Search USGS⌕ Search

SEARCH · Search USGS

Results for “Molecular Biology”

Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 55 records · Page 3Linked to original sources
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↗
USGS2023

Wildlife ecological risk assessment in the 21st century: Promising technologies to assess toxicological effects

Despite advances in toxicity testing and development of new approach methodologies (NAMs) for hazard assessment, the ecological risk assessment (ERA) framework for terrestrial wildlife (i.e., air-breathing amphibians, reptiles, birds, and mammals) has remained unchanged for decades. While survival, growth, and reproductive endpoints derived from whole animal toxicity tests are central to hazard assessment, non-standard measures of biological effects at multiple levels of biological organization (e.g., molecular, cellular, tissue, organ, organism, population, community, ecosystem) have potential to enhance the relevance of prospective and retrospective wildlife ERAs. Other factors (e.g., indirect effects of contaminants on food supplies and infectious disease processes) are influenced by toxicants at individual, population, and community levels, and need to be factored into chemically-based risk assessments to enhance the “eco” component of ERAs. Regulatory and logistical challenges often relegate such non-standard endpoints and indirect effects to post-registration evaluations of pesticides and industrial chemicals, and contaminated site evaluations. While NAMs are being developed, to date their applications in ERAs focused on wildlife have been limited. No single magic tool or model will address all uncertainties in hazard assessment. Modernizing wildlife ERAs will likely entail combinations of laboratory and field-derived data at multiple levels of biological organization, knowledge collection solutions (e.g., systematic review, adverse outcome pathway frameworks), and inferential methods that facilitate integrations and risk estimations focused on species, populations, interspecific extrapolations, and ecosystem services modeling, with less dependence on whole animal data and simple hazard ratios.

Integrated Environmental Assessment and Management↗
USGS2012

Analogues of doxanthrine reveal differences between the dopamine D1 receptor binding properties of chromanoisoquinolines and hexahydrobenzo[a]phenanthridines

Efforts to develop selective agonists for dopamine D 1 -like receptors led to the discovery of dihydrexidine and doxanthrine, two bioisosteric β-phenyldopamine-type full agonist ligands that display selectivity and potency at D 1 -like receptors. We report herein an improved methodology for the synthesis of substituted chromanoisoquinolines (doxanthrine derivatives) and the evaluation of several new compounds for their ability to bind to D 1 - and D 2 -like receptors. Identical pendant phenyl ring substitutions on the dihydrexidine and doxanthrine templates surprisingly led to different effects on D 1 -like receptor binding, suggesting important differences between the interactions of these ligands with the D 1 receptor. We propose, based on the biological results and molecular modeling studies, that slight conformational differences between the tetralin and chroman-based compounds lead to a shift in the location of the pendant ring substituents within the receptor.

European Journal of Medicinal Chemistry↗
USGS1976

Amino acids and gases in some springs and an oil field in California

Samples of water and gas were collected from six springs and two wells in the Upper Cretaceous Great Valley sequence and Franciscan Formation underlying the Coast Range of northern California and from four oil wells penetrating Tertiary sedimentary rocks in the Kettleman North Dome oil field. Comparison of the dissolved free amino acid compositions of the waters from the two locations show overlapping ranges with many more similarities than differences. The detection of nonprotein amino acids (sarcosine, β -amino n -butyric acid, and others) indicates the protein degradation is partly chemical rather than strictly biological. Other low molecular weight degradation products (methane, ethane, nonvolatile organic acids, and other organic chelating agents) were found. This may be one mechanism for the transportation of organic matter from the source rocks to the reservoir rocks of an oil deposit.

