between defense and attack

The scientists of the institute are looking for natural antibiotics based on the fighting strategies of the bacteria Dr. Rotem Sorek. The champions of survival

Bacteria are warlike types. Although they cause diseases in humans, most of the time they are engaged in wars and struggles with other microorganisms. In the battles they conduct among themselves for food and living spaces, the bacteria use sophisticated weapons and defenses. Bacterial attack and defense strategies are at the center of the research of Dr. Rotem Shurk, who recently joined the Department of Molecular Genetics at the Weizmann Institute of Science. "We have a lot to learn from the bacteria, which are the champions of survival," he says. "These microscopic creatures exist on Earth much longer than more developed creatures, such as fungi, plants, animals and humans, and they know how to adapt and adapt themselves to the changing environment impressively."

Dr. Shurk believes that through an in-depth study of the secrets of bacterial warfare, scientists will be able to find new biological strategies and develop advanced ways to deal with bacteria that have developed resistance to antibiotics. This is one of the main health problems of the 21st century: for example, the amount of antibiotic-resistant bacteria strains in US hospitals has increased tenfold in the last two decades, from 2% in 1990 to approximately 20% today.

One way to deal with drug-resistant bacteria may be based on "natural antibiotics" - proteins that certain bacteria produce to kill other bacteria. Dr. Sorek: "If we manage to locate these proteins and understand their mechanisms of action, we may be able to turn these weapons back against the bacteria themselves." In his post-doctoral research, which he carried out at the Lawrence Berkeley National Laboratory in California, Dr. Sorek discovered an original method for the rapid detection of such weapon proteins, based on the process of deciphering the genome of bacteria.

In order to decode the genetic material of the bacterium, the scientists break down its genome into short segments, which they combine, using genetic engineering methods, with the genetic load of the bacterium E. coli, which they use as an "instrument" for DNA replication. After that, the segments are connected to each other and the complete genome is "read". This process presented the researchers with a permanent problem - gaps were created in the genome that do not allow continuous reading. Dr. Sorek believed that this problem is actually an advantage, and that the gaps arise because certain DNA segments contain genes that produce proteins that kill the E bacteria. coli within them were supposed to multiply. He developed a computational method that makes it possible to read the missing DNA segments, thus locating the sequence of the lethal genes.

In his new laboratory at the Weizmann Institute of Science, Dr. Sorek continues to develop and apply his method. Another of his research deals with a natural system called CRISPR, which allows bacteria that carry it to defend themselves against virus attack. This system was discovered by French scientists in 2007. A better understanding of the system may help to develop effective ways to protect "desirable" bacteria, which play different roles in industry (such as those that produce various dairy products, or are used to clean areas contaminated with oil), from viruses . As in many cases in human history, Dr. Sorek is also looking for ways to turn this defensive weapon into an offensive weapon, which will cause harmful bacteria to destroy themselves.

Many of Dr. Sorek's studies are based on innovative technologies for DNA decoding, which revolutionized life science research.

The Solexa systems currently operating at the Weizmann Institute of Science are capable of deciphering 600 million genetic letters every day. For comparison, the systems used to decipher the human genome operated at a rate of about half a million DNA letters per day. The cost of genetic decoding in the new systems is about 4 dollars per million letters, compared to 2,000 dollars in older systems. Along with the decoding systems, Dr. Sorek's laboratory also has about 40 computers, including about 300 processors, which make it possible to analyze the flow of information emitted from the decoding systems using computational methods developed by the group members.
These advanced measures allow his group to decipher both entire genomes of bacteria and many RNA molecules. This research may lead to the development of more accurate replacements for the DNA chips currently used for genetic research. Such studies - which reveal the evolutionary processes taking place in bacteria, and their genetic control mechanisms - will allow scientists to perform various manipulations in the genetic material of the bacteria - for the benefit of humans.

The question: How do you fight bacteria that have developed resistance to antibiotic drugs?

The findings: A method of using natural antibiotic substances - proteins that certain bacteria produce to kill other bacteria, may indicate a direction for the development of drugs that will overcome the resistant bacteria.

Rotem Shurk was born in Tel Aviv in 1975 and studied for a first, second and third degree at Tel Aviv University. At the same time as his studies, Sorek worked for five years at the biotechnology company Compugen. After doing post-doctoral research in the USA, he joined the Department of Molecular Genetics at the Weizmann Institute of Science as a senior researcher. He won many awards, including the 2008 Clore Research Award, and registered nine patent applications. He is married to Zahar, who completed her doctoral studies at the Institute, under the guidance of Prof. Jacob Englister. The couple lives in Rehovot with their four-year-old son Uri. In his spare time, Dr. Sorek enjoys windsurfing and mountain biking.