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"Cook, Joseph A."
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Tourism : the business of travel
\"Tourism, the world's largest industry, continues to grow worldwide. With this growth comes a wealth of opportunities and challenges. In their fourth edition, Cook, Yale, and Marqua invite you to join them in exploring the many changes that are shaping the future of this exciting industry.\" \"The authors designed this book so that it engages students in the learning experience. Its appealing writing style and hundreds of current industry examples make it the perfect text for students taking their first tourism class as well as anyone who wants to know more about this exciting industry. Based on popular demand, a variety of readings, exercises, and cases augment the expanded content, providing students with even more opportunities to apply their knowledge.\"--Jacket.
The next generation of natural history collections
2018
The last 50 years have witnessed rapid changes in the ways that natural history specimens are collected, preserved, analyzed, and documented. Those changes have produced unprecedented access to specimens, images, and data as well as impressive research results in organismal biology. The stage is now set for a new generation of collecting, preserving, analyzing, and integrating biological samples-a generation devoted to interdisciplinary research into complex biological interactions and processes. Next-generation collections may be essential for breakthrough research on the spread of infectious diseases, feeding Earth's growing population, adapting to climate change, and other grand research challenges. A decade-long investment in research collection infrastructure will be needed.
Journal Article
Digitization and the Future of Natural History Collections
by
HEBERLING, J. MASON
,
GRASSA, CHRISTOPHER J.
,
DAVIS, CHARLES C.
in
Annotations
,
Anthropocene
,
Anthropogenic factors
2020
Natural history collections (NHCs) are the foundation of historical baselines for assessing anthropogenic impacts on biodiversity. Along these lines, the online mobilization of specimens via digitization—the conversion of specimen data into accessible digital content—has greatly expanded the use of NHC collections across a diversity of disciplines. We broaden the current vision of digitization (Digitization 1.0)—whereby specimens are digitized within NHCs—to include new approaches that rely on digitized products rather than the physical specimen (Digitization 2.0). Digitization 2.0 builds on the data, workflows, and infrastructure produced by Digitization 1.0 to create digital-only workflows that facilitate digitization, curation, and data links, thus returning value to physical specimens by creating new layers of annotation, empowering a global community, and developing automated approaches to advance biodiversity discovery and conservation. These efforts will transform large-scale biodiversity assessments to address fundamental questions including those pertaining to critical issues of global change.
Journal Article
Preserve a Voucher Specimen! The Critical Need for Integrating Natural History Collections in Infectious Disease Studies
by
Ferguson, Adam W.
,
Paul, Deborah L.
,
Simmons, Nancy B.
in
Animals
,
Archives & records
,
Biodiversity
2021
Despite being nearly 10 months into the COVID-19 (coronavirus disease 2019) pandemic, the definitive animal host for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the causal agent of COVID-19, remains unknown. Unfortunately, similar problems exist for other betacoronaviruses, and no vouchered specimens exist to corroborate host species identification for most of these pathogens. Despite being nearly 10 months into the COVID-19 (coronavirus disease 2019) pandemic, the definitive animal host for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the causal agent of COVID-19, remains unknown. Unfortunately, similar problems exist for other betacoronaviruses, and no vouchered specimens exist to corroborate host species identification for most of these pathogens. This most basic information is critical to the full understanding and mitigation of emerging zoonotic diseases. To overcome this hurdle, we recommend that host-pathogen researchers adopt vouchering practices and collaborate with natural history collections to permanently archive microbiological samples and host specimens. Vouchered specimens and associated samples provide both repeatability and extension to host-pathogen studies, and using them mobilizes a large workforce (i.e., biodiversity scientists) to assist in pandemic preparedness. We review several well-known examples that successfully integrate host-pathogen research with natural history collections (e.g., yellow fever, hantaviruses, helminths). However, vouchering remains an underutilized practice in such studies. Using an online survey, we assessed vouchering practices used by microbiologists (e.g., bacteriologists, parasitologists, virologists) in host-pathogen research. A much greater number of respondents permanently archive microbiological samples than archive host specimens, and less than half of respondents voucher host specimens from which microbiological samples were lethally collected. To foster collaborations between microbiologists and natural history collections, we provide recommendations for integrating vouchering techniques and archiving of microbiological samples into host-pathogen studies. This integrative approach exemplifies the premise underlying One Health initiatives, providing critical infrastructure for addressing related issues ranging from public health to global climate change and the biodiversity crisis.
