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Researchers have genetically transformed the Common Primrose (Primula vulgaris) for the first time in a development that could shed light on one of the plant world's most renowned reproductive systems.

Credit: John Innes Historical Collection

The complicated sex life of Primula was a subject that fascinated Charles Darwin and generations of geneticists that followed because it's one of the best examples of heteromorphic flower development.

Heteromorphy (or heterostyly) is a phenomenon in which plants exhibit two or three distinct forms of flowers based on the position of the male and female sex organs. Now, some of the secrets that eluded Darwin could be revealed following the biotechnological success announced by researchers from the John Innes Centre, the University of East Anglia (UEA) and the Earlham Institute.

The technology known as Agrobacterium-mediated plant transformation involves using soil bacteria to insert or modify genes in a plant genome. Genetic transformation is a valuable tool that allows researchers to study gene function and genetically controlled characteristics in organisms.

It is a research method routinely used on model organisms such as Nicotiana benthamiana and Arabidopsis thaliana to understand the molecular workings of plants. However, these species cannot be used to study heteromorphy because their flowers are all homomorphic which means they are able to self-fertilise.

"Now we have a transformation system we can use gene editing tools such as CRISPR-Cas9 to work out exactly what the gene function is that controls heteromorphy in the Primula family," says Sadiye Hayta, of the John Innes Centre.

"Longer term, there may be implications for commercial crops. If we understand the roles of these different genes we could take them over to a commercial crop and use it in a hybrid system," she adds.

Until now attempts to transform Primula have been unsuccessful because the plant has proved resistant to laboratory regeneration of whole plants from tissue culture.

The new transformation protocols reported in the peer-reviewed journal Plant Methods will allow the scientists of today to study the Primula at a molecular level.

The flowering plant is one of the best-known examples of heteromorphic flower development. This reproductive system enthralled not only Darwin but many leading geneticists from the early 1900s including William Bateson, the first director of the John Innes Centre and colleagues JBS Haldane, Cyril Darlington and Dorothea de Winton.

Darwin, in a landmark paper of 1862, worked out the functional significance of the different anatomical formations: they made the plants self-incompatible. This is Nature's way of promoting cross-pollination to maintain genetic variation in the population, driving natural selection.

Fundamental research into heteromorphy has continued. In a research paper in 2016 a John Innes Centre - University of East Anglia team led by Professor Philip Gilmartin identified the S-Locus supergene that controls heteromorphy as described by Darwin.

Armed with this fundamental knowledge and a the newly announced transformation system, scientists can delve deeper into the mysteries of heteromorphy.

Co-author Mark Smedley, of the John Innes Centre says: "It is not every day you get to work on a paper that references Darwin. This is a fundamental story that scientists have been trying to unravel for 200 years."

Professor Philip Gilmartin of the UEA whose laboratory started out on this scientific mission more than 20 years ago, said: "The development of a Primula transformation system is an important component of our lab's long-term study to identify and characterise the genes that control development of the two forms of Primula flower studied by Charles Darwin."

It's a piece of research that would have excited Darwin. Towards the end of his illustrious career the author of On the Origin of Species remarked:

"I do not think anything in my scientific life has given me so much satisfaction as making out the meaning of the structure of these plants."

Source: John Innes Centre [December 11, 2018]

A QUT-led collaboration with University of Adelaide reveals that Australia's pint-sized banded hare-wallaby is the closest living relative of the giant short-faced kangaroos which roamed the continent for millions of years, but died out about 40,000 years ago.

The diminutive banded hare-wallaby linked to the giant Sthenurinae kangaroos [Credit: Queensland University of Technology]

Published in Systematic Biology, the research involved the first near-complete mitochondrial (mt) genome sequencing from extinct Australian megafauna.

- DNA was sequenced from inner ear bones (petrous bones) of a 45,000-year-old giant short-faced kangaroo, Simosthenurus occidentalis, part of the Sthenurinae sub-family, found at Mt Cripps in Tasmania

- These are the longest DNA sequences ever recovered from Australia's extinct megafauna, with more than 16,000 base pairs of mtDNA, which is used to help understand evolutionary relationships

- The results support an evolutionary link between giant short-faced kangaroos (Sthenurinae) and the threatened banded hare-wallaby, Lagostrophus fasciatus

- The study also combined the DNA evidence with fossil and anatomical data to trace body size change over the evolutionary history of kangaroos and wallabies

The analysis was conducted by QUT evolutionary biologists Ph.D. researcher Manuela Cascini and Associate Professor Matthew Phillips, from the Science and Engineering Faculty, in collaboration with University of Adelaide's Professor Alan Cooper and Dr. Kieren Mitchell, who undertook the DNA sequencing at the Australian Centre for Ancient DNA.

Credit: Queensland University of Technology

Lead author Ms Cascini, a molecular biologist who moved from Italy to undertake her Ph.D. research with Associate Professor Phillips, said her project also involved analysis of mtDNA sequenced from the inner ear bones of another ancient extinct macropod that was found in Tasmania – the giant wallaby, Protemnodon anak, which weighed up to 150 kilograms.

Small fragments of ancient DNA sequenced from this giant wallaby species and from the giant short-faced kangaroo were first reported on by University of Adelaide scientists in 2015.

"Our analysis confirmed their conclusion that the giant wallabies are close relatives of the iconic living Macropus genus of kangaroos and wallabies," Ms Cascini said.

"However that earlier study provided insufficient DNA to confidently place the giant short-faced kangaroos on the evolutionary tree.

"We've now been able to show the strongest evidence yet that the closest living relative of these massive Sthenurinae kangaroos, which weighed up to about 240 kilograms, is the tiny, 2-kilogram banded hare-wallaby. These wallabies live in the wild only on islands off Western Australia and are classified as vulnerable."

Largest of the extinct giant short-faced kangaroos, Procoptodon goliah, featured on an Australia Post stamp  [Credit: Queensland University of Technology]

Associate Professor Phillips said the larger amount of mtDNA sequenced in this study by the University of Adelaide collaborators helped enable the strong finding on the banded hare-wallaby link.

