Tag Archives: genome

Wheat.

Wheat’s genetic secrets could lead to better, more resilient crops

Wheat has a genome five times longer than yours — and now, it’s been fully sequenced.

Wheat.

Image credits Brad Higham / Flickr.

Staying true to their name, researchers at the International Wheat Genome Sequencing Consortium have published a paper containing the complete sequence of the wheat (genus Triticum) genome, a dataset that could help breed new crops.

Food-nome

Having access to the plant’s genome should help speed up the breeding of more resilient, disease-resistant, and higher-yield crops. Wheat is currently the most widely grown crop, providing more protein than meat in the human diet, and supplying roughly one-fifth of the total calories people consume. It’s also surprisingly complex from a genetic standpoint: its genome includes some 16 million base pairs, over five times larger than yours or mine.

Despite its genetic beefiness, wheat is quite vulnerable to floods, droughts, and several diseases (such as wheat rust) that can claim whole crops at a time. Luckily, now that we know the structure of its genome, we can modify it to add a whole lot of desirable characteristics — resilience to pests, higher yields, more nutritional value — into our crops.

Actually sequencing the genome, however, proved to be a significant challenge. Not only was it huge, it also included three sub-genomes — a large part of which included repetitive elements. This makes long stretches of the genome identical or very similar to each other, making it difficult to distinguish individual chains and re-constructing the overall genome.

The sequencing effort is detailed in two papers. The first, published by researchers from the. International Wheat Genome Sequencing Consortium, details the sequence of the plant’s 21 chromosomes. It also lists the location of 107,891 genes, more than 4 million molecular markers, as well as sequence elements between the genes that regulate their expression.

The second paper, led by a team at the John Innes Centre (JIC), aims to help breeders and researchers understand what trait each gene affects. This work is largely based on a technique known as ‘speed breeding’, previously developed at the JIC. Speed breeding involves the use of glasshouses to shorten the breedings cycles of plants. Combined with the wealth of genome information from the first paper, this helped the team significantly shorten the time required to test what each gene does.

“Genomic knowledge of other crops has driven progress in selecting and breeding important traits,” says Cristobal Uauy, Project Leader in crop genetics at the John Innes Centre says.

“Tackling the colossal wheat genome has been a Herculean challenge, but completing this work means we can identify genes controlling traits of interest more rapidly. This will facilitate and make more effective the breeding for traits like drought or disease resistance. Where previously we had a broad view and could spot areas of interest, we can now zoom into the detail on the map.”

Uauy cites past research estimating that the world will need 60% more wheat by 2050 to meet global demand. The research his team performed can be instrumental towards reaching that goal.

It’s not the first time researchers have fully decoded the genome of a cereal: just last year, an international research team published the full genome of barley.

The first paper, “Shifting the limits in wheat research and breeding using a fully annotated reference genome”, has been published in the journal Science.

The second paper “The transcriptional landscape of polyploid wheat” has been published in the journal Science.

Machu Pichu, the 15th-century Inca citadel situated on a mountain ridge 2,430 metres (7,970 ft) above sea level. Credit: MaxPexel.

Genes of living descendents might solve mystery of the Inca Empire’s origin

Machu Pichu, the 15th-century Inca citadel situated on a mountain ridge 2,430 metres (7,970 ft) above sea level. Credit: MaxPexel.

Machu Pichu, the 15th-century Inca citadel situated on a mountain ridge 2,430 metres (7,970 ft) above sea level. Credit: MaxPexel.

The Inca founded the largest empire in pre-Columbian America, and possibly the largest empire in the world in the early 16th century. Its origin, however, has always been shrouded in mystery — much to the vexation of scholars.

But although written records are few and far between, each and every one of us carries a record of our ancestors in our genes. Recently, an international team led by researchers at the University of San Martin de Porres in Peru used genetic sequencing techniques to show that there’s credence to two of the most popular Inca origin legends, and that they might even be linked.

The Inca combined their mythology with the Aymara, an indigenous nation in the Andes and Altiplano regions, which has obscured their origin myth even further. According to the most popular legend, the Inca state was founded by Manco Capac, who brought his people from Lake Titicaca, in Puno. According to another legend, the four Ayar brothers emerged out of the Pacaritambo mountain in Cusco. Later, the tribe gradually established its hegemony over other people.

Researchers in Peru, Brazil, and Bolivia sequenced the genomes of 3,000 samples from present-day families known to be descended from the Incas. These indigenous families, known as ‘Panakas’, are one of the few living relatives of the old Inca nobility, whose DNA is very difficult to obtain from archaeological samples as the Spanish Conquistadors destroyed burial sites and Inca mummies during their conquest.

When the Panakas DNA was compared to those of people living in Puno and Cusco, there were significant genetic similarities suggesting both legends have at least an ounce of truth to them, as reported in the journal Molecular Genetics and Genomics. What’s more, the two legends might actually be linked.

“After three years of tracking the genetic fingerprints of the descendants, we confirm that the two legends explaining the origin of the Inca civilization could be related,” Ricardo Fujita from the University of San Martin de Porres in Peru told to AFP.

“Probably the first migration came from the Puno region and was established in Pacaritambo for a few decades before heading to Cusco and founding Tahuantinsuyo.”

Inca Empire borders during its greatest extent. Credit: Wikimedia Commons.

Inca Empire borders at the time of its greatest extent. Credit: Wikimedia Commons.

These preliminary results will be improved once the researchers manage to identify old Inca mummies and have their DNA sequenced. Whatever they find will either cement the idea of a multiple-lineage origin theory or force the researchers back to the drawing board.

“We have arrived at the conclusion that Tahuantinsuyo nobility descends from two lineages, one from Lake Titicaca in the Puno area and the other from the Pacaritambo mountain in Cusco. That tells us the legends about the foundation are true and that they could’ve been a single scenario,” Jose Sandoval, a researcher of the University of San Martin de Porres, explained to the AFP.

A genetic bed of roses: scientists sequence the complete genome of the rose

In a new study, researchers have sequenced the genome of the rose flowers. Roses exhibit a high diversity of flower fragrance and color, and scientists weren’t exactly sure what biochemical determinants were responsible for this — until now.

Roses are important both culturally and economically, being used as ornamental plants and as a prime material in the perfume industry. They’ve been grown by humans since antiquity, probably for their aesthetic qualities, and are widely grown in all areas of the world today. However, modern roses have complex genomes and previous rose genome assemblies were highly fragmented and therefore difficult to decipher.

Mohammed Bendahmane and colleagues produced a very high-quality rose genome sequence of Rosa chinensis, a modern rose species known as ‘Old Blush’. Old Bush is a rose from China, a major ancestor of modern rose varieties, that blooms several times a year.

They were able to sequence and decipher all the genetic information carried by the seven pairs of the rose chromosomes and to characterize all of its 36,377 genes. This enabled researchers to better understand what gives roses their cherished properties.

“Thanks to the high-quality genome assembly, we have now information on the gene regulatory pathways involved in many processes including scent biosynthesis, color, flowering, resistance to biotic and abiotic stresses,” Bendahmane told ZME Science.

The researchers also performed comparative analyses of other plants such as strawberry, apricot, peach, apple, and pear, to assess the evolutionary history and ancestry or roses. This has shown that rose, strawberry, and raspberry plants are evolutionarily very close.

“Comparative genomic investigation allowed us to assess rose paleohistory within the Rosaceae family,” researchers wrote in the study.

This work also identifies the main genes and biosynthetic pathways involved in flowering, flower development, reproduction, fragrance and pigment synthesis. The team successfully reconstructed the biosynthetic pathways in which these genes intervene. In particular, they highlighted a group of genes involved simultaneously in the regulation of the flower’s color and fragrance.

