Student brings home new expertise to answer question in antibiotic resistance

Working out the structure of a complex formed when a protein binds to DNA has proved to be key in understanding how an antibiotic-producing organism controls resistance to its own antibiotic, and may be an example of how other antibiotic producers regulate export to prevent self-toxicity.

The natural production of antibiotics by certain microorganisms is a complex and highly regulated process, not least because the organism making these compounds must protect itself from their toxic effects. Researchers at the John Innes Centre, which is strategically funded by the Biotechnology and Biological Sciences Research Council (BBSRC), have been studying the production of simocyclinone, produced by Streptomyces antibioticus, and in particular how the production of this potent antibiotic triggers an efficient pumping mechanism that exports the antibiotic from the cell.

Much of the work elucidating this protection mechanism has been carried out by Tung Le, a Vietnamese PhD student enrolled in the JIC's four-year rotation PhD programme. Tung, working under the supervision of Mark Buttner and David Lawson, showed that SimR, the protein Streptomyces antibioticus uses to regulate antibiotic export, can bind either to DNA or to the antibiotic itself, but crucially cannot bind to both. This means that when the antibiotic is around, SimR releases the DNA, which allows the expression of a gene that encodes a pump responsible for removing simocyclinone from the cell.

"This provides a mechanism that couples the potentially lethal biosynthesis of the antibiotic to its export, which has wider implications for resistance to clinically important antibiotics," commented Prof. Buttner. "However, we needed to know more detail about the interaction between SimR and DNA."

In this latest research, published in the journal Nucleic Acids Research, they show that the SimR protein has a novel 'arm' and that cutting off this arm unexpectedly weakened SimR binding to DNA. To determine the function of this arm, the researchers needed to work out the crystal structure of the protein bound to DNA, something which hadn't been achieved in Norwich before.

To overcome this skills gap, Tung won both a Korner Travelling Fellowship and an EMBO Short-Term Travel Fellowship to visit the University of Texas M.D. Anderson Cancer Center, home to one of the leading laboratories specialising in this technique. Tung spent three months working in the labs of Richard Brennan and Maria Schumacher, learning how to solve the structures of protein-DNA complexes. He was then able to apply this to his own project.

"I learned a lot and it was a great experience," said Tung. "The knowledge I brought back was not only useful for my project but will also be beneficial for others, and I feel very proud about that."

Usually, the SimR arm is unstructured, but in the presence of DNA they saw that it becomes ordered and binds into the minor groove of the DNA molecule. The crystal structure also shows how other parts of the SimR protein form sequence-specific interactions with a binding site in front of the export pump gene.

SimR is a member of a large family of regulatory proteins found in bacteria, and is the fifth one to have its structure solved when bound to DNA. The way these proteins recognise their target DNA sequences differs. This new example has wider implications, as a bioinformatic search of this family of regulators showed that many of them also have arms similar to the one characterised in this study.

Tung submitted his PhD thesis in early August, and his research has already produced four first-author papers. He is due to take up a post-doctoral position at the Massachusetts Institute of Technology in January.

"It can be very difficult for non-EU students to find the funding to study for a PhD in the UK, and so I was delighted to be offered a place on the JIC rotation programme. I am keen to encourage and help build relations between JIC and Vietnam. I was very happy to see the JIC is involved in joint work with Vietnam to sequence the genomes of different varieties of rice" said Tung, who left Vietnam at the age of seventeen for a bioscience career in the UK.

The researchers have also recently received a grant from the BBSRC to continue investigating the complexities of the regulation of antibiotic biosynthetic pathways, focussing on SimR and two other antibiotic-responsive transcription factors encoded in the simocyclinone biosynthetic cluster. This will establish the roles that the antibiotic plays in regulating self-resistance and its own biosynthesis. With the ever-growing problem of resistance, this kind of fundamental research is vital.

Provided by Norwich BioScience Institutes

Student turns paper mill waste into ‘green’ material for industrial applications

A method to use paper mill waste to produce ecologically friendly, industrial foams from renewable resources has been developed by a graduate student in agriculture at the Hebrew University of Jerusalem.

Foams are used for numerous day-to-day uses, including in the manufacture of furniture and car interiors. In many composite material applications, they are used as core material in "sandwich" panels to achieve high strength, weight reduction, energy dissipation and insulation. Conventional foams are produced from polymers such as polyurethane, polystyrene, polyvinyl chloride (PVC) and polyethylene terephthalate (PET). Since all of these current foams rely on fossil oil, they present a clear environmental disadvantage.