California↗
USGS2019

Biological and mineralogical controls over cycling of low molecular weight organic compounds along a soil chronosequence

Low molecular weight organic compounds (LMWOC) represent a small but critical component of soil organic matter (SOM) for microbial growth and metabolism. The fate of these compounds is largely under microbial control, yet outside the cell, intrinsic soil properties can also significantly influence their turnover and retention. Using a chronosequence representing 1200 ka of pedogenic development, we compared physicochemical vs biological controls on the turnover and retention of fast-cycling carbon (C), e.g. glucose (GLU) and p-hydroxybenzoic acid (PHBA). Along the chronosequence, we observed mineralogical gradients whereby amorphous constituents were greatest in intermediate-aged sites, while older sites demonstrated soils with more ordered and less reactive mineralogy. Soil microbial community composition varied along the soil chronosequence and we observed reductions in total biomass and fungal biomass from younger to older sites, but this did not affect the turnover of LMWOC. Microbial utilization of LMWOC was substrate- and soil-dependent; amorphous Fe and Al oxides reduced the respiration of PHBA but respiration from glucose remained less affected. Variation in soil mineralogy did not significantly alter recovery of PHBA within microbial biomass or fungal vs. bacterial biomarkers, suggesting that reduced respiration of the phenolic resulted from direct mineral interaction with ionizable functional groups rather than changes to microbial allocation of PHBA. We conclude patterns of soil carbon storage observed across chronosequences are moderated by mineralogical effects on microbial access to LMWOC, independent of variation in microbial community composition. Keywords: 13C; Glucose; Microbial biomass C; Organo-mineral interactions; p-Hydroxybenzoic acid; Selective dissolution mineralogical analyses

Soil Biology and Biochemistry↗
USGS2016

Comments to Middle Miocene closure of the Central American Seaway

In a recent paper proposing an early (mid-Miocene) closure of the Central American Seaway (CAS), Montes et al. 2015 (1) disregard existing paleogeographic data that invalidate Panama as a source for zircons, and inappropriately ignore the evidence for trans-isthmian marine connections until 4-3 Ma. They also fail to cite previous work (2, 3), that had reconstructed the Central American arc already docked with South America by 12 Ma. Montes et al. 2015 (1) (Fig. 1) disregard the Atrato-San Juan sedimentary basin (3), a shallowing Oligocene to Pliocene, Pacific to Caribbean seaway (3, 4, 5). This deep graben (6) is filled with thousands of meters of Pre-Pliocene marine sediments (3, 5, 6) that now occupy a lowland between the Baudo uplift to the west and the Western Cordillera to the east. The Mande Batholith and numerous Eocene and younger volcanic rocks (4), the most proximal source of the zircons, are situated to the east of this seaway and would have shed zircons eastward towards the Cordillera Central. There is no evidence for any rivers crossing the seaway (3, 5), and thus no Panamanian source of zircons. Instead this seaway is evidence of a significant marine connection between the Pacific and Atlantic oceans into the Pliocene. The authors assume that the middle Miocene closure of the CAS effectively creates a continuous land bridge connecting North and South America and separating the Atlantic from the Pacific. They acknowledge, but then discount, marine connections across the Isthmus until 4-3 Ma even though these satisfactorily explain (Coates and Stallard, 2014 (6)) the oceanographic, molecular and Great American Biological Interchange events ignore unexplained by Montes et al. 2015. Only by conspicuously ignoring these events can they imply that the Isthmus was formed at 15-13 Ma. References 1. C. Montes et al., Middle Miocene closure of the Central American Seaway. Science 348, 226-229 (2015). 2. A. G. Coates, R. F. Stallard, How old is the Isthmus of Panama? B Mar Sci 89, 801-813 (2013). 3. H. Duque-Caro, The Choco Block in the northwestern corner of South America: Structural, tectonostratigraphic, and paleogeographic implications. Journal of South American Earth Sciences 3, 71-84 (1990). 4. H. Duque-Caro, Neogene stratigraphy, paleoceanography and paleobiogeography in northwest South America and the evolution of the Panama Seaway. Pal

Science↗
USGS2008

Potential environmental contaminant risks to avian species at important bird areas in the northeastern United States

