27 research outputs found
Diversity and origins of bacterial and archaeal viruses on sinking particles reaching the abyssal ocean
No full text© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Luo, E., Leu, A. O., Eppley, J. M., Karl, D. M., & DeLong, E. F. Diversity and origins of bacterial and archaeal viruses on sinking particles reaching the abyssal ocean. ISME Journal, 16, : 1627–1635, https://doi.org/10.1038/s41396-022-01202-1.Sinking particles and particle-associated microbes influence global biogeochemistry through particulate matter export from the surface to the deep ocean. Despite ongoing studies of particle-associated microbes, viruses in these habitats remain largely unexplored. Whether, where, and which viruses might contribute to particle production and export remain open to investigation. In this study, we analyzed 857 virus population genomes associated with sinking particles collected over three years in sediment traps moored at 4000 m in the North Pacific Subtropical Gyre. Particle-associated viruses here were linked to cellular hosts through matches to bacterial and archaeal metagenome-assembled genome (MAG)-encoded prophages or CRISPR spacers, identifying novel viruses infecting presumptive deep-sea bacteria such as Colwellia, Moritella, and Shewanella. We also identified lytic viruses whose abundances correlated with particulate carbon flux and/or were exported from the photic to abyssal ocean, including cyanophages. Our data are consistent with some of the predicted outcomes of the viral shuttle hypothesis, and further suggest that viral lysis of both autotrophic and heterotrophic prokaryotes may play a role in carbon export. Our analyses revealed the diversity and origins of prevalent viruses found on deep-sea sinking particles and identified prospective viral groups for future investigation into processes that govern particle export in the open ocean.This project is funded by grants from the Simons Foundation (#329108 to EFD and DMK, #721223 to EFD, and #721252 to DMK) and the Gordon and Betty Moore Foundation (GBMF3777 to EFD and GBMF3794 to DMK). Partial support for EL was provided by the Natural Sciences and Engineering Research Council of Canada (PGSD3-487490-2016)
In search of lost spacetime: philosophical issues arising in quantum gravity
No full textThis paper issues a call to arms and seeks to entice the reader with some of the most captivating philosophical puzzles arising in quantum gravity. The analysis will be prefaced, in Section 1, by general considerations concerning the need for finding a quantum theory of gravity and the methods used in the pursuit of this goal. After mapping the field in Section 2, loop quantum gravity is introduced as an important competitor and particularly rich source of philosophical trouble in Section 3. The so-called problem of time, i.e. the puzzle that no genuine physical quantity can change, is discussed in Section 4. Finally, Section 5 analyzes how the familiar continuous spacetime structure might re-emerge from the fundamental, non-spatiotemporal structure
Multidirectional photodiode array for the measurement of solar radiances
No full textFebruary, 1980.Sponsored by grant by the Eppley Laboratory, Inc.Sponsored by the National Science Foundation ATM 78-12631
Microbial sources of exocellular DNA in the ocean
No full text© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Linney, M. D., Eppley, J. M., Romano, A. E., Luo, E., DeLong, E. F., & Karl, D. M. Microbial sources of exocellular DNA in the ocean. Applied and Environmental Microbiology, 88(7), (2022): e02093-21, https://doi.org/10.1128/aem.02093-21.Exocellular DNA is operationally defined as the fraction of the total DNA pool that passes through a membrane filter (0.1 μm). It is composed of DNA-containing vesicles, viruses, and free DNA and is ubiquitous in all aquatic systems, although the sources, sinks, and ecological consequences are largely unknown. Using a method that provides separation of these three fractions, we compared open ocean depth profiles of DNA associated with each fraction. Pelagibacter-like DNA dominated the vesicle fractions for all samples examined over a depth range of 75 to 500 m. Viral DNA consisted predominantly of myovirus-like and podovirus-like DNA and contained the highest proportion of unannotated sequences. Euphotic zone free DNA (75 to 125 m) contained primarily bacterial and viral sequences, with bacteria dominating samples from the mesopelagic zone (500 to 1,000 m). A high proportion of mesopelagic zone free DNA sequences appeared to originate from surface waters, including a large amount of DNA contributed by high-light Prochlorococcus ecotypes. Throughout the water column, but especially in the mesopelagic zone, the composition of free DNA sequences was not always reflective of cooccurring microbial communities that inhabit the same sampling depth. These results reveal the composition of free DNA in different regions of the water column (euphotic and mesopelagic zones), with implications for dissolved organic matter cycling and export (by way of sinking particles and/or migratory zooplankton) as a delivery mechanism.This work was supported by the Simons Collaboration on Ocean Processes and Ecology (awards 329108 to D.M.K. and E.F.D., 721252 to D.M.K., and 721223 to E.F.D.)
