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James P. Bennett

Publications and source records attributed to James P. Bennett.

At least 19 recordsLinked to original sources
USGS2014

Lichens: Unexpected anti-prion agents?

The prion diseases sheep scrapie and cervid chronic wasting disease are transmitted, in part, via an environmental reservoir of infectivity; prions released from infected animals persist in the environment and can cause disease years later. Central to controlling disease transmission is the identification of methods capable of inactivating these agents on the landscape. We have found that certain lichens, common, ubiquitous, symbiotic organisms, possess a serine protease capable of degrading prion protein (PrP) from prion-infected animals. The protease functions against a range of prion strains from various hosts and reduces levels of abnormal PrP by at least two logs. We have now tested more than 20 lichen species from several geographical locations and from various taxa and found that approximately half of these species degrade PrP. Critical next steps include examining the effect of lichens on prion infectivity and cloning the protease responsible for PrP degradation. The impact of lichens on prions in the environment remains unknown. We speculate that lichens could have the potential to degrade prions when they are shed from infected animals onto lichens or into environments where lichens are abundant. In addition, lichens are frequently consumed by cervids and many other animals and the effect of dietary lichens on prion disease transmission should also be considered.

Arkansas, California, Michigan, Missouri, Oregon, ↗
USGS2012

Prion protein degradation by lichens of the genus Cladonia

It has recently been discovered that lichens contain a serine protease capable of degrading the pathogenic prion protein, the etiological agent of prion diseases such as sheep scrapie and cervid chronic wasting disease. Limited methods are available to degrade or inactivate prion disease agents, especially in the environment, and lichens or their serine protease could prove important for management of these diseases. Scant information is available regarding the presence or absence of the protease responsible for degrading prion protein (PrP) in lichen species and, in this study, we tested the hypothesis that PrP degradation activity in lichens is phylogenetically-based by testing 44 species of Cladonia lichens, a genus for which a significant portion of the phylogeny is well established. We categorized PrP degradation activity among the 44 species (high, moderate, low or none) and found that activity in Cladonia species did not correspond with phylogenetic position of the species. Degradation of PrP did correspond, however, with three classical taxonomic characters within the genus: species with brown apothecia, no usnic acid, and the presence of a cortex. Of the 44 species studied, 18 (41%) had either high or moderate PrP degradation activity, suggesting the protease may be frequent in this genus of lichens.

North America↗
USGS2011

Degradation of the disease-associated prion protein by a serine protease from lichens.

The disease-associated prion protein (PrP TSE ), the probable etiological agent of the transmissible spongiform encephalopathies (TSEs), is resistant to degradation and can persist in the environment. Lichens, mutualistic symbioses containing fungi, algae, bacteria and occasionally cyanobacteria, are ubiquitous in the environment and have evolved unique biological activities allowing their survival in challenging ecological niches. We investigated PrP TSE inactivation by lichens and found acetone extracts of three lichen species ( Parmelia sulcata , Cladonia rangiferina and Lobaria pulmonaria ) have the ability to degrade prion protein (PrP) from TSE-infected hamsters, mice and deer. Immunoblots measuring PrP levels and protein misfolding cyclic amplification indicated at least two logs of reductions in PrP TSE . Degradative activity was not found in closely related lichen species or in algae or a cyanobacterium that inhabit lichens. Degradation was blocked by Pefabloc SC, a serine protease inhibitor, but not inhibitors of other proteases or enzymes. Additionally, we found that PrP levels in PrP TSE -enriched preps or infected brain homogenates are also reduced following exposure to freshly-collected P. sulcata or an aqueous extract of the lichen. Our findings indicate that these lichen extracts efficiently degrade PrP TSE and suggest that some lichens could have potential to inactivate TSE infectivity on the landscape or be a source for agents to degrade prions. Further work to clone and characterize the protease, assess its effect on TSE infectivity and determine which organism or organisms present in lichens produce or influence the protease activity is warranted.

Michigan, Minnesota, Oregon, Wisconsin↗
USGS2010

Lichen diversity changes along the Mississippi River in the Minneapolis-St. Paul urban area

Lichen diversity along the Mississippi River in the Minneapolis-St. Paul urban area was studied in 2008 by sampling 37 localities along the 110-kilometer river basin, resulting in 76 species, which are thought to represent 80% of the complete flora. A significant decrease in lichen diversity toward the urban part of the river basin, as well as the presence of only one cyanolichen suggests that urban factors, e.g. air pollutants and habitat destruction may be affecting lichen diversity. In addition, lichen diversity has significantly decreased from that of 112 years ago, when a study by Fink reported 113 species, and a higher number of genera represented by a single species.

