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Article: Multi-Domain Touchscreen-Based Cognitive Assessment of C57BL/6J Female Mice Shows Whole-Body Exposure to

Soler, Ivan / Yun, Sanghee / Reynolds, Ryan P / Whoolery, Cody W / Tran, Fionya H / Kumar, Priya L / Rong, Yuying / DeSalle, Matthew J / Gibson, Adam D / Stowe, Ann M / Kiffer, Frederico C / Eisch, Amelia J

Frontiers in behavioral neuroscience

2021 Volume 15, Page(s) 722780

Abstract: Astronauts during interplanetary missions will be exposed to galactic cosmic radiation, including charged particles ... ...

Abstract	Astronauts during interplanetary missions will be exposed to galactic cosmic radiation, including charged particles like
Language	English
Publishing date	2021-10-11
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2452960-6
ISSN	1662-5153
ISSN	1662-5153
DOI	10.3389/fnbeh.2021.722780
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Article ; Online: A natural history museum visitor survey of perception, attitude and knowledge (PAK) of microbes and antibiotics.

Zichello, Julia / Gupta, Preeti / Scott, Monique / Desai, Bella / Cohen, Ruth / Halderman, Lauri / Perkins, Susan / Porzecanski, Ana / Planet, Paul J / Wyner, Yael / Blaser, Martin / Burk, Robert / Diamond, Judy / Kennett, Rod / Borland, Jennifer / DeSalle, Rob

PloS one

2021 Volume 16, Issue 9, Page(s) e0257085

Abstract: A kiosk-based survey at the American Museum of Natural History in New York City in 2016-2018 allowed us to assess public knowledge of antibiotics and public attitudes toward microbes in museum goers. Over 22,000 visitors from 172 countries and ... ...

Abstract	A kiosk-based survey at the American Museum of Natural History in New York City in 2016-2018 allowed us to assess public knowledge of antibiotics and public attitudes toward microbes in museum goers. Over 22,000 visitors from 172 countries and territories answered several carefully designed questions about microbes and antibiotics. These visitors also entered age, gender, and country demographic data that allowed for stratification along these demographic and geographic divisions. Because museum goers are likely to be better informed about these and other science-based topics, the results described here can set a potential upper bound for public knowledge on these topics. Surprisingly, the results of our analysis of museum goers' answers about microbes and antibiotics indicate a substantial lack of familiarity with both topics. For example, overall only about 50% of respondents can correctly identify penicillin as an antibiotic and less than 50% of museum visitors view microbes as beneficial. The results described here suggest that we are perhaps off target with our educational efforts in this area and that a major shift in approach toward more basic microbial topics is warranted in our educational efforts.
MeSH term(s)	Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects ; Data Analysis ; Health Knowledge, Attitudes, Practice ; Humans ; Language ; Museums ; Natural History ; Perception ; Surveys and Questionnaires
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2021-09-22
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0257085
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Article ; Online: Plant ecological genomics at the limits of life in the Atacama Desert.

Eshel, Gil / Araus, Viviana / Undurraga, Soledad / Soto, Daniela C / Moraga, Carol / Montecinos, Alejandro / Moyano, Tomás / Maldonado, Jonathan / Díaz, Francisca P / Varala, Kranthi / Nelson, Chase W / Contreras-López, Orlando / Pal-Gabor, Henrietta / Kraiser, Tatiana / Carrasco-Puga, Gabriela / Nilo-Poyanco, Ricardo / Zegar, Charles M / Orellana, Ariel / Montecino, Martín /

Maass, Alejandro / Allende, Miguel L / DeSalle, Robert / Stevenson, Dennis W / González, Mauricio / Latorre, Claudio / Coruzzi, Gloria M / Gutiérrez, Rodrigo A

Proceedings of the National Academy of Sciences of the United States of America

2021 Volume 118, Issue 46

Abstract: ... microbe diversity at 22 sites (every 100 m of altitude) along the TLT over a 10-y period. We quantified ...

