Wednesday, October 04, 2023

 

Aston University engineering graduate launches first AI powered grill

Business Announcement

ASTON UNIVERSITY

Suraj Sudera 

IMAGE: 

SURAJ SUDERA

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CREDIT: SURAJ SUDERA



  • Graduate Suraj Sudera created an AI powered grill to cook the perfect steak.
  • His love of engineering led him to create the device called Perfecta™
  • He founded Birmingham based start-up SEERGRILLS which applies AI and advanced technologies to improve cooking.

 

An Aston University engineering graduate has created the world’s first AI powered grill.

Suraj Sudera has created a cooking device called Perfecta™ which cooks the perfect steak in 90 seconds.

Suraj graduated from Aston University in 2015 with a BEng in Mechanical Engineering and again in 2018 with an MSc Ophthalmic Engineering.

He initially worked for Aston University spinout, EYOTO, which develops medical devices. He worked his way up to vice president of engineering, before setting up, and then selling, another company.

However, it was his love of engineering and product development that sparked his ‘light bulb’ moment which led him to create an AI powered grill which can cook food to an individual’s exact preference.

He founded SEERGRILLS, a Birmingham based start-up, which applies AI and advanced technologies to improve cooking.

Suraj said: “We noticed there is often difficulty and inconsistency in cooking food; it’s mostly always overcooked and dry, taking a long time.

“So, we decided to use our skills and knowledge to apply AI to cook the perfect steak and set up SEERGRILLS.

“We developed our first product called Perfecta™ which is the world’s first AI powered grill, the world’s fastest grill, the world’s most intelligent grill and the world’s most efficient grill.”

The device is powered by NeuralFire™ technology, which is AI combined with a proprietary cooking system which can cook more than 50 types of food in under three minutes.

AI calculates the time needed to cook the food based on size, surface area and fat content, and the burners adapt as needed.

Suraj’s Birmingham-based company now employs 48 people, many of whom are Aston University alumni, and his product is available to pre-order in the US.

Suraj said as well as providing him with an education his time at Aston University helped grow his technical skillset and demonstrated to him the importance of networking.

He said: “Creating a company or a product is a bit like putting a man on the moon. One has to visualise the future, and then work backwards, breaking down the journey into its most fundamental components and organise these in a pragmatic way which balances priority, cost and resource.

“Think of a five-dimensional moving jigsaw puzzle in your head - It gets very difficult very quickly, therefore planning, focus, hard work and grit are essential.

“Equally, serendipity and networking are powerful, so exploring, constantly learning and putting yourself in new situations can be pivotal. Entrepreneurship is very rewarding process – to do what nobody else has, you must do what nobody else does.”

 

Organizing can give tenants power to effect change


Peer-Reviewed Publication

CORNELL UNIVERSITY




ITHACA, N.Y. – A renter doesn’t generally hold much sway with a landlord or management company, but when tenants organize, their power can be formidable.

Jamila Michener, associate professor of government and public policy, who has spent years researching tenant organizing, asserts that tenants acting collectively can wield power in “Racism, Power, And Health Equity: The Case Of Tenant Organizing,” which published Oct. 2 in Health Affairs.

“It can feel like these families are so helpless and we need government agencies and political leaders to intervene in order for anything to be changed,” Michener said. “That’s not untrue, but one thing that was striking to me was that tenants, when they work collectively, can actually get an immediate resolution to a direct problem.”

Michener interviewed 79 tenants for her research, which appears in Health Affairs’ October issue, dedicated to “Tackling Structural Racism in Health.” She chose tenants across two critical dimensions: geography and race. Interviewees hailed from 25 states, from large metro areas and rural farm country. Interviewees were 50% white, 40% Black, 6% Asian, 3% Latino and 1% mixed race.

Michener used information gleaned from the interviewees to illustrate that it’s possible for organized tenants to wield power in ways that help advance health equity in the face of structural racism.

“It gives me hope,” Michener said. “When you focus on how people can build and exercise power, that’s part of the path to solutions.”

For additional information, see this Cornell Chronicle story.

Cornell University has dedicated television and audio studios available for media interviews.