Minnesota↗
USGS2009

Changes in macrolichens of Douglas County, Wisconsin

Macrolichens collected in Douglas County, Wisconsin in the 1940s, 1970s and 2009 are compared in order to determine floristic changes. Species sensitive to disturbance, land use change, and possibly climate that have changed over these time spans are identified and suggested for further monitoring. The total lichen flora of Douglas County is compared with Harris’ 1977 publication of the lichens of the Straits of Mackinac.

Wisconsin↗
USGS2008

Discrimination of lichen genera and species using element concentrations

The importance of organic chemistry in the classification of lichens is well established, but inorganic chemistry has been largely overlooked. Six lichen species were studied over a period of 23 years that were growing in 11 protected areas of the northern Great Lakes ecoregion, which were not greatly influenced by anthropogenic particulates or gaseous air pollutants. The elemental data from these studies were aggregated in order to test the hypothesis that differences among species in tissue element concentrations were large enough to discriminate between taxa faithfully. Concentrations of 16 chemical elements that were found in tissue samples from Cladonia rangiferina, Evernia mesomorpha, Flavopunctelia flaventior, Hypogymnia physodes, Parmelia sulcata, and Punctelia rudecta were analyzed statistically using multivariate discriminant functions and CART analyses, as well as t-tests. Genera and species were clearly separated in element space, and elemental discriminant functions were able to classify 91-100 of the samples correctly into species. At the broadest level, a Zn concentration of 51 ppm in tissues of four of the lichen species effectively discriminated foliose from fruticose species. Similarly, a S concentration of 680 ppm discriminated C. rangiferina and E. mesomorpha , and a Ca concentration of 10 436 ppm discriminated H. physodes from P. sulcata . For the three parmelioid species, a Ca concentration >32 837 ppm discriminated Punctelia rudecta from the other two species, while a Zn concentration of 56 ppm discriminated Parmelia sulcata from F. flaventior . Foliose species also had higher concentrations than did fruticose species of all elements except Na. Elemental signatures for each of the six species were developed using standardized means. Twenty-four mechanisms explaining the differences among species are summarized. Finally, the relationships of four species based on element concentrations, using additive-trees clustering of a Euclidean-distance matrix, produced identical relationships as did analyses based on secondary product chemistry that used additive-trees clustering of a Jaccard similarity matrix. At least for these six species, element composition has taxonomic significance, and may be useful for discriminating other taxa.

Great Lakes↗
USGS2005

A pre-dam-removal assessment of sediment transport for four dams on the Kalamazoo River between Plainwell and Allegan, Michigan

Four dams on the Kalamazoo River between the cities of Plainwell and Allegan, Mich., are in varying states of disrepair. The Michigan Department of Environmental Quality (MDEQ) and U.S. Environmental Protection Agency (USEPA) are considering removing these dams to restore the river channels to pre-dam conditions. This study was initiated to identify sediment characteristics, monitor sediment transport, and predict sediment resuspension and deposition under varying hydraulic conditions. The mathematical model SEDMOD was used to simulate streamflow and sediment transport using three modeling scenarios: (1) sediment transport simulations for 730 days (Jan. 2001 to Dec. 2002), with existing dam structures, (2) sediment transport simulations based on flows from the 1947 flood at the Kalamazoo River with existing dam structures, and (3) sediment transport simulations based on flows from the 1947 flood at the Kalamazoo River with dams removed. Sediment transport simulations based on the 1947 flood hydrograph provide an estimate of sediment transport rates under maximum flow conditions. These scenarios can be used as an assessment of the sediment load that may erode from the study reach at this flow magnitude during a dam failure. The model was calibrated using suspended sediment as a calibration parameter and root mean squared error (RMSE) as an objective function. Analyses of the calibrated model show a slight bias in the model results at flows higher than 75 m 3 /s; this means that the model-simulated suspended-sediment transport rates are higher than the observed rates; however, the overall calibrated model results show close agreement between simulated and measured values of suspended sediment. Simulation results show that the Kalamazoo River sediment transport mechanism is in a dynamic equilibrium state. Model results during the 730-day simulations indicate significant sediment erosion from the study reach at flow rates higher than 55 m 3 /s. Similarly, significant sediment deposition occurs during low to average flows (monthly mean flows between 25.49 m 3 /s and 50.97 m 3 /s) after a high-flow event. If the flow continues to stay in the low to average range the system shifts towards equilibrium, resulting in a balancing effect between sediment deposition and erosion rates. The 1947 flood-flow simulations show approximately 30,000 m 3 more instream sediments erosion for the first 21 days of the dams removed scenario than for the existing-dams scenario, with the same initial conditions for both scenarios. Application of a locally weighted regression smoothing (LOWESS) function to simulation results of the dams removed scenario indicates a steep downtrend with high sediment transport rates during the first 21 days. In comparison, the LOWESS curve for the existing-dams scenario shows a smooth transition of sediment transport rates in response to the change in streamflow. The high erosion rates during the dams-removed scenario are due to the absence of the dams; in contrast, the presence of dams in the existing-dams scenario helps reduce sediment erosion to some extent. The overall results of 60-day simulations for the 1947 flood show no significant difference in total volume of eroded sediment between the two scenarios, because the dams in the study reach have low heads and no control gates. It is important to note that the existing-dams and dams-removed scenarios simulations are run for only 60 days; therefore, the simulations take into account the changes in sediment erosion and deposition rates only during that time period. Over an extended period, more erosion of instream sediments would be expected to occur if the dams are not properly removed than under the existing conditions. On the basis of model simulations, removal of dams would further lower the head in all the channels. This lowering of head could produce higher flow velocities in the study reach, which ultimately would result in accelerated erosion rates.

