#genomic data

[trendynewsnow]

Ryoji Ikeda's Solo Exhibition at the Estonian National Museum

As part of the vibrant programme celebrating Tartu as the 2024 European Capital of Culture, renowned artist Ryoji Ikeda has unveiled his solo exhibition at the Estonian National Museum (ENM) in Tartu. Ikeda is celebrated for his innovative integration of data and technology into his artistic creations. The exhibition showcases two groundbreaking works that have been specifically developed for…

[poojascmi]

Sequencing for Tomorrow: Sustainability and Growth in the DNA Sequencing Market

The title "Sequencing for Tomorrow: Sustainability and Growth in the DNA Sequencing Market" encapsulates the dynamic intersection of scientific innovation, economic expansion, and environmental responsibility within the realm of DNA sequencing. As the DNA sequencing market continues to advance, it is essential to explore how sustainability practices and growth strategies coalesce to shape the future of this transformative industry.

The DNA sequencing market is a dynamic and transformative force that has redefined our understanding of genetics and catalyzed innovations across diverse disciplines. Its impact on healthcare, research, and various industries is unparalleled, and it promises to unlock even more insights and possibilities in the future. As the market evolves and expands, the collaborative efforts of scientists, researchers, and stakeholders will continue to shape the trajectory of genetic exploration and discovery.

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 The DNA sequencing market stands at the forefront of scientific and technological innovation, revolutionizing our understanding of genetics, medicine, and various fields of research. This market encompasses a diverse range of techniques and technologies aimed at deciphering the genetic code of living organisms, enabling researchers to unravel intricate biological information and drive advancements that have far-reaching implications.

Global DNA Sequencing Market is estimated to be valued at US$ 6,802.2 million in 2023 and is expected to exhibit a CAGR of 11.7% during the forecast period (2023-2030), recent study by Coherent Market Insights. Over the forecast period, increasing demand for precision medicine is anticipated to fuel market expansion. For instance, Mount Sinai, a network of hospitals in New York City, announced a cooperation with Regeneron Genetics Center, a division of a biotechnology company based in the United States, in August 2022 to launch a genetic sequencing project that will advance the field of precision medicine research.  

At its core, DNA sequencing involves determining the precise order of nucleotide bases – adenine (A), thymine (T), cytosine (C), and guanine (G) – that make up an organism's DNA. This process holds the key to unlocking a wealth of insights, from identifying genetic mutations and variations to understanding the genetic basis of diseases and traits.

The DNA sequencing market has witnessed exponential growth and transformative breakthroughs since its inception. What was once a laborious and time-consuming endeavor has been streamlined and automated, leading to increased efficiency and affordability. This accessibility has democratized genetic research, allowing scientists, clinicians, and even individuals to harness the power of DNA sequencing for a myriad of applications.

However, growth in the DNA sequencing market must also be balanced with sustainability considerations. The energy-intensive nature of sequencing processes and the production of sequencing reagents can place a burden on the environment. Consequently, industry leaders are increasingly focusing on implementing sustainable practices, such as energy-efficient sequencing platforms, reduced chemical waste, and eco-friendly materials. The pursuit of sustainability not only aligns with global environmental goals but also enhances the long-term viability of the market itself.

Furthermore, sustainability extends beyond environmental concerns to encompass economic and social dimensions. The growth of the DNA sequencing market fosters job creation, drives technological advancements, and stimulates economic development. It also serves as a catalyst for collaboration among diverse sectors, including academia, industry, and government, leading to a holistic approach in addressing complex challenges.

In summary, "Sequencing for Tomorrow: Sustainability and Growth in the DNA Sequencing Market" signifies a harmonious blend of scientific progress, responsible stewardship, and economic vitality. By embracing sustainable practices and fostering growth, the DNA sequencing market can chart a course towards a future where genetic insights and technological innovation drive positive outcomes for humanity and the planet.

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[cbirt]

PCA (Principle Component Analysis) is a commonly used technique in biomedical research to identify similarities and differences between groups of samples. Though conventional PCA is a great tool, it still has some limitations in visualizing and quantifying batch effects; therefore, to overcome these limitations, researchers from the Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, USA, developed PCA-Plus. 

It is an enhanced version of conventional PCA with advanced and additional features for improved diagnosis, detection, and quantification of differences in a group of samples. It appears to be a useful and valuable tool for researchers working on large datasets, particularly in the field of bioinformatics and related areas, where batch effects and group differences are important considerations.

To untangle the complexities of datasets with many variables, PCA (Principal Component Analysis) is an important tool to help researchers in data analysis. PCA is a powerful statistical technique that sorts data into a simpler and much more understandable form. It identifies the main components that explain the most variance in the given dataset. PCA reduces the complexity of your data while preserving the essential information by focusing on the main components. This makes it easier to visualize trends and patterns, dimensionality reduction, feature extraction, and anomaly detection. It has been used in a wide variety of contexts, for example, image processing and compression, characterization of molecular dynamics, linguistic information retrieval, and assessment of batch effects.