Tropical field stations yield high conservation return on investment
No full textConservation funding is currently limited; cost-effective conservation solutions are essential. We suggest that the thousands of field stations worldwide can play key roles at the frontline of biodiversity conservation and have high intrinsic value. We assessed field stations’ conservation return on investment and explored the impact of COVID-19. We surveyed leaders of field stations across tropical regions that host primate research; 157 field stations in 56 countries responded. Respondents reported improved habitat quality and reduced hunting rates at over 80% of field stations and lower operational costs per km2 than protected areas, yet half of those surveyed have less funding now than in 2019. Spatial analyses support field station presence as reducing deforestation. These “earth observatories” provide a high return on investment; we advocate for increased support of field station programs and for governments to support their vital conservation efforts by investing accordingly.Additional co-authors: Ekwoge Abwe, Tanvir Ahmed, Marc Ancrenaz, Raphali R. Andriantsimanarilafy, Andie Ang, Filippo Aureli, Louise Barrett, Jacinta C. Beehner, Marcela E. Benítez, Bruna M. Bezerra, Júlio César Bicca-Marques, Dominique Bikaba, Robert Bitariho, Christophe Boesch, Laura M. Bolt, Ramesh Boonratana, Thomas M. Butynski, Gustavo R. Canale, Susana Carvalho, Colin A. Chapman, Dilip Chetry, Susan M. Cheyne, Marina Cords, Fanny M. Cornejo, Liliana Cortés-Ortiz, Camille N. Z. Coudrat, Margaret C. Crofoot, Drew T. Cronin, Alvine Dadjo, S. Chrystelle Dakpogan, Emmanuel Danquah, Tim R. B. Davenport, Yvonne A. de Jong, Stella de la Torre, Andrea Dempsey, Judeline C. Dimalibot, Rainer Dolch, Giuseppe Donati, Alejandro Estrada, Rassina A. Farassi, Peter J. Fashing, Eduardo Fernandez-Duque, Maria J. Ferreira da Silva, Julia Fischer, César F. Flores-Negrón, Barbara Fruth, Terence Fuh Neba, Lief Erikson Gamalo, Jörg U. Ganzhorn, Paul A. Garber, Smitha D. Gnanaolivu, Mary Katherine Gonder, Sery Ernest Gonedelé Bi, Benoit Goossens, Marcelo Gordo, Juan M. Guayasamin, Diana C. Guzmán-Caro, Andrew R. Halloran, Jessica A. Hartel, Eckhard W. Heymann, Russell A. Hill, Kimberley J. Hockings, Gottfried Hohmann, Naven Hon, Mariano G. Houngbédji, Michael A. Huffman, Rachel A. Ikemeh, Inaoyom Imong, Mitchell T. Irwin, Patrícia Izar, Leandro Jerusalinsky, Gladys Kalema-Zikusoka, Beth A. Kaplin, Peter M. Kappeler, Stanislaus M. Kivai, Cheryl D. Knott, Intanon Kolasartsanee, Kathelijne Koops, Martin M. Kowalewski, Deo Kujirakwinja, Ajith Kumar, Quyet K. Le, Rebecca J. Lewis, Aung Ko Lin, Andrés Link, Luz I. Loría, Menladi M. Lormie, Edward E. Louis Jr., Ngwe Lwin, Suchinda Malaivijitnond, Lesley Marisa, Gráinne M. McCabe, W. Scott McGraw, Addisu Mekonnen, Pedro G. Méndez-Carvajal, Tânia Minhós, David M. Montgomery, Citlalli Morelos-Juárez, David Morgan, Amancio Motove Etingüe, Papa Ibnou Ndiaye, K. Anne-Isola Nekaris, Nga Nguyen, Vincent Nijman, Radar Nishuli, Marilyn A. Norconk, Luciana I. Oklander, Rahayu Oktaviani, Julia Ostner, Emily Otali, Susan E. Perry, Eduardo J. Pinel Ramos, Leila M. Porter, Jill D. Pruetz, Anne E. Pusey, Helder L. Queiroz, Mónica A. Ramírez, Guy Hermas Randriatahina, Hoby Rasoanaivo, Jonah Ratsimbazafy, Joelisoa Ratsirarson, Josia Razafindramanana, Onja H. Razafindratsima, Vernon Reynolds, Rizaldi Rizaldi, Martha M. Robbins, Melissa E. Rodríguez, Marleny Rosales-Meda, Crickette M. Sanz, Dipto Sarkar, Anne Savage, Amy L. Schreier, Oliver Schülke, Gabriel H. Segniagbeto, Juan Carlos Serio-Silva, Arif Setiawan, John Seyjagat, Felipe E. Silva, Elizabeth M. Sinclair, Rebecca L. Smith, Denise Spaan, Fiona A. Stewart, Shirley C. Strum, Martin Surbeck, Magdalena S. Svensson, Mauricio Talebi, Luc Roscelin Tédonzong, Bernardo Urbani, João Valsecchi, Natalie Vasey, Erin R. Vogel, Robert B. Wallace, Janette Wallis, Siân Waters, Roman M. Wittig, Richard W. Wrangham, Patricia C. Wright, Russell A. Mittermeie
