cellular level
Humans Are on Track to Achieve Immortality in 7 Years, Futurist Says
Futurist Ray Kurzweil is still making waves years after his initial singularity claims as artificial intelligence continues to progress. With singularity milestones coming, Kurzweil believes immortality is achievable by 2030. Kurzweil's predictions are met with a healthy dose of skepticism. A new video from the YouTube channel Adagio revisits futurist Ray Kurzweil's ideas about how for humans, both singularity and immortality are shockingly imminent--as in, potentially just seven years away. Both concepts may take a stretch of reality to attain, but Kurzweil and his supporters are quite limber.
New research enables a key step toward personalized medicine: Modeling biological systems
A new study by the Oregon State University College of Engineering shows that machine learning techniques can offer powerful new tools for advancing personalized medicine, care that optimizes outcomes for individual patients based on unique aspects of their biology and disease features. The research with machine learning, a branch of artificial intelligence in which computer systems use algorithms and statistical models to look for trends in data, tackles long-unsolvable problems in biological systems at the cellular level, said Oregon State's Brian D. Wood, who conducted the study with then OSU Ph.D. student Ehsan Taghizadeh and Helen M. Byrne of the University of Oxford. "Those systems tend to have high complexity--first, because of the vast number of individual cells and second, because of the highly nonlinear way in which cells can behave," said Wood, a professor of environmental engineering. "Nonlinear systems present a challenge for upscaling methods, which is the primary means by which researchers can accurately model biological systems at the larger scales that are often the most relevant." A linear system in science or mathematics means any change to the system's input results in a proportional change to the output; a linear equation, for example, might describe a slope that gains 2 feet vertically for every foot of horizontal distance.
OSU research enables key step toward personalized medicine: modeling biological systems
CORVALLIS, Ore. โ A new study by the Oregon State University College of Engineering shows that machine learning techniques can offer powerful new tools for advancing personalized medicine, care that optimizes outcomes for individual patients based on unique aspects of their biology and disease features. The research with machine learning, a branch of artificial intelligence in which computer systems use algorithms and statistical models to look for trends in data, tackles long-unsolvable problems in biological systems at the cellular level, said Oregon State's Brian D. Wood, who conducted the study with then OSU Ph.D. student Ehsan Taghizadeh and Helen M. Byrne of the University of Oxford. "Those systems tend to have high complexity โ first because of the vast number of individual cells and second, because of the highly nonlinear way in which cells can behave," said Wood, a professor of environmental engineering. "Nonlinear systems present a challenge for upscaling methods, which is the primary means by which researchers can accurately model biological systems at the larger scales that are often the most relevant." A linear system in science or mathematics means any change to the system's input results in a proportional change to the output; a linear equation, for example, might describe a slope that gains 2 feet vertically for every foot of horizontal distance.
Researchers use deep learning to identify gene regulation at single-cell level
Scientists at the University of California, Irvine have developed a new deep-learning framework that predicts gene regulation at the single-cell level. In a study published recently in Science Advances, UCI researchers describe how their deep-learning technique can also be successfully used to observe gene regulation at the cellular level. Until now, that process had been limited to tissue-level analysis. According to co-author Xiaohui Xie, UCI professor of computer science, the framework enables the study of transcription factor binding at the cellular level, which was previously impossible due to the intrinsic noise and sparsity of single-cell data. A transcription factor (TF) is a protein that controls the translation of genetic information from DNA to RNA; TFs regulate genes to ensure they're expressed in proper sequence and at the right time in cells.