This could ultimately enable growers and botanists to select and develop particular rose traits they are looking for, Bendahmane explains.

“One way would be to use the sequence of the gene alleles associated with a typical trait to select during breeding the individuals that have the capacity to develop trait. In another word marker-assisted selection.”

“[Growers can] use the identified genes as markers to select the best genitor roses (parents) that can then be used for crosses and breeding. This will increase the chances to identify in the sibling new rose cultivars with the most desirable traits and/or their combinations.”

The study, “The Rosa genome provides new insights into the domestication of modern roses”, has been published in the journal Nature Genetics.

Credit: Wikimedia Commons.

Scientists double the number of Neanderthal genomes, gleaning new tribal insights

Credit: Wikimedia Commons.

Credit: Wikimedia Commons.

After scientists sequenced the first Neanderthal genome, we were surprised to learn that our extinct cousins actually interbred with modern humans. It’s believed all non-Subsaharan individuals alive today carry about 2% Neanderthal DNA. But our Neanderthal ancestry might be even richer than we thought: five new Neanderthal genomes sourced from Belgium, France, Croatia, and Russia have been recently sequenced. This effectively doubles the number of genomes available.

The samples were taken from bones and teeth, ground into a fine powder, and treated with a mild hypochlorite solution to remove any contaminants. All the new genomes are 39,000 to 47,000 years old, which makes them latecomers in the species’ history.

“Our work demonstrates that the generation of genome sequences from a large number of archaic human individuals is now technically feasible, and opens the possibility to study Neandertal populations across their temporal and geographical range”, says Janet Kelso, the senior author of the new study.

After the researchers at the Max Planck Institute for Evolutionary Anthropology analyzed the five Neanderthals, they compared them to previously sequenced Neanderthals (whole-genome sequencing was available for only four Neanderthal individuals prior to this study), but also a Denisovan, and samples from our own species.

Upper molar of a male Neandertal from Spy, Belgium.Credit: I. Crevecoeur.

Upper molar of a male Neandertal from Spy, Belgium.Credit: I. Crevecoeur.

They found that the five individuals shared a common ancestor about 150,000 years ago with another Neanderthal individual whose remains were recovered from a Siberian cave. According to the researchers, they can now identify 10 to 20 percent more Neanderthal DNA in people living today than it was possible when everything scientists had at their disposal was the Altai Neanderthal genome, the first Neanderthal genome to be sequenced.

Very curiously, none of these individuals had any modern human DNA contained their genomes, despite having shared the same timeline. This suggests that the gene flow may have been strictly unidirectional — from Neanderthals to humans, but not the other way around. It’s not clear whether the gene flow comes from male or female Neanderthals, so there are still open questions concerning the intimate dynamic between the two species.

It also seems that these late Neanderthals were more related to the Neanderthals that mated with the ancestors of modern-day Europeans and Asians than the older Neanderthal populations found in Siberia.

For thousands of years, the Mezmaiskaya Cave, laying near the border between Russia and Georgia in the Caucasus mountains, had offered Neanderthals shelter. The newly extracted genetic information allowed the researchers to compare two individuals who had lived approximately 20,000 years apart. To the researchers’ surprise, the two individuals were not closely related.

Instead of both being distantly related to Western European Neanderthals, the team found that the younger Neanderthal was more genetically similar to Croatian, Belgian, and French Neanderthals than to the older Neanderthal found at the cave. This suggests that the more recent individual was part of a new population that replaced the former ones, which were likely wiped out. The authors believed that “extreme cold periods in northern Europe may have triggered the local extinction of Neanderthal populations.” Eventually this population, too, collapsed with the extinction of its own species — only to be replaced by our own.

“We see that the genetic similarity between these Neandertals is well-correlated with their geographical location. By comparing these genomes to the genome of an older Neandertal from the Caucasus we show that Neandertal populations seem to have moved and replaced each other towards the end of their history”, says first author, Mateja Hajdinjak.

The findings appeared in the journal Nature.

Scientists discover why cockroaches are such good survivors

Researchers sequenced the American cockroach‘s genome for the first time, discovering what makes them such great survivors.

Periplaneta americana Via Flickr

The American cockroach, also known as Periplaneta americana, possesses widely expanded gene families related to taste and smell, detoxification and immunity, compared with other insects, found a team of researchers who published their discovery on March 20 in the journal Nature Communications.

“It makes total sense in the context of the lifestyle,” said Coby Schal, an entomologist at North Carolina State University who was part of a team that last month reported an analysis of the genome of the German cockroach (Blattella germanica). “Many of the gene families that expanded in the American cockroach were also expanded in the German cockroach”, Schal said.

That actually makes sense because both species are omnivorous scavengers that can thrive on altered food in extremely unsanitary environments — at least by human standards.

The American cockroach originally comes from Africa but was introduced to the Americas in the 1500s. Unlike the German cockroach, which is found almost exclusively in human dwellings, the American cockroach only tends to venture into the basements or bottom levels of buildings, according to Schal.

In China, the cockroach is often called “xiao qiang,” meaning “little mighty,” according to Sheng Li, an entomology professor at South China Normal University in Guangzhou and lead author of the paper. “It’s a tiny pest, but has very strong vitality,” he said.

The two species are remarkable survivors and their mysterious abilities appear to lie within their genes. In the new paper, professor Sheng Li and his team found that American cockroaches have the second-largest genome of any insect ever sequenced, right behind the migratory locust (Locusta migratoria). Curiously enough, 60% of the insect’s genome consists of repetitive segments. Gene families related to taste and smell were much larger than those of other bugs, and scientists counted 522 taste receptors in the roach. German cockroaches possess a similar number of taste receptors (545), Schal said.

“They need very elaborate smell and taste systems in order to avoid eating toxic stuff,” Schal added.

Source: Flickr

Interestingly, American cockroaches also have large gene families responsible for metabolization of toxic substances, including some chemicals found in insecticides — their ‘cousins’, the German cockroaches have them too. Schal said that both roaches evolved this way long before humans ruled the world. Resistance to toxic substances developed in roaches thanks to the abundance of toxin-producing bacteria in their environments and their tendency to eat rotten plant matter, he explained.

In addition, the American cockroach has a large number of immunity genes, perhaps another adaptation to unsanitary environments and fermenting food sources, Li and colleagues wrote.

Finally, the team discovered that the insect had a large number of genes devoted to physical development, such as genes responsible for synthesizing the insect’s juvenile hormone or the proteins in its exoskeleton. Authors were not surprised by this since American cockroaches can measure up to 2 inches (53 millimeters) long.

A greater understanding of the cockroach genome could help researchers come up with new ways to control theses pest species. One interesting research interest, Schal said, is the Asian cockroach (Blattella asahinai), a close relative of the pesky German cockroach that lives outdoors and doesn’t really bother humans. It would be interesting to see what are the differences between the Asian and German cockroach genomes.

Still, there’s a long way to go before we can see the broad picture of cockroach genetics.

“There are 5,000 described species of cockroaches, and now we have two [full] genomes,” Schal concluded. “So we need more.”

Scientist decode the largest genome so far – and it belongs to the axolotl

The Mexican axolotl Ambystoma mexicanum. Credit: IMP.

The Mexican axolotl Ambystoma mexicanum. Credit: IMP.

The axolotl (Ambystoma mexicanum), also known as the Mexican salamander, is one of the most peculiar animals on Earth. Its superpower is similar to that of Wolverine’s: extreme regeneration. Axolotl, this smily-faced amphibian, can regrow missing limbs, spinal chord segments, brain tissue, nerves, and retina.

Scientists have long been fascinated about this creature’s mysterious abilities. Now, a team composed of researchers from Vienna, Dresden, and Heidelberg has successfully decoded the entire genetic information of the axolotl. This data may help decipher the miracle of limb re-growth.

