Culture

New research suggests that the first dinosaurs laid soft-shelled eggs--a finding that contradicts established thought. The study, led by the American Museum of Natural History and Yale University and published today in the journal Nature, applied a suite of sophisticated geochemical methods to analyze the eggs of two vastly different non-avian dinosaurs and found that they resembled those of turtles in their microstructure, composition, and mechanical properties. The research also suggests that hard-shelled eggs evolved at least three times independently in the dinosaur family tree.

"The assumption has always been that the ancestral dinosaur egg was hard-shelled," said lead author Mark Norell, chair and Macaulay Curator in the Museum's Division of Paleontology. "Over the last 20 years, we've found dinosaur eggs around the world. But for the most part, they only represent three groups--theropod dinosaurs, which includes modern birds, advanced hadrosaurs like the duck-bill dinosaurs, and advanced sauropods, the long-necked dinosaurs. At the same time, we've found thousands of skeletal remains of ceratopsian dinosaurs, but almost none of their eggs. So why weren't their eggs preserved? My guess--and what we ended up proving through this study--is that they were soft-shelled."

Amniotes--the group that includes birds, mammals, and reptiles--produce eggs with an inner membrane or "amnion" that helps to prevent the embryo from drying out. Some amniotes, such as many turtles, lizards, and snakes, lay soft-shelled eggs, whereas others, such as birds, lay eggs with hard, heavily calcified shells. The evolution of these calcified eggs, which offer increased protection against environmental stress, represents a milestone in the history of the amniotes, as it likely contributed to reproductive success and so the spread and diversification of this group. Soft-shelled eggs rarely preserve in the fossil record, which makes it difficult to study the transition from soft to hard shells. Because modern crocodilians and birds, which are living dinosaur, lay hard-shelled eggs, this eggshell type has been inferred for all non-avian dinosaurs.

The researchers studied embryo-containing fossil eggs belonging to two species of dinosaur: Protoceratops, a sheep-sized plant-eating dinosaur that lived in what is now Mongolia between about 75 and 71 million years ago, and Mussaurus, a long-necked, plant-eating dinosaur that grew to 20 feet in length and lived between 227 and 208.5 million years ago in what is now Argentina. The exceptionally preserved Protoceratops specimen includes a clutch of at least 12 eggs and embryos, six of which preserve nearly complete skeletons. Associated with most of these embryos--which have their backbones and limbs flexed--consistent with the position the animals would assume while growing inside of the egg--is a diffuse black-and-white egg-shaped halo that obscures some of the skeleton. In contrast, two potentially hatched Protoceratops newborns in the specimen are largely free of the mineral halos. When they took a closer look at these halos with a petrographic microscope and chemically characterized the egg samples with high-resolution in situ Raman microspectroscopy, the researchers found chemically altered residues of the proteinaceous eggshell membrane that makes up the innermost eggshell layer of all modern archosaur eggshells. The same was true for the Mussaurus specimen. And when they compared the molecular biomineralization signature of the dinosaur eggs with eggshell data from other animals, including lizards, crocodiles, birds, and turtles, they determined that the Protoceratops and Mussaurus eggs were indeed non-biomineralized--and, therefore, leathery and soft.

"It's an exceptional claim, so we need exceptional data," said study author and Yale graduate student Jasmina Wiemann. "We had to come up with a brand-new proxy to be sure that what we were seeing was how the eggs were in life, and not just a result of some strange fossilization effect. We now have a new method that can be applied to all other sorts of questions, as well as unambiguous evidence that complements the morphological and histological case for soft-shelled eggs in these animals."

With data on the chemical composition and mechanical properties of eggshells from 112 other extinct and living relatives, the researchers then constructed a "supertree" to track the evolution of the eggshell structure and properties through time, finding that hard-shelled, calcified eggs evolved independently at least three times in dinosaurs, and probably developed from an ancestrally soft-shelled type.

"From an evolutionary perspective, this makes much more sense than previous hypotheses, since we've known for a while that the ancestral egg of all amniotes was soft," said study author and Yale graduate student Matteo Fabbri. "From our study, we can also now say that the earliest archosaurs--the group that includes dinosaurs, crocodiles, and pterosaurs--had soft eggs. Up to this point, people just got stuck using the extant archosaurs--crocodiles and birds--to understand dinosaurs."

Because soft eggshells are more sensitive to water loss and offer little protection against mechanical stressors, such as a brooding parent, the researchers propose that they were probably buried in moist soil or sand and then incubated with heat from decomposing plant matter, similar to some reptile eggs today.

Baltimore, MD-- New work from a team of Carnegie cell, genomic and developmental biologists solves a longstanding marine science mystery that could aid coral conservation. The researchers identified the type of cell that enables a soft coral to recognize and take up the photosynthetic algae with which it maintains a symbiotic relationship, as well as the genes responsible for this transaction.

Their breakthrough research is published in Nature.

Corals are marine invertebrates that build large exoskeletons from which reefs are constructed. But this architecture is only possible because of a mutually beneficial relationship between the coral and various species of single-celled algae called dinoflagellates that live inside individual coral cells.

"For years, researchers have been trying to determine the mechanism by which the coral host is able to recognize the algal species with which is compatible--as well as to reject other, less-desirable species--and then to ingest and maintain them in a symbiotic arrangement," explained Carnegie Embryology Director Yixian Zheng who, with colleagues Chen-ming Fan, Minjie Hu, and Xiaobin Zheng, conducted this research.

These dinoflagellates are photosynthetic, which means that, like plants, they can convert the Sun's energy into chemical energy. An alga will share the sugars it synthesizes with its coral host, which in turn provides the alga with the inorganic carbon building blocks it needs, as well as phosphorous, nitrate, and sulfur.

