This document summarizes a study that examined soil samples from 17 bat hibernacula caves in Oklahoma for the presence of Pseudogymnoascus destructans, the fungus that causes white-nose syndrome. 83 soil samples were tested using real-time polymerase chain reaction analysis and none were found to contain genetic material from P. destructans. The study suggests that P. destructans has not yet reached Oklahoma based on these results and previous negative tests of bats in the state.
Comparative analysis of genome sequences from six strains of Streptococcus agalactiae (Group B Streptococcus; GBS), representing the five major disease-causing serotypes, and two previously sequenced genomes suggests that a bacterial species can be described by its "pan-genome". The pan-genome includes a core genome of genes present in all strains and a dispensable genome of strain-specific and partially shared genes. While 80% of any single genome is shared among all isolates (core genome), sequencing additional strains revealed unique genes, and extrapolation predicts more unique genes will be found with further sequencing. Multiple independent genome sequences are thus required to fully understand the genomic complexity of a bacterial species.
This document summarizes a study that used PCR and cloning to analyze the 16S rRNA genes present in a natural marine bacterioplankton population from the Sargasso Sea. Researchers constructed a library of 51 small-subunit rRNA genes and sequenced five unique genes. In addition to genes from known marine Synechococcus and SAR11 lineages, they identified two new classes of genes belonging to alpha- and gamma-proteobacteria, confirming that many planktonic bacteria have not been previously recognized by microbiologists.
The document describes a meta-analysis of microbial community samples collected by the Earth Microbiome Project (EMP) that used coordinated protocols and analytical methods to explore patterns of diversity at an unprecedented scale. By tracking individual bacterial and archaeal ribosomal RNA gene sequences across multiple studies, the analysis resulted in both a reference database providing global context to DNA sequence data and an analytical framework for incorporating future study data to further characterize Earth's microbial diversity. The meta-analysis found that standardized environmental descriptors and new analytical methods, particularly using exact sequences instead of clustered operational taxonomic units, enabled comparisons across studies and exploration of large-scale ecological patterns.
UC Davis EVE161 Lecture 18 by @phylogenomicsJonathan Eisen
This document contains slides for a lecture on metagenomics. It discusses student presentation guidelines, summarizes a published article on characterizing genes from the human gut microbiome, provides details on the methods used in that study to extract and sequence DNA from fecal samples of 124 individuals, and includes some results tables. The study generated over 500 GB of sequence data and identified over 3 million non-redundant microbial genes from the gut microbiome.
This document describes the sequencing and analysis of the small subunit ribosomal RNA gene from an unusual form of the protistan parasite Ichthyophonus found infecting yellowtail flounder off Nova Scotia. Phylogenetic analysis shows it is distinct from two isolates of I. hoferi, supporting it being a separate species named I. irregularis. This finding raises the possibility that ichthyophoniasis in fish could be caused by different but related pathogens, in some cases concurrently.
This document summarizes a study that reconstructed 7,903 bacterial and archaeal genomes from over 1,500 public metagenomes. Key findings include:
- The genomes increase phylogenetic diversity of bacterial and archaeal trees by over 30% and provide first representatives for 17 bacterial and 3 archaeal candidate phyla.
- 245 genomes were recovered from the Patescibacteria superphylum.
- The genomes vary substantially in quality, with 43.5% considered near-complete, 43.8% medium quality, and 12.7% partial.
- The genomes expand representation of underrepresented phyla like Aminicenantes, Gemmatimonadetes, and Lentisphaera
The document contains slides from a course on microbial phylogenomics taught by Jonathan Eisen at UC Davis in winter 2016. The slides discuss various topics relating to metagenomics including the environmental genome shotgun sequencing of the Sargasso Sea, methods for binning sequences from metagenomic data like aligning to reference genomes or assembly, and examples of projects that used shotgun sequencing like the Wolbachia and glassy-winged sharpshooter projects. It also discusses challenges with assembly for metagenomic data due to variations in coverage and the DeLong lab's early work characterizing uncultured marine microbes.
Comparative analysis of genome sequences from six strains of Streptococcus agalactiae (Group B Streptococcus; GBS), representing the five major disease-causing serotypes, and two previously sequenced genomes suggests that a bacterial species can be described by its "pan-genome". The pan-genome includes a core genome of genes present in all strains and a dispensable genome of strain-specific and partially shared genes. While 80% of any single genome is shared among all isolates (core genome), sequencing additional strains revealed unique genes, and extrapolation predicts more unique genes will be found with further sequencing. Multiple independent genome sequences are thus required to fully understand the genomic complexity of a bacterial species.
This document summarizes a study that used PCR and cloning to analyze the 16S rRNA genes present in a natural marine bacterioplankton population from the Sargasso Sea. Researchers constructed a library of 51 small-subunit rRNA genes and sequenced five unique genes. In addition to genes from known marine Synechococcus and SAR11 lineages, they identified two new classes of genes belonging to alpha- and gamma-proteobacteria, confirming that many planktonic bacteria have not been previously recognized by microbiologists.
The document describes a meta-analysis of microbial community samples collected by the Earth Microbiome Project (EMP) that used coordinated protocols and analytical methods to explore patterns of diversity at an unprecedented scale. By tracking individual bacterial and archaeal ribosomal RNA gene sequences across multiple studies, the analysis resulted in both a reference database providing global context to DNA sequence data and an analytical framework for incorporating future study data to further characterize Earth's microbial diversity. The meta-analysis found that standardized environmental descriptors and new analytical methods, particularly using exact sequences instead of clustered operational taxonomic units, enabled comparisons across studies and exploration of large-scale ecological patterns.
UC Davis EVE161 Lecture 18 by @phylogenomicsJonathan Eisen
This document contains slides for a lecture on metagenomics. It discusses student presentation guidelines, summarizes a published article on characterizing genes from the human gut microbiome, provides details on the methods used in that study to extract and sequence DNA from fecal samples of 124 individuals, and includes some results tables. The study generated over 500 GB of sequence data and identified over 3 million non-redundant microbial genes from the gut microbiome.
This document describes the sequencing and analysis of the small subunit ribosomal RNA gene from an unusual form of the protistan parasite Ichthyophonus found infecting yellowtail flounder off Nova Scotia. Phylogenetic analysis shows it is distinct from two isolates of I. hoferi, supporting it being a separate species named I. irregularis. This finding raises the possibility that ichthyophoniasis in fish could be caused by different but related pathogens, in some cases concurrently.
This document summarizes a study that reconstructed 7,903 bacterial and archaeal genomes from over 1,500 public metagenomes. Key findings include:
- The genomes increase phylogenetic diversity of bacterial and archaeal trees by over 30% and provide first representatives for 17 bacterial and 3 archaeal candidate phyla.
- 245 genomes were recovered from the Patescibacteria superphylum.
- The genomes vary substantially in quality, with 43.5% considered near-complete, 43.8% medium quality, and 12.7% partial.
- The genomes expand representation of underrepresented phyla like Aminicenantes, Gemmatimonadetes, and Lentisphaera
The document contains slides from a course on microbial phylogenomics taught by Jonathan Eisen at UC Davis in winter 2016. The slides discuss various topics relating to metagenomics including the environmental genome shotgun sequencing of the Sargasso Sea, methods for binning sequences from metagenomic data like aligning to reference genomes or assembly, and examples of projects that used shotgun sequencing like the Wolbachia and glassy-winged sharpshooter projects. It also discusses challenges with assembly for metagenomic data due to variations in coverage and the DeLong lab's early work characterizing uncultured marine microbes.
This document summarizes key points from a class on microbial phylogenomics taught by Jonathan Eisen. It discusses reading scientific papers, specifically beginning with the introduction rather than the abstract. It also provides guidance on identifying the big question a field is trying to answer, summarizing the background and limitations of prior work, stating the specific questions authors are addressing, and identifying their experimental approach. The document does not summarize any specific paper.
