genetics Archives

Seeing the polymerase molecule that transcribes photosynthetic genes in the plant chloroplast. Images of individual molecules collected with an electron microscope were sorted and aligned to reveal details of the structural architecture of the protein complex. CREDIT Michael Webster & Ishika Pramanick

Biochemistry & Organic Chemistry, Biophysics, Biosignatures & Paleobiology, Microbiology & Virology, Origin & Evolution of Life, Plant Biology, Press Release

Photosynthetic Secrets Come To Light

by Keith CowingMarch 5, 2024March 5, 2024

Secrets of photosynthesis have been discovered at atomic level, shedding important new light on this plant super-power that greened the earth more than a billion years ago.

Scatterplots show the evolving populations of hammerheads across multiple rounds of evolution. Hammerheads copied by the lower-fidelity polymerase (52-2) drift away from the original RNA sequence (white contours) and lose their function. Hammerheads copied by the new higher-fidelity polymerase (71-89) retain function, with new functional sequences emerging over time. -- Salk Institute

Biochemistry & Organic Chemistry, Biosignatures & Paleobiology, Genomics, Proteomics, Bioinformatics, Origin & Evolution of Life, Press Release

Modeling The Origins Of Life: New evidence For An RNA World

by Keith CowingMarch 5, 2024March 5, 2024

Charles Darwin described evolution as “descent with modification.” Genetic information in the form of DNA sequences is copied and passed down from one generation to the next. But this process […]

NASA astronaut Kate Rubins prepares a run of Biomolecule Sequencer experiment, which sequenced DNA in space for the first time. -- NASA

Biophysics, Biosignatures & Paleobiology, Commercial & Private Sector, Genomics, Proteomics, Bioinformatics, Microbiology & Virology, Microgravity, Space Life Science, Space Physiology & Medicine, Space Stations, Status Report

Offworld Genomics Research On the ISS: Studying DNA in Space

by Keith CowingFebruary 8, 2024February 8, 2024

Long-term space exploration exposes humans to radiation that can damage deoxyribonucleic acid or DNA, which carries the genetic information for our development and functioning. Conditions in space also affect the […]

Work plan: RNA oligomers (upper left box, also DNA and DNA-RNA hybrid constructs) for their ligation (upper right box, also untemplated elongation) and their peptidylation with relatively lipophilic peptide mixtures (lower left box) to give amphiphilic peptide–oligonucleotide chimeras (lower right box) outside or inside the lumen of mixed-lipid giant vesicles (GVs). A = adenylate (or 2′-deoxyadenylate), G = guanylate (or 2′-deoxyguanylate), C = uridylate, T = thymidylate, Fluo = fluorophore, P = terminal phosphate, OH = terminal hydroxy group, EDC = 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide, CDI = N,N’-carbonyldiimidazole, ImH = imidazole, R = H (Gly), CH3 (Ala), isopropyl (Val), isobutyl (Leu), CH2OPO3H2 (phosphoserine), CH2N3 (β-azido-alanine). -- Life

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

From the RNA-Peptide World: Prebiotic Reaction Conditions Compatible with Lipid Membranes for the Formation of Lipophilic Random Peptides in the Presence of Short Oligonucleotides, and More

by Keith CowingJanuary 29, 2024January 29, 2024

Deciphering the origins of life on a molecular level includes unravelling the numerous interactions that could occur between the most important biomolecules being the lipids, peptides and nucleotides. They were […]

scRNA-seq reveals a global pattern of replication-associated gene covariance. A) PETRI-seq workflow20. Bacterial cells were fixed and permeabilized, then subjected to three rounds of cDNA barcoding to give transcripts of each cell a unique barcode combination. This method is highly scalable to multiple samples and tens of thousands of cells. B) Local operon structure is captured by gene-gene correlations (Spearman’s r). Operons are indicated by shared colors of genes. Gray genes indicate those removed by low-count filtering. Names of SAUSA300_RS04760 and SAUSA300_RS04765 are truncated. C & D) Global gene-gene correlations reflect chromosomal position in (C) exponential phase and (D) stationary phase S. aureus. Spearman correlations were calculated based on scVI-smoothed expression averaged in 50 kb bins by chromosome position. E) Simulated correlation patterns in unsynchronized E. coli populations at three different growth rates. F) Spearman correlations between scaled data averaged into 50 kb bins, as for (C) but for E. coli grown at three growth rates. G) Introducing ectopic origins of replication in E. coli leads to predictable perturbations in gene expression heterogeneity. Top: schematic of predicted replication patterns based on previous studies25–27. Middle: Predicted correlation patterns based on the copy number simulation. Bottom: Real correlation patterns in oriX and oriZ mutant strains, as in (C). Heatmaps of correlations without chromosome position-dependent binning are shown in Fig. S2D.

Genomics, Proteomics, Bioinformatics, Microbiology & Virology, Press Release

New Tool Reveals Gene Behavior In Bacteria

by Keith CowingJanuary 25, 2024January 24, 2024

Bacterial infections cause millions of deaths each year, with the global threat made worse by the increasing resistance of the microbes to antibiotic treatments.

