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Sample records for woodrat neotoma micropus

  1. Besnoitia neotomofelis n. sp. (Protozoa: Apicomplexa) from the southern plains woodrat ( Neotoma micropus).

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    Dubey, J P; Yabsley, M J

    2010-10-01

    Certain species of the protozoan genus Besnoitia cause clinical disease in livestock and wildlife. In the present paper a new species, Besnoitia neotomofelis is described from the southern planes woodrat (Neotoma micropus). The parasite was detected by bioassay of woodrat tissues in outbred Swiss Webster mice in an attempt to isolate Toxoplasma gondii. Initially, the organism was misdiagnosed as T. gondii because it was highly pathogenic for mice and its tachyzoites resembled T. gondii tachyzoites. Further studies revealed that it differed structurally and biologically from T. gondii. Tachyzoites were successfully cultivated and maintained in vitro in bovine monocytes and African green monkey kidney cells, and in vivo in mice. Non-dividing, uninucleate tachyzoites were approximately 1 x 5 μm in size. Longitudinally-cut bradyzoites in tissue sections measured 1.5-1.6 x 7.7-9.3 μm. Tissue cysts were microscopic, up to 210 μm long, and were infective orally to mice. Cats fed tissue cysts shed unsporulated 13 x 14 μm sized oocysts. All mice inoculated with B. neotomofelis died of acute besnoitiosis, irrespective of the dose, and Norwegian rats became infected but remained asymptomatic. Entero-epithelial stages (schizonts, gamonts) were found in cats fed tissue cysts. Large (up to 40 x 50 μm) first-generation schizonts developed in the lamina propria of the small intestine of cats. A second generation of small sized (8 μm) schizonts containing 4-8 merozoites was detected in enterocytes of the small intestine. Gamonts and oocysts were seen in goblet cells of the small intestinal epithelium. Tachyzoites were present in mesenteric lymph nodes of cats. Phylogenetic analysis indicated that B. neotomofelis was related to other Besnoitia species from rodents, rabbits, and opossums. Besnoitia neotomofelis is distinct from the 3 other species of Besnoitia, B. wallacei, B. darlingi and B. oryctofelisi that utilize cats as a definitive host.

  2. Temporal and spatial distribution of Leishmania mexicana infections in a population of Neotoma micropus

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    Raymond Russell W

    2003-01-01

    Full Text Available A 19-month mark-release-recapture study of Neotoma micropus with sequential screening for Leishmania mexicana was conducted in Bexar County, Texas, USA. The overall prevalence rate was 14.7% and the seasonal prevalence rates ranged from 3.8 to 26.7%. Nine incident cases were detected, giving an incidence rate of 15.5/100 rats/year. Follow-up of 101 individuals captured two or more times ranged from 14 to 462 days. Persistence of L. mexicana infections averaged 190 days and ranged from 104 to 379 days. Data on dispersal, density, dispersion, and weight are presented, and the role of N. micropus as a reservoir host for L. mexicana is discussed.

  3. Persistence of Allegheny woodrats Neotoma magister across the mid-Atlantic Appalachian Highlands landscape, USA

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    W. Mark Ford; Steven B. Castleberry; Michael T. Mengak; Jane L. Rodrigue; Daniel J. Feller; Kevin R. Russell

    2006-01-01

    We examined a suite of macro-habitat and landscape variables around active and inactive Allegheny woodrat Neotoma magister colony sites in the Appalachian Mountains of the mid-Atlantic Highlands of Maryland, Virginia, and West Virginia using an information-theoretic modeling approach. Logistic regression analyses suggested that Allegheny woodrat presence was related...

  4. Genetic relatedness and spatial associations of dusky-footed woodrats (Neotoma fuscipes)

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    Robin J. Innes; Mary Brooke McEachern; Dirk H. Van Vuren; John M. Eadie; Douglas A. Kelt; Michael L. Johnson

    2012-01-01

    We studied the association between space sharing and kinship in a solitary rodent, the dusky-footed woodrat (Neotoma fuscipes). Genetic relatedness was inversely correlated with geographic distance for female woodrats but not for males, a pattern consistent with female philopatry and male dispersal. However, some female neighbors were unrelated, suggesting the...

  5. Allegheny woodrat (Neotoma magister) use of rock drainage channels on reclaimed mines in southern West Virginia

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    Chamblin, H.D.; Wood, P.B.; Edwards, J.W.

    2004-01-01

    Allegheny woodrats (Neotoma magister) currently receive protected status throughout their range due to population declines. Threats associated with habitat fragmentation (e.g., introduced predators, disease, loss of connectivity among subpopulations and habitat loss) may explain why Allegheny woodrats are no longer found in many areas where they existed just 25 y ago. In southern West Virginia, surface coal mining is a major cause of forest fragmentation. Furthermore, mountaintop mining, the prevalent method in the region, results in a loss of rock outcrops and cliffs within forested areas, typical habitat of the Allegheny woodrat To determine the extent that Allegheny woodrats make use of reclaimed mine land, particularly rock drainages built during reclamation, we sampled 24 drainage channels on reclaimed surface mines in southern West Virginia, collected habitat data at each site and used logistic regression to identify habitat variables related to Allegheny woodrat presence. During 187 trap nights, 13 adult, 2 subadult and 8 juvenile Allegheny woodrats were captured at 13 of the 24 sites. Percent of rock as a groundcover and density of stems >15 cm diameter-at-breast-height (DBH) were related to Allegheny woodrat presence and were significantly greater at sites where Allegheny woodrats were present than absent. Sites where Allegheny woodrats were present differed substantially from other described habitats in West Virginia, though they may simulate boulder piles that occur naturally. Our findings suggest the need for additional research to examine the dynamics between Allegheny woodrat populations inhabiting rock outcrops in forests adjacent to mines and populations inhabiting constructed drainage channels on reclaimed mines. However, if Allegheny woodrats can use human-created habitat, our results will be useful to surface mine reclamation and to other mitigation efforts where rocky habitats are lost or disturbed.

  6. The draft genome sequence and annotation of the desert woodrat Neotoma lepida

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    Michael Campbell

    2016-09-01

    Full Text Available We present the de novo draft genome sequence for a vertebrate mammalian herbivore, the desert woodrat (Neotoma lepida. This species is of ecological and evolutionary interest with respect to ingestion, microbial detoxification and hepatic metabolism of toxic plant secondary compounds from the highly toxic creosote bush (Larrea tridentata and the juniper shrub (Juniperus monosperma. The draft genome sequence and annotation have been deposited at GenBank under the accession LZPO01000000.

  7. Creosote bush (Larrea tridentata) resin increases water demands and reduces energy availability in desert woodrats (Neotoma lepida).

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    Mangione, Antonio M; Dearing, M Denise; Karasov, William H

    2004-07-01

    Although many plant secondary compounds are known to have serious consequences for herbivores, the costs of processing them are generally unknown. Two potential costs of ingestion and detoxification of secondary compounds are elevation of the minimum drinking water requirement and excretion of energetically expensive metabolites (i.e., glucuronides) in the urine. To address these impacts, we studied the costs of ingestion of resin from creosote bush (Larrea tridentata) on desert woodrats (Neotoma lepida). The following hypotheses were tested: ingestion of creosote resin by woodrats (1) increases minimum water requirement and (2) reduces energy available by increasing fecal and urinary energy losses. We tested the first hypothesis, by measuring the minimum water requirement of woodrats fed a control diet with and without creosote resin. Drinking water was given in decreasing amounts until woodrats could no longer maintain constant body mass. In two separate experiments, the minimum drinking water requirement of woodrats fed resin was higher than that of controls by 18-30% (about 1-1.7 ml/d). We tested several potential mechanisms of increased water loss associated with the increase in water requirement. The rate of fecal water loss was higher in woodrats consuming resin. Neither urinary water nor evaporative water loss was affected by ingestion of resin. Hypothesis 2 was tested by measuring energy fluxes of woodrats consuming control vs. resin-treated diets. Woodrats on a resin diet had higher urinary energy losses and, thus, metabolized a lower proportion of the dietary energy than did woodrats on control diet. Fecal energy excretion was not affected by resin. The excretion of glucuronic acid represented almost half of the energy lost as a consequence of resin ingestion. The increased water requirement and energy losses of woodrats consuming a diet with resin could have notable ecological consequences.

  8. Functional characterization of cytochromes P450 2B from the desert woodrat Neotoma lepida

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    Wilderman, P. Ross; Jang, Hyun-Hee; Malenke, Jael R.; Salib, Mariam; Angermeier, Elisabeth; Lamime, Sonia; Dearing, M. Denise; Halpert, James R.

    2014-01-01

    Mammalian detoxification processes have been the focus of intense research, but little is known about how wild herbivores process plant secondary compounds, many of which have medicinal value or are drugs. cDNA sequences that code for three enzymes of the cytochrome P450 (CYP) 2B subfamily, here termed 2B35, 2B36, and 2B37 have been recently identified from a wild rodent, the desert woodrat (Malenke et al., 2012). Two variant clones of each enzyme were engineered to increase protein solubility and to facilitate purification, as reported for CYP2B enzymes from multiple species. When expressed in Escherichia coli each of the woodrat proteins gave the characteristic maximum at 450 nm in a reduced carbon monoxide difference spectrum but generally expressed at lower levels than rat CYP2B1. Two enzymes, 2B36 and 2B37, showed dealkylation activity with the model substrates 7-ethoxy-4-(trifluoromethyl)coumarin and 7-benzyloxyresorufin, whereas 2B35 was inactive. Binding of the monoterpene (+)-α-pinene produced a Type I shift in the absorbance spectrum of each enzyme. Mutation of 2B37 at residues 114, 262, or 480, key residues governing ligand interactions with other CYP2B enzymes, did not significantly change expression levels or produce the expected functional changes. In summary, two catalytic and one ligand-binding assay are sufficient to distinguish among CYP2B35, 2B36, and 2B37. Differences in functional profiles between 2B36 and 2B37 are partially explained by changes in substrate recognition site residue 114, but not 480. The results advance our understanding of the mechanisms of detoxification in wild mammalian herbivores and highlight the complexity of this system. - Highlights: • Three CYP2B enzymes from Neotoma lepida were cloned, engineered, and expressed. • A mix of catalytic and binding assays yields unique results for each enzyme. • Mutational analysis indicates CYP 2 B substrate recognition remains to be clarified. • Reported N. lepida gene

  9. Functional characterization of cytochromes P450 2B from the desert woodrat Neotoma lepida

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    Wilderman, P. Ross, E-mail: pwilderman@ucsd.edu [Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA (United States); Jang, Hyun-Hee [Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA (United States); Malenke, Jael R. [Department of Biology, University of Utah, Salt Lake City, UT (United States); Salib, Mariam; Angermeier, Elisabeth; Lamime, Sonia [Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA (United States); Dearing, M. Denise [Department of Biology, University of Utah, Salt Lake City, UT (United States); Halpert, James R. [Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA (United States)

    2014-02-01

    Mammalian detoxification processes have been the focus of intense research, but little is known about how wild herbivores process plant secondary compounds, many of which have medicinal value or are drugs. cDNA sequences that code for three enzymes of the cytochrome P450 (CYP) 2B subfamily, here termed 2B35, 2B36, and 2B37 have been recently identified from a wild rodent, the desert woodrat (Malenke et al., 2012). Two variant clones of each enzyme were engineered to increase protein solubility and to facilitate purification, as reported for CYP2B enzymes from multiple species. When expressed in Escherichia coli each of the woodrat proteins gave the characteristic maximum at 450 nm in a reduced carbon monoxide difference spectrum but generally expressed at lower levels than rat CYP2B1. Two enzymes, 2B36 and 2B37, showed dealkylation activity with the model substrates 7-ethoxy-4-(trifluoromethyl)coumarin and 7-benzyloxyresorufin, whereas 2B35 was inactive. Binding of the monoterpene (+)-α-pinene produced a Type I shift in the absorbance spectrum of each enzyme. Mutation of 2B37 at residues 114, 262, or 480, key residues governing ligand interactions with other CYP2B enzymes, did not significantly change expression levels or produce the expected functional changes. In summary, two catalytic and one ligand-binding assay are sufficient to distinguish among CYP2B35, 2B36, and 2B37. Differences in functional profiles between 2B36 and 2B37 are partially explained by changes in substrate recognition site residue 114, but not 480. The results advance our understanding of the mechanisms of detoxification in wild mammalian herbivores and highlight the complexity of this system. - Highlights: • Three CYP2B enzymes from Neotoma lepida were cloned, engineered, and expressed. • A mix of catalytic and binding assays yields unique results for each enzyme. • Mutational analysis indicates CYP{sub 2}B substrate recognition remains to be clarified. • Reported N. lepida gene

  10. Parasite prevalence and community diversity in sympatric and allopatric populations of two woodrat species (Sigmodontinae: Neotoma) in central California.

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    Bechtel, Molly J; Teglas, Michael B; Murphy, Peter J; Matocq, Marjorie D

    2015-04-01

    Patterns of host-parasite association may vary across the landscape in part because of host and parasite diversity, divergence, local ecology, or interactions among these factors. In central coastal California, we quantified parasite prevalence, infection intensity, and diversity in two sister species of woodrats (Neotoma fuscipes and Neotoma macrotis) where the species co-occur (sympatry) and where each species exists alone (allopatry). In feces from 50 adults we identified seven taxa: the protozoans Eimeria, Giardia, and Cryptosporidium, the nematodes Trichuris, Aspicularis, and Eucoleus, and a cestode in the family Anoplocephalidae. Gastrointestinal parasite infection intensity and diversity were higher in males than in females, a difference that was most pronounced in the more aggressive N. fuscipes. Both species had lower infection intensity in sympatry than in allopatry and in sympatry the two species did not differ in infection intensity in total but did maintain distinct parasite communities. Taken together, our findings suggest that host evolutionary differences, including perhaps species-specific patterns of aggressive behavior, as well as local ecology, influence the likelihood of infection by these endoparasite taxa.