"However, ocean warming due to climate change is causing many coral hosts to lose their algal tenants--along with the nutrients that they provide--a phenomenon called bleaching," explained lead author Hu. "Without algae there to increase its food supply, the coral can die. This makes it particularly critical to understand the symbiotic mechanism now, as coral communities are increasingly jeopardized."

Building on Carnegie biologists' longstanding tradition of using a model organism approach to study complicated biological processes, the research team set out to use the pulsing, feathery, lavender-colored, soft coral Xenia to reveal the cell types and pathways that orchestrate the symbiotic relationship between a coral and its algae. This knowledge can then be applied to increase our understanding of other coral species and allow for further research into how these fragile ecosystems are threatened by warming oceans.

Applying a wide range of genomic, bioinformatic, and developmental biology tools, the researchers identified the type of cell that is required for the symbiotic relationship to occur. They discovered that it expresses a distinct set of genes, which enable it to identify, "swallow," and maintain an alga in a specialized compartment, as well as to prevent the alga from being attacked by its immune system as a foreign invader. Furthermore, the researchers showed that the uptake process occurs over five stages, with stage three representing mature, alga-hosting cells, and stage one being pre-symbiotic-relationship and stage five being post-alga-expulsion.

Looking ahead, the team wants to understand how environmental stress affects progression through the five stages, and which stage is most crucial for recovery after a bleaching event, and the genes that function at each stage.

Earlier this year, Zheng was selected as one of 15 scientists awarded a grant from the Gordon and Betty Moore Foundation to support research on symbiosis in aquatic systems. The foundation launched its Symbiosis in Aquatic Systems Initiative last year. Current and emerging leaders in aquatic symbiosis research--as well as scientists who will apply their deep expertise from other areas of science to aquatic symbiosis--were selected from a competitive pool.

"Dr. Zheng's work using the soft coral, Xenia, is an exemplar of how model systems research can advance our understanding of fundamental processes in nature. We look forward to continued discovery as part of her Symbiosis in Aquatic Systems Initiative investigator award," Said Dr. Sara J. Bender, program officer, Science Program, Gordon and Betty Moore Foundation.

When Pulitzer Prize and Grammy award winner Kendrick Lamar rapped "I got millions, I got riches buildin' in my DNA," he almost certainly wasn't talking about the humble tomato. But a new study unveiling more than 230,000 DNA differences across 100 tomato varieties which will allow breeders and scientists to engineer larger, juicier, more profitable plants, proves that tomatoes indeed have riches buildin' in their DNA, too.

The study will be published June 17 in Cell.

"The vast majority of the DNA differences we discovered are completely new," says Michael Schatz, Bloomberg Distinguished Associate Professor of Computer Science and Biology at Johns Hopkins University and the study's co-corresponding author.

As one of the largest fruit crops in the world, the commercially growing tomatoes is an $190 billion global industry that relies pinpointing which large-scale difference between genomes, or structural variants, are responsible for the variety of tomato shapes, colors and tastes we see at the store.

Previous technologies, however, didn't allowed scientists to read large portions of a genome, only allowing for small bits to be read at a time in a piecemeal fashion.

"Like a big jigsaw puzzle with hundreds of millions of small pieces, maybe you manage to put together the corners, but not the big blue sky. The new technology used in this study allowed us to zoom in and get larger, clearer puzzle pieces," says Schatz.

Using new DNA sequencing technology and software to 'sharpen' their view, Schatz and more than 30 collaborators around the world in a self-proclaimed "tomato consortium" were able to sequence and compare the genomes of 100 different tomato types. In doing so, they found more than 230,000 structural variants.

From there, the team dove deeper with detailed genetic experiments to understand how some of those variants affect tomato traits. In one experiment, they found that duplication of a particular gene causes a plant's tomatoes to be about 20% larger. Next, they discovered a gene that contributes to a smoky flavor in some tomatoes. And in a third set of experiments, the researchers uncovered a complex interaction involving four structural variants that can mitigate a potential trade-off between a feature that simplifies tomato harvesting and another that reduces productivity.

The scale of their investigation has never been accomplished for any other crop, says Cold Spring Harbor Laboratory professor and Howard Hughes Medical Institute investigator Zachary Lippman, who co-led the project.

"I think it sets the foundation for what other crops and people in those working on those crops should be thinking about," says Lippman.

"All crops are based on mutations. Everything that we eat is based on mutations and up until now it's pretty been pretty slow process to identify and evaluate the importance of those mutations."

Adds Schatz: "We've taken processes that used to take hundreds, or in some cases, even thousands of years, and performed them very rapidly. From here, we can apply our understanding of genetics to very rapidly domesticate some of the species related to tomatoes and create new crops to feed the world with."

An expansive new analysis of genetic variation among tomatoes has uncovered 230,000 previously hidden large-scale differences in DNA between varieties. As tomato plants evolved, segments of DNA were deleted, duplicated, or rearranged. These genomic "structural variations" underpin the vast diversity among tomatoes, changing flavors, altering yield, and shaping other important traits.

The study, a collaborative effort led by Cold Spring Harbor Laboratory Professor and Howard Hughes Medical Institute investigator Zachary Lippman and Johns Hopkins University (JHU) Professor Michael Schatz, is the most comprehensive analysis to date of structural genome variation for a major crop. Breeders and scientists will be able to apply the information to breed or engineer new, more desirable plants with greater efficiency.

Large-scale differences between genomes, known collectively as structural variants, are likely responsible for a wide range of plant features that breeders care about, but these elements have been notoriously difficult to study, leaving much of the genetic origins of tomato diversity unexplained, says Xingang Wang, a postdoctoral researcher in Lippman's lab. New DNA sequencing technology along with powerful new genome editing technology has recently made structural variants easier to detect and study how they affect crop traits. Lippman's team, in collaboration with scientists at Johns Hopkins University, the University of Georgia, the Boyce Thompson Institute, and others, seized the opportunity to investigate. Lippman notes,

"There was a whole massive amount of natural genetic variation that we were blind to. And the only way to get at it was through this new technology. And there were already quite a few examples in the literature of how some of that hidden--what we call structural variation--was important. And it was probably being grossly underestimated in terms of its importance. So we really just needed to walk through that door. And the only way to do it was to do it at scale with a hundred different genomes."