Environmental contaminants can have profound effects on birds, acting from the molecular through population levels of biological organization. An analysis of potential contaminant threats was undertaken at 52 Important Bird Areas (IBAs) within the northeastern Atlantic coast drainage. Using geographic information system methodology, data layers describing or integrating contamination (impaired waters, fish or wildlife consumption advisories, toxic release inventory sites, and estimates of pesticide use) were overlaid on buffered IBA boundaries, and the relative threat at each site was ranked. The most threatened sites include Jefferson National Forest (NF), Stewart B. McKinney National Wildlife Refuge (NWR), Great Dismal Swamp NWR, Blue Ridge Parkway, Shenandoah National Park (NP), Adirondack Park, Edwin B. Forsythe NWR, George Washington NF, Green Mountain NF, Long Island Piping Plover Beaches, and Merrymeeting Bay. These sites exhibited moderate to high percentages of impaired waters and had fish consumption advisories related to mercury and polychlorinated biphenyls, and were located in counties with substantial pesticide use. Endangered, threatened and Watch List bird species are present at these sites. The Contaminant Exposure and Effects--Terrestrial Vertebrates database was searched within buffered IBA boundaries, and for a moderate number of sites there was concordance between the perceived risk and contaminant exposure. Several of the IBAs with apparently substantial contaminant threats had no avian ecotoxicological data (e.g., George Washington NF, Shenandoah NP). Based upon this screening level risk assessment, contaminant biomonitoring is warranted at such sites, and data generated from these efforts should foster natural resource management activities.

Integrated Environmental Assessment and Management↗
USGS2007

Potential environmental contaminant risks to avian species at important bird areas in the northeastern United States

Environmental contaminants, acting at molecular through population levels of biological organization, can have profound effects upon birds. A screening level risk assessment was conducted that examined potential contaminant threats at 52 Important Bird Areas (IBAs) in the northeastern Atlantic coast drainage. Using geographic information system methodology, data layers describing or integrating pollutant hazards (impaired waters, fish or wildlife consumption advisories, toxic release inventory data, estimated pesticide use and hazard) were overlaid on buffered IBA boundaries, and the relative contaminant threat for each site was ranked. The 10 sites identified as having the greatest contaminant threats included Jefferson National Forest, Stewart B. McKinney National Wildlife Refuge, Great Dismal Swamp National Wildlife Refuge, Blue Ridge Parkway, Shenandoah National Park, Adirondack Park, Edwin B. Forsythe National Wildlife Refuge, George Washington National Forest, Green Mountain National Forest, and Long Island Piping Plover Beaches. These sites accounted for over 50% of the entire study area, and in general had moderate to high percentages of impaired waters, fish consumption advisories related to mercury and PCBs, and were located in counties with substantial application rates of pesticides known to be toxic to birds. Avian species at these IBAs include Federally endangered Roseate terns (Sterna dougallii), threatened piping plovers (Charadrius melodus), neotropical migrants, Bicknell?s thrush (Catharus bicknelli), Swainson?s warbler (Limnothlypis swainsonii) and wintering brant geese (Branta bernicla). Extant data for free-ranging birds from the Contaminant Exposure and Effects--Terrestrial Vertebrates database were examined within the buffered boundaries of each IBA, and for a moderate number of sites there was qualitative concordance between the perceived risk and actual contaminant exposure data. However, several of the IBAs with substantial contaminant hazards (e.g., Blue Ridge Parkway, George Washington National Forest, Shenandoah National Park) had no recent avian ecotoxicological data. Contaminant biomonitoring is warranted at such sites, and data generated from such efforts should foster natural resource management activities.

Book chapter↗
USGS1999

Tadpoles: the Biology of Anuran Larvae

The recent alarming declines in amphibian populations worldwide and the suitability of amphibians for use in answering research questions in disciplines as diverse as molecular systematics, animal behavior, ecology, and evolutionary biology have focused enormous attention on tadpoles. Yet despite this growing interest, relatively little is known about these fascinating creatures. n this invaluable reference, leading experts on tadpole biology relate what we currently know about tadpoles and what we might learn from them in the future. Tadpoles provides detailed summaries of tadpole morphology, development, behavior, ecology, and environmental physiology; explores the evolutionary consequences of the tadpole stage; synthesizes available information on their biodiversity, and presents a standardized terminology and an exhaustive literature review of tadpole biology.

