Biotechnology

Event Date: 
Wednesday, January 28, 2015 - 19:00 - 19:45
Institution: 
University of Sydney
Title: 

The use of genomics in diagnostic and public health microbiology

Abstract: 

Since 2004 technological advances have enabled us to sequence more nucleic acid and generate more data in a shorter amount of time. Decreases in cost per nucleotide sequenced, the initial price of sequencing machines and the complexity of library construction means that whole genome sequencing (WGS) is available in many research labs and an increasing number of public health microbiology labs. I will examine the use of WGS in public health microbiology, particularly the possibility of investigating organisms without culture, the interrogation of genomes where PCR may be unavailable, outbreak investigation, tracking resistance mutations and novel pathogen discovery.

Event Date: 
Wednesday, March 26, 2014 - 18:00 - 18:15
Institution: 
UNSW
Title: 

Insights into the stress response of the biomining bacterium Acidithiobacillus ferrooxidans using gene expression and proteomic analysis

Abstract: 

Bioleaching is a simple and effective process used for metal extraction from low grade ores and mineral concentrates using microorganisms. The extraction of some metals such as copper from low grade ore is becoming necessary because of gradual depletion of high grade ore. The traditional methods used for extraction of copper are either Pyrometallurgy or Hydrometallurgy. However both the methods are not environmental friendly. There are many techniques proposed to extract metals but these are not practically suitable, as these requires a very high energy input as well as most of them creates environmental pollution problem, that also rises the cost of environmental protection throughout the world. Therefore, bioleaching is recognizable as the most environmentally friendly method of separating metals since it requires less energy and it reduces the amount of greenhouse gasses released to the atmosphere. Bioleaching is also a fairly simple process that does not require a lot of expertise to operate or complicated machinery.
The most commonly used bacterium in bioleaching is Acidithiobacillus ferrooxidans (former Thiobacillus ferrooxidans) and this is due to its capacity to oxidize metal sulphides. A. ferroxidans is a chemolithotrophic bacterium capable of utilizing ferrous iron or reduced sulphur compounds as the sole source of energy for its growth. It thrives optimally around pH 2.0 and 30ºC. During Bioleaching process, A. ferrooxidans is often subject to changes in the ideal growth pH and temperature, and to nutrients starvation. These changes can affect the bacterial physiology and as a consequence, the efficiency of bioleaching. Then, the stress response of this bacterium subject to heat stress and phosphate starvation has been investigated using different approaches, namely, gene expression and proteomic analysis, Fourier transform infrared spectroscopy (FT-IR), as well as morphological analysis by scanning electron microscopy (SEM).
The results showed that under the tested stress conditions A. ferrooxidans cells suffer elongation, a common stress response in bacteria. Alterations in carbohydrates, phospholipids and phosphoproteins were detected by FT-IR. By proteomic analyses (2-DE and tandem mass spectrometry), many differentially expressed protein spots were visualized and identified as proteins belonging to 11 different functional categories. Indeed, the up-regulated proteins were mainly from the protein fate category. Real time quantitative PCR was employed to analyze changes in the expression patterns of heat shock genes, as well as many other genes encoding proteins related to several functional categories in A. ferrooxidans. Cells were submitted to long-term growth and to heat shock, both at 40°C. The results evidenced that heat shock affected the expression levels of most genes while long-term growth at 40°C caused minimal changes in gene expression patterns – with exception of some iron transport related genes, which were strongly down-regulated. Further bioinformatic analysis indicated a putative transcriptional regulation, by the σ32 factor, in most heat-affected genes. These results evidence that A. ferrooxidans has an efficient range of stress-responses, which explains its ability for biotechnological purposes.
 

Event Date: 
Wednesday, November 27, 2013 - 19:00 - 20:00
Institution: 
Deptartment of Civil and Environmental Engineering, MIT
Title: 

The Ocean....from the microscale

Abstract: 

At a time when microbial ecology is largely traveling along genomic roads, we cannot forget that the functions and services of microbes depend greatly on their behaviors, encounters, and interactions with their environment. New technologies, including microfluidics, high-speed video-microscopy and image analysis, provide a powerful opportunity to spy on the lives of microbes, directly observing their behaviors at the spatiotemporal resolution most relevant to their ecology. I will illustrate this 'natural history approach to microbial ecology' by focusing on marine bacteria, unveiling striking adaptations in their motility and chemotaxis and describing how these are connected to their incredibly dynamic, gradient-rich microenvironments. Specifically, I will present (i) direct evidence for a diverse gallery of microscale microbial hotspots in the ocean; (ii) a new framework for understanding the evolution of microbial diversity in the ocean; and (iii) microfluidic experiments to capture the dramatic chemotactic abilities of bacterial pathogens towards the roiling surface of coral hosts. Through these examples, I hope to show that direct visualization can foster a new layer of understanding in microbial ecology and can help us unlock the ocean's microscale.

Event Date: 
Wednesday, January 30, 2013 - 18:00 - 18:15
Institution: 
University Technology Sydney
Title: 

Development of an electrochemical biosensor for bacteria detection coupling immuno-capture with magnetic particles and amperometry at flow-channel microband electrodes.

