Life Sciences Commons^™

A Climatological Dataset Of Nutrient, Chlorophyll, And Particulate Matter Distributions On The Ross Sea Continental Shelf Derived From Cruise-Based Measurements Spanning 1967 To 2016, Walker O. Smith Jr., Daniel E. Kaufman

Data

This dataset includes data used in the publication Smith and Kaufman (2018), Progress in Oceanography, which examines the temporal and spatial distributions of nutrients and particulate matter in the Ross Sea continental Shelf using cruise-based observations, and compares the resulting annual productivity estimates with previously reported satellite-based estimates. Specifically, these data represent distributions of nutrients, chlorophyll, particulate organic carbon, particulate organic nitrogen, and biogenic silica that were compiled from 42 cruises (from 1967 - 2016) to the Ross Sea continental shelf to generate a comprehensive climatological dataset for November, December, January, and February. This climatology provides a novel look at …

Presence/Absence And Density Data For Epipelagic Tows Collected During R/V Blazing Seven Cruises Lf2016a And Lf2016b, Northern Gulf Of Mexico From 2016-06-09 To 2016-07-28, Jay R. Rooker, David Wells

DEEPEND Datasets

This dataset reports presence/absence and density data for epipelagic tows collected in the northern Gulf of Mexico during R/V Blazing Seven cruises LF2016A and LF2016B (2016-06-09 to 2016-07-28). Larval fishes were sampled from 48 stations and cruise data were collected at each site including latitude/longitude, date, time, environmental data (temperature, salinity, dissolved oxygen) and Sargassum dry weight. Larval catch data before and after the oil spill will be compared to improve our understanding of the causes of temporal variability as it relates to the Deep-Water Horizon oil spill (DWHOS). Habitat associations of selected taxa (billfishes, tunas, dolphinfishes, flyingfishes) will be …

Inventory Of Oceanic Fauna Data Including Species, Weight, And Measurements From R/V Point Sur (Cruise Dp05) In The Gulf Of Mexico From 2017-05-01 To 2017-05-11, April Cook, Tracey Sutton

DEEPEND Datasets

This dataset includes an inventory of Gulf of Mexico oceanic fauna data including species, weight, and measurements collected from R/V Point Sur (Cruise DP05) from 2017-05-01 to 2017-05-11. The main gear type used was a 10-m2 Multiple Opening Closing Net and Environmental Sensing System (MOCNESS). The MOCNESS was fitted with 6 nets which were opened according to the following depth scheme: net 0 from the surface to 1500m, net 1 from 1500-1200m, net 2 from 200-1000m, net 3 from 1000-600m, net 4 from 600-200m, and net 5 from 200m to the surface. Two trawls were conducted at each station sampled …

Microtubule Seams Are Not Mechanically Weak Defects, Taviare Hawkins

Physics Faculty Scholarship

Microtubule rigidity is important for many cellular functions to support extended structures and rearrange materials within the cell. The arrangement of the tubulin dimers within the microtubule can be altered to affect the protofilament number and the lattice type. Prior electron microscopy measurements have shown that when polymerized in the presence of a high concentration of NaCl, microtubules were more likely to be ten protofilaments with altered intertubulin lattice types. Specifically, such high-salt microtubules have a higher percentage of seam defects. Such seams have long been speculated to be a mechanically weak location in the microtubule lattice, yet no experimental …

Microbiome And Bacterioplankton Rrna Gene Sequence Data Collected From Gulf Of Mexico Seawater Samples, Cruises Dp03 And Dp04 From April - August 2016, Cole Easson, Lindsey Freed

DEEPEND Datasets

Seawater was collected and filtered for microbiome and bacterioplankton sequencing and analyses at various depths during planned DEEPEND cruise expeditions to the GOM in 2016. Filters were stored and then processed for total environmental genomic DNA according to standard methods (see earthmicrobiome.org). 16S rRNA amplicon libraries covering the V4 hypervariable regions were generated with universal PCR primers and then sequenced on an Illumina MiSeq DNA sequencing platform. Raw paired-end sequences were joined and quality filtered in the bioinformatics program, QIIME. Vertical baseline characterizations will track alpha and beta diversity at different depths ranging from 0 – 1500 m, assess seasonal …

Mitochondrial Dna Sequence Alignments And Raw Fastq Files For The Population Genetic Analysis Of The Deep Sea Isopod, Bathynomus Giganteus, Laura Timm, Barbara Moahamed

DEEPEND Datasets

This data set includes three alignments (12S, 16S, COI) of mitochondrial DNA sequences, as well as two raw fastq files generated through the next-generation sequencing (NGS) method ddRADseq. This data was collected from Bathynomus giganteus specimens collected from throughout the northeastern Gulf of Mexico.