Book↗
USGS1978

Rock pushing and sampling under rocks on Mars

Viking Lander 2 acquired samples on Mars from beneath two rocks, where living organisms and organic molecules would be protected from ultraviolet radiation. Selection of rocks to be moved was based on scientific and engineering considerations, including rock size, rock shape, burial depth, and location in a sample field. Rock locations and topography were established using the computerized interactive video-stereophotogrammetric system and plotted on vertical profiles and in plan view. Sampler commands were developed and tested on Earth using a full-size lander and surface mock-up. The use of power by the sampler motor correlates with rock movements, which were by plowing, skidding, and rolling. Provenance of the samples was determined by measurements and interpretation of pictures and positions of the sampler arm. Analytical results demonstrate that the samples were, in fact, from beneath the rocks. Results from the Gas Chromatograph-Mass Spectrometer of the Molecular Analysis experiment and the Gas Exchange instrument of the Biology experiment indicate that more adsorbed(?) water occurs in samples under rocks than in samples exposed to the sun. This is consistent with terrestrial arid environments, where more moisture occurs in near-surface soil un- der rocks than in surrounding soil because the net heat flow is toward the soil beneath the rock and the rock cap inhibits evaporation. Inorganic analyses show that samples of soil from under the rocks have significantly less iron than soil exposed to the sun. The scientific significance of analyses of samples under the rocks is only partly evaluated, but some facts are clear. Detectable quantities of martian organic molecules were not found in the sample from under a rock by the Molecular Analysis experiment. The Biology experiments did not find definitive evidence for Earth-like living organisms in their sample. Significant amounts of adsorbed water may be present in the martian regolith. The response of the soil from under a rock to the aqueous nutrient in the Gas Exchange instrument indicates that adsorbed water and hydrates play an important role in the oxidation potential of the soil. The rock surfaces are strong, because they did not scratch, chip or spall when the sampler pushed them. Fresh surfaces of soil and the undersides of rocks were exposed so that they could be imaged in color. A ledge of soil adhered to one rock that tilted, showing that a crust forms near the surface of Mars. The reason for low amounts of iron in the sampIes from under the rocks is not known at this time.

Professional Paper↗
USGS2026

Effects of carbamazepine to visual function in early life stage fish

The frequent detection of pharmaceuticals and personal care products (PPCPs) in the environment raises concern for aquatic systems. Carbamazepine (CBZ), an antiepileptic drug, is among the most detected PPCP globally, with concentrations in surface water exceeding those that induce toxicity to aquatic organisms. Non-targeted transcriptomic profiling was conducted in zebrafish ( Danio rerio ) larvae exposed to 0, 1, 5, 10, or 50 μg/L CBZ from 2 h post fertilization (hpf) through hatching, and then sampled at 48, 72, or 144 hpf. Transcriptomic profiles were annotated and characterized with in silico bioinformatic software to assess top enriched pathways and identify targets of environmentally relevant concentrations of CBZ and anchor molecular effects to higher levels of biological organization. Based on this analysis, CBZ was predicted to impair visual perception and sensory system development. The number of eye saccades, determined with a visually mediated behavioral assay, optokinetic response, was significantly reduced in 144 hpf larvae exposed to concentrations as low as 1 μg/L CBZ. These results indicate that environmentally relevant concentrations of CBZ may target and impact processes involved in visual function in fish.

Environmental Research↗
USGS2006

Integrating bioavailability approaches into waste rock evaluations

The presence of toxic metals in soils affected by mining, industry, agriculture and urbanization, presents problems to human health, the establishment and maintenance of plant and animal habitats, and the rehabilitation of affected areas. A key to managing these problems is predicting the fraction of metal in a given soil that will be biologically labile, and potentially harmful ('bioavailable'). The molecular form of metals and metalloids, particularly the uncomplexed (free) form, controls their bioavailability and toxicity in solution. One computational approach for determining bioavailability, the biotic ligand model (BLM), takes into account not only metal complexation by ligands in solution, but also competitive binding of hardness cations (Ca 2+,Mg 2+,) and metal ions to biological receptor sites. The more direct approach to assess bioavailability is to explicitly measure the response of an organism to a contaminant. A number of microbial enzyme tests have been developed to assess the impact of pollution in a rapid and procedurally simple way. These different approaches in making bioavailability predictions may have value in setting landuse priorities, remediation goals, and habitat reclamation strategies.

