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At least 1,027 records · Page 57Linked to original sources

Characterization of a linear DNA plasmid from the filamentous fungal plant pathogen Glomerella musae [Anamorph: Colletotrichum musae (Berk. and Curt.) arx.]

A 7.4-kilobase (kb) DNA plasmid was isolated from Glomerella musae isolate 927 and designated pGML1. Exonuclease treatments indicated that pGML1 was a linear plasmid with blocked 5' termini. Cell-fractionation experiments combined with sequence-specific PCR amplification revealed that pGML1 resided in mitochondria. The pGML1 plasmid hybridized to cesium chloride-fractionated nuclear DNA but not to A + T-rich mitochondrial DNA. An internal 7.0-kb section of pGML1 was cloned and did not hybridize with either nuclear or mitochondrial DNA from G. musae. Sequence analysis revealed identical terminal inverted repeats (TIR) of 520 bp at the ends of the cloned 7.0-kb section of pGML1. The occurrence of pGML1 did not correspond with the pathogenicity of G. musae on banana fruit. Four additional isolates of G. musae possessed extrachromosomal DNA fragments similar in size and sequence to pGML1.

Current Genetics↗

Cutaneous and diphtheritic avian poxvirus infection in a nestling Southern Giant Petrel (Macronectes giganteus) from Antarctica

The Southern giant petrel ( Macronectes giganteus ) is declining over much of its range and currently is listed as vulnerable to extinction by the International Union for the Conservation of Nature (IUCN). Island-specific breeding colonies near Palmer Station, Antarctica, have been monitored for over 30 years, and because this population continues to increase, it is critically important to conservation. In austral summer 2004, six diseased giant petrel chicks were observed in four of these colonies. Diseased chicks were 6–9 weeks old and had multiple proliferative nodules on their bills and skin. One severely affected chick was found dead on the nest and was salvaged for necropsy. Histopathological examination of nodules from the dead chick revealed epithelial cell hyperplasia and hypertrophy with numerous eosinophilic intracytoplasmic inclusions (Böllinger bodies). A poxvirus was isolated from multiple nodules. Poxviral infection has not been reported in this species, and the reason for its emergence and its potential impact on the population are not yet known.

Polar Biology↗

Characterizing lesions in corals from American Samoa

The study of coral disease has suffered from an absence of systematic approaches that are commonly used to determine causes of diseases in animals. There is a critical need to develop a standardized and portable nomenclature for coral lesions in the field and to incorporate more commonly available biomedical tools in coral disease surveys to determine the potential causes of lesions in corals. We characterized lesions in corals from American Samoa based on gross and microscopic morphology and classified them as discoloration, growth anomalies, or tissue loss. The most common microscopic finding in corals manifesting discoloration was the depletion of zooxanthellae, followed by necrosis, sometimes associated with invasive algae or fungi. The most common microscopic lesion in corals manifesting tissue loss was cell necrosis often associated with algae, fungi, or protozoa. Corals with growth anomaly had microscopic evidence of hyperplasia of gastrovascular canals, followed by necrosis associated with algae or metazoa (polychaete worms). Several species of apparently normal corals also had microscopic changes, including the presence of bacterial aggregates or crustacea in tissues. A single type of gross lesion (e.g., discoloration) could have different microscopic manifestations. This phenomenon underlines the importance of using microscopy to provide a more systematic description of coral lesions and to detect potential pathogens associated with these lesions.

Coral Reefs↗

Pathological drivers of coral diseases across the Arabian Peninsula

Increasing trends of coral mortality are a challenge to coral reef management worldwide, and a need exists to identify the causes and pathways involved. Pathology is useful to help decipher potential causes of mortality in animals, because it illuminates agents associated with lesions and gives insights on the nature of how a host responds to said agents. To better understand the nature of threats facing corals in the Arabian Peninsula, we performed gross and microscopic pathology on corals from Saudi Arabia, Qatar, and the United Arab Emirates. Among 321 coral fragments examined from 21 genera, tissue loss was the most common lesion seen in 31% of samples, reflecting its widespread presence on reefs from the Arabian Peninsula. Histologically, 68% of lesions exhibited necrosis, predominantly in the basal body wall and surface body wall. Endolithic filamentous microalgae and sponges, originating from the skeleton, were associated with 57% and 39% of lesions, respectively, and were often linked to necrosis and hyaline membrane formation. Cell-associated microbial aggregates and coccidia were detected mainly in Acropora, Pocillopora , and Porites but were not associated with adverse host response. Notably, 69–100% of fragments showing lesions were female likely reflecting the temporal reproductive life history of corals in the region. Our findings highlight endolithic organisms as major contributors to coral tissue degradation in the Arabian Peninsula. Future studies might focus on drivers of endolithic microalgal and sponge dynamics in the region and their role in coral reef health.

