biorxiv.org Archives

Cell-free Protein Synthesis Aboard ISS -- biorxiv.org

Genomics, Proteomics, Bioinformatics, Microgravity, Nanotechnology & SynBio, Space Life Science, Space Stations, Status Report, Tricorders & Sensors

Validation Of Cell-free Protein Synthesis Aboard The International Space Station

by Keith CowingDecember 9, 2023December 9, 2023

Cell-free protein synthesis (CFPS) is a rapidly maturing in vitro gene expression platform that can be used to transcribe and translate nucleic acids at the point of need, enabling on-demand […]

Snowball Earth - Artist's concept - NASA.gov

Biophysics, Genomics, Proteomics, Bioinformatics, Origin & Evolution of Life, Status Report

Physical Constraints During Snowball Earth Drive The Evolution Of Multicellularity

by Keith CowingDecember 9, 2023December 9, 2023

Molecular and fossil evidence suggest that complex eukaryotic multicellularity evolved during the late Neoproterozoic era, coincident with Snowball Earth glaciations, where ice sheets covered most of the globe.

Illustration of the modeling combination between a Genome-Scale Model (GSM), i.e., Prochlorococcus MED4 GSM, and an Earth Systems Model (ESM), i.e., NEMO-PISCES, and comparison between growth rates estimated from ESM and GSM. a |From a metabolic network, we defined a solution space embedding all possible fluxes that go through each network reaction. These fluxes satisfy the quasi-steady states assumption and other thermodynamic constraints defined in the GSM. This set of constraints (C1) is defined as biotic constraints, and they affect inner reactions, as well as exchange reactions responsible for the uptake or secretion of nutrients, and a biomass reaction simulating the growth of the organism (color scale similar to panel d., see Appendix 1 for details). b |Earth Systems Models predict global ocean biogeochemistry across space and time. Here the ESM provides uptake fluxes of nutrients for each grid point for each modeled organism. In our framework, these uptake values are used as a set of constraints (C2) on the exchange reactions of the GSM. These are defined as the set of abiotic constraints that are applied in the model. c |C1 and C2 are combined to constrain further exchanged metabolite fluxes at each grid point of the global ocean. As a result, we can estimate the organismal growth rate and all feasible inner fluxes corresponding to a given environment as proposed by the ESM. d |Description of growth rates (h−1) at 5 m depth estimated from NEMO-PISCES picophytoplankton (top) and Prochlorococcus MED4 GSM (bottom). The dashed line shows the transect described in the following panel. e |Distribution of respective growth rates across latitudes and depths at longitude -24o. Grey areas indicate latitudes that do not allow Prochlorococcus MED4 growth because of thermal limits; the GSM does not consider them. The relationship between growth rates across space (above 500 m) and time (i.e., without gray areas) shows R2:0.80 and slope: 0.787 (see Extended Fig. 11). -- biorxiv.org

Biochemistry & Organic Chemistry, Biogeochemical Cycles & Geobiology, Biosignatures & Paleobiology, Gaia - Planetary Perspectives, Genomics, Proteomics, Bioinformatics, Microbiology & Virology, Status Report, Water/Hycean Worlds & Oceanography

Modeling Genome-scale Knowledge In Earth’s Global Ocean

by Keith CowingDecember 4, 2023December 3, 2023

Editor’s note: As we make plans to do orbital and surface sorties on other worlds searching for life it is certainly useful to use Earth and its diverse biota as […]

Images of filters with a layer of wild type and transformed Nostoc punctiforme

Commercial & Private Sector, Genomics, Proteomics, Bioinformatics, Microbiology & Virology, Microgravity, Nanotechnology & SynBio, Space Stations, Status Report

Desiccated Cyanobacteria Serve As Efficient Plasmid DNA Carrier In Space Flight

by Keith CowingNovember 7, 2023December 3, 2023

Effective transport of biological systems as cargo during space travel is a critical requirement to use synthetic biology and biomanufacturing in outer space.