This document describes a study that analyzed the transcriptome of the gut epithelium in Helicoverpa zea (corn earworm) larvae 24 hours after being infected with Helicoverpa zea single nucleopolyhedrovirus (HzSNPV) or a mock treatment. The study found 1,139 genes were differentially expressed between the two groups, with 63% downregulated and 37% upregulated in infected larvae. Genes related to digestion, detoxification, and some immune responses like viral recognition were generally downregulated upon infection, while antimicrobial peptides and prophenoloxidase were upregulated. This provided insight into how baculovirus infection alters gene expression in the gut, likely the most heavily
EveMicrobial Phylogenomics (EVE161) Class 9Jonathan Eisen
Microbial Phylogenomics (EVE161) at UC Davis Spring 2016. Co-taught by Jonathan Eisen and Holly Ganz.
Class 9:
Era II: rRNA Case Study: Built Environment Metaanalysis
Marine Host-Microbiome Interactions: Challenges and OpportunitiesJonathan Eisen
This document summarizes a talk given by Jonathan Eisen on marine host-microbiome interactions. It discusses various topics researched in Eisen's lab, including phylogenomic methods and tools, microbial phylogenomics and evolvability, reference data resources, communication in science, and model systems. Specific projects are mentioned, such as automated genome trees, phylogenetic marker genes, the GEBA project, and dark matter microbes. The document then introduces the concept of the host-microbiome stress triangle and gives examples of stress types including nutrient acquisition, pathogens, and environmental change. It concludes by discussing a potential project on seagrass microbiomes in collaboration with Jay Stachowicz's lab.
The largest virus in the oceans oceans yeastGervynFajardo1
Researchers discovered the largest virus known to inhabit the oceans. They collected samples from the Atlantic and Pacific oceans and sequenced the genomes of single-celled eukaryotes. They found a virus, called ChoanoVirus, that infects choanoflagellates, which are predatory protists. ChoanoVirus has the largest viral genome discovered so far, containing hundreds of protein sequences and genes involved in harvesting energy from light. This virus appears to help its host cell obtain energy from the sun, a novel function not previously seen in a predatory cell.
This document describes a study that developed and validated a multiplex real-time PCR assay to distinguish between human, bovine, and swine fecal contamination in water samples. Species-specific primers and probes were created to target the NADH dehydrogenase subunit 5 (ND5) gene in the mitochondrial DNA of each species. The assay was able to correctly identify the species in spiked effluent samples 83% of the time with no false positives. Some carry-over mitochondrial DNA signal was detected in human feces after consuming beef but not pork products. The multiplex real-time PCR provides a promising new tool for identifying the source of fecal contamination in environmental samples.
This document contains lecture slides for a course on microbial phylogenomics taught by Jonathan Eisen at UC Davis in winter 2014. The slides discuss the use of rRNA PCR and sequencing to study major microbial groups based on 16S rRNA gene sequences. They provide phylogenetic trees comparing sequences from cultivated vs uncultivated microbes in various bacterial divisions. The slides also address issues with phylogenetic analysis like unseen changes over evolutionary time and limitations in representing diversity due to a lack of cultivated microbes. Overall, the slides aim to provide students with an understanding of how rRNA gene sequencing has expanded knowledge of microbial diversity beyond what was known from culture and the challenges that remain in fully resolving deep phylogenetic relationships.
UC Davis EVE161 Lecture 14 by @phylogenomicsJonathan Eisen
This document contains slides from a lecture on metagenomics and microbial phylogenomics. The lecture discusses the history and development of metagenomics, which involves studying the collective genomes of microbes in an environment. It reviews key papers on metagenomics and the discovery of proteorhodopsin and the SAR11 lineage of bacteria from environmental samples. The slides also discuss previous findings on marine microbes from rRNA studies and introduce two new lineages of alpha- and gamma-proteobacteria identified from an analysis of 16S rRNA genes cloned from Sargasso Sea bacterioplankton DNA.
1) The study isolated and identified soil microbes from an area affected by an underground mine fire in Centralia, Pennsylvania that has been burning since 1962.
2) Unique bacterial colonies were isolated from soil samples taken at different temperatures. Through DNA sequencing, isolates were identified as species of Bacillus, Brevibacillus, Streptomyces, and potentially a novel Geobacillus species.
3) Further analysis of a Geobacillus isolate (unknown 2) that showed antimicrobial properties suggests it may produce a thermostable antibiotic and represent a novel Geobacillus species adapted to high soil temperatures due to the mine fire.
The researchers collected blue crabs from a polluted wetland (experimental group) and unpolluted dock (control group) to compare bacteria levels in their blood. They found higher bacteria counts in the male crab from the polluted site, including a salt-tolerant Bacillus species and Micrococcus species. However, further samples did not produce reliable bacteria counts, possibly due to differences in crab size and sex between trials. The study aimed to correlate environmental pollution to bacteria levels in crab blood but yielded inconclusive results requiring more sampling.
Arthropods emerged near the base of the Cambrian period based on early trace fossils and body fossils from the Cambrian. Molecular evidence indicates arthropods are monophyletic and part of the Ecdysozoa clade. Key insights include hexapods being crustaceans rather than allies of myriapods, and lobopodians representing stem lineages rather than relatives of onychophorans. The diversity of Cambrian lobopodians and anomalocaridids sheds light on the stem group leading to crown-group euarthropods.
This extended essay examines whether a deficiency in the AWB olfactory neuron affects the ability of C. elegans worms to differentiate between pathogenic and non-pathogenic bacteria. The author conducted a chemotaxis assay comparing the behavior of wild-type N2 worms and AWB-deficient PY2223 worms when exposed to the non-pathogenic bacteria E. coli OP50 and the pathogenic bacteria S. marcescens. Results showed N2 worms were able to differentiate between the bacteria, while PY2223 worms were not. This suggests the AWB neuron is important for C. elegans to distinguish between harmful and harmless bacteria.
BIS2C. Biodiversity and the Tree of Life. 2014. L14. FungiJonathan Eisen
The document is a set of lecture slides about fungi. It discusses several types of fungi, including microsporidia, chytrids, zygospore fungi, glomeromycota, and dikarya. It provides details on the characteristics, life cycles, and evolution of these groups. It specifically examines the life cycles of sac fungi, noting they have a haploid stage, form a dikaryotic mycelium through plasmogamy, undergo karyogamy and meiosis within ascocarps to produce haploid ascospores.
Microbial source tracking markers for detection of fecal contaminationFatima Batool
MST ( Microbial Source Tracking Markers) are being used nowadays for the detection of fecal contamination in water bodies. Conventionally, Fecal Inhibitor Bacteria (FIB) were used for detection of fecal contamination but there are many limitations of this method.
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive functioning. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms.
La gestión de proyectos es un área de conocimiento que permite planificar, organizar y controlar los recursos para completar proyectos de manera efectiva y eficiente. Incluye conceptos como la definición de alcance, estimación de tiempo y costos, y control de calidad.
This document summarizes key points from a class on microbial phylogenomics taught by Jonathan Eisen. It discusses reading scientific papers, specifically beginning with the introduction rather than the abstract. It also provides guidance on identifying the big question a field is trying to answer, summarizing the background and limitations of prior work, stating the specific questions authors are addressing, and identifying their experimental approach. The document does not summarize any specific paper.
This document describes a study that analyzed the transcriptome of the gut epithelium in Helicoverpa zea (corn earworm) larvae 24 hours after being infected with Helicoverpa zea single nucleopolyhedrovirus (HzSNPV) or a mock treatment. The study found 1,139 genes were differentially expressed between the two groups, with 63% downregulated and 37% upregulated in infected larvae. Genes related to digestion, detoxification, and some immune responses like viral recognition were generally downregulated upon infection, while antimicrobial peptides and prophenoloxidase were upregulated. This provided insight into how baculovirus infection alters gene expression in the gut, likely the most heavily
EveMicrobial Phylogenomics (EVE161) Class 9Jonathan Eisen
Microbial Phylogenomics (EVE161) at UC Davis Spring 2016. Co-taught by Jonathan Eisen and Holly Ganz.
