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Recent Additions: New and Updated Entries in the Past 60 Days
Displaying entries 46 through 60 of 108 found.


Ecosmomics: Independent, UniVersal, Complex Network Systems and a Generative Code-Script Source

Cosmic Code > Genetic Info > DNA word

Lin, Yigun, et al.. Exploiting Hierarchical Interactions for Protein Surface Learning. arXiv:2401.10144. Hong Kong University of Science and Technology, and Nanyang Technological University, Singapore computer scientists post another frontier instance of creative ways to learn to read and write life’s amino acid metabolism.

Predicting interactions between proteins is a main project in structural bioinformatics which is often based on geometric and chemical features. Here, we propose key properties of a more effective learning process: 1) relationship atoms linked by covalent bonds to form biomolecules 2): a residue effect that validates hierarchical feature interactions among atoms and surface points). In this paper, we present a principled framework based on deep learning techniques, namely Hierarchical Chemical and Geometric Feature Interaction Network (HCGNet), for protein surface analysis by bridging chemical and geometric features with hierarchical interactions. (Excerpt)

In this work, we highlight the importance of the multiscale relationship between atoms and the hierarchical interaction between chemical and geometric features. To this end, we propose HCGNet, a novel learning architecture for protein surface analysis. HCGNet takes atoms and surface points of a given protein as the input. Then two hierarchical branches are used to learn chemical features from atoms and geometric features from surface points in parallel. In addition, features are hierarchically propagated from the chemical branch to the geometric branch for multi-modality feature fusion. (9)

Cosmic Code > Genetic Info > DNA word

Liu, Jiajia, et al. Large language models in bioinformatics: applications and perspective.. arXiv:2401.04155. We cite this entry by Center for Computational Systems Medicine, University of Texas Health Science Center, Zhengzhou University, Southwest Jiaotong University and Center of Gerontology and Geriatrics, West China Hospital, Sichuan University computational biologists ast an example of the on-going interplay of bioinformatic studies and these novel linguistic programs, as the quote notes.

Large language models (LLMs) as based on AI deep learning perform well on various tasks such as natural language processing (NLP). LLMs are composed of artificial neural networks with many parameters trained on unlabeled input using self- or semi- supervised learning. However, their potential for bioinformatics studies may even exceed this proficiency. In this review, we review the prominent LLMs such as BERT and GPT, and explore their applications at different omics levels in bioinformatics like transcriptomics, proteomics, drug discovery and single cell analysis. (excerpt)

Cosmic Code > Genetic Info > DNA word

Maggi, Luca. The main role of fractal-like nature of conformational space in subdiffusion in protein. arXiv:2306.07825. A Barcelona Institute of Science and Technology bioinformatics disease mechanism researcher provides a latest report of how vital self-similarities appear to suffuse their metabolic activities. See also The Evolution of Fractal Protein Modules in Multicellular Development by Harry Booth and Peter Bentley in Artificial Life Conference Proceedings (MIT Press 2022).

Protein dynamics studies their biological functions but a theoretical picture of their relevant features is still missing. For example, a prime property exhibited by this dynamic is its subdiffusivity. Here, by comparing all-atom molecular simulations and theory we show that this behavior arises from the fractal network of the network of metastable conformational states over which protein diffusion processes take place. (Excerpt)

Cosmic Code > Genetic Info > DNA word

Sondka, Zbyslaw, et al.. COSMIC: a curated database of somatic variants and clinical data for cancer.. Nucleic Acids Research. 52/D1, 2024. Wellcome Sanger Institute geneticists describe the latest four year version of their extensive, actively used informational resource for treating this malady.


The Catalogue Of Somatic Mutations In Cancer (COSMIC), https://cancer.sanger.ac.uk/cosmic, is an expert-curated knowledgebase providing data on somatic variants in cancer, supported by a comprehensive suite of tools for interpreting genomic data, discerning the impact of somatic alterations on disease, and facilitating translational research. Within the last 4 years, COSMIC has substantially expanded its utility by adding new resources: the Mutational Signatures catalogue, the Cancer Mutation Census, and Actionability.

Data curation is the organization and integration of data collected from various sources. It involves annotation, publication and presentation of the data so that the value of the data is maintained over time, and the data remains available for reuse and preservation. In science, data curation may indicate the process of extraction of important information from scientific texts, such as research articles to be converted into an electronic format.