For quite some time, salamanders such as axolotl have been intensely studied because of their remarkable regeneration ability. If the amphibian loses a limb, in a few weeks, it will grow a new one, from scratch. The limb will be just like the old one, with no scar tissue whatsoever. These salamanders can also receive implants from their kin with no problems. A research team even performed axolotl head transplants in 1968. One of the animals lived up to 65 weeks with two functioning heads.

A key factor in understanding this type of regeneration is the animal’s genome (genetic material). So far, scientists couldn’t sequence all of it due to its length — at 32 billion base pairs, it is more than ten times larger than the human genome.

Male albino axolotl. Source: Pixabay/Tinwe

Researchers used the PacBio-platform, a sequencing technology that produces long reads to span large repetitive regions. A total of 72.435.954 reads were sequenced. Next, Gene Myers and Siegfried Schloissnig together with colleagues developed software systems that can assemble the genome from the 72 million pieces.

This is how they found that the uniqueness of the axolotl resides in its genes — the salamander only shares several genes expressed in regenerating limb tissue with other amphibian species. An essential developmental gene that plays key roles in neural and muscle development — PAX3 — is completely missing. Another gene, named PAX7, has taken over its functions.

“We now have the map in our hands to investigate how complicated structures such as legs can be re-grown”, says Sergej Nowoshilow, co-first author of the study. “This is a turning point for the community of scientists working with axolotl, a real milestone in a research adventure that started more than 150 years ago.”

Because of their incredible regenerative abilities, axolotls are of great interest to scientists. Because they can not only regenerate limbs and organs, but also brain tissue, many researchers hope that they might one day be able to do the same for human tissue in certain conditions. The implications in medical practice would be immensenly beneficial.  One challenging aspect has always been the axolotl’s huge genome size but now that it’s been sequenced, a whole new avenue of discoveries await.

Scientific reference: The axolotl genome and the evolution of key tissue formation regulators. Sergej Nowoshilow, Siegfried Schloissnig, Ji-Feng Fei, Andreas Dahl, Andy W.C. Pang, Martin Pippel, Sylke Winkler, Alex R. Hastie, George Young, Juliana G. Roscito, Francisco Falcon, Dunja Knapp, Sean Powell, Alfredo Cruz, Han Cao, Bianca Habermann, Michael Hiller, Elly M. Tanaka, and Eugene Myers. Nature, doi: 10.1038/nature25458.

Infant skeleton sheds new light on early Native American populations

The remains of a six-week-old infant cast new light upon the Native American founding population.

Scientists divided the ancient American populations into two categories: the Southern and the Northern Native Americans. The two groups are related, but a link between them and an ancient Siberian population was missing, until now.

Pictures were taken at Upward Sun River site. Credit: Ben Potter

“It’s the first time that we have had direct genomic evidence that all Native Americans can be traced back to one source population, via a single, founding migration event.” said evolutionary geneticist Eske Willerslev from the University of Cambridge in the UK, the research team leader, in a press release.

Researchers named this population “Ancient Beringians” after Beringia, the land bridge that connected northeast Asia with northwestern North America, during the Pleistocene epoch — sometimes called the Ice Age.

Via Wikipedia

The girl was named Xach’itee’aanenh t’eede gaay, or Sunrise Child-girl, by the local Native community. Her skeleton was discovered at the Upward Sun River archaeological site in Alaska in 2013. Scientists say the child lived 11,500 years ago, long after the first wave of migration occurred, but her genome was consistently different from the two types of ancient Native Americans.

“The Ancient Beringians diversified from other Native Americans before any ancient or living Native American population sequenced to date. It’s basically a relict population of an ancestral group which was common to all Native Americans, so the sequenced genetic data gave us enormous potential in terms of answering questions relating to the early peopling of the Americas,” Eske Willerslev said.

The excavation site from Alaska. Credit: Ben Potter

This is the first ancient skeleton ever discovered in Alaska — acidic soils make bone tissue and DNA preservation very difficult.

“We were able to show that people probably entered Alaska before 20,000 years ago. It’s the first time that we have had direct genomic evidence that all Native Americans can be traced back to one source population, via a single, founding migration event.” said Professor Willerslev.

The Northern and the Southern branches are thought to have separated somewhere between 17,000-14,000 years ago. The two groups probably went separate ways as they passed through or around the Cordilleran and Laurentide ice sheets that covered present-day Canada and a part of northern United States.

Scientists believe that the Ancient Beringians were left behind the ice sheets and remained in Alaska. Next, the population was absorbed by other Native groups derived from the Northern branch, that migrated back after the ice had melted away.

“One significant aspect of this research is that some people have claimed the presence of humans in the Americas dates back earlier – to 30,000 years, 40,000 years, or even more. We cannot prove that those claims are not true, but what we are saying, is that if they are correct, they could not possibly have been the direct ancestors to contemporary Native Americans”, added Willerslev.

The paper was published in the Nature journal on the 3rd of January 2018.

 

Cannabis.

Cannabis genome project will allow for new crops, better medicine

Marijuana is slowly gaining public and legal acceptance, but there’s still a lot to be learned about the plant. With that in mind, researchers from the University of California Davis have started a project to map the cannabis genome.

Cannabis.

Image credits Wally Crawfish.

Hemp and marijuana are two different species, but they’re both strains of the cannabis (Cannabis sativa) plant. The main difference between the two is that marijuana has higher levels of THC (tetrahydrocannabinol), the substance that gets you ‘high’. Both species have a long history of human selective breeding, with marijuana getting a lot more of attention from farmers and breeders in recent times, due to the plant’s high market value.

Parts of the cannabis genome have been studied in the past, too, and now researchers from UC Davis have set out to map it out in its entirety, keeping an eye out for portions of the genome that confer it’s medicinal and nutritional value.

“People have gotten really good at breeding high-THC [weed] for the recreational side,” said Jon Vaught, the CEO and co-founder of Front Range Biosciences, a cannabis biotech company that has partnered with the university on the study.

“There’s really not a lot of work to do there. We’re not really focused on that.”

Instead, Vaught believes cannabis could be the next big commercial crop. It has potential in the field of medicine, pharmaceuticals, health supplements such as CBD oil, or nutritional products like hemp-derived protein powders. However, given that most work on cannabinoids was performed (probably domestically) and with the goal of increasing their THC content, growing it as easily and profitably as corn can be challenging.

Open source genome

This is where the UC Davis team steps in. Led by assistant professor in the department of viticulture and enology at UC Davis Dario Cantu, they have previously mapped the genomes of the arabica coffee bean and the cabernet sauvignon grape, so they should not lack for experience in tackling that of the hemp plant.

“We have successfully applied cutting-edge DNA sequencing technologies and computational approaches to study challenging genomes of diverse crops and associated microorganisms,” said Dario Cantu.

“We are now excited to have the opportunity to study the genome of hemp. Decoding the genome will allow us to gain new insight into the genetic bases of complex pathways of secondary metabolism in plants.”

Because they’re both cannabis plants, the underlying genome information will be broadly applicable. As a public university, UC Davis will make all the findings open to the public, meaning breeders of all kinds of cannabis will benefit from the research. Using this database, breeders will be able to isolate new varieties of cannabis or make existing ones better able to withstand different stressors, like pests or drought, or foster other desirable traits — “a big step forward and consistent with our public mission,” according to UC Davis spokesperson Dan Flynn.

There’s another benefit to be had from this research: right now research into cannabis is slow at best. Since it’s listed as a Schedule I drug at the federal level, researchers need to get approval from the Drug Enforcement Agency to work with the plant. Until regulation for this plant relaxes or goes away completely, having its full genome at hand would be a good way to work around that issue.

easter-island

Easter Island natives may not have sailed all the way to South America after all

easter-island

Credit: Pixabay.