Conference Paper↗
USGS2014

Genetic tools for wildlife management

Granted interim status in November, 2013, The Wildlife Society’s (TWS) Molecular Ecology Working Group aims to promote scientific advancement by applying molecular techniques to wildlife ecology, management, and conservation. The working group—composed of sci - entists from diverse backgrounds—met for the first time in Pittsburgh at the TWS Annual Conference held in October. Our overarching goal is to enhance awareness of molecular ecology and genetic applica - tions to wildlife biology and act as an informational and networking resource. During the group’s interim status, which runs for three years, we intend to focus on a broad scope of molecular ecology that is applicable to wildlife including genetic and ge - nomic methods, conservation genetics, non-invasive genetic population monitoring, landscape genetics, evolutionary genetics, and molecular forensics

The Wildlife Professional↗
USGS1971

Fluid inclusions in quartz crystals from South-West Africa

Quartz crystals from calcite veins of unknown age in Precambrian metasedimentary rocks at Geiaus No. 6 and Aukam farms in South-West Africa contain both primary and secondary inclusions filled with one or a variable combination of: organic liquid, moderately saline aqueous liquid, dark-colored solid, and vapor. Analysis of these materials by microscopy and by gas chromatography and mass spectrometry shows the presence of constituents of both low and high molecular weights. The former include CH 4 , C 2 H 6 , C 3 H 8 and possibly C 4 H 10 as well as CO, CO 2 , H 2 O, N 2 and H 2 . High molecular weight components are dominantly n-alkanes and isoprenoid hydrocarbons. The n-alkanes range from at least n-C 10 to n-C 33 . Concentrations of n-alkanes larger than n-C 17 decrease regularly with increasing carbon number. An homologous series of isoprenoid hydrocarbons ranging from at least C 14 to C 20 is present in unusually high concentrations. Pristane (C 19 ) is most abundant, and C 17 isoprenoid is least abundant. The molecular composition and distribution of hydrocarbons suggest biological precursors for these components. Consideration of data provided by freezing, crushing and heating experiments suggests that the pressures at the time these in part supercritical fluids were trapped probably exceeded 30–40 atm, and the minimum trapping temperature was about 120–160°C. Both primary and secondary inclusions apparently containing only organic materials were trapped by the growth of the host quartz from aqueous solution. The data obtained neither prove nor preclude Precambrian, Paleozoic or younger sources for the organic materials.

Geochimica et Cosmochimica Acta↗
USGS2015

Trust Species and Habitat Branch: using the innovative approaches of today to conserve biodiversity for tomorrow

Some of the biggest challenges facing wildlife today are changes to their environment from both natural and anthropogenic causes. Natural resource managers, planners, policy makers, industry and private landowners must make informed decisions and policies regarding management, conservation, and restoration of species, habitats, and ecosystem function in response to these changes. Specific needs include (1) a better understanding of population status and trends; (2) understanding of species’ habitat needs and roles in supporting ecosystem functions; (3) the ability to assess species’ responses to environmental changes and predict future responses; and (4) the development of innovative techniques and tools to better understand, minimize or prevent any unintended consequences of environmental change. The Trust Species and Habitats Branch of the Fort Collins Science Center includes a diverse group of scientists encompassing both traditional and specialized expertise in wildlife biology, ecosystem ecology, quantitative ecology, disease ecology, molecular genetics, and stable isotope geochemistry. Using our expertise and collaborating with others around the world, our goal is to provide the information, tools, and technologies that our partners need to support conservation, management, and restoration of terrestrial vertebrate populations, habitats, and ecosystem function in a changing world.

Fact Sheet↗
USGS2013

How old is the Isthmus of Panama?