Cosmic Code > Genetic Info > Genome CS

Ghorbani, Mahboobeh, et al. Gene Expression Is Not Random: Scaling, Long-Range Cross-Dependence, and Fractal Characteristics of Gene Regulatory Network.. Frontiers in Physiology. October, 2018. University of Southern California system theorists including Paul Bogdan describe how of a self-similar topology is evident in complex genomes.

Understanding the dynamics of gene expression is crucial to unraveling the physical complexities of this process. Here, we report the scaling properties of gene expression time series in Escherichia coli. Our results demonstrate that the gene expression time series display fractal and long-range dependence characteristics. The interplay between genes and transcription factors in regulatory networks are also fractal and cross-correlated. (Excerpt)

Lastly, mathematical and analytical investigation of the relation between structure and dynamics of processes are also fundamental in theory. Answering to the question of how long-range dependency transfers between structure and dynamics and how the degree of fractality/multifractality of structure and dynamics are like each other would have a huge impact on predicting the behavior of complex systems.

Life's Corporeal Evolution Develops, Encodes and Organizes Itself: An EarthWinian Genesis Synthesis

Quickening Evolution

Adami, Christoph. The Evolution of Biological Information: How Evolution Creates Complexity, from Viruses to Brains. Princeton: Princeton University Press, 2024. A senior authority in computational biology for over 20 years based at Michigan State University contributes his unique, 600 page opus. Its comprehensive chapters flow from the subject theory to biotic precursors, its genetic prescription, digital lab experiments, physiologic robustness, RNA origins, all the way to ascendant intelligence and social cooperation. As these aspects unfold in thorough turn they are braced by many equations.

An overall course becomes evident from the earliest replicants to metabolic biomolecules, cellular animals and relative linguistic knowledge. Although not a theme, it does trace a central trend that winds up with our sentient, observant selves. While Caleb Scharf and Yavul Harari write of algorithms that pass on from the human phase, for Adami the plot thickens and quickens as life’s genomic heredity proceeds from simple cells to neural cognizance. By 2024, a temporal progression may come into view of a procreative ecosmos were trying to decipher and read its own hereditary endowment.

In this final chapter I discussed three prime scales of life: how information is the key element that distinguishes life from nonlife, how the communication of information is the main factor that makes cooperation possible from cells to societies and how information is used to predict the future state of the world. Just as I wrote in the chapter introduction, once we look at biology in the light of information, it is hard not to see the fundamental importance of this concept. (519)

In this book, Christoph Adami adds a 21st century perspective to Darwinian evolution through the lens of an informational quality. This novel theoretical stance sheds light on how cells evolve to communicate, intelligence arises and viruses evolve drug resistance, By this account, information emerges as the central unifying principle which allows us to think about the origin of life on Earth and elsewhere. A leader in the field of computational biology, Adami especially considers the information theory of biomolecules and its content in genetic sequences and proteins. After viewing bacteria and digital organisms, he goes onto explain cooperation among cells, animals, and people. (MIT)

Christoph Adami is professor of microbiology and molecular genetics at Michigan State University. A pioneer in the application of methods from information theory to the study of evolution, he designed the Avida system that launched the use of digital life as a tool for investigating basic questions in evolutionary biology.

Quickening Evolution

Hoyal Cuthill, Jennifer and Simon Conway Morris.. Fractal branching organizations of Ediacaran rangeomorph fronds reveal a lost Proterozoic body plan. PNAS. 111/36, 2014. Cambridge University paleobiologists report a pre-Cambrium presence of a physiological fractal geometry whose self-similarity served to improve creaturely sustenance.

Rangeomorph fronds characterize the late Ediacaran Period (575–541 Ma), representing some of the earliest large organisms. As such, they offer key insights into the early evolution of multicellular eukaryotes. However, their extraordinary branching morphology differs from other organisms and is highly enigmatic. Here we provide a unified mathematical model, allowing us to reconstruct 3D morphologies of 11 taxa and measure their functional properties. This reveals an adaptive radiation of fractal morphologies which maximized body surface area, consistent with diffusive nutrient uptake. Rangeomorphs were adaptively optimal for the low-competition, high-nutrient conditions of Ediacaran oceans. (Abstract)

