Finding biological data sets to stifle bacterial growth

October 24, 2016 23:32
4 minute read.

A spiral galaxy known as NGC 1433 is seen in an undated image captured by the NASA/ESA Hubble Space Telescope. (photo credit: REUTERS)

Natural evolutionary processes prevent the presence of dangerous and potentially deadly molecular interactions by avoiding the presence of specific protein sequences in microorganisms. A study from the lab of chemistry Prof. Noam Adir at Haifa’s Technion-Israel Institute of Technology found these sequences by a novel method – looking for what is missing in biological data sets.

The group then experimentally showed that when these sequences are present in a protein, bacterial growth is indeed affected. The study was recently published in the Proceedings of the [US] National Academy of Sciences.

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Evolution is an ongoing process in which those individuals of species that are the most fit for their environment have more offspring and thus outcompete less fit individuals. The individual’s fitness is a product of the quality of its cellular biochemistry, made possible by the thousands of enzymes that allow its physiology to perform all of the necessary life-giving chemical reactions.

Problems in these molecular functions can lead to disease, loss of adaptability to environmental changes or weakness against other organisms. The molecular machines that make life possible are large polymers made up of linear sequences of building blocks that contain different chemical functions – proteins, DNA and RNA. Biological variety is a result of the evolutionary changes in these polymers, first and foremost the result of the astronomic number of possible permutations in the order of the 20 naturally occurring amino acid (AA) residues that are the building blocks of proteins.

There are 8,000 possible sequences of three AAs, 160,000 sequences of four AAs, more than three million sequences of five AAs and so on. Since proteins can contain between hundreds to thousands of AAs, the possibilities are endless. The millions of different protein sequences found in all organisms determine the three-dimensional structures that give proteins the ability to function correctly. Proteins in cells can work alone or associate correctly with other cellular components, while avoiding incorrect and harmful associations with other components.

Changes to the sequences naturally occur due to mutations of an organism’s DNA.

Changes due to mutations can lead to new positive characteristics, or they may have negative consequences to the organism’s viability.

A mutation that has a negative effect may prevent the organism from competing with other organisms in its environment, eventually leading to its death. One could predict that over time, evolutionary pressure would work against the presence of organisms containing these internally lethal sequences, causing them to disappear.

Over the past few years, there has been a worldwide effort to obtain the entire DNA sequences (genomes) of many organisms.

These data have given us the ability to predict all of the possible protein sequences (the proteome) that might exist in organisms as simple as bacteria or as complicated as humans.

Adir and his students, Dr. Sharon Penias- Navon and Tali Schwartzman, hypothesized that the huge amount of data made available by modern genomics would allow them to look for short sequences that occur less often than expected or are completely missing in the organism’s proteome. They developed a computer program that searched the many existing data sets to identify short sequences that are underrepresented (URSs).

While they found that most of the sequences of three or four AAs indeed do exist at their expected frequency in the proteins of different organisms, URSs do exist. They used the program to search for URSs in the proteomes of many different and found that different organisms have different URSs.

ASTRONOMY SET IN STANDING STONE The earliest standing stone monuments of Britain – the great circles – were constructed specifically in line with the movements of the sun and moon 5,000 years ago, according to researchers at Australia’s University of Adelaide. The study was recently published for the first time in the Journal of Archeological Science: Reports, detailing the use of innovative 2D and 3D technology to construct quantitative tests of the patterns of alignment of the standing stones.

“Nobody before this has ever statistically determined that a single stone circle was constructed with astronomical phenomena in mind – it was all supposition,” said project leader Dr. Gail Higginbottom.

They examined the oldest great stone circles built in Scotland (Callanish, on the Isle of Lewis, and Stenness, on the Isle of Orkney – both predating Stonehenge’s standing stones by about 500 years). The researchers found a great concentration of alignments towards the sun and moon at different times of their cycles. 2,000 years later in Scotland, much simpler monuments were still being built that had at least one of the same astronomical alignments found at the great circles.

The stones, however, are not just connected with the sun and the moon. The researchers discovered a complex relationship between the alignment of the stones, the surrounding landscape and horizon, and the movements of the sun and the moon across that landscape.

“This research is finally proof that the ancient Britons connected the Earth to the sky with their earliest standing stones, and that this practice continued in the same way for 2,000 years,” said Higginbottom.

Detailed examination showed that about half the sites were surrounded by one landscape pattern and the other half by the complete reverse.

“These chosen surroundings would have influenced the way the sun and moon were seen, particularly in the timing of their rising and setting at special times, like when the moon appears at its most northerly position on the horizon, which only happens every 18.6 years,” she said.

“These people chose to erect these great stones very precisely within the landscape and in relation to the astronomy they knew.

They invested a tremendous amount of effort and work to do so. It tells us about their strong connection with their environment, and how important it must have been to them, for their culture and for their culture’s survival.”

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