Easter Island is one of the most mysterious cultural landmarks in the world. Located smack in the middle of the South Pacific Ocean and a staggering 2,300 miles away from South America, the island is littered with over 1,000 massive carved statues called Moai. Easter Island became even more interesting in 2014 when a paleogenomics analysis found Polynesian natives had mixed with Native Americans at least 19 generations ago, between 1280 and 1495 or long-before Europeans had set foot on the island for the first time in 1722. However, a new study published today in Current Biology contradicts the findings suggesting the islanders remained isolated until they made contact with Europeans.

Buzzkill

Lars Fehren-Schmitz, associate professor of anthropology at UC Santa Cruz, led the team that analyzed bone fragments from the ancient skeletal remains of five individuals. Three individuals lived prior to European contact, and two lived after.

Fehren-Schmitz had expected to find evidence of Native American gene flow in the pre-European contact individuals but none of the individuals who lived between the 13th and 19th centuries showed any sign of Native American ancestry.

“We were really surprised we didn’t find anything. There’s a lot of evidence that seems plausible, so we were convinced we would find direct evidence of pre-European contact with South America, but it wasn’t there,” Fehren-Schmitz said in a press release.

The 2014 study made waves, finding that the genomes of 28 modern Rapanui (Easter Island natives) inherited 8% of their DNA from Native American ancestors. Signs pointed towards mixing between the two populations many generations before any European set foot on the island. This immediately conjured the image of daredevil Polynesians manning their wooden outrigger canoes, making a spectacular journey more than 2,000 miles across the ocean where they made contact with American Natives. The presence of crops native to the Americas in Polynesia, including the Andean sweet potato, long before the first reported European contact, strengthened this image.

The new findings, however, dispell this theory.

It could be that the pre-Columbian individuals that Fehren-Schmitz et al. analyzed came from isolated families that had yet to contact the Native American genetic signature, which would have already been present on the island in other individuals. After all, the initial study sampled 28 individuals while this time only five individuals were analyzed. Maybe, but Fehren-Schmitz’s hypothesis is far more plausible.

“This study highlights the value of ancient DNA to test hypotheses about past population dynamics,” said Fehren-Schmitz. “We know the island’s modern populations have some Native American ancestry, and now we know that early inhabitants did not. So the big questions remain: Where and when did these groups interact to change the genetic signature of Easter Islanders?

When Europeans first made contact with Native Americans in the 16th century, they made sure to “civilize” the locals with their way of life. Slavery and mass deportation soon followed. By the time the first Native American slaves arrived at Easter Island in the 18th century, they would have already had short-bursts of European and Native American DNA in their genomes. So after Polynesian Rapanui mixed with the continental people, the genetic analysis could have fooled us that the Native American genome was present on the island long before Europeans made contact.

The bottom line is that ascertaining the history of a whole culture of people is an extremely complex affair if genes are all you have to work with. It’s likely, however, that this is not the last word on the matter.

“We want to do more work to determine more precisely when this gene flow between Native Americans and the people of Rapa Nui occurred, and where in the Americas it originated,” Fehren-Schmitz said. “The population dynamics of these regions are fascinating. We need to study the ancient populations of other islands—if remains exist.”

Scientific reference: Current Biology, Fehren-Schmitz and Jarman et al.: “Genetic Ancestry of Rapanui before and after European Contact” DOI: 10.1016/j.cub.2017.09.029. 

Gene cutting.

Second gene-silencing mechanism found, could lead to viable clones and safer in vitro

A new cellular gene-silencing mechanism has been identified and could hold the key to safer in vitro fertilization, even the cloning of animals.

Gene cutting.

Image credits Arek Socha.

We each inherit two working copies of most genes from our parents, one from the maternal and one from the paternal side. But for a tiny minority of genes, or allele, only one copy can be allowed to function while the other remains inactivated from inception until the moment we die. This mechanism is called imprinting, and faulty imprinting can cause a host of genetic syndromes, such as Angelman’s (too much imprinting, so both genes are inactivated) or Beckwith-Wiedemann syndrome (too little imprinting, so both alleles are expressed).

Imprinting is why a lion and a tiger can have two types of offspring. If the female is lion, the couple will sire a tigon, which generally-speaking are smaller than both the parent species. But if the female is a tiger, they will sire a liger — which is much larger in general than any of the initial two. The differences in size and appearance come down, in part, to imprinting differences in maternal- and paternal-inherited genes.Usually, imprinting takes place naturally during inception, through a process called methylation — basically, methyl groups are added to a gene to shut it down.

But in artificial fertilization methods, such as in vitro for humans or straight-up cloning of mammals, imprinting can sometimes be faulty or bypassed altogether. However, a new discovery from the Howard Hughes Medical Institute might hold the key to reversing faulty imprinting. The team, whose correspondent author is Investigator Yi Zhang, found another mechanism cells can use to silence imprinted genes — by attaching specially-modified proteins called histones to the problematic alleles.

These genes are histone-y

The researchers succeeded in shutting down the activity of some imprinted genes in mice by modifying a histone known as H3K27 to carry methyl groups. They also identified 76 genes in mice that likely belong to the imprinted gene group, which is a pretty big number: until now, roughly 150 imprinted genes have been found in mice and roughly half that in humans.

There’s still a lot of work to be done on imprinting, Zhang says, but finding a second mechanism underpinning it just goes to show how important imprinting is from evolution’s point of view. It’s possible that the one the team describes in their paper evolved as a back-up to catch any improperly-imprinted alleles before they can cause any damage.

Imprinting disorders seem to develop more often in children conceived in vitro or through similar methods, the paper notes. It’s still unclear as to why. It could be that imprinting problems are inherently tied to infertility itself, or it may well be that these procedures somehow interfere with imprinting and we just don’t know it yet. But Zhao thinks their findings could give hope to couples who’re having difficulties conceiving and are pursuing assisted reproductive technologies that their child will be healthy.

Furthermore, improper imprinting could be why we’ve had so little success in cloning a healthy animal. Usually, the process requires that imprinting marks be scrapped in the precursor cells and then re-added in the eggs and sperm. Previous research lends weight to the idea that even minor bugs in this erase-rewrite phase can have dramatic effects on the development of clone embryos.

“The new imprinting mechanism may eventually offer a target for treating such developmental failures,” Zhang concludes.

The paper “Maternal H3K27me3 controls DNA methylation-independent imprinting” has been published in the journal Nature.

Barley’s full genome sequenced after decade-long research effort

After more than a decade of work, an international team consisting of over 70 researchers is poised to make your beer fuller and your Scotch neater — they have successfully sequenced the complete genome of barley, a major crop and key ingredient in the two brews.

Barley.

Image credits Hans Braxmeier.

We’ve got a long and alcohol-imbibed history with barley. It has been a staple crop for us and animal feed as well as underpinned breweries ever since the agricultural revolution. Today, barley is a major component in all-purpose flour for bread and pastries, graces breakfast tables as an ingredient in cereals, is the prime ingredient in single malt Scotch, lends beer its color, body, the protein to form a good head, and the natural sugars needed for its fermentation.

Selective breeding has allowed farmers to develop tastier, more nutritious barley with a greater yield over that time – but there’s still room for improvement, as the crop’s genome was barley known, limiting the effectiveness of breeding efforts.

Now, the International Barley Genome Sequencing Consortium (IBSC) a team of 77 researchers from around the world report that they’ve successfully sequenced the full genome of barley families heavily relied on for malting processes. This allowed them to pinpoint the bits of code that formed “genetic bottlenecks” during domestication, and further breeding efforts focus on increasing diversity in these areas and make the crops even better. It should also help scientists working with other crops in the grass family such as rice, wheat, or oats.