A hypothetical evolutionary scenario of the origin and fold switch of ribosom protein msL1/msL2. The Sewall Wright’s adaptive fitness landscape shows a possible order o events in which degeneration of rRNA in microsporidian species was compensated by the orig and subsequent evolution of a new ribosomal protein. In this hypothetical order of event microsporidian species have undergone a progressive reduction of their ribosomal RNA, whic was likely caused by the accumulation of deleterious mutations in microsporidian genomes du to frequent genetic drifts. Then a new protein msL1 could originate through the spontaneous d novo birth of a gene that was retained in microsporidia due to its ability to counterbalance th rRNA reduction. As rRNA continued to evolve and reduce in size, protein msL1 then underwe a fold switch to yield protein msL2, which three-dimensional structure allowed msL2 to regain i high affinity to its further reduced binding site (rRNA helix H52). -- biorxiv.org

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

A Conserved Ribosomal Protein Has Entirely Dissimilar Structures In Different Organisms

by Keith CowingJanuary 11, 2024January 10, 2024

Ribosomes from different species can markedly differ in their composition by including dozens of ribosomal proteins that are unique to specific lineages but absent in others. However, it remains unknown […]

The two major field sites: Eldfell, a decade-old eruption site on the island of Heimaey, and Fimmvörðuháls, a region between glaciers with access to both very recent and much older lava fields. At each major site, triplicate samples were taken at each point in a 1 m triangle; this pattern was repeated at 2–3 locations 10 m apart, and then that nested pattern was repeated 2–3 times at locations 100 m apart. -- Astrobiology via PubMed

Analog Studies, Arctic / Antarctic / Alpine, Biosignatures & Paleobiology, Caves, Craters, Mountains, Subsurface, Lava Tubes, Exploration Gear & Tech, Extremeophiles and Extreme Environments, Fossils & Paleontology, Genomics, Proteomics, Bioinformatics, Imaging & Spectroscopy, Microbiology & Virology, Status Report, Tricorders & Sensors

Correlations Between Life-Detection Techniques and Implications for Sampling Site Selection in Planetary Analog Missions

by Keith CowingDecember 20, 2023December 20, 2023

We conducted an analog sampling expedition under simulated mission constraints to areas dominated by basaltic tephra of the Eldfell and Fimmvörðuháls lava fields (Iceland).

a Overall structure of E.coli RNA polymerase EC. αI, αII, β′, β and ω subunit of RNAP were colored in green, cyan, gray, yellow, and red, respectively. RNA, template strand DNA (TS), non-template strand DNA (NTS) are shown in red, blue and dark green, respectively. b Model and map of three unnatural base pairs; dB:STP, dB:UTP and dS:BTP are shown with Cryo-EM density maps. c Active site of three UBP EC structures. Bridge helix (BH) is colored in green. UBP in +1 position were colored yellow. Other parts of the structures are colored white. The nitrogen, oxygen, phosphate, and carbon atoms of the base pair at i + 1 position are colored in blue, red, orange, and yellow, respectively. -- Nature Communications

Astropharmacy / Biotechnology, Biochemistry & Organic Chemistry, Genomics, Proteomics, Bioinformatics, Origin & Evolution of Life, Status Report

Expanding The Natural Genetic Code – Implications For SynBio And Origin Of Life?

by Keith CowingDecember 19, 2023January 10, 2026

Editor’s note: The genetic code of all life (with a few minor exceptions) on our home world is based on a genomic code consisting of 4 standard nucleotides. It is […]

Analog Studies, Away Teams & Field Reports, Biosignatures & Paleobiology, Gaia - Planetary Perspectives, Genomics, Proteomics, Bioinformatics, Habitable Zones, Status Report

Planetary Scale Assay Of Earth Life: The Monarch Initiative In 2024: An Analytic Platform Integrating Phenotypes, Genes And Diseases Across Species

by Keith CowingDecember 3, 2023December 2, 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 […]

On the left panel, we have Himmelblau’s function, while the center panel displays its contour diagram. The red points on the contours represent the global minima of the function. On the right panel, we can observe the application of the genetic algorithm with niching and sharing, specifically for Himmelblau’s function. -- astro-ph.CO

AI - Data - Apps - Cybernetics, Astronomy & Telescopes, Genomics, Proteomics, Bioinformatics, Status Report

Cosmological Parameter Estimation With Genetic Algorithms

by Keith CowingNovember 14, 2023November 14, 2023

The search for the optimal values, maxima or minima, of a complex function is an essential task in several fields where mathematical modeling is required. Genetic algorithms (GAs) are a […]

genetics

Photosynthetic Secrets Come To Light

Modeling The Origins Of Life: New evidence For An RNA World

Offworld Genomics Research On the ISS: Studying DNA in Space

From the RNA-Peptide World: Prebiotic Reaction Conditions Compatible with Lipid Membranes for the Formation of Lipophilic Random Peptides in the Presence of Short Oligonucleotides, and More

New Tool Reveals Gene Behavior In Bacteria

A Conserved Ribosomal Protein Has Entirely Dissimilar Structures In Different Organisms

Correlations Between Life-Detection Techniques and Implications for Sampling Site Selection in Planetary Analog Missions

Expanding The Natural Genetic Code – Implications For SynBio And Origin Of Life?

Planetary Scale Assay Of Earth Life: The Monarch Initiative In 2024: An Analytic Platform Integrating Phenotypes, Genes And Diseases Across Species

Cosmological Parameter Estimation With Genetic Algorithms

NASA Spaceline Current Awareness List #1,215 4 September 2026 (Space Life Science Research Results)

The Metallicity Of Giant Exoplanets Around Low-mass Stars And How Ariel Can Help

Two Extremely Irradiated Volatile-rich Sub-Neptunes With Companions In The TOI-426 And TOI-1839 Systems: Insights Into Arrival And Survival Near The Lower Edge Of The Neptunian Desert

Mapping the WISPIT2 Planet-Hosting Cavity at Sub-Hill-Radius scales

Contrasting C/O Ratios in Uranus and Neptune From Disequilibrium Chemistry: A Clue To Distinct Evolutionary Pathways?