Coral Reefs↗

Modeling the mid-Piacenzian warm climate using the water isotope-enabled Community Earth System Model (iCESM1.2-ITPCAS)

The mid-Piacenzian Warm Period (MPWP, ~ 3.264–3.025 Ma) is the most recent example of a persistently warmer climate in equilibrium with atmospheric CO 2 concentrations similar to today. Towards studying patterns and dynamics of a warming climate the MPWP is often compared to today. Following the Pliocene Model Intercomparison Project, Phase 2 (PlioMIP2) protocol we prepare a water isotope-enabled Community Earth System Model (iCESM1.2) simulation that is warmer and wetter than the PlioMIP2 multi-model ensemble (MME). While our simulation resembles PlioMIP2 MME in many aspects we find added insights. (1) Considerable warmth at high latitudes exceeds previous simulations. Polar amplification (PA) is comparable to proxies, enabled by iCESM1.2’s high climate sensitivity and a distinct method of ocean initialization. (2) Major driver of warmth is the downward component of clear-sky surface long-wave radiation (Δ T rlds_clearsky ). (3) In iCESM1.2 modulated dominance of dynamic (δDY) processes causes different low-latitude (~ 30 S°–10°N) precipitation response than the PlioMIP2 MME, where thermodynamic processes (δTH) dominate. (4) Modulated local condensation leads to lower δ18O p across tropical Indian Ocean and surrounding Asian-African-Australian monsoon regions. (5) We find contrasting changes in tropical atmospheric circulations (Hadley and Walker cells). Anomalous regional meridional (zonal) circulation, forced by changes in tropical-subtropical (tropical) diabatic processes, presents a more comprehensive perspective than explaining weakened and expanded Hadley circulation (strengthened and westward-shifted Walker circulation) via static stability. (6) Enhanced Atlantic meridional overturning circulation owes to a closed Bering Strait.

Climate Dynamics↗

Associations of intestinal helminth infections with health parameters of spring-migrating female lesser scaup (Aythya affinis) in the upper Midwest, USA

Thousands of lesser scaup ( Aythya affinis ) die during spring and fall migrations through the upper Midwest, USA, from infections with Cyathocotyle bushiensis and Sphaeridiotrema spp. (Class: Trematoda) after ingesting infected intermediate hosts, such as non-native faucet snails ( Bithynia tentaculata ). The lesser scaup is a species of conservation concern and is highly susceptible to these infections. We collected female lesser scaup from spring migratory stopover locations throughout Illinois and Wisconsin and assessed biochemical and morphological indicators of health in relation to intestinal helminth loads. Helminth species diversity, total trematode abundance, and the infection intensities of the trematodes C. bushiensis and Sphaeridiotrema spp. were associated with percent body fat, blood metabolites, hematological measures, and an index of foraging habitat quality. Helminth diversity was negatively associated with percent body fat, albumin concentrations, and monocytes, whereas glucose concentrations displayed a slight, positive association. Total trematode abundance was negatively associated with blood concentrations of non-esterified fatty acids and albumin. Infections of C. bushiensis were positively related to basophil levels, whereas Sphaeridiotrema spp. infection intensity was negatively associated with packed cell volume and foraging habitat quality. Thus, commonly measured health metrics may indicate intestinal parasite infections and help waterfowl managers understand overall habitat quality. Intestinal parasitic loads offer another plausible mechanism underlying the spring condition hypothesis.