The Standard Model of the formation of the Isthmus of Panama proposes that final closure occurred at 4–3 Ma. The model is based on evidence from studies of marine stratigraphy, fossil sequences, divergent molecular phylogenies, the timing of the Great American Biological Interchange (GABI), and proxies for marine paleosalinity, paleobathymetry, productivity, and paleotemperatures. The new model uses cooling of magmas in the Cretaceous to Early Miocene Central American Volcanic arc to propose Eocene emergence of the discrete structural blocks of the arc and then U/Pb dating, paleomagnetic pole rotations, and atlantic sea-floor anomalies to reconfigure the blocks for different time slices back to 25 Ma. Closure is proposed at 15 Ma, because by this time the alignment of the blocks leaves no space for trans-isthmian marine passages. We propose that the Indonesian Australian Archipelago (IAA) provides a model for the Central American arc between 15 and 3 Ma because it accounts for the extensive marine interchange between the Pacific and Indian oceans through few and narrow passages while maintaining a complete separation of the terrestrial faunas (Wallace and Lydekker lines) of the two continental platforms of Sunda and Sahul. Using the Indonesian Volcanic arc as a model, we can now accommodate the general tectonic configuration and much of the emergence of the new model, while accounting for the marine fossil record, the molecular evidence of rapid recent speciation, and the delayed Great American Biotic Interchange that the New Model fails to explain.

Bulletin of Marine Science↗
USGS2014

Tick control: Trapping, bio-control, host management and other alternative strategies

Biology of Ticks is the most comprehensive work on tick biology and tick-borne diseases. This second edition is a multi-authored work, featuring the research and analyses of renowned experts across the globe. Spanning two volumes, the book examines the systematics, biology, structure, ecological adaptations, evolution, genomics and the molecular processes that underpin the growth, development and survival of these important disease-transmitting parasites. Also discussed is the remarkable array of diseases transmitted (or caused) by ticks, as well as modern methods for their control. This book should serve as a modern reference for students, scientists, physicians, veterinarians and other specialists. Volume II includes chapters on the ecology of non-nidicolous and nidicolous ticks, genetics and genomics (including the genome of the Lyme disease vector Ixodes scapularis) and immunity, including host immune responses to tick feeding and tick-host interactions, as well as the tick's innate immune system that prevents and/or controls microbial infections. Six chapters cover in depth the many diseases caused by the major tick-borne pathogens, including tick-borne protozoa, viruses, rickettsiae of all types, other types of bacteria (e.g., the Lyme disease agent) and diseases related to tick paralytic agents and toxins. The remaining chapters are devoted to tick control using vaccines, acaricides, repellents, biocontrol, and, finally, techniques for breeding ticks in order to develop tick colonies for scientific study.

Book chapter↗
USGS2015

Fecal indicator organism modeling and microbial source tracking in environmental waters: Chapter 3.4.6

Mathematical models have been widely applied to surface waters to estimate rates of settling, resuspension, flow, dispersion, and advection in order to calculate movement of particles that influence water quality. Of particular interest are the movement, survival, and persistence of microbial pathogens or their surrogates, which may contaminate recreational water, drinking water, or shellfish. Most models devoted to microbial water quality have been focused on fecal indicator organisms (FIO), which act as a surrogate for pathogens and viruses. Process-based modeling and statistical modeling have been used to track contamination events to source and to predict future events. The use of these two types of models require different levels of expertise and input; process-based models rely on theoretical physical constructs to explain present conditions and biological distribution while data-based, statistical models use extant paired data to do the same. The selection of the appropriate model and interpretation of results is critical to proper use of these tools in microbial source tracking. Integration of the modeling approaches could provide insight for tracking and predicting contamination events in real time. A review of modeling efforts reveals that process-based modeling has great promise for microbial source tracking efforts; further, combining the understanding of physical processes influencing FIO contamination developed with process-based models and molecular characterization of the population by gene-based (i.e., biological) or chemical markers may be an effective approach for locating sources and remediating contamination in order to protect human health better.

Book chapter↗