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[thatshowthingstarted]

Jebel Irhoud !

Jebel Irhoud or Adrar n Ighoud, is an archeological site located just north of the locality known as Tlet Ighoud, approximately 50 km (30 mi) south-east of the city of Safi in Morocco.

It is noted for the hominin fossils that have been found there since the discovery of the site in 1960.

Originally thought to be Neanderthals, the specimens have since been assigned to Homo Sapiens and, as reported in 2017, have been dated to roughly 300,000 years ago (286±32 ka for the Irhoud 3 mandible, 315±34 ka based on other fossils and the flint artefacts found nearby).

[inheritance-beyond-genes]

20.5.24

My amazing and supportive pi sent me a pic of blue tit for inspo. Need to share alongside with my finally emerging metadata table ⭐

[megumi-fm]

inside you there are two wolves. the science enthusiast wolf is beyond overeager and wants to pick every elective on the course list. the perpetually burnt out wolf is begging you to choose the minimum number of credits needed to graduate.

[dailycupofcreativitea]

This is a shameless pitch for my field of work but if you like biology and you like coding...consider bioinformatics as a career  👀  Especially if you live in the US, as it's well-known for its bionformatics scene.

[thepastisalreadywritten]

[impactofhealth]

Health Research & News: Navigating the Sea of Information

Staying informed about health research and news is crucial for making informed decisions about our well-being. With the abundance of information available, it’s essential to navigate through the sea of data and distinguish between reliable sources and misinformation. Let’s delve into the world of health research and news, exploring its significance, challenges, and impact on society. Read More...

[jcmarchi]

A protein found in human sweat may protect against Lyme disease

New Post has been published on https://thedigitalinsider.com/a-protein-found-in-human-sweat-may-protect-against-lyme-disease/

A protein found in human sweat may protect against Lyme disease

Lyme disease, a bacterial infection transmitted by ticks, affects nearly half a million people in the United States every year. In most cases, antibiotics effectively clear the infection, but for some patients, symptoms linger for months or years.

Researchers at MIT and the University of Helsinki have now discovered that human sweat contains a protein that can protect against Lyme disease. They also found that about one-third of the population carries a genetic variant of this protein that is associated with Lyme disease in genome-wide association studies.

It’s unknown exactly how the protein inhibits the growth of the bacteria that cause Lyme disease, but the researchers hope to harness the protein’s protective abilities to create skin creams that could help prevent the disease, or to treat infections that don’t respond to antibiotics.

“This protein may provide some protection from Lyme disease, and we think there are real implications here for a preventative and possibly a therapeutic based on this protein,” says Michal Caspi Tal, a principal research scientist in MIT’s Department of Biological Engineering and one of the senior authors of the new study.

Hanna Ollila, a senior researcher at the Institute for Molecular Medicine at the University of Helsinki and a researcher at the Broad Institute of MIT and Harvard, is also a senior author of the paper, which appears today in Nature Communications. The paper’s lead author is Satu Strausz, a postdoc at the Institute for Molecular Medicine at the University of Helsinki.

A surprising link

Lyme disease is most often caused by a bacterium called Borrelia burgdorferi. In the United States, this bacterium is spread by ticks that are carried by mice, deer, and other animals. Symptoms include fever, headache, fatigue, and a distinctive bulls-eye rash.

Most patients receive doxycycline, an antibiotic that usually clears up the infection. In some patients, however, symptoms such as fatigue, memory problems, sleep disruption, and body aches can persist for months or years.

Tal and Ollila, who were postdocs together at Stanford University, began this study a few years ago in hopes of finding genetic markers of susceptibility to Lyme disease. To that end, they decided to run a genome-wide association study (GWAS) on a Finnish dataset that contains genome sequences for 410,000 people, along with detailed information on their medical histories.

This dataset includes about 7,000 people who had been diagnosed with Lyme disease, allowing the researchers to look for genetic variants that were more frequently found in people who had had Lyme disease, compared with those who hadn’t.

This analysis revealed three hits, including two found in immune molecules that had been previously linked with Lyme disease. However, their third hit was a complete surprise — a secretoglobin called SCGB1D2.

Secretoglobins are a family of proteins found in tissues that line the lungs and other organs, where they play a role in immune responses to infection. The researchers discovered that this particular secretoglobin is produced primarily by cells in the sweat glands.

To find out how this protein might influence Lyme disease, the researchers created normal and mutated versions of SCGB1D2 and exposed them to Borrelia burgdorferi grown in the lab. They found that the normal version of the protein significantly inhibited the growth of Borrelia burgdorferi. However, when they exposed bacteria to the mutated version, twice as much protein was required to suppress bacterial growth.

The researchers then exposed bacteria to either the normal or mutated variant of SCGB1D2 and injected them into mice. Mice injected with the bacteria exposed to the mutant protein became infected with Lyme disease, but mice injected with bacteria exposed to the normal version of SCGB1D2 did not.