Together, the group sequenced and compared the genomes of 100 different varieties of tomato, including robust varieties suitable for industrial agriculture, succulent heirlooms, and wild relatives of cultivated tomatoes. Within those genomes, the team identified more than 230,000 structural variants.

To gain a better understanding of structural variants' role in diversity, the team showed that thousands of genes were changed by the structural changes. Then they used CRISPR--the genome editing tool that can make targeted changes in DNA--to show that duplication of a particular gene causes a plant's tomatoes to increase in size by about 30 percent. According to Schatz:

"Previous studies had identified this one gene called KLUH as being relevant. It makes the plant smaller. So it's the HULK, y'know superhero, spelled backwards. Previous studies had sort of thought they had identified a single nucleotide variant. But we really came to appreciate, it was not a single nucleotide variant--it was one of these structural variants that had never been detected before. And what it turns out is that there was a so-called copy number variant, where if you have extra copies of this KLUH gene, it tends to make all of the cells in the plants bigger, makes the fruits bigger. So we think that this is going to have an enormous impact in agricultural science, where we sort of did this in tomato, but the experimental design could be executed in basically every crop species of interest."

Investigating another variant, they tracked down a gene that contributes to a smoky flavor in some tomatoes. Wang says:

"By identifying the causal gene and the causal mutations of this flavor, in the future, breeders can have a more precise target to either increase the smoky flavor or try to remove the smoky flavor."

And in a third set of experiments, the researchers used CRISPR to tease out a complex interaction involving four structural variants that can mitigate a potential trade-off between a feature that simplifies tomato harvesting and another that reduces productivity.

Understanding how structural variants influence tomatoes, a $190 billion global industry, gives breeders new power to improve the properties of tomatoes, and shows how structural variants that can enhance breeding are likely hidden in the complex genomes of many other important crops, like corn, rice, and soybeans.

What The Study Did: This observational study examined the risk of cardiovascular death and sudden cardiac death associated with use of the antibiotic azithromycin compared with amoxicillin.

Authors: Jonathan G. Zaroff, M.D., of Kaiser Permanente Northern California in Oakland, is the corresponding author.

To access the embargoed study: Visit our For The Media website at this link https://media.jamanetwork.com/

(doi:10.1001/jamanetworkopen.2020.8199)

Editor's Note: The article includes conflicts of interest and funding/support disclosures. Please see the article for additional information, including other authors, author contributions and affiliations, conflicts of interest and financial disclosures, and funding and support.

In 2011, Chilean scientists discovered a mysterious fossil in Antarctica that looked like a deflated football. For nearly a decade, the specimen sat unlabeled and unstudied in the collections of Chile's National Museum of Natural History, with scientists identifying it only by its sci-fi movie-inspired nickname - "The Thing."

An analysis led by researchers at The University of Texas at Austin has found that the fossil is a giant, soft-shell egg from about 66 million years ago. Measuring in at more than 11 by 7 inches, the egg is the largest soft-shell egg ever discovered and the second-largest egg of any known animal.

The specimen is the first fossil egg found in Antarctica and pushes the limits of how big scientists thought soft-shell eggs could grow. Aside from its astounding size, the fossil is significant because scientists think it was laid by an extinct, giant marine reptile, such as a mosasaur -- a discovery that challenges the prevailing thought that such creatures did not lay eggs.

"It is from an animal the size of a large dinosaur, but it is completely unlike a dinosaur egg," said lead author Lucas Legendre, a postdoctoral researcher at UT Austin's Jackson School of Geosciences. "It is most similar to the eggs of lizards and snakes, but it is from a truly giant relative of these animals."

A study describing the fossil egg was published in Nature on June 17.

Co-author David Rubilar-Rogers of Chile's National Museum of Natural History was one of the scientists who discovered the fossil in 2011. He showed it to every geologist who came to the museum, hoping somebody had an idea, but he didn't find anyone until Julia Clarke, a professor in the Jackson School's Department of Geological Sciences, visited in 2018.

"I showed it to her and, after a few minutes, Julia told me it could be a deflated egg!" Rubilar-Rogers said.

Using a suite of microscopes to study samples, Legendre found several layers of membrane that confirmed that the fossil was indeed an egg. The structure is very similar to transparent, quick-hatching eggs laid by some snakes and lizards today, he said. However, because the fossil egg is hatched and contains no skeleton, Legendre had to use other means to zero in on the type of reptile that laid it.

He compiled a data set to compare the body size of 259 living reptiles to the size of their eggs, and he found that the reptile that laid the egg would have been more than 20 feet long from the tip of its snout to the end of its body, not counting a tail. In both size and living reptile relations, an ancient marine reptile fits the bill.

Adding to that evidence, the rock formation where the egg was discovered also hosts skeletons from baby mosasaurs and plesiosaurs, along with adult specimens.

"Many authors have hypothesized that this was sort of a nursery site with shallow protected water, a cove environment where the young ones would have had a quiet setting to grow up," Legendre said.

The paper does not discuss how the ancient reptile might have laid the eggs. But the researchers have two competing ideas.

One involves the egg hatching in the open water, which is how some species of sea snakes give birth. The other involves the reptile depositing the eggs on a beach and hatchlings scuttling into the ocean like baby sea turtles. The researchers say that this approach would depend on some fancy maneuvering by the mother because giant marine reptiles were too heavy to support their body weight on land. Laying the eggs would require the reptile to wriggle its tail on shore while staying mostly submerged, and supported, by water.