Tracking development at the cellular level
We each developed from a single cellโa fertilized eggโthat divided and divided and eventually gave rise to the trillions of cells, of hundreds of types, that constitute the tissues and organs of our adult bodies. Advancing our understanding of the molecular programs underlying the emergence and differentiation of these diverse cell types is of fundamental interest and will affect almost every aspect of biology and medicine. Recently, technological advances have made it possible to directly measure the gene expression patterns of individual cells ([ 1 ][1]). Such methods can be used to clarify cell types and to determine the developmental stage of individual cells ([ 2 ][2]). Single-cell transcriptional profiling of successive developmental stages has the potential to be particularly informative, as the data can be used to reconstruct developmental processes, as well as characterize the underlying genetic programs ([ 3 ][3], [ 4 ][4]). ![Figure][5] A genomic technique for tracking cellular development High-throughput single-cell genomic methods enable a global view of cell type diversifcation by transcriptome and epigenome CREDIT: N. DESAI/ SCIENCE FROM CAO ET AL. ([7][6]) AND BIORENDER When I began my doctoral studies in Jay Shendure's lab at the University of Washington, available single-cell sequencing techniques relied on the isolation of individual cells within physical compartments and thus were limited in terms of both throughput and cost. As a graduate student, I developed four high-throughput single-cell genomic techniques to overcome these limitations ([ 5 ][7]โ[ 8 ][8]). Leveraging these methods, I profiled millions of single-cell transcriptomes from organisms, in species that included worms, mice, and humans. By quantifying the dynamics of embryonic development at single-cell resolution, I was able to map out the global genetic programs that control cell proliferation and differentiation at the whole-organism scale. By the 1980s, biologists had documented every developmental step in the nematode Caenorhabditis elegans , from a single-cell embryo to the adult worm, and mapped the connections of all of the worm's neurons ([ 9 ][9]). However, although the nematode worm has a relatively small cell number (558 cells at hatching), a comprehensive understanding of the molecular basis for the specification of these cell types remains difficult. To resolve cellular heterogeneity, I first developed a method to specifically label the transcriptomes of large numbers of single cells, which we called sci-RNA-seq (single-cell combinatorial indexing RNA sequencing) ([ 5 ][7]). This method is based on combinatorial indexing, a strategy using split-pool barcoding of nucleic acids to label vast numbers of single cells within a single experiment ([ 9 ][9]). In this study, I profiled nearly 50,000 cells from C. elegans at the L2 stage, which is more than 50-fold โshotgun cellular coverageโ of its somatic cell composition. We further defined consensus expression profiles for 27 cell types and identified rare neuronal cell types corresponding to as few as one or two cells in the L2 worm. This was the first study to show that single-cell transcriptional profiling is sufficient to separate all major cell types from an entire animal. C. elegans development follows a tightly controlled genetic program. Other multicellular organisms, such as mice and humans, have much more developmental flexibility. However, conventional approaches for mammalian single-cell profiling lack the throughput and resolution to obtain a global view of the molecular states and trajectories of the rapidly diversifying and expanding cell types. To investigate cell state dynamics in mammalian development, I developed an even more scalable single-cell profiling technique, sci-RNA-seq3 ([ 7 ][6]), and used it to trace the development path of 2 million mouse cells as they traversed diverse paths in a 4-day window of development corresponding to organogenesis (embryonic day 9.5 to embryonic day 13.5). From these data, we characterized the dynamics of cell proliferation and key regulators for each cell lineage, a potentially foundational resource for understanding how the hundreds of cell types forming a mammalian body are generated in development. This was, and remains, the largest publicly available single-cell transcriptional dataset. The sci-RNA-seq3 method enabled this dataset to be generated rapidly, within a few weeks, by a single individual. A major challenge regarding current single-cell assays is that nearly all such methods capture just one aspect of cellular biology (typically mRNA expression), limiting the ability to relate different components to one another and to infer causal relationships. Another technique that I developed, sci-CAR (single-cell combinatorial indexing chromatin accessibility and mRNA) ([ 6 ][10]), was created with the goal of overcoming this limitation, allowing the user to jointly profile the epigenome (chromatin accessibility) and transcriptome (mRNA). I applied sci-CAR to the mouse whole kidneys, recovering all major cell types and linking cis-regulatory sites to their target genes on the basis of the covariance of chromatin accessibility and