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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

YeastWGD2025

Supplementary data for Discovery of additional ancient genome duplications in yeasts wgd_syn / - directory containing wgd syn output for all contiguous genomes [dataset] Tree - phylogeny [dataset]Duplications - duplication table from OrthoFinder output KOannotations - KEGG annotations used for enrichment analysis IPRannotations - InterPro annotations used for enrichment analysis DipodascalesOrthogroups - formatted orthogroup assignments for Dipodascales genes.fa and .gff3 files for each new genome assembly are also provided, those these are not required to replicate the analysis

Genomics↗
NASA NTRS1991

LinkFinder: An expert system that constructs phylogenic trees

An expert system has been developed using the C Language Integrated Production System (CLIPS) that automates the process of constructing DNA sequence based phylogenies (trees or lineages) that indicate evolutionary relationships. LinkFinder takes as input homologous DNA sequences from distinct individual organisms. It measures variations between the sequences, selects appropriate proportionality constants, and estimates the time that has passed since each pair of organisms diverged from a common ancestor. It then designs and outputs a phylogenic map summarizing these results. LinkFinder can find genetic relationships between different species, and between individuals of the same species, including humans. It was designed to take advantage of the vast amount of sequence data being produced by the Genome Project, and should be of value to evolution theorists who wish to utilize this data, but who have no formal training in molecular genetics. Evolutionary theory holds that distinct organisms carrying a common gene inherited that gene from a common ancestor. Homologous genes vary from individual to individual and species to species, and the amount of variation is now believed to be directly proportional to the time that has passed since divergence from a common ancestor. The proportionality constant must be determined experimentally; it varies considerably with the types of organisms and DNA molecules under study. Given an appropriate constant, and the variation between two DNA sequences, a simple linear equation gives the divergence time.

Inglehart, James↗
NASA NTRS1992

On the nature of global classification

Molecular sequencing technology has brought biology into the era of global (universal) classification. Methodologically and philosophically, global classification differs significantly from traditional, local classification. The need for uniformity requires that higher level taxa be defined on the molecular level in terms of universally homologous functions. A global classification should reflect both principal dimensions of the evolutionary process: genealogical relationship and quality and extent of divergence within a group. The ultimate purpose of a global classification is not simply information storage and retrieval; such a system should also function as an heuristic representation of the evolutionary paradigm that exerts a directing influence on the course of biology. The global system envisioned allows paraphyletic taxa. To retain maximal phylogenetic information in these cases, minor notational amendments in existing taxonomic conventions should be adopted.

NASA Program Exobiology↗
NASA NTRS2003

Biosignatures of early earths

A major goal of NASA's Origins Program is to find habitable planets around other stars and determine which might harbor life. Determining whether or not an extrasolar planet harbors life requires an understanding of what spectral features (i.e., biosignatures) might result from life's presence. Consideration of potential biosignatures has tended to focus on spectral features of gases in Earth's modern atmosphere, particularly ozone, the photolytic product of biogenically produced molecular oxygen. But life existed on Earth for about 1(1/2) billion years before the buildup of atmospheric oxygen. Inferred characteristics of Earth's earliest biosphere and studies of modern microbial ecosystems that share some of those characteristics suggest that organosulfur compounds, particularly methanethiol (CH(3)SH, the sulfur analog of methanol), may have been biogenic products on early Earth. Similar production could take place on extrasolar Earth-like planets whose biota share functional chemical characteristics with Earth life. Since methanethiol and related organosulfur compounds (as well as carbon dioxide) absorb at wavelengths near or overlapping the 9.6-microm band of ozone, there is potential ambiguity in interpreting a feature around this wavelength in an extrasolar planet spectrum.

