Tag: Life Sciences

Since the agricultural revolution, mankind has strived to enhance plant varieties through genetic diversity. However, until recently, our understanding was limited to the functions of individual genes, which account for just 20% of the genome. The remaining 80%, comprised of genes grouped in families, remained a mystery on a large genomic scale.

In a groundbreaking achievement, Tel Aviv University researchers have harnessed the power of CRISPR technology to develop an innovative and scalable genetic modification method. This breakthrough allows us to uncover the roles and characteristics of duplicated genes in plants. As a result, the team has successfully identified numerous overlooked features, paving the way for a revolutionary approach to crop improvement. This remarkable development has the potential to revolutionize agricultural practices across a wide range of crops and traits, including increased yields and enhanced resistance to drought and pests.

Overcoming Genetic Redundancy

This groundbreaking research was led by postdoctoral student Dr. Yangjie Hu, under the guidance of Prof. Eilon Shani and Prof. Itay Mayrose from the School of Plant Sciences and Food Security at TAU’s The George S. Wise Faculty of Life Sciences. Collaborating with scientists from France, Denmark, and Switzerland, the team utilized the CRISPR gene editing technology along with bioinformatics and molecular genetics methods to develop this novel gene-location method. The research was published in the prestigious journal Nature Plants.

“We wanted to apply this technique to improve the control of creating mutations in plants for the purposes of agricultural improvement, and specifically to overcome the common limitation posed by genetic redundancy.” – Prof. Itay Mayrose

Genetic redundancy, caused by gene families, has long posed a challenge in plant research. Previous methods of genetic intervention were limited by the inability to precisely identify genes responsible for specific traits. The accepted method to address this challenge is to produce mutations, that is, to modify genes in different ways, and then to examine changes in the plant’s traits as a result of the mutation in the DNA and to learn from this about the function of the gene.

Thus, for example, if a plant with sweeter fruit develops, it can be concluded that the altered gene determines the sweetness of the fruit. This strategy has been used for decades, and has been very successful, but it also has a fundamental problem: an average plant such as tomato or rice has about 30,000 genes, but about 80% of them do not work alone but are grouped in families of similar genes. Therefore, if a single gene from a certain gene family is mutated, there is a high probability that another gene from the same family (actually a copy very similar to the mutated gene) will mask the phenotypes in place of the mutated gene. Due to this phenomenon, called genetic redundancy, it is difficult to create a change in the plant itself, and to determine the function of the gene and its link to a specific trait.

The research team

The team addressed this challenge by using CRISPR and designing sgRNA sequences that guide an enzyme called Cas9 found naturally in bacteria to cut specific genetic sequences associated with entire gene families. Prof. Mayrose explains that “this genetic editing method allows us to design different sgRNA sequences to allow Cas9 to cut almost any gene that we want to change. We wanted to apply this technique to improve the control of creating mutations in plants for the purposes of agricultural improvement, and specifically to overcome the common limitation posed by genetic redundancy.”

In the first stage, a bioinformatics study was carried out on a computer, which, unlike most studies in the field, initially covered the entire genome. The researchers chose to focus on the Arabidopsis plant, which is used as a model in many studies and has about 30,000 genes. First, they identified and isolated about 8,000 individual genes, which have no family members, and therefore no copies in the genome. The remaining 22,000 genes were divided into families, and for each family appropriate sgRNA sequences were computationally designed. Each sgRNA sequence was designed to guide the Cas9 cutting enzyme to a specific genetic sequence that characterizes the entire family, with the aim of creating mutations in all family members so that these genes can no longer overlap each other. In this way, a library was built that totaled approximately 59,000 sgRNA sequences, where each sgRNA by itself can simultaneously modify 2-10 genes at once from each gene family, thereby effectively neutralizing the phenomenon of genetic redundancy.

In addition, the sgRNA sequences were divided into ten sub libraries of approximately 6,000 sgRNA sequences each, according to the presumed role of the genes – such as coding for enzymes, receptors, transcription factors, etc. According to the researchers, establishing the libraries allowed them to focus and optimize the search for genes responsible for desired traits, a search that until now has been largely random.