Michigan↗
USGS2005

Simulation of flow and sediment transport in the white sturgeon spawning habitat of the Kootenai River near Bonners Ferry, Idaho

Characterization of sediment transport of the Kootenai River in the white sturgeon spawning reach is needed by the Kootenai River White Sturgeon Recovery Team to predict sediment-transport conditions that improve spawning conditions for the white sturgeon (Acipenser transmontanus) in the Kootenai River near Bonners Ferry, Idaho. The decreasing population and spawning failure of the white sturgeon has led to much concern. Few wild juvenile sturgeon are found in the river today. The Kootenai River begins in British Columbia, Canada, and flows through Montana, Idaho, and back into British Columbia. A 15-mile reach of the Kootenai River in Idaho was studied, including the white sturgeon spawning reach that has been designated as a critical habitat near Bonners Ferry, Idaho, and a 1-mile long side channel around the western side of Shorty Island. A one-dimensional sediment-transport model of the study reach was developed, calibrated, and used to simulate the response of the hydraulic and sediment system to varying discharges and water-surface elevations. The model comprises 79 cross sections, most of which came from a previous river survey conducted in 2002-03. Bed-sediment samples collected in 2002 and additional samples collected for this study in 2004 were used in the model. The model was calibrated to discharge and water-surface elevations at two U.S. Geological Survey gaging stations. The model also was calibrated to suspended-sediment discharge at several sites in the study reach. The calibrated model was used to simulate six different management alternatives to assess erosion and deposition under varying hydraulic conditions at the end of 21 days of simulation. Alternative 1 was simulated with a discharge of 6,000 cubic feet per second (ft3/s), alternative 2 with 20,000 ft3/s, alternative 3 with 40,000 ft3/s, and alternatives 4 through 6 with 60,000 ft3/s and represents low to high discharges in the river since the construction of Libby Dam. Sediment deposition was dominant in management alternatives 1 through 4. The streambed in the sandbed reach changed little or not at all. The gravel-cobble reach was more dynamic. In alternatives 1 through 4, deposition was the dominant feature because increasing river discharge alone did not produce boundary shear stresses that can erode and transport streambed sediments. Water-surface slope probably was the limiting factor in these alternatives because backwater conditions flattens the stage throughout the reach. High flows in the river probably would be more effective in eroding the streambed and transporting sediments if water-surface slope was increased. One practical method for increasing the slope is to lower the water level in Kootenay Lake. Two additional alternatives (5 and 6) were simulated to demonstrate the effects of a steeper slope in the study reach. Simulation results from management alternatives 5 and 6 (a discharge of 60,000 ft3/s) were quite different than those from alternatives 1-4. Erosion was the dominant feature in these simulations because water-surface slopes were increased by lowering water levels in Kootenay Lake. Slopes in alternatives 5 and 6 were 2.4 and 3.5 times, respectively, greater than slope in alternative 4. For alternatives 5 and 6, sediment deposition dominated in the gravel-cobble reach while erosion dominated in the sandbed reach. Downstream of Ambush Rock (river mile 151.8) in the sandbed reach, maximum streambed decreased 2 and 3 feet in alternatives 5 and 6, respectively. Decreases also were prevalent in the side channel and averaged 1 foot or greater. White sturgeon eggs have been collected in the study reach since 1994. The largest number of eggs have been collected in the reach adjacent to Shorty Island. Another large number of eggs was located between river miles 149 and 146. Although these reaches for alternatives 5 and 6 were erosional, these reaches are still considered unsuitable spawning habitat because