Quickening Evolution > Systems Biology

Nuno de la Rosa, Laura and Gerd Muller, eds.. Evolutionary Developmental Biology: A Reference Guide. International: Springer, 2021. The editors are biophilosophers at Complutense University of Madrid, and at the University of Vienna. Muller is also president of the Konrad Lorenz Institute. The 1260 page volume rates as the most comprehensive topical source to date. It is arranged into ten main aspects such as Philosophy of EvoDevo, Evo-Devo of Basic Mechanisms, Vertebrate Evo-Devo, EvoDevo and Population Genetics and Extensions of EvoDevo. Some 86 chapters inform about Developmental Homology, Convergence (G. McGhee), Evo-Devo Lessons Learned from Honeybees, Inherency (S. Newman), Evo-Devo’s Contributions to the Extended Evolutionary Synthesis (G. Muller), and Evo-Devo of Language and Cognition.

In regard then, as these many contributions now possible in the third 21st century decade proceed from conceptual views and basic biological features all the way to social behaviors and linguistic cognition, an impression occurs in broad survey that life’s long arduous emergence can well take on a developmental guise of a quickening gestation.

Quickening Evolution > Recapitulation > Life Origin

Douglas, Jordan, et al. Douglas, Jordan, et al. Enzymic recognition of amino acids drove the evolution of primordial genetic codes. Nucleic Acids Research. 52/2, 2024. Into this late year, University of Auckland and University of North Carolina paleobiologists including Peter Wills and Charles Carter (search each) are able todelve deeper to reach better quantified reasons of how and why prebiotic precursors and reactions formed biomolecular systems that could replicate themselves. And as one reads along, an impression grows that our Earthuman retrospective has indeed come upon a preordained ecosmic fertility as it proceeds to complexify, reproduce, develop and evolve.

How genetic information gained its control over chemical processes which build living cells remains to be understood. Today, the aminoacyl-tRNA synthetases (AARS) are known to foster the genetic codes in all living systems. A phylogenetic reconstruction of extant AARS genes, enhanced by modular acquisitions, reveals six AARS with distinct bacterial, archaeal, eukaryotic, or organellar clades. The resulting model shows a tendency for less elaborate enzymes, with simpler catalytic domains, to activate amino acids that did not appear until later. A probable evolutionary route for an amino acid type to find a place in the code was by recruiting older, less specific AARS. (excerpt)

Quickening Evolution > Recapitulation > Life Origin

Helmbrecht, Vanessa, et al. White and green rust chimneys accumulate RNA in a ferruginous chemical garden. Geobiology. 21/6, 2023. Ludwig-Maximilians University paleo-geoscientists return to thermal vent environs with 2020s analytical techniques to be able to explain how they could be a plausible origin site.

Mechanisms of nucleic acid accumulation were likely critical to life's emergence in the ferruginous oceans of the early Earth. How prebiotic geological settings accumulated nucleic acids from dilute aqueous solutions is poorly understood. We, simulated low-temperature alkaline hydrothermal vents in co-precipitation experiments to investigate chemical gardens via sorption. RNA was only extractable from the ferruginous solution in the presence of a phosphate buffer, suggesting RNA in solution was bound to Fe2+ ions. This represents a new mechanism for nucleic acid accumulation in the ferruginous oceans of the early Earth and may have helped to concentrate RNA in a dilute prebiotic ocean.

Quickening Evolution > Recapitulation > Life Origin

Yu, Jinhan, et al. Prebiotic access to enantioenriched amino acids via peptide-mediated transamination reactions.. PNAS. 121/7, 2024. As life origin retro-studies continue to gain a finer focus, Scripps Research, La Jolla, CA biochemists including Donna Blackmond report how these appropriate metabolic biomaterials played their vital role early on. And once again, the whole animate process seems to be unfolding by its own innate merits.

The kinetic resolution of racemic amino acids mediated by dipeptides and pyridoxal provides a prebiotically plausible route to enantioenriched proteinogenic amino acids. The enzymatic transamination cycles that are key to modern biochemical formation of enantiopure amino acids may have evolved from this half of the reversible reaction couple. Kinetic resolution of racemic precursors emerges as a general route to enantioenrichment under prebiotic conditions. (Abstract)

Transamination is the process by which amino groups are removed from amino acids and transferred to acceptor keto-acids to generate the amino acid version of the keto-acid and the keto-acid version of the original amino acid.