Parasitology Research↗

Novel avian papillomaviruses identified in a south polar skua sampled on Ross Island, Antarctica

Papillomaviruses are small circular DNA viruses that infect epithelial cells of their hosts. Avian papillomaviruses are poorly sampled/documented compared to those infecting humans. We used a viral metagenomic approach to identify viruses from the oral swab taken from a deceased south polar skua ( Stercorarius maccormicki ) found at Cape Royds, Ross Island, Antarctica in late 2024. We identified three papillomaviruses and determined their complete genomes, Stercorarius maccormicki papillomavirus (SmacPV) 1-3. SmacPV1 is the most divergent of the three SmacPVs, sharing 62% genome-wide pairwise identity to SmacPV2 and SmacPV3 and <63.5% to other avian papillomaviruses. The genomes of SmacPV2 and SmacPV3 represent two new papillomavirus types sharing 82.4% genome-wide pairwise identity with each other and <72% to other papillomaviruses. SmacPV2 and SmacPV3 phylogenetically cluster with sequences of the Rissa tridactyla papillomavirus 1 from black-legged kittiwake ( Rissa tridactyla ), Larus smithsonianus papillomavirus 1 from American herring gull ( Larus smithsonianus ) and Fratercula arctica papillomavirus 1 from Atlantic puffin ( Fratercula arctica ), and they collectively represent a new papillomavirus species. These are the first papillomaviruses to be identified in Stercorarius spp . and add to the handful of known papillomaviruses in identified avian species. We also expand the known host range of papillomaviruses in Antarctic animals, which previously included Adélie penguins ( Pygoscelis adeliae ), Weddell seals ( Leptonychotes weddellii ), Antarctic fur seals ( Arctocephalus gazella ), leopard seals ( Hydrurga leptonyx ) and emerald notothen ( Trematomus bernacchii ).

Archives of Virology↗

Adaptive inference for distinguishing credible from incredible patterns in nature

Strong inference is a powerful and rapid tool that can be used to identify and explain patterns in molecular biology, cell biology, and physiology. It is effective where causes are single and separable and where discrimination between pairwise alternative hypotheses can be determined experimentally by a simple yes or no answer. But causes in ecological systems are multiple and overlapping and are not entirely separable. Frequently, competing hypotheses cannot be distinguished by a single unambiguous test, but only by a suite of tests of different kinds, that produce a body of evidence to support one line of argument and not others. We call this process "adaptive inference". Instead of pitting each member of a pair of hypotheses against each other, adaptive inference relies on the exuberant invention of multiple, competing hypotheses, after which carefully structured comparative data are used to explore the logical consequences of each. Herein we present an example that demonstrates the attributes of adaptive inference that have developed out of a 30-year study of the resilience of ecosystems.

Ecosystems↗

Ecosystem responses to nitrogen deposition in the Colorado Front Range

We asked whether 3–5 kg N y −1 atmospheric N deposition was sufficient to have influenced natural, otherwise undisturbed, terrestrial and aquatic ecosystems of the Colorado Front Range by comparing ecosystem processes and properties east and west of the Continental Divide. The eastern side receives elevated N deposition from urban, agricultural, and industrial sources, compared with 1–2 kg N y −1 on the western side. Foliage of east side old-growth Englemann spruce forests have significantly lower C:N and lignin:N ratios and greater N:Mg and N:P ratios. Soil % N is higher, and C:N ratios lower in the east side stands, and potential net N mineralization rates are greater. Lake NO 3 concentrations are significantly higher in eastern lakes than western lakes. Two east side lakes studied paleolimnologically revealed rapid changes in diatom community composition and increased biovolumes and cell concentrations. The diatom flora is now representative of increased disturbance or eutrophication. Sediment nitrogen isotopic ratios have become progressively lighter over the past 50 years, coincident with the change in algal flora, possibly from an influx of isotopically light N volatilized from agricultural fields and feedlots. Seventy-five percent of the increased east side soil N pool can be accounted for by increased N deposition commensurate with human settlement. Nitrogen emissions from fixed, mobile, and agricultural sources have increased dramatically since approximately 1950 to the east of the Colorado Front Range, as they have in many parts of the world. Our findings indicate even slight increases in atmospheric deposition lead to measurable changes in ecosystem properties.

