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At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals

Background. In octocorals (Cnidaria Octocorallia), the functional relationship between host health and its symbiotic consortium has yet to be determined. Here, we employed comparative metagenomics to uncover the distinct functional and phylogenetic features of the microbiomes of healthy Eunicella gazella, Eunicella verrucosa, and Leptogorgia sarmentosa tissues, in contrast with the microbiomes found in seawater and sediments. We further explored how the octocoral microbiome shifts to a pathobiome state in E. gazella. Results. Multivariate analyses based on 16S rRNA genes, Clusters of Orthologous Groups of proteins (COGs), Protein families (Pfams), and secondary metabolite-biosynthetic gene clusters annotated from 20 Illumina-sequenced metagenomes each revealed separate clustering of the prokaryotic communities of healthy tissue samples of the three octocoral species from those of necrotic E. gazella tissue and surrounding environments. While the healthy octocoral microbiome was distinguished by so-far uncultivated Endozoicomonadaceae, Oceanospirillales, and Alteromonadales phylotypes in all host species, a pronounced increase of Flavobacteriaceae and Alphaproteobacteria, originating from seawater, was observed in necrotic E. gazella tissue. Increased abundances of eukaryotic-like proteins, exonucleases, restriction endonucleases, CRISPR/Cas proteins, and genes encoding for heat-shock proteins, inorganic ion transport, and iron storage distinguished the prokaryotic communities of healthy octocoral tissue regardless of the host species. An increase of arginase and nitric oxide reductase genes, observed in necrotic E. gazella tissues, suggests the existence of a mechanism for suppression of nitrite oxide production by which octocoral pathogens may overcome the host’s immune system. Conclusions. This is the first study to employ primer-less, shotgun metagenome sequencing to unveil the taxonomic, functional, and secondary metabolism features of prokaryotic communities in octocorals. Our analyses reveal that the octocoral microbiome is distinct from those of the environmental surroundings, is host genus (but not species) specific, and undergoes large, complex structural changes in the transition to the dysbiotic state. Host-symbiont recognition, abiotic-stress response, micronutrient acquisition, and an antiviral defense arsenal comprising multiple restriction endonucleases, CRISPR/Cas systems, and phage lysogenization regulators are signatures of prokaryotic communities in octocorals. We argue that these features collectively contribute to the stabilization of symbiosis in the octocoral holobiont and constitute beneficial traits that can guide future studies on coral reef conservation and microbiome therapy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Diversity, taxonomy, and evolution of archaeal viruses of the class Caudoviricetes

The archaeal tailed viruses (arTV), evolutionarily related to tailed double-stranded DNA (dsDNA) bacteriophages of the class Caudoviricetes , represent the most common isolates infecting halophilic archaea. Only a handful of these viruses have been genomically characterized, limiting our appreciation of their ecological impacts and evolution. Here, we present 37 new genomes of haloarchaeal tailed virus isolates, more than doubling the current number of sequenced arTVs. Analysis of all 63 available complete genomes of arTVs, which we propose to classify into 14 new families and 3 orders, suggests ancient divergence of archaeal and bacterial tailed viruses and points to an extensive sharing of genes involved in DNA metabolism and counterdefense mechanisms, illuminating common strategies of virus–host interactions with tailed bacteriophages. Coupling of the comparative genomics with the host range analysis on a broad panel of haloarchaeal species uncovered 4 distinct groups of viral tail fiber adhesins controlling the host range expansion. The survey of metagenomes using viral hallmark genes suggests that the global architecture of the arTV community is shaped through recurrent transfers between different biomes, including hypersaline, marine, and anoxic environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Sphagnum diabolicum sp. nov. and S. magniae sp. nov.; morphological variation and taxonomy of the “S. magellanicum complex”

Until a few years ago, Sphagnum magellanicum was understood to be a single widespread species with an intercontinental range. Recent work by Norwegian sphagnologists showed that S. magellanicum s.str. is restricted to southern South America and plants known as S. magellanicum in Europe should be referred to S. divinum and S. medium. In a separate publication, we showed that there are two additional major clades in eastern North America, and we describe them herein as S. diabolicum and S. magniae. These species are very hard to distinguish morphologically (and also from S. divinum and S. medium) but are distinct phylogenetically, ecologically and geographically, and are important units of biodiversity. Here, morphological variation within and between species is photographically documented.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Non-Powered Dam Custom Analysis and Taxonomy (NPDamCAT) Framework

Over 85,000 non-powered dams (NPDs) exist in the United States that provide services such as flood control, navigation, and water storage for irrigation/domestic water use (USACE 2019). The existing infrastructure of NPDs poses an opportunity for improving economic and environmental performance and generating electricity, as well as a challenge for maintaining aging structures and remediating fragmented river systems. NPD stakeholders interested in the rehabilitation, retrofit, or removal of NPDs must have the relevant information about the population of dams to support decision-making. Each NPD has unique characteristics describing its design, operation, environmental impacts, social impacts, and economic potential. The large number of dams, the diversity of interests related to dams, the variety of dam characteristics, and the types of data required to describe dams all pose major challenges to an analysis of the entire dam population.