It may not sound like a huge accomplishment until you consider that barley’s genome is almost double the size of a human’s, and large swathes of it (around 80%) is composed of highly repetitive sequences, which made it incredibly hard for the team to focus on specific locations in the genome. The team had to make major advances in and sequencing technology, algorithmic design, and computing for the task at hand. Their findings provide knowledge of more than 39,000 barley genes.

“This takes the level of completeness of the barley genome up a huge notch,” said Timothy Close, a professor of genetics at UC Riverside and co-author of the paper.

“It makes it much easier for researchers working with barley to be focused on attainable objectives, ranging from new variety development through breeding to mechanistic studies of genes.”

One finding, in particular, surprised the scientists, and it has to do with the malting process. This involves germinating and then crushing the grains and is a key step in brewing. During germination, seeds produce amylase, a protein which breaks down their store of starch into simple sugars – which will ferment into alcohol. The team’s sequencing efforts revealed there was much more variability than expected in the genes encoding the amylase.

The full paper “A chromosome conformation capture ordered sequence of the barley genome” has been published in the journal Nature.

Ladybugs.

If you like having sex, you should thank pathogens for making it possible

The arms race between pathogens and the organisms they infect may be the fundamental reason why animals have taken to having sex and then stuck with it, a new paper reports.

So why do we have sex? Well, it’s obvious isn’t it — we do it to make more humans. But there is a small chink in that explanation, something which has been bothering evolutionary geneticists for about as long there have been any around: sexual reproduction is hard work, whereas asexual reproduction is easy and much more efficient — so why bother with it?

Ladybugs.

Image via Pixabay.

That’s something we’ve all asked ourselves at one point or another but Dr. Jack da Silva and James Galbraith from the University of Adelaide have actually set out to get an answer. After using a computer model to simulate how the genomes of Caenorhabditis elegans (non-parasitic roundworms) shift throughout several generations, the duo suggests that sexual reproduction imposed itself because organisms needed to constantly adapt their genomes to fight off co-evolving pathogens.

“Asexual reproduction, such as laying unfertilised eggs or budding off a piece of yourself, is a much simpler way of reproducing,” says Dr da Silva, Senior Lecturer in the University of Adelaide’s School of Biological Sciences.

“It doesn’t require finding a mate, and the time and energy involved in that, nor the intricate and complicated genetics that come into play with sexual reproduction. It’s hard to understand why sex evolved at all.”

One decades-old theory has been attracting more attention recently, da Silva said. Known as the Hill-Robertson Interference, it holds that sexual reproduction evolved because it allows DNA recombination between mates, allowing offspring to ‘hoard’ more beneficial mutations. In the case of asexual reproduction, where there is no pooling of genes, beneficial mutations compete with each other and natural selection grinds down.

But de Silva says this theory doesn’t explain why sexual reproduction would be maintained in a stable, well-adapted population — where maintaining the status quo makes more evolutionary sense.

 

“It is hard to imagine why this sort of natural selection should be ongoing, which would be required for sex to be favoured,” he says.

“Most mutations in an adapted population will be bad. For a mutation to be good for you, the environment needs to be changing fairly rapidly. There would need to be some strong ongoing selective force for sex to be favoured over asexual reproduction.”

The team’s suggestion is to bring another, less influential evolutionary theory into the mix. Known as the Red Queen theory, it holds that because bacteria, viruses, or parasites are continuously trying to adapt and overcome our natural or artificial defenses, our genomes are also trying to keep one step ahead by continuously mutating, becoming more resistant to them.

‘Good enough’ is better than ‘the best’

While we may be really well adapted to our environments, there’s a constant sort of biological arms race going on. Staying unpredictable — by having the ability to develop new mutations and pool them in offspring — thus becomes more advantageous than reaching a hypothetical ‘best-adapted’ genome and keeping with it.

So in the end, organisms may have chosen sexual reproduction over cloning because, although it’s harder and (on those lonely Saturday nights) more frustrating to pull off, it keeps us all similar but different enough so the germs can’t get us all in one shot. Which I feel is win for us.

“These two theories have been pushed around and analysed independently but we’ve brought them together,” says Dr da Silva. “Either on their own can’t explain sex, but looking at them together we’ve shown that the Red Queen dynamics of co-evolving pathogens produces that changing environment that makes sex advantageous through the simple genetic mechanism of the Hill-Robertson theory.”

“This is not a definitive test but it shows our model is consistent with the best experimental evidence that exists.”

The paper “Hill-Robertson Interference Maintained by Red Queen Dynamics Favours the Evolution of Sex” has been published in the Journal of Evolutionary Biology.

Researchers complete 30% of the synthetic yeast chromosome — synthetic life is just around the corner

An international research effort to construct the first fully synthetic yeast is well under way. The scientists have fully designed the fungus’ genome and have already built five of its final sixteen chromosomes — planning to have the rest completed by the end of the year.

Image credits Paul / Pixabay.

Yeast has to be humanity’s favorite fungus. Sure, other shrooms taste better in a saute or make for a much more entertaining way to spend some free time, but yeast has been by our side since times immemorial. Whenever we’ve needed something fermented, yeast had our back. Without it, there would be no alcohol, no bread, no fish sauce!

Since modern industries need to ferment more stuff much faster and into a more varied range of end products than ever before (think biofuels, insulin, antibiotics, THC), scientists have spent the last two decades sequencing yeast genome to produce different strains useful for all these products. That still leaves us limited by much of the yeast’s genome, however, which nature sadly didn’t design for industrial applications — but not for long.

Led by NYU Langone geneticist Jef Boeke, PhD, and a team of more than 200 authors, the Synthetic Yeast Project (Sc2.0) has designed a full genome for a functioning synthetic version of Baker’s yeast (S. cerevisiae). The latest issue of seven papers coming from the group shows that they’ve successfully constructed almost one third of this genome — 5 out of 16 chromosomes. They plan to have the rest ready by the end of the year. The new round of papers consists of an overview paper and five individual ones describing the first assembly of synthetic yeast chromosomes synII, synV, synVI, synX, and synXII. A seventh paper provides a first look at the 3D structures of synthetic chromosomes in the cell nucleus.

“This work sets the stage for completion of designer, synthetic genomes to address unmet needs in medicine and industry,” says Boeke, director of NYU Langone’s Institute for Systems Genetics.

“Beyond any one application, the papers confirm that newly created systems and software can answer basic questions about the nature of genetic machinery by reprogramming chromosomes in living cells.”

Learning the A’s and C’s

Apart from the immediate utility of having a tailorable yeast strain to apply in industry, Baker’s yeast was selected because of it’s relative simplicity and similarity to human cells. Sc2.0’s researchers are akin to a group of genetic programmers — they add or remove parts of DNA from chromosomes to dictate new function or prevent diseases or weakness to various factors. It makes sense to start with a simple ‘program’ until you learn the basics, which you can then apply to more complex systems.

Three years ago, Sc2.0 successfully assembled the first synthetic chromosome (chromosome 3 or synIII) out of 272,871 base pairs — the blocks which make up DNA. This process starts with the researchers screening libraries of yeast strains to find which genes are most likely to have useful features. Then, they planning thousands of permutations in the genome in a process somewhat similar to very rapid evolution. Some of these changes introduce the new genes to make the yeast exhibit desired features, others remove bits of DNA which were shown not to have a function in past trials.

Stained polytene chromosomes.
Image credits Doc. RNDr. Josef Reischig, CSc.

After the computer models are finished, the team starts assembling the edited DNA sequence bit by bit until they have the whole thing. The completed sequences are then introduced into yeast cells, which handle synthesizing and finish building the chromosomes — the latest round of papers describes a major innovation in this last step.