Colorado↗

Map visualization of groundwater withdrawals at the sub-basin scale

A simple method is proposed to visualize the magnitude of groundwater withdrawals from wells relative to user-defined water-resource metrics. The map is solely an illustration of the withdrawal magnitudes, spatially centered on wells—it is not capture zones or source areas contributing recharge to wells. Common practice is to scale the size (area) of withdrawal well symbols proportional to pumping rate. Symbols are drawn large enough to be visible, but not so large that they overlap excessively. In contrast to such graphics-based symbol sizes, the proposed method uses a depth-rate index (length per time) to visualize the well withdrawal rates by volumetrically consistent areas, called “footprints”. The area of each individual well’s footprint is the withdrawal rate divided by the depth-rate index. For example, the groundwater recharge rate could be used as a depth-rate index to show how large withdrawals are relative to that recharge. To account for the interference of nearby wells, composite footprints are computed by iterative nearest-neighbor distribution of excess withdrawals on a computational and display grid having uniform square cells. The map shows circular footprints at individual isolated wells and merged footprint areas where wells’ individual footprints overlap. Examples are presented for depth-rate indexes corresponding to recharge, to spatially variable stream baseflow (normalized by basin area), and to the average rate of water-table decline (scaled by specific yield). These depth-rate indexes are water-resource metrics, and the footprints visualize the magnitude of withdrawals relative to these metrics.

Hydrogeology Journal↗

The potential for free and mixed convection in sedimentary basins

Free thermal convection and mixed convection are considered as potential mechanisms for mass and heat transport in sedimentary basins. Mixed convection occurs when horizontal flows (forced convection) are superimposed on thermally driven flows. In cross section, mixed convection is characterized by convection cells that migrate laterally in the direction of forced convective flow. Two-dimensional finite-element simulations of variable-density groundwater flow and heat transport in a horizontal porous layer were performed to determine critical mean Rayleigh numbers for the onset of free convection, using both isothermal and semi-conductive boundaries. Additional simulations imposed a varying lateral fluid flux on the free-convection pattern. Results from these experiments indicate that forced convection becomes dominant, completely eliminating buoyancy-driven circulation, when the total forced-convection fluid flux exceeds the total flux possible due to free convection. Calculations of the thermal rock alteration index (RAI=q·∇T) delineate the patterns of potential diagenesis produced by fluid movement through temperature gradients. Free convection produces a distinct pattern of alternating positive and negative RAIs, whereas mixed convection produces a simpler layering of positive and negative values and in general less diagenetic alteration.

Hydrogeology Journal↗

Carbon isotope turnover as a measure of arrival time in migratory birds

Arrival time on breeding or non-breeding areas is of interest in many ecological studies exploring fitness consequences of migratory schedules. However, in most field studies, it is difficult to precisely assess arrival time of individuals. Here, we use carbon isotope turnover in avian blood as a technique to estimate arrival time for birds switching from one habitat or environment to another. Stable carbon isotope ratios (&delta; 13 C) in blood assimilate to a new equilibrium following a diet switch according to an exponential decay function. This relationship can be used to determine the time a diet switch occurred if &delta; 13 C of both the old and new diet are known. We used published data of captive birds to validate that this approach provides reliable estimates of the time since a diet switch within 1&ndash;3 weeks after the diet switch. We then explored the utility of this technique for King Eiders ( Somateria spectabilis ) arriving on terrestrial breeding grounds after wintering and migration at sea. We estimated arrival time on breeding grounds in northern Alaska (95% CI) from red blood cell &delta; 13 C turnover to be 4&ndash;9 June. This estimate overlapped with arrival time of birds from the same study site tracked with satellite transmitters (5&ndash;12 June). Therefore, we conclude that this method provides a simple yet reliable way to assess arrival time of birds moving between isotopically distinct environments.

Journal of Ornithology↗

Observations on the use of membrane filtration and liquid impingement to collect airborne microorganisms in various atmospheric environments