  11. Small-Scale Die-Offs in Woodrats Support Long-Term Maintenance of Plague in the U.S. Southwest.

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    Kosoy, Michael; Reynolds, Pamela; Bai, Ying; Sheff, Kelly; Enscore, Russell E; Montenieri, John; Ettestad, Paul; Gage, Kenneth

    2017-09-01

    Our longitudinal study of plague dynamics was conducted in north-central New Mexico to identify which species in the community were infected with plague, to determine the spatial and temporal patterns of the dynamics of plague epizootics, and to describe the dynamics of Yersinia pestis infection within individual hosts. A total of 3156 fleas collected from 535 small mammals of 8 species were tested for Y. pestis DNA. Nine fleas collected from six southern plains woodrats (Neotoma micropus) and from one rock squirrel (Otospermophilus variegatus) were positive for the pla gene of Y. pestis. None of 127 fleas collected from 17 woodrat nests was positive. Hemagglutinating antibodies to the Y. pestis-specific F1 antigen were detected in 11 rodents of 6 species. All parts of the investigated area were subjected to local disappearance of woodrats. Despite the active die-offs, some woodrats always were present within the relatively limited endemic territory and apparently were never exposed to plague. Our observations suggest that small-scale die-offs in woodrats can support maintenance of plague in the active U.S. Southwestern focus.

  12. Mammalian species - Neotoma magister

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    Steven B. Castleberry; Michael T. Mengak; W. Mark Ford

    2006-01-01

    External morphology of N. magister (Fig. 1) is similar to that of N. floridana, the only parapatric Neotoma. Although N. magister generally is larger in mass and with longer vibrissae, identification based on single measurements is unreliable because of morphometric overlap (Ray 2000)....

  13. The Neotoma Paleoecology Database

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    Grimm, E. C.; Ashworth, A. C.; Barnosky, A. D.; Betancourt, J. L.; Bills, B.; Booth, R.; Blois, J.; Charles, D. F.; Graham, R. W.; Goring, S. J.; Hausmann, S.; Smith, A. J.; Williams, J. W.; Buckland, P.

    2015-12-01

    The Neotoma Paleoecology Database (www.neotomadb.org) is a multiproxy, open-access, relational database that includes fossil data for the past 5 million years (the late Neogene and Quaternary Periods). Modern distributional data for various organisms are also being made available for calibration and paleoecological analyses. The project is a collaborative effort among individuals from more than 20 institutions worldwide, including domain scientists representing a spectrum of Pliocene-Quaternary fossil data types, as well as experts in information technology. Working groups are active for diatoms, insects, ostracodes, pollen and plant macroscopic remains, testate amoebae, rodent middens, vertebrates, age models, geochemistry and taphonomy. Groups are also active in developing online tools for data analyses and for developing modules for teaching at different levels. A key design concept of NeotomaDB is that stewards for various data types are able to remotely upload and manage data. Cooperatives for different kinds of paleo data, or from different regions, can appoint their own stewards. Over the past year, much progress has been made on development of the steward software-interface that will enable this capability. The steward interface uses web services that provide access to the database. More generally, these web services enable remote programmatic access to the database, which both desktop and web applications can use and which provide real-time access to the most current data. Use of these services can alleviate the need to download the entire database, which can be out-of-date as soon as new data are entered. In general, the Neotoma web services deliver data either from an entire table or from the results of a view. Upon request, new web services can be quickly generated. Future developments will likely expand the spatial and temporal dimensions of the database. NeotomaDB is open to receiving new datasets and stewards from the global Quaternary community

  14. The woodrat gut microbiota as an experimental system for understanding microbial metabolism of dietary toxins

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    Kevin D. Kohl

    2016-07-01

    Full Text Available The microbial communities inhabiting the alimentary tracts of mammals, particularly those of herbivores, are estimated to be one of the densest microbial reservoirs on Earth. The significance of these gut microbes in influencing the physiology, ecology and evolution of their hosts is only beginning to be realized. To understand the microbiome of herbivores with a focus on nutritional ecology, while evaluating the roles of host evolution and environment in sculpting microbial diversity, we have developed an experimental system consisting of the microbial communities of several species of herbivorous woodrats (genus Neotoma that naturally feed on a variety of dietary toxins. We designed this system to investigate the long-standing, but experimentally neglected hypothesis that ingestion of toxic diets by herbivores is facilitated by the gut microbiota. Like several other rodent species, the woodrat stomach has a sacculated, nongastric foregut portion. We have documented a dense and diverse community of microbes in the woodrat foregut, with several genera potentially capable of degrading dietary toxins and/or playing a role in stimulating hepatic detoxification enzymes of the host. The biodiversity of these gut microbes appears to be a function of host evolution, ecological experience and diet, such that dietary toxins increase microbial diversity in hosts with experience with these toxins while novel toxins depress microbial diversity. These microbial communities are critical to the ingestion of a toxic diet as reducing the microbial community with antibiotics impairs the host’s ability to feed on dietary toxins. Furthermore, the detoxification capacity of gut microbes can be transferred from Neotoma both intra and interspecifically to naïve animals that lack ecological and evolutionary history with these toxins. In addition to advancing our knowledge of complex host-microbes interactions, this system holds promise for identifying microbes that

  15. Brucella neotomae Infection in Humans, Costa Rica.

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    Suárez-Esquivel, Marcela; Ruiz-Villalobos, Nazareth; Jiménez-Rojas, César; Barquero-Calvo, Elías; Chacón-Díaz, Carlos; Víquez-Ruiz, Eunice; Rojas-Campos, Norman; Baker, Kate S; Oviedo-Sánchez, Gerardo; Amuy, Ernesto; Chaves-Olarte, Esteban; Thomson, Nicholas R; Moreno, Edgardo; Guzmán-Verri, Caterina

    2017-06-01

    Several species of Brucella are known to be zoonotic, but B. neotomae infection has been thought to be limited to wood rats. In 2008 and 2011, however, B. neotomae was isolated from cerebrospinal fluid of 2 men with neurobrucellosis. The nonzoonotic status of B. neotomae should be reassessed.

  16. Serological response of cats to experimental Besnoitia darlingi and Besnoitia neotomofelis infections and prevalence of antibodies to these parasites in cats from Virginia and Pennsylvania

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    Besnoitia darlingi and B. neotomofelis are tissue cyst-forming apicomplexan parasite that use domestic cats (Felis domesticus) as definitive hosts and opossums (Didelphis virginiana) and southern planes woodrats (Neotoma micropus) as intermediate hosts, respectively. Nothing is known about the preva...

  17. Spatial clustering of Borrelia burgdorferi sensu lato within populations of Allen's chipmunks and dusky-footed woodrats in northwestern California.

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    Hacker, Gregory M; Brown, Richard N; Fedorova, Natalia; Girard, Yvette A; Higley, Mark; Clueit, Bernadette; Lane, Robert S

    2018-01-01

    The ecology of Lyme borreliosis is complex in northwestern California, with several potential reservoir hosts, tick vectors, and genospecies of Borrelia burgdorferi sensu lato. The primary objective of this study was to determine the fine-scale spatial distribution of different genospecies in four rodent species, the California ground squirrel (Otospermophilus beecheyi), northern flying squirrel (Glaucomys sabrinus), dusky-footed woodrat (Neotoma fuscipes), and Allen's chipmunk (Neotamias senex). Rodents were live-trapped between June 2004 and May 2005 at the Hoopa Valley Tribal Reservation (HVTR) in Humboldt County, California. Ear-punch biopsies obtained from each rodent were tested by polymerase chain reaction (PCR) and sequencing analysis. The programs ArcGIS and SaTScan were used to examine the spatial distribution of genospecies. Multinomial log-linear models were used to model habitat and host-specific characteristics and their effect on the presence of each borrelial genospecies. The Akaike information criterion (AICc) was used to compare models and determine model fit. Borrelia burgdorferi sensu stricto was primarily associated with chipmunks and B. bissettiae largely with woodrats. The top model included the variables "host species", "month", and "elevation" (weight = 0.84). Spatial clustering of B. bissettiae was detected in the northwestern section of the HVTR, whereas B. burgdorferi sensu stricto was clustered in the southeastern section. We conclude that the spatial distribution of these borreliae are driven at least in part by host species, time-of-year, and elevation.

  18. Bushy-tailed woodrat abundance in dry forests of eastern Washington.

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    John F. Lehmkuhl; Keith D. Kistler; James S. Begley

    2006-01-01

    We studied bushy-tailed woodrats (Neotonza cinerea occidentalis) in the eastern Washington Cascade Range to estimate their density and survival in 3 typical dry forest cover types. We predicted woodrat density to be high, moderate, and low in mature mixed-conifer forests, young mixed-conifer forests, and open ponderosa pine forests, respectively....

  19. The Neotoma Paleoecology Database: An International Community-Curated Resource for Paleoecological and Paleoenvironmental Data

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    Williams, J. W.; Grimm, E. C.; Ashworth, A. C.; Blois, J.; Charles, D. F.; Crawford, S.; Davis, E.; Goring, S. J.; Graham, R. W.; Miller, D. A.; Smith, A. J.; Stryker, M.; Uhen, M. D.

    2017-12-01

    The Neotoma Paleoecology Database supports global change research at the intersection of geology and ecology by providing a high-quality, community-curated data repository for paleoecological data. These data are widely used to study biological responses and feedbacks to past environmental change at local to global scales. The Neotoma data model is flexible and can store multiple kinds of fossil, biogeochemical, or physical variables measured from sedimentary archives. Data additions to Neotoma are growing and include >3.5 million observations, >16,000 datasets, and >8,500 sites. Dataset types include fossil pollen, vertebrates, diatoms, ostracodes, macroinvertebrates, plant macrofossils, insects, testate amoebae, geochronological data, and the recently added organic biomarkers, stable isotopes, and specimen-level data. Neotoma data can be found and retrieved in multiple ways, including the Explorer map-based interface, a RESTful Application Programming Interface, the neotoma R package, and digital object identifiers. Neotoma has partnered with the Paleobiology Database to produce a common data portal for paleobiological data, called the Earth Life Consortium. A new embargo management is designed to allow investigators to put their data into Neotoma and then make use of Neotoma's value-added services. Neotoma's distributed scientific governance model is flexible and scalable, with many open pathways for welcoming new members, data contributors, stewards, and research communities. As the volume and variety of scientific data grow, community-curated data resources such as Neotoma have become foundational infrastructure for big data science.

  20. Promotion and Rescue of Intracellular Brucella neotomae Replication during Coinfection with Legionella pneumophila.

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    Kang, Yoon-Suk; Kirby, James E

    2017-05-01

    We established a new Brucella neotomae in vitro model system for study of type IV secretion system-dependent (T4SS) pathogenesis in the Brucella genus. Importantly, B. neotomae is a rodent pathogen, and unlike B. abortus , B. melitensis , and B. suis , B. neotomae has not been observed to infect humans. It therefore can be handled more facilely using biosafety level 2 practices. More particularly, using a series of novel fluorescent protein and lux operon reporter systems to differentially label pathogens and track intracellular replication, we confirmed T4SS-dependent intracellular growth of B. neotomae in macrophage cell lines. Furthermore, B. neotomae exhibited early endosomal (LAMP-1) and late endoplasmic reticulum (calreticulin)-associated phagosome maturation. These findings recapitulate prior observations for human-pathogenic Brucella spp. In addition, during coinfection experiments with Legionella pneumophila , we found that defective intracellular replication of a B. neotomae T4SS virB4 mutant was rescued and baseline levels of intracellular replication of wild-type B. neotomae were significantly stimulated by coinfection with wild-type but not T4SS mutant L. pneumophila Using confocal microscopy, it was determined that intracellular colocalization of B. neotomae and L. pneumophila was required for rescue and that colocalization came at a cost to L. pneumophila fitness. These findings were not completely expected based on known temporal and qualitative differences in the intracellular life cycles of these two pathogens. Taken together, we have developed a new system for studying in vitro Brucella pathogenesis and found a remarkable T4SS-dependent interplay between Brucella and Legionella during macrophage coinfection. Copyright © 2017 American Society for Microbiology.

  1. Brucellosis caused by the wood rat pathogen Brucella neotomae: two case reports.

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    Villalobos-Vindas, Juan M; Amuy, Ernesto; Barquero-Calvo, Elías; Rojas, Norman; Chacón-Díaz, Carlos; Chaves-Olarte, Esteban; Guzman-Verri, Caterina; Moreno, Edgardo

    2017-12-19

    Brucellosis is a chronic bacterial disease caused by members of the genus Brucella. Among the classical species stands Brucella neotomae, until now, a pathogen limited to wood rats. However, we have identified two brucellosis human cases caused by B. neotomae, demonstrating that this species has zoonotic potential. Within almost 4 years of each other, a 64-year-old Costa Rican white Hispanic man and a 51-year-old Costa Rican white Hispanic man required medical care at public hospitals of Costa Rica. Their hematological and biochemical parameters were within normal limits. No adenopathies or visceral abnormalities were found. Both patients showed intermittent fever, disorientation, and general malaise and a positive Rose Bengal test compatible with Brucella infection. Blood and cerebrospinal fluid cultures rendered Gram-negative coccobacilli identified by genomic analysis as B. neotomae. After antibiotic treatment, the patients recovered with normal mental activities. This is the first report describing in detail the clinical disease caused by B. neotomae in two unrelated patients. In spite of previous claims, this bacterium keeps zoonotic potential. Proposals to generate vaccines by using B. neotomae as an immunogen must be reexamined and countries housing the natural reservoir must consider the zoonotic risk.