"This is by far the most genetic data that anyone has extracted out of Australian megafauna, and it was taken from the petrous bones which are denser and often seem to hold DNA better," he said.
"You find a lot of ancient DNA studies of megafauna from permafrost in northern Europe and northern America because the cold helps preserve the DNA. But in Australia the hotter climate and older age of the megafauna is far less favourable for DNA preservation."

Dr. Mitchell said Tasmania's cooler climate and higher-altitude caves "make for much better DNA preservation than we find elsewhere in Australia, so we focused our hunt for high-quality megafaunal DNA there".

Associate Professor Phillips said other findings of the study on the evolution of kangaroos and wallabies (macropods) included:

- The macropod ancestors diverged from tree-living possums around 41 to 46 million years ago

- They remained small, in the 2-15 kg range, while Australia was more dominated by rainforest

- As the climate cooled and dried, and as the forests opened up over the past 10 million years, at least four different kangaroo lineages independently evolved to megafaunal size (more than 44 kg)

- This includes the short-faced kangaroos, the giant Protemnodon wallabies, and the living red and grey kangaroos.

Author: Rose Trapnell | Source: Queensland University of Technology [December 10, 2018]

Barely living "zombie" bacteria and other forms of life constitute an immense amount of carbon deep within Earth's subsurface -- 245 to 385 times greater than the carbon mass of all humans on the surface, according to scientists nearing the end of a 10-year international collaboration to reveal Earth's innermost secrets.

A nematode (eukaryote) in a biofilm of microorganisms. This unidentified nematode (Poikilolaimus sp.) from Kopanang gold mine in South Africa, lives 1.4 km below the surface [Credit: Gaetan Borgonie, Extreme Life Isyensya, Belgium]

On the eve of the American Geophysical Union's annual meeting, scientists with the Deep Carbon Observatory today reported several transformational discoveries, including how much and what kinds of life exist in the deep subsurface under the greatest extremes of pressure, temperature, and low nutrient availability.

Drilling 2.5 kilometers into the seafloor, and sampling microbes from continental mines and boreholes more than 5 km deep, scientists have used the results to construct models of the ecosystem deep within the planet.

With insights from now hundreds of sites under the continents and seas, they have approximated the size of the deep biosphere -- 2 to 2.3 billion cubic km (almost twice the volume of all oceans) -- as well as the carbon mass of deep life: 15 to 23 billion tonnes (an average of at least 7.5 tonnes of carbon per cu km subsurface).

The work also helps determine types of extraterrestrial environments that could support life.

Among many key discoveries and insights:

- The deep biosphere constitutes a world that can be viewed as a sort of "subterranean Galapagos" and includes members of all three domains of life: bacteria and archaea (microbes with no membrane-bound nucleus), and eukarya (microbes or multicellular organisms with cells that contain a nucleus as well as membrane-bound organelles)

- Two types of microbes -- bacteria and archaea -- dominate Deep Earth. Among them are millions of distinct types, most yet to be discovered or characterized. This so-called microbial "dark matter" dramatically expands our perspective on the tree of life. Deep Life scientists say about 70% of Earth's bacteria and archaea live in the subsurface

- Deep microbes are often very different from their surface cousins, with life cycles on near-geologic timescales, dining in some cases on nothing more than energy from rocks

- The genetic diversity of life below the surface is comparable to or exceeds that above the surface

- While subsurface microbial communities differ greatly between environments, certain genera and higher taxonomic groups are ubiquitous -- they appear planet-wide

- Microbial community richness relates to the age of marine sediments where cells are found -- suggesting that in older sediments, food energy has declined over time, reducing the microbial community

- The absolute limits of life on Earth in terms of temperature, pressure, and energy availability have yet to be found. The records continually get broken. A frontrunner for Earth's hottest organism in the natural world is Geogemma barossii, a single-celled organism thriving in hydrothermal vents on the seafloor. Its cells, tiny microscopic spheres, grow and replicate at 121 degrees Celsius (21 degrees hotter than the boiling point of water). Microbial life can survive up to 122°C, the record achieved in a lab culture (by comparison, the record-holding hottest place on Earth's surface, in an uninhabited Iranian desert, is about 71°C -- the temperature of well-done steak)

- The record depth at which life has been found in the continental subsurface is approximately 5 km; the record in marine waters is 10.5 km from the ocean surface, a depth of extreme pressure; at 4000 meters depth, for example, the pressure is approximately 400 times greater than at sea level

- Scientists have a better understanding of the impact on life in subsurface locations manipulated by humans (e.g., fracked shales, carbon capture and storage)

Candidatus Desulforudis audaxviator (the purplish, blue rod-shaped cells straddling orange carbon spheres) is a species of bacteria that survives on hydrogen. Scientists found it living within a fluid and gas-filled fracture 2.8 km beneath Earth's surface at a mine near Johannesburg, South Africa. The genus name Desulforudis comes from the Latin for "from sulfur"  and "rod," noting its shape and its ability to get energy from sulfates. And audaxviator? From Jules Verne's Journey to the Center of the Earth, and a message in Latin deciphered by Verne's protagonist, Professor Lidenbrock, which read  in part: "descend, bold traveler, and attain the center of the Earth" [Credit: Greg Wanger, California Institute of Technology, USA, and Gordon Southam University of Queensland, Australia]

Ever-increasing accuracy and the declining cost of DNA sequencing, coupled with breakthroughs in deep ocean drilling technologies (pioneered on the Japanese scientific vessel Chikyu, designed to ultimately drill far beneath the seabed in some of the planet's most seismically-active regions) made it possible for researchers to take their first detailed look at the composition of the deep biosphere.

There are comparable efforts to drill ever deeper beneath continental environments, using sampling devices that maintain pressure to preserve microbial life (none thought to pose any threat or benefit to human health).