"We can't exclude the idea that they shoved their tail end up on shore because nothing like this has ever been discovered," Clarke said.

Information technology continues to progress at a rapid pace. However, the growing demands of data centers have pushed electrical input-output systems to their physical limit, which has created a bottleneck. Maintaining this growth will require a shift in how we built computers. The future is optical.

Over the last decade, the field of photonics has provided a solution to the chip-to-chip bandwidth problem in the electronic world by increasing the link distance between servers with higher bandwidth, far less energy, and lower latency compared to electrical interconnects.

One element of this revolution, silicon photonics, was advanced fifteen years ago when UC Santa Barbara and Intel demonstrated silicon laser technology. This has since triggered an explosion of this field. Intel is now delivering millions of silicon photonic transceivers for data centers all around the world.

Now, a collaboration between UC Santa Barbara, Caltech, and EPFL have made another revolutionary discovery in the field. The group managed to simplify and condense a complex optical system onto a single silicon photonic chip. The achievement, published in Nature, significantly lowers the cost of production and allows for easy integration with traditional, silicon chip production.

"The entire internet is driven by photonics now," says John Bowers, who holds the Fred Kavli Chair in Nanotechnology at UC Santa Barbara and directs the campus's Institute for Energy Efficiency and led the collaborative research effort.

Despite the great success of photonics in the internet's backbone, there are still challenges. The explosion of data traffic also means growing requirements for the data rates that silicon photonic chip can handle. So far, most efficient way to address this demand is to use multicolor laser lights to transmit information: the more laser colors, the more information can be carried.

But this poses a problem for integrated lasers, which can generate only one color of laser light at a time. "You might literally need fifty or more lasers in that chip for that purpose," says Bowers. And using fifty lasers is expensive and inefficient in terms of power. Also, noise and heat can cause the frequency of light that each laser produces to fluctuate. Finally, with multiple lasers, the frequencies can even drift into each other, much like early radio stations did.

A solution can be found in the technology of "optical frequency combs", which are collections of equally spaced frequencies of laser light. Plotting the frequencies reveals spikes and dips that resemble a hair comb -- hence the name.

Generating combs used to require bulky and expensive equipment, but this can be now managed using the recently emerged microresonator-based soliton frequency combs, which are miniaturized frequency comb sources built on CMOS photonic chips. Using this "integrated photonics" approach, the collaborating team has developed the smallest comb generator in the world, which essentially resolves all of these issues.

The system is rather simple, consisting of a commercially available feedback laser and a silicon nitride photonic chip. "What we have is a source that generates all these colors out of one laser and one chip," says Bowers. "That's what's significant about this."

The simple structure means small scale, less power, and lower cost. The entire setup now fits in a package smaller than a match box whose overall price and power consumption are smaller than previous systems.

The new technology is also much more convenient to operate. Previously, generating a stable comb had been a tricky endeavor. Researchers would have to adjust frequency and power just right to produce a coherent soliton comb, and even then, the process was not guaranteed to generate a comb every time. "The new approach makes the process as easy as switching on a room light," says Kerry Vahala, Professor of Applied Physics and Information Science and Technology at Caltech, where the new soliton generation scheme was discovered.

"What is remarkable about the result is the full photonic integration and reproducibility with which frequency combs can be generated on demand," adds Tobias J. Kippenberg, Professor of Physics at EPFL who leads the Laboratory and Photonics and Quantum Measurement (LPQM), and whose laboratory first observed microcombs more than a decade ago.

The EPFL team has provided the ultralow-loss silicon nitride photonic chips, which were fabricated in at EPFL Center of MicroNanoTechnology (CMi) and serve as the key component for soliton comb generation. The low-loss silicon nitride photonics technology has been commercialized via the lab startup LIGENTEC.

The "magic" behind all these improvements lies in an interesting physical phenomenon: when the pump laser and resonator are integrated, their interaction forms a highly coupled system that is self-injection-locking and simultaneously generates "solitons" - pulses that circulate indefinitely inside the resonator and give rise to optical frequency combs.

The new technology is expected to have an extensive impact on photonics. In addition to addressing the demands of multicolor light sources in communication-related products, it also opens up a lot of new opportunities in many applications. One example is optical clocks, which provide the most accurate time standard in the world and are used in a number of applications, from navigation to measuring physical constants.

"Optical clocks used to be large, heavy, and expensive," says Bowers. "There are only a few in the world. With integrated photonics, we can make something that could fit in a wristwatch, and you could afford it."

"Low-noise integrated optical microcombs will enable a new generation of optical clocks, communications and sensors," says Gordon Keeler, the project's manager at the Defense Advanced Research Projects Agency (DARPA). "We should see more compact, more sensitive GPS receivers coming out of this approach."

All in all, the future looks bright for photonics. "It is the key step to transfer the frequency comb technology from the laboratory to the real world," says Bowers. "It will change photonics and our daily lives."

The Earth hosts an abundance of life forms - from well-known animals and plants to small, more hardy life forms such as archaea, viruses and bacteria. These life forms are fundamentally different all the way down to the cell level. Or so scientists thought.

Now an international team of researchers has analysed the proteins found in 100 different species - from bacteria and archaea to plants and humans. It is the largest protein mapping ever to be conducted across different species.

They have learned that these life forms in fact have a number of common characteristics. The study is a collaboration between researchers in Professor Matthias Mann's group in the Novo Nordisk Foundation Center for Protein Research and the Max Planck Institute of Biochemistry. It has been published in the top scientific journal Nature.

'We have mapped the proteins, together called the proteome of 100 different species. And it is obvious that they are extremely different. At the same time, though, they have more in common than we thought. In all these life forms, a large share of the proteins focus on metabolism and on maintaining a protein balance', says Professor Matthias Mann.