Journal Article
Advancing the central role of non-model biorepositories in predictive modeling of emerging pathogens
by
Colella, Jocelyn P.
,
Salinas, Irene
,
Cook, Joseph A.
in
Analysis
,
Archives & records
,
Artificial intelligence
2023
The COVID-19 pandemic demonstrated the insufficiency of a reactive approach to emerging zoonotic pathogens. With spillover increasing in frequency as environments change and the human footprint continues to grow, pandemic prevention will require predictive models that can identify (i) potential zoonoses with a high likelihood of emergence and (ii) environmental or other features that may trigger a shift in host, vector, or pathogen baselines associated with emergence and/or spillover. Artificial intelligence (AI), and particularly its machine learning and deep learning branches, holds enormous potential for detecting shifts in large-scale biodiversity and disease datasets (genomic, ecological, geospatial, etc.). Such algorithms can be trained to identify subtle patterns in large volumes of data to yield insights into complex phenomena for which we have limited knowledge of the true cause(s) or predictor(s), as is the case for emerging infectious diseases.
Journal Article
Biospecimen Repositories and Integrated Databases as Critical Infrastructure for Pathogen Discovery and Pathobiology Research
by
Armien, Blas
,
Johnson, Karl M.
,
Dunnum, Jonathan L.
in
Archives & records
,
Biological Specimen Banks - organization & administration
,
Biology
2017
In addition to providing wide taxonomic sampling, museums and associated databases critically tie discoveries of new pathogens to permanent host records and samples and to a series of other informatics resources (e.g., GenBank and GIS applications) that facilitate future exploration, tracking, and mitigation of novel zoonotic pathogens. Because a fundamental requirement for the designation of a new pathogen is precise identification of the reservoir taxon [1], we advocate formal incorporation of museum biorepositories and integrated databases as critical infrastructure for pathogen discovery and pathobiology research. Advantages and Disadvantages of Museum Biorepositories and Integrated Databases Advantages: * Maintains spatially broad, temporally deep and site-intensive archives of ultra-frozen vertebrate tissues * Permanently links host specimens and tissues, microbial and host genetic sequences, associated publications, and other related data or materials * Ensures that pathogen reservoir identity is not lost due to taxonomic revision * Establishes best practices for loan agreements and specimen tracking * Facilitates inclusion of museum catalog numbers in GenBank accessions prior to accepting manuscripts for publication Disadvantages: * Necessitates long-term institutional commitment to support personnel and physical infrastructure * Requires periodic inventory of the number and condition of biospecimens
Journal Article
A human pathogenic hantavirus circulates and is shed in taxonomically diverse rodent reservoirs
by
Suriyamongkol, Thanchira
,
Mali, Ivana
,
Dunnum, Jonathan L.
in
Animals
,
Archives & records
,
Disease Reservoirs - virology
2025
Orthohantaviruses are negative-sense RNA viruses that can cause hantavirus cardiopulmonary syndrome (HCPS) in humans. In the United States, Sin Nombre orthohantavirus (SNV) is the primary cause of HCPS, with a fatality rate of 36% and most cases occuring in the southwestern states. The western deer mouse, Peromyscus sonoriensis, is the primary reservoir for SNV; however, it remains unclear if alternative reservoirs exist.
We conducted an extensive survey of SNV genetic prevalence in wild-caught small mammal communities throughout New Mexico and observed that 27% of all animals were positive for SNV. Through longitudinal trapping at a site of patient exposure, we found that SNV circulates at a high rate in multiple species over time. Furthermore, we isolated live SNV from tissues and feces from multiple small mammal species, demonstrating infectious virus in alternative and novel reservoirs.
Altogether, this work shows that SNV is widely prevalent and persistent throughout New Mexico in multiple small mammal reservoirs that can harbor and shed infectious virus. This encourages future work for additional surviellance efforts and revaluates host-species dynamics for New World hantaviruses.
Journal Article
Arctos: Community-driven innovations for managing natural and cultural history collections
by
McDonald, Dusty L.
,
Witt, Christopher C.