Foraging Radii and Energetics of Least Auklets ( Aethia pusilla ) Breeding on Three Bering Sea Islands
No full textThe authors studied the relationship between the foraging radius and energy economy of A. pusilla breeding in colonies on three islands in the Bering Sea (St Lawrence, St Matthew, and St George Islands). The distance to which auklets commuted on foraging trips varied by more than an order of magnitude c5-56 km), but mean field metabolic rate did not vary significantly among birds from the three islands. The authors modeled the partitioning of energy to various activities and hypothesized that the added cost of commuting incurred by auklets from St Lawrence Island (foraging radius, 56 km) was offset by reduced energy costs while foraging at sea. Data indicated that auklets from St Lawrence Island fed on larger, more energy-rich copepods than auklets from St Matthew Island (foraging radius, 5 km). -from Author
Longitudinal progesterone profiles in baleen from female North Atlantic right whales (Eubalaena glacialis) match known calving history
No full text© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Conservation Physiology 4 (2016): cow014, doi:10.1093/conphys/cow014.Reproduction of mysticete whales is difficult to monitor, and basic parameters, such as pregnancy rate and inter-calving interval, remain unknown for many populations. We hypothesized that baleen plates (keratinous strips that grow downward from the palate of mysticete whales) might record previous pregnancies, in the form of high-progesterone regions in the sections of baleen that grew while the whale was pregnant. To test this hypothesis, longitudinal baleen progesterone profiles from two adult female North Atlantic right whales (Eubalaena glacialis) that died as a result of ship strike were compared with dates of known pregnancies inferred from calf sightings and post-mortem data. We sampled a full-length baleen plate from each female at 4 cm intervals from base (newest baleen) to tip (oldest baleen), each interval representing ∼60 days of baleen growth, with high-progesterone areas then sampled at 2 or 1 cm intervals. Pulverized baleen powder was assayed for progesterone using enzyme immunoassay. The date of growth of each sampling location on the baleen plate was estimated based on the distance from the base of the plate and baleen growth rates derived from annual cycles of stable isotope ratios. Baleen progesterone profiles from both whales showed dramatic elevations (two orders of magnitude higher than baseline) in areas corresponding to known pregnancies. Baleen hormone analysis shows great potential for estimation of recent reproductive history, inter-calving interval and general reproductive biology in this species and, possibly, in other mysticete whales.This work was supported by the Eppley Foundation for Research, the National Oceanographic and Atmospheric Administration Marine Mammal Health and Stranding Program and the Woods Hole Oceanographic Institution Ocean Life Institute
Multi-year longitudinal profiles of cortisol and corticosterone recovered from baleen of North Atlantic right whales (Eubalaena glacialis)
No full text© The Author(s), 2017. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in General and Comparative Endocrinology 254 (2017): 50-59, doi:10.1016/j.ygcen.2017.09.009.Research into stress physiology of mysticete whales has been hampered by difficulty in
obtaining repeated physiological samples from individuals over time. We investigated whether
multi-year longitudinal records of glucocorticoids can be reconstructed from serial sampling
along full-length baleen plates (representing ~10 years of baleen growth), using baleen recovered
from two female North Atlantic right whales (Eubalaena glacialis) of known reproductive
history. Cortisol and corticosterone were quantified with immunoassay of subsamples taken
every 4 cm (representing ~60 d time intervals) along a full-length baleen plate from each female.