Class 9:
Era II: rRNA Case Study: Built Environment Metaanalysis
Marine Host-Microbiome Interactions: Challenges and OpportunitiesJonathan Eisen
This document summarizes a talk given by Jonathan Eisen on marine host-microbiome interactions. It discusses various topics researched in Eisen's lab, including phylogenomic methods and tools, microbial phylogenomics and evolvability, reference data resources, communication in science, and model systems. Specific projects are mentioned, such as automated genome trees, phylogenetic marker genes, the GEBA project, and dark matter microbes. The document then introduces the concept of the host-microbiome stress triangle and gives examples of stress types including nutrient acquisition, pathogens, and environmental change. It concludes by discussing a potential project on seagrass microbiomes in collaboration with Jay Stachowicz's lab.
The largest virus in the oceans oceans yeastGervynFajardo1
Researchers discovered the largest virus known to inhabit the oceans. They collected samples from the Atlantic and Pacific oceans and sequenced the genomes of single-celled eukaryotes. They found a virus, called ChoanoVirus, that infects choanoflagellates, which are predatory protists. ChoanoVirus has the largest viral genome discovered so far, containing hundreds of protein sequences and genes involved in harvesting energy from light. This virus appears to help its host cell obtain energy from the sun, a novel function not previously seen in a predatory cell.
This document describes a study that developed and validated a multiplex real-time PCR assay to distinguish between human, bovine, and swine fecal contamination in water samples. Species-specific primers and probes were created to target the NADH dehydrogenase subunit 5 (ND5) gene in the mitochondrial DNA of each species. The assay was able to correctly identify the species in spiked effluent samples 83% of the time with no false positives. Some carry-over mitochondrial DNA signal was detected in human feces after consuming beef but not pork products. The multiplex real-time PCR provides a promising new tool for identifying the source of fecal contamination in environmental samples.
This document contains lecture slides for a course on microbial phylogenomics taught by Jonathan Eisen at UC Davis in winter 2014. The slides discuss the use of rRNA PCR and sequencing to study major microbial groups based on 16S rRNA gene sequences. They provide phylogenetic trees comparing sequences from cultivated vs uncultivated microbes in various bacterial divisions. The slides also address issues with phylogenetic analysis like unseen changes over evolutionary time and limitations in representing diversity due to a lack of cultivated microbes. Overall, the slides aim to provide students with an understanding of how rRNA gene sequencing has expanded knowledge of microbial diversity beyond what was known from culture and the challenges that remain in fully resolving deep phylogenetic relationships.
UC Davis EVE161 Lecture 14 by @phylogenomicsJonathan Eisen
This document contains slides from a lecture on metagenomics and microbial phylogenomics. The lecture discusses the history and development of metagenomics, which involves studying the collective genomes of microbes in an environment. It reviews key papers on metagenomics and the discovery of proteorhodopsin and the SAR11 lineage of bacteria from environmental samples. The slides also discuss previous findings on marine microbes from rRNA studies and introduce two new lineages of alpha- and gamma-proteobacteria identified from an analysis of 16S rRNA genes cloned from Sargasso Sea bacterioplankton DNA.
1) The study isolated and identified soil microbes from an area affected by an underground mine fire in Centralia, Pennsylvania that has been burning since 1962.
2) Unique bacterial colonies were isolated from soil samples taken at different temperatures. Through DNA sequencing, isolates were identified as species of Bacillus, Brevibacillus, Streptomyces, and potentially a novel Geobacillus species.
3) Further analysis of a Geobacillus isolate (unknown 2) that showed antimicrobial properties suggests it may produce a thermostable antibiotic and represent a novel Geobacillus species adapted to high soil temperatures due to the mine fire.
The researchers collected blue crabs from a polluted wetland (experimental group) and unpolluted dock (control group) to compare bacteria levels in their blood. They found higher bacteria counts in the male crab from the polluted site, including a salt-tolerant Bacillus species and Micrococcus species. However, further samples did not produce reliable bacteria counts, possibly due to differences in crab size and sex between trials. The study aimed to correlate environmental pollution to bacteria levels in crab blood but yielded inconclusive results requiring more sampling.
Arthropods emerged near the base of the Cambrian period based on early trace fossils and body fossils from the Cambrian. Molecular evidence indicates arthropods are monophyletic and part of the Ecdysozoa clade. Key insights include hexapods being crustaceans rather than allies of myriapods, and lobopodians representing stem lineages rather than relatives of onychophorans. The diversity of Cambrian lobopodians and anomalocaridids sheds light on the stem group leading to crown-group euarthropods.
This extended essay examines whether a deficiency in the AWB olfactory neuron affects the ability of C. elegans worms to differentiate between pathogenic and non-pathogenic bacteria. The author conducted a chemotaxis assay comparing the behavior of wild-type N2 worms and AWB-deficient PY2223 worms when exposed to the non-pathogenic bacteria E. coli OP50 and the pathogenic bacteria S. marcescens. Results showed N2 worms were able to differentiate between the bacteria, while PY2223 worms were not. This suggests the AWB neuron is important for C. elegans to distinguish between harmful and harmless bacteria.
BIS2C. Biodiversity and the Tree of Life. 2014. L14. FungiJonathan Eisen
The document is a set of lecture slides about fungi. It discusses several types of fungi, including microsporidia, chytrids, zygospore fungi, glomeromycota, and dikarya. It provides details on the characteristics, life cycles, and evolution of these groups. It specifically examines the life cycles of sac fungi, noting they have a haploid stage, form a dikaryotic mycelium through plasmogamy, undergo karyogamy and meiosis within ascocarps to produce haploid ascospores.
Microbial source tracking markers for detection of fecal contaminationFatima Batool
MST ( Microbial Source Tracking Markers) are being used nowadays for the detection of fecal contamination in water bodies. Conventionally, Fecal Inhibitor Bacteria (FIB) were used for detection of fecal contamination but there are many limitations of this method.
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive functioning. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms.
La gestión de proyectos es un área de conocimiento que permite planificar, organizar y controlar los recursos para completar proyectos de manera efectiva y eficiente. Incluye conceptos como la definición de alcance, estimación de tiempo y costos, y control de calidad.
Student teacher Jane Doe had a school experience week beginning date at an unnamed school. The area for discussion between the student teacher and subject mentor was formative assessment. The tutorial topic was the school-based curriculum for years 7 to 9. The main points discussed in the tutorial included autonomy and feedback in the classroom, curriculum planning and progression, and differentiation of activities. The student teacher's progression toward Teachers' Standards included standards 2, 3, 4, 5, and 6. Progression toward personal targets included planning engaging lessons and receiving student feedback.
El documento describe las características y funcionalidades de OMP, una plataforma libre para gestionar el proceso editorial de publicaciones académicas. OMP automatiza tareas como la revisión de manuscritos, la creación de un catálogo en línea y la venta de publicaciones. Permite a editoriales universitarias mejorar la calidad y profesionalización de sus procesos de publicación.
Paul H. Smaal is seeking a position that utilizes his educational background in business administration and industrial engineering as well as his extensive technical experience. He has over 40 years of experience in large-scale business optimization, developing programs and processes to achieve growth and productivity. His expertise includes multi-site management, staff workflow prioritization, project management, and client/business relations. He has held various leadership roles at Caterpillar supporting dealers globally in areas like product support, service engineering, and operations.
Justin Bieber released his debut EP "My World" in 2009 featuring his first hit single. His early music videos featured a similar style with forward bangs and bright colors as he sang about teen romance. His second studio album "My World 2.0" continued this theme. Bieber's later albums showed a matured style, like his Christmas album "Under the Mistletoe" featuring nighttime outdoor shots and darker colors. His third album "Believe" marked a change with a black and white cover and spikier hair, signifying Bieber's transition from teen pop to a more mature sound and image.
Architecture Construction Portfolio 17 x 11Al Bacon
This document provides construction documents for renovations and upgrades to a bus garage and police department facility. The bus garage scope includes converting a freight area to a lounge and bathrooms, expanding a single door garage to two doors, and installing engine warming stations. The police department scope is to construct ADA compliant sidewalks, walkways, and grading to maintain compliance. Photos are included from a website showing the bus garage renovations currently underway.
