An investigation into the characteristics and sources of light emission at deep-sea hydrothermal vents

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution June 2000A spectral camera (ALISS - Ambient Light Imaging and Spectral System) was used to image ambient light from high-temperature vents at 9°N East Pacific Rise and the Juan de Fuca Ridge during 1997 and 1998 Alvin dive cruises. ALISS is a low-light digital camera with custom-designed optics. A set of nine lenses, each covered by an individual bandpass filter (50 and 100 nm nominal bandwidths), allows vents to be imaged in nine wavelength bands simultaneously spanning the range of 400-1 000 nm. Thus, both spatial and spectral information are obtained. ALISS was used to image three types of vents: black smokers, flange pools, and beehives. The primary source of light is thermal radiation due to the high temperature of the hydrothermal fluid (-350°C). This light is dominant at wavelengths greater than 700 nm. At flange pools, where the fluid is relatively stable, only thermal radiation is present. Black smokers and beehives, however, are subject to mixing with ambient seawater (2°C) leading to mineral precipitation. Data from these types of vents show the existence of non-thermal, temporally varying light in the 400-700 nm region. This light is probably caused by mechanisms related to mixing and precipitation, such as chemiluminescence, crystalloluminescence and triboluminescence

Laser Raman spectroscopy as a technique for identification of seafloor hydrothermal and cold seep minerals

Author Posting. © Elsevier B.V., 2009. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Chemical Geology 259 (2009): 240-252, doi:10.1016/j.chemgeo.2008.11.008.In situ sensors capable of real-time measurements and analyses in the deep ocean are necessary to fulfill the potential created by the development of autonomous, deep-sea platforms such as autonomous and remotely operated vehicles, and cabled observatories. Laser Raman spectroscopy (a type of vibrational spectroscopy) is an optical technique that is capable of in situ molecular identification of minerals in the deep ocean. The goals of this work are to determine the characteristic spectral bands and relative Raman scattering strength of hydrothermally- and cold seep-relevant minerals, and to determine how the quality of the spectra are affected by changes in excitation wavelength and sampling optics. The information learned from this work will lead to the development of new, smaller sea-going Raman instruments that are optimized to analyze minerals in the deep ocean. Many minerals of interest at seafloor hydrothermal and cold seep sites are Raman active, such as elemental sulfur, carbonates, sulfates and sulfides. Elemental S8 sulfur is a strong Raman scatterer with dominant bands at ~219 and 472 Δcm-1. The Raman spectra of carbonates (such as the polymorphs calcite and aragonite) are dominated by vibrations within the carbonate ion with a primary band at ~1085 Δcm-1. The positions of minor Raman bands differentiate these polymorphs. Likewise, the Raman spectra of sulfates (such as anhydrite, gypsum and barite) are dominated by the vibration of the sulfate ion with a primary band around 1000 Δcm-1 (~1017 for anhydrite, ~1008 for gypsum, and ~988 for barite). Sulfides (pyrite, marcasite, chalcopyrite, isocubanite, sphalerite, and wurtzite) are weaker Raman scatters than carbonate and sulfate minerals. They have distinctive Raman bands in the ~300-500 Δcm-1 region. Raman spectra from these mineral species are very consistent in band position and normalized band intensity. High quality Raman spectra are obtained from all of these minerals using both green and red excitation lasers, and using a variety of sampling optics. The highest quality spectra (highest signal to noise) were obtained using green excitation (532 nm Nd:YAG laser) and a sampling optic with a short depth of focus (and thus high power density). Significant fluorescence was not observed for the minerals analyzed using green excitation. Spectra were also collected from pieces of active and inactive hydrothermal chimneys, recovered from the Kilo Moana vent field in 2005 and 11ºN on the East Pacific Rise in 1988, respectively. Profiles of sample J2-137-1-r1-a show the transition from the chalcopyrite-rich “inner” wall to the sphalerite-dominated “outer” wall, and indicate the presence of minor amounts of anhydrite. Spectra collected from sample A2003-7-1a5 identify Cu-S tarnishes present on the surface of the sample.This work was funded by the Cecil H. and Ida M. Green Technology Innovation Fund. Additional support was provided by the James S. Coles and Cecily C. Selby Endowed Fund in Support of Scientific Staff and the Penzance Endowed Fund in Support of Assistant Scientists

