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Hamilton, New Zealand

Hobbs J.K.,University of Waikato | Shepherd C.,University of Otago | Saul D.J.,ZyGEM Corporation Ltd | Demetras N.J.,University of Waikato | And 4 more authors.
Molecular Biology and Evolution | Year: 2012

Thermophily is thought to be a primitive trait, characteristic of early forms of life on Earth, that has been gradually lost over evolutionary time. The genus Bacillus provides an ideal model for studying the evolution of thermophily as it is an ancient taxon and its contemporary species inhabit a range of thermal environments. The thermostability of reconstructed ancestral proteins has been used as a proxy for ancient thermal adaptation. The reconstruction of ancestral "enzymes" has the added advantages of demonstrable activity, which acts as an internal control for accurate inference, and providing insights into the evolution of enzymatic catalysis. Here, we report the reconstruction of the structurally complex core metabolic enzyme LeuB (3-isopropylmalate dehydrogenase, E. C. 1.1.1.85) from the last common ancestor (LCA) of Bacillus using both maximum likelihood (ML) and Bayesian inference. ML LeuB from the LCA of Bacillus shares only 76% sequence identity with its closest contemporary homolog, yet it is fully functional, thermophilic, and exhibits high values for k cat, k cat/K M, and ΔG ‡ for unfolding. The Bayesian version of this enzyme is also thermophilic but exhibits anomalous catalytic kinetics. We have determined the 3D structure of the ML enzyme and found that it is more closely aligned with LeuB from deeply branching bacteria, such as Thermotoga maritima, than contemporary Bacillus species. To investigate the evolution of thermophily, three descendents of LeuB from the LCA of Bacillus were also reconstructed. They reveal a fluctuating trend in thermal evolution, with a temporal adaptation toward mesophily followed by a more recent return to thermophily. Structural analysis suggests that the determinants of thermophily in LeuB from the LCA of Bacillus and the most recent ancestor are distinct and that thermophily has arisen in this genus at least twice via independent evolutionary paths. Our results add significant fluctuations to the broad trend in thermal adaptation previously proposed and demonstrate that thermophily is not exclusively a primitive trait, as it can be readily gained as well as lost. Our findings also demonstrate that reconstruction of complex functional Precambrian enzymes is possible and can provide empirical access to the evolution of ancient phenotypes and metabolisms. © The Author 2011. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved.


Patent
ZyGEM CORPORATION LTD. and Lockheed Martin | Date: 2013-12-04

A microfluidic chip includes one or more reaction chambers to hold fluids for chemical or biochemical reactions, such as PCR. A non-contact heat source heats the reaction chamber and the fluid, such that the heat source does not contact the reaction chamber or the fluid. The heat source can heat the reaction chamber and the fluid separately, where the reaction chamber and the fluid separately absorb heat radiation from the heat source. A temperature sensor acquires a temperature of the reaction chamber and/or the fluid. Control circuitry controls the heat source according to a cycling profile for the reaction in the fluid to cycle the heat source between heating and not heating the reaction chamber and the fluid based on the temperature acquired by the temperature sensor. Cooling can be provided passively or actively.


Trademark
Zygem Corporation Ltd | Date: 2008-06-03

CHEMICAL PREPARATIONS CONTAINING ENZYMES FOR SCIENTIFIC PURPOSES, NAMELY FOR AGRICULTURAL PURPOSES, OR DNA ANALYSIS, OR BIO-SECURITY PURPOSES OR FORENSIC PURPOSES; CHEMICAL PREPARATIONS FOR SCIENTIFIC PURPOSES, NAMELY FOR AGRICULTURAL PURPOSES, OR DNA ANALYSIS, OR BIO -SECURITY PURPOSES, OR FORENSIC PURPOSES; DIAGNOSTIC PREPARATIONS OTHER THAN FOR MEDICAL OR VETERINARY PURPOSES; CHEMICAL REAGENTS FOR NON-MEDICAL PURPOSES; ENZYMES AND BUFFERS FOR NON-MEDICAL PURPOSES, NAMELY FOR AGRICULTURAL PURPOSES, OR DNA ANALYSIS, OR BIO SECURITY PURPOSES OR FOR FORENSIC PURPOSES; DILUTION SOLUTIONS FOR DILUTING NUCLEIC ACIDS, NAMELY ANY SOLUTION USED TO BUFFER, DILUTE OR PRESERVE NUCLEIC ACIDS, FOR NON-MEDICAL PURPOSES, NAMELY FOR AGRICULTURAL PURPOSES, OR DNA ANALYSIS, OR BIO-SECURITY PURPOSES, OR FORENSIC PURPOSES; CHEMICAL PREPARATIONS WHICH FACILITATE THE RELEASE OF NUCLEIC ACIDS OTHER THAN FOR MEDICAL OR VETERINARY PURPOSES. CHEMICAL PREPARATIONS CONTAINING ENZYMES FOR MEDICAL OR VETERINARY PURPOSES; CHEMICAL PREPARATIONS FOR MEDICAL OR VETERINARY PURPOSES, NAMELY FOR USE IN MEDICAL DNA ANALYSIS OR PROTEIN DETECTION FOR MEDICAL OR VETERINARY PURPOSES; DIAGNOSTIC PREPARATIONS FOR MEDICAL OR VETERINARY PURPOSES; REAGENTS FOR MEDICAL OR VETERINARY DIAGNOSTIC PURPOSES; ENZYMES AND BUFFERS FOR MEDICAL OR VETERINARY PURPOSES, NAMELY FOR MOLECULAR DIAGNOSTICS, GENETIC TESTING, PATHOGEN DETECTION, OR NUCLEIC ACID ISOLATION; DILUTION SOLUTIONS FOR DILUTING NUCLEIC ACIDS, NAMELY ANY SOLUTION USED TO BUFFER, DILUTE OR PRESERVE NUCLEIC ACIDS FOR MEDICAL OR VETERINARY PURPOSES, NAMELY MOLECULAR DIAGNOSTICS, GENETIC TESTING, PATHOGEN DETECTION, OR NUCLEIC ACID ISOLATION; CHEMICAL PREPARATIONS WHICH FACILITATE THE RELEASE OF NUCLEIC ACIDS FOR MEDICAL OR VETERINARY USE..