The influence of sample-collection-time on the recovery of culturable airborne microorganisms using a low-flow-rate membrane-filtration unit and a high-flow-rate liquid impinger were investigated. Differences in recoveries were investigated in four different atmospheric environments, one mid-oceanic at an altitude of ~10.0 m, one on a mountain top at an altitude of ~3,000.0 m, one at ~1.0 m altitude in Tallahassee, Florida, and one at ~1.0 m above ground in a subterranean-cave. Regarding use of membrane filtration, a common trend was observed: the shorter the collection period, the higher the recovery of culturable bacteria and fungi. These data also demonstrated that lower culturable counts were common in the more remote mid-oceanic and mountain-top atmospheric environments with bacteria, fungi, and total numbers averaging (by sample time or method categories) <3.0 colony-forming units (CFU) m −3 . At the Florida and subterranean sites, the lowest average count noted was 3.5 bacteria CFU m −3 , and the highest averaged 140.4 total CFU m −3 . When atmospheric temperature allowed use, the high-volume liquid impinger utilized in this study resulted in much higher recoveries, as much as 10× greater in a number of the categories (bacterial, fungal, and total CFU). Together, these data illustrated that (1) the high-volume liquid impinger is clearly superior to membrane filtration for aeromicrobiology studies if start-up costs are not an issue and temperature permits use; (2) although membrane filtration is more cost friendly and has a ‘typically’ wider operational range, its limits include loss of cell viability with increased sample time and issues with effectively extracting nucleic acids for community-based analyses; (3) the ability to recover culturable microorganisms is limited in ‘extreme’ atmospheric environments and thus the use of a ‘limited’ methodology in these environments must be taken into account; and (4) the atmosphere culls, i.e., everything is not everywhere.

Aerobiologia↗

Extracellular enzyme kinetics scale with resource availability

Microbial community metabolism relies on external digestion, mediated by extracellular enzymes that break down complex organic matter into molecules small enough for cells to assimilate. We analyzed the kinetics of 40 extracellular enzymes that mediate the degradation and assimilation of carbon, nitrogen and phosphorus by diverse aquatic and terrestrial microbial communities (1160 cases). Regression analyses were conducted by habitat (aquatic and terrestrial), enzyme class (hydrolases and oxidoreductases) and assay methodology (low affinity and high affinity substrates) to relate potential reaction rates to substrate availability. Across enzyme classes and habitats, the scaling relationships between apparent V max and apparent K m followed similar power laws with exponents of 0.44 to 0.67. These exponents, called elasticities, were not statistically distinct from a central value of 0.50, which occurs when the K m of an enzyme equals substrate concentration, a condition optimal for maintenance of steady state. We also conducted an ecosystem scale analysis of ten extracellular hydrolase activities in relation to soil and sediment organic carbon (2,000–5,000 cases/enzyme) that yielded elasticities near 1.0 (0.9 ± 0.2, n = 36). At the metabolomic scale, the elasticity of extracellular enzymatic reactions is the proportionality constant that connects the C:N:P stoichiometries of organic matter and ecoenzymatic activities. At the ecosystem scale, the elasticity of extracellular enzymatic reactions shows that organic matter ultimately limits effective enzyme binding sites. Our findings suggest that one mechanism by which microbial communities maintain homeostasis is regulating extracellular enzyme expression to optimize the short-term responsiveness of substrate acquisition. The analyses also show that, like elemental stoichiometry, the fundamental attributes of enzymatic reactions can be extrapolated from biochemical to community and ecosystem scales.

Biogeochemistry↗

Projections and downscaling of 21st century temperatures, precipitation, radiative fluxes and winds for the southwestern US, with focus on the Lake Tahoe basin

Recent projections of global climate changes in response to increasing greenhouse-gas concentrations in the atmosphere include warming in the Southwestern US and, especially, in the vicinity of Lake Tahoe of from about +3°C to +6°C by end of century and changes in precipitation on the order of 5-10 % increases or (more commonly) decreases, depending on the climate model considered. Along with these basic changes, other climate variables like solar insolation, downwelling (longwave) radiant heat, and winds may change. Together these climate changes may result in changes in the hydrology of the Tahoe basin and potential changes in lake overturning and ecological regimes. Current climate projections, however, are generally spatially too coarse (with grid cells separated by 1 to 2° latitude and longitude) for direct use in assessments of the vulnerabilities of the much smaller Tahoe basin. Thus, daily temperatures, precipitation, winds, and downward radiation fluxes from selected global projections have been downscaled by a statistical method called the constructed-analogues method onto 10 to 12 km grids over the Southwest and especially over Lake Tahoe. Precipitation, solar insolation and winds over the Tahoe basin change only moderately (and with indeterminate signs) in the downscaled projections, whereas temperatures and downward longwave fluxes increase along with imposed increases in global greenhouse-gas concentrations.

