Some Bacteria Like it Hot

Benjamin Kumwenda from Malawi began his scientific career studying undergraduate biology at the University of Malawi – Chancellor College in Zomba. But as he made his way through the course requirements for his Bachelor of Science degree, he felt equally drawn to Computer Science, and took as many interesting CS courses as he could fit into his schedule.

“In this part of Africa people think that Computer Science is just about maintaining computers,” he said. “But my interest was in the application of Computer Science to my major understanding of genes, genomes, and proteins to solve biological and medical problems. These are intensively data-driven activities that require a lot of computation.”

When he earned his Bachelor of Science degree at an honors level, the next logical step was to combine his two interests. He was able to do that at the University of the Witwatersrand in South Africa, where he moved to study computational biology at the master’s level. His work there gave him a solid background in bioinformatics, and the opportunity to join the RISE-SABINA network at the University of Pretoria nearby. There he found a kindred spirit in Prof. Oleg Reva, a native of the Ukraine and specialist in bioinformatics who welcomed Benjamin and his enthusiasm for the subject.

Benjamin’s work at Pretoria does not require huge computing power, but his dual background of biology and computer science is well suited to the challenges of bioinformatics. These include the study and modeling of individual genes and whole genomes. The knowledge of these complex systems can open the way to the design of valuable new chemicals for industry and drugs for medicine. For example, detailed knowledge of protein structure can allow the design of a drug that will bind tightly to a site and prevent another agent, such as a disease organism, from binding to the same site and causing disease. In the same way, a researcher might study the genome of a little-known bacterium and identify a genetic trait that is known from other organisms and that might be useful for industry.

When Benjamin arrived, he had several options for moving ahead at the PhD level. One was to concentrate his work in the area of natural products, which is the main thrust of SABINA. But he knew that Prof. Reva was working on bacteria, and he saw an opportunity to become expert in the exciting new area of thermophilic bacteria and its many practical applications.

Once a curiosity, this special class of living organisms (“thermophilic” derives from the Greek for heat-loving) is now drawing attention from researchers around the world. Benjamin is interested partly in discovering how they are equipped to survive at such high temperatures; most species function best at temperatures somewhat above 50 degrees Celsius (122 degree Fahrenheit), but some of them, often called “extremophiles,” flourish at temperatures near and sometimes above the boiling point of water, 100 degrees Celsius (212 degrees Fahrenheit). These bacteria are familiar to many travelers who have visited Yellowstone National Park in the USA or other sites of geysers, fumaroles, or hot springs where these organisms thrive and create colorful patterns and textures against rocky backgrounds.

At a more practical level, he is also learning how these bacteria synthesize proteins, and how those proteins, especially the enzymes that catalyze chemical reactions, might be useful. Many industrial processes, such as generation of biofuels, occur most efficiently at high temperatures, where many bacteria do not perform well. Thermophilic species are the exception in preferring hot environments, and much sought-after as powerful catalytic tools. The higher the temperature, the more efficient their enzymes tend to be, and the faster their reactions with other chemicals.

Some thermophilic species are already proving valuable in producing paper, dairy products, clothing, and other products. A goal in making shoe leather, for example, is to make the leather soft. This can be done with enzymes that partially break down the skins of the leather, and the enzymes of thermophilic bacteria can do it fastest. In the same way, the food industry uses enzymes to tenderize meat, and the laundry industry uses thermophilic bacteria to make detergent more efficient. In addition, the bacteria has good ability to clean up water than has been polluted by heavy metals such as chromium, iron, and zinc, and to reduce the toxicity of heavy metals in food.

Benjamin has been working in particular on South African species of bacteria, seeking to  understand them in the context of others that have been studied previously. He is especially interested in finding genetic patterns that determine thermo-stable behavior at high temperatures. This exercise in comparative genomics helps him identify sections of the genome that seem likely to be useful for industrial needs, especially new ones.

More specifically, his project focuses on the completely sequenced genome of the bacterium Thermus scotoductus strain SA-01, which was isolated at a depth of 3.2 kilometers in a goldmine at Witwatersrand. The goal is to compare its genome against other bacteria and understand its features. He has examined the enzymes it produces and determined the properties of those enzymes, especially the temperatures at which they can function efficiently in the laboratory.