  2. Identification of a single-nucleotide insertion in the promoter region affecting the sodC promoter activity in Brucella neotomae.

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    Dina A Moustafa

    Full Text Available Brucella neotomae is not known to be associated with clinical disease in any host species. Previous research suggested that B. neotomae might not express detectable levels of Cu/Zn superoxide dismutase (SOD, a periplasmic enzyme known to be involved in protecting Brucella from oxidative bactericidal effects of host phagocytes. This study was undertaken to investigate the genetic basis for the disparity in SOD expression in B. neotomae. Our Western blot and SOD enzyme assay analyses indicated that B. neotomae does express SOD, but at a substantially reduced level. Nucleotide sequence analysis of region upstream to the sodC gene identified a single-nucleotide insertion in the potential promoter region. The same single-nucleotide insertion was also detected in the sodC promoter of B. suis strain Thomsen, belonging to biovar 2 in which SOD expression was undetectable previously. Examination of the sodC promoter activities using translational fusion constructs with E. coli β-galactosidase demonstrated that the B. neotomae and B. suis biovar 2 promoters were very weak in driving gene expression. Site-directed mutation studies indicated that the insertion of A in the B. neotomae sodC promoter reduced the promoter activity. Increasing the level of SOD expression in B. neotomae through complementation with B. abortus sodC gene did not alter the bacterial survival in J774A.1 macrophage-like cells and in tissues of BALB/c and C57BL/6 mice. These results for the first time demonstrate the occurrence of a single-nucleotide polymorphism affecting promoter function and gene expression in Brucella.

  3. Oral immunization of mice with gamma-irradiated Brucella neotomae induces protection against intraperitoneal and intranasal challenge with virulent B. abortus 2308.

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    Dabral, Neha; Martha-Moreno-Lafont; Sriranganathan, Nammalwar; Vemulapalli, Ramesh

    2014-01-01

    Brucella spp. are Gram-negative, facultative intracellular coccobacilli that cause one of the most frequently encountered zoonosis worldwide. Humans naturally acquire infection through consumption of contaminated dairy and meat products and through direct exposure to aborted animal tissues and fluids. No vaccine against brucellosis is available for use in humans. In this study, we tested the ability of orally inoculated gamma-irradiated B. neotomae and B. abortus RB51 in a prime-boost immunization approach to induce antigen-specific humoral and cell mediated immunity and protection against challenge with virulent B. abortus 2308. Heterologous prime-boost vaccination with B. abortus RB51 and B. neotomae and homologous prime-boost vaccination of mice with B. neotomae led to the production of serum and mucosal antibodies specific to the smooth LPS. The elicited serum antibodies included the isotypes of IgM, IgG1, IgG2a, IgG2b and IgG3. All oral vaccination regimens induced antigen-specific CD4(+) and CD8(+) T cells capable of secreting IFN-γ and TNF-α. Upon intra-peritoneal challenge, mice vaccinated with B. neotomae showed the highest level of resistance against virulent B. abortus 2308 colonization in spleen and liver. Experiments with different doses of B. neotomae showed that all tested doses of 10(9), 10(10) and 10(11) CFU-equivalent conferred significant protection against the intra-peritoneal challenge. However, a dose of 10(11) CFU-equivalent of B. neotomae was required for affording protection against intranasal challenge as shown by the reduced bacterial colonization in spleens and lungs. Taken together, these results demonstrate the feasibility of using gamma-irradiated B. neotomae as an effective and safe oral vaccine to induce protection against respiratory and systemic infections with virulent Brucella.

  4. Building connected data standards to promote interdisciplinary research in the paleogeosciences- PalEON, Neotoma, THROUGHPUT

    Science.gov (United States)

    Goring, S. J.; Richard, S. M.; Williams, J. W.; Dawson, A.

    2017-12-01

    A broad array of data resources, across disciplines, are needed to study Earth system processes operating at multiple spatial or temporal scales. Data friction frequently delays this integrative and interdisciplinary research, while sustainable solutions may be hampered as a result of academic incentives that penalize technical "tool building" at the expense of research publication. The paleogeosciences, in particular, often integrate data drawn from multiple sub-disciplines and from a range of long-tail and big data sources. Data friction can be lowered and the pace of scientific discovery accelerated through the development and adoption of data standards, both within the paleogeosciences and with allied disciplines. Using the PalEON Project (https://sites.nd.edu/paleonproject/) and the Neotoma Paleoecological Database (https://neotomadb.org) as focal case studies, we first illustrate the advances possible through data standardization. We then focus on new efforts in data standardization and building linkages among paleodata resources underway through the EarthCube-funded Throughput project. A first step underway is to analyze existing standards across paleo-data repositories and identify ways in which the adoption of common standards can promote connectivity, reducing barriers to interdisciplinary research, especially for early career researchers. Experience indicates that standards tend to emerge by necessity and from a mixture of bottom-up and top-down processes. A common pathway is when conventions developed to solve specific problems within a community are extended to address challenges that are more general. The Throughput project will identify, document, and promote such solutions to foster wider adoption of standards for data interchange and reduce data friction in the paleogeosciences.

  5. Food habits of rodents inhabiting arid and semi-arid ecosystems of central New Mexico

    Science.gov (United States)

    Hope, Andrew G.; Parmenter, Robert R.

    2007-01-01

    In this study, we describe seasonal dietary composition for 15 species of rodents collected in all major habitats on the Sevilleta National Wildlife Refuge (Socorro County) in central New Mexico. A comprehensive literature review of food habits for these species from throughout their distribution also is provided. We collected rodents in the field during winter, spring and late summer in 1998 from six communities: riparian cottonwood forest; piñon-juniper woodland; juniper-oak savanna; mesquite savanna; short-grass steppe; and Chihuahuan Desert scrubland. Rodents included Spermophilus spilosoma (Spotted Ground Squirrel), Perognathus flavescens (Plains Pocket Mouse), Perognathus flavus (Silky Pocket Mouse), Dipodomys merriami (Merriam’s Kangaroo Rat), Dipodomys ordii (Ord’s Kangaroo Rat), Dipodomys spectabilis (Banner-tailed Kangaroo Rat), Reithrodontomys megalotis (Western Harvest Mouse), Peromyscus boylii (Brush Mouse), Peromyscus eremicus (Cactus Mouse), Peromyscus leucopus (White-footed Mouse), Peromyscus truei (Piñon Mouse), Onychomys arenicola (Mearn’s Grasshopper Mouse), Onychomys leucogaster (Northern Grasshopper Mouse), Neotoma albigula/leucodon (White-throated Woodrats), and Neotoma micropus (Southern Plains Woodrat). We collected stomach contents of all species, and cheek-pouch contents of heteromyids, and quantified them in the laboratory. We determined seasonal diets in each habitat by calculating mean percentage volumes of seeds, arthropods and green vegetation (plant leaves and stems) for each species of rodent. Seeds consumed by each rodent were identified to genus, and often species, and quantified by frequency counts. Comparisons of diets between and among species of rodents, seasons, and ecosystems were also examined. We provide an appendix of all plant taxa documented.

  6. Prevalence of Trypanosoma cruzi infection in dogs and small mammals in Nuevo León, Mexico.

    Science.gov (United States)

    Galaviz-Silva, Lucio; Mercado-Hernández, Roberto; Zárate-Ramos, José J; Molina-Garza, Zinnia J

    Chagas disease, caused by the protozoan Trypanosoma cruzi, is an important public health concern in areas extending from South America northward into the southern United States of America. Although this hemoflagellate has many wild and domestic mammalians reported as reservoir hosts, studies on this subject are scarce in Nuevo León state, a region located in northeastern Mexico. This cross-sectional study showed that the general prevalence of T. cruzi infection in Nuevo León state was 14.5% (35/241), this percentage matching the ones determined by PCR and traditional diagnostics. Localities and infected mammals did not significantly differ (χ 2 =6.098, p=0.192); however the number of infected animals was highly correlated with mammalian species (p=0.009). Striped skunks (Mephitis mephitis) were found to be the most infected overall (11/34, 32.3%), while dogs (Canis familiaris) had the lowest prevalence. In conclusion, although the prevalence of T. cruzi infection in small mammals was lower in Nuevo León than in other states of Mexico, our results provide new locality records, including striped skunks, opossums (Didelphis marsupialis) and dogs, and extend the recorded area to woodrats (Neotoma micropus). Copyright © 2017 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.

  7. Novel Hepatozoon in vertebrates from the southern United States.

    Science.gov (United States)

    Allen, Kelly E; Yabsley, Michael J; Johnson, Eileen M; Reichard, Mason V; Panciera, Roger J; Ewing, Sidney A; Little, Susan E

    2011-08-01

    Novel Hepatozoon spp. sequences collected from previously unrecognized vertebrate hosts in North America were compared with documented Hepatozoon 18S rRNA sequences in an effort to examine phylogenetic relationships between the different Hepatozoon organisms found cycling in nature. An approximately 500-base pair fragment of 18S rDNA common to Hepatozoon spp. and some other apicomplexans was amplified and sequenced from the tissues or blood of 16 vertebrate host species from the southern United States, including 1 opossum (Didelphis virginiana), 2 bobcats (Lynx rufus), 1 domestic cat (Felis catus), 3 coyotes (Canis latrans), 1 gray fox (Urocyon cinereoargenteus), 4 raccoons (Procyon lotor), 1 pet boa constrictor (Boa constrictor imperator), 1 swamp rabbit (Sylvilagus aquaticus), 1 cottontail rabbit (Sylvilagus floridanus), 4 woodrats (Neotoma fuscipes and Neotoma micropus), 3 white-footed mice (Peromyscus leucopus), 8 cotton rats (Sigmodon hispidus), 1 cotton mouse (Peromyscus gossypinus), 1 eastern grey squirrel (Sciurus carolinensis), and 1 woodchuck (Marmota monax). Phylogenetic analyses and comparison with sequences in the existing database revealed distinct groups of Hepatozoon spp., with clusters formed by sequences obtained from scavengers and carnivores (opossum, raccoons, canids, and felids) and those obtained from rodents. Surprisingly, Hepatozoon spp. sequences from wild rabbits were most closely related to sequences obtained from carnivores (97.2% identical), and the sequence from the boa constrictor was most closely related to the rodent cluster (97.4% identical). These data are consistent with recent work identifying prey-predator transmission cycles in Hepatozoon spp. and suggest this pattern may be more common than previously recognized.

  8. BMDO Raptor/Talon Program

    Science.gov (United States)

    1993-06-01

    has been graded and covered with gravel. Vegetation adjacent to and surrounding the tower consists of low growing desert shrubs (creosote bush (Larrea...lucida) White Sands wood rat (Neotoma micropus leucophaeus) Plants Mosquito plant (Agastache cana) Supreme sage (Sälvia summa) Dune unicorn plant

  9. Comparison of six commercial DNA extraction kits for detection of Brucella neotomae in Mexican and Central American-style cheese and other milk products.

    Science.gov (United States)

    Lusk, Tina S; Strain, Errol; Kase, Julie A

    2013-05-01

    Raw or inadequately pasteurized milk from infected animals and cheese made with such milk are a frequent vehicle for human brucellosis infection. Also, biological terrorism is a concern with certain Brucella spp. Due to matrix-associated real-time polymerase chain reaction (qPCR) inhibitors, robust sample preparations are crucial. We compared six commercial nucleic acid extraction kits using nine Mexican and Central American-style soft cheeses or creams and three liquid milk products inoculated with Brucella neotomae, a surrogate for pathogenic Brucella spp. Kits were evaluated by purity and quantity of DNA as determined by qPCR Ct values, reproducibility across cheese and milk types, and cost. At 10(7) CFU/g in four different cheeses, Qiagen statistically outperformed all other kits. When two cheese styles were inoculated at dual levels, Qiagen and High Pure kit extracted samples at 1.5 × 10(5) CFU/g produced average Ct values of 34-39, while PrepSEQ and MagMAX kit extracted samples exhibited higher or no Ct values. High Pure and Qiagen kits excelled also with liquid milk products. Considering matrices, inoculation levels, and kits evaluated, High Pure and Qiagen products produced Brucella DNA of high quality and quantity indicated by the lowest Ct values and were the least expensive. Copyright © 2012 Elsevier Ltd. All rights reserved.

  10. Environmental Assessment for the Orbital Reentry Corridor for Generic Unmanned Lifting Entry Vehicle Landing at Edwards Air Force Base

    Science.gov (United States)

    2002-12-01

    mouse (Onychomys torridus), little pocket mouse (Perognathus longimembris), Merriam’s kangaroo rat (Dipodymus merriami), and desert woodrat (Neotoma...mild, such as an increase in heart rate, to more severe, such as effects on metabolism and hormone balance. Behavioral responses can also be mild

  11. Environmental Assessment for Armed Munitions Integration Testing on the Precision Impact Range Area

    Science.gov (United States)

    2005-05-01

    Perognathus 11 longimembris), Merriam’s kangaroo rat (Dipodymus merriami), and desert woodrat (Neotoma lepida). 12 Common bats include the western pipistrelle...or behavioral. Physiological effects can be mild, such as 3 an increase in heart rate, to more severe, such as effects on metabolism and hormone

  12. Environmental Impact Analysis Process. Environmental Impact Statement, Flight Operations in the Sells Airspace Overlying the Tohono O’Odham Indian Reservation & Organ Pipe Cactus National Monument, Southern Arizona. Revised Draft

    Science.gov (United States)

    1986-06-06

    al. 1970. Endocrine and metabolic effects of noise in normal, hypertensive and psychotic subjects. IN: Physiological Effects of Noise. Welch, B. L...Perognathus baileyi Bannertail Kangaroo Rat Dipodomys spectabilis Cactus Mouse Peromyscus eremicus Canyon Mousea Peromyscus crinitus Desert Kangaroo Rat...Dipodomys deserti Desert Pocket Mouse Perognathus penicillatus Desert Woodrat Neotoma lepida Merriam Kangaroo Rat Dipodomys merriami Merriam Mouse

  13. The detection of hemorrhagic proteins in snake venoms using monoclonal antibodies against Virginia opossum (Didelphis virginiana) serum.