Until now, the researchers had to finish building once piece of a chromosome before work could begin on the latter, severely limiting their speed. These sequential requirements bottle-necked the process and increased cost, Boeke said. So the team made efforts to “parallelize” chromosome assembly, with different labs around the world synthesizing different bits in strains which were then mated. The resulting yeast strains would in some instances have even more than one fully synthetic chromosome. A paper led by Leslie Mitchell, PhD, a post-doctoral fellow from Boeke’s lab at NYU Langone, described the construction of a strain containing three synthetic chromosomes.

“Steps can be accomplished at the same time in many locales and then assembled at the end, like networking laptops to create a global super computer,” says Mitchell.

Another paper describes how a team at Tsinghua University used the same parallelized method to synthesize chromosome synXII, which formed a molecule with more than a million base pairs (one megabase) in length when fully assembled — the longest synthetic chromosome ever made by humans. It’s still only 1/3,000 the length of a human chromosome, but it’s closer than we’ve ever come before.

The researchers also found that they can edit some dramatic changes into the yeast genome without killing the cells. They survived even when the team moved whole sections of DNA from one chromosome to another, DNA swaps between yeast species, often with very little effects on the cells.

There’s a huge potential to synthetic yeast. Scientists could tailor their genome to produce anything we need from drugs, to food, new materials, almost anything — just from sugar and raw materials. It could fundamentally change how we think about a lot of industries, potentially churning the same products as factories and labs from a humble barrel.

But the work performed under the Sc2.0 project also revolutionizes how we know about genome building and synthetic life. Yeast is simple, but the end goal is to one day move on to tailor-made plants, maybe even to perfect the human genome. But we’re still a long way from that. Right now, the team will focus on getting their yeast’s final A’s, T’s, G’s, and C’s in place.

 

smoking

Smoking damages DNA, altering more than 7,000 genes

Smoking is bad for your health, and that includes genes too. This is the conclusion of one of the most comprehensive studies involving the effects of smoking and human DNA — and there are a few.

smoking

Credit: Pixabay

The Harvard Medical School researchers tracked DNA modifications in 16,000 current and ex-smokers who had participated in various studies involving smoking, some of which go as far back as 1971. Besides filling questionnaires about smoking, diet, lifestyle and their health histories, the blood of each participant was collected and had its DNA extracted for sequencing.

The results suggest smokers have a pattern of methylation changes that affected more than 7,000 genes. Methylation modifies the function of a gene, either changing the way it functions or by (in)activating it.

“Our study has found compelling evidence that smoking has a long-lasting impact on our molecular machinery, an impact that can last more than 30 years,” said Roby Joehanes of Hebrew SeniorLife and Harvard Medical School.

With such a huge number of genes affected by smoking, it’s no wonder that smokers are highly at risk of developing heart disease and cancer, both caused by genetic damage.

Now, if all of this might sound highly concerning for those of you who stop smoking, there is some good news. The researchers say that not all DNA damage is permanent. In fact, most of the damage disappeared in people who had stopped smoking for at least five years. Some genes, including the TIAM2 gene linked to lymphoma, still had changes caused by smoking 30 years later, as reported in the journal Circulation: Cardiovascular Genetics.

[panel style=”panel-warning” title=”You should know” footer=””]Smoking is the most contributor to preventable illnesses, killing 480,000 Americans yearly and roughly six million people worldwide.

While smoking was very popular in the United States, the habit has been kicked by the nation. Only 15 percent of American adults and 11 percent of high school teenagers smoke nowadays. [/panel]

“These results are important because methylation, as one of the mechanisms of the regulation of gene expression, affects what genes are turned on, which has implications for the development of smoking-related diseases,” says Dr. Stephanie J. London, the deputy chief of the Epidemiology Branch at the National Institute of Environmental Health Sciences.

“Equally important is our finding that even after someone stops smoking, we still see the effects of smoking on their DNA,” she adds.

 

human genome

Leading scientists will synthesize human genomes from scratch by 2026

Around 130 leading scientists, entrepreneurs and key government officials met behind closed doors at Harvard University a couple of weeks ago. The whole meeting was shrouded in secrecy and speculations ran amok. Now, this ad-hoc convention has made public its most ambitious plan: build and deploy a fully synthetic human genome in human cell lines within 10 years.

human genome

Credit: YouTube

The Human Genome Project Write (HGP-Write), is the next obvious step after the roaring success of the Human Genome Project (HGP-Read) launched in the 1990s. HGP-Read was one of the most serious scientific ventures in history. Instead of focusing outward, like studying the mechanics of the physical universe, HGP-Read ventured inward so that we might understand how genes code the human body.

HGP-read was finally completed in April 2003, thirteen years and $3 billion later from its launch. Today, however, the cost of sequencing a person’s DNA has fallen below the $1,000 threshold. DNA sequencing is now widely used in anything from crop breeding to forensics, to medical research.

While HGP-Read enabled us to read the human genome, HGP-Write ought to lend us the necessary knowledge and tools to write code in the human genome.

“The ability to write the genome, essentially by typing it into a computer, would be revolutionary. If it were possible, it can be used for many applications – from engineering microbes that can produce industrially relevant chemical and biological compounds to generating engineered human cells for therapeutic applications, such as for treating cancer and tissue regeneration,” said Dr. Kris Saha, Assistant Professor of Biomedical Engineering, University of Wisconsin-Madison.

Scientists will work on HGP-Write over a decade-long period, and the Center of Excellence for Engineering Biology — the non-profit that coordinates the whole affair — will seek to raise $100 million this year. The largest genome synthesis project to date is Sc 2.0, which aims to create an entirely synthetic yeast in the next five years.  The size of even the smallest human chromosome is 48 million base pairs which is 22 times the size of the largest yeast chromosome at 2.2 million base pairs.

“Relative to Sc2.0, HGP-write is 200x larger and includes a much higher proportion of difficult-to-synthesize ‘low complexity’ DNA,” said Dr. Samuel Deutsch, Head of DNA Synthesis and Assembly, DOE Joint Genome Institute.

The authors of the announcement claim fabricating synthetic human genomes, or at least regions or parts of it, will provide significant advances in medicine and biology. It could, for instance, lead to the manufacturing of pig organs that are compatible with the human body, hence fit for transplant.

DNA_Sequencing_Cost_per_Genome_Over_Time

A lot of critics have voiced ethical concerns over the project, especially during the first meetings which were shrouded in the utmost secrecy. The lead proponents of HGP-Write said they were required to keep the meetings confidential to avoid unnecessary publicity until the announcement could be made in a peer-reviewed journal. The project was officially announced on Thursday, in the journal Science.

Many are concerned that HGP-Write will open the flood gates to engineering humans. Indeed, this could be theoritically possible, but is not the scope of the project.

“It is very important to make a clear distinction between synthesizing a human genome in somatic cell lines as is proposed, and modifying human germline cells that could be hereditably transmitted, which is not in the scope of this project. Nevertheless, all technology that could be potentially used to modify human genomes needs to proceed in the context of open and transparent dialogue with many societal stakeholders, and under a regulatory framework that governs how such technology can be used in a safe and ethically acceptable manner,” Deutsch said.

“The authors propose that a percentage of all funding raised for this project be dedicated to ethical, legal and social issues. This is not only advisable but also essential. By starting a broad, transparent and inclusive conversation early on, both the scientific community and society in general will be better positioned to address the societal implications of HGP-write as the technology comes of age,” he added.