Este documento describe la productividad y los factores que la afectan. Define la productividad parcial, de factor total y total. Explica que la productividad es importante para el progreso económico y los salarios. Identifica factores externos, del producto, del proceso, de capacidad, de la fuerza laboral y de calidad que impactan la productividad. Además, discute cómo medir la productividad a nivel internacional, nacional y de empresa.
O documento contém 9 exercícios sobre cartografia e curvas de nível. Os exercícios pedem para identificar informações sobre relevo, altitude, declividade e localização geográfica a partir de mapas topográficos representados por curvas de nível. O documento também fornece as respostas corretas para cada exercício.
Salt Lake City December 11 Executive Roundtable Final Flyer 120115John Priecko
This document announces an executive roundtable discussion on international trade, export controls, regulatory compliance and enforcement. The roundtable will be held on December 11, 2015 at the World Trade Center Utah and will feature presentations from the President and CEO of WTCU, the Director of the Utah US Export Assistance Center, and the Director of the Export Enforcement Coordination Center at the US Department of Homeland Security. The target audience includes CEOs, COOs, CFOs, CIOs and other senior executives involved in technology protection and international trade. Attendees must RSVP by December 9th.
La nueva versión de la KTM 690 Duke presenta mejoras significativas, incluyendo un motor más potente de 73 CV, una parte ciclo más ligera y solvente, y una electrónica avanzada nunca antes vista en una moto de esta categoría. La Duke ahora es más divertida de conducir, con una respuesta más enérgica del motor y mayor fiabilidad del ciclo, además de contar con características tecnológicas que la convierten en la monocilíndrica más avanzada del mercado.
This document lists common question words in English and Catalan including: which, what, what kind, who, why, were, when, and wh. It provides the question words to ask questions seeking more information on a topic, event, or situation.
White Nose Syndrome is a condition affecting multiple bat species in the eastern US and Canada. It is associated with a newly identified cold-tolerant fungus that grows on the bats' skin. Signs include white fungal growth on the nose, wings and other areas. Infected bats exhibit abnormal behaviors like flying outside during winter. Mortality rates can be as high as 90%. Over 400,000 bats have died from WNS since 2006 when it first appeared. The fungus may have been recently introduced and is spreading from bat to bat and potentially through human transmission to new caves. Research is ongoing to understand and address this emerging threat facing bat populations.
This document summarizes a study on the phylogeography of placozoans in the Caribbean Sea. Researchers performed both coarse and fine-scale surveys of placozoan distribution. For the coarse survey, they sampled placozoans from five Caribbean locations and sequenced the 16S rDNA to identify four of the five known placozoan clades. They also discovered two new haplotypes. For the fine-scale study, they intensively sampled the mangroves of Twin Cays, Belize and found evidence of placozoan diversity within this small island. The studies provide molecular evidence of species diversity within the Phylum Placozoa in the Caribbean region.
This document summarizes a study that characterized the toxicity of acid metalliferous water (AMW) in mallards. 221 bird deaths were investigated at 3 mine sites and were assumed to be from consumption of AMW. A synthetic AMW (SAMW) was formulated based on the contaminant profile of a pond where many carcasses were found. An acute oral toxicity trial with mallards found that 7 of 9 birds exposed to SAMW died within 12 hours of consuming doses of 69.8-270.1 mL/kg. Clinical signs and lesions in SAMW-exposed birds were consistent with acute metal toxicosis, especially copper toxicity. Blood and kidney copper levels were much higher in SAMW
This document examines various life history traits of dicyemids to understand their reproductive strategies and adaptations to living as endoparasites in cephalopod renal organs. It finds that dicyemids have a hermaphroditic gonad that produces roughly equal numbers of eggs and sperm. Fecundity increases with adult body size. Embryo size correlates with host size, suggesting host factors influence dispersal and infection of new hosts. While individual fecundity is low, total reproductive capacity per community is high due to asexual multiplication within the host. Adult size appears constrained by the volume and features of the renal habitat within different host species.
The first case of forensic entomology applied to a roadkill dog carcase. ShahrukhKhan373491
This document describes the first case of applying forensic entomology to analyze a roadkill dog carcass in Colombia. Entomological samples, including maggots, were collected from the dog's skull. The maggots and flesh samples were reared in the lab. Previous research on pig carcasses in the same area found eggs and adults of the fly Chrysomya macellaria from the bloating to dry decomposition stages. This suggests the minimum postmortem interval for the dog was likely around 37 days prior, based on the typical decomposition timetable for an animal body in that environment to become dry remains. The study demonstrates the potential of wildlife forensic entomology to provide evidence for investigations into threats to endangered
London Great Plague DNA identified for first timeDarren Pauli
Five out of 20 samples from individuals excavated from a mass burial pit from the 1665 Great Plague of London tested positive for Yersinia pestis, confirming plague as the cause of death. Isotopic analysis of the remains provided information on diet and migration, while C14 dating confirmed the mid-17th century timeframe. Archaeological and historical evidence, including accounts of overburdened burial grounds and mass pits, support the pit as a plague burial site. While names of victims could not be identified, one headstone revealed was of plague victim Mary Godfrey. There is no modern risk of plague from the remains.
First discovery of dicyemida (mesozoa) in caribbean cephalopodsdreicash
This document summarizes the first discovery of Dicyemida (Mesozoa) parasites in Caribbean cephalopods. Thirteen octopuses from Venezuela were found to be heavily infected by dicyemids, representing the first records of these parasites in the tropical Caribbean region. Previously, dicyemids were thought to be limited to temperate waters and rare in the tropics. However, this finding suggests dicyemids may be more common in tropical areas than previously believed and encourages further searching in other tropical localities.
A survey on the ectoparasites and haemoparasites ofAlexander Decker
This document summarizes a study on the ectoparasites and haemoparasites of grasscutters (Thryonomys swinderianus) reared under captive conditions. Ten grasscutters were examined for ectoparasites by brushing their fur and for haemoparasites through blood smear analysis. Three ectoparasite species were identified: Ixodes aulacodi, Rhipicephalus sanguineus ticks and Xenopsylla cheopis fleas. Ixodes aulacodi had the highest prevalence at 50%. Two haemoparasite species were found: Plasmodium and Trypanosoma, each at 10% prevalence. The anterior body regions of
This study examined three species of aquatic freshwater turtles in Costa Rica for haemogregarine infections. All turtles sampled were positive for intraerythrocytic haemogregarines, representing the first report of these parasites in turtles from Central America. Black river turtles had a significantly higher average parasitemia (0.34%) than white-lipped mud turtles (0.05%). Parasites in the single scorpion mud turtle examined were smaller and did not displace the host cell nucleus like those in the other two species. This is the first report of haemogregarines in the white-lipped mud turtle, scorpion mud turtle, and any Rhinoclemm
This study examined the presence of Borrelia burgdorferi, the bacterium that causes Lyme disease, in blacklegged ticks and rodents across five sites on the Outer Banks of North Carolina over an 18-year period from 1991 to 2009. B. burgdorferi was detected in questing blacklegged ticks and isolated from white-footed mice, rice rats, and marsh rabbits sampled at the sites. Sequence analysis confirmed the isolates were B. burgdorferi sensu stricto. The long-term detection of the bacterium across multiple years and locations indicates it is stably transmitted between ticks and rodent populations in this region.
- The document summarizes a study that used environmental DNA (eDNA) analysis to assess the biodiversity of restored bivalve populations at two sites in New York City - Soundview Park and Freshkills Park.
- eDNA was extracted from water and sediment samples to identify eukaryotic organisms without directly observing them. This allows for a more efficient biodiversity analysis compared to traditional methods.
- The study aims to compare biodiversity between restored areas with bivalves and control sites without bivalves to evaluate the impact of restoration efforts. Preliminary results from Soundview Park found over 270 eukaryotic orders present based on eDNA sequencing.
The document summarizes a study that collected cloacal swab samples from 200 waterfowl in Erie and Mercer counties in Pennsylvania to test for avian influenza virus (AIV) subtypes. Using RT-PCR analysis, the study found that AIV was not present in the sampled waterfowl. While no AIV was detected, previous studies have found AIV in waterfowl populations at the same field sites. The lack of detection could be because AIV is only shed for a limited time after infection. Continued surveillance is important to assess the risk AIV poses to wildlife and humans.
