Cruise Report C-200 : Scientific data collected aboard SSV Corwith Cramer, Woods Hole, MA – Sable Island, Canada – Halifax, Nova Scotia – Woods Hole, MA, 6 July, 2005 – 2 August, 2005

Woods Hole, MA – Sable Island, Canada – Halifax, Nova Scotia – Woods Hole, MA, 6 July, 2005 – 2 August, 2005This cruise report provides a record of data collected during C200 aboard the SSV Corwith Cramer from Woods Hole, MA, USA to Sable Island, Canada, continuing on to Halifax, Nova Scotia, Canada and returning to Woods Hole (Figure 1). We collected samples or data with 98 individual deployments from 37 discrete stations (Table 2) along our cruise track. In addition we continuously sampled water depth, sub-bottom profiles and Acoustic Doppler Current Profiles (ADCP) along with flow-through sea surface temperature, salinity and in vivo fluorescence. This report summarizes physical, chemical and biological characteristics at the sea surface (Table 3, Figure 2) and at depth (Tables 4 and 5, Figure 3a) along our cruise track. A complete oceanographic survey of two submarine canyons (Hydrographer’s canyon south of Georges bank and The Gully, east of Sable Island) were completed. Bathymetry and surface currents for each seamount are available on request. Temperature, salinity and fluorescence profiles are presented (Figures 3b and 3c). Large scale hydrography is summarized by contour plots of temperature, salinity and fluorescence (Figure 4); whereas large scale current patterns are summarized by contour plots of current direction, magnitude and echo amplitude (Figure 5). In addition, the distribution and density of zooplankton at the sea surface (Table 6) and at depth (Figures 7 and 8) are presented. Sediment samples were sieved and grain size percentage of each fraction was determined (Figure 9). Additional CTD, bathymetry (CHIRP), current (ADCP) and biological data are not reported here but are available on request through Sea Education Association (SEA) and the Chief Scientist. The information in this report is not intended to represent final interpretation of the data and should not be excerpted or cited without written permission from SEA. Unpublished data can be made available by arrangement with the SEA archivist by contacting: Erik R. Zettler, Science Coordinator Sea Education Association, P.O. Box 6, Woods Hole, MA 02543, U.S.A. 508-540-3954 x29 fax 508-457-4673 email: [email protected] website: www.sea.edu As part of SEA’s educational program, undergraduates conducted student-designed oceanographic research during the cruise. Project topics included physical, chemical, biological and geological oceanography (Table 10). Student research efforts culminated in a written report and public presentation to the ship’s company. These papers are available on request from SEA.NS

Cruise Report S-207 : Scientific data collected aboard SSV Robert C. Seamans, San Diego, California – La Paz, Baja California Sur – Puerto Vallarta, Mexico. 12 October – 20 November, 2006

