A5088298029- Origins and Evolution of Life
- Microbial Metabolic Engineering and Bioproduction
- Photoreceptor and optogenetics research
- Genomics and Phylogenetic Studies
- Photosynthetic Processes and Mechanisms
- Molecular spectroscopy and chirality
- Protein Structure and Dynamics
- Microbial Community Ecology and Physiology
- Metabolomics and Mass Spectrometry Studies
- Enzyme Structure and Function
- Gene Regulatory Network Analysis
- Protist diversity and phylogeny
- Bioinformatics and Genomic Networks
- Plant and Biological Electrophysiology Studies
- Anaerobic Digestion and Biogas Production
- Earth Systems and Cosmic Evolution
- Microbial Natural Products and Biosynthesis
- Machine Learning in Materials Science
- Complex Network Analysis Techniques
- Methane Hydrates and Related Phenomena
- Scientific Research and Discoveries
- Biofuel production and bioconversion
- Fractal and DNA sequence analysis
- Sexual function and dysfunction studies
- Chemical Reactions and Isotopes
Imperial College London
2023-2024
University College London
2022
Heinrich Heine University Düsseldorf
2018-2021
IPO Porto
2021
Hospital de São João
2021
University of Minho
2014-2018
European Molecular Biology Laboratory
2018
European Molecular Biology Laboratory
2014-2016
Institute for Biotechnology and Bioengineering
2014
Modern cells embody metabolic networks containing thousands of elements and form autocatalytic sets molecules that produce copies themselves. How the first self-sustaining arose at life's origin is a major open question. Autocatalytic smaller than were proposed as transitory intermediates life, but evidence for their role in prebiotic evolution lacking. Here, we identify reflexively food-generated (RAFs)—self-sustaining collectively catalyse all reactions—embedded within microbial...
Research on the origin of life is highly heterogeneous. After a peculiar historical development, it still includes strongly opposed views which potentially hinder progress. In 1st Interdisciplinary Origin Life Meeting, early-career researchers gathered to explore commonalities between theories and approaches, critical divergence points, expectations for future. We find that even though classical approaches theories-e.g. bottom-up top-down, RNA world vs. metabolism-first-have been prevalent...
The composition of a cell in terms macromolecular building blocks and other organic molecules underlies the metabolic needs capabilities species. Although some core biomass components such as nucleic acids proteins are evident for most species, essentiality pool molecules, especially cofactors prosthetic groups, is yet unclear. Here we integrate compositions from 71 manually curated genome-scale models, 33 large-scale gene datasets, enzyme-cofactor association data vast array publications,...
Self-sustaining autocatalytic networks play a central role in living systems, from metabolism at the origin of life, simple RNA and modern cell, to ecology cognition. A collectively network that can be sustained an ambient food set is also referred more formally as ‘reflexively food-generated’ (RAF) set. In this paper, we first investigate simplified setting for studying RAFs, which nevertheless relevant real biochemistry allows exact mathematical analysis based on graph-theoretic concepts....
Abstract Several studies have shown that neither the formal representation nor functional requirements of genome-scale metabolic models (GEMs) are precisely defined. Without a consistent standard, comparability, reproducibility, and interoperability across groups software tools cannot be guaranteed. Here, we present memote ( https://github.com/opencobra/memote ) an open-source containing community-maintained, standardized set me tabolic mo del te sts. The tests cover range aspects from...
Abstract Bacteria are the most abundant cells on Earth. They generally regarded as ancient, but due to striking diversity in their metabolic capacities and widespread lateral gene transfer, physiology of first bacteria is unknown. From 1089 reference genomes bacterial anaerobes, we identified 146 protein families that trace last common ancestor, LBCA, form conserved predicted core its network, which requires only nine genes encompass all universal metabolites. Our results indicate LBCA...
Though all theories for the origin of life require a source energy to promote primordial chemical reactions, nature that drove emergence metabolism at origins is still debated. We reasoned evidence should be preserved in biochemical reactions itself, whereby changes free energy, Δ G , which determine whether reaction can go forward or not, help specify source. By calculating values across conserved and universal core 402 individual synthesize amino acids, nucleotides cofactors from H 2 CO NH...