Scientific Investigations Report↗
USGS2003

Bedrock, soil, and lichen geochemistry from Isle Royale National Park, Michigan

Isle Royale National Park, Michigan, is a large island in northeastern Lake Superior that became a national park in 1940 and was designated as a wilderness area in 1976. The relative isolation of Isle Royale (Figure 1), 25 kilometers out in Lake Superior from the Canadian mainland, its generally harsh climate, and its status as a wilderness national park have minimized human influence on the geochemical evolution of its landscape. USGS sampling on Isle Royale began in 1996 as part of a larger project on the geology of the Midcontinent rift in the Lake Superior region and continued through 2000. Sampling began with collecting bedrock samples to characterize the geochemistry of the volcanic rocks that make up the much of the island, as well as samples representative of the minor native copper mineralization found on the island. Preliminary results from the bedrock study indicated, among other findings, that basaltic bedrock on the island had no detectable mercury, but that there was an association between native copper mineralization and trace amounts of mercury (Cannon and Woodruff, 1999). This finding and the recognition by the National Park Service that 6 of 32 inland lakes on Isle Royale have mercury levels in game fish that exceed State of Michigan acceptable levels for human consumption (Kallemeyn, 2000) resulted in renewed sampling on the island focused more on environmental issues. To evaluate atmospheric inputs of mercury and other elements to soil geochemistry, regionally distributed samples of both soils and lichens were collected as paired samples across the entire island. At each soil sample site, three epiphytic (grows in trees) lichen species, Evernia mesomorpha , Hypogymnia plysodes , and Parmelia sucata , were always collected. At some sites Cladina rangiferina , a lichen that grows on bare bedrock and soil surfaces, was also collected. The occurrence of Cladina rangiferina on the island is somewhat limited, and so this lichen species was not collected at all sites. A high density of soil samples was collected within three individual watersheds (Sargent Lake, Lake Wagejo, and Lake Richie) for a localized study that evaluated the terrestrial distribution of mercury and other elements of environmental concern. These lakes were chosen using data from Kallemeyn (2000) that showed that Sargent Lake and Lake Wagejo have high mercury in fish, whereas Lake Richie, which is similar in size to Sargent Lake, does not. As part of this study on the terrestrial contribution of mercury to lakes, long cores of lake sediments were recovered from Sargent Lake and Lake Richie using a modified Livingston piston sampler. For an ancillary study that evolved from the study on the distribution of mercury in certain watersheds, some soil samples were collected to evaluate the impact of forest fire on soil geochemistry, deliberately sampling within and outside areas on the island that burned in severe forest fires in 1936. To complete bedrock sampling on the island, rock samples from the Copper Harbor Formation, a sedimentary unit that occurs on the southeastern part of the island were collected in 1999. This report presents all the geochemical data from samples collected by the USGS during this period (Figures 1 and 2). A number of reports presenting data interpretation are in preparation

Michigan↗
USGS1999

Geothermal elements in lichens of Yellowstone National Park, USA

Geothermal features (e.g. geysers, fumaroles, vents, and springs) emit gaseous mercury, sulfur and heavy metals and therefore, are natural sources of these elements in the atmosphere. Field studies of heavy metals in lichens in Italy have detected elevated concentrations near geothermal power plants, and have determined that the origin of mercury is from soil degassing, not soil particles. We studied this phenomenon in a geothermal area without power plants to determine the natural levels of mercury and other elements. Two common and abundant species of epiphytic lichens, Bryoria fremontii and Letharia vulpina , were collected at six localities in Yellowstone National Park, USA in 1998 and analyzed for 22 chemical elements. Thirteen elements differed significantly between species. Some elements were significantly higher in the southern part of the park, while others were higher in the north. Levels of most elements were comparable with those in other national parks and wilderness areas in the region, except Hg, which was unusually high. The most likely sources of this element are the geothermal features, which are known emitters of Hg. Multivariate analyses revealed strong positive associations of Hg with S, and negative associations with soil elements, providing strong evidence that the Hg in the lichens is the result of soil degassing of elemental Hg rather than particulate Hg directly from soils. Average Hg levels in the lichens were 140 p.p.b. in Bryoria and 110 p.p.b. in Letharia , but maxima were 291 and 243 p.p.b., respectively. In spite of this, both species were healthy and abundant throughout the park.

Idaho, Montana, Wyoming↗