Doubling of Experimentally Confirmed Proteins

Previously, researchers were mainly interested in the DNA of various organisms. For example, how much genetic material humans share with different animals. However, with advancements in the technology used for studying organisms at molecular level, researchers have turned to proteins the workhorses of the cell.

'A common characteristic of all these life forms is the fact that a high percentage of their proteomes focus on maintaining a sort of balance, what is called as homeostasis. Another common characteristic is the fact that a large share of the proteins help to generate energy. Even though the ways in which this is done differ - from photosynthesis to carbohydrate burning', says Alberto Santos Delgado who during the studies was employed at the Novo Nordisk Foundation Center for Protein Research.

The researchers have used an advanced technology called mass spectrometry to study all 100 species. The technology enabled them to double the number of proteins confirmed experimentally.

Previous research has predicted how many and which proteins exist based only on the genetic code and bioinformatic calculations. However, the new protein mapping has provided actual data on the existence of a very large number of new proteins.

Machine Learning Can Reveal New Correlations

'Our work connecting quantitative mass spectrometry-based proteomics with database resources has resulted in a data set of eight million data points with 53 million interconnections. We made all the data publicly available, enabling other researchers to use it to identify new correlations. New technologies enabled by machine learning are on the rise and we expect those to benefit from the large and uniform dataset we provide publicly', says PhD Student Johannes Mueller from the Max Planck Institute of Biochemistry.

The researchers at the University of Copenhagen focussed on data processing and bioinformatics analysis, while the researchers at the Max Planck Institute of Biochemistry in Munich focussed on mass spectrometry.

On the website Proteomes of Life, the researchers made all data from the project publicly available.

The study was funded by the Max Planck Society for the Advancement of Science, the EU Horizon 2020 programme and the Novo Nordisk Foundation.

Soybean oil is one of the world's most important vegetable oils and soybeans are a key protein feed crop. Cultivated soybeans were domesticated from wild relatives in China approximately 5,000 years ago. At present, over 60,000 accessions adapted to different ecoregions have been developed. Extensive genetic diversity among soybean germplasms has shown the need for construction of a complete pan-genome from diverse soybean accessions.

Recently, the research group led by Prof. TIAN Zhixi from the Institute of Genetics and Developmental Biology (IGDB) of the Chinese Academy of Sciences (CAS), in cooperation with Profs. LIANG Chengzhi and ZHU Baoge's team, Prof. HAN Bin's team from the Center for Excellence in Molecular Plant Sciences of CAS, Prof. HUANG Xuehui's team from Shanghai Normal University, and the Berry Genomics Corporation, individually de novo assembled 26 soybean genomes and constructed a high quality graph-based soybean pan-genome.

Based on a phylogenetic analysis of 2,898 soybean accessions, they selected 26 accessions and performed de novo genome assembly for each accession. The contig N50 sizes of the 26 whole-genome assemblies ranged from 18.8 to 26.8 Mb pairs with a mean of 22.6 Mb, and scaffold N50 sizes ranged from 50.3 to 52.3 Mb with a mean of 51.2 Mb.

Through a comparative genome analysis of the 26 genomes plus three previously reported genomes, the scientists identified a total of 14,604,953 SNPs and 12,716,823 small insertions and deletions, 723,862 present and absent variations, 27,531 copy number variations, 21,886 translocation events, and 3,120 inversion events.

Subsequently, by integrating these structural variations, a graph-based genome was built using the ZH13 genome as a standard linear reference genome.

Further investigations illuminated that these structural variations play important roles in driving genome evolution, gene structure variation and gene functional divergence, which in turn contribute to agronomic trait variations in the soybean population.

Having a reference genome opens the door to functional genomics and molecular design breeding for a species. However, an increasing number of reports has suggested that one or a few reference genomes cannot represent the full range of genetic diversity of a species. Therefore, pan-genome construction is becoming increasingly necessary.

In addition, conventional linear references are limited since they are unable to show the genotypes of different alleles from each locus. How to integrate the genotypes from different alleles into a new form of genome is a challenge.

This is the first reported graph-based genome in a plant. This graph-based genome can be used to reanalyze previously resequenced data, which will generate more comprehensive information than ever and rejuvenate those data. In turn, this will greatly facilitate functional study and breeding. An anonymous reviewer said this work is "a landmark paper for genomics."

Acute myeloid leukemia (AML) is a hematological malignancy which incidence increases with age, that is biologically, phenotypically, and genetically very heterogeneous. Its treatment uses to combine chemotherapy followed by allogenic Hematopoietic Stem and Progenitor Cells transplant (allo-HSCT), based on the patient's eligibility, to consolidate complete remission and prevent relapse. Yet, except for a few subgroups, so-called low-risk AMLs, relapses are frequent after consolidation therapy and transplant. Chemotherapy-related toxicity, refractoriness, and failure to eradicate leukemia-initiating cells are the major causes underlying AML progression and relapse. Unfortunately, improved AML treatments have only experienced minor developments over the last four decades, and current 5-year event-free survival remains in a 20% in adults and less than 70% in children, highlighting the desperate need for safer and more efficient therapeutics.

Lately, cellular immunotherapy based on CAR-Ts has generated unprecedented expectations in cancer treatment. CARTs immunotherapy consists of the engineering of human T-cells with chimeric antigen receptors (CARs) that direct the T-cells against the cell surface tumor antigens. CARTs have shown robust clinical responses in patients with B-cell malignancies thanks to its high efficacy, specificity, and persistence.

AML patients are challenging because of the absence of a universal AML target antigen to direct the CART and of the shared expression of target antigens with healthy hematopoietic stem and progenitor cells (HSPC), which may lead to life-threatening on target off-tumor cytotoxicity. Despite this, past studies have found that CD33- and CD123-redirected CARTs for AML exhibit robust anti-leukemic activity, and are in advanced preclinical and clinical development.