Chlorophyll Concentration And Optical Absorption Spectra Of Particulate And Dissolved Material, Collected At Several Depths On Deepend Cruises Dp05 From January-December 2017, Chuanmin Hu

DEEPEND Datasets

The optical absorption spectra from seawater’s particulate and dissolved components can be used to compute the penetration of light to various depths, estimate the proportion of living to non-living particulate matter, assess photosynthetic light availability and the type of phytoplankton present, and to validate satellite or airborne ocean color measurements. Chlorophyll and phaeopigment concentrations are often used to estimate the amount of phytoplankton present, and to allow extrapolation of in situ fluorometric measurements. Water was collected using a CTD rosette near the surface and from several depths at each sampling station occupied by the DEEPEND cruise DP05 (see GRIIDC dataset …

16s And Coi Barcoding Sequences For Crustaceans Collected From The Northern Gulf Of Mexico For Cruises Dp02, Dp03, And Dp04 From August 2015 - August 2016, Heather Bracken-Grissom Dr.

DEEPEND Datasets

These are the 16S and COI barcoding sequences for crustaceans collected on cruises DP02, DP03, and DP04. These barcodes, obtained from the species we collected, will be used to aid in species identification efforts, evolutionary relationships analyses, adult-larval linkages, and new species discoveries. Samples were taken from animals collected during cruises that took place in the northern Gulf of Mexico from August 2015 - August 2016.

Habitat Classification Of The Gulf Of Mexico (Gom) Using The Hybrid Coordinate Ocean Model (Hycom) And Salinity/Temperature Profiles, Cruises Dp01-Dp04, May 2015 To August 2016, Matt Johnston, Rosanna Milligan, Cole Easson, Sergio Derada, Brad Penta, Tracey Sutton

DEEPEND Datasets

Deep pelagic habitat from the entire Gulf of Mexico (GOM) was classified using the deviation of sea surface height (SSH) from mean SSH for the entire GOM and water temperature at 300 m water depth, founded on ocean condition data from the 1/25° GOM HYbrid Coordinate Ocean Model (HYCOM). Pelagic habitats were segregated into anticyclonic, mixed boundaries, and common water units – all of which likely produce varying levels of forage for deep-sea fauna and may be trophic drivers. Model classifications were compared to classifications based on water column temperature and salinity at depth, as measured by CTD casts during …

Control Of Molecular Shuttles By Designing Electrical And Mechanical Properties Of Microtubules, Taviare Hawkins

Physics Faculty Scholarship

Kinesin-driven microtubules have been focused on to serve as molecular transporters, called “molecular shuttles,” to replace micro/nanoscale molecular manipulations necessitated in micro total analysis systems. Although transport, concentration, and detection of target molecules have been demonstrated, controllability of the transport directions is still a major challenge. Toward broad applications of molecular shuttles by defining multiple moving directions for selective molecular transport, we integrated a bottom-up molecular design of microtubules and a top-down design of a microfluidic device. The surface charge density and stiffness of microtubules were controlled, allowing us to create three different types of microtubules, each with different gliding …

Inventory Of Gulf Of Mexico Oceanic Fauna Data Including Species, Weight, And Measurements From R/V Point Sur (Cruises Dp03 And Dp04) May-August, 2016, April Cook, Tracey Sutton

DEEPEND Datasets

This data set includes the biological and environmental data for all of the species collected during the DP03 (May 2016) and DP04 cruises (August 2016). The main gear type used was a 10-m2 Multiple Opening Closing Net and Environmental Sensing System (MOCNESS). The MOCNESS was fitted with 6 nets which were opened according to the following depth scheme: net 0 from the surface to 1500m, net 1 from 1500-1200m, net 2 from 200-1000m, net 3 from 1000-600m, net 4 from 600-200m, and net 5 from 200m to the surface. Two trawls were conducted at each station sampled to capture diel …

Chlorophyll Concentration And Optical Absorption Spectra Of Particulate And Dissolved Material, Collected At Several Depths On Deepend Cruises Dp03 And Dp04 From January-December 2016, Chuanmin Hu, Jenifer Cannizzaro, David English

DEEPEND Datasets

The optical absorption spectra from seawater’s particulate and dissolved components can be used to compute the penetration of light to various depths, estimate the proportion of living to non-living particulate matter, assess photosynthetic light availability and the type of phytoplankton present, and the validate of satellite or airborne ocean color measurements. Chlorophyll and phaeopigment concentrations are often used to estimate the amount of phytoplankton present, and to allow extrapolation of in situ fluorometric measurements. Water was collected using a CTD rosette near the surface and from several depths at each sampling station occupied by the DEEPEND cruises DP03 & DP04 …