13 HYDRO ENERGY↗
DOE OSTI2021

New Data Define the Molecular Phylogeny and Taxonomy of Four Freshwater Suctorian Ciliates With Redefinition of Two Families Heliophryidae and Cyclophryidae (Ciliophora, Phyllopharyngea, Suctoria)

Four suctorian ciliates, Cyclophrya magna Gönnert, 1935, Peridiscophrya florea (Kormos & Kormos, 1958) Dovgal, 2002, Heliophrya rotunda (Hentschel, 1916) Matthes, 1954 and Dendrosoma radians Ehrenberg, 1838, were collected from a freshwater lake in Ningbo, China. The morphological redescription and molecular phylogenetic analyses of these ciliates were investigated. Phylogenetic analyses inferred from SSU rDNA sequences show that all three suctorian orders, Endogenida, Evaginogenida, and Exogenida, are monophyletic and that the latter two clusters as sister clades. The newly sequenced P. florea forms sister branches with C. magna , while sequences of D. radians group with those from H. rotunda within Endogenida. The family Heliophryidae, which is comprised of only two genera, Heliophrya and Cyclophrya , was previously assigned to Evaginogenida. There is now sufficient evidence, however, that the type genus Heliophrya reproduces by endogenous budding, which corresponds to the definitive feature of Endogenida. In line with this and with the support of molecular phylogenetic analyses, we therefore transfer the family Heliophryidae with the type genus Heliophrya to Endogenida. The other genus, Cyclophrya , still remains in Evaginogenida because of its evaginative budding. Therefore, combined with morphological and phylogenetic analysis, Cyclophyidae are reactivated, and it belongs to Evaginogenida.

Ma, Mingzhen↗
DOE OSTI2021

IoT Intrusion Detection Taxonomy, Reference Architecture, and Analyses

This paper surveys the deep learning (DL) approaches for intrusion-detection systems (IDSs) in Internet of Things (IoT) and the associated datasets toward identifying gaps, weaknesses, and a neutral reference architecture. A comparative study of IDSs is provided, with a review of anomaly-based IDSs on DL approaches, which include supervised, unsupervised, and hybrid methods. All techniques in these three categories have essentially been used in IoT environments. To date, only a few have been used in the anomaly-based IDS for IoT. For each of these anomaly-based IDSs, the implementation of the four categories of feature(s) extraction, classification, prediction, and regression were evaluated. We studied important performance metrics and benchmark detection rates, including the requisite efficiency of the various methods. Four machine learning algorithms were evaluated for classification purposes: Logistic Regression (LR), Support Vector Machine (SVM), Decision Tree (DT), and an Artificial Neural Network (ANN). Therefore, we compared each via the Receiver Operating Characteristic (ROC) curve. The study model exhibits promising outcomes for all classes of attacks. The scope of our analysis examines attacks targeting the IoT ecosystem using empirically based, simulation-generated datasets (namely the Bot-IoT and the IoTID20 datasets).

97 MATHEMATICS AND COMPUTING↗
NASA NTRS1975

Sporulation and ultrastructure in a late Proterozoic cyanophyte - Some implications for taxonomy and plant phylogeny

Electron microscopical studies of a morphologically diverse, coccoid, presumably late Proterozoic blue-green alga are here reported. They show, together with light microscopy, that the form studied is widespread in the Cordilleran geosyncline, extend the record of well-defined endosporangia perhaps 700 million years into the past, and reveal previously unrecorded ultrastructural details. Coming from northeastern Utah, southwestern Alberta, and east central Alaska, these minute fossils belong to the recently described, morphologically diverse taxon Sphaerocongregus variabilis Moorman, are related to living entophysalidaceans, and have affinities with both the chroococcalean and chamaesiphonalean cyanophytes. Included in the morphological modes displayed by this alga are individual unicells, coenobial clusters of unicells, and a range of endosporangia comparable to those described for living entophysalidaceans. Scanning and transmission electron microscopy reveal that the endospores are commonly embedded in a vesicular matrix, that some of them show what appears to be a bilaminate or perhaps locally multilaminate wall structure, and that some remain together to mature as coenobial clones or 'colonies'. Taxonomic classification and phylogeny are discussed.