Abstract	The Atacama Desert in Chile-hyperarid and with high-ultraviolet irradiance levels-is one of the harshest environments on Earth. Yet, dozens of species grow there, including Atacama-endemic plants. Herein, we establish the Talabre-Lejía transect (TLT) in the Atacama as an unparalleled natural laboratory to study plant adaptation to extreme environmental conditions. We characterized climate, soil, plant, and soil-microbe diversity at 22 sites (every 100 m of altitude) along the TLT over a 10-y period. We quantified drought, nutrient deficiencies, large diurnal temperature oscillations, and pH gradients that define three distinct vegetational belts along the altitudinal cline. We deep-sequenced transcriptomes of 32 dominant plant species spanning the major plant clades, and assessed soil microbes by metabarcoding sequencing. The top-expressed genes in the 32 Atacama species are enriched in stress responses, metabolism, and energy production. Moreover, their root-associated soils are enriched in growth-promoting bacteria, including nitrogen fixers. To identify genes associated with plant adaptation to harsh environments, we compared 32 Atacama species with the 32 closest sequenced species, comprising 70 taxa and 1,686,950 proteins. To perform phylogenomic reconstruction, we concatenated 15,972 ortholog groups into a supermatrix of 8,599,764 amino acids. Using two codon-based methods, we identified 265 candidate positively selected genes (PSGs) in the Atacama plants, 64% of which are located in Pfam domains, supporting their functional relevance. For 59/184 PSGs with an
MeSH term(s)	Altitude ; Chile ; Climate Change ; Desert Climate ; Ecosystem ; Genomics/methods ; Phylogeny ; Plants/genetics ; Soil ; Soil Microbiology
Chemical Substances	Soil
Language	English
Publishing date	2021-11-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2101177118
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Article ; Online: Whole-Body

Zanni, Giulia / Deutsch, Hannah M / Rivera, Phillip D / Shih, Hung-Ying / LeBlanc, Junie A / Amaral, Wellington Z / Lucero, Melanie J / Redfield, Rachel L / DeSalle, Matthew J / Chen, Benjamin P C / Whoolery, Cody W / Reynolds, Ryan P / Yun, Sanghee / Eisch, Amelia J

International journal of molecular sciences

2018 Volume 19, Issue 10

Abstract: High-charge and -energy (HZE) particles comprise space radiation and they pose a challenge to astronauts on deep space missions. While exposure to most HZE particles decreases neurogenesis in the hippocampus-a brain structure important in memory-prior ... ...

Abstract	High-charge and -energy (HZE) particles comprise space radiation and they pose a challenge to astronauts on deep space missions. While exposure to most HZE particles decreases neurogenesis in the hippocampus-a brain structure important in memory-prior work suggests that
MeSH term(s)	Animals ; Biomarkers ; Carbon Isotopes ; Cell Count ; Cell Proliferation ; Cell Survival ; Dentate Gyrus/cytology ; Dentate Gyrus/radiation effects ; Immunohistochemistry ; Ki-67 Antigen/metabolism ; Mice ; Neurogenesis ; Pyramidal Cells/cytology ; Pyramidal Cells/metabolism ; Pyramidal Cells/radiation effects ; Whole-Body Irradiation
Chemical Substances	Biomarkers ; Carbon Isotopes ; Ki-67 Antigen
Language	English
Publishing date	2018-10-09
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms19103078
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Article ; Online: Mitochondrial lipid droplet formation as a detoxification mechanism to sequester and degrade excessive urothelial membranes.

Molecular biology of the cell

2019 Volume 30, Issue 24, Page(s) 2969–2984

Abstract: The apical surface of the terminally differentiated mammalian urothelial umbrella cell is mechanically stable and highly impermeable, in part due to its coverage by urothelial plaques consisting of 2D crystals of uroplakin particles. The mechanism for ... ...

Abstract	The apical surface of the terminally differentiated mammalian urothelial umbrella cell is mechanically stable and highly impermeable, in part due to its coverage by urothelial plaques consisting of 2D crystals of uroplakin particles. The mechanism for regulating the uroplakin/plaque level is unclear. We found that genetic ablation of the highly tissue-specific sorting nexin Snx31, which localizes to plaques lining the multivesicular bodies (MVBs) in urothelial umbrella cells, abolishes MVBs suggesting that Snx31 plays a role in stabilizing the MVB-associated plaques by allowing them to achieve a greater curvature. Strikingly, Snx31 ablation also induces a massive accumulation of uroplakin-containing mitochondria-derived lipid droplets (LDs), which mediate uroplakin degradation via autophagy/lipophagy, leading to the loss of apical and fusiform vesicle plaques. These results suggest that MVBs play an active role in suppressing the excessive/wasteful endocytic degradation of uroplakins. Failure of this suppression mechanism triggers the formation of mitochondrial LDs so that excessive uroplakin membranes can be sequestered and degraded. Because mitochondrial LD formation, which occurs at a low level in normal urothelium, can also be induced by disturbance in uroplakin polymerization due to individual uroplakin knockout and by arsenite, a bladder carcinogen, this pathway may represent an inducible, versatile urothelial detoxification mechanism.
MeSH term(s)	Animals ; Female ; Lipid Droplets/metabolism ; Lipid Droplets/physiology ; Membrane Glycoproteins/metabolism ; Membranes/metabolism ; Mice ; Mice, Inbred C57BL ; Mitochondria/metabolism ; Multivesicular Bodies/metabolism ; Sorting Nexins/metabolism ; Urinary Bladder/metabolism ; Uroplakins/metabolism ; Uroplakins/physiology ; Urothelium/metabolism
Chemical Substances	Membrane Glycoproteins ; Sorting Nexins ; Uroplakins
Language	English
Publishing date	2019-10-02
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1098979-1
ISSN	1939-4586 ; 1059-1524
ISSN (online)	1939-4586
ISSN	1059-1524
DOI	10.1091/mbc.E19-05-0284
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Article: Regulation of the G1 to S transition by the ubiquitin pathway.

