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10 recordsLinked to original sources
USGS1997

Fungal life-styles and ecosystem dynamics: Biological aspects of plant pathogens, plant endophytes and saprophytes

This chapter discusses various biochemical, genetic, ecological, and evolutionary aspects of fungi that express either symbiotic or saprophytic life-styles. An enormous pool of potential pathogens exists in both agricultural and natural ecosystems, and virtually all plant species are susceptible to one or more fungal pathogens. Fungal pathogens have the potential to impact on the genetic structure of populations of individual plant species, the composition of plant communities and the process of plant succession. Endophytic fungi exist for at least part of their life cycles within the tissues of a plant host. This group of fungi is distinguished from plant pathogens because they do not elicit significant disease symptoms. However, endophytes do maintain the genetic and biochemical mechanisms required for infection and colonization of plant hosts. Fungi that obtain chemical nutrients from dead organic matter are known as saprophytes and are critical to the dynamics and resilience of ecosystems. There are two modes of saprophytic growth: one in which biomolecules that are amenable to transport across cell walls and membranes are directly absorbed, and another in which fungi must actively convert complex biopolymers into subunit forms amenable to transportation into cells. Regardless of life-style, fungi employ similar biochemical mechanisms for the acquisition and conversion of nutrients into complex biomolecules that are necessary for vegetative growth, production and dissemination of progeny, organismal competition, and survival during periods of nutrient deprivation or environmental inclemency.

Advances in Botanical Research↗
USGS2021

Sex- and developmental stage-related differences in the hepatic transcriptome of Japanese quail (Coturnix japonica) exposed to 17β-Trenbolone

Endocrine-disrupting chemicals can cause transcriptomic changes that may disrupt biological processes associated with reproductive function including metabolism, transport, and cell growth. We investigated effects from in ovo and dietary exposure to 17β-trenbolone (at 0, 1, and 10 ppm) on the Japanese quail ( Coturnix japonica ) hepatic transcriptome. Our objectives were to identify differentially expressed hepatic genes, assess perturbations of biological pathways, and examine sex- and developmental stage–related differences. The number of significantly differentially expressed genes was higher in embryos than in adults. Male embryos exhibited greater differential gene expression than female embryos, whereas in adults, males and females exhibited similar numbers of differentially expressed genes (>2-fold). Vitellogenin and apovitellenin-1 were up-regulated in male adults exposed to 10 ppm 17β-trenbolone, and these birds also exhibited indications of immunomodulation. Functional grouping of differentially expressed genes identified processes including metabolism and transport of biomolecules, enzyme activity, and extracellular matrix interactions. Pathway enrichment analyses identified as perturbed peroxisome proliferator–activated receptor pathway, cardiac muscle contraction, gluconeogenesis, growth factor signaling, focal adhesion, and bile acid biosynthesis. One of the primary uses of 17β-trenbolone is that of a growth promoter, and these results identify effects on mechanistic pathways related to steroidogenesis, cell proliferation, differentiation, growth, and metabolism of lipids and proteins.

Environmental Toxicology and Chemistry↗
USGS2021

Spatial and temporal dynamics of phytoplankton assemblages in the upper Mississippi River

Phytoplankton provide large quantities of organic carbon and biomolecules that support large river ecosystems. However, when certain groups become overabundant (e.g., cyanobacteria), they can pose a risk to human health and river biota. The purpose of this study was to examine the spatial and temporal dynamics of phytoplankton community composition within the upper Mississippi River. More specifically, we analyzed samples from main channel, impounded, and backwater areas of Navigation Pools 8 and 13 to examine lateral variability within each of these pools. We analyzed samples from the main channel of Pool 26 to examine longitudinal variation among Pools 8, 13, and 26. Phytoplankton and water quality samples were collected during the summer months of 2006–2009. The main channels of Pool 8 and Pool 13 were generally dominated by diatoms, although cyanobacteria were (at times) more abundant. The backwaters were generally dominated by cyanobacteria and typified by flagellated species (e.g., cryptomonads and euglenoids). The main channel of Pool 26 was always dominated by diatoms. Discharge influenced phytoplankton community composition. In Pool 26, taxonomic richness tended to increase with increasing discharge. There were no linear correlations between cyanobacteria total or proportional biovolume and nutrient concentrations, indicating that nutrient limitation was not common. Differences in phytoplankton communities were generally associated with physical factors such as discharge, turbidity, and residence time.