Cloud, P.↗
NASA NTRS1978

Physical observations and taxonomy of asteroids

Physical asteroid observations are summarized and the classification scheme to describe asteroid surfaces in relation to mineralogical composition is detailed. The principle classes, distinguished on the basis of a number of parameters involving albedo and color, are called C, S, and M.

Morrison, D.↗
NASA NTRS1978

Taxonomy of asteroids

A taxonomic system for asteroids is discussed which is based on seven directly observable parameters from polarimetry, spectrophotometry, radiometry, and UBV photometry. The classification scheme is entirely empirical and independent of specific mineralogical interpretations. Five broad classes (designated C, S, M, E, and R), as well as an 'unclassifiable' designation, are defined on the basis of observational data for 523 asteroids. Computer-generated type classifications and derived diameters are given for the 523 asteroids, and the application of the classification procedure is illustrated. Of the 523 asteroids classified, 190 are identified as C objects, 141 as S type, 13 as type M, three as type E, three as type R, 55 as unclassifiable, and 118 as ambiguous. The present taxonomic system is compared with several other asteroid classification systems.

Bowell, E.↗
NASA NTRS1979

Asteroid taxonomy and the distribution of the compositional types

Physical observations of minor planets documented in the TRIAD computer file are used to classify 752 objects into the broad compositional types C, S, M, E, R, and U (unclassifiable) according to the prescriptions adopted by Bowell et al. (1978). Diameters are computed from the photometric magnitude using radiometric and/or polarimetric data where available, or else from albedos characteristic of the indicated type. An analysis of the observational selection effects leads to tabulation of the actual number of asteroids, as a function of type and diameter, in each of 15 orbital element zones. For the whole main belt the population is 75% of type C, 15% of type S, and 10% of other types, with no belt-wide dependence of the mixing ratios on diameter. In some zones the logarithmic diameter-frequency relations are decidedly nonlinear. The relative frequency of S-type objects decreases smoothly outward through the main belt, with exponential scale length 0.5 AU. The rarer types show a more chaotic, but generally flatter, distribution over distance. Characteristic type distributions, contrasting with the background population, are found for the Eos, Koronis, Nysa and Themis families.

Zellner, B.↗
NASA NTRS1982

The peculiar, luminous early-type emission line stars of the Magellanic clouds: A preliminary taxonomy

A sample of some 20 early type emission supergiants in the Magellanic clouds was observed with both the SWP and LWR low resolution mode of IUE. All stars have strong H-emission, some showing P-Cygni structure as well with HeI, HeII, FeII and other ions also showing strong emission. It is found that the stars fall into three distinct groups on the basis of the HeII/HeI and HeI/HI strengths: (1) HeII strong, HeI, HI; (2) HeII absent, HeI, HI strong; (3) HeI absent, HI, FeII, FeII, strong in addition to low excitation ions. The two most extreme emission line stars found in the Clouds S 134/LMC and S 18/SMC are discussed. Results for the 2200A feature in these supergiants, and evidence for shells around the most luminous stars in the clouds are also described.

Shore, S. N.↗
NASA NTRS1985

Chemical compositional study of 35 iron meteorites and its application in taxonomy

Structural and compositional data are reported as a guide to the classification of 35 iron meteorites. The Xinjiang iron meteorite, previously classified as III AB, is reclassified as III E on the basis of its lower Ga/Ni and Ge/Ni ratios, its wider, swollen kamacite bands, and the ubiquitous presence of haxonite, (Fe,Ni)22C. The Dongling (III CD) appears not to be a new meteorite, but to be paired with the Nantan. Four Antarctic iron meteorites, IAB Allan Hills A77250, A77263, A77289, and A77290, are classified as a paired meteorite because of their similarities in structure and in concentrations of various elements. It is shown that Cu shares certain properties with Ga and Ge, which makes them excellent taxonomic parameters.

Wang, D.↗
NASA NTRS1989

A three-parameter asteroid taxonomy

Broadband U, V, and x photometry together with IRAS asteroid albedos have been used to construct an asteroid classification system. The system is based on three parameters (U-V and v-x color indices and visual geometric albedo), and it is able to place 96 percent of the present sample of 357 asteroids into 11 taxonomic classes. It is noted that all but one of these classes are analogous to those previously found using other classification schemes. The algorithm is shown to account for the observational uncertainties in each of the classification parameters.

Tedesco, Edward F.↗