transcription across large numbers of single cells. To further explore the gene regulatory mechanisms, I invented sci-fate ([ 8 ][8]), a new method that identifies the temporal dynamics of transcription by distinguishing newly synthesized mRNA transcripts from โolderโ mRNA transcripts in thousands of individual cells. Applying the strategy to cancer cell state dynamics in response to glucocorticoids, we were able to link transcription factors (TFs) with their target genes on the basis of the covariance between TF expression and the amount of newly synthesized RNA across thousands of cells. In summary, my dissertation involved developing the technical framework for quantifying gene expression and chromatin dynamics across thousands to millions of single cells and applying these technologies to profile complex, developing organisms. The methods that I developed enable such projects to be achievable by a single individual, rather than requiring large consortia. Looking ahead, I anticipate that the integration of single-cell views of the transcriptome, epigenome, proteome, and spatial-temporal information throughout development will enable an increasingly complete view of how life is formed. GRAND PRIZE WINNER Junyue Cao Junyue Cao received his undergraduate degree from Peking University and a Ph.D. from the University of Washington. After completing his postdoctoral fellowship at the University of Washington, Junyue Cao started his lab as an assistant professor and lab head of single-cell genomics and population dynamics at the Rockefeller University in 2020. His current research focuses on studying how a cell population in our body maintains homeostasis by developing genomic techniques to profile and perturb cell dynamics at single-cell resolution. CATEGORY WINNER: ECOLOGY AND EVOLUTION Orsi Decker Orsi Decker completed her undergraduate degree at Eรถtvรถs Lorรกnd University in Budapest, Hungary. She went on to receive her master's degree in Ecology and Evolution at the University of Amsterdam. Decker completed her doctoral research at La Trobe University in Melbourne, Australia, where she investigated the extinctions of native digging mammals and their context-dependent impacts on soil processes. She is currently a postdoctoral researcher at La Trobe University, where she is examining how land restoration efforts could be improved to regain soil functions through the introduction of soil fauna to degraded areas. [www.sciencemag.org/content/370/6519/925.1][11] CATEGORY WINNER: MOLECULAR MEDICINE Dasha Nelidova Dasha Nelidova completed her undergraduate degrees at the University of Auckland, New Zealand. She completed her Ph.D. in neurobiology at the Friedrich Miescher Institute for Biomedical Research in Basel, Switzerland. Nelidova is currently a postdoctoral researcher at the Institute of Molecular and Clinical Ophthalmology Basel, where she is working to develop new translational technologies for treating retinal diseases that lead to blindness. [www.sciencemag.org/content/370/6519/925.2][12] CATEGORY WINNER: CELL AND MOLECULAR BIOLOGY William E. Allen William E. Allen received his undergraduate degree from Brown University in 2012, M.Phil. in Computational Biology from the University of Cambridge in 2013, and Ph.D. in Neurosciences from Stanford University in 2019. At Stanford, he worked to develop new tools for the large-scale characterization of neural circuit structure and function, which he applied to understand the neural basis of thirst. After completing his Ph.D., William started as an independent Junior Fellow in the Society of Fellows at Harvard University, where he is developing and applying new approaches to map mammalian brain function and dysfunction over an animal's life span. [www.sciencemag.org/content/370/6519/925.3][13] 1. [โต][14]1. D. Ramskรถld et al ., Nat. Biotechnol. 30, 777 (2012). [OpenUrl][15][CrossRef][16][PubMed][17] 2. [โต][18]1. C. Trapnell , Genome Res. 25, 1491 (2015). [OpenUrl][19][Abstract/FREE Full Text][20] 3. [โต][21]1. D. E. Wagner et al ., Science 360, 981 (2018). [OpenUrl][22][Abstract/FREE Full Text][23] 4. [โต][24]1. K. Davie et al ., Cell 174, 982 (2018). [OpenUrl][25][CrossRef][26][PubMed][27] 5. [โต][28]1. J. Cao et al ., Science 357, 661 (2017). [OpenUrl][29][Abstract/FREE Full Text][30] 6. [โต][31]1. J. Cao et al ., Science 361, 1380 (2018). [OpenUrl][32][Abstract/FREE Full Text][33] 7. [โต][34]1. J. Cao et al ., Nature 566, 496 (2019). [OpenUrl][35][CrossRef][36][PubMed][37] 8. [โต][38]1. J. Cao, 2. W. Zhou, 3. F. Steemers, 4. C. Trapnell, 5. J. Shendure , Nat. Biotechnol. 38, 980 (2020). [OpenUrl][39][CrossRef][40][PubMed][41] 9. [โต][42]1. D. A. Cusanovich et al ., Science 348, 910 (2015). 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Transparent human organs allow 3-D maps at the cellular level
For the first time, researchers have managed to make intact human organs transparent. Using microscopic imaging, they revealed complex underlying structures of the transparent organs at the cellular level. The resulting organ maps can serve as templates for 3-D bioprinting technologies. In the future, this could lead to the creation of on-demand artificial organs for many patients in need. The findings have been published in Cell.