Earth (Planet)↗
NASA NTRS2002

The Radiata and the evolutionary origins of the bilaterian body plan

The apparent conservation of cellular and molecular developmental mechanisms observed in a handful of bilaterian metazoans has spawned a "race" to reconstruct the bilaterian ancestor. Knowledge of this ancestor would permit us to reconstruct the evolutionary changes that have occurred along specific bilaterian lineages. However, comparisons among extant bilaterians provide an unnecessarily limited view of the ancestral bilaterian. Since the original bilaterians are believed by many to be derived from a radially symmetrical ancestor, additional evidence might be obtained by examining present-day radially symmetrical animals. We briefly review pertinent features of the body plans of the extant radial eumetazoan phyla, the Cnidaria, and Ctenophora, in the context of revealing potential evolutionary links to the bilaterians.

NASA Discipline Evolutionary Biology↗
NASA NTRS2004

Evidence of pathogenic microbes in the International Space Station drinking water: reason for concern?

Molecular analyses were carried out on four preflight and six postflight International Space Station (ISS)-associated potable water samples at various stages of purification, storage, and transport, to ascertain their associated microbial diversities and overall microbial burdens. Following DNA extraction, PCR amplification, and molecular cloning procedures, rDNA sequences closely related to pathogenic species of Acidovorax, Afipia, Brevundimonas, Propionibacterium, Serratia, and others were recovered in varying abundance. Retrieval of sequences arising from the iodine (biocide)-reducing Delftia acidovorans in postflight waters is also of concern. Total microbial burdens of ISS potable waters were derived from data generated by an ATP-based enumeration procedure, with results ranging from 0 to 4.9 x 10(4) cells/ml. Regardless of innate biases in sample collection and analysis, such circumstantial evidence for the presence of viable, intact pathogenic cells should not be taken lightly. Implementation of new cultivation approaches and/or viability-based assays are requisite to confirm such an occurrence.

STS-113 Shuttle Project↗
NASA NTRS2005

Recurrent isolation of hydrogen peroxide-resistant spores of Bacillus pumilus from a spacecraft assembly facility

While the microbial diversity of a spacecraft assembly facility at the Jet Propulsion Laboratory (Pasadena, CA) was being monitored, H2O2-resistant bacterial strains were repeatedly isolated from various surface locations. H2O2 is a possible sterilant for spacecraft hardware because it is a low-temperature process and compatible with various modern-day spacecraft materials, electronics, and components. Both conventional biochemical testing and molecular analyses identified these strains as Bacillus pumilus. This Bacillus species was found in both unclassified (entrance floors, anteroom, and air-lock) and classified (floors, cabinet tops, and air) locations. Both vegetative cells and spores of several B. pumilus isolates were exposed to 5% liquid H2O2 for 60 min. Spores of each strain exhibited higher resistance than their respective vegetative cells to liquid H2O2. Results indicate that the H2O2 resistance observed in both vegetative cells and spores is strain-specific, as certain B. pumilus strains were two to three times more resistant than a standard Bacillus subtilis dosimetry strain. An example of this trend was observed when the type strain of B. pumilus, ATCC 7061, proved sensitive, whereas several environmental strains exhibited varying degrees of resistance, to H2O2. Repeated isolation of H2O2-resistant strains of B. pumilus in a clean-room is a concern because their persistence might potentially compromise life-detection missions, which have very strict cleanliness and sterility requirements for spacecraft hardware.

Spacecraft↗
NASA NTRS1998

A natural view of microbial biodiversity within hot spring cyanobacterial mat communities