San Diego, California – La Paz, Baja California Sur – Puerto Vallarta, Mexico. 12 October – 20 November, 2006This cruise report provides a record of data collected during S207 aboard the SSV Robert C. Seamans from San Diego, California to Puerto Vallarta, Mexico (Figure 1) with a stop at La Paz on the southeastern shore of Baja California Sur. We collected samples or data with 170 individual deployments from 91 discrete stations (Table 2) along our cruise track. In addition we continuously sampled water depth, sub-bottom profiles and Acoustic Doppler Current Profiles (ADCP) along with flow-through sea surface temperature, salinity and in vivo fluorescence. This report summarizes physical, chemical and biological characteristics along our cruise track and around surveyed seamounts and islands. The S207 cruise track traversed several oceanic regions that can be distinguished by their sea surface temperature, salinity, density and fluorescence values (Figures 2a-b). Sub-surface water masses and their chemical properties were also surveyed using a CTD and 12 bottle carousel (Tables 4 and 5). Large scale hydrography are summarized by contour plots of temperature, salinity and sound velocity along our cruise track (Figure 3) and for specific transects across key oceanic features (Figures 4a-e) and around surveyed seamounts and islands (Figures 5a-c). Large scale current patterns are summarized by contour plots of current direction, magnitude and echo amplitude (Figure 6). The distribution of neuston net, meter net, and Tucker trawl stations and corresponding zooplankton density and numbers of select nekton species are presented (Tables 6-8). Location and relevant station depths for sediment samples are shown in Table 9. Secchi depth at various locations is also provided (Table 10). A complete oceanographic survey of Jasper seamount, Cerralvo seamount and the coastal waters of Isla Guadalupe were completed. Additional CTD, CHIRP, ADCP and biological data not reported here are available on request through Sea Education Association (SEA) and the Chief Scientist. The information in this report is not intended to represent final interpretation of the data and should not be excerpted or cited without written permission from SEA. In addition, vertical and horizontal distribution patterns of myctophids (lantern fish), and the marine insect Halobates were studied in relation to environmental characteristics. Results, not reported here, are available upon request through SEA. As part of SEA’s educational program, undergraduates conducted independent oceanographic research during the cruise. Project explored regionally, relevant topics in the disciplines of physical, chemical, biological and geological oceanography (Table 11). Student research efforts culminated in a written report and public presentation to the ship’s company. These papers are available on request from SEA.NS

Cruise Report S-203 : Scientific data collected aboard SSV Robert C. Seamans, Papeete, Tahiti – Rangiroa Atoll, Tuamoto Archipelago – Nuku Hiva, Marquesas – Honolulu, Hawaii. 7 February, 2006 - 18 March, 2006

Papeete, Tahiti – Rangiroa Atoll, Tuamoto Archipelago – Nuku Hiva, Marquesas – Honolulu, Hawaii. 7 February, 2006 - 18 March, 2006This cruise report provides a record of data collected during S203 aboard the SSV Robert C. Seamans from Papeete, Tahiti to Honolulu, Hawaii (Figure 1) with stops at Rangiroa Atoll, and Nuku Hiva, Marquesas. We collected samples or data with 189 individual deployments from 69 discrete stations (Table 2) along our cruise track. In addition we continuously sampled water depth, sub-bottom profiles and Acoustic Doppler Current Profiles (ADCP) along with flow-through sea surface temperature, salinity and in vivo fluorescence. This report summarizes physical, chemical and biological characteristics at the sea surface (Table 3, Figure 2) and at depth (Tables 4 and 5, Figure 3a) along our cruise track and around surveyed seamounts (Figure 3b). Large scale hydrography are summarized by contour plots of temperature, salinity and sound velocity or fluorescence along our cruise track (Figure 4a) and around surveyed seamounts (Figure 4b and c); whereas large scale current patterns are summarized by contour plots of current direction, magnitude and echo amplitude (Figure 5a - c). The distribution of neuston net stations, meter net stations and corresponding zooplankton density and numbers of select nekton species are presented (Table 6 and 7). Distribution and depth of phytoplankton drift nets are also provided (Table 8). Location and relevant station depths for bathyphotometer, secchi disc and shipek grab (atop seamount summits) deployments are shown in tables 9-11 respectively. A complete oceanographic survey of two seamounts, west of the Marquesan Islands was completed. Additional CTD, CHIRP, ADCP and biological data not reported here are available on request through Sea Education Association (SEA) and the Chief Scientist. The information in this report is not intended to represent final interpretation of the data and should not be excerpted or cited without written permission from SEA. In addition, diel patterns of myctophids (lantern fish), pteropods and bioluminescence potential were studied in relation to the lunar phase. Results, not reported here, are available upon request through SEA. As part of SEA’s educational program, undergraduates conducted idependent oceanographic research during the cruise. Project topics explored physical, chemical, biological and geological oceanography (Table 12). Student research efforts culminated in a written report and public presentation to the ship’s company. These papers are available on request from SEA.NS

Cruise Report S-206 : Scientific data collected aboard SSV Robert C. Seamans, Seattle, WA – Victoria, British Columbia – Skung Gwaii, Anthony Island – Tahsis, British Columbia – San Francisco, CA. 7 July – 2 August, 2006

