A male’s genome contains information that can help scientists guess his surname, American and Israeli researchers have discovered. The findings have serious implications for data privacy; intelligence services around the world are bound to be interested.
In the study published in the journal Science, researchers have developed a formula for an algorithm that can discover men’s surnames by looking at the Y chromosome, the male chromosome. The Y chromosome, which is transmitted from father to son from generation to generation, includes markers called short tandem repeats, which form a kind of fingerprint.
The researchers, headed by Dr. Yaniv Erlich of the Whitehead Institute for Biomedical Research in Cambridge, Massachusetts, fed 40 markers into a computer and compared them to Y-chromosome sequences on websites. In the United States, there are companies that show people’s genome sequences derived from saliva samples; this makes it possible to determine a person’s origins and locate relatives around the world.
“Even though there isn’t a unified database of all genetic sequences on the Internet, comparing a subject’s Y chromosome with information from existing databases could help locate his family,” says Israeli team member Eran Halperin, a professor at Tel Aviv University’s Department of Molecular Microbiology and Biotechnology.
In addition to the Whitehead Institute, the research was carried out by experts at Harvard, MIT and the International Computer Science Institute in Berkeley, California.
The researchers and doctoral student David Golan of Tel Aviv University’s statistics department developed the formula for the algorithm, which was tested on 911 men in the United States. The numbers were compared to Internet databases containing genetic sequences of 135,000 men with the most common surnames in the United States, most of them of European origin. The algorithm identified the surname 12 percent of the time, a success rate it later boosted to 18 percent.
The researchers, for example, applied the algorithm to the genome sequence of American geneticist Craig Venter, the head of a research institute in San Diego who was one of the first to sequence the human genome.
In the U.S.-Israeli experiment, the algorithm identified the Venter surname, and after crossing the data with other discoveries, figured out his age. Knowing that he lives in California, the researchers showed that only one other person in the state shares the unique spots on his chromosomes.
The researchers also scanned Y chromosomes of 10 residents of Utah, without knowing their last names; the algorithm helped them figure out the surnames of five of them, all of them Mormons.
“The identification technique could have a number of useful applications such as locating relatives and identifying corpses in natural disasters,” says Halperin. “But the research also reveals a fundamental problem: If a person publishes his genome on the Internet, even when this is done anonymously, his identity is pretty much exposed.”
Halperin adds that the ability to find a surname is based only on the Y chromosome, one of the body’s 46 chromosomes. The study also raises questions about sharing genetic information from various sources.
“We take a positive view of sharing genetic information on public databases – with permission, of course,” says Halperin. “Sharing information is essential to science, and there are many advantages to users of these services. But it’s important that all organizations involved in the data sharing be aware of the possible exposure and weigh their decisions accordingly.”
Erlich adds: “The obvious conclusion from the study is that biometrics can produce unexpected situations. We believe legislators must proceed with great caution when they plan such databases.”
Researchers at the Hebrew University of Jerusalem have discovered a new pathway by which cells in the body become cancerous. The discovery is expected to facilitate the development of new treatment methods that could block this process and prevent the spread of cancerous growths as well as new diagnostic tools to distinguish between normal and malignant tumors.
In their article in the scientific journal “Cell Reports,” the researchers describe a gene found in every cell of the body that manufactures an enzyme called S6K1. This enzyme appears in two forms, one long and one short. It is the latter variant of the enzyme, which like all enzymes is a protein, that is involved in the process of tumor formation.
While the long variant of the S6K1 enzyme is composed of more than 500 different amino acids, the short form contains only 300. In the article, “S6K1 Alternative Splicing Modulates Its Oncogenic Activity and Regulates mTORC1,” the short variation, or isoform, of the protein is described for the first time. Healthy cells contain a relatively small number of this form of S6K1, which the researchers discovered encourages nearby cells to become cancerous. The research team, led by Ph.D. candidate Vered Ben-Hur and adviser Dr. Rotem Karni of the Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, demonstrated that an additional protein found in the body, SRSF1, depresses the activity of the long variation of S6K1 and activates its short form – the one implicated in the cancer process.
The short variation of S6K1 activates the signaling pathway between cells. This pathway encourages nearby cells to divide in an unregulated manner and thereby become cancerous, spreading and invading various tissues within the body.
The researchers identified the short variform of S6K1 first in mice and then in cell cultures taken from women with breast cancer. They later found significant levels of the short variation in cultures taken from people with lung cancer and from people with cancer of the colon. “We found that the pathway we have described is very important and that it takes place in nearly all types of cancerous tumors,” Karni said.
In a related discovery, the researchers found that in laboratory conditions the long variation of S6K1 actually depresses tumor activity and even prevents healthy cells from becoming cancerous, just the reverse of the effect of this enzyme’s short version. “We showed that the [S6K1] protein causes damage when it is truncated, whereas damage to the long form could actually intensify the disease,” Karni explained.