River Research and Applications↗
USGS1998

Sources and age of aquatic humus

As aquatic scientists have recognized the diversity of processes controlled by or dependent upon aquatic humus, it has become important to learn more about the genesis, chemical properties, and concentration of humic substances in aquatic ecosystems. There are three classes of aquatic humus (fulvic acids, humic acids, and humin), all of which share the characteristics of being heterogeneous biomolecules which are yellow to brown or black in color, high to moderate molecular weight, and biologically recalcitrant. Fulvic acids are organic acids which are soluble at any pH; humic acids are soluble above pH 2; and humin is insoluble under the full range of pH. Aquatic humus occurs in both dissolved and solid phases, with molecular weights ranging from about 500 D for dissolved fulvic acid to greater than 100,000 D for humic acids in sediments. Although the heterogeneity of these humic fractions makes rigorous chemical studies challenging, there are sufficient analytical methods at hand to make progress toward understanding the sources, formation pathways, and fate of aquatic humus.

Book chapter↗
USGS2018

Unifying concepts linking dissolved organic matter composition to persistence in aquatic ecosystems

The link between composition and reactivity of dissolved organic matter (DOM) is central to understanding the role aquatic systems play in the global carbon cycle; yet, unifying concepts driving molecular composition have yet to be established. We characterized 37 DOM isolates from diverse aquatic ecosystems, including their stable and radiocarbon isotopes (δ 13 C-dissolved organic carbon (DOC) and Δ 14 C-DOC), optical properties (absorbance and fluorescence), and molecular composition (ultrahigh resolution mass spectrometry). Isolates encompassed end-members of allochthonous and autochthonous DOM from sites across the United States, the Pacific Ocean, and Antarctic lakes. Modern Δ 14 C-DOC and optical properties reflecting increased aromaticity, such as carbon specific UV absorbance at 254 nm (SUVA 254 ), were directly related to polyphenolic and polycyclic aromatic compounds, whereas enriched δ 13 C-DOC and optical properties reflecting autochthonous end-members were positively correlated to more aliphatic compounds. Furthermore, the two sets of autochthonous end-members (Pacific Ocean and Antarctic lakes) exhibited distinct molecular composition due to differences in extent of degradation. Across all sites and end-members studied, we find a consistent shift in composition with aging, highlighting the persistence of certain biomolecules concurrent with degradation time.

Environmental Science & Technology↗
USGS2001

Search for life on Mars in surface samples: Lessons from the 1999 Marsokhod rover field experiment

The Marsokhod 1999 field experiment in the Mojave Desert included a simulation of a rover-based sample selection mission. As part of this mission, a test was made of strategies and analytical techniques for identifying past or present life in environments expected to be present on Mars. A combination of visual clues from high-resolution images and the detection of an important biomolecule (chlorophyll) with visible/near-infrared (NIR) spectroscopy led to the successful identification of a rock with evidence of cryptoendolithic organisms. The sample was identified in high-resolution images (3 times the resolution of the Imager for Mars Pathfinder camera) on the basis of a green tinge and textural information suggesting the presence of a thin, partially missing exfoliating layer revealing the organisms. The presence of chlorophyll bands in similar samples was observed in visible/NIR spectra of samples in the field and later confirmed in the laboratory using the same spectrometer. Raman spectroscopy in the laboratory, simulating a remote measurement technique, also detected evidence of carotenoids in samples from the same area. Laboratory analysis confirmed that the subsurface layer of the rock is inhabited by a community of coccoid Chroococcidioposis cyanobacteria. The identification of minerals in the field, including carbonates and serpentine, that are associated with aqueous processes was also demonstrated using the visible/NIR spectrometer. Other lessons learned that are applicable to future rover missions include the benefits of web-based programs for target selection and for daily mission planning and the need for involvement of the science team in optimizing image compression schemes based on the retention of visual signature characteristics.