“The second part of that subtitle is the ethical framework. The project is not as controversial as some observers might be saying. First we already replace segments of human genes in cells growing in culture dishes. This is well regulated and is the very core of the new advances in medical genetics.  Making large and larger pieces of human chromosomes and putting them into host cells in culture dishes will enable more deeper understanding of what all the genes and the non-coding DNA actually does. On the route to the final goal of this new initiative will be a myriad of new therapies for treating medical conditions from genetic diseases to viral infections.  There is no call to make an entire human being just as there is no push for doing that with current studies using human embryos,” Prof John Ward, Professor of Synthetic Biology for Bioprocessing, The Advanced Centre for Biochemical Engineering, UCL, said in a statement.

“The 25 scientists propose that this project would be carried out with public involvement using the framework of Responsible Innovation where common goals of both the public and the science are identified and worked on from the beginning. The debate by scientists at a recent meeting gave rise to this white paper and it’s fascinating to see the speed of progress from that debate only 23 days ago to this carefully formulated proposal.”

Right now, scientists are already able to insert new genes or modify existing ones to breed genetically modified organisms. Genome editing tools, like the famous Crispr, have made genomic engineering even easier. Though counterintuitive, in many instances building a synthethic genome from scratch could be more efficient than modifying existing genomes, besides opening avenues of opportunity unavailable using today’s tech.

If successful HGP-Write will make history, and ought to help science at least as much as HGP-Read. Many ethical challenges have to be addressed first, though. At some point, we might even have to consider pulling the plug.

venter face prediction genome

How DNA can predict what you look and sound like

venter face prediction genome
On Monday, Dr. J. Craig Venter, regarded as one of the leading scientists of the 21st century, delivered a lecture at Washington State University. During the lecture, Venter talked about some of the most exciting projects he and colleagues are involved in. If you don’t know who Venter is, I’ll lend you a hand. He’s the pioneer who made the first synthetic life form; invested $100 million to race the government and sequence a human genome, which turned out to be his own; currently planning ‘biological teleportation’ (imagine printing life, antibiotics, whatever with a protein 3D printer, on Earth, Mars, anywhere — that’s the idea) and the recipient of countless awards. His hour-long lecture is packed with gems, wisdom and mind-bending findings from science, but maybe the most groundbreaking project Verter shared had to do with using one’s genome to predict what your face must look like, or even the sound of your voice! The results speak for themselves — just check out the video below.

The way it works is Venter and colleagues have found a way to isolate those set of genes that determine our appearance. DNA samples from thousands of people were taken, which were then sequenced and correlated with 3D models of the volunteers’ faces.

“We can now predict eye colour better than people can self describe it. There’s an 80% difference between the left and right eye that they’re not even aware of,” Venter said during the lecture
“It’s totally logical that your genome predicts exactly what we look like,” he added.

Logical indeed — it’s just that we weren’t expecting it this soon. Personally, I’m not even sure what he’s showing here (which is freaking amazing) is as precise as Venter might want us to think. Facial features may be shaped by hundreds or thousands of genes — each with very tiny effects.Hair, eye and skin color, as well as ethnic background, are relatively easy to pin down. But the genetic roots of other traits, such as height and face shape, are scattered throughout people’s DNA like dandelion seeds in the wind. If Venter managed to pull this off, well cheers!

If it’s as precise and effective as Venter says it is, than this tech can transform forensics, on one hand. It could also usher in a crazy age in which every person has his DNA in a database — information on everything that nature offered you when you entered this world.

“The forensic applications of this are , obviously, tremendous. From a DNA sample right now we use statistics to see whether it matches someone perhaps who committed a rape. But we’re limited by a DNA database. We use these images we have, at least, to scan the whole internet. We use these image scanners and then we use them to find that person on the internet.”
“We can also predict what a couple’s child looks like roughly at age 18. The genome predicts what a person looks like post-puberty but we now have software that can age or de-age photos.”

“It’s harder to predict voice from the genome. From a digital recording of your voice we can tell whether it’s male or female, and we can predict your age highly accurately. Now we can predict your height all from a voice recording. We’re finding a correlation between voice and face shape.”

Not coincidentally, a genome bank is the object of Venter’s latest business venture: Human Longevity Inc. (HLI), a startup the pioneering American inventor founded 18 months ago. Already, HLI is considered the world’s largest genome sequencing lab. Most recently, HLI partnered with South African health insurers to sequence the medically important genes of its clients for just $250. The client would then receive a list of diseases or afflictions that he risks developing in the course of life. Sounds quite the business – the African insurer can better assess its clients and decide who can be insured and on what terms, while HLI is gaining a massive genetic database which it can then use to fine-tune its projects, especially considering African genomes are lacking in the global DNA sequence bank.

Largest genetic complement identified, owned by the water bear

Also known as the water bear, the tardigrade has a lot to be proud of — this tiny organism is nigh-indestructible, known to have survived in extreme temperatures ( -272C to +151C / -457.6F to 303.8F) and to be the only animal that can brave the vacuum of space unprotected and live to tell the tale. A team from the University of North Carolina at Chapel Hill, curious as to how the tardigrade can accomplish such incredible feats, sequenced the genome of the microorganism. Their paper, published in the journal PNAS, reveals that a huge chunk of its DNA is of foreign origin — nearly 17.5% of the water bear’s genome (some 6000 genes) are primarily of bacterial origin, though genes from fungi and plants have also been identified.

Looks fluffy.
Image via wikimedia

Defined as the shifting of genetic material materially between organisms, horizontal gene transfer is widespread in the microscopic world. The process occurs in humans too but in a limited fashion, and via transposons and viruses. Microscopic animals however are known to have large complements of foreign genes.

Until today, the rotifer held the title for ” the greatest complement of foreign DNA of any microscopic organism,” but the newly-sequenced tardigrade genome includes twice as many genes as those boasted by the rotifer. And the authors have a theory as to why this extremely extensive gene transfer may have occurred.

Tardigrades have long been known to undergo and survive the process of desiccation (extreme drying out). The authors believe that this process is extremely harsh on the tardigrade’s genome, with strands of DNA suffering significant sheering and breakage, causing a general loss of integrity and leakiness of the water bear’s nucleus. This may allow foreign genetic material to easily exploit such gaps in the genome and integrate themselves, similar to the gene-transfer procedure known as electroportation.

For now, the tardigrade has a dual claim to fame, being the only known animal to survive the vacuum of space, and being the animal with the largest genetic complement.

Not bad for a 1.5mm long bug.

An early embryo

UK scientists want to modify genes inside a human embryo

A team working at the Francis Crick Institute in London applied to the Human Fertilisation and Embryology Authority for a permit that would allow them to edit genes in a human embryo. If allowed, this would lead to the very first genetically modified embryo in the UK. The scientists claim they need approval to do basic research that may ” improve embryo development after in vitro fertilization (IVF) and might provide better clinical treatments for infertility,” and not for clinical research. Either way, the controversial practice is banned in all Western countries and virtually banned, although not explicitly, in the US.

An early embryo

The Crick group leader,  Dr Kathy Niakan, wants to make specific alterations to the genomes of human embryos using a new technique called CRIPSR/Cas9. This technique makes it a lot more easy and cheap to split and stitch DNA into the genome. A lot of biotech companies now use this technique for a wide array of innovative research. For instance, there’s Edita – startup backed by Bill Gates – which uses CRIPSR to edit somatic cells collected from live patients. These cells, like the T-cells (a type of white cells), have their genes edited or repaired to correct an abnormality and inserted back into the patient through a simple blood transfusion. Research that manipulates human embryo genomes, many consider, is unethical and is an eugenic line that shouldn’t be crossed.