Shaul Lapidot, a Ph.D. student of Prof. Oded Shoseyov, along with his laboratory colleagues at the Robert H. Smith Faculty of Agriculture, Food and Environment of the Hebrew University in Rehovot, has formulated a procedure for production of nano-crystalline cellulose (NCC) from paper mill waste. NCC is further processed into composite foams for applications in the composite materials industry as bio-based replacement for synthetic foams.

The process of paper production involves loss of all fibers with dimensions lower than the forming fabric mesh. Consequently around 50% of the total fibers initially produced are washed away as sludge. In Europe alone, 11 million tons of waste are produced annually by this industry, creating an incentive for finding alternative uses and different applications for the wastes.

Lapidot has found that fibers from paper mill sludge are a perfect source for NCC production due to their small dimensions which require relatively low energy and chemical input in order to process them into NCC. He also developed the application of NCC into nano-structured foams. This is further processed into composite foams for applications in the composite materials industry to be used as bio-based replacement for synthetic foams.

NCC foams that Lapidot and his colleagues have recently developed are highly porous and lightweight. Additional strengthening of the foams was enabled by infiltration of furan resin, a hemicellulose-based resin produced from raw crop waste, such as that remaining from sugar cane processing, as well as oat hulls, corn cobs and rice hulls.

The new NCC reinforced foams display technical performance which matches current high-end synthetic foams. The technology was recently licensed from Yissum, the technology transfer company of the Hebrew University, by Melodea Ltd., an Israeli-Swedish start-up company which aims to develop it for industrial scale production.

Lapidot's development has led to his being awarded one of the Barenholz Prizes that were presented on June 21 at the Hebrew University Board of Governors meeting. The award is named for its donor, Prof. Yehezkel Barenholz of the Hebrew University-Hadassah Medical School.

Story Source:

The above story is reprinted (with editorial adaptations) from materials provided by Hebrew University of Jerusalem, via AlphaGalileo.

Student creates clothes that trap harmful gases

 A new Cornell cloth that can selectively trap noxious gases and odors has been fashioned by a senior into a mask and hooded shirts inspired by the military.

The garments use metal organic framework molecules (MOFs) and cellulose fibers that were assembled in assistant fiber science professor Juan Hinestroza's lab to create the special cloth.

MOFs, which are clustered crystalline compounds, can be manipulated at the nanolevel to have cages that are the exact same size as the gas they are trying to capture, said Jennifer Keane '11, a fiber science and apparel design (FSAD) major in the College of Human Ecology.

Keane worked with Hinestroza and fiber science postdoctoral associate Marcia Da Silva Pinto to create the gas-absorbing hood and mask. Some of the basic science behind this project was funded by the U.S. Department of Defense.

"The initial goal of attaching the MOFs to fibers was sponsored by the Defense Threat Reduction Agency. We wanted to harness the power of these molecules to absorb gases and incorporate these MOFs into fibers, which allows us to make very efficient filtration systems," Hinestroza said.

Da Silva Pinto first created MOF fabrics in Hinestroza's lab, working in collaboration with chemists from Professor Omar Yaghi's group at the University of California-Los Angeles; Yaghi is one of the pioneers and leaders of MOF chemistry, said Hinestroza.

At first the process did not work smoothly. "These crystalline molecules are like a powder that cannot easily become part of cloth," Da Silva Pinto noted. After months of trying to attach the particles to the fiber, the researchers realized that, "The key was to bring the fiber to the particle ... It was a real paradigm shift," she said.

"Now we can make large surfaces of fabric coated with MOFs, and we are looking at scaling up this technology to nanofibers," said Hinestroza. "This type of work would only be possible at a place like Cornell where you have this unique merging of disciplines, where a fashion designer can interact easily with a chemist or a materials scientist."

Though trained as a chemical engineer, Hinestroza said he likes "to work with designers because they think very differently than scientists. I love that because that's where the real creativity comes, when you have this collision of styles and thinking processes."

Keane, who took Hinestroza's Textiles, Apparel and Innovation class, said she started Cornell as a pre-med major but switched to FSAD because she enjoyed the creative aspect of sewing and designing her own clothing in high school. She has since interned with Nike and recently received a job offer from Adidas.

She noted that while her MOF hood and mask will not be showcased in the upcoming Cornell Fashion Collective spring fashion show at Barton Hall, April 16, 7-9:30 p.m., her line of comfortable women's sportswear will be. It includes many geometric patterns and bright jewel tones.

"It's a lot of knits, jersey and this brushed denim, which is really soft ... It was based off of jewelry designs that I saw in Italy," she said.

Provided by Cornell University (news : web)