“We believe that this is the future of agriculture: controlled and targeted crop improvement on a large scale. Today, we are applying the method we developed to rice and tomato plants with great success, and we intend to apply it to other crops as well.” – Prof. Eilon Shani

In the next step, the researchers moved from the computer to the laboratory. Here they generated all 59,000 sgRNA sequences designed by the computational method and engineered them into new plasmid libraries (i.e., circular DNA segments) in combination with the cutting enzyme. The researchers then generated thousands of new plants containing the libraries – where each plant was implanted with a single sgRNA sequence directed against a specific gene family.

The researchers observed the traits that were manifested in the plants following the genome modifications, and when an interesting phenotype was observed in a particular plant, it was easy to know which genes were responsible for the change based on the sgRNA sequence that was inserted into it. Also, through DNA sequencing of the identified genes, it was possible to determine the nature of the mutation that caused the change and its contribution to the plant’s new properties.

In this way, many new traits were mapped that until now were blocked due to genetic redundancy. Specifically, the researchers identified specific proteins that comprise a mechanism related to the transport of the hormone cytokinin, which is essential for optimal plant development.

Commercialization and Future Impact

Prof. Shani concludes: “The new method we developed is expected to be of great help to basic research in understanding processes in plants, but beyond that, it has enormous significance for agriculture: it makes it possible to efficiently and accurately reveal the pool of genes responsible for traits we seek to improve – such as resistance to drought, pests, and diseases, or increasing yields. We believe that this is the future of agriculture: controlled and targeted crop improvement on a large scale. Today we are applying the method we developed to rice and tomato plants with great success, and we intend to apply it to other crops as well.”

Recognizing the transformative potential of this breakthrough, Tel Aviv University’s technology commercialization company, Ramot, partnered with the AgChimedes group to establish DisTree, a company dedicated to applying this technology to different crops. This collaboration, along with financial investment and professional support, aims to revolutionize agricultural genetics and ensure nutritional security in the face of climate crises.

A new study led by the paleogenetic laboratory of the Steinhardt Museum of Natural History at Tel Aviv University and the University of Haifa analyzed DNA from ancient local winegrape seeds discovered at archaeological excavations in the Negev. One seed was found to be almost identical to the Syriki variety used today to make high-quality red wine in Greece and Lebanon, while another seed is a relative of the white variety called Be’er, still growing in deserted vineyards in the dunes of Palmachim.

Exported to Europe

The genetic study was led by Dr. Pnina Cohen and Dr. Meirav Meiri of the paleogenetic lab at the Steinhardt Museum of Natural History at Tel Aviv University. The seeds were found at archaeological excavations led by Prof. Guy Bar-Oz from the School of Archaeology and Maritime Cultures at the University of Haifa, in collaboration with researchers from the Israel Antiquities Authority. Other participants included researchers from the University of Haifa, the Weizmann Institute, Bar-Ilan University, and research institutions in France, Denmark, and the UK. The paper was published in the leading scientific journal PNAS.

“The findings include large winepresses, jugs in which the exclusive wine, exported to Europe, was stored, and grape seeds preserved for more than a thousand years. This industry gradually declined following the Muslim conquest in the 7th century, since Islam forbids the consumption of wine.” – Prof. Guy Bar-Oz

“Archaeological excavations conducted in the Negev [in Israel] in recent years have revealed a flourishing wine industry from the Byzantine and early Arab periods (around the fourth to ninth centuries A.D.), especially at the sites of Shivta, Haluza, Avdat, and Nizana, which were large, thriving cities at the time,” says Prof. Guy Bar-Oz from the University of Haifa.

“The findings include large winepresses, jugs in which the exclusive wine, exported to Europe, was stored, and grape seeds preserved for more than a thousand years. This industry gradually declined following the Muslim conquest in the 7th century, since Islam forbids the consumption of wine.”

“The cultivation of winegrapes in the Negev was renewed only in modern times, in the state of Israel, mostly since the 1980s. This industry, however, relies mainly on winegrape varieties imported from Europe.”

Avdat Excavation (photo: Tali. Erickson-Gini and Scott Bucking)

Extracting DNA

One especially interesting finding was a large hoard of grape seeds, discovered on the floor of a sealed room at Avdat. The researchers explain that these seeds have been relatively well preserved thanks to protection from climatic phenomena such as extreme temperatures, flooding, or dehydration. To learn more about the seeds, in the hope of discovering which varieties they might belong to, the researchers prepared to extract their DNA in the paleogenetic lab.