    Science.gov (United States)

    Sánchez, E E; García, C; Pérez, J C; De La Zerda, S J

    1998-10-01

    Most snakes and a few warm-blooded animals have a resistance to snake venoms because of naturally occurring antihemorrhagins found in their sera. The antihemorrhagins in serum of Virginia opossum (Didelphis virginiana) neutralize hemorrhagic activity by binding to hemorrhagins in snake venoms. The binding characteristic of antihemorrhagins in D. virginiana serum was used to develop a five-step western blot. The detection of hemorrhagic proteins were measured indirectly with antihemorrhagins in Virginia opossum serum and with DV-2LD#2, a monoclonal antibody specific for Virginia opossum antihemorrhagins. Snake venoms were separated by native-PAGE, transferred to a Millipore Immobilon-P membrane and then incubated with crude Virginia opossum serum. The hemorrhagins in snake venom bind to antihemorrhagins in Virginia opossum serum which react with DV-2LD#2 a monoclonal antibody that is specific for Virginia opossum antihemorrhagins. DV-2LD#2 monoclonal antibody inhibits antihemorrhagic activity in Virginia opossum serum when mixed in equal amounts. The inhibition of antihemorrhagins by DV-2LD#2 monoclonal antibody suggests specificity. DV-2LD#2 monoclonal antibody does not recognize antihemorrhagins in gray woodrat (Neotoma micropus) serum. The five-step western blot reveals two well-defined bands which represent hemorrhagins found in Western diamondback rattlesnake (Crotalus atrox) venom. Venoms from 15 different snake species were examined to determine the usefulness of the five-step western blot. Other hemorrhagic venoms (Great Basin rattlesnake (C. viridis lutosus), Prairie rattlesnake (C. viridis viridis), Tancitaran dusky rattlesnake (C. pusillus), Northern Mojave rattlesnake (C. scutulatus scutulatus type B) and Northern Pacific rattlesnake (C. v. oreganus)) had one single band in the five-step western blot. DV-2LD#2 did not bind to the non-hemorrhagic venoms and reacted with 50% of the hemorrhagic venoms used in this study. The monoclonal antibody, CAH

  14. Late Holocene expansion of Ponderosa pine (Pinus ponderosa) in the Central Rocky Mountains, USA

    Science.gov (United States)

    Norris, Jodi R; Betancourt, Julio L.; Jackson, Stephen T.

    2016-01-01

    "Aim: Ponderosa pine (Pinus ponderosa) experienced one of the most extensive and rapid post-glacial plant migrations in western North America. We used plant macrofossils from woodrat (Neotoma) middens to reconstruct its spread in the Central Rocky Mountains, identify other vegetation changes coinciding with P. ponderosa expansion at the same sites, and relate P. ponderosa migrational history to both its modern phylogeography and to a parallel expansion by Utah juniper (Juniperus osteosperma).

  15. Evidence for functional convergence in genes upregulated by herbivores ingesting plant secondary compounds

    Science.gov (United States)

    2014-01-01

    Background Nearly 40 years ago, Freeland and Janzen predicted that liver biotransformation enzymes dictated diet selection by herbivores. Despite decades of research on model species and humans, little is known about the biotransformation mechanisms used by mammalian herbivores to metabolize plant secondary compounds (PSCs). We investigated the independent evolution of PSC biotransformation mechanisms by capitalizing on a dramatic diet change event—the dietary inclusion of creosote bush (Larrea tridentata)—that occurred in the recent evolutionary history of two species of woodrats (Neotoma lepida and N. bryanti). Results By comparing gene expression profiles of two populations of woodrats with evolutionary experience to creosote and one population naïve to creosote, we identified genes either induced by a diet containing creosote PSCs or constitutively higher in populations with evolutionary experience of creosote. Although only one detoxification gene (an aldo-keto reductase) was induced by both experienced populations, these populations converged upon functionally equivalent strategies to biotransform the PSCs of creosote bush by constitutively expressing aldehyde and alcohol dehydrogenases, Cytochromes P450s, methyltransferases, glutathione S-transferases and sulfotransferases. The response of the naïve woodrat population to creosote bush was indicative of extreme physiological stress. Conclusions The hepatic detoxification system of mammals is notoriously complex, with hundreds of known biotransformation enzymes. The comparison herein of woodrat taxa that differ in evolutionary and ecological experience with toxins in creosote bush reveals convergence in the overall strategies used by independent species after a historical shift in diet. In addition, remarkably few genes seemed to be important in this dietary shift. The research lays the requisite groundwork for future studies of specific biotransformation pathways used by woodrats to metabolize the

  16. Evaluating nest supplementation as a recovery strategy for the endangered rodents of the Florida Keys

    Science.gov (United States)

    Cove, Michael V.; Simons, Theodore R.; Gardner, Beth; Maurer, Andrew S.; O'Connell, Allan F.

    2017-01-01

    The Key Largo woodrat (Neotoma floridana smalli) and Key Largo cotton mouse (Peromyscus gossypinus allapaticola) are federally endangered subspecies endemic to the tropical hardwood hammocks of Key Largo, Florida. Woodrats are considered generalists in habitat and diet, yet a steady decline in natural stick nests and capture rates over the past several decades suggests that they are limited by the availability of nesting habitat due to habitat loss and fragmentation. The more specialized Key Largo cotton mouse appears to rely on old growth hammock, a habitat type that is rare following past land clearing. In 2004, the U.S. Fish and Wildlife Service started building supplemental nest structures to restore habitat quality and connectivity for these endangered rodents, but nest use requires evaluation. We used camera traps and occupancy models to evaluate the factors influencing woodrat and cotton mouse use of the supplemental nests. We detected woodrats at 65 and cotton mice at 175 of 284 sampled nest structures, with co-occurrence at 38 nests. Woodrat nest use followed a gradient from low nest use in the north to high nest use in the south, which might relate to the proximity of free-ranging domestic cat (Felis catus) colonies in residential developments. Cotton mouse nest use, however, was related positively to mature hammock and related negatively to disturbed areas (e.g. scarified lands). The two species occurred independently of each other. Stick-stacking behavior was observed at supplemental nests and, although it was correlated with detection of woodrats, it was not a strong predictor of their occurrence. We suggest that nest supplementation can be an important tool for species recovery as habitat quality continues to improve with succession.

  17. Experience matters: prior exposure to plant toxins enhances diversity of gut microbes in herbivores.

    Science.gov (United States)

    Kohl, Kevin D; Dearing, M D

    2012-09-01

    For decades, ecologists have hypothesised that exposure to plant secondary compounds (PSCs) modifies herbivore-associated microbial community composition. This notion has not been critically evaluated in wild mammalian herbivores on evolutionary timescales. We investigated responses of the microbial communities of two woodrat species (Neotoma bryanti and N. lepida). For each species, we compared experienced populations that independently converged to feed on the same toxic plant (creosote bush, Larrea tridentata) to naïve populations with no exposure to creosote toxins. The addition of dietary PSCs significantly altered gut microbial community structure, and the response was dependent on previous experience. Microbial diversity and relative abundances of several dominant phyla increased in experienced woodrats in response to PSCs; however, opposite effects were observed in naïve woodrats. These differential responses were convergent in experienced populations of both species. We hypothesise that adaptation of the foregut microbiota to creosote PSCs in experienced woodrats drives this differential response. © 2012 Blackwell Publishing Ltd/CNRS.

  18. Late holocene climate derived from vegetation history and plant cellulose stable isotope records from the Great Basin of western North America

    International Nuclear Information System (INIS)

    Wigand, P.E.; Hemphill, M.L.; Patra, S.M.

    1994-01-01

    Integration of pollen records, and fossil woodrat midden data recovered from multiple strata of fossil woodrat (Neotoma spp.) dens (middens) in both northern and southern Nevada reveal a detailed paleoclimatic proxy record for the Great Basin during the last 45,000 years in growing detail. Clear, late Holocene climate-linked elevational depressions of plant species' distributions have occurred throughout the Great Basin of up to 200 m below today's and by as much as 1000 m below what they were during the middle Holocene. Horizontal plant range extentions during the Holocene reflecting the final northern most adjustments to Holocene climates range up to several hundred kilometers in the Great Basin. Well documented lags evidenced in the late Holocene response of vegetation communities to increased precipitation indicate reduced effectiveness in the ability of plant communities to assimilate excess precipitation. This resulted in significant runoff that was available for recharge. These responses, although indicating both rapid and dramatic fluctuations of climate for the Holocene, fall far short of the scale of such changes during the late Pleistocene. Extension of these results to Pleistocene woodrat den and pollen data evidence spans lasting several hundred to a thousand or more years during which significantly greater amounts of precipitation would have been available for runnoff or recharge

  19. Estudos sobre a resistência ao jejum e aspectos nutricionais de Triatoma lecticularia (Stal, 1859 (Hemiptera, Reduviidae, Triatominae Studies on the resistance to fasting and nutritional aspects of Triatoma lecticularia (Stal, 1859 (Hemiptera, Reduviidae, Triatominae

    Directory of Open Access Journals (Sweden)

    José Jurberg

    1989-09-01

    Full Text Available Foi feito um estudo sobre a resistência ao jejum em todas as fases evolutivas e pesagens em diferentes situações nutricionais de Triatoma lecticularia (alimentado; não alimentado; na morte após o jejum com temperatura e umidade registradas. Observou-se que os períodos de resistência das fases ninfais apresentaram médias (dias crescentes: 1º: 45,84; 2º: 61; 3º: 88,74; 4º: 123,47; 5º 162,30. Na fase adulta as médias foram aproximadas à do 3º estádio (para os machos 88,94 e para as fêmeas 83,66. O procedimento de pesagens permitiu registrar a quantidade de sangue ingerido, a perda de peso durante o jejum e o respectivo percentual em relação ao peso inicial. Esta espécie tem assinalada sua distribuição geográfica na região Neártica, onde tem sido encontrda infectada com Trypanosoma cruzi associada a Neotoma micropus Baird e Spermophilus variagatus (Erxeleben.The resistance to fasting of Triatoma lecticularia was studied in all phases of the life cycle and the insect weighed in different nutritional situations (fed, not fed, death after starvation. The temperature and humidity level were also recorded. The nymphal phases showed increasing resistance to fasting as demonstrated by the following averages (days 1st 45.84; 2nd 61; 3rd 88.74; 4th 123.44; 5th 162.30. Upon the adult phase, the averages were similar to those of the 3rd stage for the male insects 88.94 and for females 83.66. The weighing technique allowed for the measeurement of the quantity of blood ingested, the weight loss during the fast and the percentage weight lost as related to the initial weight. The species is found in the Neartic region where it has been found infected with Trypanosoma cruzi and is associated with the terrestial rodents Neotoma micropus Baird and Spermophilus variagatus (Erxelebem.

  20. Scat removal: A source of bias in feces-related studies

    Science.gov (United States)

    Livingston, T.R.; Gipson, P.S.; Ballard, W.B.; Sanchez, D.M.; Krausman, P.R.

    2005-01-01

    Consumption of feces (coprophagy) may alter findings of dietary studies and population estimates based on fecal analyses, but its magnitude is poorly understood. We investigated seasonal incidence of scat removal on Fort Riley, Kansas, from January through December 2000. We placed feces from captive bobcats (Lynx rufus), captive coyotes (Canis latrans), and free-ranging coyotes randomly on tracking stations in forest and prairie landscapes to determine rates of scat removal by local wildlife. Rates of removal of feces from captive bobcats, captive coyotes, and free-ranging coyotes varied from 7% during spring to 50% during summer. We identified opossums (Didelphis virginiana) as the most common species present at stations where scat removal occurred. Feces may be an important seasonal source of food for opossums and may provide seasonal dietary supplements for other species. Other factors responsible for disturbance of feces included a woodrat (Neotoma floridana) caching coyote feces, removal of captive coyote feces by free-ranging coyotes accompanied by deposition of fresh feces, a bobcat burying a captive bobcat sample and depositing fresh feces, and rain storms. Dietary studies based on fecal analyses could be biased by scat removal, assuming that contents in feces are representative of the proportion of foods consumed.

  1. Modeling time-series data from microbial communities.

    Science.gov (United States)

    Ridenhour, Benjamin J; Brooker, Sarah L; Williams, Janet E; Van Leuven, James T; Miller, Aaron W; Dearing, M Denise; Remien, Christopher H

    2017-11-01

    As sequencing technologies have advanced, the amount of information regarding the composition of bacterial communities from various environments (for example, skin or soil) has grown exponentially. To date, most work has focused on cataloging taxa present in samples and determining whether the distribution of taxa shifts with exogenous covariates. However, important questions regarding how taxa interact with each other and their environment remain open thus preventing in-depth ecological understanding of microbiomes. Time-series data from 16S rDNA amplicon sequencing are becoming more common within microbial ecology, but methods to infer ecological interactions from these longitudinal data are limited. We address this gap by presenting a method of analysis using Poisson regression fit with an elastic-net penalty that (1) takes advantage of the fact that the data are time series; (2) constrains estimates to allow for the possibility of many more interactions than data; and (3) is scalable enough to handle data consisting of thousands of taxa. We test the method on gut microbiome data from white-throated woodrats (Neotoma albigula) that were fed varying amounts of the plant secondary compound oxalate over a period of 22 days to estimate interactions between OTUs and their environment.