These CARTs have generated some preclinical and clinical controversy on whether they can be myeloablative, as they could also target healthy HSPC, which are essential for hematopoiesis or blood cell production. This suspicion lies in the fact that HSPC also expresses to a various degree these antigens, so these CARTs could also attack them.

Although some isolated short-term studies have been performed in vitro and in vivo to prove the safety of this CARTs therapy on healthy HSPC, there was no substantial evidence of mid- or long-term in vivo studies yet.

Matteo Baroni, researcher of the Stem Cell Biology, Developmental Leukemia and Immunotherapy Research Group of the Josep Carreras Leukaemia Research Institute, hypothesized with his colleagues that the time for a CART to be effective against a healthy HSPC could be longer than against a leukemic cell. They thought that the results provided from previous studies on the potential myelotoxicity of redirecting T-cells against CD123 underestimated the on-target off-tumor potential of these CARTs.

Baroni and his team provided extensive evidence, in a 6-week in vivo study, that the presence of anti CD123 CAR T-cells strongly inhibited normal hematopoiesis, causing irreversible impediments in the formation of new blood cells. These results have been recently published in the Journal for Immunotherapy of Cancer.

"We call for the caution of using CAR T-cells against CD123 in another way than before an allogenic transplant of AML patients that have experienced therapy refractoriness of disease recurrence or relapse, and cannot further benefit from standard chemotherapy. For these patients is a great alternative. We believe that these results will help clinicians to consider critical long-term effects if CAR-T CD123 cells remain, and prevent for other uses." States Baroni.

This research has been funded by the European Research Council (CoG-2014-646903, PoC-2018-811220), the Spanish Ministry of Economy and Competitiveness (MINECO, SAF2016-80481-R), the Spanish Cancer Research Association (AECC-Semilla19)

To defend the body, the immune system makes proteins known as antibodies that latch onto the perceived threat, be it HIV, the new coronavirus or, as is the case in autoimmune disease, part of the body itself. In a new proof-of-concept study in ACS Sensors, researchers describe a new system for detecting antibodies within a pinprick of blood within minutes, using an unlikely combination of cotton thread, glowing proteins and a smartphone camera. 

While some tests simply detect the presence of an antibody, sometimes doctors want to know how much is circulating in the blood. Such quantitative tests are used to diagnose a number of conditions, including infections and autoimmune diseases. Although a quantitative antibody test is not yet approved for use in the U.S., such a test could potentially aid in assessing immunity to SARS-CoV-2. However, quantitative testing currently requires expensive, sophisticated instruments in labs, and efforts to make it more accessible have had only limited success. So, Maarten Merkx, Daniel Citterio and colleagues tested an approach that could provide a small, inexpensive alternative.  

The researchers' microfluidic thread-based analytical device (μTAD) relies on light-emitting sensor proteins held on a thread. In the presence of the right antibodies, the color of the light emitted by the sensors changes. The shift, from green to blue, correlates with the concentration of antibodies in a sample. Using a finger-prick-sized drop of pigs' blood spiked with antibodies against HIV, the team showed that their system could successfully detect antibody levels within five minutes. In addition, the device can test for the amounts of several different antibodies in a single blood sample and doesn't require extensive handling and incubation steps. They found that a smartphone camera, outfitted with an adaptor, could pick up on the shifts in the light's color, while the device itself could convert color data into test results and transmit that information. With further development, this combination of technologies could provide user-friendly, one-step analysis of antibody concentration, according to the researchers.

URBANA, Ill. - Like antibiotic-resistant bacteria, some herbicide-resistant weeds can't be killed by available chemicals. The problem affects more than just the errant weed in our driveways; herbicide-resistant weeds threaten our food supply, stealing resources and outcompeting the crops that make up our breakfast cereal and feed the nation's livestock.

The weed that represents the biggest threat to Midwestern corn and soybean production, waterhemp, has outsmarted almost every kind of herbicide on the market today.

University of Illinois scientists are working to reveal waterhemp's tricks. Through years of research, they discovered the weed can ramp up production of detoxifying enzymes that neutralize certain herbicides before they can disrupt essential cellular processes. Metabolic resistance, as this strategy is known, is just one process by which waterhemp evades herbicides. Unfortunately, because there may be hundreds of detoxifying enzymes involved, metabolic resistance is hard to identify and even harder to combat.

In two recent studies, Illinois researchers explain metabolic resistance to three commonly used herbicides in waterhemp, getting closer to finding important genetic cues. Results also confirm the importance of using a multi-pronged approach to waterhemp control.

"These waterhemp populations are adapting and evolving incredible abilities to metabolize everything. It's bad news, but at least we understand the mechanisms better. And ultimately, that understanding could potentially be exploited to use waterhemp's metabolic arsenal against itself," says Dean Riechers, professor in the Department of Crop Sciences at Illinois and co-author on both studies. "That's one interesting way our research could be directly applied to controlling this weed."

Last year, Illinois researchers documented resistance to Group 15 herbicides in waterhemp. This group of herbicides, including S-metolachlor, targets very-long-chain fatty acid production in sensitive plants. The researchers suspected it was also a case of metabolic resistance, and the Illinois team, led by graduate student Seth Strom, has now confirmed it in a study published in Pest Management Science.

"We were the first group in the world to show resistance to Group 15 herbicides in waterhemp, and now we have identified the mechanism behind it," Riechers says. "Again, it's not good news because it means we're running out of herbicides, and in this case it involves pre-emergence herbicides."

The study suggests two classes of detoxifying enzymes, known as GSTs and P450s, appear to neutralize S-metolachlor in resistant waterhemp.

Group 15 herbicides can be safely used in corn because the crop uses GSTs to naturally detoxify the chemicals; in other words, corn has a natural tolerance to these chemicals. Strom's research suggests waterhemp is not only able to mimic corn's natural detoxification mechanism, but it evolved an additional way to avoid being harmed by S-metolachlor.