Arizona;California;Idaho;Nevada;Oregon;Utah↗

Histologic, immunologic and endocrine biomarkers indicate contaminant effects in fishes of the Ashtabula River

The use of fish as sentinels of aquatic ecosystem health is a biologically relevant approach to environmental monitoring and assessment. We examined the health of the Ashtabula River using histologic, immunologic, and endocrine biomarkers in brown bullhead (BB; Ameiurus nebulosus) and largemouth bass (Micropterus salmoides) and compared fish collected from a reference site (Conneaut Creek). Seasonal analysis was necessary to distinguish differences in fish between the two rivers. Overall BB from the Ashtabula River had a lower condition factor and significantly more macrophage aggregates than those from the reference site. Reduced bactericidal and cytotoxic-cell activity was observed in anterior kidney leukocytes from both BB and largemouth bass from the Ashtabula River. Lower plasma thyroxine and triiodo-L-thyronine in both species in the Ashtabula River indicated disruption of the thyroid axis. Differences in physiological biomarker responses were supported by body burden chemical concentrations when data were analyzed on a seasonal basis. The use of two fish species added a level of rigor that demonstrated biological effects were not exclusive to a single species. The results provide strong evidence that contaminants have affected fish in the Ashtabula River, a Great Lakes Area of Concern, and provide a baseline by which to evaluate remediation activities.

Ohio↗

Effects of urban land-use on largescale stonerollers in the Mobile River Basin, Birmingham, AL

During the spring and fall of 2001 and the spring of 2002 a study was conducted to evaluate the health of the largescale stoneroller ( Campostoma oligolepis) populations in streams along an urban land-use gradient. Sites were selected from a pool of naturally similar sub-basins (eco-region, basin size, and geology) of the Mobile River basin (MRB), using an index of urban intensity derived from infrastructure, socioeconomic, and land-use data. This urban land-use gradient (ULUG) is a multimetric indicator of urban intensity, ranging from 0 (background) to 100 (intense urbanization). Campostoma sp. have been used previously as indicators of stream health and are common species found in all sites within the MRB. Endpoints used to determine the effects of urban land-use on the largescale stoneroller included total glutathione, histology, hepatic apoptosis, condition factor and external lesions. Liver glutathione levels were positively associated with increasing urban land-use (r 2 = 0.94). Histopathological examination determined that some abnormalities and lesions were correlated with the ULUG and generally increased in prevalence or severity with increasing urbanization. Liver macrophage aggregates were positively correlated to the ULUG. The occurrence of nucleosomal ladders (indicating apoptotic cell death) did not correspond with urban intensity in a linear fashion. Apoptosis, as well as prevalence and severity of a myxozoan parasite, appeared to have a hormetic dose–response relationship. The majority of the biomarkers suggested fish health was compromised in areas where the ULUG ≥ 36.

Alabama↗

Biomarker responses of Peromyscus leucopus exposed to lead and cadmium in the Southeast Missouri Lead Mining District

Biomarker responses and histopathological lesions have been documented in laboratory mammals exposed to elevated concentrations of lead and cadmium. The exposure of white-footed mice ( Peromyscus leucopus ) to these metals and the potential associated toxic effects were examined at three contaminated sites in the Southeast Missouri Lead Mining District and at a reference site in MO, USA. Mice from the contaminated sites showed evidence of oxidative stress and reduced activity of red blood cell δ-aminolevulinic acid dehydratase (ALAD). Histological examinations of the liver and kidney, cytologic examination of blood smears, and biomarkers of lipid peroxidation and DNA damage failed to show indications of toxic effects from lead. The biomagnification factor of cadmium (hepatic concentration/soil concentration) at a site with a strongly acid soil was 44 times the average of the biomagnification factors at two sites with slightly alkaline soils. The elevated concentrations of cadmium in the mice did not cause observable toxicity, but were associated with about a 50% decrease in expected tissue lead concentrations and greater ALAD activity compared to the activity at the reference site. Lead was associated with a decrease in concentrations of hepatic glutathione and thiols, whereas cadmium was associated with an increase. In addition, to support risk assessment efforts, we developed linear regression models relating both tissue lead dosages (based on a previously published a laboratory study) and tissue lead concentrations in Peromyscus to soil lead concentrations.

Missouri↗