The document summarizes baseline ecological surveys conducted in 2014 at the University of Portland's River Campus riparian zone, a former Superfund site undergoing restoration. Surveys inventoried 22 woody plant species (90% in poor health), recorded 139 herbaceous plant species from 42 families including 29% natives, and observed 31 avian species and 3988 invertebrates from 16 orders. Methods were developed to monitor vegetation, birds, and insects to establish baseline data and assess ecological recovery over time. While mainly exotic species were present, several native plants and species were colonizing. Future surveys will compare data to these baselines to evaluate restoration success and riparian habitat recovery.
The document summarizes a study that examined differences in decomposition and insect activity on pig carrion placed in sunlit versus shaded locations during winter in Canberra, Australia. 8 pig carcasses were placed in cages either in full sun or full shade and observed over approximately 3 months. No significant difference was found in temperature or decomposition rate between sunlit and shaded carrion. However, the insect populations and species present did vary strongly, with more insects and larger populations observed on the sunlit carrion. Forensic entomology methods were used to analyze the insect data and determine estimates of the post mortem interval.
This document summarizes a study of mosquito surveillance conducted in Eau Claire County, Wisconsin in 2015. The study aimed to identify mosquito species that could potentially carry West Nile Virus (WNV), including Aedes vexans, Culex pipiens/restuans, and Coquillettidia perturbans. Mosquitoes were collected from six sites using CO2-baited traps from June through August. The highest mosquito counts were observed in June and July. Over 1,300 mosquitoes were collected, consisting primarily of Aedes and C. perturbans. No Culex mosquitoes were found. The results provide information on mosquito populations and distribution to assess WNV risk
This document discusses using environmental DNA (eDNA) to analyze zooplankton distribution in Monterey Bay, California from 2010-2015. Water samples were collected and eDNA was extracted and sequenced to identify species. Results found copepods but little krill DNA. This could be due to methodological errors or krill DNA being misidentified as flies. While eDNA has potential, improvements are needed as it is a new technique prone to errors. Climate change is reducing biodiversity, making monitoring important for conservation.
Succession of Arthropods on White Rat Carcasses in Ile Ife, Southwestern Nigeriaijtsrd
The forensic information provided by decomposition of small carcasses often goes unnoticed, even in advanced economies, due to frequent neglect. This paper reports the succession pattern of arthropod species that associated with carcasses of white rat, Rattus norvegicus Berkenhout Rodentia Muridae , in Ile Ife, southwestern Nigeria. Four bushy sites were chosen for the study and nine rat carcasses were placed at each site once a season for two seasons. The carcasses were monitored daily until the process of decay was over. The visiting and colonizing invertebrates were collected daily and identified. Immatures were also collected and reared in the laboratory till adult emergence for easy identification. The carcasses went through five stages of decay and the arthropods arrived in the order Diptera early fresh stage , Hymenoptera late fresh stage , Coleoptera and Dermaptera active decay stage , and Araneae and Oribatida advanced decay stage . Dipteran flies were the first arthropods to interact with the remains but ants were the only arthropods that associated with all the five stages of decay. A total of 9828 arthropods 4415 adults and 5413 immatures belonging to six orders in two classes of the phylum were collected in the study. The proportion of faunal abundance was Diptera 75.10 , Hymenoptera 22.90 , Coleoptera 1.80 , Dermaptera 0.10 , Oribatida 0.08 and Araneae 0.02 . Rate of decay was faster and faunal population was higher on carcasses during the dry season compared to the wet. Faunal population was also higher on carcasses placed in close proximity to the Zoological garden. The implications of these results on accuracy of estimated postmortem interval PMI and applicability in law were discussed. Aminat Adeola Adesina | Olalekan Joseph Soyelu "Succession of Arthropods on White Rat Carcasses in Ile-Ife, Southwestern Nigeria" Published in International Journal of Trend in Scientific Research and Development (ijtsrd), ISSN: 2456-6470, Volume-4 | Issue-6 , October 2020, URL: https://www.ijtsrd.com/papers/ijtsrd35737.pdf Paper Url: https://www.ijtsrd.com/biological-science/zoology/35737/succession-of-arthropods-on-white-rat-carcasses-in-ileife-southwestern-nigeria/aminat-adeola-adesina
This study analyzed the vocalizations of black-capped chickadees in three populations along a river in Colorado over two winter seasons. The researchers recorded the "gargle" vocalizations of 46 individual birds to identify their unique call repertoires. They identified 56 distinct syllables used to construct the birds' various gargle calls. Each population shared some call types with nearby populations, but also had unique calls. Sharing of both full calls and their component syllables was greater within populations than between populations. The frequencies of calls and syllables were correlated over the two study years, with stronger correlation for syllables.
This document summarizes a study that investigated the response of the invasive Asian cockroach, Blattella asahinai, to blattellaquinone, the sex pheromone of its closest relative the German cockroach. Electroantennogram analysis revealed that the antennae of both male B. asahinai and B. germanica responded strongly to blattellaquinone. Field trapping experiments then showed that male B. asahinai were most attracted to blattellaquinone-baited traps, especially those containing 10 micrograms of the pheromone. These results suggest that blattellaquinone may function as a component of the female B. asahin
1. BioOne sees sustainable scholarly publishing as an inherently collaborative enterprise connecting authors, nonprofit publishers, academic institutions, research
libraries, and research funders in the common goal of maximizing access to critical research.
Examination of several Oklahoma bat hibernacula cave soils for
Pseudogymnoascus destructans, the causative agent of White-Nose Syndrome
Author(s): James P. Creecy, William Caire, and Kylie A. Gilcrest
Source: The Southwestern Naturalist, 60(2-3):213-217.
Published By: Southwestern Association of Naturalists
DOI: http://dx.doi.org/10.1894/JKF-53.1
URL: http://www.bioone.org/doi/full/10.1894/JKF-53.1
BioOne (www.bioone.org) is a nonprofit, online aggregation of core research in the biological, ecological, and
environmental sciences. BioOne provides a sustainable online platform for over 170 journals and books published
by nonprofit societies, associations, museums, institutions, and presses.
Your use of this PDF, the BioOne Web site, and all posted and associated content indicates your acceptance of
BioOne’s Terms of Use, available at www.bioone.org/page/terms_of_use.
Usage of BioOne content is strictly limited to personal, educational, and non-commercial use. Commercial inquiries
or rights and permissions requests should be directed to the individual publisher as copyright holder.
2. THE SOUTHWESTERN NATURALIST 60(2-3): 213–217 JUNE-SEPTEMBER 2015
EXAMINATION OF SEVERAL OKLAHOMA BAT HIBERNACULA CAVE
SOILS FOR PSEUDOGYMNOASCUS DESTRUCTANS, THE CAUSATIVE
AGENT OF WHITE-NOSE SYNDROME
JAMES P. CREECY, WILLIAM CAIRE,* AND KYLIE A. GILCREST
Biology Department, University of Central Oklahoma, 100 North University Drive, Edmond, OK 73034
*Correspondent: wcaire@uco.edu
ABSTRACT—White-nose syndrome is an often lethal fungal infection of bats that is caused by the fungus
Pseudogymnoascus destructans, formerly Geomyces destructans. The fungal spores can persist for extended periods
of time in the soil and on surfaces in caves where it might be found even after the bats depart. In 2010, a single
bat, Myotis velifer, from a western Oklahoma gypsum cave, was initially diagnosed by the U.S. Geological Survey
National Wildlife Health Center, as ‘‘suspect white-nose syndrome.’’ Based on this, we decided to examine soil
samples from various bat caves across Oklahoma for the presence of P. destructans. We used Real-time
Polymerase Chain Reaction to analyze 83 soil samples from 17 caves in Oklahoma. None of the soil samples
were found to contain genetic material from P. destructans. We postulate that P. destructans has not yet reached
Oklahoma because of the negative Real-time Polymerase Chain Reaction results, because a National Wildlife
Health Center reexamination of the original bat suggested the bat was negative for P. destructans, and
subsequent analyses of bat nose and wing swabs, bat tissues, and physical examination of hibernating bats have
all been negative for white-nose syndrome.