DeSalle, L M / Pagano, M

FEBS letters

2001 Volume 490, Issue 3, Page(s) 179–189

Abstract: This year the most prestigious prize in medical sciences, the Lasker Award, has been presented to the three scientists who discovered the ubiquitin pathway: Aaron Ciechanover, Avram Hershko, and Alexander Varshavsky [Nature Med. 6 (2000) 1073-1081]. ... ...

Abstract	This year the most prestigious prize in medical sciences, the Lasker Award, has been presented to the three scientists who discovered the ubiquitin pathway: Aaron Ciechanover, Avram Hershko, and Alexander Varshavsky [Nature Med. 6 (2000) 1073-1081]. During a time when the scientific community was focused on understanding how proteins were synthesized, they intently pursued the novel idea that cells were programmed to selectively destroy proteins. Their work led to the identification of an elaborate system of protein degradation targeting a myriad of cellular substrates. A small protein called ubiquitin is at the center of this process. Although the ubiquitin pathway was first described in the early 1980s, it has only more recently advanced to the forefront of basic research as a significant regulatory network within the cell. The field continues to grow as new ubiquitination enzymes and novel functions of this system are identified. Scientists are focused on elucidating the mechanisms by which cells deploy the ubiquitin pathway to control levels of selected proteins, such as cell cycle regulatory proteins, transcription factors and signaling molecules. Accelerated or decelerated rates of degradation of particular substrates participate in the genesis of many human diseases. Thus, understanding the mechanisms that confer specificity to the ubiquitin system will allow the development of novel therapeutic approaches to target aberrations in this pathway underlying tumorigenesis and other human pathologies.
MeSH term(s)	Animals ; Cell Cycle Proteins/metabolism ; Cysteine Endopeptidases/metabolism ; F-Box Proteins ; F-Box-WD Repeat-Containing Protein 7 ; G1 Phase ; Humans ; Ligases/chemistry ; Ligases/metabolism ; Multienzyme Complexes/metabolism ; Peptide Synthases/chemistry ; Peptide Synthases/metabolism ; Proteasome Endopeptidase Complex ; Protein Subunits ; S Phase ; SKP Cullin F-Box Protein Ligases ; Saccharomyces cerevisiae/enzymology ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins ; Ubiquitin-Conjugating Enzymes ; Ubiquitin-Protein Ligases ; Ubiquitins/metabolism
Chemical Substances	CDC4 protein, S cerevisiae ; Cell Cycle Proteins ; F-Box Proteins ; F-Box-WD Repeat-Containing Protein 7 ; FBXW7 protein, human ; Multienzyme Complexes ; Protein Subunits ; Saccharomyces cerevisiae Proteins ; Ubiquitins ; ubiquitin carrier proteins ; Ubiquitin-Conjugating Enzymes (EC 2.3.2.23) ; SKP Cullin F-Box Protein Ligases (EC 2.3.2.27) ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; Cysteine Endopeptidases (EC 3.4.22.-) ; Proteasome Endopeptidase Complex (EC 3.4.25.1) ; Ligases (EC 6.-) ; Peptide Synthases (EC 6.3.2.-)
Language	English
Publishing date	2001-02-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S. ; Review
ZDB-ID	212746-5
ISSN	1873-3468 ; 0014-5793
ISSN (online)	1873-3468
ISSN	0014-5793
DOI	10.1016/s0014-5793(01)02121-4
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Article ; Online: Colonization and diversification of aquatic insects on three Macaronesian archipelagos using 59 nuclear loci derived from a draft genome.

