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Draft genome sequence of Therminicola potens strain JR

Description: 'Thermincola potens' strain JR is one of the first Gram-positive dissimilatory metal-reducing bacteria (DMRB) for which there is a complete genome sequence. Consistent with the physiology of this organism, preliminary annotation revealed an abundance of multiheme c-type cytochromes that are putatively associated with the periplasm and cell surface in a Gram-positive bacterium. Here we report the complete genome sequence of strain JR.
Date: July 1, 2010
Creator: Byrne-Bailey, K.G.; Wrighton, K.C.; Melnyk, R.A.; Agbo, P.; Hazen, T.C. & Coates, J.D.
Partner: UNT Libraries Government Documents Department


Description: A small number of type I supernovae exhibit well defined peculiarities. In particular some type I supernovae do not have the characteristic 6150 {angstrom} feature and some do not have the 1.2 {micro}m absorption. It is noted that all SN which lack the infrared absorption also lack the 6150 {angstrom} feature which is attributed to Si II. It is proposed that these supernovae constitute a single sub-class and that Si could be responsible for the strong unidentified infrared absorption which is characteristic of classical SNI. Si I has a dense array of strong lines in the near infrared so this ion could be responsible for the dominant features of SNIa IR behaviour. If this hypothesis is vindicated by subsequent observations or by calculation of synthetic spectra then it is most likely that the difference between ordinary supernovae and these peculiar ones is the abundance of Si.
Date: November 1, 1985
Creator: Graham, J.R.
Partner: UNT Libraries Government Documents Department

Measuring solar abundances

Description: This is the rapporteur paper of Working Group 2 on Measuring Solar Abundances. The working group presented and discussed the different observations and methods for obtaining the elemental and isotopic composition of the Sun, and critically reviewed their results and the accuracies thereof. Furthermore, a few important yet unanswered questions were identified, and the potential of future missions to provide answers was assessed.
Date: January 1, 2001
Creator: Reisenfeld, D. B. (Daniel B.); Von Steiger, R. (Rudolf); Vial, J.-C. (Jean-Claude); Bochsler, P.; Chaussidon, M.; Cohen, C. M. S. et al.
Partner: UNT Libraries Government Documents Department

Short sequence motifs, overrepresented in mammalian conservednon-coding sequences

Description: Background: A substantial fraction of non-coding DNAsequences of multicellular eukaryotes is under selective constraint. Inparticular, ~;5 percent of the human genome consists of conservednon-coding sequences (CNSs). CNSs differ from other genomic sequences intheir nucleotide composition and must play important functional roles,which mostly remain obscure.Results: We investigated relative abundancesof short sequence motifs in all human CNSs present in the human/mousewhole-genome alignments vs. three background sets of sequences: (i)weakly conserved or unconserved non-coding sequences (non-CNSs); (ii)near-promoter sequences (located between nucleotides -500 and -1500,relative to a start of transcription); and (iii) random sequences withthe same nucleotide composition as that of CNSs. When compared tonon-CNSs and near-promoter sequences, CNSs possess an excess of AT-richmotifs, often containing runs of identical nucleotides. In contrast, whencompared to random sequences, CNSs contain an excess of GC-rich motifswhich, however, lack CpG dinucleotides. Thus, abundance of short sequencemotifs in human CNSs, taken as a whole, is mostly determined by theiroverall compositional properties and not by overrepresentation of anyspecific short motifs. These properties are: (i) high AT-content of CNSs,(ii) a tendency, probably due to context-dependent mutation, of A's andT's to clump, (iii) presence of short GC-rich regions, and (iv) avoidanceof CpG contexts, due to their hypermutability. Only a small number ofshort motifs, overrepresented in all human CNSs are similar to bindingsites of transcription factors from the FOX family.Conclusion: Human CNSsas a whole appear to be too broad a class of sequences to possess strongfootprints of any short sequence-specific functions. Such footprintsshould be studied at the level of functional subclasses of CNSs, such asthose which flank genes with a particular pattern of expression. Overallproperties of CNSs are affected by patterns in mutation, suggesting thatselection which causes their conservation is not always verystrong.
Date: February 21, 2007
Creator: Minovitsky, Simon; Stegmaier, Philip; Kel, Alexander; Kondrashov,Alexey S. & Dubchak, Inna
Partner: UNT Libraries Government Documents Department

Experimental factors affecting PCR-based estimates of microbial species richness and evenness

Description: Pyrosequencing of 16S rRNA gene amplicons for microbial community profiling can, for equivalent costs, yield greater than two orders of magnitude more sensitivity than traditional PCR-cloning and Sanger sequencing. With this increased sensitivity and the ability to analyze multiple samples in parallel, it has become possible to evaluate several technical aspects of PCRbased community structure profiling methods. We tested the effect of amplicon length and primer pair on estimates of species richness number of species and evenness relative abundance of species by assessing the potentially tractable microbial community residing in the termite hindgut. Two regions of the 16S rRNA gene were sequenced from one of two common priming sites, spanning the V1-V2 or V8 regions, using amplicons ranging n length from 352 to 1443 bp. Our results demonstrate that both amplicon length and primer pair markedly influence estimates of richness and evenness. However, estimates of species evenness are consistent among different primer pairs targeting the same region. These results highlight the importance of experimental methodology when comparing diversity estimates across communities.
Date: December 1, 2009
Creator: Engelbrektson, Anna; Kunin, Victor; Wrighton, Kelly C.; Zvenigorodsky, Natasha; Chen, Feng; Ochman, Howard et al.
Partner: UNT Libraries Government Documents Department