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A prehistoric cosmic airburst preceded the advent of agriculture in the Levant



Peer-Reviewed Publication

UNIVERSITY OF CALIFORNIA - SANTA BARBARA




Agriculture in Syria started with a bang 12,800 years ago as a fragmented comet slammed into the Earth’s atmosphere. The explosion and subsequent environmental changes forced hunter-gatherers in the prehistoric settlement of Abu Hureyra to adopt agricultural practices to boost their chances for survival.

That’s the assertion made by an international group of scientists in one of four related research papers, all appearing in the journal Science Open: Airbursts and Cratering Impacts. The papers are the latest results in the investigation of the Younger Dryas Impact Hypothesis, the idea that an anomalous cooling of the Earth almost 13 millennia ago was the result of a cosmic impact.

“In this general region, there was a change from more humid conditions that were forested and with diverse sources of food for hunter-gatherers, to drier, cooler conditions when they could no longer subsist only as hunter-gatherers,” said Earth scientist James Kennett, a professor emeritus of UC Santa Barbara . The settlement at Abu Hureyra is famous among archaeologists for its evidence of the earliest known transition from foraging to farming. “The villagers started to cultivate barley, wheat and legumes,” he noted. “This is what the evidence clearly shows.”


These days, Abu Hureyra and its rich archaeological record lie under Lake Assad, a reservoir created by construction of the Taqba Dam on the Euphrates River in the 1970s. But before this flood, archaeologists managed to extract loads of material to study. “The village occupants,” the researchers state in the paper, “left an abundant and continuous record of seeds, legumes and other foods.” By studying these layers of remains, the scientists were able to discern the types of plants that were being collected in the warmer, humid days before the climate changed and in the cooler, drier days after the onset of what we know now as the Younger Dryas cool period.


Before the impact, the researchers found, the inhabitants’ prehistoric diet involved wild legumes and wild-type grains, and “small but significant amounts of wild fruits and berries.” In the layers corresponding to the time after cooling, fruits and berries disappeared and their diet shifted toward more domestic-type grains and lentils, as the people experimented with early cultivation methods. By about 1,000 years later, all of the Neolithic “founder crops” — emmer wheat, einkorn wheat, hulled barley, rye, peas, lentils, bitter vetch, chickpeas and flax — were being cultivated in what is now called the Fertile Crescent. Drought-resistant plants, both edible and inedible, become more prominent in the record as well, reflecting a drier climate that followed the sudden impact winter at the onset of the Younger Dryas.

The evidence also indicates a significant drop in the area’s population, and changes in the settlement’s architecture to reflect a more agrarian lifestyle, including the initial penning of livestock and other markers of animal domestication.

To be clear, Kennett said, agriculture eventually arose in several places on Earth in the Neolithic Era, but it arose first in the Levant (present-day Syria, Jordan, Lebanon, Palestine, Israel and parts of Turkey) initiated by the severe climate conditions that followed the impact.

And what an impact it must have been

In the 12,800-year-old layers corresponding to the shift between hunting and gathering and agriculture, the record at Abu Hureyra shows evidence of massive burning. The evidence includes a carbon-rich “black mat” layer with high concentrations of platinum, nanodiamonds and tiny metallic spherules that could only have been formed under extremely high temperatures — higher than any that could have been produced by man’s technology at the time. The airburst flattened trees and straw huts, splashing meltglass onto cereals and grains, as well as on the early buildings, tools and animal bones found in the mound — and most likely on people, too. 

This event is not the only such evidence of a cosmic airburst on a human settlement. The authors previously reported a smaller but similar event which destroyed the biblical city at Tall el-Hammam in the Jordan Valley about 1600 BCE.

The black mat layer, nanodiamonds and melted minerals have also been found at about 50 other sites across North and South America and Europe, the collection of which has been called the Younger Dryas strewnfield. According to the researchers, it’s evidence of a widespread simultaneous destructive event, consistent with a fragmented comet that slammed into the Earth’s atmosphere. The explosions, fires and subsequent impact winter,  they say, caused the extinction of most large animals, including the mammoths, saber-toothed cats, American horses, and American camels, as well as the collapse of the North American Clovis culture.

Because the impact appears to have produced an aerial explosion there is no evidence of craters in the ground. “But a crater is not required,” Kennett said. “Many accepted impacts have no visible crater.” The scientists continue to compile evidence of relatively lower-pressure cosmic explosions — the kind that occur when the shockwave originates in the air and travels downward to the Earth’s surface. 