  2. Induced and constitutive responses of digestive enzymes to plant toxins in an herbivorous mammal.

    Science.gov (United States)

    Kohl, Kevin D; Dearing, M Denise

    2011-12-15

    Many plants produce plant secondary compounds (PSCs) that bind and inhibit the digestive enzymes of herbivores, thus limiting digestibility for the herbivore. Herbivorous insects employ several physiological responses to overcome the anti-nutritive effects of PSCs. However, studies in vertebrates have not shown such responses, perhaps stemming from the fact that previously studied vertebrates were not herbivorous. The responses of the digestive system to dietary PSCs in populations of Bryant's woodrat (Neotoma bryanti) that vary in their ecological and evolutionary experience with the PSCs in creosote bush (Larrea tridentata) were compared. Individuals from naïve and experienced populations were fed diets with and without added creosote resin. Animals fed diets with creosote resin had higher activities of pancreatic amylase, as well as luminal amylase and chymotrypsin, regardless of prior experience with creosote. The experienced population showed constitutively higher activities of intestinal maltase and sucrase. Additionally, the naïve population produced an aminopeptidase-N enzyme that was less inhibited by creosote resin when feeding on the creosote resin diet, whereas the experienced population constitutively expressed this form of aminopeptidase-N. Thus, the digestive system of an herbivorous vertebrate responds significantly to dietary PSCs, which may be important for allowing herbivorous vertebrates to feed on PSC-rich diets.

  3. Anthropogenic water sources and the effects on Sonoran Desert small mammal communities

    Directory of Open Access Journals (Sweden)

    Aaron B. Switalski

    2017-11-01

    Full Text Available Anthropogenic water sources (AWS are developed water sources used as a management tool for desert wildlife species. Studies documenting the effects of AWS are often focused on game species; whereas, the effects on non-target wildlife are less understood. We used live trapping techniques to investigate rodent abundance, biomass, and diversity metrics near AWS and paired control sites; we sampled vegetation to determine rodent-habitat associations in the Sauceda Mountains of the Sonoran Desert in Arizona. A total of 370 individual mammals representing three genera and eight species were captured in 4,800 trap nights from winter 2011 to spring 2012. A multi-response permutation procedure was used to identify differences in small mammal community abundance and biomass by season and treatment. Rodent abundance, biomass, and richness were greater at AWS compared to control sites. Patterns of abundance and biomass were driven by the desert pocket mouse (Chaetodipus penicillatus which was the most common capture and two times more numerous at AWS compared to controls. Vegetation characteristics, explored using principal components analysis, were similar between AWS and controls. Two species that prefer vegetation structure, Bailey’s pocket mouse (C. baileyi and white-throated woodrat (Neotoma albigula, had greater abundances and biomass near AWS and were associated with habitat having high cactus density. Although small mammals do not drink free-water, perhaps higher abundances of some species of desert rodents at AWS could be related to artificial structure associated with construction or other resources. Compared to the 30-year average of precipitation for the area, the period of our study occurred during a dry winter. During dry periods, perhaps AWS provide resources to rodents related to moisture.

  4. Anthropogenic water sources and the effects on Sonoran Desert small mammal communities.

    Science.gov (United States)

    Switalski, Aaron B; Bateman, Heather L

    2017-01-01

    Anthropogenic water sources (AWS) are developed water sources used as a management tool for desert wildlife species. Studies documenting the effects of AWS are often focused on game species; whereas, the effects on non-target wildlife are less understood. We used live trapping techniques to investigate rodent abundance, biomass, and diversity metrics near AWS and paired control sites; we sampled vegetation to determine rodent-habitat associations in the Sauceda Mountains of the Sonoran Desert in Arizona. A total of 370 individual mammals representing three genera and eight species were captured in 4,800 trap nights from winter 2011 to spring 2012. A multi-response permutation procedure was used to identify differences in small mammal community abundance and biomass by season and treatment. Rodent abundance, biomass, and richness were greater at AWS compared to control sites. Patterns of abundance and biomass were driven by the desert pocket mouse ( Chaetodipus penicillatus ) which was the most common capture and two times more numerous at AWS compared to controls. Vegetation characteristics, explored using principal components analysis, were similar between AWS and controls. Two species that prefer vegetation structure, Bailey's pocket mouse ( C. baileyi ) and white-throated woodrat ( Neotoma albigula) , had greater abundances and biomass near AWS and were associated with habitat having high cactus density. Although small mammals do not drink free-water, perhaps higher abundances of some species of desert rodents at AWS could be related to artificial structure associated with construction or other resources. Compared to the 30-year average of precipitation for the area, the period of our study occurred during a dry winter. During dry periods, perhaps AWS provide resources to rodents related to moisture.

  5. Wildfires alter rodent community structure across four vegetation types in southern California, USA

    Science.gov (United States)

    Brehme, Cheryl S.; Clark, Denise R.; Rochester, Carlton J.; Fisher, Robert N.

    2011-01-01

    We surveyed burned and unburned plots across four habitat reserves in San Diego County, California, USA, in 2005 and 2006, to assess the effects of the 2003 wildfires on the community structure and relative abundance of rodent species. The reserves each contained multiple vegetation types (coastal sage scrub, chaparral, woodland, and grassland) and spanned from 250 m to 1078 m in elevation. Multivariate analyses revealed a more simplified rodent community structure in all burned habitats in comparison to unburned habitats. Reduction in shrub and tree cover was highly predictive of changes in post-fire rodent community structure in the burned coastal sage scrub and chaparral habitats. Reduction in cover was not predictive for the less substantially burned woodlands and grasslands, for which we hypothesized that interspecific competition played a greater role in post-fire community structure. Across vegetation types, generalists and open habitat specialists typically increased in relative abundance, whereas closed habitat specialists decreased. We documented significant increases in relative abundance of the deer mouse (Peromyscus maniculatus Wagner) and Dulzura kangaroo rat (Dipodomys simulans Merriam). In contrast, we found significant decreases in relative abundance for the California mouse (Peromyscus californicus Gambel), San Diego pocket mouse (Chaetodipus fallax Merriam), desert woodrat (Neotoma lepida Thomas), and brush mouse (Peromyscus boylii Baird). Currently, our research program involves assessment of whether habitat conservation plans (HCPs) in southern California provide long-term protection to HCP covered species, as well as preserve ecosystem function. The scenario of increased wildfires needs to be incorporated into this assessment. We discuss our results in relation to management and conservation planning under a future scenario of larger and more frequent wildfires in southern California.

  6. Community-Supported Data Repositories in Paleobiology: A 'Middle Tail' Between the Geoscientific and Informatics Communities

    Science.gov (United States)

    Williams, J. W.; Ashworth, A. C.; Betancourt, J. L.; Bills, B.; Blois, J.; Booth, R.; Buckland, P.; Charles, D.; Curry, B. B.; Goring, S. J.; Davis, E.; Grimm, E. C.; Graham, R. W.; Smith, A. J.

    2015-12-01

    Community-supported data repositories (CSDRs) in paleoecology and paleoclimatology have a decades-long tradition and serve multiple critical scientific needs. CSDRs facilitate synthetic large-scale scientific research by providing open-access and curated data that employ community-supported metadata and data standards. CSDRs serve as a 'middle tail' or boundary organization between information scientists and the long-tail community of individual geoscientists collecting and analyzing paleoecological data. Over the past decades, a distributed network of CSDRs has emerged, each serving a particular suite of data and research communities, e.g. Neotoma Paleoecology Database, Paleobiology Database, International Tree Ring Database, NOAA NCEI for Paleoclimatology, Morphobank, iDigPaleo, and Integrated Earth Data Alliance. Recently, these groups have organized into a common Paleobiology Data Consortium dedicated to improving interoperability and sharing best practices and protocols. The Neotoma Paleoecology Database offers one example of an active and growing CSDR, designed to facilitate research into ecological and evolutionary dynamics during recent past global change. Neotoma combines a centralized database structure with distributed scientific governance via multiple virtual constituent data working groups. The Neotoma data model is flexible and can accommodate a variety of paleoecological proxies from many depositional contests. Data input into Neotoma is done by trained Data Stewards, drawn from their communities. Neotoma data can be searched, viewed, and returned to users through multiple interfaces, including the interactive Neotoma Explorer map interface, REST-ful Application Programming Interfaces (APIs), the neotoma R package, and the Tilia stratigraphic software. Neotoma is governed by geoscientists and provides community engagement through training workshops for data contributors, stewards, and users. Neotoma is engaged in the Paleobiological Data Consortium

  7. The bush Karoo rat Otomys unisulcatus on the Cape West coast

    African Journals Online (AJOL)

    1987-06-05

    Jun 5, 1987 ... In its habit of constructing lodges O. unisulcatus parallels the woodrats ..... crustacean, and three of arachnids were represented. On a numerical basis ..... activity patterns, food and feeding behaviour of. Parotomys brantsii ...

  8. Sensitivity of Coastal Environments and Wildlife to Spilled Oil: Hudson River: T_MAMMAL (Terrestrial Mammal Polygons)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains sensitive biological resource data for small terrestrial mammals (woodrats, myotis, muskrat, mink) for the Hudson River. Vector polygons in...

  9. Paleomadrigueras de roedores, un nuevo método para el estudio del Cuaternario en zonas áridas de Sudamérica Rodent middens, a new method for Quaternary research in arid zones of South America

    Directory of Open Access Journals (Sweden)

    Julio L. Betancourt

    2002-09-01

    formadores. Basados en la experiencia Norteamericana entregamos además, un resumen de los métodos existentes para la detección y análisis de dichos depósitos, los sesgos asociados, así como el aporte potencial que su análisis podría representar en futuros estudios paleoecológicos en las zonas áridas y semiáridas de SudaméricaIn arid and semi-arid regions of South America, historical evidence for climate and vegetation change is scarce despite its importance for determining reference conditions and rates of natural variability in areas susceptible to modern desertification. Normal lines of evidence, such as pollen stratigraphies from lakes, are either rare or unobtainable in deserts; studies of late Quaternary vegetation history are few and generally inconclusive. This gap in knowledge may be corrected with discovery and development of fossil rodent middens in rocky environments throughout arid South America. These middens, mostly the work of Lagidium, Phyllotis, Abrocoma and Octodontomys, are rich in readily identifiable plant macrofossils, cuticles and pollen, as well as vertebrate and insect remains. In the North American deserts, more than 2,500 woodrat (Neotoma middens analyzed since 1960 have yielded a detailed history of environmental change during the past 40,000 years. Preliminary work in the pre-puna, Monte and Patagonian Deserts of western Argentina, the Atacama Desert of northern Chile/southern Peru, the Mediterranean matorral of central Chile, and the Puna of the Andean altiplano suggest a similar potential for rodent middens in South America. Here we borrow from the North American experience to synthesize methodologies and approaches, summarize preliminary work, and explore the potential of rodent midden research in South America

  10. Food habits of the Northern Spotted Owl (Strix occidentalis caurina) at six nest sites in Washington?s east Cascades

    Science.gov (United States)

    Kenneth R. Bevis; Jo Ellen Richards; Gina M. King; Eric E. Hanson

    1997-01-01

    This paper reports on 245 pellet samples containing 479 identified prey items collected at six Northern Spotted Owl (Strix occidentalis caurina) breeding sites in the eastern portion of its range. The majority of prey (biomass) came from four species; northern flying squirrels (Glaucomys sabrinus), bushy-tailed woodrats (...

  11. Hantavirus en roedores de la Octava Región de Chile Hantavirus in rodents of the VIII Region of Chile

    Directory of Open Access Journals (Sweden)

    JUAN CARLOS ORTIZ

    2004-06-01

    Full Text Available La Octava Región de Chile corresponde a la segunda región con el mayor número de casos de Síndrome Cardiopulmonar por Hantavirus (SCPH. Por tal motivo se realizó un estudio para detectar la presencia de anticuerpos contra hantavirus en roedores y su distribución local en la Octava Región. El estudio comprendió las cuatro provincias de la región y consideró once sitios de muestreo. Se capturaron siete especies de roedores, Abrothrix olivaceus fue la más abundante seguida de Oligoryzomys longicaudatus. De los 300 roedores analizados, cinco ejemplares (1,66 % resultaron ser positivos a hantavirus y correspondieron a tres especies de sigmodontinos: a saber, Loxodontomys micropus, que corresponde al único registro de este tipo para la especie en Chile, Abrotrix longipilis y Oligoryzomys longicaudatusThe Eight Region has the second highest number of cases of Hantavirus Cardiopulmonary Syndrome (HCPS in humans for Chile. A study was performed to identify the number of rodents serologically positive to hantavirus and their local distribution in this region. To achieve this goal, we sampled eleven sites in the four provinces of the region. Seven rodents species were collected, with Abrothrix olivaceus presenting the largest number of captures followed by Oligoryzomys longicaudatus. Of the 300 rodents analyzed, five (1.66 % were sero-positives to hantavirus and belonged to three different sigmodontine species: Abrothrix longipilis, O. longicaudatus, and Loxodontomys micropus. No previous records of seropositive L. micropus existed.

  12. Databases and their application

    NARCIS (Netherlands)

    Grimm, E.C.; Bradshaw, R.H.W; Brewer, S.; Flantua, S.; Giesecke, T.; Lézine, A.M.; Takahara, H.; Williams, J.W.,Jr; Elias, S.A.; Mock, C.J.