Inventory Of Gulf Oceanic Fauna Data Including Species, Weight, And Measurements. Cruises Dp01 May 1-8, 2015 And Dp02 August 9-21, 2015 R/V On The Point Sur In The Northern Gulf Of Mexico, April Cook, Tracey Sutton

DEEPEND Datasets

This data set includes the biological and environmental data for all of the species collected during the DP01 (May 2015) and DP02 cruises (August 2015). The main gear type used was a 10-m2 Multiple Opening Closing Net and Environmental Sensing System (MOCNESS). The MOCNESS was fitted with 6 nets which were opened according to the following depth scheme: net 0 from the surface to 1500m, net 1 from 1500-1200m, net 2 from 1200-1000m, net 3 from 1000-600m, net 4 from 600-200m, and net 5 from 200m to the surface. Two trawls were conducted at each station sampled to capture diel …

Code For "Noise-Enhanced Coding In Phasic Neuron Spike Trains", Cheng Ly, Brent D. Doiron

Statistical Sciences and Operations Research Data

This zip file contains Matlab scripts and ode (XPP) files to calculate the statistics of the models in "Noise-Enhanced Coding in Phasic Neuron Spike Trains". This article is published in PLoS ONE.

Associated Dataset: Assimilating Bio-Optical Glider Data During A Phytoplankton Bloom In The Southern Ross Sea, Daniel E. Kaufman, Marjorie A.M. Friedrichs, John C.P. Hemmings, Walker O. Smith

Data

No abstract provided.

Silencing Science.Pptx, Kai Hung

Faculty Research & Creative Activity

This is a non-peer reviewed teaching resource.

A Study Of Defensive Mechanisms Employed By Two Species Of Nudibranchs Using Toxicity And Unpalatability Analyses, Sean Youn

Independent Study Project (ISP) Collection

Nudibranchs are marine invertebrates that have developed an intriguing defense mechanism, including warning coloration and the use of chemicals accumulated through their sponge diet. The goal of this study was to determine whether the strength of chemical defenses differs between dietary and accumulated secondary metabolites for two species: Glossodoris vespa and Ceratosoma brevicaudatum. First, NMR spectroscopy was used to not only identify specific compounds in the mantle (outer covering) and the viscera (gut) but also to analyze the possibility of nudibranch species transporting more toxic compounds for defensive purposes. Next, toxicity (brine shrimp) and palatability (Palaemon shrimp) assays were used …

Land Cover Data For The Mississippi-Alabama Barrier Islands, 2010-2011 Arcgis V10.3 Geodatabase, Gregory A. Carter, Carlton P. Anderson, Kelly L. Lucas, Nathan L. Hopper

Land Cover Data for the Mississippi-Alabama Barrier Islands, 2010-2011

Land cover on the Mississippi-Alabama barrier islands was surveyed in 2010-2011 as part of continuing research on island geomorphic and vegetation dynamics following the 2005 impact of Hurricane Katrina. Results of the survey include sub-meter GPS location, a listing of dominant vegetation species and field photographs recorded at 375 sampling locations distributed among Cat, West Ship, East Ship, Horn, Sand, Petit Bois and West Dauphin Islands. The survey was conducted in a period of intensive remote sensing data acquisition over the northern Gulf of Mexico by federal, state and commercial organizations in response to the 2010 Macondo Well (Deepwater Horizon) …

2016-01-A3dsrinp-Csc-Sta-Cmb-522-Bps-542, Raymond Pulver, Neal Buxton, Xiaodong Wang, John Lucci, Jean Yves Hervé, Lenore Martin

Bioinformatics Software Design Projects

Cholesterol is carried and transported through bloodstream by lipoproteins. There are two types of lipoproteins: low density lipoprotein, or LDL, and high density lipoprotein, or HDL. LDL cholesterol is considered “bad” cholesterol because it can form plaque and hard deposit leading to arteries clog and make them less flexible. Heart attack or stroke will happen if the hard deposit blocks a narrowed artery. HDL cholesterol helps to remove LDL from the artery back to the liver.