“Shocked quartz is well known and is probably the most robust proxy for a cosmic impact,” he continued. Only forces on par with cosmic-level explosions could have produced the microscopic deformations within quartz sand grains at the time of the impacts, and these deformations have been found in abundance in the minerals gathered from impact craters.

This “crème de la crème” of cosmic impact evidence has also been identified at Abu Hureyra and at other Younger Dryas Boundary (YDB) sites, despite an absence of craters. However, it has been argued that the kind of shock-fractured quartz found in the YDB sites is not equivalent to that found in the large crater-forming sites, so the researchers worked to link these deformations to lower-pressure cosmic events.

To do so, they turned to manmade explosions of the magnitude of cosmic airbursts: nuclear tests conducted at the Alamogordo Bombing Range in New Mexico in 1945 and in Kazakhstan, in 1949 and 1953. Similar to cosmic airbursts, the nuclear explosions occurred above ground, sending shockwaves toward Earth.

“In the papers, we characterize what the morphologies are of these shock fractures in these lower-pressure events,” Kennett said. “And we did this because we wanted to compare it with what we have in the shock-fractured quartz in the Younger Dryas Boundary, to see if there was any comparison or similarities between what we see at the Trinity atomic test site and other atomic bomb explosions.” Between the shocked quartz at the nuclear test sites and the quartz found at Abu Hureyra, the scientists found close associations in their characteristics, namely glass-filled shock fractures, indicative of temperatures greater than 2,000 degrees Celsius, above the melting point of quartz.

“For the first time, we propose that shock metamorphism in quartz grains exposed to an atomic detonation is essentially the same as during a low-altitude, lower-pressure cosmic airburst,” Kennett said. However, the so-called “lower pressure” is still very high — probably greater than 3 GPa or about 400,000 pounds per square inch, equivalent to about five 737 airplanes stacked on a small coin. The novel protocol the researchers developed for identifying shock fractures in quartz grains will be useful in identifying previously unknown airbursts that are estimated to recur every few centuries to millennia.

Taken together, the evidence presented by these papers, according to the scientists, “implies a novel causative link among extraterrestrial impacts, hemispheric environmental and climatic change, and transformative shifts in human societies and culture, including agricultural development.”

Watch how hammerhead sharks get their hammer


Peer-Reviewed Publication

UNIVERSITY OF FLORIDA

Hammerhead development 

IMAGE: A BABY HAMMERHEAD DURING DEVELOPMENT WITH A NASCENT HAMMERHEAD SNOUT. view more 

CREDIT: GARETH FRASER




For weeks, you’d be hard pressed to tell if the rapidly growing animal was going to become a chicken, a fish, a frog, or even a human.

Then out of nowhere: the hammer.

In an unprecedented look at perhaps the strangest, most captivating animals in the ocean, University of Florida scientists have documented how hammerhead sharks stretch and distort their skulls into their namesake hammer-like shape.

“This is a look at how monsters form,” said Gareth Fraser, a UF professor of biology who supervised the new study. “This is an insight into the development of a wonder of nature that we haven’t seen before and may not be able to see again.”

In a series of striking pictures, the study reveals how, roughly halfway through gestation, two-inch-long bonnethead shark embryos suddenly widen their heads. The growing skull pushes out their still-growing eyes at unnatural-looking angles. In the following weeks, the front of the hammer rounds out as it pushes backward toward the gills, creating the final shovel-like shape.

A couple months later, the fully-formed, foot-long shark is born.

Fraser and his graduate student Steven Byrum led the work to document in careful detail the development of bonnetheads, the smallest hammerhead shark species. Bonnetheads are abundant in the Gulf of Mexico and the Atlantic Ocean and spend time near shore, making them relatively easy to study.

But this detailed look at hammerhead development had previously escaped scientists. Most fish, and many sharks, lay eggs that can be easily collected and examined back at the lab. Hammerheads give birth to live young, which makes it exceedingly difficult to watch embryos develop. Many species are endangered, prohibiting the harvesting of sharks to study their young.

Fraser’s team made the most of existing specimens. Through their collaborators, they gained access to embryos that were preserved from bonnetheads caught during other biological studies. No additional sharks were harmed to complete the study.