Abstract The last eukaryote common ancestor (LECA) possessed mitochondria and all key traits that make eukaryotic cells more complex than their prokaryotic ancestors, yet the timing of mitochondrial acquisition role in origin complexity remain debated. Here, we report evidence from gene duplications LECA indicating an early mitochondria. Among 163,545 24,571 trees spanning 150 sequenced genomes, identify 713 duplication events occurred LECA. LECA’s bacterial-derived genes include numerous...
Life and the genetic code are self-referential so autocatalytic networks made of simpler, small molecules. Several origins life theories postulate chemical preceding primordial code, yet demonstration with biochemical systems is lacking. Here, small-molecule reflexively food-generated (RAFs) ranging in size from 3 to 619 reactions were found all 6683 prokaryotic metabolic searched. The average maximum RAF 275 for a rich organic medium 93 single cofactor, NAD. In medium, universally essential...
The metabolism of cells contains evidence reflecting the process by which they arose. Here, we have identified ancient core autotrophic encompassing 404 reactions that comprise reaction network from H2, CO2, and ammonia (NH3) to amino acids, nucleic acid monomers, 19 cofactors required for their synthesis. Water is most common reactant in core, indicating arose an aqueous environment. Seventy-seven involve hydrolysis high-energy phosphate bonds, furthermore suggesting presence a...
Carbon dioxide enters metabolism via six known CO 2 fixation pathways, of which only one is linear, exergonic in the direction ‐assimilation, and present both bacterial archaeal anaerobes – Wood‐Ljungdahl ( WL ) or reductive acetyl‐CoA pathway. monoxide plays a central role pathway as an energy rich intermediate. Here, we scan major biochemical reaction databases for reactions involving . We identified 415 corresponding to enzyme commission EC numbers , are non‐randomly distributed across...
The concept of an autocatalytic network reactions that can form and persist, starting from just available food source, has been formalized by the notion a reflexively food-generated (RAF) set. theory algorithmic results concerning RAFs have applied to range settings, metabolic questions arising at origin life, ecological networks, cognitive models in cultural evolution. In this article, we present new structural RAF sets, studying more complex modes catalysis allow certain require multiple...
Metabolism across all known living systems combines two key features. First, of the molecules that are required either available in environment or can be built up from resources via other reactions within system. Second, proceed a fast and synchronized fashion catalysts also produced Building on early work by Stuart Kauffman, precise mathematical model for describing such self-sustaining autocatalytic (RAF theory) has been developed to explore origins organization general formal framework....
Essential metabolic reactions are shaping constituents of networks, enabling viable and distinct phenotypes across diverse life forms. Here we analyse compare modelling predictions essential functions with experimental data thereby identify core pathways in prokaryotes. Simulations 15 manually curated genome-scale models were integrated 36 large-scale gene essentiality datasets encompassing a wide variety species bacteria archaea. Conservation genes was estimated by analysing 79...
Understanding the origin(s) of life (OoL) is a fundamental challenge for science in 21st century. Research on OoL spans many disciplines, including chemistry, physics, biology, planetary sciences, computer science, mathematics and philosophy. The sheer number different scientific perspectives relevant to problem has resulted coexistence diverse tools, techniques, data, software studies. This made communication between disciplines extremely difficult because interpretation analyses, or...
The origins of life probably involved autocatalysis. Kauffman’s 1986 description collectively autocatalytic sets—self-replicating reaction networks—and related ideas have influenced efforts to study the properties networks that may given rise life. Here, researchers discuss impact sets on field.
Abstract A closer look at Wilhelm Ostwald's articles that originally proposed the concept of autocatalysis reveals he accepted reactants, not just products, as potential autocatalysts. Therefore, a process is catalyzed by some its which common definition autocatalysis, only proper subset what Ostwald meant “Autokatalyse.” As result, it necessary to reconsider especially important for origins‐of‐life research because provides an abiotic mechanism yields reproduction‐like dynamics. Here, we...
Abstract Modern cells embody metabolic networks containing thousands of elements and form autocatalytic molecule sets that produce copies themselves. How the first self-sustaining arose at life’ s origin is a major open question. Autocatalytic smaller than were proposed as transitory intermediates life, but evidence for their role in prebiotic evolution lacking. Here we identify reflexively food-generated (RAFs)—self-sustaining collectively catalyze all reactions—embedded within microbial...