Honing in on the two classes of detoxifying enzymes is not the end of the story, however. Because plants have hundreds of enzymes in each class, the researchers have more work ahead of them to identify the specific genes that are activated.

In a separate study, Riechers and another group of Illinois scientists revealed more of waterhemp's metabolic secrets.

"We have known for the last 10 years that whenever we see waterhemp with resistance to an HPPD inhibitor in the field, such as mesotrione, it has always shown metabolic atrazine resistance, too. However, it is possible for waterhemp to be resistant to atrazine and not mesotrione," Riechers says.

The apparent association between mesotrione and metabolic atrazine resistance could be coincidental, but given how often the resistances co-occur, Riechers thought the genes controlling resistance for the two chemicals might be shared or linked.

In a study published in Weed Science, graduate student Kip Jacobs demonstrated an overlap in the genes responsible for metabolic atrazine and mesotrione resistance. Because researchers already knew the single gene for metabolic atrazine resistance, the results get them closer to understanding the genes conferring mesotrione resistance.

"Whenever we find out whether it's two or three or four genes involved in mesotrione resistance, our results tell us one of them should be the metabolic atrazine resistance gene," Riechers says. "We know which one that is."

Unfortunately, even if researchers are able to trace each resistance trait back to the genetic level, that won't ensure an easy solution to the problem. Experts say there are no new herbicide sites-of-action coming into the marketplace, so farmers will need to consider alternative methods of weed control.

"With metabolic resistance, our predictability is virtually zero. We have no idea what these populations are resistant to until we get them under controlled conditions. It's just another example of how we need a more integrated system, rather than relying on chemistry only. We can still use the chemistry, but have to do something in addition," says Aaron Hager, associate professor in the Department of Crop Sciences at Illinois and co-author on the Pest Management Science study. "We have to rethink how we manage waterhemp long term."

Recent devastating fires in the Amazon rain forest and the Australian bush highlight the need to detect forest fires at early stages, before they blaze out of control. Current methods include infrared imaging satellites, remote sensing, watchtowers and aerial patrols, but by the time they sound the alarm, it could be too late. Now, researchers reporting in ACS Applied Materials & Interfaces have developed self-powered "paper chips" that sense early fires and relay a signal.

Previously, scientists have proposed placing a network of sensors in the forest that could detect changes in temperature, smoke or humidity and wirelessly transmit a signal to responders. However, such a system hasn't yet seemed practical because all of the sensing components require power. Batteries would eventually go dead and need to be replaced. Thermoelectric materials, which convert temperature differences into electricity, could simultaneously detect temperature increases from fires and power themselves. However, most of these materials are solid inorganic semiconductors, which are often expensive, rigid and environmentally unfriendly. Yapei Wang and colleagues wanted to find out if ionic liquids could be used as thermoelectric materials for fire sensing. These fluids are salts in the liquid state, and two different types of ionic liquids can be connected in series to generate signals.

To make paper-based thermoelectric sensors, the researchers chose two ionic liquids that behaved differently when the temperature increased: One adsorbed to the surface of gold electrodes, while the other desorbed, producing opposite (positive or negative) voltages. They deposited each ionic liquid like an ink between two gold electrodes that were sputtered onto a piece of ordinary paper. When connected in series, the two ionic liquids produced an electric signal when a large temperature difference occurred, as would happen in a fire. In a pilot test of the new sensor, the researchers attached one to a houseplant. When they placed a flaming cotton ball close to the plant's roots, the temperature at the bottom of the sensor quickly increased, producing a voltage signal that an attached microcomputer chip wirelessly transmitted to a receiver. Upon picking up the signal, the receiver activated a sound alarm and a red light. The thermoelectric paper chips are cheap ($0.04), and the materials are eco-friendly, the researchers say.

Researchers at UConn's Center of Excellence in Vaccine Research (CEVR) have made a breakthrough in vaccine development for a common and difficult to treat pneumonia-causing pathogen. Their research was recently published in the Nature Partner Journal - Vaccines.

For Mycoplasma pneumoniae, vaccine development has been stalled since the 1960s due to a phenomena called vaccine-enhanced disease (VED) or vaccine induced disease exacerbation. A vaccine for this type of community acquired pneumonia has been sought after since the illness can pose problems for closed community settings such as military bases, hospitals, ships, college dormitories, and prisons.

"Two different vaccines were developed by the National Institutes of Health," says Assistant Professor in Pathobiology and Veterinary Science Steven Szczepanek. "In trials, most vaccinated subjects were protected from infection and showed no symptoms. However, for some vaccinated and infected subjects, symptoms were actually worse than those observed in people that did not receive the vaccine. This is vaccine-enhanced disease and is of course really bad."

A vaccine must strike a balance. The formulation needs just enough potency to ensure the immune system will be able to recognize a pathogen and easily kill it if the patient re-encounters it. If all goes according to plan, vaccinated patients are able to easily clear a reinfection without even knowing they were re-exposed. However, a vaccine can sometimes lead to an overreaction by the immune system upon reinfection. This vaccine-enhanced disease has been seen with other pathogens such as respiratory syncytial virus (RSV), Dengue fever, and in animals models in SARS vaccine research, says Steven Geary Department Head of Pathobiology and Veterinary Science and Director of CEVR.

VED is contradictory to the very basis of vaccination.

"We're trying to develop prophylactic vaccines to prevent infections from occurring in healthy people. If the vaccines we develop will actually make infections worse in 1/3 people that get the vaccine, then most people are not going to take the vaccine - and rightfully so," says Szczepanek. "We're not talking about cancer therapeutics where the subject is already sick, where the potential benefit of finding a cure often outweighs the risk of an adverse event occurring. The medical community, and people in general, have very little tolerance for adverse events occurring in a product that is given to otherwise healthy individuals."