RESUME—El s´ındrome de nariz blanca es una infecci´on mic´otica a menudo letal en murci´elagos que es
causada por el hongo Pseudogymnoascus destructans, anteriormente Geomyces destructans. Las esporas de los
hongos pueden persistir por largos per´ıodos de tiempo en el suelo y en superficies en las cuevas donde se
pueden encontrar incluso despu´es de que los murci´elagos se van. En 2010, un s´olo murci´elago Myotis velifer, de
una cueva de yeso al oeste de Oklahoma fue diagnosticado inicialmente por el USGS Nacional Wildlife Health
Center (NWHC), como ‘‘sospechoso del s´ındrome de nariz blanca’’. Bas´andonos en esto, decidimos examinar
las muestras de suelo de varias cuevas de murci´elagos a trav´es de Oklahoma por la presencia de P. destructans.
Se utiliz´o PCR en tiempo real para analizar 83 muestras de suelo de 17 cuevas en Oklahoma. Ningunas de las
muestras de suelo conten´ıa el material gen´etico del P. destructans. Postulamos que P. destructans todav´ıa no ha
llegado a Oklahoma debido a los resultados negativos de PCR en tiempo real, debido a que una
reexaminaci´on del NWHC del murci´elago original sugiri´o que el murci´elago result´o negativo para el P.
destructans y debido a que unos an´alisis posteriores de hisopos de nariz y ala de murci´elagos, tejidos de
murci´elagos, y el examen f´ısico de murci´elagos en hibernaci´on han sido negativos para el s´ındrome de nariz
blanca.
White-nose syndrome (WNS) is an often lethal
parasitic infection of bats that is caused by Pseudogymnoas-
cus destructans, formerly Geomyces destructans (Minnis and
Linder, 2013), a psychrophilic and keratinophylic asco-
mycete fungus (Blehert et al., 2009, 2011; Cryan et al.,
2010). WNS has been described as the most devastating
disease ever reported for hibernating bats (Moore et al.,
2011) and it has caused widespread mortality to millions
of bats in the United States (Verant et al., 2012). The
disease has progressively, since the initial discovery in New
York in 2006 (Blehert et al., 2009), spread to the south
and west. In 2014, bats with WNS were confirmed in
Missouri and Arkansas near the border with Oklahoma
(White-Nose Syndrom.org; http://whitenosesyndrome.
org/resources/map).
A cave myotis, Myotis velifer, found with white crusty
material on the skin, was submitted from Woodward
County in western Oklahoma to the United States
Geological Service National Wildlife Health Center
(NWHC) to determine whether the white material was
attributed to P. destructans. In May 2010, the NWHC
reported that the submitted bat was ‘‘suspect WNS’’ for P.
destructans (NWHC Diagnostic Final Report 23042, May
2010). For four years following the initial report from the
NWHC, hibernating M. velifer in the same cave where the
suspect WNS bat was found, as well as several other major
hibernation sites in western Oklahoma, were examined
3. during late hibernation (January and February) for visible
signs of WNS. To date, no bats have been seen that appear
to have WNS (W. Caire, pers. observ.).
The absence of signs of WNS on the bats was an
encouraging observation for the health of the bat
hibernacula, but it is known that P. destructans produces
spores that can persist for extended periods in the soil
and on surfaces in caves where bats hibernate even after
the bats depart (Lorch et al., 2013). Because of the report
of a WNS suspect bat from western Oklahoma mentioned
earlier, we analyzed soils from selected bat hibernacula in
Oklahoma in 2011 and 2012 to determine whether
genetic material indicative of P. destructans might be
present.
METHODS AND MATERIALS—Sample Collection and DNA
Extraction—During the 2011 and 2012 bat hibernation
season, we collected 83 soil samples from 17 Oklahoma
cave systems (Table 1) known to be inhabited by bat
colonies. We followed universal precautions to prevent
the spread of P. destructans (U.S. Fish and Wildlife Service,
http://www.fws.gov/WhiteNoseSyndrome/) during cave
visits and the processing of soil samples. Procedures for
sampling in the bat caves were approved by the
Institutional Animal Care and Use Committee of the
University of Central Oklahoma. We also followed
guidelines of the American Society of Mammalogists for
the Use of Wild Mammals in Research (Sikes et al., 2011).
The soil collections taken in the caves and near the bats
were under the auspices of a Scientific Collecting Permit
issued by the Oklahoma Department of Wildlife Conser-
vation or the United States Fish and Wildlife Service.
During each soil sample collection, we took care to
prevent cross-contamination (sterilized sample contain-
ers, a new pair of latex gloves, use of sterilized soil-
collecting spatulas, placing each sample in a separate
ziplock bag, etc.) among soil samples and to minimize the
impact to the hibernacula. We collected 1–4 soil samples;
usually 1 from the entrance to the cave, in the twilight
region, and usually 2 from separate interior locations in
TABLE 1—Caves in Oklahoma from which 83 soil samples were screened for Pseudogymnoascus destructans DNA, the causative agent
of white-nose syndrome. Included are locations in the caves where soil samples were analyzed: E, entrance; TW, twilight; UB, under
bats; BC, back of cave in total darkness. AD-6, AD-7, AD-14, DL-39 and DL-91 are cave codes used by the U.S. Fish and Wildlife Service
to protect the location of caves with endangered species of bats. Touchdown PCR and Real-time PCR analysis was conducted to detect
Geomyces or a closely related fungal species and P. destructans DNA, respectively. All samples that were analyzed using Real-time PCR
(represented as RT) were negative for P. destructans DNA. Three of the sixteen soil samples analyzed by touchdown PCR (represented
as PCR) were positive for Geomyces or a closely related fungal species DNA and are identified by an *. The remaining samples analyzed
by touchdown PCR were negative. No data is indicated by the em dash (—).
Year Cave, Provenience
Soil sample sites and method of PCR analysis
E TW UB BC
2011 AD-6, Adair Co. RT RT RT RT
2011 AD-7, Adair Co. RT RT RT RT
2011 AD-14, Adair Co. (Back Door) RT RT RT RT
2011 AD-14, Adair Co. (Main Entrance) RT RT RT RT
2011 AD-14, Adair Co. (Third Cave) RT RT RT RT
2011 AD-14, Adair Co. (Side Door) RT RT RT RT
2011 Alabaster Caverns, Woodward Co. — — PCR/RT PCR/RT
2011 Broken Horn, Woodward Co. RT — — —
2011 Cattle Cave, Woodward Co. — — RT RT
2011 DL-39, Delaware Co. — RT RT —
2011 DL-91, Delaware Co. RT RT — —
2011 Faulkner Cave, Woods Co. — — PCR/RT PCR/RT
2011 Jester Cave, Greer Co. RT RT RT RT
2011 Merihew Cave, Woods Co. RT RT PCR/RT PCR/RT
2011 Nescatunga Cave, Major Co. — — PCR/RT PCR/RT
2011 Selman Bat Cave, Woodward Co. RT RT RT RT
2011 Selman Cave System-Skylight, Woodward Co. RT RT PCR*/RT PCR/RT
2011 Selman Cave System-Skunkeater, Woodward Co. RT RT RT RT
2011 Washita Cave Bat Cave, Washita Co. — — PCR/RT PCR*/RT
2012 Gnarled Knuckle, Murray Co. RT RT RT —
2012 Jester Cave, Greer Co. RT RT RT RT
2012 Nescatunga Cave, Major Co. RT RT PCR/RT PCR*/RT
2012 Selman Bat Cave, Woodward Co. RT RT RT —
2012 Selman Cave System-Skunkeater, Woodward Co. RT RT RT RT
2012 Washita Cave Bat Cave, Washita Co. RT RT PCR/RT PCR/RT
2012 Vickery Bat Cave, Major Co. RT RT — —
214 vol. 60, no. 2-3The Southwestern Naturalist
4. total darkness. If bats were present, we took a soil sample
from under or near where the bats were roosting. Soil
samples were kept cool and transported to the University
of Central Oklahoma (Edmond, Oklahoma) where they
were stored at -808C until DNA was extracted. Although
the cave environments were not a focus of this study, we
included the air temperatures and relative humidities
recorded (HOBO data loggers; Onset Computer Corpo-
ration, Bourne, Maine) on 28 January 2011 from near the
soil collection sites in the Selman Cave System. This is the
cave where the NWHC, (Diagnostic Services Case report
23042, May 2010) first indicated that P. destructans was
present in western Oklahoma.