ROS species generation for the NSRL GCRSim Proton simulation in AMMPER. ROS specie,s are shown as green dots; each point corresponds to a single molecule of either OH∙ 270 or H2O2. ROS species are generated due to 271 the ionization of water molecules by the energy depositions from the ions of the radiation tracks. -- biorxiv

Genomics, Proteomics, Bioinformatics, Microbiology & Virology, Radiation, Status Report

Agent-based Model For Microbial Populations Exposed To Radiation (AMMPER) Simulates Yeast Growth For Deep-space Experiments

by Keith CowingNovember 6, 2023November 5, 2023

Space radiation poses a substantial health risk to humans traveling beyond Earth’s orbit to the Moon and Mars. As microbes come with us to space as model organisms for studying […]

Event data for E. coli ribosome in 2M LiCl. Panel A shows heat map of change in conductance vs. dwell time (time molecule spends disrupting nanopore’s ionic current). Heat map color scale corresponds to a probability of an event being in that region of the heat map. Panel B shows example events interpreted to be an intact ribosome (corresponding to Panel C) and a ribosomal fragment (corresponding to Panel D). Panels C and D show overlaid events within the red boxes C and D on Panel A, plotting all events with a signal-to-noise ratio greater than 10, with time scaled to 1. Event data around a current baseline of 0 pA can be observed in C and D throughout the middle of the scaled events (e.g. events with a current signal close to the baseline along time axis points of 0.4 - 0.6). This is due to instances of the automatic event extraction selecting an event with 2 translocations (due to the translocations happening close to each other temporally). -- biorxiv.org

AI - Data - Apps - Cybernetics, Biosignatures & Paleobiology, Genomics, Proteomics, Bioinformatics, Status Report, Tricorders & Sensors, Water/Hycean Worlds & Oceanography

Tricorder Tech: Translation As A Biosignature

by Keith CowingAugust 18, 2023August 18, 2023

Life on Earth relies on mechanisms to store heritable information and translate this information into cellular machinery required for biological activity. In all known life, storage, regulation, and translation are […]

Maximum likelihood phylogenetic tree of [NiFe]-hydrogenase gene sequences obtained from our MAGs (n = 2433), with reference sequences obtained from the HydB and previous phylogenetic analysis. Branches and reference gene labels are colored according to the group of [NiFe]-hydrogenase. Bootstrap values >90% are depicted as filled circles on branches, with size reflecting value, and 1000 ultrafast bootstrap iterations applied. The phyla of the originating MAGs assembled in this study are displayed in a color-coded outer ring. In cases where RuBisCO large subunit gene/s co-occurred within these genomes, the proportion of forms present is indicated by external pie charts. -- biorxiv.org

Arctic / Antarctic / Alpine, Genomics, Proteomics, Bioinformatics, Habitable Zones, Icy Worlds, Microbiology & Virology, Status Report

Metagenomics Untangles Metabolic Adaptations Of Antarctic Endolithic Bacteria At The Fringe Of Habitability

by Keith CowingAugust 18, 2023August 18, 2023

Background: Endolithic niches offer an ultimate refuge, supplying buffered conditions for microorganisms that dwell inside rock airspaces. Yet, survival and growth strategies of Antarctic endolithic microbes residing in Earths’ driest […]

Microeukaryotic cells captured with epifluorescence (DAPI filter) from FLP uptake experiments conducted in this study. All images are derived from shipboard experiments and scale bars are located within each panel. (a-c) Eukaryotic cells from grazing experiments conducted at vent site X-18. The cell in panel (a) contained a consumed FLP cell. Imaged cells from (d) Mustard Stand, (e) Shrimpocalypse, and (f) the plume at Von Damm. Two FLP cells are imaged inside the eukaryotic cell in (f). -- biorxiv.org

Biochemistry & Organic Chemistry, Biogeochemical Cycles & Geobiology, Extremeophiles and Extreme Environments, Microbiology & Virology, Status Report

Microbial Eukaryotic Predation Pressure And Biomass At Deep-sea hydrothermal Vents: Implications For Deep-sea Carbon Cycling

by Keith CowingAugust 18, 2023August 18, 2023

Deep-sea hydrothermal vent geochemistry shapes the foundation of the microbial food web by fueling chemolithoautotrophic microbial activity. Microbial eukaryotes (or protists) play a critical role in hydrothermal vent food webs […]