California↗
USGS2009

Peptide synthesis in early earth hydrothermal systems

We report here results from experiments and thermodynamic calculations that demonstrate a rapid, temperature-enhanced synthesis of oligopeptides from the condensation of aqueous glycine. Experiments were conducted in custom-made hydrothermal reactors, and organic compounds were characterized with ultraviolet-visible procedures. A comparison of peptide yields at 260??C with those obtained at more moderate temperatures (160??C) gives evidence of a significant (13 kJ ?? mol -1 ) exergonic shift. In contrast to previous hydrothermal studies, we demonstrate that peptide synthesis is favored in hydrothermal fluids and that rates of peptide hydrolysis are controlled by the stability of the parent amino acid, with a critical dependence on reactor surface composition. From our study, we predict that rapid recycling of product peptides from cool into near-supercritical fluids in mid-ocean ridge hydrothermal systems will enhance peptide chain elongation. It is anticipated that the abundant hydrothermal systems on early Earth could have provided a substantial source of biomolecules required for the origin of life. Astrobiology 9, 141-146. ?? 2009 Mary Ann Liebert, Inc. 2009.

Astrobiology↗
USGS2023

The founding charter of the Omic Biodiversity Observation Network (Omic BON)

Omic BON is a thematic Biodiversity Observation Network under the Group on Earth Observations Biodiversity Observation Network (GEO BON), focused on coordinating the observation of biomolecules in organisms and the environment. Our founding partners include representatives from national, regional, and global observing systems; standards organizations; and data and sample management infrastructures. By coordinating observing strategies, methods, and data flows, Omic BON will facilitate the co-creation of a global omics meta-observatory to generate actionable knowledge. Here, we present key elements of Omic BON's founding charter and first activities.

GigaScience↗
USGS2011

Response to comments on "A bacterium that can grow using arsenic instead of phosphorus"

Concerns have been raised about our recent study suggesting that arsenic (As) substitutes for phosphorus in major biomolecules of a bacterium that tolerates extreme As concentrations. We welcome the opportunity to better explain our methods and results and to consider alternative interpretations. We maintain that our interpretation of As substitution, based on multiple congruent lines of evidence, is viable.

Science↗
USGS2019

Generation of lamprey monoclonal antibodies (Lampribodies) using the phage display system

The variable lymphocyte receptors (VLRs) consist of leucine rich repeats (LRRs) and comprise the humoral antibodies produced by lampreys and hagfishes. The diversity of the molecules is generated by stepwise genomic rearrangements of LRR cassettes dispersed throughout the VLRB locus. Previously, target-specific monovalent VLRB antibodies were isolated from sea lamprey larvae after immunization with model antigens. Further, the cloned VLR cDNAs from activated lamprey leukocytes were transfected into human cell lines or yeast to select best binders. Here, we expand on the overall utility of the VLRB technology by introducing it into a filamentous phage display system. We first tested the efficacy of isolating phage into which known VLRB molecules were cloned after a series of dilutions. These experiments showed that targeted VLRB clones could easily be recovered even after extensive dilutions (1 to 10 9 ). We further utilized the system to isolate target-specific “lampribodies” from phage display libraries from immunized animals and observed an amplification of binders with relative high affinities by competitive binding. The lampribodies can be individually purified and ostensibly utilized for applications for which conventional monoclonal antibodies are employed.

Biomolecules↗