“The theory,” he said, “is that as proteins are being created, they fold into a structure that is thermodynamically stable. This means that the most stable structures are the ones that expend the least amount of energy as they fold. The energetic features of various configurations of proteins are already known, so when we find the protein of thermophilic bacteria fold in a certain way in nature, we calculate the energy and know that will be stable. Then we have a good idea of what properties, or chemical reactions, it will have, and think about designing enzymes that do the same things.”

Benjamin started his PhD work in April 2010, and expects to complete his degree shortly. He has already completed a paper on his studies for BMC Genomics apr 29, 2009 – an open access, peer-reviewed journal.

Story: Alan Anderson, SIG blog- April 2013

Modernizing the Horticulture of Tea

Godwil Madamombe, a native of Zimbabwe, earned his bachelor’s degree in crop science and his master’s degree in crop protection at the University of Zimbabwe, based in Harare. During his first major crop protection project, he worked for the government as a plant pathologist. He was tasked with conducting research on many common and injurious diseases, including Fusarium bark disease, coffee berry disease, leaf rust and others; he used cultural, biological, and host plant resistance and chemical methods in developing integrated disease management programs.

A significant part of his MSc studies were aimed at determining the extent to which smallholder farmers planted soybean seed that had been kept from the previous year’s crop. The reason they retained seed was that they could not afford to buy fresh seed each year, and they would usually continue to plant the retained seed for as long as it lasted. But this habit brought many drawbacks. The most direct of these was the introduction of seed-borne pathogens to the next year’s crop. In addition, while these “free” seeds did germinate, they usually lost more and more of their genetic disease resistance and vigor during each successive year. For example, Godwil found that most farmers following this practice would lose between 15 and 30 percent of their crop during the first year. By the third or fourth year, the yields would be too low to support the farmer. At that point, unless the government provided new seed for free, they would have nothing to plant. Sometimes a seed company would bring them new seed, but they had to agree to sell their entire crop back to the company at a low price, and also to pay for transporting the harvested beans to the company.

“We offered the farmers herbicides and fungicides to reduce the losses,” said Godwil, “but they couldn’t afford them. We felt very helpless. All we could do was to recommend keeping the fields clear of weeds, drying the seed they harvested, and storing it in a moisture-free environment, which they usually didn’t have.”

After completing his master’s studies in 2003 he was offered a job in Zimbabwe with the Tea Research Foundation of Central Africa (TRFCA). With some variation by year, Zimbabwe is the third-, fourth-, or fifth-largest tea producer in Africa, producing about 18,000 tons of tea annually – more than Zambia or Mozambique, but less than the 40,000 tons of Malawi and the 345,000 tons of Kenya, the world’s third-largest producer after China and India. But Zimbabwe tea is known for high quality and high yields, and as the country struggles to emerge from a period of political strife, its growers are eager to maintain that reputation.

During his work for the TFRCA, Godwil saw that a significant problem for the Zimbabwe tea industry was the shortage of labor, which had become a problem in nearby Malawi as well. The tea industry had long depended on labor from Mozambique, which was plentiful during the years of civil war there, from 1977 to 1992. Many workers sought to escape the violence in Mozambique and were willing to work hard and cheaply in neighboring countries. After the war, however, these laborers were quick to abandon the arduous, low-paying job of picking tea in favor of jobs closer to home. The supply of labor declined, and tea growers were forced to turn to the mechanization of tea harvesting.

After using the machines for some time, the growers realized that their yields were declining, but they did not know why. Godwil was asked to search for the reason, and he quickly identified several problems. First, the machine harvesters were non-selective, taking the immature leaves/shoots as well as the mature shoots and in the process damaging the bush. However, the tea industry had no other option besides mechanical harvesting now that labor was either not available or, if available, more expensive than it had been during wartime. In addition, Godwil knew there were many other reasons for yield decline that were not understood. For example, the growers wanted to compensate for the reduced yield by making the plants grow faster and produce more mature leaves – but without losing flavor. This raised many basic questions of horticulture. For example, no one knew how much of the products of photosynthesis was going to the shoots and how much to the roots under mechanical harvesting. Also, growers knew that more nutrients are removed from fields through machine harvesting, but they did not know how much of the fertilizer was taken up by the roots and how much was taken up by the plant for shoot growth. Of the solid nitrate scattered between rows, how much was actually made available to the plant? During harvesting, how much of the fertilizer leached into the soil or was removed by different harvesting methods?

Through his work at the TRFCA, Godwil heard about the SABINA network in biotechnology and informatics, which was already involved in tea research from a genetic viewpoint. For example, SABINA students are searching for the genes that control drought resistance and other desirable traits. He was accepted in 2010 as a PhD student in horticultural science, gaining access to the advanced research facilities and expert researchers at the University of Pretoria and the nearby Council for Scientific and Industrial Research.