,
Koo, Michelle S.
in
Archives & records
,
Biodiversity
,
Biology
2024
More than tools for managing physical and digital objects, museum collection management systems (CMS) serve as platforms for structuring, integrating, and making accessible the rich data embodied by natural history collections. Here we describe Arctos, a scalable community solution for managing and publishing global biological, geological, and cultural collections data for research and education. Specific goals are to: (1) Describe the core features and implementation of Arctos for a broad audience with respect to the biodiversity informatics principles that enable high quality research; (2) Highlight the unique aspects of Arctos; (3) Illustrate Arctos as a model for supporting and enhancing the Digital Extended Specimen concept; and (4) Emphasize the role of the Arctos community for improving data discovery and enabling cross-disciplinary, integrative studies within a sustainable governance model. In addition to detailing Arctos as both a community of museum professionals and a collection database platform, we discuss how Arctos achieves its richly annotated data by creating a web of knowledge with deep connections between catalog records and derived or associated data. We also highlight the value of Arctos as an educational resource. Finally, we present the financial model of fiscal sponsorship by a nonprofit organization, implemented in 2022, to ensure the long-term success and sustainability of Arctos.
Journal Article
Decades-old studies of fungi associated with mammalian lungs and modern DNA sequencing approaches help define the nature of the lung mycobiome
by
Hamm, Paris S.
,
Taylor, John W.
,
Cook, Joseph A.
in
Asthma
,
Biology
,
Biology and Life Sciences
2020
About the Authors: Paris S. Hamm Affiliation: Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America ORCID logo http://orcid.org/0000-0002-6168-5723 John W. Taylor Affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America ORCID logo http://orcid.org/0000-0002-5794-7700 Joseph A. Cook Affiliations Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America, Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, United States of America ORCID logo http://orcid.org/0000-0003-3985-0670 Donald O. Natvig * E-mail: dnatvig@unm.edu Affiliation: Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America ORCID logo http://orcid.org/0000-0003-0891-6534 Introduction The vertebrate lung is the organ with the largest surface area presented to the external environment. Lung surface areas and inhalation volumes for small mammals are comparable to those of humans when scaled for size. [...]many small mammals live in microenvironments (notably burrows and understories) where they are exposed to high densities of airborne spores derived from the growth of fungi on substrates in soil and litter. [...]next-generation sequencing efforts now provide important new contexts for the study of lung-inhabiting fungi that began more than seven decades ago. Initial investigations of the human lung mycobiome involved individuals with lung diseases such as cystic fibrosis (CF) [7], asthma, and chronic obstructive pulmonary disease.
Journal Article
Evolutionary Insights from a Genetically Divergent Hantavirus Harbored by the European Common Mole (Talpa europaea)
2009
The discovery of genetically distinct hantaviruses in shrews (Order Soricomorpha, Family Soricidae) from widely separated geographic regions challenges the hypothesis that rodents (Order Rodentia, Family Muridae and Cricetidae) are the primordial reservoir hosts of hantaviruses and also predicts that other soricomorphs harbor hantaviruses. Recently, novel hantavirus genomes have been detected in moles of the Family Talpidae, including the Japanese shrew mole (Urotrichus talpoides) and American shrew mole (Neurotrichus gibbsii). We present new insights into the evolutionary history of hantaviruses gained from a highly divergent hantavirus, designated Nova virus (NVAV), identified in the European common mole (Talpa europaea) captured in Hungary.
Pair-wise alignment and comparison of the full-length S- and L-genomic segments indicated moderately low sequence similarity of 54-65% and 46-63% at the nucleotide and amino acid levels, respectively, between NVAV and representative rodent- and soricid-borne hantaviruses. Despite the high degree of sequence divergence, the predicted secondary structure of the NVAV nucleocapsid protein exhibited the characteristic coiled-coil domains at the amino-terminal end, and the L-segment motifs, typically found in hantaviruses, were well conserved. Phylogenetic analyses, using maximum-likelihood and Bayesian methods, showed that NVAV formed a distinct clade that was evolutionarily distant from all other hantaviruses.
Newly identified hantaviruses harbored by shrews and moles support long-standing virus-host relationships and suggest that ancestral soricomorphs, rather than rodents, may have been the early or original mammalian hosts.
Journal Article