In both whales, corticosterone was significantly elevated during known pregnancies (inferred
from calf sightings and necropsy data) as compared to intercalving intervals; cortisol was
significantly elevated during pregnancies in one female but not the other. Within intercalving
intervals, corticosterone was significantly elevated during the first year (lactation year) and/or
the second year (post-lactation year) as compared to later years of the intercalving interval, while
cortisol showed more variable patterns. Cortisol occasionally showed brief high elevations
(“spikes”) not paralleled by corticosterone, suggesting that the two glucocorticoids might be
differentially responsive to certain stressors. Generally, immunoreactive corticosterone was
present in higher concentration in baleen than immunoreactive cortisol; corticosterone:cortisol
ratio was usually >4 and was highly variable in both individuals. Further investigation of baleen
cortisol and corticosterone profiles could prove fruitful for elucidating long-term, multi-year
patterns in stress physiology of large whales, determined retrospectively from stranded or
archived specimens.This work was supported by the Eppley Foundation for Research, the NOAA Marine Mammal
Health and Stranding Program, the Woods Hole Oceanographic Institution Ocean Life Institute,
and the New England Aquarium
Relevance of amyloid precursor-like protein 2 C-terminal fragments in pancreatic cancer cells
No full textIn some cellular systems, particularly neurons, amyloid precursor-like protein 2 (APLP2), and its highly homologous family member amyloid precursor protein (APP), have been linked to cellular growth. APLP2 and APP undergo regulated intramembrane proteolysis to produce C-terminal fragments. In this study, we found comprehensive expression of APLP2 C-terminal fragments in a panel of pancreatic cancer cell lines; however, APP C-terminal fragments were notably limited to the BxPC3 cell line. Extensive glycosaminoglycan modification on APLP2 was also found in the majority of pancreatic cancer cell lines. Glycosaminoglycan-modified and -unmodified APLP2, and particularly APLP2 C-terminal fragments, also demonstrated increased expression in oncogene-transformed pancreatic ductal cells. Additionally, elevated APLP2 levels were confirmed in human pancreatic cancer tissue. Downregulation of APLP2 and APP expression, alone or in combination, caused a decrease in the growth of a pancreatic cancer cell line with representatively low APP C-terminal fragment expression, the S2-013 cell line. Furthermore, we found that treatment with beta-secretase inhibitors to block formation of APLP2 C-terminal fragments decreased the growth and viability of S2-013 cells, without affecting the survival of a non-transformed pancreatic ductal cell line. In conclusion, our studies demonstrate that abundant APLP2, but not APP, C-terminal fragment expression is conserved in pancreatic cancer cell lines; however, APP and APLP2 equally regulated the growth of S2-013 pancreatic cancer cells. Chiefly, our discoveries establish a role for APLP2 in the growth of pancreatic cancer cells and show that inhibitors preventing APLP2 cleavage reduce the viability of pancreatic cancer cells.OncologySCI(E)2ARTICLE41464-14744
Observation of meson nuclear modifications in Au+Au collisions at = 200 GeV
No full text7 pages including author list, 4 figures ; see paper for full list of authorsWe report the first measurement of charmed-hadron () production via the hadronic decay channel () in Au+Au collisions at = 200\,GeV with the STAR experiment. The charm production cross-section per nucleon-nucleon collision at mid-rapidity scales with the number of binary collisions, , from + to central Au+Au collisions. The meson yields in central Au+Au collisions are strongly suppressed compared to those in + scaled by , for transverse momenta p_{T}>3 GeV/, demonstrating significant energy loss of charm quarks in the hot and dense medium. An enhancement at intermediate is also observed. Model calculations including strong charm-medium interactions and coalescence hadronization describe our measurements