Godwil joined the RISE program in 2010 but had to delay his research in order to take several advanced courses in Pretoria. He was able to begin field work in Zimbabwe in 2011, visiting Pretoria every three months to consult with Prof. Zeno Apostolides, Dr. Nicolette Taylor, Dr. Eyob Tesfamariam, and other mentors and colleagues. In the lab, he is about to do the kinds of complex biochemistry not possible in the field, such as starch analysis. He has access to such instrumentation as centrifuges, a photospectrometer to measure starch level, ceptometer to measure the amount of light reaching the tea plant, photosynthesis system to measure the rate of photosynthesis with the tea bush canopy, sensitive scales and pH meters, and a controlled temperature water bath. He has faced numerous logistical delays, including the slow arrival of new equipment and implementation of reliable weather station tracking on the tea farms. He also needs to obtain data through the full tea pruning cycle, which spans three years. But he has been cleared to extend his research to June 2013, and he is optimistic that it will bring value to the tea growers. At a recent professional presentation on his work at the 2nd All-Africa Horticultural Congress at Skukuza,  Kruger National Park, attended by horticultural experts from all over Africa, his presentation won first prize.

Source: Alan Anderson-Science Initiative Group (SIG) Blog

Key Find for Acid Mine Drainage on World Water Day

A newly developed membrane used to separate waste from water could become key in the treatment of pollutants ranging from acid mine drainage to oil-containing wastewater, as well as in processes ranging from desalination to kidney dialysis.

The research was published in Scientific Reports (Nature Publishing Group) on Friday, 22 March, coinciding with World Water Day and falling within South Africa’s National Water Week.

The technology – which was developed by a team of researchers from Wits University, in

collaboration with NASA – will make it easier to filter pure water from waste produced during mining, oil and gas exploration and production, and nuclear exploration, to name a few. Even medical purification processes such as kidney dialysis could benefit.

A commercial product will hopefully be developed soon, and there are plans to approach the US government regarding their problems with contaminants such as arsenic, mercury, and other heavy metals in their water. Closer to home, the technology could make huge inroads in dealing with the major issue of acid mine drainage.

According to the Head of the School of Chemical and Metallurgical Engineering, Prof. Sunny Iyuke, who developed the product in collaboration with two PhD students, the membrane module (similar to a household water filter) could be used to catch water waste from mines before it entered drains or the water table. Water flow analytics could be used to track the direction and location of any escaped wastewater, where another membrane module (in the form of a borehole) could be stationed.

The nanocomposite membrane gives two products: a smaller amount of concentrated waste and water so clean it could be drinkable. The waste can be reused, as in the case of arsenic, which is used in preservatives for wood and leather, ammunitions manufacturing, and pest control. Even the waste from acid mine drainage could be reused.

“Water is critical to sustaining life, and water scarcity is becoming a huge problem not just in South Africa, but all over the world,” said Iyuke. “This technology produces a win win situation, for industry and the environment.”

Source: Wits Newsroom, April 2013

CMEG researchers head for the Namib Desert

In late April 2013, Don Cowan will lead the 20-strong Centre for Microbial Ecology and Genomics (CMEG) team, along with researchers from the University of the Western Cape (UWC), the University of Cape Town (UCT), Heriot-Watt University, Karlsruhe Institute of Technology and the Spanish National Research Council (Consejo Superior de Investigaciones Científicas – CSIC), on a week-long field research programme to the Gobabeb Research and Training Centre in the Namib Desert.
Building on the work done during two previous visits, the team will undertake the first comprehensive survey of Namib Desert microbiology, using the latest molecular phylogenetic measurements.

of Samples recovered during the week will be returned to the CMEG laboratory at the University Pretoria for chemical, physical and molecular analyses. These studies will rely heavily on genomic and metagenomic methods and will extensively employ next generation DNA sequencing.

Individual research projects will focus on the gravel desert soils, the dune and inter-dune environments, the microbiology of different soil types and soil ages, and specialised niche environments such as spear-grass mounds, saline springs, ‘fairy circles’ and hypoliths. Macro and microclimatic effects, soil chemistry, carbon turnover and other factors are all expected to influence microbial community structures. These studies will include surveys of bacterial, fungal and bacteriophage diversity.

Source: Prof Don Cowan, UP news April 2013