The main problem with germline embryo modification is that these modifications, which can be repairs or upgrades (genes that make you smarter, faster, stronger, less prone to diseases etc.), are passed on to subsequent generations without consent. This is an extremely grey area which often loops into non-sense. One could argue that you can’t ask an embryo anything. “So, future baby, what do you think of mommy and daddy? Do you consent of them as your parents? Do you consent being born a “Christian” or “Muslim”?” Wouldn’t be funny if a newborn baby was like “heeeey, I’m out of here!”. Of course, other issues are far more serious. An artificially induced genetic defect could make its way into the gene pool and there’s no way you can pull it out, unless you manage to isolate populations, then a whole slew of complications arise. Then, there’s always a background complaint: modified human embryos is playing God. It’s like sidetracking evolution to create a human super race, one that’s immune to disease, is super smart and, possibly, can’t die of old age. This sounds scary and impressive at the same time. It’s really hard to pick sides, so it’s no wonder that most countries have decided to solve this issue in the easiest way possible: ban it!

Well, everyone except China it seems. This April, the world learnt that Chinese researchers, again using CRIPSR, edited the genome of human embryonic cells, a world first. The cells never survived but it was the first practical demonstration, one that immediately sent shivers at the prospect of “designer children”. The Chinese embryos also bore unwanted mutations as a result of the intervention. Since 1999, the Beijing Genomics Institute is carrying research to find out which genes, if any, are responsible for human genius. The project spawned wild accusations of eugenics plots, as well as more measured objections by social scientists who view such research as a distraction from pressing societal issues.

In the US, things are pretty clear: “NIH will not fund any use of gene-editing technologies in human embryos. The concept of altering the human germline in embryos for clinical purposes … has been viewed almost universally as a line that should not be crossed,” said Francis Collins, director of the US National Institutes of Health. As for the UK, the Crick study might receive approval, but it most likely won’t due to public pressure. If it does, it would mark a huge milestone in genetics. Let’s just hope that it’s a fortunate milestone.

Junk DNA

Only 8.2% of our DNA is actually useful, the rest is ‘junk’ apparently

It’s been only a decade since the Human Genome Project finished its task of mapping all the code that makes up our DNA. The hard part came later, though – identifying what each piece of code does or, oddly enough, does not. According to the most recent estimate for instance, only 8.2% of the code embedded in the human genome is actually useful, in the sense that it performs a function whether activating a gene, regulating it, and so on. The rest is what scientists class as “junk DNA”.

Junk DNA

Image: Institute for Creation Research

Genomes are like biological books, written in genetic letters known as bases; the human genome contains about 3.2 billion bases. The study led by researchers at University of Oxford in England found only 250 million of these letters are functional, and 2 billion or so are not. This might not seem like a really tiny amount, but it’s still considerably higher than a previous estimates which had the figure hovering between 3 and 5 percent. That’s not to say that previous findings were wrong. Instead, it has more to do with how each group classes functional DNA. For instance, a research published by the Encyclopedia of DNA Elements Project (ENCODE) found 80% of our DNA is ‘useful’. But the researchers counted all pieces of DNA on which some protein activity occurred, whether or not this was useful to the cell. The problem is that protein activity occurs all the time. When a cell divides, the DNA replicates and causes protein activity, but this doesn’t mean that particular code is useful.

“Whether people like it or not, the vast majority of our genome is junk,” said Dan Graur for LiveScience, a professor of molecular evolutionary biology at the University of Houston in Texas, who was not involved with the new study. “We know that because we have so many organisms that have much smaller genomes than we do and organisms that have much larger genomes than we have. The size of your genome is not really what matters.”

In this new study, the researchers used an evolutionary model to estimate which part of the DNA is useful or otherwise. This consideration was applied not only to the human genome, but others as well like cattle, ferrets, rabbits or pandas. This sort of novel analysis looks at how DNA has changed since all these mammals, including us humans, split from a common ancestor some 100 million years ago. The reasoning is that by looking at how many genes suffered the least amount of mutations you can count the useful ones – the less mutations the better the chance that the gene in question is useful. Like humans, just 8.2 percent of the DNA in each of these animals is functional, the findings suggest.

Even more interesting, just 1% of our genes code proteins that handle our day to day bodily functions, while the rest of 7% regulate these genes by turning on and off – which is just as vital, granted.

Some might be surprised by these kind of findings. How can it be possible such a thing as “junk DNA” exists? Wouldn’t nature find a way to eliminate redundancy? Why clutter DNA if there’s no use to it? Nobody knows for sure why, but the simplest answer is that nature isn’t perfect and life can be a mess. It’s enough to look at other organisms to understand that more DNA doesn’t equal more complexity. An onion’s genome is five times larger; the wheat’s is eleven times larger. Over millions of years, the human genome has spontaneously gotten bigger, swelling with useless copies of genes and new transposable elements. Our ancestors tolerated all that extra baggage because it wasn’t actually all that heavy. This is at least one side of the story.

40,000-year-old modern human jawbone reveals that this man had a Neandertal ancestor as recently as four to six generations back. Image: Credit: MPI f. Evolutionary Anthropology/ Paabo

An ancient human who lived in Romania had almost 9% Neanderthal DNA

DNA analysis of the jawbone of a human who lived in modern day Romania some 40,000 years ago has the most Neanderthal ancestry ever seen. Up to 9% of the ancient man’s DNA was Neanderthal, suggesting interbreeding occurred much earlier than previously thought. In fact, this European human had a Neanderthal ancestor four to six generations back in his family tree. How would it be to have a Neanderthal for a  great-great-great-grandfather?

40,000-year-old modern human jawbone reveals that this man had a Neandertal ancestor as recently as four to six generations back. Image:  Credit: MPI f. Evolutionary Anthropology/ Paabo

40,000-year-old modern human jawbone reveals that this man had a Neandertal ancestor as recently as four to six generations back. Image: Credit: MPI f. Evolutionary Anthropology/ Paabo

Most people living outside sub-Saharan Africa today have about 1 to 3 percent Neanderthal DNA. The study published today by a team of international researchers suggests, however, that the ancient Romanian’s genome contained 6 to 9% Neanderthal genes, as reported in Nature. Neanderthals lived in Europe until about 35,000 years ago, disappearing at the same time modern humans were spreading across the continent.

The jawbone was found in 2002 along with the skull of another individual in a cave in Romania called Pestera cu Oase. There were no artifacts found nearby, no clues that could indicate some cultural trademark to help identify who the individuals were or how they lived. From the start, the researchers knew there was something special to the jawbone, though. It predominantly had physical features resembling those of modern humans, but there were some uncanny Neanderthal traits that were also apparent. Radiocarbon dating determined the jawbone was between 37,000 and 42,000 years old.

David Reich at Harvard Medical School and Svante Pääbo at the Max Planck Institute in Germany then got involved and performed the genome sequencing.

“Some Neanderthals clearly became incorporated in modern human societies,” said Pääbo, director of the Department of Evolutionary Genetics at the Max Planck Institute for Evolutionary Anthropology. “It is still unclear exactly how much of the complete Neanderthal genome exists today in people, but it seems to approach something like 40 percent.”

“But, of course, the Neanderthals are clearly extinct in the sense that they do not exist as an independent, separate group since some 30,000 or 40,000 years.”

“The sample is more closely related to Neanderthals than any other modern human we’ve ever looked at before,” Reich says.

“It’s an incredibly unexpected thing,” Reich says. “In the last few years, we’ve documented interbreeding between Neanderthals and modern humans, but we never thought we’d be so lucky to find someone so close to that event.”

Interesting enough, the Oase individual didn’t pass his Neanderthal ancestry to the present population, according to Reich.

“This sample, despite being in Romania, doesn’t yet look like Europeans today,” he says. “It is evidence of an initial modern human occupation of Europe that didn’t give rise to the later population. There may have been a pioneering group of modern humans that got to Europe, but was later replaced by other groups.”