The researchers have not yet identified the environmental factors affecting the production of either the short or the long variations of the S6K1 enzyme, but the assumption is that environmental factors that have been associated with the development of cancer, such as prolonged exposure to sun or to known carcinogens, could accelerate the production of the short form. Further study will be needed to test this hypothesis.
The research team is now working on turning the short form of S6K1 into its long form and then testing whether this could prevent or at least slow the growth of cancerous tumors.
“We are developing materials that could switch off the splicing mechanism in order to create more of the long form of the protein and fewer of the short ones,” Karni said, adding, “Today we can do this in the laboratory, and the intention is to develop a drug therapy based on this discovery.”
The team has already determined that new cancer drugs, recently approved for use in Europe, can affect the activity of the short form of S6K1.
Scientists at the Hebrew University of Jerusalem have taken a giant step forward in unlocking one of the great mysteries of science: what the unconscious is for, anyway. While that question remains open, what’s sure is that even if you think you can’t do simple sums – your unconscious can.
The studies proved that humans can do some pretty complex thinking without even being aware of it. For instance, we can read words and phrases, and do complicated math requiring multiple steps without realizing it, researchers at the Psychology Department at the Hebrew University of Jerusalem report.
Note that these processes happen in our subconscious, not in a state of unconsciousness. The findings challenge existing theories, like the notion that one had to consciously strain the brain in order to read or solve mathematical formulas. Not so, evidently. The findings not only surprise, they open a window to a richness of future studies on the power of the subconscious brain.
The study was headed by Dr. Ran Hassin, head of the cognition sciences department at the Hebrew University. It encompassed 372 students who were asked to carry out 13 tasks on a computer. But how is one to present sentences and equations to the unconscious part of the mind, while the subject is awake and alert? The solution lies in separating what each of the subject’s two eyes sees, a technique called Continuous Flash Suppression.
This involved exposing the right eye to rapidly changing images, while the left eye was shown a constant image, with a word, a phrase, or a math problem. The eye seeing the rapid changes dominates consciousness, thus the image presented to the other eye is not experienced consciously.
In the first round of tests the students were shown semantically nonsensical phrases, such as “The bench ate a zebra.” They were also shown sensible phrases such as “the lion ate a zebra”. In addition they were shown pairs of words, some negative (“concentration camp”) and some positive (“ironed shirt”).
The students were told to press a button when the sentence broke through to their conscious. It turns out that the negative and nonsensical break through faster than the positive and sensible phrases.
Everyone’s a critic, including your subconscious
This indicates a definite “pickup” by the unconscious of something negative and out of the ordinary, the scientists explain.
The set of tests for math was conducted the same way. The left eye was shown simple math problems while the right eye was shown static dominating images. Later both eyes were shown a number. The testee was supposed to say the number aloud.
It turned out that subjects were able to say the number faster if it was the solution to the problem their left eye had seen.
Evidently, ergo, humans can solve complex, rule-based mathematical problems unconsciously, say the researchers.
“Therefore,” said Dr. Hassin, “current theories of the unconscious processes and human consciousness need to be revised. These revisions would bring us closer to solving one of the biggest scientific mysteries of the 21st century: What are the functions of human consciousness?”
Now what? The scientists hope to continue testing the power of the unconscious. A study starting shortly will check if the human unconscious can be asked questions, and answer them. Hassin believes these studies could shed light on that great mystery: Why, if at all, we need our unconscious mind.
Make no bones about this technology: Bonus Biogroup, a regenerative medicine company in Israel, has found a way to grow human bone from a patient’s own fat, culled during liposuction.
Following successful pre-clinical testing, clinical trials will begin within the next year in Europe or in Israel on applications ranging from growing bones for dental surgery to replacing bone tissue lost through trauma or illness.
“The standard of care today is autologous bone grafting — taking bone from other parts of the body, breaking it and putting it in where needed,” Bonus founder and CEO Shai Meretzki tells ISRAEL21c. “Two operations are needed for the treatment of harvesting bone from another part of the body,” he says. Obviously, this solution isn’t optimal.
“Our advantage is that the healing process is much faster, and patients of course don’t have to suffer the harvesting procedure,” he adds.
The new innovation pioneered by Bonus evolved from years of research and development at the NASDAQ-traded company Pluristem Therapeutics, which Meretzki founded previously. The technology involves extracting stem cells from a person’s own fat tissues, and transferring them to a special matrix that coaxes the cells to grow into real human bone.
Using a 3D imaging scan of the area of missing or damaged bone, the Bonus methodology builds a “scaffold” of the correct shape. Then, a live culture of cells is introduced onto the scaffold inside a unique bioreactor that mimics the cellular environment of the human body. After a few months, bone in the correct shape and size, compatible with the patient’s own body, is ready and can be sent by courier to wherever it is needed.