The science of paleogenomic uses a range of advanced technologies to analyze ancient genomes, primarily from archaeological findings,” explains Dr. Meiri from the Steinhardt Museum of Natural History at Tel Aviv University. “Since the DNA molecule is very sensitive and disintegrates over time, especially under high temperatures, we usually get only small pieces of DNA, often in a poor state of preservation. To protect them we work under special conditions: the paleogenetic lab is an isolated clean laboratory, with positive air pressure that keeps contaminants out, and we enter it in sterilized ‘spacesuits’ familiar to everyone from the COVID pandemic.” 

To begin with, the researchers looked for any organic matter remaining in the seeds. For this purpose, they used FTIR (Fourier-transform infrared spectroscopy) – a chemical technique applying infrared radiation to produce a light spectrum that identifies the sample’s content. Finding remnants of organic matter in 16 seeds, the researchers went on to extract DNA from these samples.

Ancient local winegrape seeds from Shivta, Israel (photo: Prof. Guy Bar-Oz, The University of Haifa)

Ancient Grapes – Still Around Today

The extracted DNA was sequenced, with an emphasis on about 10,000 genomic sites where variety-specific features are usually found, and the results were compared to databases of modern grapevines from around the world: In 11 samples, the quality of genetic material was too poor to allow any definite conclusions. Three of the remaining samples were identified as generally belonging to local varieties. Finally, the two samples of the highest quality, both from around 900 A.D., were identified as belonging to specific local varieties that still exist today.

The discovery was quite extraordinary:

• One seed was found to belong to Syriki, a known Middle Eastern variety with a long history of cultivation in the Southern Levant and Crete, still used today to make high-quality red wine in Greece (where it is known to have arrived from the east) and in Lebanon. Since winegrapes are usually named after their place of origin, it is quite possible that the name Syriki is derived from Nahal Sorek, an important stream in the Judean Hills. Moreover, this variety may even appear in the Bible – in Jacob’s blessing to his son Judah: “He will tether his donkey to a vine, his colt to the choicest branch (soreka); he will wash his garments in wine, his robes in the blood of grapes (Genesis 49, 11); and perhaps also suggested in the giant cluster of grapes brought back by the men sent by Moses to explore the land:  “When they reached the Valley of Eshkol (identified by some as Nahal Sorek), they cut off a branch bearing a single cluster of grapes. Two of them carried it on a pole between them” (Numbers 13, 23).
• The other high-quality seed was identified as related to Be’er, a white winegrape variety still growing in the sands of Palmachim on Israel’s seashore, in remnants of vineyards probably abandoned in the mid- 20th century. For the first time ever, the researchers were able to use the genome of a grape seed to determine the color of the fruit, discovering that it was in fact a white grape – the oldest botanical specimen of a white variety ever identified. Be’er, a unique local variety, endemic to the land of Israel, is used today by the Barkan winery to make a special white wine of its own.

“The wonderful thing about paleogenetics is that sometimes, tiny items can tell a big story. This is exactly what happened in this study. With just a bit of DNA extracted from two grape seeds we were able to trace continuity in the local wine industry – from the Byzantine period, more than a thousand years ago, to the present day.” – Dr. Meirav Meiri

Tiny Items Tell a Big Story

“The wonderful thing about paleogenetics is that sometimes, tiny items can tell a big story,” says Dr. Meiri. “This is exactly what happened in this study. With just a bit of DNA extracted from two grape seeds we were able to trace continuity in the local wine industry – from the Byzantine period, more than a thousand years ago, to the present day.”

“We believe that our findings are also significant for Israel’s modern wine industry, which has been growing and thriving in recent decades. Today, most varieties grown here have been imported from Europe, so that the local conditions are not optimal for them. Local varieties can be more suitable for the local climate and soil, especially in the desert region of the Negev. Our study opens new paths for restoring and improving ancient local varieties, to create winegrapes that are more suitable for challenging climatic conditions such as high temperatures and little rainfall.”