    2013-01-01

    During the past 20 years, several pollen database cooperatives have been established. These databases are now constituent databases of the Neotoma Paleoecology Database, a public domain, multiproxy, relational database designed for Quaternary-Pliocene fossil data and modern surface samples. The

  13. Competitive interactions and resource partitioning between northern spotted owls and barred owls in western Oregon

    Science.gov (United States)

    Wiens, J. David; Anthony, Robert G.; Forsman, Eric D.

    2014-01-01

    with minimal spatial overlap among core-use areas. We used an information-theoretic approach to rank discrete-choice models representing alternative hypotheses about the influence of forest conditions, topography, and interspecific interactions on species-specific patterns of nighttime resource selection. Spotted owls spent a disproportionate amount of time foraging on steep slopes in ravines dominated by old (>120 yr) conifer trees. Barred owls used available forest types more evenly than spotted owls, and were most strongly associated with patches of large hardwood and conifer trees that occupied relatively flat areas along streams. Spotted and barred owls differed in the relative use of old conifer forest (greater for spotted owls) and slope conditions (steeper slopes for spotted owls), but we found no evidence that the 2 species differed in their use of young, mature, and riparian-hardwood forest types. Mean overlap in proportional use of different forest types between individual spotted owls and barred owls in adjacent territories was 81% (range = 30–99%). The best model of habitat use for spotted owls indicated that the relative probability of a location being used was substantially reduced if the location was within or in close proximity to a core-use area of a barred owl. We used pellet analysis and measures of food-niche overlap to determine the potential for dietary competition between spatially associated pairs of spotted owls and barred owls. We identified 1,223 prey items from 15 territories occupied by spotted owls and 4,299 prey items from 24 territories occupied by barred owls. Diets of both species were dominated by nocturnal mammals, but diets of barred owls included many terrestrial, aquatic, and diurnal prey species that were rare or absent in diets of spotted owls. Northern flying squirrels (Glaucomys sabrinus), woodrats (Neotoma fuscipes, N. cinerea), and lagomorphs (Lepus americanus, Sylvilagus bachmani) were primary prey for both owl

  14. Examination of Habitat Fragmentation and Effects on Species Persistence in the Vicinity of Naval Base Pt. Loma and Marine Corps Air Station Miramar, San Diego, CA and Development of a Multi-Species Planning Framework for Fragmented Landscapes

    Science.gov (United States)

    2011-02-01

    Chaparral. Ecological Monographs 70:149-169. Pausas, J. G. 2004. Changes in fire and climate in the eastern Iberian Peninsula (Mediterranean basin...3.2.1  Current Climate and Future Climate Projections ...................................................... 19  3.2.2  Future Habitat Loss and...study area—1953, 1974, 1984, 1995, and 2005. .................. 37  Figure 21. Maxent projections for Neotoma macrotis and underlying climate variables

  15. The Power of Comparative Physiology: Evolution, Integration and Applied

    Science.gov (United States)

    2003-03-01

    and olive ridley marine turtle hatchlings. T.T. Jones, R.R. Reina Symposium and P.L. Lutz. Florida Atlantic Univ., Boca 44.0 REGULATION OF VERTEBRATE... preference of 16[deg]C acclimated emabs was a genseralist woodrat, with a choice bersween control anod 50% juniper diet under Wsarm (26 1 4.6fdeg]C and thsey...and Olive Ridley Marine Turtle Harvey B. Lillywhite’, Jaishri G. Mceon2, Gopinathan K. Menon’. Ming C. Tuo: ’University, Hatchllngs of Florida

  16. Environmental Impact Analysis Process. Deployment Area Selection and Land Withdrawal/Acquisition DEIS. Chapter III. Part I. Affected Environment.

    Science.gov (United States)

    1980-12-01

    oodrat x Yeootos ;epxda K Porcupine £retizon dorsatux RABITS Black-tailed Jackrabbit x x Lepus californicu$ Desert Cottontail a x x Slv ilaqu...Neocoma sucropus X K White-throated Woodrat .V. uIb~qula K K X 1orway Bt RCtus no*#eqieoa K K 4UMOUS oiS -Nba ms~gc-1.8 x Porcupine tre Chison Soreatum K...and 200 in Potter counties (Travis, 1980). An annual aerial census of pronghorn shows that the bulk of the antelope herd is found in the northern

  17. ORF Alignment: NC_003318 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_003318 gi|17989189 >1bxwA 4 170 40 240 2e-16 ... gb|AAN33618.1| outer membrane protein Omp3...1 [Brucella suis 1330] gb|AAS84567.1| ... Omp31 [Brucella cetaceae] gb|AAS84566.1| Omp31 [Br...ucella ... cetaceae] gb|AAS84565.1| Omp31 [Brucella pinnipediae] ... gb|AAS84564.1| Omp31 [Bru...nsis] ... gb|AAL27297.1| outer membrane protein Omp31 [Brucella ... melitensis biovar Neotomae...] gb|AAL27290.1| outer ... membrane protein Omp31 [Brucella melitensis biovar Suis] ... gb|AAL

  18. ORF Alignment: NC_004310 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_004310 gi|23502485 >1bxwA 4 170 45 261 5e-15 ... gb|AAN30527.1| outer membrane protein Omp3...1 [Brucella suis 1330] gb|AAS84575.1| ... Omp31b [Brucella cetaceae] gb|AAS84574.1| Omp31b ... ... ... [Brucella cetaceae] gb|AAS84573.1| Omp31b [Brucella ... cetaceae] gb|AAS84572.1| Omp31b [Br...ucella pinnipediae] ... gb|AAS84571.1| Omp31b [Brucella melitensis biovar ... ... Neotomae] ref|NP_698612.1| outer membrane protein Omp31 ... [Brucella suis 1330] ...

  19. Borrelia bissettiae sp. nov. and Borrelia californiensis sp. nov. prevail in diverse enzootic transmission cycles.

    Science.gov (United States)

    Margos, Gabriele; Lane, Robert S; Fedorova, Natalia; Koloczek, Johannes; Piesman, Joseph; Hojgaard, Andrias; Sing, Andreas; Fingerle, Volker

    2016-03-01

    Two species of the genus Borrelia , Borrelia bissettiae sp. nov. and Borrelia californiensis sp. nov., were first described by Postic and co-workers on the basis of genetic analyses of several loci. Multilocus sequence analysis of eight housekeeping loci confirmed that these two Borrelia genomospecies are distinct members of the Borrelia burgdorferi sensu lato complex. B. bissettiae sp. nov. was initially described in transmission cycles involving Neotoma fuscipes wood rats and Ixodes pacificus ticks in California, and Neotoma mexicana and Ixodes spinipalpis in Colorado. The preferred host of B. californiensis sp. nov. appears to be the California kangaroo rat, Dipodomys californicus ; Ixodes jellisoni , I. spinipalipis and I. pacificus ticks are naturally infected with it. Thus, the ecological associations of the two genomospecies and their genetic distance from all other known Borrelia genomospecies species justify their description as separate genomospecies: B. bissettiae sp. nov. (type strain DN127 T  = DSM 17990 T  =  CIP 109136 T ) and B. californiensis (type strain CA446 T  = DSM 17989 T  = ATCC BAA-2689 T ).

  20. Identification of Brucella genus and eight Brucella species by Luminex bead-based suspension array.

    Science.gov (United States)

    Lusk Pfefer, Tina S; Timme, Ruth; Kase, Julie A

    2018-04-01

    Globally, unpasteurized milk products are vehicles for the transmission of brucellosis, a zoonosis responsible for cases of foodborne illness in the United States and elsewhere. Existing PCR assays to detect Brucella species are restricted by the resolution of band sizes on a gel or the number of fluorescent channels in a single real-time system. The Luminex bead-based suspension array is performed in a 96-well plate allowing for high throughput screening of up to 100 targets in one sample with easily discernible results. We have developed an array using the Bio-Plex 200 to differentiate the most common Brucella species: B. abortus, B. melitensis, B. suis, B. suis bv5, B. canis, B. ovis, B. pinnipedia, and B. neotomae, as well as Brucella genus. All probes showed high specificity, with no cross-reaction with non-Brucella strains. We could detect pure DNA from B. abortus, B. melitensis, and genus-level Brucella at concentrations of ≤5 fg/μL. Pure DNA from all other species tested positive at concentrations well below 500 fg/μL and we positively identified B. neotomae in six artificially contaminated cheese and milk products. An intra-laboratory verification further demonstrated the assay's accuracy and robustness in the rapid screening (3-4 h including PCR) of DNA. Published by Elsevier Ltd.

  1. The role of adaptations in two-strain competition for sylvatic Trypanosoma cruzi transmission.

    Science.gov (United States)

    Kribs-Zaleta, Christopher M; Mubayi, Anuj

    2012-01-01

    This study presents a continuous-time model for the sylvatic transmission dynamics of two strains of Trypanosoma cruzi enzootic in North America, in order to study the role that adaptations of each strain to distinct modes of transmission (classical stercorarian transmission on the one hand, and vertical and oral transmission on the other) may play in the competition between the two strains. A deterministic model incorporating contact process saturation predicts competitive exclusion, and reproductive numbers for the infection provide a framework for evaluating the competition in terms of adaptive trade-off between distinct transmission modes. Results highlight the importance of oral transmission in mediating the competition between horizontal (stercorarian) and vertical transmission; its presence as a competing contact process advantages vertical transmission even without adaptation to oral transmission, but such adaptation appears necessary to explain the persistence of (vertically-adapted) T. cruzi IV in raccoons and woodrats in the southeastern United States.

  2. Pneumocystosis in wild small mammals from California

    Science.gov (United States)

    Laakkonen, Juha; Fisher, Robert N.; Case, Ted J.

    2001-01-01

    Cyst forms of the opportunistic fungal parasite Pneumocystis carinii were found in the lungs of 34% of the desert shrew, Notiosorex crawfordi (n = 59), 13% of the ornate shrew, Sorex ornatus (n = 55), 6% of the dusky-footed wood rat, Neotoma fuscipes (n = 16), 2.5% of the California meadow vole,Microtus californicus (n = 40), and 50% of the California pocket mouse, Chaetodipus californicus (n= 2) caught from southern California between February 1998 and February 2000. Cysts were not found in any of the harvest mouse, Reithrodontomys megalotis (n = 21), California mouse,Peromyscus californicus (n = 20), brush mouse, Peromyscus boylii (n = 7) or deer mouse, Peromyscus maniculatus (n = 4) examined. All infections were mild; extrapulmonary infections were not observed. Other lung parasites detected were Hepatozoon sp./spp. from M. californicus andNotiosorex crawfordi, Chrysosporium sp. (Emmonsia) from M. californicus, and a nematode from S. ornatus.

  3. Multivariate spatiotemporal visualizations for mobile devices in Flyover Country

    Science.gov (United States)

    Loeffler, S.; Thorn, R.; Myrbo, A.; Roth, R.; Goring, S. J.; Williams, J.

    2017-12-01

    Visualizing and interacting with complex multivariate and spatiotemporal datasets on mobile devices is challenging due to their smaller screens, reduced processing power, and limited data connectivity. Pollen data require visualizing pollen assemblages spatially, temporally, and across multiple taxa to understand plant community dynamics through time. Drawing from cartography, information visualization, and paleoecology, we have created new mobile-first visualization techniques that represent multiple taxa across many sites and enable user interaction. Using pollen datasets from the Neotoma Paleoecology Database as a case study, the visualization techniques allow ecological patterns and trends to be quickly understood on a mobile device compared to traditional pollen diagrams and maps. This flexible visualization system can be used for datasets beyond pollen, with the only requirements being point-based localities and multiple variables changing through time or depth.

