This publication documents the scientific advances associated with new instrument systems and accessories built to improve aboveand in-water observations of the apparent optical properties (AOPs) for a diversity of water masses, including optically complex waters. The principal objective is to be prepared for the launch of next-generation ocean color satellites with the most capable commercial off-the-shelf (COTS) instrumentation in the shortest time possible. The technologies described herein are entirely new hybrid sampling capabilities, so as to satisfy the requirements established for next-generation missions. Both aboveand in-water instruments are documented with software options for autonomous control of data collection activities as applicable. The instruments were developed for the Hybridspectral Alternative for Remote Profiling of Optical Observations for NASA Satellites (HARPOONS) vicarious calibration project. The state-of-the-art accuracy required for vicarious calibration also led to the development of laboratory instruments to ensure the field observations were within uncertainty requirements. Separate detailed presentations of the individual instruments provide the hardware designs, accompanying software for data acquisition and processing, and examples of the results achieved.

A novel Gram-stain-negative, rod-shaped, motile, non-spore-forming, facultatively anaerobic marine bacterium was isolated from the gastrointestinal tract of the sandworm Alitta succinea collected from Grice Cove, South Carolina, USA. The strain was arginine dihydrolase-positive, and oxidase- and catalase-positive. Growth occurred between 10 and 37 degrees C, with optimal growth occurring between 30 and 32 degrees C. Comparative 16S rRNA gene sequence analysis showed its nearest neighbours are members of the genus Kistimonas of the family Hahellaceae, which is found in the order Oceanospirillales, class Gammaproteobacteria. The closest related species was Kistimonas asteriae KMD 001(T) with 16S rRNA gene sequence similarity of 99.0 %. However, DNA-DNA hybridization between these strains revealed less than 70 % DNA-DNA relatedness, supporting the novel species status of the strain. The major fatty acids were C-16:0, C-18:0, C-18:1 omega 7c and a summed feature that contained C-16:1 omega 6c/C-16:1 omega 7c. The major respiratory quinone was ubiquinone-9 and the predominant polar lipids were phosphatidylserine, phosphoethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The genomic DNA G+C content was 52.5 mol%. Based on the data presented, strain BGP-2(T) is considered to represent a novel member of the genus Kistimonas, for which the name Kistimonas alittae sp. nov. is proposed. The type strain is BGP-2(T) (=CCUG 65711(T)=JCM 30010(T)).

This publication documents the scientific advances associated with new instrument systems and accessories built to improve aboveand in-water observations of the apparent optical properties (AOPs) of aquatic ecosystems. The perspective is to obtain high quality data in offshore, nearshore, and inland waters with equal efficacy. The principal objective is to be prepared for the launch of the next-generation ocean color satellites with the most capable commercial off-the-shelf (COTS) instrumentation in the shortest time possible. The technologies described herein are designed to either improve legacy radiometric systems or to provide entirely new hybrid sampling capabilities, so as to satisfy the requirements established for diverse remote sensing requirements. Both aboveand in-water instrument suites are documented with software options for autonomous control of data collection activities. The latter includes an airborne instrument system plus unmanned surface vessel (USV) and buoy concepts.

The RNA component of the RNase P complex is found throughout most branches of the tree of life and is principally responsible for removing the 5' leader sequence from pre-tRNA transcripts during tRNA maturation. RNase P RNA has a number of universal core features, however variations in sequence and structure found in homologs across the tree of life require multiple Rfam covariance search models to detect accurately. We describe a new Rfam search model to enable efficient detection of the diminutive archaeal Type T RNase P RNAs, which are missed by existing Rfam models. Using the new model, we establish effective score detection thresholds, and detect four new RNase P RNA genes in recently completed genomes from the crenarchaeal family Thermoproteaceae.

The rationale behind the current workshop, which was hosted by Biospherical Instruments Inc. (BSI), was to update the community and get community input with respect to the following: topics not addressed during the first workshop, specifically the processing of above-water apparent optical property (AOP data) within the Processing of Radiometric Observations of Seawater using Information Technologies (PROSIT) architecture; PROSIT data processing issues that have developed or tasks that have been completed, since the first workshop; and NASA instrumentation developments, both above- and in-water, that are relevant to both workshops and next generation mission planning. The workshop emphasized presentations on new AOP instrumentation, desired and required features for processing above-water measurements of the AOPs of seawater, working group discussions, and a community update for the in-water data processing already present in PROSIT. The six working groups were organized as follows: a) data ingest and data products; b) required and desired features for optically shallow and optically deep waters; c) contamination rejection (clouds), corrections, and data filtering; d) sun photometry and polarimetry; e) instrumentation networks; and f) hyperspectral versus fixed-wavelength sensors. The instrumentation networks working group was intended to provide more detailed information about desired and required features of autonomous sampling systems. Plenary discussions produced a number of recommendations for evolving and documenting PROSIT.