Because of the difficulty of studying hammerheads, the scientists say that such a close look at their development may never happen again.

“It’s the perfect qualities of the bonnethead that allowed us do it with this species,” said Byrum. “This was a unique opportunity we may not be able to get for very much longer with bonnetheads and may not be able to get in any other species of hammerhead.”

Byrum and Fraser worked with Gavin Naylor, director of the Florida Program for Shark Research at the Florida Museum of Natural History, and scientists from the South Carolina Department of Natural Resources and Florida State University to publish their findings Sept. 28 in the journal Developmental Dynamics.

The documentation sets up future experiments to determine how hammerheads control their head shape and why they evolved their unusual features, which are thought to amplify their field of vision and ability to detect electrical movements of prey.

Hammerhead transformation [VIDEO] |

 

Intense lasers shine new light on the electron dynamics of liquids


Peer-Reviewed Publication

TOHOKU UNIVERSITY

Figure 1 

IMAGE: 

AN INTENSE LASER PULSE (IN RED) HITS A FLOW OF WATER MOLECULES, INDUCING AN ULTRAFAST DYNAMICS OF THE ELECTRONS IN THE LIQUID

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CREDIT: J. HARMS, MPSD




The behavior of electrons in liquids plays a big role in many chemical processes that are important for living things and the world in general. For example, slow electrons in liquid have the capacity to cause disruptions in the DNA strand.

But electron movements are extremely hard to capture because they take place within attoseconds: the realm of quintillionths of a second. Since advanced lasers now operate at these timescales, they can offer scientists glimpses of these ultrafast processes via a range of techniques.

An international team of researchers has now demonstrated that it is possible to probe electron dynamics in liquids using intense laser fields and to retrieve the electron's mean free path - the average distance an electron can travel before colliding with another particle.

"We found that the mechanism by which liquids emit a particular light spectrum, known as the high-harmonic spectrum, is markedly different from the ones in other phases of matter like gases and solids," said Zhong Yin from Tohoku University's International Center for Synchrotron Radiation Innovation Smart (SRIS) and co-first author of the paper. "Our findings open the door to a deeper understanding of ultrafast dynamics in liquids."

Details of the group's research was published in the journal Nature Physics on September 28, 2023.

Using intense laser fields to generate high-energy photons, a phenomenon known as high-harmonic generation (HHG), is a widespread technique used in many different areas of science, for instance for probing electronic motion in materials, or tracking chemical reactions in time. HHG has been studied extensively in gases and more recently in crystals, but much less is known about liquids.

The research team, which also included researchers from the Max Planck Institute for the Structure and Dynamics of Matter (MPSD) in Hamburg and ETH Zurich, reported on the unique behavior of liquids when irradiated by intense lasers. Until now, almost nothing is known about these light-induced processes in liquids, which surround us everywhere and are present in every chemical reaction. In contrast, scientists have made significant strides in recent years in exploring the behavior of solids under irradiation. Therefore, the experimental team at ETH Zurich developed a unique apparatus to specifically study the interaction of liquids with intense lasers. The researchers discovered a distinctive behavior where the maximum photon energy obtained through HHG in liquids was independent of the laser's wavelength. What, then, was the responsible factor?

Setting out to answer this question, the researchers identified a connection that had not been uncovered so far. "The distance an electron can travel in the liquid before colliding with another particle is the crucial factor which imposes a ceiling on the photon energy," said MPSD researcher Nicolas Tancogne-Dejean, a co-author of the study. "We were able to retrieve this quantity - known as the effective electron mean free path - from the experimental data thanks to a specifically developed analytical model which accounts for the scattering of the electrons."

By combining experimental and theoretical results in their study of HHG in liquids, the scientists not only pinpointed the key factor that determines the maximum photo energy but also provide an intuitive model to elucidate the fundamental mechanism.

"Measuring the effective mean free path of the electrons is very challenging in the low kinetic energy region, as was done in this study, added Yin. "Ultimately, our collaborative effort establishes HHG as a new spectroscopical tool to study liquids and is therefore an important stepping stone in the quest to understand the dynamics of electrons in liquids."

The research was a continuation of Yin's previous work.