Patent
Zygem Corporation Ltd. and Lockheed Martin | Date: 2014-03-27

A cartridge interface module (CIM), configured to engage with a removable microfluidic cartridge in a nucleic acid analyzer system can include a fluidics component, which is configured to initiate and support a liquid extraction of nucleic acids from a biological sample contained in the removable microfluidic cartridge. The CIM also includes a polymerase chain reaction (PCR) assembly component which can be configured to initiate and support amplification of the extracted nucleic acids. The CIM may also include a high voltage electrodes component that is configured to initiate and support separation of the amplified nucleic acids into nucleic acid fragments in a separation channel of the removable microfluidic cartridge. The CIM also includes a detection optics component that can be configured to collect, detect, and direct label nucleic acid fragments. The CIM is configured to integrate with a microfluidic chip architecture of an inserted removable microfluidic cartridge.


Trademark
Zygem Corporation Ltd | Date: 2009-06-16

CHEMICAL PREPARATIONS CONTAINING ENZYMES FOR SCIENTIFIC PURPOSES, NAMELY FOR AGRICULTURAL PURPOSES, OR DNA ANALYSIS, OR BIO-SECURITY PURPOSES OR FORENSIC PURPOSES; CHEMICAL PREPARATIONS FOR SCIENTIFIC PURPOSES, NAMELY FOR AGRICULTURAL PURPOSES, OR DNA ANALYSIS, OR BIO -SECURITY PURPOSES, OR FORENSIC PURPOSES; DIAGNOSTIC PREPARATIONS OTHER THAN FOR MEDICAL OR VETERINARY PURPOSES; CHEMICAL REAGENTS FOR NON-MEDICAL PURPOSES; ENZYMES AND BUFFERS FOR NON-MEDICAL PURPOSES, NAMELY FOR AGRICULTURAL PURPOSES, OR DNA ANALYSIS, OR BIO SECURITY PURPOSES OR FOR FORENSIC PURPOSES; DILUTION SOLUTIONS FOR DILUTING NUCLEIC ACIDS, NAMELY ANY SOLUTION USED TO BUFFER, DILUTE OR PRESERVE NUCLEIC ACIDS, FOR NON-MEDICAL PURPOSES, NAMELY FOR AGRICULTURAL PURPOSES, OR DNA ANALYSIS, OR BIO-SECURITY PURPOSES, OR FORENSIC PURPOSES; CHEMICAL PREPARATIONS WHICH FACILITATE THE RELEASE OF NUCLEIC ACIDS OTHER THAN FOR MEDICAL OR VETERINARY PURPOSES. CHEMICAL PREPARATIONS FOR MEDICAL OR VETERINARY PURPOSES;NAMELY FOR USE IN MEDICAL DNA ANALYSIS OR PROTEIN DETECTION FOR MEDICAL OR VETERINARY PURPOSES; DIAGNOSTIC PREPARATIONS FOR MEDICAL OR VETERINARY PURPOSES; REAGENTS FOR MEDICAL OR VETERINARY DIAGNOSTIC PURPOSES; ENZYMES AND BUFFERS FOR MEDICAL OR VETERINARY PURPOSES, namely, FOR MOLECULAR DIAGNOSTICS, GENETIC TESTING, PATHOGEN DETECTION, OR NUCLEIC ACID ISOLATION; DILUTION SOLUTIONS FOR DILUTING NUCLEIC ACIDS, namely, ANY SOLUTION USED TO BUFFER, DILUTE OR PRESERVE NUCLEIC ACIDS FOR MEDICAL OR VETERINARY PURPOSES, namely, MOLECULAR DIAGNOSTICS, GENETIC TESTING, PATHOGEN DETECTION, OR NUCLEIC ACID ISOLATION; CHEMICAL PREPARATIONS WHICH FACILITATE THE RELEASE OF NUCLEIC ACIDS FOR MEDICAL OR VETERINARY USE; ALL WITH THE AFOREMENTIONED GOODS SPECIALLY EXCLUDING ALL ANTI VIRAL PREPARATIONS AND SUBSTANCES FOR THE TREATMENT AND/OR ALLEVIATION OF ALL VIRAL DISEASES AND DISORDERS; ALL THE AFOREMENTIONED GOODS SPECIFICALLY EXCLUDING ALL PHARMACEUTICALS AND PHARMACEUTICAL PREPARATIONS.

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