Abstract: 

 
Current technology is insufficient for rapid on-site identification of the causative agents for waterborne diseases and existing time-consuming detection results in delayed management decisions. Fast, reliable and low-cost methods for the screening of pathogens are paramount in fields such as the environment, food industry, healthcare and defense. With the constant progress of scientific knowledge, a fast diversification of detection techniques is occurring, brought about by the appearance of imaginative new concepts within the scientific community. Biosensors are a perfect example of the combination of multidisciplinary knowledge. They encompass many fundamental, technological and scientific advances in biology, chemistry and physics.
Here, we describe a recently developed electrochemical biosensor for the detection of bacteria cells in aqueous samples. The technology used for this detection combines immuno-magnetic capture and amperometric detection in a one-step sandwich format, and in a microfluidic environment. The whole assay could be completed in 1 h and the experiments performed with Escherichia coli evidenced a linear response for concentrations ranging 102–108 cell ml−1.

Event Date: 
Wednesday, November 28, 2012 - 07:00 - 08:00
Institution: 
University of Sydney
Title: 

Biodegradation of dichloroethane by aerobic bacteria at the Botany Industrial Park

Abstract: 

The chlorinated hydrocarbon 1,2-dichloroethane (DCA) is a common pollutant of groundwater, and poses both human and environmental health risks. The Botany Industrial Park in south Sydney is heavily contaminated with DCA and other organochlorines. The main user of the site (Orica Ltd) operates a large groundwater treatment plant (GTP) on site to contain and remediate the DCA-contaminated groundwater. At present, remediation is done by air-stripping and thermal oxidation, but this is very costly and energy-intensive. Orica is interested in alternative technologies for treating the groundwater, including bioremediation. In 2010, a pilot scale membrane bioreactor (MBR) was set up to treat a fraction of the groundwater. The aims of our study were to identify DCA-degrading bacteria and genes in the GTP and on the site at large, define the community structure and ecological successions occurring in the MBR, develop a qPCR for catabolic genes in the DCA biodegradation pathway, and field-test this qPCR assay in the MBR and in a survey of groundwater in monitoring wells on the site. We discovered that DCA-degrading bacteria using a hydrolytic pathway (dhlA/dhlB genes) were widespread and diverse at this site, and that the dhlA gene was carried on a catabolic plasmid. The community in the MBR was dominated by alpha- and beta-proteobacteria, and was highly dynamic, changing dramatically in composition as the percentage of raw groundwater in the feed was increased. By combining dhlA qPCR and 16S pyrosequencing data, we found evidence that thus-far-uncultured species of Azoarcus may play a major role in DCA bioremediation in situ in the MBR.

 
Prepared by Valentina Wong (UNSW PhD student)
On a cold Tuesday night, Adrian Low from University of New South Wales warmed the JAMS audience with his passion on bioremediation of organochlorine contaminated groundwater. Adrian described the discovery of Australia’s first 1,2-dichloroethane (DCA) degrading consortium, AusDCA. His work in the field demonstrated the efficacy and sustainability of using organochlorine respiring bacteria to remediate organochlorine contaminants in situ. He plans to isolate the bacterial species responsible for performing this unique task.

Event Date: 
Tuesday, July 24, 2012 - 18:15 - 18:30
Institution: 
University of NSW
Title: 

Development of an Australian 1,2-Dichloroethane degrading culture

Abstract: 

 
1,2-Dichloroethane (DCA) is one of the most common organochlorine groundwater contaminants worldwide. The successes of bioremediation field studies with organochlorine respiring bacteria have proved the efficacy of the method to degrade such contaminants in situ. The objective of this study was to demonstrate that a DCA degrading consortium, named AusDCA could be used to bioaugment a DCA contaminated acidic aquifer in situ. Functional characterisation experiments of AusDCA in batch cultures showed that the culture could dechlorinate high concentrations of DCA (6.3 mM) to ethene anaerobically at pH 5.5 and pH 6.5 and was not inhibited by approximately 15 µM of chloroform (CF). 

Event Date: 
Wednesday, June 27, 2012 - 18:15 - 18:30
Institution: 
University of Western Sydney
Title: 

The Taguchi methods, or how to quickly and efficiently optimise PCR conditions.

Abstract: 

Originally, the Taguchi methods were formulated for the optimisation of industrial processes, where several factors (3 to 50) of complex multifactorial experiments were tested at different levels (Taguchi, 1986). The Taguchi methods use orthogonal arrays to organise the ‘control’ parameters/factors affecting a process and the levels at which they should vary. A particular algorithm (quadratic loss function) is then applied in order to predict the optimum conditions of a process, whilst accounting for performance variations due to ‘noise’ factors beyond the control of the design. In a normal factorial strategy, every parameter should be individually tested at several levels, thus becoming extremely time-consuming, labour-intensive and expensive. The Taguchi methodology allows for testing only a few combinations, therefore dramatically decreasing the total number of experiments and simultaneously identifying the optimum condition of several factors.
Because some functional genes are present only in small fractions of microbial communities, and only few copies can be present in each genome, their detection by classical PCR methods can be challenging. Optimisation of the experimental conditions of a PCR includes the different components of the reaction mix (concentrations of salt, primers, enzyme, DNA template, etc.) as well as the cycling features (time and temperature of the denaturation, annealing and extension steps, number of cycles, etc.). We used this approach for the optimisation of the detection by PCR of functional genes of non-cultivable microorganisms present in environmental samples. In particular, we tested the different parameters involved in a (touchdown/nested) PCR and estimated the optimum settings for the detection of the functional gene pmoA, coding for the putative active site of the particulate methane monooxygenase, involved in the oxidation of methane by methanotrophic bacteria. The application of the Taguchi method allowed the suppression of a nesting step and thus a significant reduction in the amplification time, as well as reagent cost.
 

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