 

A lethal parasite’s secret weapon: Infecting non-immune cells


Finding defies textbook understanding of leishmaniasis infection

Peer-Reviewed Publication

OHIO STATE UNIVERSITY




COLUMBUS, Ohio – The organisms that cause visceral leishmaniasis, a potentially deadly version of the parasitic disease that most often affects the skin to cause disfiguring disease, appear to have a secret weapon, new research suggests: They can infect non-immune cells and persist in those uncommon environments.

Researchers found the Leishmania donovani parasites in blood-related stem cells in the bone marrow of chronically infected mice – precursor cells that can regenerate all types of cells in the blood-forming system. The finding may help explain why some people who develop visceral leishmaniasis, which is fatal if left untreated, often also have blood disorders such as anemia.

Identifying these cells and other unexpected locations in which these parasites live improves scientists’ understanding of the disease and may lead to new treatment options, said senior study author Abhay Satoskar, professor of pathology in The Ohio State University College of Medicine.

“Treating a patient with leishmania drugs never eliminates every parasite from the body – they persist for the rest of a patient’s life,” Satoskar said. “Perhaps these uncommon cells are the cells responsible for harboring these parasites in low numbers. Some drugs may not reach these cells properly or may not be effective with those parasites, and maybe the parasites in these kinds of cells are different compared to parasites in immune cells because they can adapt. It would be important to eliminate these hidden parasites if we want to stop the transmission of the disease.

“It changes the way we think about this parasite: If uncommon cells are infected, what is the cells’ role? What are the parasites doing there? How did they evade the drug treatment? Are they different from parasites in other cells, or the same? There are lots of questions.”

The research was published recently in the journal Cell Reports.

Cutaneous leishmaniasis is a disfiguring skin disease caused by Leishmania major parasites that affects up to 1.2 million people annually in the tropics, while L. donovani parasites cause the less common visceral leishmaniasis that attacks internal organs, affecting an estimated 100,000 people per year. Scientists have suspected L. donovani may stray beyond their immune cell hosts because they linger in the body, but those suspicions have been difficult to confirm with most conventional technologies because the number of infected cells is low.

Satoskar and colleagues used single-cell RNA sequencing in their search for parasites in spleen and bone marrow cells of chronically infected mice. The technique allowed the team to identify individual cell types based on the thousands of genes expressed by cells that function as a signature of each cell type. Simultaneously, the researchers identified which types of cells were – and were not – infected by L. donovani parasites based on the presence or lack of genes known to be expressed by these organisms.

In the spleen, most of the infected cells detected were frontline immune cells – macrophages and monocytes – known as phagocytes whose job is to swallow up invading organisms.

“Textbooks say Leishmania are parasites of immune cells, mainly phagocytes, that hijack those cells and live there. That is what we’ve learned for many years,” said Satoksar, also a professor of microbiology at Ohio State. “Though that was the dogma, it appears during chronic infection that they’re also infecting other cell types.”

The study showed that these infectious organisms weren’t restricted to only phagocytic cells in either organ – in bone marrow, the blood-related (hematopoietic) stem cells were the main parasitized cells, a surprising finding that was verified through a separate single-cell analysis. The fact their outer surfaces feature some of the same receptors as typical immune cell targets hints at why and how they harbor the parasites, Satoskar said.

Other types of cells in both organs whose gene expression signature suggested they contained L. donovani parasites included white blood cells that assist the immune system – but don’t engulf infectious organisms – and cells responsible for the production of platelets.

“Finding Leishmania genes linked to other cell signatures gives us clues of which cells to look for next in follow-up protocols,” Satoskar said.

This work has potential for rapid translation to human tissue testing in some tropical regions, where taking needle aspiration spleen and bone marrow samples is a routine procedure for people at risk for leishmaniasis. Such samples could be used to help determine if non-immune cells are occupied by parasites in humans as well.

“These are organs where these parasites persist for many, many years after an infection as cleared and a person who becomes immune suppressed can develop disease again,” Satoskar said. “With our animal data and what we find in human samples, we hope to understand the pathways that are assisting parasites to survive and use that knowledge to develop new therapies targeting those pathways.”

This work was funded by the Global Health Innovative Technology Fund and the National Institute of Allergy and Infectious Diseases.

Co-authors include Konstantinos Karagiannis, Sreenivas Gannavaram, Thalia Pacheco-Fernandez, Parna Bhattacharya and Hira Nakhasi of the Food and Drug Administration and Chaitenya Verma of Ohio State.