Seattle, WA – Victoria, British Columbia – Skung Gwaii, Anthony Island – Tahsis, British Columbia – San Francisco, CA. 7 July – 2 August, 2006This cruise report provides a record of data collected during S206 aboard the SSV Robert C. Seamans from Seattle, Washington to San Francisco, California (Figure 1) with stops at Victoria, British Columbia, Skung Gwaii village on Anthony Island and Tahsis, British Columbia. We collected samples or data with 110 individual deployments from 60 discrete stations (Table 2) along our cruise track. In addition we continuously sampled water depth, sub-bottom profiles and Acoustic Doppler Current Profiles (ADCP) along with flow-through sea surface temperature, salinity and in vivo fluorescence. This report summarizes physical, chemical and biological characteristics along our cruise track. The S206 cruise track traversed several coastal regions that can be distinguished by their sea surface temperature, salinity, and fluorescence values (Figures 2). Inshore-offshore transects of surface stations revealed the distribution of nutrients, chlorophyll-a and bacteria near river outflows Table 3). Detailed views of specific transects through specific coastal regions reveal dynamic spatial (nautical miles) and temporal (days) variability (Figures 3 a-d). Sub-surface water masses and their chemical properties were also surveyed using a CTD and 12 bottle carousel (Tables 4 and 5). Regional scale hydrography is summarized by T-S plots (Figure 4). Surface currents throughout our cruise track were generally weak except for regionally isolated phenomena (Figure 5). The distribution of neuston and meter net stations and corresponding zooplankton density and numbers of select nekton species are presented (Tables 6-7). Location and relevant station depths for sediment samples are shown in Table 8. In addition, a complete biomass and compositional survey of lower tropic levels was completed in several regions; from enumeration of bacterial communities using epifluorescence microscopy through phytoplankton, zooplankton and meroplankton communities to myctophids (lantern fish) and other micronekton. Results, not reported here, are available upon request through SEA. As part of SEA’s educational program, undergraduates conducted independent oceanographic research during the cruise. Project explored regionally, relevant topics in the disciplines of physical, chemical, biological and geological oceanography (Table 9). Student research efforts culminated in a written report and public presentation to the ship’s company. These papers are available on request from SEA.NS

Comparative mitochondrial and chloroplast genomics of a genetically distinct form of Sargassum contributing to recent “Golden Tides” in the Western Atlantic

© The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ecology and Evolution 7 (2017): 516–525, doi:10.1002/ece3.2630.Over the past 5 years, massive accumulations of holopelagic species of the brown macroalga Sargassum in coastal areas of the Caribbean have created “golden tides” that threaten local biodiversity and trigger economic losses associated with beach deterioration and impact on fisheries and tourism. In 2015, the first report identifying the cause of these extreme events implicated a rare form of the holopelagic species Sargassum natans (form VIII). However, since the first mention of S. natans VIII in the 1930s, based solely on morphological characters, no molecular data have confirmed this identification. We generated full-length mitogenomes and partial chloroplast genomes of all representative holopelagic Sargassum species, S. fluitans III and S. natans I alongside the putatively rare S. natans VIII, to demonstrate small but consistent differences between S. natans I and VIII (7 bp differences out of the 34,727). Our comparative analyses also revealed that both S. natans I and S. natans VIII share a very close phylogenetic relationship with S. fluitans III (94- and 96-bp differences of 34,727). We designed novel primers that amplified regions of the cox2 and cox3 marker genes with consistent polymorphic sites that enabled differentiation between the two S. natans forms (I and VIII) from each other and both from S. fluitans III in over 150 Sargassum samples including those from the 2014 golden tide event. Despite remarkable gene synteny and sequence conservation, the three Sargassum forms differ in morphology, ecology, and distribution patterns, warranting more extensive interrogation of holopelagic Sargassum genomes as a whole.This work was supported by a US National Science Foundation (NSF) collaborative grant to LAA-Z (OCE-1155571) and ERZ (OCE-1155379), and an NSF TUES grant (DUE-1043468) to LAA-Z and ER