To get to the root cause of VED with M. pneumoniae vaccination, the researchers analyzed the building blocks of the bacteria -- the proteins, lipids, and lipoproteins -- to determine if they elicited an immune response.

"We decided to systematically tear the bug apart using different chemical and physical approaches and test different components as vaccines to see if we could identify what, exactly, was causing VED after infection. Before we started this process, we hypothesized that it was the membrane bound surface lipoproteins that were causing VED," says Szczepanek.

The team also studied details about the host immune system and what qualities of the pathogen would lead to the occurrence of VED.

"That's the $64,000 question. The short answer is that we don't know the full picture. Chemical signals used by the immune system called "cytokines" help to drive specific types of immune responses to different pathogens," says Szczepanek.

A confounding trend the researchers have found is the cytokines that play a key role in vaccine protection to another pneumonia-causing bacteria, Streptococcus pneumoniae, are the same cytokines driving VED with M. pneumoniae. This is an example of the nuances and complexities behind vaccine development explains Szczepanek.

"We can't even use what we know about immunity from one bacterial pathogen that causes a similar disease to understand what happens during infection with a different species. Each pathogen is complex and unique, so it seems that we will stay employed for many years to come."

The researchers were able to narrow down the candidates to certain lipoproteins on the surface of the bacteria to test their hypothesis about the immune-inducing culprit.

"After some pretty extensive testing we found out that we were right," says Szczepanek. "Chemical removal of the lipid portion of purified M. pneumoniae lipoproteins eliminated VED, and even drove some level of protection from infection. We still have some work to do to fully optimize the efficacy of a vaccine formulation, but we have identified and eliminated the cause of the nagging roadblock of VED that plagued the field for over half a century. Safety problems are no longer a concern for M. pneumoniae vaccines."

The road to a safe and effective vaccine is a long one, but the researchers at CEVR are excited to be moving forward after overcoming the difficult hurdle of VED, says Geary.

"We have to prepare and refine candidate M. pneumoniae vaccines that do not contain lipoproteins, and test them in our animal model. We will also be testing different adjuvants (compounds that are added to vaccines to increase the proper immune response). Once we have defined the precise vaccine formulation we will proceed with a phase 1 clinical trial in humans. If successful, we will continue on the FDA proscribed phase 2 and 3 clinical trials required for all human vaccines and hopefully then find a partner to produce and market it."

It is a team effort Geary adds, "The majority of the hands-on experimentation and data evaluation to date has been conducted by PhD candidates Arlind Mara and Tyler Gavitt, who will continue to perform the immunologic and vaccine efficacy analysis as this project progresses to the point of a successful vaccine."

UConn has filed a provisional patent application and the technology is available for licensing or partnering. For further information please contact Amit Kumar at a.kumar@uconn.edu.

Coffee is very popular around the world despite or perhaps because of its bitter taste. Compounds contained in the coffee such as caffeine contribute to the bitterness to varying degrees. A recent study conducted by the Leibniz-Institute for Food Systems Biology and the Technical University of Munich (TUM) provides new insights into the molecular interactions between bitter substances and bitter receptors. This is of relevance not only for taste perception.

Caffeine is surely the best-known bitter coffee constituent. However, this stimulating substance is not solely responsible for the bitter taste of the beverage. The latest findings from a study conducted by the Freising team of scientists confirm this. Using a cell-based testing system - a type of artificial tongue - and docking analyses, the team investigated five different bitter coffee constituents. The tests included the bitter substance mozambioside identified in Arabica beans, its roast product bengalensol, and the well-known coffee compounds cafestol, kahweol, and caffeine.

Based on the results of their study, the research team assumes that mainly two of the 25 human bitter taste receptors respond to the coffee's constituents. Whereas a relatively high concentration of caffeine is necessary to stimulate the receptors TAS2R46 and TAS2R43, considerably smaller amounts of the other four substances are needed. The caffeine concentration required to activate the bitter taste receptor TAS2R43 to the same degree as mozambioside or bengalensol was about 30 and 300 times higher, respectively, says lead author Tatjana Lang from the Leibniz-Institute for Food Systems Biology.

Bitter substance reduces bitter taste?

Further studies conducted by the researchers suggest that the bitter substances contained in coffee interact with each other. These studies showed that kahweol and mozambioside exhibit similar binding properties for the bitter taste receptor TAS2R43. Compared to mozambioside, however, kahweol receptor activation was relatively weak and, depending on the dose, was capable of inhibiting the mozambioside-induced activation of the bitter taste receptor. "We therefore assume that kahweol can reduce the bitter taste elicited by TAS2R43 by suppressing more effective bitter substances at the receptor," says principal investigator Maik Behrens, who is head of the research group Taste Systems Reception & Biosignals at the Leibniz-Institute.

Behrens adds that this effect could play a role in coffee preparations that do not include a filtering step like espresso or Turkish coffee, which are beverages that contain kahweol.

Bitter receptor affects gastric acid secretion

Behrens says the study results are exciting from another perspective as well, adding that: "All of our findings indicate that bitter coffee substances quite specifically activate two of the 25 bitter taste receptors. We furthermore know that both types of receptors are present not only in taste cells. TAS2R43 is also present in the stomach and in conjunction with caffeine plays a role in the regulation of gastric acid secretion. The question now arises as to how coffee constituents like bengalensol, which activate the receptor with much higher potency, might be involved in this regulatory process."

It is also interesting that many people do not possess the bitter taste receptor TAS2R43 due to a genetic variation. This could explain the differences in individual coffee taste perception or its tolerability says Veronika Somoza, director of the Leibniz-Institute for Systems Biology. She adds that much more research is needed to elucidate the complex interaction of bitter substances, bitter receptors, and their effects on the human body.