This review summarizes a decade of research in which we have used molecular methods, in conjunction with more traditional approaches, to study hot spring cyanobacterial mats as models for understanding principles of microbial community ecology. Molecular methods reveal that the composition of these communities is grossly oversimplified by microscopic and cultivation methods. For example, none of 31 unique 16S rRNA sequences detected in the Octopus Spring mat, Yellowstone National Park, matches that of any prokaryote previously cultivated from geothermal systems; 11 are contributed by genetically diverse cyanobacteria, even though a single cyanobacterial species was suspected based on morphologic and culture analysis. By studying the basis for the incongruity between culture and molecular samplings of community composition, we are beginning to cultivate isolates whose 16S rRNA sequences are readily detected. By placing the genetic diversity detected in context with the well-defined natural environmental gradients typical of hot spring mat systems, the relationship between gene and species diversity is clarified and ecological patterns of species occurrence emerge. By combining these ecological patterns with the evolutionary patterns inherently revealed by phylogenetic analysis of gene sequence data, we find that it may be possible to understand microbial biodiversity within these systems by using principles similar to those developed by evolutionary ecologists to understand biodiversity of larger species. We hope that such an approach guides microbial ecologists to a more realistic and predictive understanding of microbial species occurrence and responsiveness in both natural and disturbed habitats.

Review↗
NASA NTRS2000

Horizontal transfer of archaeal genes into the deinococcaceae: detection by molecular and computer-based approaches

Members of the Deinococcaceae (e.g., Thermus, Meiothermus, Deinococcus) contain A/V-ATPases typically found in Archaea or Eukaryotes which were probably acquired by horizontal gene transfer. Two methods were used to quantify the extent to which archaeal or eukaryotic genes have been acquired by this lineage. Screening of a Meiothermus ruber library with probes made against Thermoplasma acidophilum DNA yielded a number of clones which hybridized more strongly than background. One of these contained the prolyl tRNA synthetase (RS) gene. Phylogenetic analysis shows the M. ruber and D. radiodurans prolyl RS to be more closely related to archaeal and eukaryal forms of this gene than to the typical bacterial type. Using a bioinformatics approach, putative open reading frames (ORFs) from the prerelease version of the D. radiodurans genome were screened for genes more closely related to archaeal or eukaryotic genes. Putative ORFs were searched against representative genomes from each of the three domains using automated BLAST. ORFs showing the highest matches against archaeal and eukaryotic genes were collected and ranked. Among the top-ranked hits were the A/V-ATPase catalytic and noncatalytic subunits and the prolyl RS genes. Using phylogenetic methods, ORFs were analyzed and trees assessed for evidence of horizontal gene transfer. Of the 45 genes examined, 20 showed topologies in which D. radiodurans homologues clearly group with eukaryotic or archaeal homologues, and 17 additional trees were found to show probable evidence of horizontal gene transfer. Compared to the total number of ORFs in the genome, those that can be identified as having been acquired from Archaea or Eukaryotes are relatively few (approximately 1%), suggesting that interdomain transfer is rare.

Non-NASA Center↗
NASA NTRS2001

Analysis of the myosins encoded in the recently completed Arabidopsis thaliana genome sequence

BACKGROUND: Three types of molecular motors play an important role in the organization, dynamics and transport processes associated with the cytoskeleton. The myosin family of molecular motors move cargo on actin filaments, whereas kinesin and dynein motors move cargo along microtubules. These motors have been highly characterized in non-plant systems and information is becoming available about plant motors. The actin cytoskeleton in plants has been shown to be involved in processes such as transportation, signaling, cell division, cytoplasmic streaming and morphogenesis. The role of myosin in these processes has been established in a few cases but many questions remain to be answered about the number, types and roles of myosins in plants. RESULTS: Using the motor domain of an Arabidopsis myosin we identified 17 myosin sequences in the Arabidopsis genome. Phylogenetic analysis of the Arabidopsis myosins with non-plant and plant myosins revealed that all the Arabidopsis myosins and other plant myosins fall into two groups - class VIII and class XI. These groups contain exclusively plant or algal myosins with no animal or fungal myosins. Exon/intron data suggest that the myosins are highly conserved and that some may be a result of gene duplication. CONCLUSIONS: Plant myosins are unlike myosins from any other organisms except algae. As a percentage of the total gene number, the number of myosins is small overall in Arabidopsis compared with the other sequenced eukaryotic genomes. There are, however, a large number of class XI myosins. The function of each myosin has yet to be determined.

NASA Discipline Plant Biology↗