Traditionally, particle counts of LDL and HDL plays an important role to understanding and prediction of heart disease risk. But recently research suggested that …

Perturbations In Microtubule Mechanics From Tubulin Preparation, Taviare Hawkins

Physics Faculty Scholarship

Microtubules are essential structures for cellular organization. They support neuronal processes and cilia, they are the scaffolds for the mitotic spindle, and they are the tracks for intracellular transport that actively organizes material and information within the cell. The mechanical properties of microtubules have been studied for almost 30 years, yet the results from different groups are startlingly disparate, ranging over an order of magnitude. Here we present results demonstrating the effects of purification, associated-protein content, age, and fluorescent labeling on the measured persistence length using the freely fluctuating filament method. We find that small percentages (<1%) of residual microtubule-associated proteins left over in the preparation can cause the persistence length to double, and that these proteins also affect the persistence length over time. Interestingly, we find that the fraction of labeled tubulin dimers does not affect the measured persistence length. Further, we have enhanced the analysis method established by previous groups. We have added a bootstrapping with resampling analysis to estimate the error in the variance data used to determine the persistence length. Thus, we are able to perform a weighted fit to the data to more accurately determine the persistence length.

Examining Trends In Taste Preferences, Market Demand, And Annual Catch In An Indigenous Marine Turtle Fishery In Southwest Madagascar, Kristin Jones

Independent Study Project (ISP) Collection

The worldwide exploitation of marine turtles has been common throughout human history, turtle products including carapaces for decoration and use, skin for leather, and eggs and meat for consumption. The hunting of marine turtles has long established economic importance among Madagascar's coastal inhabitants and is an activity traditionally associated with integral cultural and spiritual values. Due to overexploitation and a combination of relatively newer threats such as pollution, habitat loss, and incidental fisheries take, however, all marine turtle species in the Indian Ocean are considered to be endangered or critically endangered. Although Madagascar's marine turtles have been legally protected from …

Ma, Connecticut River, Holyoke Dam, Brett Towler

Fish Passage Data Archive

No abstract provided.

Understanding The Physical Properties That Control Protein Crystallization By Analysis Of Largescale Experimental Data, W. Nicholson Price Ii, Yang Chen, Samuel K. Handelman, Helen Neely, Philip Manor, Richard Karlin, Rajesh Nair, Jinfeng Liu, Michael Baran, John Everett, Saichiu N. Tong, Farhad Forouhar, Swarup S. Swaminathan, Thomas Acton, Rong Xiao, Joseph R. Luft, Angela Lauricella, George T. Detitta, Burkhard Rost, Gaetano T. Montelione, John T. Hunt

Law Faculty Scholarship

Crystallization is the most serious bottleneck in high-throughput protein-structure determination by diffraction methods. We have used data mining of the large-scale experimental results of the Northeast Structural Genomics Consortium and experimental folding studies to characterize the biophysical properties that control protein crystallization. This analysis leads to the conclusion that crystallization propensity depends primarily on the prevalence of well-ordered surface epitopes capable of mediating interprotein interactions and is not strongly influenced by overall thermodynamic stability. We identify specific sequence features that correlate with crystallization propensity and that can be used to estimate the crystallization probability of a given construct. Analyses of …

The Malina Oceanographic Expedition: How Do Changes In Ice Cover, Permafrost And Uv Radiation Impact On Biodiversity And Biogeochemical Fluxes In The Arctic Ocean?, Phillippe Massicotte, Rainer Amon, David Antoine, Philippe Archambault, Sergio Balzano, Simon Bélanger, Ronald Benner, Dominique Boeuf, Annick Bricaud, Flavienne Bruyant, Gwenaëlle Chaillou, Malik Malik, Bruno Charrière, Jing Chen, Hervé Claustre, Pierre Coupel, Nicole Delsaut, David Doxaran, Et. Al.

Faculty Publications

The MALINA oceanographic campaign was conducted during summer 2009 to investigate the carbon stocks and the processes controlling the carbon fluxes in the Mackenzie River estuary and the Beaufort Sea. During the campaign, an extensive suite of physical, chemical and biological variables was measured across seven shelf–basin transects (south-north) to capture the meridional gradient between the estuary and the open ocean. Key variables such as temperature, absolute salinity, radiance, irradiance, nutrient concentrations, chlorophyll-a concentration, bacteria, phytoplankton and zooplankton abundance and taxonomy, and carbon stocks and fluxes were routinely measured onboard the Canadian research icebreaker CCGS Amundsen and from a barge …

A Working Plan For The Woodlands Of The New Haven Water Company; Prepared After Five Years Of Forest Practice, 1908 To 1912, Ralph C. Hawley

Yale School of the Environment Bulletin Series

Soon after the establishment of the Yale Forest School in 1900, the necessity developed for finding forest lands near the city of NewHaven upon which to conduct field work. It was found that many of the most accessible and best timbered tracts were owned by the New Haven Water Company....about 250 acres near the Maltby Lakes were placed under the management of the Yale Forest School. ...a written plan is desirable. The plan is divided into two parts: the first, descriptive of present conditions and passt accomplishments; the second, treating of the policy to be pursued.