The Wonderful Ways Artificial Intelligence Is Transforming Genomics and Gene Editing
By 2021, consultant firm Frost & Sullivan expects that artificial intelligence (AI) systems will generate $6.7 billion in revenue from healthcare globally. One area that machine learning is significantly evolving is genomics--the study of the complete set of genes within an organism. While much attention has been paid to the implications for human health, genetic sequencing and analysis could also be ground-breaking for agriculture and animal husbandry. When researchers can sequence and analyze DNA, something that artificial intelligence systems make faster, cheaper and more accurate, they gain perspective on the particular genetic blueprint that orchestrates all activities of that organism. With this insight, they can make decisions about care, what an organism might be susceptible to in the future, what mutations might cause different diseases and how to prepare for the future.
Machine learning provides insight into the human brain โ Physics World
A research collaboration headed up at the National University of Singapore (NUS) has successfully employed machine learning to investigate the cellular architecture of the human brain. The approach uses functional MRI (fMRI) data to automatically estimate brain parameters, enabling neuroscientists to infer the cellular properties of different brain regions without having to surgically probe the brain. The researchers say that their technique could potentially be used to assess treatment of neurological disorders or develop new therapies (Science Advances 10.1126/sciadv.aat7854). "The underlying pathways of many diseases occur at the cellular level, and many pharmaceuticals operate at the microscale level," explains team leader Thomas Yeo. "To know what really happens at the innermost levels of the human brain, it is crucial for us to develop methods that can delve into the depths of the brain non-invasively." Currently, most human brain studies employ non-invasive approaches such as MRI, which limits examination of the brain at a cellular level.
The Amazing Ways Artificial Intelligence Is Transforming Genomics and Gene Editing
By 2021, consultant firm Frost & Sullivan expects that artificial intelligence (AI) systems will generate $6.7 billion in revenue from healthcare globally. One area that machine learning is significantly evolving is genomics--the study of the complete set of genes within an organism. While much attention has been paid to the implications for human health, genetic sequencing and analysis could also be ground-breaking for agriculture and animal husbandry. When researchers can sequence and analyze DNA, something that artificial intelligence systems make faster, cheaper and more accurate, they gain perspective on the particular genetic blueprint that orchestrates all activities of that organism. With this insight, they can make decisions about care, what an organism might be susceptible to in the future, what mutations might cause different diseases and how to prepare for the future.
Killer Nanorobots Are Coming For Your Cancer
Hong Kong researchers have successfully developed a 3D-printed nanoscale robot that can maneuver at a cellular level. In Jun, Science Robotics, a leading robotics technical journal, published a report about the exploits of the City University engineers. It shows that targeted, personalized medicine with tiny robots is no longer science fiction . Precision medicine, as a field, has grown tremendously with the arrival of gene-editing strategies and more-affordable DNA sequencing. WASHINGTON, DC - FEBRUARY 25: U.S. Secretary of Veterans Affairs Robert A. McDonald speaks during the White House Precision Medicine Initiative Summit, in the South Court Auditorium in the Eisenhower Executive Office Building, February 25, 2016 in Washington, DC.