied Biosystems ProFlex™ 3x32-Well PCR machine

  • Applied Biosystems QuantStudio™ 7 Flex Real-Time PCR System

  • Dionex™ ICS-5000+ with Electrochemical and UV Detector

  • BioTek ELx405™ Plate Washer

  • GE AKTA Fast Performance Liquid Chromatography Protein Purification system

  • New Brunswick BioFlo 110 Fermentation System

  • Opentrons OT-One S Automatic microplate-based pipetting station

  • Confocal laser scanning microscope

  • Fluorescence Imaging Microscope

  • Powder X-ray diffraction machine

  • Multiple photobioreactors (1 gal to 25 gallons) to cultivate algae.

  • A bench-scale and mobile continuous flow reactor connected with an online sampling arrangement connected to a gas chromatograph (TCD & FID) for the gas analysis.

  • A high temperature (500°C) and high pressure (5000 psi) 500 mL batch reactor (Parr Reactor)

  • Multiple high-pressure tubular reactors

  • Two 9.5-liter complete mix batch reactors for anaerobic digestion

  • Fluidized sand bath (Techne) for batch reactions

  • A bench-scale automated bioreactor

  • The Automatic Methane Potential Test System (AMPTS)

  • Labconco freeze dryer.

  • Rotary vacuum evaporator

Resources

Plant growth and tissue culture room:

A room in Khan’s lab contains 14 shelves of lights for growing plants in highly controlled conditions.

In addition, the same room is also annexed with a separate plant tissue culture facility that hosts Biosafety Type-A2 benches and air-lift bioreactors.

 

Field station:

The University of Houston Coastal Center (UHCC) is a 1,000-acre facility containing natural and modified ecosystems. An on-site building contains office space, a 900-ft2 laboratory, and a garage for storage. The UHCC maintains a fleet of vehicles and a tractor for prepping and maintaining experiments. One full-time employee lives at the UHCC and assists with field prep for experiments. There is also a greenhouse at the UHCC for plant propagation and two micrometeorology towers.

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