Rutschmann, Sereina / Detering, Harald / Simon, Sabrina / Funk, David H / Gattolliat, Jean-Luc / Hughes, Samantha J / Raposeiro, Pedro M / DeSalle, Rob / Sartori, Michel / Monaghan, Michael T

Molecular phylogenetics and evolution

2017 Volume 107, Page(s) 27–38

Abstract: ... species complex, Cloeon dipterum L. 1761 (Ephemeroptera: Baetidae), in Macaronesia. Whole ...

Abstract	The study of processes driving diversification requires a fully sampled and well resolved phylogeny, although a lack of phylogenetic markers remains a limitation for many non-model groups. Multilocus approaches to the study of recent diversification provide a powerful means to study the evolutionary process, but their application remains restricted because multiple unlinked loci with suitable variation for phylogenetic or coalescent analysis are not available for most non-model taxa. Here we identify novel, putative single-copy nuclear DNA (nDNA) phylogenetic markers to study the colonization and diversification of an aquatic insect species complex, Cloeon dipterum L. 1761 (Ephemeroptera: Baetidae), in Macaronesia. Whole-genome sequencing data from one member of the species complex were used to identify 59 nDNA loci (32,213 base pairs), followed by Sanger sequencing of 29 individuals sampled from 13 islands of three Macaronesian archipelagos. Multispecies coalescent analyses established six putative species. Three island species formed a monophyletic clade, with one species occurring on the Azores, Europe and North America. Ancestral state reconstruction indicated at least two colonization events from the mainland (to the Canaries, respectively Azores) and one within the archipelago (between Madeira and the Canaries). Random subsets of the 59 loci showed a positive linear relationship between number of loci and node support. In contrast, node support in the multispecies coalescent tree was negatively correlated with mean number of phylogenetically informative sites per locus, suggesting a complex relationship between tree resolution and marker variability. Our approach highlights the value of combining genomics, coalescent-based phylogeography, species delimitation, and phylogenetic reconstruction to resolve recent diversification events in an archipelago species complex.
MeSH term(s)	Animals ; Biodiversity ; Biological Evolution ; DNA/chemistry ; DNA/isolation & purification ; DNA/metabolism ; Europe ; Genetic Loci ; Genome ; Insecta/classification ; Insecta/genetics ; Islands ; North America ; Phylogeny ; Phylogeography ; Sequence Analysis, DNA
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2017-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	33610-5
ISSN	1095-9513 ; 1055-7903
ISSN (online)	1095-9513
ISSN	1055-7903
DOI	10.1016/j.ympev.2016.10.007
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Article: Tumor outbreaks in marine turtles are not due to recent herpesvirus mutations.

Herbst, Larry / Ene, Ada / Su, Mei / Desalle, Rob / Lenz, Jack

Current biology : CB

2004 Volume 14, Issue 17, Page(s) R697–9

MeSH term(s)	Animals ; Base Sequence ; Bayes Theorem ; Disease Outbreaks ; Evolution, Molecular ; Herpesviridae/genetics ; Herpesviridae/pathogenicity ; Herpesviridae Infections/epidemiology ; Herpesviridae Infections/veterinary ; Models, Genetic ; Molecular Sequence Data ; Mutation/genetics ; Papilloma/epidemiology ; Papilloma/veterinary ; Phylogeny ; Sequence Analysis, DNA ; Skin Neoplasms/epidemiology ; Skin Neoplasms/veterinary ; Species Specificity ; Turtles/virology
Language	English
Publishing date	2004-09-07
Publishing country	England
Document type	Comparative Study ; Letter
ZDB-ID	1071731-6
ISSN	1879-0445 ; 0960-9822
ISSN (online)	1879-0445
ISSN	0960-9822
DOI	10.1016/j.cub.2004.08.040
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Article: Colonization and diversification of aquatic insects on three Macaronesian archipelagos using 59 nuclear loci derived from a draft genome

Rutschmann, Sereina / David H. Funk / Harald Detering / Jean-Luc Gattolliat / Michael T. Monaghan / Michel Sartori / Pedro M. Raposeiro / Rob DeSalle / Sabrina Simon / Samantha J. Hughes

Molecular phylogenetics and evolution. 2017 Feb., v. 107

2017

Abstract: ... species complex, Cloeon dipterum L. 1761 (Ephemeroptera: Baetidae), in Macaronesia. Whole ...