To estimate the total mass of Earth's subcontinental deep life, for example, scientists compiled data on cell concentration and microbial diversity from locations around the globe.

Led by Cara Magnabosco of the Flatiron Institute Center for Computational Biology, New York, and an international team of researchers, subsurface scientists factored in a suite of considerations, including global heat flow, surface temperature, depth and lithology -- the physical characteristics of rocks in each location -- to estimate that the continental subsurface hosts 2 to 6 × 10^29 cells.

Combined with estimates of subsurface life under the oceans, total global Deep Earth biomass is approximately 15 to 23 petagrams (15 to 23 billion tonnes) of carbon.

Says Mitch Sogin of the Marine Biological Laboratory Woods Hole, USA, co-chair of DCO's Deep Life community of more than 300 researchers in 34 countries: "Exploring the deep subsurface is akin to exploring the Amazon rainforest. There is life everywhere, and everywhere there's an awe-inspiring abundance of unexpected and unusual organisms.

"Molecular studies raise the likelihood that microbial dark matter is much more diverse than what we currently know it to be, and the deepest branching lineages challenge the three-domain concept introduced by Carl Woese in 1977. Perhaps we are approaching a nexus where the earliest possible branching patterns might be accessible through deep life investigation.

"Ten years ago, we knew far less about the physiologies of the bacteria and microbes that dominate the subsurface biosphere," says Karen Lloyd, University of Tennessee at Knoxville, USA. "Today, we know that, in many places, they invest most of their energy to simply maintaining their existence and little into growth, which is a fascinating way to live.

"Today too, we know that subsurface life is common. Ten years ago, we had sampled only a few sites - the kinds of places we'd expect to find life. Now, thanks to ultra-deep sampling, we know we can find them pretty much everywhere, albeit the sampling has obviously reached only an infinitesimally tiny part of the deep biosphere."

"Our studies of deep biosphere microbes have produced much new knowledge, but also a realization and far greater appreciation of how much we have yet to learn about subsurface life," says Rick Colwell, Oregon State University, USA. "For example, scientists do not yet know all the ways in which deep subsurface life affects surface life and vice versa. And, for now, we can only marvel at the nature of the metabolisms that allow life to survive under the extremely impoverished and forbidding conditions for life in deep Earth."

"A decade ago, we had no idea that the rocks beneath our feet could be so vastly inhabited. Experimental investigations told us that microbes could potentially survive to great depth; at that time, we had no evidence, and this has become real ten years later. This is simply fascinating and will surely foster enthusiasm to look for the biotic-abiotic fringe on Earth and elsewhere," said Isabelle Daniel, University of Lyon 1, France.

This is a species of Methanobacterium, which produces methane. Found in samples from a buried coal bed 2 km below the  Pacific Ocean floor off the coast of Japan, this specimen was retrieved during an Integrated Ocean Drilling Program  (now the International Ocean Discovery Program) expedition aboard the Drilling Vessel Chikyu. Bar represents 10 μm (micrometers, or 0.0004 inch) [Credit: Hiroyuki Imachi (Japan Agency for Marine-Earth Science and Technology (JAMSTEC)]

Among the many remaining enigmas of deep life on Earth:

Movement: How does deep life spread -- laterally through cracks in rocks? Up, down? How can deep life be so similar in South Africa and Seattle, Washington? Did they have similar origins and were separated by plate tectonics, for example? Or do the communities themselves move? What roles do big geological events (such as plate tectonics, earthquakes; creation of large igneous provinces; meteoritic bombardments) play in deep life movements?

Origins: Did life start deep in Earth (either within the crust, near hydrothermal vents, or in subduction zones) then migrate up, toward the sun? Or did life start in a warm little surface pond and migrate down? How do subsurface microbial zombies reproduce, or live without dividing for millions to tens of millions of years?

Energy: Is methane, hydrogen, or natural radiation (from uranium and other elements) the most important energy source for deep life? Which sources of deep energy are most important in different settings? How do the absence of nutrients, and extreme temperatures and pressure, impact microbial distribution and diversity in the subsurface?

"Even in dark and energetically challenging conditions, intraterrestrial ecosystems have uniquely evolved and persisted over millions of years. Expanding our knowledge of deep life will inspire new insights into planetary habitability, leading us to understand why life emerged on our planet and whether life persists in the Martian subsurface and other celestial bodies,"  according to Fumio Inagaki, Japan Agency for Marine-Earth Science and Technology.

"While we are far from being able to quantify it, we believe Deep Life has an important impact on global biogeochemical cycles and chemical equilibria in habitable rocks. Deep Life plays a role in aquifer quality, for example, or carbon capture and storage (CCS). Unfortunately, the deep biosphere is very poorly considered in engineering operations carried out in the subsurface. We recently demonstrated the high reactivity of deep biota to CO2 injections (CCS), which ultimately led to the bioclogging of the injection well, and surrounding reservoir," adds Benedicte Menez, Institut de Physique du Globe de Paris, France.

Source: Deep Carbon Observatory [December 10, 2018]

University of Otago researchers have discovered information about a gene that sets primates—great apes and humans—apart from other mammals, through the study of a rare developmental brain disorder.

Brain organoids, or "mini-brains" growing in culture [Credit: Dr Adam O'Neill]

Dr. Adam O'Neill carried out the research as part of his Ph.D. at the University of Otago, under the supervision of Professor Stephen Robertson, discovering that the PLEKHG6 gene has qualities that drives aspects of brain development differently in primates compared to other species.

"Broadly speaking, this gene can be thought of as one of the genetic factors that make us human in a neurological sense," Dr. O'Neill who now works in the Department of Physiological Genomics at Ludwig Maximilian Universität in Munich, Germany, explains.

Professor Robertson says the research, just published in international journal Cell Reports, aimed to address the idea that there must be genes that humans have that have made our brains bigger and better functioning in some respects than other animals. However, that increased complexity could come at a cost, potentially predisposing humans to the development of a whole suite of neurological or psychiatric conditions.