 

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Contact: Abhay Satoskar, Abhay.Satoskar@osumc.edu

Written by Emily Caldwell, Caldwell.151@osu.edu; 614-292-8152

 

 

Can ChatGPT help us form personal narratives?


Peer-Reviewed Publication

UNIVERSITY OF PENNSYLVANIA




Research has shown that personal narratives—the stories we tell ourselves about our lives—can play a critical role in identity and help us make sense of the past and present. Research has also shown that by helping people reinterpret narratives, therapists can guide patients toward healthier thoughts and behaviors.

Now, researchers from the Positive Psychology Center at the University of Pennsylvania have tested the ability of ChatGPT-4 to generate individualized personal narratives based on stream-of-consciousness thoughts and demographic details from participants, and showed that people found the language model’s responses accurate.

In a new study in The Journal of Positive Psychology, Abigail Blyler and Martin Seligman found that 25 of the 26 participants rated the AI-generated responses as completely or mostly accurate, 19 rated the narratives as very or somewhat surprising, and 19 indicated they learned something new about themselves. Seligman, the Zellerbach Family Professor of Psychology, is the director of the Positive Psychology Center, and Blyler is his research manager. 

“This is a rare moment in the history of scientific psychology: Artificial intelligence now promises much more effective psychotherapy and coaching,” Seligman says.

For each participant, the researchers fed ChatGPT-4 recorded stream-of-consciousness thoughts, which Blyler likened to diary entries with thoughts as simple as “I’m hungry” or “I’m tired.” In a second study published concurrently in The Journal of Positive Psychology, they fed five narratives rated “completely accurate” into ChatGPT-4, asked for specific interventions, and found that the chatbot generated highly plausible coaching strategies and interventions. 

“Since coaching and therapy typically involve a great deal of initial time spent fleshing out such an identity, deriving this automatically from 50 thoughts represents a major savings,” the authors write. 

Abigail Blyler and Martin Seligman, Zellerbach Family Professor of Psychology and director of Penn’s Positive Psychology Center.

Blyler, the first author and a student in the Master of Applied Positive Psychology Program, shares more about the studies in a Q & A.

Q: What are personal narratives, how do they shape identity, and what is their role in therapeutic approaches?

Stories of the self, the way people talk about the journey of their lives and who they are, is really what pulled me into psychology. I’ve come to understand that these narratives impact our behaviors, how we view the world and others, and, importantly, our well-being. One thing Marty [Seligman] and I have discussed a lot is, How do we get to knowing what our narratives are? Narratives help to construct a coherent story, make sense of everything in our lives. 

We found that ChatGPT was able to, with just 50 of those thoughts and very basic demographic information, come up with a highly accurate and detailed personal narrative. This could be a tool for helping people gain self-insight. We see this as something that can be used in the therapeutic context, not as something that would replace a therapist. Can the coach use this to help understand the client better, and can the client in turn understand themselves better? We’re hoping there’s this reciprocal relationship, where this speeds up the process of getting to mutual understanding, so the deep work can take place.

Q: How did you come up with the idea of using ChatGPT-4 to create personal narratives?

I really credit Marty [Seligman]. He has been such a leader in the field of positive psychology for so long. To me, he is the paragon of curiosity, particularly when it comes to the cutting-edge, and so he’s been really steeped in the things that people are doing with AI and psychology. The idea came from a series of discussions we were having around my interest in personal narratives, asking, What are the things we’re consistently telling ourselves? Might that give us a window into the narratives that play on a loop in people’s minds? Can AI be of use here?

Q: The personal narratives were generated from 50 stream-of-consciousness thoughts the participants recorded. What instructions were they given?

We didn’t give any description of what the content of the thoughts should be, just that they should be fairly automatic. We asked that people try not to edit them in their minds. We gave them the option to record it via a voice memo or write it down in a Word document or Notes app. However they chose to do it, we gave them 48 hours to just collect 50 of them.

Q: How did you determine the coaching strategies and interventions ChatGPT-4 generated were highly plausible?