“In the paper we show they stayed healthy until day 10, but we followed the mice for over a month, and they never got infected. This wasn’t a delay, this was a full stop. That was really exciting,” Tal says.

Preventing infection

After the MIT and University of Helsinki researchers posted their initial findings on a preprint server, researchers in Estonia replicated the results of the genome-wide association study, using data from the Estonian Biobank. These data, from about 210,000 people, including 18,000 with Lyme disease, were later added to the final Nature Communications study.

The researchers aren’t sure yet how SCGB1D2 inhibits bacterial growth, or why the variant is less effective. However, they did find that the variant causes a shift from the amino acid proline to leucine, which may interfere with the formation of a helix found in the normal version.

They now plan to investigate whether applying the protein to the skin of mice, which do not naturally produce SCGB1D2, could prevent them from being infected by Borrelia burgdorferi. They also plan to explore the protein’s potential as a treatment for infections that don’t respond to antibiotics.

“We have fantastic antibiotics that work for 90 percent of people, but in the 40 years we’ve known about Lyme disease, we have not budged that,” Tal says. “Ten percent of people don’t recover after having antibiotics, and there’s no treatment for them.”

“This finding opens the door to a completely new approach to preventing Lyme disease in the first place, and it will be interesting to see if it could be useful for preventing other types of skin infections too,” says Kara Spiller, a professor of biomedical innovation in the School of Biomedical Engineering at Drexel University, who was not involved in the study.

The researchers note that people who have the protective version of SCGB1D2 can still develop Lyme disease, and they should not assume that they won’t. One factor that may play a role is whether the person happens to be sweating when they’re bitten by a tick carrying Borrelia burgdorferi.

SCGB1D2 is just one of 11 secretoglobin proteins produced by the human body, and Tal also plans to study what some of those other secretoglobins may be doing in the body, especially in the lungs, where many of them are found.

“The thing I’m most excited about is this idea that secretoglobins might be a class of antimicrobial proteins that we haven’t thought about. As immunologists, we talk nonstop about immunoglobulins, but I had never heard of a secretoglobin before this popped up in our GWAS study. This is why it’s so fun for me now. I want to know what they all do,” she says.

The research was funded, in part, by Emily and Malcolm Fairbairn, the Instrumentarium Science Foundation, the Academy of Finland, the Finnish Medical Foundation, the Younger Family, and the Bay Area Lyme Foundation.

[phagodyke]

seth was so fucking real for this I had to learn R for my degree and it fucking suuucked 😡😤

[grison-in-space]

other shower thoughts: constructing a visual model of a toy population to show how difficult it can be to measure genetic effects on complex traits without referencing environment. say, five loci each with four alleles, just to make it exciting: A, which contributes phenotype score -1 when present in Environment X and 2 in Environment Y; B, which contributes phenotype score 0 in Environment X and 1 in Environment Y; C, which contributes phenotype score 0.5 across environments, and D, which contributes phenotype score 1 in Environment X and score 0 in Environment Y.

Say, allele frequencies of each locus being 0.1 for D and 0.3 for everything else.

If I knock up a population in HWE and define my environments as, say, equally likely to be X or Y for any particular individual, how possible is it for current ACE models of behavior genetics to recapitulate a genetic effect of those alleles when measured agnostically to environment?

....I kind of want to do this to make a point to someone who has irritated me, but if I do mock this thing up, would there be interest in seeing how it plays out in a population of 100? I'm vaguely envisioning a graphic depiction with intensity of phenotype measured in darkness along a color gradient, maybe with borders of black or white to denote hidden environmental effects of X and Y.

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[cbirt]

In a remarkable corridor of achievement, the scientists of the University of Southampton have reputedly gotten the ability to conserve the complete human genomic sequence on a disruptive 5D memory crystal. This achievement is an exceptional phenomenon in data storage and has profound implications for preserving the genetic heritage of humanity and other species.

The 5D memory crystal, a creation by the university’s Optoelectronics Research Centre (ORC), bears unprecedented durability and storage longevity. Unlike the previous ways of storing data, which were subject to aging deterioration, this crystal can hold a lot of information for decades, even centuries and millennia, even in the harshest of conditions.

The crystal’s remarkable resilience stems from its composition and structure.  The crystal is equivalent to fused quartz, one of the most chemically and thermally durable materials on Earth. It withstands extremely low as well as unbearably high temperatures, extreme stress, and even radiation. It can withstand the high and low extremes of freezing, fire, and temperatures of up to 1000 °C. The crystal can also withstand a direct impact force of up to 10 tons per cm2 and is unchanged by long exposure to cosmic radiation.

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[amrtechinsights]

🌟 Unlock the Future of Medicine with Genomic Data Analysis! 🧬 Dive into cutting-edge techniques that are transforming healthcare and personalizing treatments. Join the genomic revolution! 🚀 #Genomics #DataAnalysis #PrecisionMedicine #HealthInnovation #FutureOfMedicine