"Such genes have been hard to find, but using an approach where we studied children with a certain brain malformation called periventricular nodular heterotopia, we found a 'damaged' genomic element in a child that had the attributes of such a primate specific genetic factor," he explains. In this particular condition a subset of neurons in the developing brain fail to take up their correct position resulting in a variety of symptoms including epilepsy and delayed development.

Dr. O'Neill and research collaborators from Max Planck Institute of Psychiatry, Germany, then set forth to test the point that the gene drives aspects of brain development that are unique to primates. Some amazing data was found using a novel approach through studying human "mini-brains" in culture. It is now possible to take a skin cell and transform it using a set of genetic tricks, so that it can be triggered to form a tiny brain-like structure in culture in the lab.

Their results showed that the particular genetic change that disabled a component of this gene (PLEKHG6) altered its ability to support the growth and proliferation of specialised stem cells in the developing brain. In addition, some of these cells also failed to migrate to their correct position in the growing "mini-brain" during the first few weeks of brain development.

Professor Robertson says it has been known for a while that these stem cells behave differently between primates/humans and other animals, but understanding what genes regulate these differences has been a mystery.

"Adam's achievement has been to show that this particular component of the PLEKHG6 gene is one such regulator that humans have 'acquired' very recently in their evolution to make their brains 'exceptional'."

Dr. O'Neill says there are very few genetic elements that are primate specific in our genome, so this discovery adds to a very short list of genetic factors that, at least in one sense, make us human.

"Such an understanding positions us to better understand how a brain builds itself- knowledge that will add to our ability to design strategies to repair the damaged brain, especially early in infancy where there are still lots of stem cells around," Dr. O'Neill says.

The work also helps provide more information about the list of genes that are altered to cause this particular type of brain malformation.

"Personally, I also think it does underscore how it is very subtle nuanced differences that separate us from other animals. Our anthropocentrism could be a whole lot more humble," Dr. O'Neill says.

Source: University of Otago [December 06, 2018]

Like other organisms, bacteria constantly have to fight to survive in hostile living conditions. Together with colleagues in Finland, researchers at the Max Planck Institute for Evolutionary Biology in Plön have discovered that bacteria adapt to their environment more slowly and less efficiently as soon as they are exposed to two stress factors rather than one. This is due to mutations in different genes. The slower rate of evolution led to smaller population sizes. This means that evolution can take divergent paths if an organism is exposed to several stress factors.

The single-cell organism Tetrahymena thermophila (green) with its bacterial prey (purple) [Credit: Matti Jalasvuori]

Bacteria rarely live alone; they are usually part of a community of species that is exposed to various stress factors. They can often react to these factors by adapting to new environmental conditions with astonishing speed. Antibiotics that enter soil and water via waste water and accumulate there in low concentrations can trigger the evolution of resistance in bacteria – even though these concentrations are so low that they inhibit bacterial growth only slightly or not at all. However, bacteria do not only have to fight antibiotics; they also have to deal with predators. This is why they often grow in large colonies that cannot be consumed by predatory organisms.

Typically, scientists investigate the effects that a single stress factor has on an organism. Researchers at the Max Planck Institute for Evolutionary Biology in Plön and the Universities of Helsinki and Jyväskylä, Finland, have now investigated the question of how microorganisms behave when they are confronted with more than one stress factor. "We simulated natural environmental conditions in the lab and exposed bacteria to both predators and antibiotics. This allows us to estimate how likely it is to find evolution of resistance to antibiotics outdoors," explains study leader Lutz Becks.

Antibiotics and predators

In the scientists' laboratory, the bacterium Pseudomonas fluorescence had to cope with both antibiotics and the predatory single-cell organism Tetrahymena thermophila. After just a short time, the team of researchers noticed that the bacterial population was changing: the bacteria were much slower and less effective in developing resistance and protecting themselves from being consumed than others of the species that were only exposed to one of these factors. Moreover, resistance against the antibiotic was much less common. "The bacteria were clearly unable to optimize both attributes at the same time," says Becks.

In the next step, the scientists analysed the genetic basis of these adaptations. Their results show that mutations for improved protection from predators appear in the same numbers and at the same places in the bacterial genome if only the predatory ciliates are present. The same applies to mutations that cause resistance to antibiotics. However, other mutations occur as soon as both stress factors influence the bacteria and the bacteria have to fight both predators and antibiotics. This causes both the bacteria's protection against predators and resistance to antibiotics to evolve more slowly and be less efficient.

Because the bacteria are less able to protect themselves from predators if they are confronted by the predatory ciliates and antibiotics simultaneously, their numbers are fewer than when they only have to defend themselves from predators. Several stress factors therefore appear to have a strong influence on whether and how often resistance to antibiotics develops and how large the population of bacteria can become.

"Microbial populations – whether in a lake or in the gut – are complex communities in which many species have to compete for resources. The various stress factors to which microbes are exposed have an enormous effect on their evolution and survival rate. It will take some time until we fully understand the interaction of all these factors and the influence of antibiotics and pesticides," explains Becks.

The study is published in Nature Ecology & Evolution.

Source: Max Planck Society [December 06, 2018]

Parrots are famously talkative, and a blue-fronted Amazon parrot named Moises - or at least its genome - is telling scientists volumes about the longevity and highly developed cognitive abilities that give parrots so much in common with humans. Perhaps someday, it will also provide clues about how parrots learn to vocalize so well.

This photograph shows an Amazona aestiva taking care of the nest in Pantanal [Credit: Glaucia Seixas]

Morgan Wirthlin, a BrainHub post-doctoral fellow in Carnegie Mellon University's Computational Biology Department and first author of a report to appear in the journal Current Biology, said she and her colleagues sequenced the genome of the blue-fronted Amazon and used it to perform the first comparative study of parrot genomes.