Learning probabilistic models of hydrogen bond stability from molecular dynamics simulation trajectories

Hydrogen bonds (H-bonds) play a key role in both the formation and stabilization of protein structures. H-bonds involving atoms from residues that are close to each other in the main-chain sequence stabilize secondary structure elements. H-bonds between atoms from distant residues stabilize a protein’s tertiary structure. However, H-bonds greatly vary in stability. They form and break while a protein deforms. For instance, the transition of a protein from a nonfunctional to a functional state may require some H-bonds to break and others to form. The intrinsic strength of an individual H-bond has been studied from an energetic viewpoint, but energy alone may not be a very good predictor. Other local interactions may reinforce (or weaken) an H-bond. This paper describes inductive learning methods to train a protein-independent probabilistic model of H-bond stability from molecular dynamics (MD) simulation trajectories. The training data describes H-bond occurrences at successive times along these trajectories by the values of attributes called predictors. A trained model is constructed in the form of a regression tree in which each non-leaf node is a Boolean test (split) on a predictor. Each occurrence of an H-bond maps to a path in this tree from the root to a leaf node. Its predicted stability is associated with the leaf node. Experimental results demonstrate that such models can predict H-bond stability quite well. In particular, their performance is roughly 20 % better than that of models based on H-bond energy alone. In addition, they can accurately identify a large fraction of the least stable H-bonds in a give

Control of intestinal stem cell function and proliferation by mitochondrial pyruvate metabolism.

Most differentiated cells convert glucose to pyruvate in the cytosol through glycolysis, followed by pyruvate oxidation in the mitochondria. These processes are linked by the mitochondrial pyruvate carrier (MPC), which is required for efficient mitochondrial pyruvate uptake. In contrast, proliferative cells, including many cancer and stem cells, perform glycolysis robustly but limit fractional mitochondrial pyruvate oxidation. We sought to understand the role this transition from glycolysis to pyruvate oxidation plays in stem cell maintenance and differentiation. Loss of the MPC in Lgr5-EGFP-positive stem cells, or treatment of intestinal organoids with an MPC inhibitor, increases proliferation and expands the stem cell compartment. Similarly, genetic deletion of the MPC in Drosophila intestinal stem cells also increases proliferation, whereas MPC overexpression suppresses stem cell proliferation. These data demonstrate that limiting mitochondrial pyruvate metabolism is necessary and sufficient to maintain the proliferation of intestinal stem cells

An in situ and ex situ study of χ phase formation in a hypoeutectic Fe-based hardfacing alloy

In this work, the effect of topologically close-packed χ phase on the microstructure and properties of the rapidly solidified hypoeutectic iron-based Fe-25Cr-7Mo-0.8C alloy was investigated. The novelty of the work is based on the introduction of χ phase into the Fe-based hypoeutectic alloy with the aim of reducing the mean free path of the matrix and increasing abrasive resistance. The phase composition was studied using in situ neutron and ex situ X-ray synchrotron diffraction. The microstructural evolution was analyzed via scanning and transmission electron microscopy and modelled using CALPHAD thermodynamic calculations. The mechanical behavior of the evolving microstructure was quantified using high-speed nanoindentation mapping. At low temperatures (650 °C), the χ phase nucleates mainly in dendrite areas and exhibits a needle-like morphology caused by high misfit with the ferritic matrix. At higher temperatures (800 °C), the χ phase nucleates on carbide/matrix interfaces and in dendrites and is characterized by a blocky morphology. Simultaneously, the evolution of M23C6 carbide morphology towards a continuous and solid network of precipitates was observed. Such changes in the alloy's microstructure induced an increase in hardness of about 16% and resulted in the reduction of the average scratch depth in comparison to as-cast state.ISSN:0264-1275ISSN:1873-419