The diversity of Archaea in a municipal wastewater sludge sample was investigated by amplification of ribosomal RNA genes from sludge DNA using archaeal-specific primers. Surprisingly, a large fraction (32%) of these sequences were from Halobacteriales, not previously seen in surveys of wastewater sludge. Other abundant sequences were from members of uncultivated ‘environmental’ archaeal groups that are commonly detected in sludge and sediment environments. Only a few distant relatives of Methanosarcina (which are commonly thought of as the predominant methanogenic species in sludge environments) were detected.

RNase P RNA is an ancient, nearly universal feature of life. As part of the ribonucleoprotein RNase P complex, the RNA component catalyzes essential removal of 5′ leaders in pre-tRNAs. In 2004, Li and Altman computationally identified the RNase P RNA gene in all but three sequenced microbes: Nanoarchaeum equitans , Pyrobaculum aerophilum , and Aquifex aeolicus (all hyperthermophiles) [Li Y, Altman S (2004) RNA 10:1533–1540]. A recent study concluded that N. equitans does not have or require RNase P activity because it lacks 5′ tRNA leaders. The “missing” RNase P RNAs in the other two species is perplexing given evidence or predictions that tRNAs are trimmed in both, prompting speculation that they may have developed novel alternatives to 5′ pre-tRNA processing. Using comparative genomics and improved computational methods, we have now identified a radically minimized form of the RNase P RNA in five Pyrobaculum species and the related crenarchaea Caldivirga maquilingensis and Vulcanisaeta distributa , all retaining a conventional catalytic domain, but lacking a recognizable specificity domain. We confirmed 5′ tRNA processing activity by high-throughput RNA sequencing and in vitro biochemical assays. The Pyrobaculum and Caldivirga RNase P RNAs are the smallest naturally occurring form yet discovered to function as trans -acting precursor tRNA-processing ribozymes. Loss of the specificity domain in these RNAs suggests altered substrate specificity and could be a useful model for finding other potential roles of RNase P. This study illustrates an effective combination of next-generation RNA sequencing, computational genomics, and biochemistry to identify a divergent, formerly undetectable variant of an essential noncoding RNA gene.

This report documents new technology used to measure the apparent optical properties (AOPs) of optically complex waters. The principal objective is to be prepared for the launch of next-generation ocean color satellites with the most capable commercial off-the-shelf (COTS) instrumentation. An enhanced COTS radiometer was the starting point for designing and testing the new sensors. The follow-on steps were to apply the lessons learned towards a new in-water profiler based on a kite-shaped backplane for mounting the light sensors. The next level of sophistication involved evaluating new radiometers emerging from a development activity based on so-called microradiometers. The exploitation of microradiometers resulted in an in-water profiling system, which includes a sensor networking capability to control ancillary sensors like a shadowband or global positioning system (GPS) device. A principal advantage of microradiometers is their flexibility in producing, interconnecting, and maintaining instruments. The full problem set for collecting sea-truth data--whether in coastal waters or the open ocean-- involves other aspects of data collection that were improved for instruments measuring both AOPs and inherent optical properties (IOPs), if the uncertainty budget is to be minimized. New capabilities associated with deploying solar references were developed as well as a compact solution for recovering in-water instrument systems from small boats.

Small nucleolar ribonucleoproteins (snoRNPs) are widely studied and characterized as guide RNAs for sequence-specific 2'-O-ribose methylation and psuedouridylation of ribosomal RNAs. In addition, snoRNAs have also been shown to interact with some tRNAs and direct alternative splicing in mRNA biogenesis. Recent advances in bioinformatics have resulted in new algorithms able to rapidly identify noncoding RNAs generally and snoRNAs specifically in genomic and metagenomic sequences, resulting in a rapid increase in the number and diversity of identified snoRNA sequences. The snoRNP database is a web-based collection of snoRNA and snoRNA-associated protein sequences from a wide range of species. The database currently contains 8994 snoRNA sequences from Bacteria, Archaea, and Eukaryotes and 589 snoRNA-associated protein sequences. The snoRNP database can be found at: http://evolveathome.com/snoRNA/snoRNA.php.

Ribonuclease P (RNase P) is a ribonucleoprotein comprised of a catalytic RNA subunit and one or several protein subunits. RNase P is best known for its role in 5'-processing of tRNA precursors. RNase P enzymes from almost all forms of life, including protein-synthesizing organelles, contain an RNase P with a conserved, homologous RNA. Five distinct structure classes of RNase P RNAs have been identified in bacteria and archaea; eukaryotic RNase P RNAs are not yet sufficiently well surveyed for structure classes to be defined. Here we will examine the structure variations in RNase P RNAs in bacteria, archaea, eukaryotes, plastids and mitochondria with special emphasis on the functional roles these unique secondary structures perform.