By comparing the blue-fronted Amazon with 30 other long- and short-lived birds -- including four additional parrot species -- she and colleagues at Oregon Health and Science University (OHSU), the Federal University of Rio de Janeiro and other entities identified a suite of genes previously not known to play a role in longevity that deserve further study. They also identified genes associated with longevity in fruit flies and worms.

"In many cases, this is the first time we've connected those genes to longevity in vertebrates," she said.

This photograph shows Amazona aestiva chicks in Pantanal [Credit: Glaucia Seixas]

Wirthlin, who began the study while a Ph.D. student in behavioral neuroscience at OHSU, said parrots are known to live up to 90 years in captivity -- a lifespan that would be equivalent to hundreds of years for humans. The genes associated with longevity include telomerase, responsible for DNA repair of telomeres (the ends of chromosomes), which are known to shorten with age. Changes in these DNA repair genes can potentially turn cells malignant. The researchers have found evidence that changes in the DNA repair genes of long-lived birds appear to be balanced with changes in genes that control cell proliferation and cancer.

The researchers also discovered changes in gene-regulating regions of the genome -- which seem to be parrot-specific -- that were situated near genes associated with neural development. Those same genes are also linked with cognitive abilities in humans, suggesting that both humans and parrots evolved similar methods for developing higher cognitive abilities.

This photograph shows an Amazona aestiva taking care of the nest in Pantanal [Credit: Glaucia Seixas]

"Unfortunately, we didn't find as many speech-related changes as I had hoped," said Wirthlin, whose research is focused on the evolution of vocal behaviors, including speech. Animals that learn songs or speech are relatively rare -- parrots, hummingbirds, songbirds, whales, dolphins, seals and bats -- which makes them particularly interesting to scientists, such as Wirthlin, who hope to gain a better understanding of how humans evolved this capacity.

"If you're just analyzing genes, you hit the end of the road pretty quickly," she said. That's because learned speech behaviors are thought be more of a function of gene regulation than of changes in genes themselves. Doing comparative studies of these "non-coding" regulatory regions, she added, is difficult, but she and Andreas Pfenning, assistant professor of computational biology, are working on the computational and experimental techniques that may someday reveal more of their secrets.

Author: Byron Spice | Source: Carnegie Mellon University [December 06, 2018]

Botryllus schlosseri, a marine invertebrate that lives in underwater colonies resembling fuzzy pinheads clinging to rocks, has a blood-forming system with uncanny similarities to that of humans, according to scientists at Stanford University.

Under the microscope, a Botryllus colony looks like a bouquet of flowers, although in reality each “petal” is a separate organism with its own heart, gills, digestive system, brain and blood cells [Credit: Stanford Hopkins Marine Station]

In a study published in Nature, the researchers report that these lowly sea creatures may provide a way to understand our own blood-forming system, improve our immune function and find new immune-associated tools for biological discovery.

"The mammalian and Botryllus blood-forming systems also share hundreds of homologous genes, even though the two species are separated by over 500 million years of evolution," said former postdoctoral scholar Benyamin Rosental, PhD.

Rosental shares lead authorship of the study with graduate student Mark Kowarsky. The senior authors are Irving Weissman, MD, the Virginia and D.K. Ludwig Professor for Clinical Innovation in Cancer Research and professor of pathology and of developmental biology; Stephen Quake, PhD, the Lee Otterson Professor in the School of Engineering and professor of bioengineering and of applied physics; and senior research scientist Ayelet Voskoboynik, PhD.

The researchers isolated the Botryllus stem cells that are the foundation of its blood and immune system, as well as the progenitor cells they make on their way to becoming adult blood and immune cells. "Out of all the invertebrates, the Botryllus blood stem cells and progenitors are the most similar to vertebrate blood cells, so it is possible, if not likely, that they are the 'missing link' between vertebrates and invertebrates," said Weissman, who also directs the Stanford Institute for Stem Cell Biology and Regenerative Medicine and the Ludwig Cancer Center at Stanford.

Odd characteristics

Botryllus is an organism with many odd characteristics. It lives part of its life as a free-swimming chordate "tadpole" -- an animal without vertebrae but with a spinal bundle called a notochord. Then it attaches itself to a rock, undergoes metamorphosis to lose its notochord, tail, body muscles and one of its two brains, and settles down to live in colonies with other Botryllus organisms on the subtidal surface.

The separate Botryllus organisms in the colony share a common blood supply, and even exchange cells [Credit: Stanford Hopkins Marine Station]

Under the microscope, a Botryllus colony looks like a bouquet of flowers, although in reality each "petal" is a separate organism with its own heart, gills, digestive system, brain and blood cells. The separate Botryllus organisms in the colony share a common blood supply, and even exchange cells. This blood sharing allows stem cells for sperm and eggs and stem cells for body tissues to be shared throughout the growing colony.

The researchers showed that there are close parallels between the blood systems in Botryllus and in mammals. They found that Botryllus has a sort of incubator of specialized cells, called a niche, that holds and supports blood stem cells and is a lot like the blood stem cell niche in mammalian bone marrow. They also found that Botryllus blood stem cells will find their own way from blood vessels to the niche, exactly as they do in mammals. And they found 327 genes involved in blood cell formation in Botryllus that are similar to genes involved in blood formation in mammals.

Previously, researchers in the Weissman lab showed that a single variant of a gene called BHF regulated whether separate Botryllus organisms would send out blood vessels from their own bodies and merge with adjacent individuals, or undergo an immune rejection, preventing blood cell exchanges. The new study identifies how BHF regulates whether organisms fuse together in the colony: If the protein produced by the gene is recognized as compatible by the other colony, it prevents the activation of a rejection process that is similar to the way that the human immune system's natural killer cells attacks tissues that are not "self."

An excellent model

The discovery of such strong parallels between the two systems offers researchers an excellent model for studying many biological phenomena in mammals, the researchers said. "Blood stem cells in mammals are hard to find and, when found, it's very hard to follow what is going on in the blood stem cell niche," Voskoboynik said. "Botryllus is a translucent organism, so we can easily spot the niche and visually follow the migration of each type of cell from one part of their body to the other."