Abstract	The study of processes driving diversification requires a fully sampled and well resolved phylogeny, although a lack of phylogenetic markers remains a limitation for many non-model groups. Multilocus approaches to the study of recent diversification provide a powerful means to study the evolutionary process, but their application remains restricted because multiple unlinked loci with suitable variation for phylogenetic or coalescent analysis are not available for most non-model taxa. Here we identify novel, putative single-copy nuclear DNA (nDNA) phylogenetic markers to study the colonization and diversification of an aquatic insect species complex, Cloeon dipterum L. 1761 (Ephemeroptera: Baetidae), in Macaronesia. Whole-genome sequencing data from one member of the species complex were used to identify 59 nDNA loci (32,213 base pairs), followed by Sanger sequencing of 29 individuals sampled from 13 islands of three Macaronesian archipelagos. Multispecies coalescent analyses established six putative species. Three island species formed a monophyletic clade, with one species occurring on the Azores, Europe and North America. Ancestral state reconstruction indicated at least two colonization events from the mainland (to the Canaries, respectively Azores) and one within the archipelago (between Madeira and the Canaries). Random subsets of the 59 loci showed a positive linear relationship between number of loci and node support. In contrast, node support in the multispecies coalescent tree was negatively correlated with mean number of phylogenetically informative sites per locus, suggesting a complex relationship between tree resolution and marker variability. Our approach highlights the value of combining genomics, coalescent-based phylogeography, species delimitation, and phylogenetic reconstruction to resolve recent diversification events in an archipelago species complex.
Keywords	aquatic insects ; Baetidae ; correlation ; genomics ; islands ; loci ; monophyly ; nuclear genome ; phylogeography ; sequence analysis ; Azores ; Europe ; North America
Language	English
Dates of publication	2017-02
Size	p. 27-38.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	33610-5
ISSN	1095-9513 ; 1055-7903
ISSN (online)	1095-9513
ISSN	1055-7903
DOI	10.1016/j.ympev.2016.10.007
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Article ; Online: Colonization and diversification of aquatic insects on three Macaronesian archipelagos using 59 nuclear loci derived from a draft genome

Rutschmann, Sereina / Detering, Harald / Simon, Sabrina / Funk, David H. / Gattolliat, Jean Luc / Hughes, Samantha J. / Raposeiro, Pedro M. / DeSalle, Rob / Sartori, Michel / Monaghan, Michael T.

Molecular Phylogenetics and Evolution

2017 Volume 107

Abstract: ... species complex, Cloeon dipterum L. 1761 (Ephemeroptera: Baetidae), in Macaronesia. Whole ...

Abstract	The study of processes driving diversification requires a fully sampled and well resolved phylogeny, although a lack of phylogenetic markers remains a limitation for many non-model groups. Multilocus approaches to the study of recent diversification provide a powerful means to study the evolutionary process, but their application remains restricted because multiple unlinked loci with suitable variation for phylogenetic or coalescent analysis are not available for most non-model taxa. Here we identify novel, putative single-copy nuclear DNA (nDNA) phylogenetic markers to study the colonization and diversification of an aquatic insect species complex, Cloeon dipterum L. 1761 (Ephemeroptera: Baetidae), in Macaronesia. Whole-genome sequencing data from one member of the species complex were used to identify 59 nDNA loci (32,213 base pairs), followed by Sanger sequencing of 29 individuals sampled from 13 islands of three Macaronesian archipelagos. Multispecies coalescent analyses established six putative species. Three island species formed a monophyletic clade, with one species occurring on the Azores, Europe and North America. Ancestral state reconstruction indicated at least two colonization events from the mainland (to the Canaries, respectively Azores) and one within the archipelago (between Madeira and the Canaries). Random subsets of the 59 loci showed a positive linear relationship between number of loci and node support. In contrast, node support in the multispecies coalescent tree was negatively correlated with mean number of phylogenetically informative sites per locus, suggesting a complex relationship between tree resolution and marker variability. Our approach highlights the value of combining genomics, coalescent-based phylogeography, species delimitation, and phylogenetic reconstruction to resolve recent diversification events in an archipelago species complex.
Keywords	Baetidae ; Island radiation ; Multispecies coalescent ; Phylogeny ; Phylogeography
Subject code	590
Language	English
Publishing country	nl
Document type	Article ; Online
ZDB-ID	33610-5
ISSN	1095-9513 ; 1055-7903
ISSN (online)	1095-9513
ISSN	1055-7903
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