Gas hydrate measurements at Hydrate Ridge using Raman spectroscopy

Author Posting. © Elsevier B.V., 2007. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Geochimica et Cosmochimica Acta 71: 2947-2959, doi:10.1016/j.gca.2007.03.032.Oceanic gas hydrates have been measured near the seafloor for the first time using a seagoing Raman spectrometer at Hydrate Ridge, Oregon, where extensive layers of hydrates have been found to occur near the seafloor. All of the hydrates analyzed were liberated from the upper meter of the sediment column near active gas venting sites in water depths of 770-780 m. Hydrate properties, such as structure and composition, were measured with significantly less disturbance to the sample than would be realized with core recovery. The natural hydrates measured were sI, with methane as the predominant guest component, and minor/trace amounts of hydrogen sulfide present in three of the twelve samples measured. Methane large-to-small cage occupancy ratios of the hydrates varied from 1.01 to 1.30, in good agreement with measurements of laboratory synthesized and recovered natural hydrates. Although the samples visually appeared to be solid, varying quantities of free methane gas were detected, indicating the presence of occluded gas a hydrate bubble fabric and/or partial hydrate dissociation in the under-saturated seawater.This work was supported through National Undersea Research Program grant UAF03-0098. DORISS and PUP development was funded by a grant to MBARI from the David and Lucile Packard Foundation

Optical tools for ocean monitoring and research

© 2009 The Authors. This article is distributed under the terms of the Creative Commons Attribution 3.0 License. The definitive version was published in Ocean Science 5 (2009): 661-684, doi: 10.5194/os-5-661-2009Requirements for understanding the relationships between ocean color and suspended and dissolved materials within the water column, and a rapidly emerging photonics and materials technology base for performing optical based analytical techniques have generated a diverse offering of commercial sensors and research prototypes that perform optical measurements in water. Through inversion, these tools are now being used to determine a diverse set of related biogeochemical and physical parameters. Techniques engaged include measurement of the solar radiance distribution, absorption, scattering, stimulated fluorescence, flow cytometry, and various spectroscopy methods. Selective membranes and other techniques for material isolation further enhance specificity, leading to sensors for measurement of dissolved oxygen, methane, carbon dioxide, common nutrients and a variety of other parameters. Scientists are using these measurements to infer information related to an increasing set of parameters and wide range of applications over relevant scales in space and time

Development and deployment of a precision underwater positioning system for in situ laser Raman spectroscopy in the deep ocean

Author Posting. © The Authors, 2005. This is the author's version of the work. It is posted here by permission of Elsevier B. V. for personal use, not for redistribution. The definitive version was published in Deep Sea Research Part I: Oceanographic Research Papers 52 (2005): 2376-2389, doi:10.1016/j.dsr.2005.09.002.The field of ocean geochemistry has recently been expanded to include in situ laser Raman spectroscopic measurements in the deep ocean. While this technique has proved to be successful for transparent targets, such as fluids and gases, difficulty exists in using deep submergence vehicle manipulators to position and control the very small laser spot with respect to opaque samples of interest, such as many rocks, minerals, bacterial mats, and seafloor gas hydrates. We have developed, tested, and successfully deployed by remotely operated vehicle (ROV) a precision underwater positioner (PUP) which provides the stability and precision movement required to perform spectroscopic measurements using the Deep Ocean In Situ Spectrometer (DORISS) instrument on opaque targets in the deep ocean for geochemical research. The positioner is also adaptable to other sensors, such as electrodes, which require precise control and positioning on the seafloor. PUP is capable of translating the DORISS optical head with a precision of 0.1 mm in three dimensions over a range of at least 15 cm, at depths up to 4000 m, and under the normal range of oceanic conditions (T, P, current velocity). The positioner is controlled, and spectra are obtained, in real time via Ethernet by scientists aboard the surface vessel. This capability has allowed us to acquire high quality Raman spectra of targets such as rocks, shells, and gas hydrates on the seafloor, including the ability to scan the laser spot across a rock surface in sub-millimeter increments to identify the constituent mineral grains. These developments have greatly enhanced the ability to obtain in situ Raman spectra on the seafloor from an enormous range of specimens.Funding was provided by a grant to MBARI from the David and Lucile Packard Foundation