It's also easy to observe how the cells in individual organisms interact when one mounts an immune attack against the other, or the two individuals fuse blood vessels. This could provide scientists with a better understanding of why an organism accepts or rejects foreign cells, knowledge that could give insights into organ transplant acceptance and rejection, Voskoboynik said.

"With its primitive but effective immune system, Botryllus may also give us insights into how we can boost our own immune responses to pathogens and cancer," Voskoboynik said. "But in addition to any practical benefits this research may produce, we are delighted to explore this important guidepost on the path to understanding the evolution of vertebrates, and of their blood-forming and immune systems. Isn't that what curiosity-driven science is supposed to do?"

Author: Christopher Vaughan | Source: Stanford Medicine [December 05, 2018]

Researchers at the RIKEN Center for Biosystems Dynamics (BDR) and collaborators have described for the first time the development of the hagfish inner ear. Published in the journal Nature, the study provides a new story for inner ear evolution that began with the last common ancestor of modern vertebrates.

The eel-shaped, slime-producing hagfish is a living fossil, remaining unchanged in its structure and habits for over 300 million years [Credit: Gerald & Buff Corsi/Getty Images]

Comparing organs among related animals can be helpful when trying to understand the evolutionary process, and will ultimately help us better understand organogenesis--the process through which organs develop. This underlying philosophy helped guide the collaborative effort to study the inner ear led by Shigeru Kuratani at RIKEN BDR.

The story begins with a difference between jawed and jawless vertebrates. Jawed vertebrates like humans have inner ears with three semicircular canals, which are what allow us to sense our position and stay balanced in the world, and especially to sense 3-D acceleration. The fossil record shows that a group of jawless fish from the Paleozoic era only had two semicircular canals. In order to understand the evolutionary changes that led three canals, the team looked at the only two types of jawless vertebrates that still exist on earth: lampreys and hagfish.

Lampreys are thought to have two semicircular canals, while hagfish only have one. However, hagfish are no longer thought to be more primitive than lampreys. A series of molecular biological experiments was able to clarify the issue. Analyzing the regulatory genes that control the development of the semicircular canals showed that the basic pattern of inner ear development is similar for all vertebrates, including lampreys and hagfish. Key genes, such as Tbx1 and Patched were expressed at the same places with the same timing across all three types of vertebrate.

The anterior and posterior canals in jawed vertebrates appear to be genetically homologous to the anterior and posterior parts of the lamprey canal, while the pattern for the single hagfish canal is likely an evolved trait, not a primitive condition. The difference between the jawed and lawless fish is the presence of the common crus, a structure that connects the anterior and posterior canals in jawed vertebrates. The current study could not determine whether the common crus is something that jawed vertebrates gained or something that was lost in jawless vertebrates.

Further analysis focused on the Otx1 gene. This gene is required for proper development of the lateral canal, the third canal that is unique to jawed vertebrates. The researchers found that despite the lack of a lateral canal, lampreys and hagfish both expressed Otx1 in the proper location during development. This was somewhat surprising as its expression was thought to be an advent that led to the evolution of the lateral canal. Instead, it appears that Otx1 expression in the otic vesicle is an ancient feature for all vertebrates.

A more complete understanding will be possible by performing studies with an animal that represents the lineages before jawed and jawless vertebrates diverged.

Source: RIKEN [December 05, 2018]

On 3 December 2018, the laboratory of Professor Axel Meyer, University of Konstanz published new findings of an experimental evolutionary project that ran for 30 years on the genomic mechanisms of sex determination in swordtail fish in the journal Nature Communications. Dr Paolo Franchini, evolutionary biologist and Junior Research Group Leader at the University of Konstanz is the lead author of this collaboration with the laboratory of Professor Manfred Schartl of the University of Würzburg

Xiphophorus maculatus hellerii [Credit: Manfred Schartl/Paolo Franchini]

The diversity of sex determination systems is remarkably diverse among fishes compared to mammals that all have a stereotypic XX, XY sex-chromosomal mechanism to determine sex. Why and how the genomic mechanisms and the evolutionary causes behind such diversity in sex determination in fish are so variable remained unknown.

Evolutionary biologist Dr Paolo Franchini with his collaborators has now been able to describe such a mechanism and its exact function in this study entitled "Long-term experimental hybridisation results in the evolution of a new sex chromosome in swordtail fish".

Professor Manfred Schartl, Head of the Department for Physiological Chemistry at the Biocenter of the University of Würzburg, initiated this experiment that included hybridisation with backcrossing by two Xiphophorus fish species with different sex chromosome systems three decades ago. Hybrid origins of species, the result of the crossing of two genetically different species, are found frequently in fish populations.

"What we know from the study of these systems in natural habitats is that hybridisation is a crucial mechanism for the evolution of new species", explains Paolo Franchini. In the experiment the researchers could study the effects of hybridisation on the genomic mechanism of sex-determination.

Determining the sex of these fish is easy: as its name suggests, the male swordtail fish has a sword-like elongated caudal fin; the female, on the other hand, is rounder and fuller and does not have a swordtail. In this long-term laboratory study the effects of hybridisation that is thought to have resulted in at least two swordtail species in nature on the genome and the mechanisms that determine sex could be studied in detail.

In an experimental design that makes it possible to track crossings of more than 100 generations over more than 30 years, a female Xiphophorus maculatus was crossed repeatedly with a male Xiphophorus hellerii.

These two species have different sex chromosome systems. In further steps, the new hybrid fish originating from the cross was backcrossed again with the male species, and this design was repeated for more than 100 generations.

Paolo Franchini explains further: "We found out that introgression - the movement of genetic material from one species to another - and the selection of pigmentation phenotypes results in the retention of an unexpectedly large maternally derived genomic region."

During the hybridisation process, the sex-determining region on the X chromosome of one parent was transferred to an autosome of the hybrid fish. This transfer led to the evolution of a completely new sex chromosome.