This process allows for growing bone outside the body to be used a few months down the road in bone reconstructive surgery.
While the compelling notion of harvesting stem cells from our youth to grow a complete series of replacement bones and organs for our golden years is “a little farfetched” says Meretzki, he and his team are working on bone reconstructions several centimeters in size for now. Bigger bones like femurs pose a challenge because these bones also include cartilage. But theoretically it can be done, with the right science behind it.
The key is in the growing matrix and medium. Meretzki says: “When you grow cells not in 2D but in 3D, the cells are behaving completely differently. They express different markers and cytokines and react differently with the cells around them.”
Bonus has proven that the technology works in animal models, and expects it will be a success in human clinical trials.
The impact could be enormous. Bone transplantation following hip and knee injuries and fractures amounts to two million bone grafts costing some $15 billion a year. A second application with winning potential is in grafting bone for making dental implants.
Israel-based Neuronix, which has developed a non-invasive medical device to help treat Alzheimer’s disease, expects the system to be approved by the US Food & Drug Administration in late 2014.
The device, which combines electromagnetic stimulation with computer-based cognitive training, is already approved for use in Europe, Israel and several Asian countries such as Singapore.
“You stimulate the brain on a biological level as well as on a cognitive level,” Neuronix CEO Eyal Baror told Reuters, saying this double approach created longer-lasting benefits.
The device, which consists of a chair containing an electronic system and software in the back and a coil placed at the head, has been tested on mild to moderate Alzheimer’s patients who suffer from dementia but are not totally dependent.
The system is in trials at Harvard Medical School/Beth Israel Deaconess Medical Centre. Patients are treated for one hour a day, five days a week over six weeks.
“We see improvement lasting for 9-12 months and the good thing is that patients can return and undergo treatment again,” Baror said. “If out of 10 years the patients have left to live we can keep them at home in a relatively mild state of the disease for three, four, five years, it’s a lot.”
According to Alvaro Pascual-Leone, director of the hospital’s Berenson-Allen Centre for Non-invasive Brain Stimulation, brain stimulation – or transcranial magnetic stimulation – involves a very low current applied to a specific part of the brain and is approved by the FDA for treatment of a variety of ailments and diagnostic applications.
“The application in Alzheimer’s disease and in combination with cognitive training is novel,” Pascual-Leono said in a phone interview from Boston.
About 20% of patients experience a mild headache but there are no long-term negative effects, he said.
Pascual-Leone, who is principal investigator in the Harvard trial, said that of 12 patients in the study, six received the real treatment and all showed cognitive improvement. Their improvement was significantly more than the average seen in patients taking just medication, he said.
The study’s results will be submitted for publication in the coming weeks and a follow-up study on 30 patients is planned.
Neuronix received European approval several months ago and has installations in the UK and Germany. In Israel, a few dozen patients are being treated with the device.
The US trials are expected to run till the end of 2013. Neuronix is also running a trial in Israel for pre-Alzheimer’s patients.
The company expects to sell half a dozen systems in the second half of 2012 and three dozen in 2013. In Israel, the treatment costs $6,000.
“Our target for becoming profitable is in parallel to entering the US market around 2015,” Baror said.
Neuronix has raised $8 million from private individuals as well as in grants from the Israeli Chief Scientist’s Office and is exploring options to raise more money in the coming year, including the possibility of going public.
Chaim Weizmann, the first president of Israel, discovered the process, a method of bacterial fermentation that was originally used to change starch into explosives, nearly 100 years ago. Now Cal chemists, working with others from the Energy Biosciences Institute, used this method to make diesel fuel. They think the process — still more expensive than current fossil fuels — could be commercialized in five to 10 years.
Though it would cost more, use of the new fuel would “drastically reduce greenhouse gas emissions from transportation,” UC Berkeley said.
Dean Toste, a chemistry professor at Cal, said the process can make “all sorts of renewable things, from fuels to commodity chemicals like plastics.”
The Energy Biosciences Institute, housed in UC Berkeley’s new Helios Building, is a collaboration between Cal, Lawrence Berkeley National Laboratory, and the University of Illinois at Urbana Champaign. EBI is paid for by money from oil giant BP plc (NYSE: BP), whose support caused some controversy on campus when it was first announced.
Weizmann’s procedure uses Clostridium acetobutylicum to ferment plant sugars into acetone, butanol and ethanol, and is called “ABE” as a result. Harvey Blanch andDouglas Clark, both Cal professors, figured out how to get the acetone and butanol out of the mixture, leaving most of the ethanol.
Paul Williams, a chemical engineer who works for BP and who is associate director of the EBI, first suggested connecting Blanch and Clark’s work with new types of catalysts developed by Toste.