Lessons Learned From the United States Ocean Observatories Initiative

The Ocean Observatories Initiative (OOI) is a United States National Science Foundation-funded major research facility that provides continuous observations of the ocean and seafloor from coastal and open ocean locations in the Atlantic and Pacific. Multiple cycles of OOI infrastructure deployment, recovery, and refurbishment have occurred since operations began in 2014. This heterogeneous ocean observing infrastructure with multidisciplinary sampling in important but challenging locations has provided new scientific and engineering insights into the operation of a sustained ocean observing system. This paper summarizes the challenges, successes, and failures experienced to date and shares recommendations on best practices that will be of benefit to the global ocean observing community

Guidelines for the Development of Comprehensive Care Centers for Congenital Adrenal Hyperplasia: Guidance from the CARES Foundation Initiative

Patients with rare and complex diseases such as congenital adrenal hyperplasia (CAH) often receive fragmented and inadequate care unless efforts are coordinated among providers. Translating the concepts of the medical home and comprehensive health care for individuals with CAH offers many benefits for the affected individuals and their families. This manuscript represents the recommendations of a 1.5 day meeting held in September 2009 to discuss the ideal goals for comprehensive care centers for newborns, infants, children, adolescents, and adults with CAH. Participants included pediatric endocrinologists, internal medicine and reproductive endocrinologists, pediatric urologists, pediatric surgeons, psychologists, and pediatric endocrine nurse educators. One unique aspect of this meeting was the active participation of individuals personally affected by CAH as patients or parents of patients. Representatives of Health Research and Services Administration (HRSA), New York-Mid-Atlantic Consortium for Genetics and Newborn Screening Services (NYMAC), and National Newborn Screening and Genetics Resource Center (NNSGRC) also participated. Thus, this document should serve as a “roadmap” for the development phases of comprehensive care centers (CCC) for individuals and families affected by CAH

Guidelines for the Development of Comprehensive Care Centers for Congenital Adrenal Hyperplasia: Guidance from the CARES Foundation Initiative

Patients with rare and complex diseases such as congenital adrenal hyperplasia (CAH) often receive fragmented and inadequate care unless efforts are coordinated among providers. Translating the concepts of the medical home and comprehensive health care for individuals with CAH offers many benefits for the affected individuals and their families. This manuscript represents the recommendations of a 1.5 day meeting held in September 2009 to discuss the ideal goals for comprehensive care centers for newborns, infants, children, adolescents, and adults with CAH. Participants included pediatric endocrinologists, internal medicine and reproductive endocrinologists, pediatric urologists, pediatric surgeons, psychologists, and pediatric endocrine nurse educators. One unique aspect of this meeting was the active participation of individuals personally affected by CAH as patients or parents of patients. Representatives of Health Research and Services Administration (HRSA), New York-Mid-Atlantic Consortium for Genetics and Newborn Screening Services (NYMAC), and National Newborn Screening and Genetics Resource Center (NNSGRC) also participated. Thus, this document should serve as a “roadmap” for the development phases of comprehensive care centers (CCC) for individuals and families affected by CAH

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Guidelines for the Development of Comprehensive Care Centers for Congenital Adrenal Hyperplasia: Guidance from the CARES Foundation Initiative

Abstract Patients with rare and complex diseases such as congenital adrenal hyperplasia (CAH) often receive fragmented and inadequate care unless efforts are coordinated among providers. Translating the concepts of the medical home and comprehensive health care for individuals with CAH offers many benefits for the affected individuals and their families. This manuscript represents the recommendations of a 1.5 day meeting held in September 2009 to discuss the ideal goals for comprehensive care centers for newborns, infants, children, adolescents, and adults with CAH. Participants included pediatric endocrinologists, internal medicine and reproductive endocrinologists, pediatric urologists, pediatric surgeons, psychologists, and pediatric endocrine nurse educators. One unique aspect of this meeting was the active participation of individuals personally affected by CAH as patients or parents of patients. Representatives of Health Research and Services Administration (HRSA), New York-Mid-Atlantic Consortium for Genetics and Newborn Screening Services (NYMAC), and National Newborn Screening and Genetics Resource Center (NNSGRC) also participated. Thus, this document should serve as a "roadmap" for the development phases of comprehensive care centers (CCC) for individuals and families affected by CAH