"Our results show above all the complexity of factors that contribute to patterns observed in hybrid genomes including such fundamental issues such as sex determination", summarises Paolo Franchini. The work proves that hybridisation can catalyse the rapid evolution of a new sex chromosome and thus makes an essential contribution to an experiment launched more than 30 years ago.

Source: University of Konstanz [December 05, 2018]

A UMass Boston professor and his colleagues have published new research showing that feeding on human junk food may be altering the course of evolution in Darwin's finches.

Finches eat off a plate in an urban area of the Galapagos [Credit: K. Gotanda]

Assistant Professor of Evolutionary Biology Luis De León says feeding on human foods is weakening natural selection on ground finch beaks, which is what drives the formation of new species in the wild. These findings, published in the journal Evolutionary Applications, suggest that the seemingly harmless activity of feeding birds might be altering the course of evolution in the iconic Darwin’s finches in the Galápagos islands.

“If we continue to feed finches, we’re not only affecting the individual species, but the processes that lead to the formation of new species,” De León said. “We’re getting in the way of evolution.”

Galápagos finches are famed for being the inspiration behind Charles Darwin’s pioneering work on evolution. They are an example of adaptive radiation, an evolutionary process that produces new species from a single, rapidly diversifying lineage. Their common ancestor arrived on the Galápagos about two million years ago, and since then Darwin's finches have evolved into more than a dozen recognized species differing in body size, beak shape, and feeding behavior.

De León and fellow researchers from UMass Amherst, Universidad San Francisco de Quito, McGill University, and Norwegian University of Science and Technology were on Santa Cruz Island when they found two forms of medium ground finches — a small and large version — while studying beak size at an isolated, pristine site.

When they repeated the same set of measurements at a nearby urban site, the distinction between the two beak sizes was not present. Studying data collected by other researchers in the 1970s, the researchers could see the two types of medium ground finches had been present in the area before, but something had changed in the last 40-50 years.

They hypothesized that the change might have to do with urbanization and the rapidly increasing human population in that area. In particular, the introduction of novel foods brought by humans.

Finches eat from an egg crate left by the researchers [Credit: University of Massachusetts Boston]

Using egg crates filled with natural seeds and human junk food — chips, cookies, and rice — the researchers tested to see if the finches were in fact feeding on human food and what their preference was, weighing the food before and after to see how much was eaten.

De León said they found that finches in the urban area were almost exclusively feeding on human food. When the experiment was repeated at an isolated site in nature, the finches ignored the trays.

They found that "urban" finches feed on human junk foods, and in fact prefer these foods over their natural diet. This indicates that ongoing urbanization in the Galápagos is eroding the ecological differences that originally drove the formation of species in Darwin's finches.

“In contrast to their natural diet, the finches are changing their diet to human junk food,” De León said. “We know one way finches diversify and become new species is by specializing in different food types. All three or four species of ground finches at urban sites on Santa Cruz Island seem to be converging onto the same junk food diet. If that’s the case, the selection pressures that would be naturally  keeping them apart would be weakening, possibly leading to the collapse of the adaptive radiation of ground finches.”

Researchers also found a strong preference for human foods at EG Beach, a non-urban site visited by tourists located 12 kilometers away from the town of Puerto Ayora. This suggests that human behavior, rather than human population density, is the main driver of finches’ preference for human food, expanding the impacts of urbanization beyond city centers.

Now that the researchers know that finches are changing their diets to human junk food, they need to look at the consequences for the actual evolution of the species on this island.

“When thinking about preserving biodiversity in general, we often focus on preserving individual species,” he said. “What we show with this work is we also need to consider preserving the processes that lead to the formation of species.”

Assistant Professor of Evolutionary Biology Luis De León studies Darwin's finches [Credit: University of Massachusetts Boston]

De León and a PhD student will return to the Galapagos in January.

De León said they will continue to do more genetic analysis, looking at whether there is an increase in gene flow across the four species of ground finch. Now that the birds are eating the same diet, researchers want to know if they are also interbreeding.

Elaine Montes, a second-year PhD student at UMass Boston who is working with De León, will look at the physiological consequences of human junk food on Galapagos finches by analyzing telomeres, a long chain of repetitive DNA at the end of every chromosome that can shorten due to stress and aging.

“We want to see whether they have a shorter life span than birds in nature,” he said.

De León has worked at UMass Boston for two years. He received his PhD at McGill University, where he started his work on Galapagos finches 14 years ago.

“It’s a fascinating place. Every species is so unique; it captures your imagination. You can imagine how Darwin was fascinated by looking at all those species,” he said. “I feel privileged to essentially walk in Darwin’s footsteps.”

Author: Crystal Valencia | Source: University of Massachusetts Boston [December 03, 2018]

University of Nebraska-Lincoln researchers have found revolutionary evidence that an evolutionary phenomenon at work in complex organisms is at play in their single-celled counterparts, too.

The Grand Prismatic Spring of Yellowstone National Park houses heat- and acid-loving archaea [Credit: Shutterstock]

Species most often evolve through DNA mutations inherited by successive generations. A few decades ago, researchers began discovering that multicellular species can also evolve through epigenetics: traits originating from the inheritance of cellular proteins that control access to an organism's DNA, rather than genetic changes.

Because those proteins can respond to shifts in an organism's environment, epigenetics resides on the ever-thin line between nature and nurture. Evidence for it had emerged only in eukaryotes, the multicellular domain of life that comprises animals, plants and several other kingdoms.

But a series of experiments from Nebraska's Sophie Payne, Paul Blum and colleagues has shown that epigenetics can pass along extreme acid resistance in a species of archaea: microscopic, single-celled organisms that share features with both eukaryotes and bacteria.

"The surprise is that it's in these relatively primitive organisms, which we know to be ancient," said Blum, Charles Bessey Professor of Biological Sciences at Nebraska. "We've been thinking about this as something (evolutionarily) new. But epigenetics is not a newcomer to the planet."