We isolated total environmental DNA from each soil
sample using the PowerSoil DNA Isolation Kit (MoBio
Laboratories Inc., Carlsbad, California) as recommended
by the manufacturer. We performed proper experimental
procedures and controls throughout the DNA extraction
process to evaluate the potential for contamination. All
soil samples were opened individually and never shared
time or space with another soil sample. Between each
sample, we decontaminated the laboratory bench and
applied new bench coat. We included extraction blank
controls, containing all reagents but lacking a soil sample,
with each set of extracted samples. All extraction blank
controls performed as expected, and supported the
conclusion that the samples were not contaminated
during DNA extraction. We quantified total environmen-
tal DNA from extracted samples using a Nanodrop 2000
(Thermo Scientific, Wilmington, Delaware) and stored it
at -208C prior to subsequent Polymerase Chain Reaction
(PCR) and Real-time PCR analyses.
Touchdown PCR—DNA quality and quantity obtained
from soil samples was variable; therefore, we employed
touchdown PCR as a sensitive and highly specific method
for the amplification of DNA from Geomyces and close
relatives (Don et al., 1991; Lindner and Banik, 2009).
Each touchdown PCR reaction contained a final volume
of 25 lL. Within each reaction was 3.5 lL Failsafe Buffer
I, 1.2 lL of each 10 lM PCR primer, 5U of AmpliTaq
Gold, and 5 lL template DNA (4–178 ng total DNA;
Epicentre Technologies, Madison, Wisconsin). We uti-
lized the previously published primer set nu-SSI(1506)-
184-50
-Gd and nu-5.8S-144-30
-Gd (Lorch et al., 2010)
under the following thermocycling conditions: 988C for 2
min; 40 cycles of denaturation at 958C for 30 s, 3-min
annealing period, and 728C extension for 1 min; and a
final extension at 728C for 7 min. The annealing
temperature for the first 20 cycles consisted of 0.58C
temperature step-downs every cycle (from 608C to 508C);
the annealing temperature for the final 20 cycles was
508C. Positive and negative controls were run concurrent-
ly during PCR amplification. Positive controls contained
of 10 ng of P. destructans genomic DNA purchased from
American Type Culture Collection (MYA-4855). We
evaluated PCR inhibition in an independent set of
reactions by adding 50 ng of P. destructans genomic
DNA (American Type Culture Collection MYA-4855) in
place of 1 lL of water to the reaction while keeping all
other conditions consistent.
Real-time PCR Survey for P. destructans—We subjected
DNA extracted from each soil sample to Real-time PCR
analysis using the validated Real-time IGS PCR test
established at the United States Geological Service-
National Wildlife Health Center (Muller et al., 2013).
The primers and probe published by Muller et al. (2013)
were previously characterized as specific for the IGS
region of P. destructans. Both primers and the probe were
synthesized by Biosearch Technologies Inc. (Novato,
California), and Real-time PCR of the IGS region of P.
destructans was conducted using an ABI 7500 Real-Time
PCR system (Life Technologies, Grand Island, New York)
and the QuantiFaste Probe PCR + ROX Vial Kit master
mix, (QIAGEN Inc., Valencia, California) according to
the manufacturer’s instructions. We avoided cross-con-
tamination by following standard laboratory practices and
monitored cross-contamination by analysis of reagent
blank samples. Each Real-time PCR reaction had a total
volume of 25 lL. Contained within each reaction was 12.5
lL 2· master mix, 0.5 lL 50· ROX dye solution, 0.5 lL
of each 20 lM PCR primer, 0.25 lL of 20 lM probe and 5
lL template DNA (Muller et al., 2013). We used known P.
destructans genomic DNA as a positive control for all runs.
PCR cycling conditions included a 958C for 3 min initial
activation step followed by 40 cycles of 958C for 3 s and
608C for 30 s. We classified a sample as positive if
maximum fluorescence exceeded 10% of the maximum
fluorescence of the positive control samples (King and
Guidry, 2004), and we classified failure to exceed this level
of fluorescence as a negative result.
RESULTS—Environmental DNA Extraction, Amplification
and Real-time PCR analysis—We extracted 83 total soil
samples using the Powersoil Isolation Kit, and DNA
concentration from each sample ranged from 0.8 to 35.6
ng/lL. PCR amplification of DNA obtained from soil
samples has been known to present a number of
challenges, including PCR inhibition and uncertainty of
fungal DNA abundance in the extract. As stated above, we
evaluated PCR inhibition by addition of known P.
destructans DNA to an otherwise standard PCR reaction.
For all soil samples evaluated, addition of 5 lL of DNA
extract to a traditional PCR reaction did not result in the
observation of PCR inhibition by gel electrophoresis. We
analyzed 16 soil samples from 8 cave systems by
touchdown PCR, and 3 samples indicated the presence
of DNA from Geomyces or a species closely related to
Geomyces (see Table 1). In order to more accurately
evaluate the possible presence of P. destructans DNA, we
conducted a Real-time PCR test of the species-specific IGS
region. Following Real-time PCR analysis of all 83 soil
samples collected over the 2-year period, all evidence
June 2015 Creecy et al.—Examination of bat hibernacula soils for Pseudogymnoascus destructans 215
5. indicates that there is an absence of P. destructans DNA
within the Oklahoma hibernacula tested.
DISCUSSION—This study is the first attempt to determine
whether P. destructans is present in caves soils on the
western edge of the area where WNS has been reported in
the United States. It appears that at the time of the
analysis of the soil samples, there was no P. destructans
DNA within the Oklahoma hibernacula tested. This
provides baseline chronological data should P. destructans
enter Oklahoma in the future.
Several possibilities exist as to explain why P. destructans
has not been found in any of the Oklahoma cave soils
examined. The first possibility is that the fungus has not
yet been dispersed into Oklahoma by wildlife, humans, or
other means. The single M. velifer from western Oklaho-
ma that was originally reported in 2010 as P. destructans
suspect by the NWHC was recently reexamined by
histopathology, fungal culture, and PCR, using a more
specific procedure (Muller et al., 2013); and upon review,
it was reclassified as negative for WNS (NWHC Supple-
mental Report for Diagnostic Final Report 23042, April
2014). During the hibernating season of 2010–2011, five
M. velifer, from the same cave in northwestern Oklahoma
from which the first suspect WNS bat was reported, were
submitted to the NWHC for testing. Those bats also
yielded negative results (NWHC, Diagnostic Final Report
23571, June 2011). A tri-colored bat (Perimyotis subflavus),
collected in Adair County in eastern Oklahoma in 2011,
also tested negative for WNS (NWHC, Diagnostic Final
Report 23570, July 2011). In addition, 81 combination
wing/muzzle swabs from hibernating M. velifer in Wood-
ward, Washita, and Greer counties in Oklahoma were
submitted to the NWHC during the winter of 2014 for
testing, and all were negative for P. destructans (NWHC
Diagnostic Services Final Reports Case Reports 24764,
24765, 24766, 24767, April 2014). Thus it appears likely
that P. destructans has not yet spread to western Oklahoma
bats and thus would not be in the soils.
A second possibility is that P. destructans reached
Oklahoma, but either did not become established or
persists at such low abundance that it was not easily
detected. Boyles and Willis (2010) suggested that local-
ized warm areas inside cold hibernacula might reduce
mortality of hibernating bats affected by WNS. Verant et
al. (2012) described temperature-dependent growth
performances of P. destructans isolates and noted that
optimal growth temperatures were between 12.58 and
15.88C, with an upper critical temperature for growth
between 19.08 and 19.88C. Above 128C, all P. destructans
isolates displayed atypical morphology. Their study
demonstrated that variations in hibernacula temperatures
could affect the growth and physiology of P. destructans,
which might impact the persistence and abundance of P.
destructans in western bat gypsum-cave hibernacula. Myotis
velifer and other bat species usually hibernate in western
Oklahoma gypsum caves from October to March.