This article presents an introduction to the history of Web-based and Web-assisted teaching, learning, and assessment. The development of the field of distance education and its relevance to nursing will be documented. Published utilization studies of one set of online nurse educational tools, the Assessment Technologies Institute content mastery and comprehensive predictor, will be reviewed and discussed. Methods by which schools of nursing can access and integrate these online nursing education resources will be explored.

It has been suggested that Alba, a well-established chromatin protein in Archaea, is also a subunit of the archaeal RNase P holoenzyme, based on the observation that the homolog of this protein in humans has been shown to be associated with RNase P activity. Using the same biochemical methods we used previously to show that four other proteins homologous to eukaryotic RNase P proteins are bona fide RNase P subunits in Archaea, we could not detect any association of the Alba homolog in Methanothermobacter thermoautotrophicus (Mth1483p) with the RNase P holoenzyme. In addition, the presence of Mth1483p did not enhance the activity of RNase P holoenzyme reconstituted from recombinant subunits. In conclusion, we find no evidence that Alba is an RNase P subunit.

Ocean County College received a New Jersey Health Initiatives grant from the Robert Wood Johnson Foundation to develop a web-assisted (hybrid) education model. By creating New Jersey's first web-assisted Associate Degree Nursing Program, the model seeks to address shortages of RNs in the hospital setting. This program allows those currently employed in the health care field to complete an RN program by attending class only 1 day per week (primarily on-site in host health care institutions) supplemented by online instruction. The initial results demonstrate a higher level of performance in the One Day per Week Nursing Program when compared with a group of students in the traditional nursing program who had nearly identical results on the entrance test (Test of Essential Academic Skills). Despite the influence of factors outside the program, the results do indicate early success and the likelihood that the program will meet its primary objectives.

Previous eucaryotic RNase P RNA secondary structural models have been based on limited diversity, representing only two of the approximately 30 phylogenetic kingdoms of the domain Eucarya. To elucidate a more generally applicable structure, we used biochemical, bioinformatic, and molecular approaches to obtain RNase P RNA sequences from diverse organisms including representatives of six additional kingdoms of eucaryotes. Novel sequences were from acanthamoeba (Acathamoeba castellanii, Balamuthia mandrillaris, Filamoeba nolandi), animals (Caenorhabditis elegans, Drosophila melanogaster), alveolates (Theileria annulata, Babesia bovis), conosids (Dictyostelium discoideum, Physarum polycephalum), trichomonads (Trichomonas vaginalis), microsporidia (Encephalitozoon cuniculi), and diplomonads (Giardia intestinalis). An improved alignment of eucaryal RNase P RNA sequences was assembled and used for statistical and comparative structural analysis. The analysis identifies a conserved core structure of eucaryal RNase P RNA that has been maintained throughout evolution and indicates that covariation in size occurs between some structural elements of the RNA. Eucaryal RNase P RNA contains regions of highly variable length and structure reminiscent of expansion segments found in rRNA. The eucaryal RNA has been remodeled through evolution as a simplified version of the structure found in bacterial and archaeal RNase P RNAs.

This chapter contains sections titled: Introduction Description Troubleshooting

Above- and in-water radiometric data were collected from two coastal platforms: a small boat and an oceanographic tower. The above-water data were processed with and without a correction for bidirectional effects (Q02 and S95, respectively). An intercomparison of water-leaving radiances over a wide range of environmental conditions showed (a) total uncertainties across the blue-green domain were to within 4%, (b) a convergence of the Q02 method with the in-water method (average Q02 intercomparisons were to within 4%), and (c) chlorophyll a concentrations derived from Q02 reflectances and the OC4V4 (Ocean Color 4 Version 4) algorithm agreed with independent high-performance liquid-chromatography determinations to within approximately 32%.

This document provides five brief reports that address several algorithm investigations sponsored by the Calibration and Validation Team (CVT) within the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) Project. This volume, therefore, has been designated as the first in a series of algorithm volumes. Chapter 1 describes the initial suite of masks, used to prevent further processing of contaminated radiometric data, and flags, which are employed to mark data whose quality (due to a variety of factors) may be suspect. In addition to providing the mask and flag algorithms, this chapter also describes the initial strategy for their implementation. Chapter 2 evaluates various strategies for the detection of clouds and ice in high latitude (polar and sub-polar regions) using Coastal Zone Color Scanner (CZCS) data. Chapter 3 presents an algorithm designed for detecting and masking coccolithophore blooms in the open ocean. Chapter 4 outlines a proposed scheme for correcting the out-of-band response when SeaWiFS is in orbit. Chapter 5 gives a detailed description of the algorithm designed to apply sensor calibration data during the processing of level-lb data.