  4. Yucca Mountain program summary of research, site monitoring and technical review activities (January 1987--June 1988)

    International Nuclear Information System (INIS)

    1988-12-01

    Although studies of orbital mechanics provide speculative notions of future climatic trends, they cannot predict how these trends will manifest themselves in the immediate area around Yucca Mountain. The generally accepted approach to this question is to consider the climatic variations that have occurred during the last 10,000 years, and use these as a guide to the likely range of future variation in climate. However, because climatic studies around the world indicate that we are potentially on the verge of another ice age, we should also consider the conditions that predominated during the Pleistocene. The specific aim of this project is to derive the climatic history of Yucca Mountain during the last 20,000 years from the vegetation history. By integrating data obtained from pollen records, woodrat dens (middens), and tree-ring sequences from the Nevada Test Site (NTS) area, a regional climatic record is being generated that can be correlated to data obtained at Yucca Mountain to formulate a local climatic sequence there. This will then be used to determine the magnitude and frequency of climatic variation that have occurred during that time at Yucca Mountain. These data can then be used by other researchers to provide estimates of rainfall, recharge and soil chemical changes for modeling the past hydrology of Yucca Mountain

  5. Tularemia, plague, yersiniosis, and Tyzzer’s disease in wild rodents and lagomorphs in Canada: A review

    Science.gov (United States)

    Wobeser, Gary; Campbell, G. Douglas; Dallaire, André; McBurney, Scott

    2009-01-01

    Information related to infection of wild rodents or lagomorphs in Canada by Francisella tularensis, Yersinia pestis, other Yersinia spp., and Clostridium piliforme was searched for this study. Reports on tularemia in humans linked to these species came from diagnostic databases, literature, wildlife health specialists, and public health agencies. Tularemia has been diagnosed in 8 species of wild rodent and 2 species in the genus Lepus in Canada. Tularemia occurred in wild animals, or in humans associated with these species, in all jurisdictions except the Yukon and Nunavut. Tularemia was diagnosed most frequently in beaver, muskrats, and snowshoe hares, and although tularemia is closely linked to cottontail rabbits in the USA, it has not been reported in cottontails in Canada. Tularemia in humans was associated with muskrats and hares more commonly than with beaver. Plague was diagnosed in bushy-tailed woodrats in British Columbia in 1988. Based on surveys, Y. pestis may occur enzootically in southern Alberta, Saskatchewan, and British Columbia. Infection with Yersinia pseudotuberculosis and Y. enterocolitica has been diagnosed in beaver, muskrats, and snowshoe hares in many provinces. Tyzzer’s disease has been diagnosed in muskrats in British Columbia, Saskatchewan, Ontario, and Quebec and in snowshoe hares in Ontario. Infection with these bacteria is likely much more frequent than indicated by diagnostic records. PMID:20190973

  6. Development of a North American paleoclimate pollen-based reconstruction database application

    Science.gov (United States)

    Ladd, Matthew; Mosher, Steven; Viau, Andre

    2013-04-01

    Recent efforts in synthesizing paleoclimate records across the globe has warranted an effort to standardize the different paleoclimate archives currently available in order to facilitate data-model comparisons and hence improve our estimates of future climate change. It is often the case that the methodology and programs make it challenging for other researchers to reproduce the results for a reconstruction, therefore there is a need for to standardize paleoclimate reconstruction databases in an application specific to proxy data. Here we present a methodology using the open source R language using North American pollen databases (e.g. NAPD, NEOTOMA) where this application can easily be used to perform new reconstructions and quickly analyze and output/plot the data. The application was developed to easily test methodological and spatial/temporal issues that might affect the reconstruction results. The application allows users to spend more time analyzing and interpreting results instead of on data management and processing. Some of the unique features of this R program are the two modules each with a menu making the user feel at ease with the program, the ability to use different pollen sums, select one of 70 climate variables available, substitute an appropriate modern climate dataset, a user-friendly regional target domain, temporal resolution criteria, linear interpolation and many other features for a thorough exploratory data analysis. The application program will be available for North American pollen-based reconstructions and eventually be made available as a package through the CRAN repository by late 2013.

  7. Carbon isotopes from fossil packrat pellets and elevational movements of Utah agave plants reveal the Younger Dryas cold period in Grand Canyon, Arizona

    Science.gov (United States)

    Cole, K.L.; Arundel, S.T.

    2005-01-01

    Carbon isotopes in rodent fecal pellets were measured on packrat (Neotoma spp.) middens from the Grand Canyon, Arizona. The pellet samples reflect the abundance of cold-intolerant C4 and Crassulacean acid metabolism (CAM) plant species relative to the predominant C3 vegetation in the packrat diet. The temporal sequence of isotopic results suggests a temperature decline followed by a sharp increase corresponding to the B??lling/Aller??d-Younger Dryas - early Holocene sequence. This pattern was then tested using the past distribution of Utah agave (Agave utahensis). Spatial analyses of the range of this temperature-sensitive CAM species demonstrate that its upper elevational limit is controlled by winter minimum temperature. Applying this paleotemperature proxy to the past elevational limits of Utah agave suggests that minimum winter temperatures were ???8??C below modern values during the Last Glacial Maximum, 4.5-6.5 ??C below modern during the B??lling/Aller??d, and 7.5-8.7 ??C below modern during the early Younger Dryas. As the Younger Dryas terminated, temperatures warmed ???4 ??C between ca. 11.8 ka and 11.5 ka. These extreme fluctuations in winter minimum temperature have not been generally accepted for terrestrial paleoecological records from the arid southwestern United States, likely because of large statistical uncertainties of older radiocarbon results and reliance on proxies for summer temperatures, which were less affected. ?? 2005 Geological Society of America.

  8. Vegetation and climates of the last 45,000 years in the vicinity of the Nevada Test Site, south-central Nevada

    International Nuclear Information System (INIS)

    1985-01-01

    Major changes in the climate of the Nevada Test Site have occurred during the last 45,000 years. Understanding this climate variability is important in assessing the region's suitability for permanent nuclear-waste repositories. Future climatic changes probably will occur within the time the waste materials are hazardous. The nature and magnitude of previous fluctuations indicate the nature of future climatic change that may impact on a nuclear waste repository. Reconstructions of past vegetation are used to infer climatic conditions during the past 45,000 years. Plant macrofossils from ancient packrat (Neotoma spp.) middens provide the data for these analyses. Middens can be older than 50,000 years, and they are common in the region. Each contains abundant mummified plant fossils, representing the plant species growing within about 30 meters of the site. Radiocarbon-dated midden samples provide detailed records of climate-induced vegetation change. Increased atmospheric carbon dioxide within the next 500 years probably will result in a 2 0 to 3 0 C increase in annual temperature and intensified rainfall in the Nevada Test Site region. Analogs with previous glacial-interglacial cycles indicate that this ''superinterglacial'' may be no more than a relatively brief reversal in the protracted trend toward the next ice age. Current models indicate that, within the next 10,000 years, climatic conditions may be similar to those of the last glacial age

  9. Shasta ground sloth ( Nothrotheriops shastense hoffstetter) at Shelter Cave, New Mexico: Environment, diet, and extinction

    Science.gov (United States)

    Thompson, Robert S.; Van Devender, Thomas R.; Martin, Paul S.; Foppe, Theresa; Long, Austin

    1980-11-01

    Seven coprolites of the extinct Shasta ground sloth ( Nothrotheriops shastense) were recently discovered in the Los Angeles County Museum collection from Shelter Cave, New Mexico. Three dung balls provided radiocarbon ages of 11,330, 12,330 and 12,430 yr B.P. Packrat ( Neotoma) middens disclose a xeric juniper woodland at Shelter Cave during the sloth's occupation. Plant cuticles from the dung indicate that the ground sloth had a diet dominated by mormon tea ( Ephedra) and other xerophytic shrubs. Pollen spectra from the coprolites have high representations of anemophilous plants and low representations of the dietary items shown in the cuticle analysis. Fifteen radiocarbon dates of sloth dung obtained since 1974 strengthen the hypothesis that sloth extinction occurred about 11,000 yr B.P. Paleoenvironmental studies indicate that ground sloths lived in juniper woodlands and montane conifer communities. Nothrotheriops commonly dined on shrubs that are still present in these habitats. It is difficult to explain the demise of the Shasta ground sloth by climatic change or dietary stress. Human predation remains as a possible explanation; ground sloth extinction appears to coincide with the time of Clovis mammoth hunters.

  10. Advancement of knowledge of Brucella over the past 50 years.

    Science.gov (United States)

    Olsen, S C; Palmer, M V

    2014-11-01

    Fifty years ago, bacteria in the genus Brucella were known to cause infertility and reproductive losses. At that time, the genus was considered to contain only 3 species: Brucella abortus, Brucella melitensis, and Brucella suis. Since the early 1960s, at least 7 new species have been identified as belonging to the Brucella genus (Brucella canis, Brucella ceti, Brucella inopinata, Brucella microti, Brucella neotomae, Brucella ovis, and Brucella pinnipedialis) with several additional new species under consideration for inclusion. Although molecular studies have found such high homology that some authors have proposed that all Brucella are actually 1 species, the epidemiologic and diagnostic benefits for separating the genus based on phenotypic characteristics are more compelling. Although pathogenic Brucella spp have preferred reservoir hosts, their ability to infect numerous mammalian hosts has been increasingly documented. The maintenance of infection in new reservoir hosts, such as wildlife, has become an issue for both public health and animal health regulatory personnel. Since the 1960s, new information on how Brucella enters host cells and modifies their intracellular environment has been gained. Although the pathogenesis and histologic lesions of B. abortus, B. melitensis, and B. suis in their preferred hosts have not changed, additional knowledge on the pathology of these brucellae in new hosts, or of new species of Brucella in their preferred hosts, has been obtained. To this day, brucellosis remains a significant human zoonosis that is emerging or reemerging in many parts of the world. © The Author(s) 2014.

  11. Role of edge effect on small mammal populations in a forest fragment

    International Nuclear Information System (INIS)

    Wike, L.D.

    2000-01-01

    In many cases, edge effect may determine the distribution and densities of small mammal populations. In 1995 and 1998, a mark and recapture study was conducted at the Savannah River Site (SRS), Aiken, SC, to evaluate the role of forest edge habitat. The area studied was an abandoned home site that had been recently isolated by a timber harvest. Harvest activities left a distinct edge of old field and planted pine contrasting with a relatively xeric, mixed hardwood stand. Trapping was conducted for 17 days in 1995 and 14 days in 1998. Three 30 m by 150 m grids were placed in the clear-cut, edge, and hardwood interior habitats. For both years the principal species captured were Peromyscus gossypinus, P. polionotus, and Neotoma floridana. The edge habitat accounted for approximately 55 percent of all captures and nearly four times as many recaptures as the interior and clear-cut habitats. In 1998, greater numbers of N. floridana were trapped than in 1995. The results indicate that the use of edge habitat can be pronounced even within simple communities. Stewards of managed or restored habitats need to carefully consider the role of edge in these systems. In managed areas such as waste sites, movement of material within the food chain could be reduced by minimizing edge habitat around the points of contamination

  12. Stable isotope time-series in mammalian teeth: In situ δ18O from the innermost enamel layer

    Science.gov (United States)

    Blumenthal, Scott A.; Cerling, Thure E.; Chritz, Kendra L.; Bromage, Timothy G.; Kozdon, Reinhard; Valley, John W.

    2014-01-01

    Stable carbon and oxygen isotope ratios in mammalian tooth enamel are commonly used to understand the diets and environments of modern and fossil animals. Isotope variation during the period of enamel formation can be recovered by intra-tooth microsampling along the direction of growth. However, conventional sampling of the enamel surface provides highly time-averaged records in part due to amelogenesis. We use backscattered electron imaging in the scanning electron microscope (BSE-SEM) to evaluate enamel mineralization in developing teeth from one rodent and two ungulates. Gray levels from BSE-SEM images suggest that the innermost enamel layer, <20 μm from the enamel-dentine junction, is highly mineralized early in enamel maturation and therefore may record a less attenuated isotopic signal than other layers. We sampled the right maxillary incisor from a woodrat subjected to an experimentally induced water-switch during the period of tooth development, and demonstrate that secondary ion mass spectrometry (SIMS) can be used to obtain δ18O values with 4-5-μm spots from mammalian tooth enamel. We also demonstrate that SIMS can be used to discretely sample the innermost enamel layer, which is too narrow for conventional microdrilling or laser ablation. An abrupt δ18O switch of 16.0‰ was captured in breath CO2, a proxy for body water, while a laser ablation enamel surface intra-tooth profile of the left incisor captured a δ18O range of 12.1‰. The innermost enamel profile captured a δ18O range of 15.7‰, which approaches the full magnitude of δ18O variation in the input signal. This approach will likely be most beneficial in taxa such as large mammalian herbivores, whose teeth are characterized by less rapid mineralization and therefore greater attenuation of the enamel isotope signal.

  13. Paleohydrologic investigations in the vicinity of Yucca Mountain: Late Quaternary paleobotanical and polynological records

    International Nuclear Information System (INIS)

    Spaulding, W.G.

    1994-01-01

    The primary objective of this research in the vicinity of the proposed Yucca Mountain Nuclear Waste Repository is the detection of episodes of increased runoff and groundwater discharge in this presently arid area. Ancient, inactive spring deposits in nearby valley bottoms (Haynes, 1967; Quade, 1986; Quade and Pratt, 1989), evidence for perennial water in presently dry canyons (Spaulding, 1992), and recent claims for extraordinary increases in precipitation during the last glacial age (Forester, 1994), provide good reason to further investigate both lowland spring-discharge habitats, and upland drainages. The ultimate purpose is to assess the long-term variability of the hydrologic system in the vicinity of Yucca Mountain in response to naturally occurring climatic changes. The data generated in the course of this study are derived from radiocarbon dated packrat (Neotoma) middens. This report presents the results of an initial assessment of the hydrologic stability of the candidate area based on a limited suite of middens from localities that, on geomorphic and hydrologic grounds, could have been close to ancient stream-side or spring environments. Paleoclimatic reconstructions are another means of studying the long-term climatic hydrologic stability of the Candidate Area include, and are also generated from packrat midden data. A different flora characterized the Candidate Area during the last glacial age in response to a cooler and wetter climate, and the plant species that comprised this flora can be used to reconstruct specific components of past climatic regimes. Thus, a secondary objective of this study is to compare the plant macrofossil data generated in this study to other records from the Candidate Area (Spaulding, 1985; Wigand, 1990) to determine if these new data are consistent with prior reconstructions. 66 refs., 4 figs., 13 tabs

  14. A repA-based ELISA for discriminating cattle vaccinated with Brucella suis 2 from those naturally infected with Brucella abortus and Brucella melitensis.