Temperatures, relative humidity, and number of bats
counted and checked for WNS in various cave sections of
the largest known M. velifer gypsum-cave hibernaculum in
western Oklahoma are presented in Table 2 for 28
January 2011. This is the cave from which the original
WNS suspect positive bat (now negative) was tested by the
NWHC. Although the stability and microhabitats of
western Oklahoma gypsum and eastern limestone bat
caves have not yet been compared, we suspect that the
limestone caves in eastern Oklahoma are probably more
similar in geology and environmental conditions to the
TABLE 2—Temperature, relative humidity, soil sample locations, and the number of bats counted (total bats = 46,988) and surveyed
for white-nose syndrome in various sections of the Selman Cave System, the largest known Myotis velifer gypsum-cave hibernaculum in
western Oklahoma (Woodward Co.), on 28 January 2011.
Skunkeater entrance total of 23,253 bats
Cave section Temperature Relative humidity No. of bats
Entrance (soil sample) 16.08C 23% 0
Twilight (soil sample) 11.78C 34% 0
Base of Chimney 8.78C 50% 18
Stream passage (soil sample) 7.28C 58% 15,277
Past First Breakdown (soil sample) 8.68C 63% 4,652
Big Dome 13.48C 58% 16
Past Big Dome 8.78C 65% 3,290
Skylight entrance total of 23,735 bats
Cave section Temperature Relative humidity No. of bats
Entrance (soil sample) 18.18C 23% 0
Twilight (soil sample) 18.18C 31% 10,075
Pass Twilight (soil sample) 8.78C 52% 13,609
Under Breakdown (soil sample) 9.38C 53% 49
Rear Entrance 9.98C 54% 2
216 vol. 60, no. 2-3The Southwestern Naturalist
6. caves farther east in the United States where WNS is
prevalent. Thus, we suspect that WNS will soon be seen in
eastern Oklahoma caves where several endangered bat
species (Myotis grisescens, Myotis sodalis, and Corynorhinus
townsendii ingens) reside. The possibility that microcli-
mates in western bat gypsum-cave hibernacula might not
be conducive for survival of P. destructans should be
examined over several seasons if no WNS is found in
western Oklahoma in the next few years. We encourage
biologists to continue to monitor Oklahoma cave soils for
the possible existence of P. destructans. This would provide
baseline information related to the ecology and physiol-
ogy of P. destructans and help improve our understanding
of the spread of P. destructans and WNS.
We appreciate the cooperative efforts of the following groups
and individuals who assisted in the field and lab work during this
project: Central Oklahoma Grotto, students and other faculty at
the University of Central Oklahoma, including: E. York, T.
Payne, L. Loucks, T. Cloud, S. Frasse, and J. Bowen. We thank
the following individuals on staff with the National Wildlife
Health Center for their help with the testing of the bats for
white-nose syndrome and providing the final diagnostic reports:
D. E. Green, V. Shearn-Boschler, D. Blehert, A. Ballmann, and C.
L. White. We appreciate the financial support from U.S. Fish
and Wildlife Service and their providing soil samples from bat
caves in eastern Oklahoma. We appreciate the help and
cooperation of the Oklahoma Department of Tourism, Alabaster
Caverns State Park, and the Oklahoma Department of Wildlife
Conservation. We are also grateful to the Oklahoma landowners
who allowed us access to the caves on their properties.
LITERATURE CITED
BLEHERT, D. S., J. M. LORCH, A. E. BALLMANN, P. M. CRYAN, AND C. U.
METEYER. 2011. Bat white-nose syndrome in North America.
Microbe 6:267–273.
BLEHERT, D. S., A. C. HICKS, M. BEHR, C. U. METEYER, B. M.
BERLOWSKI-ZIER, E. L. BUCKLES, J. T. H. COLEMAN, S. R. DARLING,
A. GARGAS, R. NIVER, J. C. OKONIEWSKI, R. J. RUDD, AND W. B.
STONE. 2009. Bat white-nose syndrome: an emerging fungal
pathogen Science 323:227.
BOYLES, J. G., AND C. K. R. WILLIS. 2010. Could localized warm
areas inside cold caves reduce mortality of hibernating bats
affected white-nose syndrome? Frontiers in Ecology and the
Environment 8:92–98.
CRYAN, P. M., C. U. METEYER, J. G. BOYLES, AND D. S. BLEHERT. 2010.
Wing pathology of white-nose syndrome in bats suggests life
threatening disruption of physiology. BioMed Central Biol-
ogy 8:135.
DON, R. H., P. T. COX, B. J. WAINWRIGHT, K. BAKER, AND J. S.
MATTICK. 1991. ’Touchdown’ PCR to circumvent spurious
priming during gene amplification. Nucleic Acids Research
19:4008.
KING, J. L., AND C. GUIDRY. 2004. M¨uller cell production of insulin-
like growth factor-binding proteins in vitro: modulation with
phenotype and growth factor stimulation. Investigative
Ophthalmology and Visual Science 45:4535–4542.
LINDNER, D. L., AND M. T BANIK. 2009. Effects of cloning and root-
tip size on observations of fungal ITS sequences from Picea
glauca roots. Mycologia 101:157–165.
LORCH, J. M., L. K. MULLER, R. E. RUSSELL, M. O’CONNOR, D. L.
LINDNER AND D. S. BLEHERT. 2013. Distribution and environ-
mental persistence of the causative agent of white-nose
syndrome, Pseudogymnoascus destructans, in bat hibernac-
ula of the Eastern United States. Applied Environmental
Microbiology 79:1293–1301.
LORCH, J. M., A. GARGAS, C. U. METEYER, B. M. BERLOWSKI-ZIER, D.
E. GREEN, V. SHEARN-BOCHSLER, N. J. THOMAS, AND D. S. BLEHERT.
2010. Rapid polymerase chain reaction diagnosis of white-
nose syndrome in bats. Journal of Veterinary Diagnostic
Investigation 22:224–230.
MINNIS, A. M., AND D. L. LINDNER. 2013. Phylogenetic evaluation
of Geomyces and allies reveals no close relatives of Pseudogym-
noascus destructans, comb. nov. in bat hibernacula of eastern
North America. Fungal Biology 117:638–649.
MOORE, M. S., J, D. REICHARD, T. D. MURTHA, B. ZAHEDI, R. M.
FALLIER, AND T. H. KUNZ. 2011. Specific alterations in
complement protein activity of Little Brown Myotis (Myotis
lucifugus) hibernating in white-nose syndrome affected sites.
PLOS ONE 6:e27430. doi:10.1371/journal.pone.0027430.
MULLER, L. K., J. M. LORCH, D. L. LINDNER, M. O’CONNOR, A.
GARGAS, AND D. S. BLEHERT. 2013. Bat white-nose syndrome: a
real-time TaqMan polymerase chain reaction test targeting
the intergenic spacer region of Geomyces destructans. Mycolo-
gia 105:253–259.
SIKES, R. S., W. L. GANNON, and The Animal Care and Use
Committee of the American Society of Mammalogists. 2011.
Guidelines of the American Society of Mammalogists for the
use of wild mammals in research. Journal of Mammalogy
92:235–253.
VERANT, M. L., J. G. BOYLES, W. WALDREP, JR., G. WIBBELT, AND D. S.
BLEHERT. 2012. Temperature-dependent growth of Pseudo-
gymnoascus destructans, the fungus that causes bat white-
nose syndrome. PLOS ONE 7:e46280. doi:10.1371/journal.
pone.0046280.
Submitted 31 May 2014.
Acceptance recommended by Associate Editor, Jennifer K. Frey, 7 October
2014.
June 2015 Creecy et al.—Examination of bat hibernacula soils for Pseudogymnoascus destructans 217