The team discovered the phenomenon in Sulfolobus solfataricus, a sulfur-eating species that thrives in the boiling, vinegar-acidic springs of Yellowstone National Park. By exposing the species to increasing levels of acidity over several years, the researchers evolved three strains that exhibited a resistance 178 times greater than that of their Yellowstone ancestors.

One of those strains evolved the resistance despite no mutations in its DNA, while the other two underwent mutations in mutually exclusive genes that do not contribute to acid resistance. And when the team disrupted the proteins thought to control the expression of resistance-relevant genes—leaving the DNA itself untouched—that resistance abruptly disappeared in subsequent generations.

Sophie Payne, doctoral student in biological sciences, has co-authored a study showing that single-celled organisms known as archaea can pass on traits even without changes in their DNA. This phenomenon, known as epigenetics, was found in a species that eats crystalline sulfur (pictured at front) [Credit: Greg Nathan/University Communication]

"We predicted that they'd be mutated, and we'd follow the mutations, and that would teach us what caused the extreme acid resistance," Blum said. "But that's not what we found."

Though epigenetics is essential to some of the most productive and destructive physiological processes in humans—the differentiation of cells into roughly 200 types, the occurrence of cancers—it remains difficult to study in eukaryotes.

The simplicity of archaea, combined with the fact that their cells resemble eukaryotes' in some important ways, should allow researchers to investigate epigenetic questions much faster and more cheaply than was possible before, Blum said.

"We don't know what flips the switch in humans that changes epigenetic traits," Blum said. "And we sure don't know how to reverse it very often. That's the first thing we'll go after: how to turn it on, how to turn it off, how to get it to switch. And that has benefits when you think about (managing) traits in us or traits in plants."

Yet the discovery also raises questions, Payne said, especially about how both eukaryotes and archaea came to adopt epigenetics as a method of inheritance.

"Maybe both of them had it because they diverged from a common ancestor that had it," said Payne, a doctoral student in biological sciences. "Or maybe it evolved twice. It's a really interesting concept from an evolutionary perspective."

Blum said the team is likewise curious about whether and how epigenetics might explain why no known archaea cause disease or wage antibiotic-armed warfare against their brethren, as bacteria do.

"There are no antibiotics going on in that world," he said. "Why is that? We're thinking (that) it's got something to do with epigenetics, and so their interactions among each other are fundamentally different than bacteria."

The research introduces an even broader question, Blum said.

"What was the benefit for them to have this? We don't know."

The team reported its findings in the journal Proceedings of the National Academy of Sciences.

Author: Scott Schrage | Source: University of Nebraska-Lincoln [December 03, 2018]

Jellyfish undergo an amazing metamorphosis, from tiny polyps growing on the seafloor to swimming medusae with stinging tentacles. This shape-shifting has served them well, shepherding jellyfish through more than 500 million years of mass extinctions on Earth.

Jellyfish are an ancient and successful group of animals. An in-depth look at the genome of the moon jelly, Aurita aurelia, shows that early jellyfish likely repurposed an existing set of genes to transition between polyp and swimming life stages [Credit: Alexander Vasenin/WikiCommons]

"Whatever they're doing has really worked for them," said David Gold, an assistant professor of paleobiology in the UC Davis College of Letters and Science.

The first in-depth look at the genome of a jellyfish -- the moon jelly Aurelia aurita -- reveals the origins of this successful survival strategy. The Aurelia genome, published online in the journal Nature Ecology and Evolution, indicates early jellyfish recycled existing genes to morph from polyp to medusa. The results suggest animals can radiate into new niches and forms fairly easily.

"These findings provide further evidence that evolution doesn't necessarily make the genetic code more complex," said Gold, a lead researcher on the genome study. "Jellyfish can build a big, complex life history using many of the same genes found in simpler animals."

The research team was led equally by Gold, who performed much of the work as a postdoctoral fellow at the California Institute of Technology, and by Takeo Katsuki, a project scientist at the Kavli Institute for Brain and Mind at UC San Diego.

The genome: a multi-use tool

Jellyfish come from one of the oldest branches on the animal family tree, the phylum Cnidaria, which includes corals and anemones. Jellyfish were probably the first muscle-powered swimmers in the open ocean. They appeared in the late Precambrian Era, a period of major geologic and ecological changes that preceded the Cambrian explosion of animal life.

At some point in their evolution, jellyfish gained the ability to transition from a stationary polyp to a swimming medusa. The transition involves major changes in the jellyfish nervous system, muscles and weaponry, aka the stinging cells called cnidocytes. To accomplish this, the medusa life stage often co-opts existing developmental gene networks and cell types present in polyps, the researchers found. In addition, Aurelia appears to pattern its different life stages using many of the same genes found in animals such as fruit flies and humans, the study reports. (all of these animals share a common ancestor, albeit an ancient one.)

There is a second, more controversial explanation for what the scientists found in the jellyfish genome. Perhaps the similarities between the moon jellyfish genome and "higher" animals demonstrates that the Cnidaria originally had a medusa life stage, which animals like corals and sea anemones lost.

"Our results can't distinguish between these two scenarios," said Gold. If the second hypothesis turns out to be correct, "Swimming, carnivorous animals may be even older than we think." In addition to questions of evolution, the Aurelia genome will prove valuable in many other areas of biology, Gold said. Aurelia is an important model for studying the development and function of nervous systems, and can offer insights into animal wound healing and regeneration. Moon jellies are also a major culprit in environmentally and economically damaging jellyfish blooms, which are becoming more common. For example, giant swarms of moon jellies have clogged water-intake pipes, forcing the shutdown of nuclear plants in Florida and Sweden. An improved understanding of Aurelia genetics could offer new ideas for controlling the blooms.

"In many ways, the ancient oceans in the late Precambrian are very much like what the modern oceans will look like in the near future," Gold said "meaning studying how jellyfish evolved in the past can tell us about their potential impact on the future."

Source: University of California - Davis [December 03, 2018]