    Science.gov (United States)

    Wang, Jing-Yu; Wu, Ning; Liu, Wan-Hua; Ren, Juan-Juan; Tang, Pan; Qiu, Yuan-Hao; Wang, Chi-Young; Chang, Ching-Dong; Liu, Hung-Jen

    2014-01-01

    The commonest ways of diagnosing brucellosis in animals include the Rose-Bengal plate agglutination test, the buffered plate agglutination test (BPA), the slide agglutination test, the complement fixation test, and the indirect enzyme linked immunosorbent assay (I-ELISA). However, these methods cannot discriminate the Brucella vaccine strain (Brucella suis strain 2; B. suis S2) from naturally acquired virulent strains. Of the six common Brucella species, Brucella melitensis, Brucella abortus, and B. suis are the commonest species occurring in China. To develop an ELISA assay that can differentiate between cows inoculated with B. suis S2 and naturally infected with B. abortus and B. melitensis, genomic sequences from six Brucella spp. (B. melitensis, B. abortus, B. suis, Brucella canis, Brucella neotomae and Brucella ovis) were compared using Basic Local Alignment Search Tool software. One particular gene, the repA-related gene, was found to be a marker that can differentiate B. suis from B. abortus and B. melitensis. The repA-related gene of B. suis was PCR amplified and subcloned into the pET-32a vector. Expressed repA-related protein was purified and used as an antigen. The repA-based ELISA was optimized and used as specific tests. In the present study, serum from animals inoculated with the B. suis S2 vaccine strain had positive repA-based ELISA results. In contrast, the test-positive reference sera against B. abortus and B. melitensis had negative repA-based ELISA results. The concordance rate between B. abortus antibody-negative (based on the repA-based ELISA) and the Brucella gene-positive (based on the 'Bruce ladder' multiplex PCR) was 100%. Therefore, the findings suggest that the repA-based ELISA is a useful tool for differentiating cows vaccinated with the B. suis S2 and naturally infected with B. abortus and B. melitensis. Copyright © 2014 Elsevier Ltd. All rights reserved.

  15. Characterisation of the genetic diversity of Brucella by multilocus sequencing

    Directory of Open Access Journals (Sweden)

    MacMillan Alastair P

    2007-04-01

    Full Text Available Abstract Background Brucella species include economically important zoonotic pathogens that can infect a wide range of animals. There are currently six classically recognised species of Brucella although, as yet unnamed, isolates from various marine mammal species have been reported. In order to investigate genetic relationships within the group and identify potential diagnostic markers we have sequenced multiple genetic loci from a large sample of Brucella isolates representing the known diversity of the genus. Results Nine discrete genomic loci corresponding to 4,396 bp of sequence were examined from 160 Brucella isolates. By assigning each distinct allele at a locus an arbitrary numerical designation the population was found to represent 27 distinct sequence types (STs. Diversity at each locus ranged from 1.03–2.45% while overall genetic diversity equated to 1.5%. Most loci examined represent housekeeping gene loci and, in all but one case, the ratio of non-synonymous to synonymous change was substantially Brucella species, B. abortus, B. melitensis, B. ovis and B. neotomae correspond to well-separated clusters. With the exception of biovar 5, B. suis isolates cluster together, although they form a more diverse group than other classical species with a number of distinct STs corresponding to the remaining four biovars. B. canis isolates are located on the same branch very closely related to, but distinguishable from, B. suis biovar 3 and 4 isolates. Marine mammal isolates represent a distinct, though rather weakly supported, cluster within which individual STs display one of three clear host preferences. Conclusion The sequence database provides a powerful dataset for addressing ongoing controversies in Brucella taxonomy and a tool for unambiguously placing atypical, phenotypically discordant or newly emerging Brucella isolates. Furthermore, by using the phylogenetic backbone described here, robust and rationally selected markers for use in

  16. The genome sequence of Brucella pinnipedialis B2/94 sheds light on the evolutionary history of the genus Brucella

    Directory of Open Access Journals (Sweden)

    Claverie Jean-Michel

    2011-07-01

    Full Text Available Abstract Background Since the discovery of the Malta fever agent, Brucella melitensis, in the 19th century, six terrestrial mammal-associated Brucella species were recognized over the next century. More recently the number of novel Brucella species has increased and among them, isolation of species B. pinnipedialis and B. ceti from marine mammals raised many questions about their origin as well as on the evolutionary history of the whole genus. Results We report here on the first complete genome sequence of a Brucella strain isolated from marine mammals, Brucella pinnipedialis strain B2/94. A whole gene-based phylogenetic analysis shows that five main groups of host-associated Brucella species rapidly diverged from a likely free-living ancestor close to the recently isolated B. microti. However, this tree lacks the resolution required to resolve the order of divergence of those groups. Comparative analyses focusing on a genome segments unshared between B. microti and B. pinnipedialis, b gene deletion/fusion events and c positions and numbers of Brucella specific IS711 elements in the available Brucella genomes provided enough information to propose a branching order for those five groups. Conclusions In this study, it appears that the closest relatives of marine mammal Brucella sp. are B. ovis and Brucella sp. NVSL 07-0026 isolated from a baboon, followed by B. melitensis and B. abortus strains, and finally the group consisting of B. suis strains, including B. canis and the group consisting of the single B. neotomae species. We were not able, however, to resolve the order of divergence of the two latter groups.

  17. The genome sequence of Brucella pinnipedialis B2/94 sheds light on the evolutionary history of the genus Brucella

    Science.gov (United States)

    2011-01-01

    Background Since the discovery of the Malta fever agent, Brucella melitensis, in the 19th century, six terrestrial mammal-associated Brucella species were recognized over the next century. More recently the number of novel Brucella species has increased and among them, isolation of species B. pinnipedialis and B. ceti from marine mammals raised many questions about their origin as well as on the evolutionary history of the whole genus. Results We report here on the first complete genome sequence of a Brucella strain isolated from marine mammals, Brucella pinnipedialis strain B2/94. A whole gene-based phylogenetic analysis shows that five main groups of host-associated Brucella species rapidly diverged from a likely free-living ancestor close to the recently isolated B. microti. However, this tree lacks the resolution required to resolve the order of divergence of those groups. Comparative analyses focusing on a) genome segments unshared between B. microti and B. pinnipedialis, b) gene deletion/fusion events and c) positions and numbers of Brucella specific IS711 elements in the available Brucella genomes provided enough information to propose a branching order for those five groups. Conclusions In this study, it appears that the closest relatives of marine mammal Brucella sp. are B. ovis and Brucella sp. NVSL 07-0026 isolated from a baboon, followed by B. melitensis and B. abortus strains, and finally the group consisting of B. suis strains, including B. canis and the group consisting of the single B. neotomae species. We were not able, however, to resolve the order of divergence of the two latter groups. PMID:21745361

  18. Development of a bead-based Luminex assay using lipopolysaccharide specific monoclonal antibodies to detect biological threats from Brucella species.

    Science.gov (United States)

    Silbereisen, Angelika; Tamborrini, Marco; Wittwer, Matthias; Schürch, Nadia; Pluschke, Gerd

    2015-10-05

    Brucella, a Gram-negative bacterium, is classified as a potential bioterrorism agent mainly due to the low dose needed to cause infection and the ability to transmit the bacteria via aerosols. Goats/sheep, cattle, pigs, dogs, sheep and rodents are infected by B. melitensis, B. abortus, B. suis, B. canis, B. ovis and B. neotomae, respectively, the six classical Brucella species. Most human cases are caused by B. melitensis and B. abortus. Our aim was to specifically detect Brucellae with 'smooth' lipopolysaccharide (LPS) using a highly sensitive monoclonal antibody (mAb) based immunological assay. To complement molecular detection systems for potential bioterror agents, as required by international biodefense regulations, sets of mAbs were generated by B cell hybridoma technology and used to develop immunological assays. The combination of mAbs most suitable for an antigen capture assay format was identified and an immunoassay using the Luminex xMAP technology was developed. MAbs specific for the LPS O-antigen of Brucella spp. were generated by immunising mice with inactivated B. melitensis or B. abortus cells. Most mAbs recognised both B. melitensis and B. abortus and antigen binding was not impeded by inactivation of the bacterial cells by γ irradiation, formalin or heat treatment, a step required to analyse the samples immunologically under biosafety level two conditions. The Luminex assay recognised all tested Brucella species with 'smooth' LPS with detection limits of 2×10(2) to 8×10(4) cells per mL, depending on the species tested. Milk samples spiked with Brucella spp. cells were identified successfully using the Luminex assay. In addition, the bead-based immunoassay was integrated into a multiplex format, allowing for simultaneous, rapid and specific detection of Brucella spp., Bacillus anthracis, Francisella tularensis and Yersinia pestis within a single sample. Overall, the robust Luminex assay should allow detection of Brucella spp. in both natural

  19. Sedimentation rates in eastern North America reveal strong links between regional climate, depositional environments, and sediment accumulation

    Science.gov (United States)

    Goring, S. J.; McLachlan, J. S.; Jackson, S. T.; Blaauw, M.; Christen, J.; Marlon, J.; Blois, J.; Williams, J. W.

    2011-12-01

    PalEON is a multidisciplinary project that combines paleo and modern ecological data with state-of-the-art statistical and modelling tools to examine the interactions between climate, fire and vegetation during the past two millennia in the northeastern United States. A fundamental challenge for PalEON (and paleo research more broadly) is to improve age modelling to yield more accurate sediment-core chronologies. To address this challenge, we assessed sedimentation rates and their controls for 218 lakes and mires in the northeastern U.S. Sedimentation rates (yr/cm) were calculated from age-depth models, which were obtained from the Neotoma database (www.neotomadb.org) and other contributed pollen records. The age models were recalibrated to IntCal09 and augmented in some cases using biostratigraphic markers (Picea decline, 16 kcal BP - 10.5 kcal BP; Quercus rise, 12 - 9.1 kcal BP; and Alnus decline, 11.5 - 10.6 kcal BP) as described in Blois et al. (2011). Relationships between sedimentation rates and sediment age, site longitude, and depositional environment (lacustrine or mire) are significant but weak. There are clear and significant links between variations in the NGRIP record of δ18O and sedimentation in mires across the PalEON region, but no links to lacustrine sedimentation rates. This result indicates that super-regional climatic control of primary productivity, and thus autochthonic sediment deposition, dominates in mires while deposition in lacustrine basins may be driven primarily by local and regional factors including watershed size, surficial materials,and regional vegetation. The shape of the gamma probability functions that best describe sedimentation rate distributions are calculated and presented here for use as priors in Bayesian age modelling applications such as BACON (Blaauw and Christen, in press). Future applications of this research are also discussed.

  20. Paleohydrologic investigations in the vicinity of Yucca Mountain: Late Quaternary paleobotanical and polynological records

    Energy Technology Data Exchange (ETDEWEB)

    Spaulding, W.G.

    1994-10-05

    The primary objective of this research in the vicinity of the proposed Yucca Mountain Nuclear Waste Repository is the detection of episodes of increased runoff and groundwater discharge in this presently arid area. Ancient, inactive spring deposits in nearby valley bottoms (Haynes, 1967; Quade, 1986; Quade and Pratt, 1989), evidence for perennial water in presently dry canyons (Spaulding, 1992), and recent claims for extraordinary increases in precipitation during the last glacial age (Forester, 1994), provide good reason to further investigate both lowland spring-discharge habitats, and upland drainages. The ultimate purpose is to assess the long-term variability of the hydrologic system in the vicinity of Yucca Mountain in response to naturally occurring climatic changes. The data generated in the course of this study are derived from radiocarbon dated packrat (Neotoma) middens. This report presents the results of an initial assessment of the hydrologic stability of the candidate area based on a limited suite of middens from localities that, on geomorphic and hydrologic grounds, could have been close to ancient stream-side or spring environments. Paleoclimatic reconstructions are another means of studying the long-term climatic hydrologic stability of the Candidate Area include, and are also generated from packrat midden data. A different flora characterized the Candidate Area during the last glacial age in response to a cooler and wetter climate, and the plant species that comprised this flora can be used to reconstruct specific components of past climatic regimes. Thus, a secondary objective of this study is to compare the plant macrofossil data generated in this study to other records from the Candidate Area (Spaulding, 1985; Wigand, 1990) to determine if these new data are consistent with prior reconstructions. 66 refs., 4 figs., 13 tabs.

  1. A rapid minor groove binder PCR method for distinguishing the vaccine strain Brucella abortus 104M.

    Science.gov (United States)

    Nan, Wenlong; Qin, Lide; Wang, Yong; Zhang, Yueyong; Tan, Pengfei; Chen, Yuqi; Mao, Kairong; Chen, Yiping

    2018-01-24

    Brucellosis is a widespread zoonotic disease caused by Gram-negative Brucella bacteria. Immunisation with attenuated vaccine is an effective method of prevention, but it can interfere with diagnosis. Live, attenuated Brucella abortus strain 104M has been used for the prevention of human brucellosis in China since 1965. However, at present, no fast and reliable method exists that can distinguish this strain from field strains. Single nucleotide polymorphism (SNP)-based assays offer a new approach for such discrimination. SNP-based minor groove binder (MGB) and Cycleave assays have been used for rapid identification of four Brucella vaccine strains (B. abortus strains S19, A19 and RB51, and B. melitensis Rev1). The main objective of this study was to develop a PCR assay for rapid and specific detection of strain 104M. We developed a SNP-based MGB PCR assay that could successfully distinguish strain 104M from 18 representative strains of Brucella (B. abortus biovars 1, 2, 3, 4, 5, 6, 7 and 9, B. melitensis biovars 1, 2 and 3, B. suis biovars 1, 2, 3 and 4, B. canis, B. neotomae, and B. ovis), four Brucella vaccine strains (A19, S19, S2, M5), and 55 Brucella clinical field strains. The assay gave a negative reaction with four non-Brucella species (Escherichia coli, Pasteurella multocida, Streptococcus suis and Pseudomonas aeruginosa). The minimum sensitivity of the assay, evaluated using 10-fold dilutions of chromosomal DNA, was 220 fg for the 104M strain and 76 fg for the single non-104M Brucella strain tested (B. abortus A19). The assay was also reproducible (intra- and inter-assay coefficients of variation = 0.006-0.022 and 0.012-0.044, respectively). A SNP-based MGB PCR assay was developed that could straightforwardly and unambiguously distinguish B. abortus vaccine strain 104M from non-104M Brucella strains. Compared to the classical isolation and identification approaches of bacteriology, this real-time PCR assay has substantial advantages in terms of