Tiny items can tell a big story. Ancient winegrape seeds under a Microscope from Avdat (photo: Prof. Guy Bar-Oz, The University of Haifa)

“Pregnancy brain” – sometimes called “brain fog” or “mommy brain” – refers to a pregnant woman’s forgetfulness during and shortly after pregnancy. And there have indeed been several studies pointing to an impairment of the cognitive abilities of pregnant women. Apparently, the condition does not just affect us humans: a new Tel Aviv University study reveals that bats, too, experience a decline in their ability to hunt and orient in space during pregnancy.

This impairment stems from the fact that they produce about 20 percent fewer calls, the sounds that allow them to orient themselves using echolocation, on top of flying at a slower pace and at a lower altitude. The researchers highlight the fact that, to the best of their knowledge, this is the first evidence of pregnancy affecting mammals’ sensory abilities.

“When a bat makes fewer calls, it gathers less information about the environment, its chance of colliding with objects increases, and its chance of finding food decreases — and this is at a time when the bat needs extra food to sustain the fetus in its womb.” Prof. Yossi Yovel

Affecting Bats’ Safety and Hunting

The study was led by Mor Taub, a research assistant in the laboratory of Prof. Yossi Yovel, head of Tel Aviv University’s Sagol School of Neuroscience and faculty member of the School of Zoology at The George S. Wise Faculty of Life Sciences. The study’s findings were published in the journal BMC Biology.

Mor Taub explains: “At the peak of pregnancy, bats carry about 20 percent more than their normal body weight, and it is clear that this excess weight impacts their flying capacity. In this study, we wanted to check whether and to what extent pregnancy affects bats’ echolocation ability, their sonar.”

“Bats’ sonar is based on the emitting and receiving of strong and frequent sounds in order to map their surroundings. To make these sounds, bats, like us humans, need to transfer high-pressure air from the lungs through the vocal cords, or vocal membranes, which involves many muscles, such as the chest and diaphragm. We wanted to see if the excess weight from pregnancy affects the production of sounds.”

Prof. Yossi Yovel

To this end, Prof. Yovel and his colleagues taught bats to search for and land on a small landing pad in a flight room in the bat laboratory at Tel Aviv University’s Garden for Zoological Research. They recorded the echolocation of two groups: pregnant bats and non-pregnant bats. The researchers found that the rate at which the pregnant bats emitted sounds was significantly lower than that of the control group, with 20% greater intervals between each sound.

Prof. Yovel explains that “bats change the rate of the sounds they make in accordance with the level of difficulty of the task. The average rate is about ten calls per second, but when the bat lands, this rate can increase to 100 calls per second. The pregnant bats produced sounds at a rate of only about seven per second and flew a little slower and lower.”

“Obviously, this slowing down is likely to affect their hunting. When a bat makes fewer calls, it gathers less information about the environment, its chance of colliding with objects increases, and its chance of finding food decreases — and this is at a time when the bat needs extra food to sustain the fetus in its womb. In the second phase of the study, we used a computer simulation to simulate the effect of the decreased rate of calls on the bats’ performance, and indeed, we saw that the slowed rate makes it more difficult for the bats to locate prey.”

“This is the only evidence we found in the professional literature showing that pregnancy affects mammals’ sensory abilities.” – Mor Taub

Preserving the Vulnerable

The bats in the experiment were of the Kuhl’s pipistrelle species, tiny bats that weigh only about six grams (when they are not pregnant). These bats are very common in Israel, and feed mainly on mosquitoes. Despite their weight, bats can live for decades, and their pregnancies are therefore also relatively long, lasting about four months.

Previous studies conducted on other species of bats have shown that during pregnancy, bats tend to change their diets. To date, the assumption was that this change in diet was due to the bats’ difficulty in flying, but the current study raises the possibility that the change may also be due to their sensory difficulty in detecting certain types of prey.

“This is the only evidence we found in the professional literature showing that pregnancy affects mammals’ sensory abilities,” says Mor Taub. “We assume that there are similar cases in other species as well, but this is the first time that researchers have been able to measure and demonstrate the impairment empirically. Beyond the scientific interest, it is important to preserve mammal species in the wild, especially during pregnancy and newborn care, since animals are particularly vulnerable during this period.”