We based it on the literature. There are very many evidence-based therapeutic interventions, and what the machine does here is select the ones that seem most appropriate to the narrative identity. This research is exploratory; there is absolutely a need to continue the research and deploy this with coaches. That’s where we are now, getting this into the hands of coaches. We have just begun collaborations to find out if therapy and coaching are more effective when assisted by our new methods.

 

Wheat's long non-coding RNAs unveiled: A leap in understanding grain development


Peer-Reviewed Publication

MAXIMUM ACADEMIC PRESS

Figure 1. 

IMAGE: COMPARISON OF PROTEIN-CODING GENES AND LNCRNAS IN WHEAT. view more 

CREDIT: SEED BIOLOGY



Wheat is a global staple food and plays a pivotal role in the livelihoods of billions of people. Although long non-coding RNAs (lncRNAs) have been recognized as crucial regulators of numerous biological processes, our knowledge of lncRNAs associated with wheat (Triticum aestivum) grain development remains minimal.

Seed Biology published an online paper entitled “A comprehensive atlas of long non-coding RNAs provides insight into grain development in wheat” on 04 September 2023.

To elucidate the landscape of lncRNAs in wheat, this study conducted genome-wide strand-specific RNA sequencing (ssRNA-seq) on grain endosperm at 10 and 15 days after pollination (DAP) and integrated 545 publicly available transcriptome datasets from various developmental stages and tissues. The analysis pipeline  was adapted from a previous study with modifications, processed RNA-seq data in three primary steps: mapping, assembly, and filtering. The results identified 20,893 lncRNAs in wheat. The characterization of these lncRNAs indicated an average transcript length of 900 bp, and were predominantly single exon structure (48%), with significant overlap with long terminal repeat retrotransposons (LTRs, 41.40%). Compared with protein-coding genes (PCGs), wheat lncRNAs exhibit shorter transcript lengths, fewer exons, and higher tissue-specific expression than PCGs, and their expression patterns were positively correlated with adjacent PCGs. Furthermore, analyzing the distribution of lncRNAs across the three wheat subgenomes (A, B, and D) revealed that 90.7% of the lncRNAs were exclusive to a single subgenome, suggesting that lncRNAs have different evolutionary trajectories compared with PCGs. To ensure efficient access to this wealth data, this study developed the comprehensive database wLNCdb (http://wheat.cau.edu.cn/wLNCdb) , which provides various tools to explore wheat lncRNA profiles, including expression patterns, co-expression networks, functional annotations, and single nucleotide polymorphisms among wheat accessions. Notably, using wLNCdb, the authors identified the lncRNA TraesLNC1D26001.1, which negatively regulates seed germination as its overexpression delayed wheat seed germination by upregulating Abscisic acid-insensitive 5 (TaABI5). Moreover, this lncRNA appears to co-express with genes associated with starch and protein biosynthesis in wheat, emphasizing its potential regulatory role in grain development and end-use quality.

In summation, this pioneering study provides a comprehensive map of wheat lncRNAs. The wLNCdb, with its plethora of information and advanced toolset, lays the groundwork for future exploration and analysis of the functions of lncRNAs. This research not only deepens our understanding of wheat lncRNAs' roles, especially during seed development, but also paves the way for leveraging this knowledge to boost wheat yields and quality in the future.

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References

Authors

Zhaoheng Zhang1,#, Ruijie Zhang1,#, Fengfan Meng1, Yongming Chen1, Wenxi Wang1, Kai Yang1, Yujiao Gao2, Mingming Xin1, Jinkun Du1, Zhaorong Hu1, Zhongfu Ni1, Qixin Sun1, Weilong Guo1,* ,  & Yingyin Yao1,*

# These authors contributed equally: Zhaoheng Zhang, Ruijie Zhang

Affiliations

1. Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China

2. Jiangsu Co-innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Lab of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou 225009, China

About Weilong Guo & Yingyin Yao

Weilong Guo: An associate professor at the College of Agriculture, China Agricultural University. He is currently taking wheat as his research object, combining bioinformatics, genomics, artificial intelligence and other means to focus on the integration and mining of multi-omics big data of crops, analysis of wheat genome variation and evolutionary laws, composition of wheat germplasm resources and utilization of excellent genes, and other issues.

Yingyin Yao: A professor at the College of Agriculture, China Agricultural University. She is mainly engaged in research of genetic improvement of wheat processing quality traits.