Quickening Evolution > Recapitulation > Microbial

Beavan, Alan, et al. Contingency, repeatability, and predictability in the evolution of a prokaryotic pangenome. PNAS. 121/1, 2024. University of Nottingham life scientists describe an extensive AI-based analysis of a microbial species by which to discern a broadly recurrent consistency in effect. While the colonial complexity of bacteria would not seem to be an orderly process, deep down nature seems to be suffused by an inherent coherence.

Pangenomes exhibit remarkable variability in many prokaryotic species through horizontal gene transfer. In this study, we present a machine learning method that predicts the presence or absence of genes in the Escherichia coli pangenome based on complex patterns of other accessory genes within a genome. We find that the presence or absence of a substantial set of genes is highly predictable, indicating that selection maintains gene–gene co-occurrence over long-term bacterial evolution. Our findings indicate that intragenomic gene fitness effects may be key drivers of prokaryotic evolution, influencing the repeated emergence of complex gene–gene relationships across the pangenome. (Abstract)

Pangenome In the fields of molecular biology and genetics, a pan-genome is the entire set of genes from all strains within a clade. More generally, it is the union of all the genomes of a clade.

Cladistics is a a method of classification of animals and plants according to the characteristics that they have in common. It is assumed that the higher the proportion that two organisms share, the more recently they diverged from a common ancestor.

Quickening Evolution > Recapitulation > Symbiotic

Rackaityte, Elze and Susan Lynch. The human microbiome in the 21st century. Nature Communications. 11/5256, 2020. A UC San Francisco biochemist and a gastroenterologist enter an introductory survey of growing realizations that our whole selves are actually multitudinous microbial ecosystems.

The human body supports a thriving diversity of microbes which comprise a dynamic, ancillary, functional system that synergistically develops in lock-step with physiological development of its host. The human microbiome field has transitioned from cataloging this rich diversity to dissecting molecular mechanisms by which microbiomes influence human health. Early life microbiome development trains immune function. Thus, vertically, horizontally, and environmentally acquired microbes and their metabolites have the potential to shape developmental trajectories with life-long implications for health. (Abstract)

Quickening Evolution > Recapitulation > Multicellular

The Origins and Consequences of Multicellularity. Google title and keywords.. Google title and keywords.. A home site for this 2014 Altenberg Workshop in Theoretical Biology organized by Karl Niklas and Stuart Newman. Speakers included Andrew Knoll, Manfred Laubicher, Alan Love and Kunihiko Kaneko. As usual a full set of Abstracts are here,

Multicellularity has evolved independently in ten different lineages, each of which had a unicellular ancestral condition. Its emergence involved physiological mechanisms resulting in cell-to-cell adhesion and sustained inter-cellular communication among adjoining cells. A comparative approach among extant lineages shows that these two requirements have been achieved among plant, animal, and fungal groups. In addition, the evolutionary transition from the unicellular to the multicellular condition is a major change in individuality since a new kind of organism emerges from the interactions and cooperation among subunits (cells).

Quickening Evolution > Recapitulation > Multicellular

Bingham, Emma and William Ratcliff. A nonadaptive explanation for macroevolutionary patterns in the evolution of complex multicellularity. PNAS. 121/7, 2024. Georgia Tech biologists (search WR) contribute additional insights into the many insistent occasions when all manner of animalia came together into reciprocal groupings as life arose on its way.

Complex multicellular organisms have evolved five times independently in eukaryotes, but never within prokaryotes. Here, we propose an alternative for this broad macroevolutionary pattern. By binning cells into groups with finite genetic bottlenecks between generations, multicellularity reduces the effective size of cellular populations, increasing the role of genetic drift in evolutionary change. While both prokaryotes and eukaryotes experience this phenomenon, they have opposite responses to drift: eukaryotes tend to undergo genomic expansion, while prokaryotes face genomic erosion. (Abstract)

Multiicellularity has evolved over 50 times independently, arising at least 3 billion years ago in cyanobacteria. Most of these lineages have remained relatively simple, with “complex multicellularity” arising only five times (animals, plants, fungi, brown, and red algae). Complex multicellularity is a term of art used to capture an important axis of multicellular organismality: the evolution of large, often relatively long-lived, multicellular organisms composed of many cell types (2).

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