Bacterial evolution through geological time. (a) The early evolution of bacterial genetic diversity in the Archaean (David and Alm 2010) is reflected by rapid increase in gene content disparity (see Supplementary Material). (b) A persistent higher diversification rate of aerobes since the GOE. The line charts the relative diversification rate (the ratio of the inverse of the waiting time to the next speciation event) for aerobic and anaerobic lineages, revealing a persistent higher diversification rate of aerobes for most of the Earth’s history since the GOE. Rates equilibrated prior to the NOE, before a return to higher diversification rates for aerobes since the GOE. The dotted line denotes a ratio of 1, where the diversification rate of aerobic and anaerobic lineages is equal. Terminal branches were omitted and ratios since 100 Mya were not calculated do to a low number of nodes. (c) Spread of aerobic metabolism by HGT. Transitions from anaerobic to aerobic lifestyles have outnumbered transitions in the reverse direction/back transitions/returns to anaerobicity for most of Earth history since the GOE. The plots show the ratio of aerobic to anaerobic transition rates on the dated species tree during each time period. The dotted line denotes a ratio of 1, where transitions occur in both directions at the same rate. The small number of nodes since ~200 Ma greatly increases uncertainty for both analyses, as reflected in the wide confidence intervals of posterior node age estimates. Ratios since 100 Mya were not calculated due to a low number of nodes. (d) shows the number of aerobic lineages according to Figure 2, e) qualitative sketch of atmospheric oxygen levels through time based on (Lyons, Reinhard, and Planavsky 2014; Poulton et al. 2021; Krause et al. 2022). The grey line shows the Moon-forming impact at ~4.52 Ga; the green line at ~3.23 Ga reflects the presence of fossil and isotopic evidence for oxygenic photosynthesis; the red line at ~2.33 Ga reflects the end of the GOE (see calibrations in Supplementary Material). --- biorxiv.org

Atmospheres, Climate, Weather, Biochemistry & Organic Chemistry, Biogeochemical Cycles & Geobiology, Biosignatures & Paleobiology, Microbiology & Virology, Origin & Evolution of Life, Status Report

An Evolutionary Timescale For Bacteria Calibrated Using The Great Oxidation Event

by Keith CowingAugust 16, 2023August 16, 2023

Most of life’s diversity and history is microbial but it has left a meagre fossil record, greatly hindering understanding of evolution in deep time.

The ciliated protozoan Paramecium caudatum. -- Wikipedia

Biochemistry & Organic Chemistry, Biophysics, Genomics, Proteomics, Bioinformatics, Origin & Evolution of Life, Status Report

A Definition Schema For Life Level And Some Associated Models

by Keith CowingAugust 16, 2023August 16, 2023

We present a mathematical definition schema for measuring life level that is to give options to describe how much a (generalized) organism is alive. It is just a definition schema, […]

biorxiv.org

Validation Of Cell-free Protein Synthesis Aboard The International Space Station

Physical Constraints During Snowball Earth Drive The Evolution Of Multicellularity

Modeling Genome-scale Knowledge In Earth’s Global Ocean

Desiccated Cyanobacteria Serve As Efficient Plasmid DNA Carrier In Space Flight

Agent-based Model For Microbial Populations Exposed To Radiation (AMMPER) Simulates Yeast Growth For Deep-space Experiments

Tricorder Tech: Translation As A Biosignature

Metagenomics Untangles Metabolic Adaptations Of Antarctic Endolithic Bacteria At The Fringe Of Habitability

Microbial Eukaryotic Predation Pressure And Biomass At Deep-sea hydrothermal Vents: Implications For Deep-sea Carbon Cycling

An Evolutionary Timescale For Bacteria Calibrated Using The Great Oxidation Event

A Definition Schema For Life Level And Some Associated Models

Astrobiologist Dale Andersen’s Antarctic Field Report: 9 November 2026: Lake Untersee Basecamp Update

From Anoxic to Oxic Earth: Detectability of Atmospheric Biosignatures Across Stellar Hosts with ELT/ANDES

The Kinetic Basis of the Genetic Code

Power Density as a Universal Biosignature: An Application to the Stellivore Hypothesis

The Limits of Tidal Circularization and Atmospheric Escape for Mini-Neptunes and Super-Earths: The Case of TOI-2257 b