Delineating the major KREEP-bearing terranes on the moon with global measurements of absolute thorium abundances

Description: The Lunar Prospector (LP) Gamma-Ray Spectrometer (GRS) has been used to map the global composition of thorium on the lunar surface. Previous LP results of relative thorium abundances demonstrated that thorium is highly concentrated in and around the nearside western maria and less so in the South Pole Aitken (SPA) basin. Using new detector modeling results and a larger data set, the authors present here a global map of absolute thorium abundances on a 2{degree} by 2{degree} equal-area pixel scale. Because thorium is a tracer of KREEP-rich material, these data provide fundamental information regarding the locations and importance of terranes that are rich in KREEP bearing materials.
Date: March 1, 1999
Creator: Lawrence, D.J.; Feldman, W.C.; Barraclough, B.L.; Elphic, R.C.; Prettyman, T.H.; Binder, A.B. et al.
Partner: UNT Libraries Government Documents Department


Description: Determining columnar water vapor is a fundamental problem in remote sensing. This measurement is important both for understanding atmospheric variability and also from removing atmospheric effects from remotely sensed data. Therefore discovering a reliable and if possible automated method for determining water vapor column abundance is important. There are two standard methods for determining precipitable water vapor during the daytime from multi-spectral data. The first method is the Continuum Interpolated Band Ratio (CIBR) (see for example King et al. 1996). This method assumes a baseline and measures the depth of a water vapor feature as compared to this baseline. The second method is the Atmospheric Pre-corrected Differential Absorption technique (APDA) (see Schlaepfer et al. 1998); this method accounts for the path radiance contribution to the top of atmosphere radiance measurement which is increasingly important at lower and lower reflectance values. We have also developed two methods of modifying CIBR. We use a simple curve fitting procedure to account for and remove any systematic errors due to low reflectance while still preserving the random spread of the CIBR values as a function of surface reflectance. We also have developed a two-dimensional look-up table for CIBR; CIBR using this technique is a function of both water vapor (as with all CIBR techniques) and surface reflectance. Here we use data recently acquired with the Multi-spectral Thermal Imager spacecraft (MTI) to compare these four methods of determining columnar water vapor content.
Date: March 1, 2001
Creator: HIRSCH, K. & AL, ET
Partner: UNT Libraries Government Documents Department


Description: Atomic Mass Evaluations have had a major impact on the values of the atomic weights for the twenty mononuclidic elements plus two elements, Thorium and Protactinium, which have no stable nuclides but a characteristic terrestrial isotopic composition. This paper reviews the history of the atomic weight values of these elements in the years, since the reference mass standard changed from {sup 16}O to {sup 12}C. There is a problem for Thorium, which is considered to have an abundance value of 100%, but is not treated as such in the Standard Atomic Weights' Table. Recommendations for handling the Standard Atomic Weight values for 2001 are presented.
Date: June 29, 2001
Creator: HOLDEN, N.E.
Partner: UNT Libraries Government Documents Department

Determination of mineral abundances in samples from the Exploratory Studies Facility, Yucca Mountain, Nevada, using x-ray diffraction

Description: Tuff samples collected from the Exploratory Studies Facility (ESF) were X-rayed to estimate relative mineral abundances. X-ray analysis was performed on sub-samples of specimens collected from both the Single Heater Test (SHT) and Drift Scale Heater Test (MT) that were used for thermomechanical measurements, as well as samples collected from cores retrieved from boreholes in the Drift Scale Test Area. The abundance of minerals that could affect the behavior of the host rock at repository relevant temperatures is of particular interest. These minerals include cristobalite, which undergoes a phase transition and volume change at elevated temperature (-250 {degree}C), and smectite and clinoptilolite that can dehydrate at elevated temperature with accompanying volume reduction. In addition, the spatial distribution of Si02 polymorphs and secondary minerals may provide evidence for deducing past fluid pathways. The mineral abundances tabulated here include data reported previously in three milestone reports but reanalyzed, as well as previously unreported data.
Date: January 13, 1998
Creator: Roberts, S. & Viani, B.
Partner: UNT Libraries Government Documents Department

Proteomics: Technology and Applications

Description: This meeting took place at the Keystone, Colorado resort from March 25-30, 2003. It was attended by 206 participants, of which 35 were students; 39% of attendees submitted abstracts. The meeting had 30% returning attendees and 70% new attendees. The group of speakers was composed of internationally recruited junior and senior experts in their respective fields. The group included representatives from academia and the private sector, highlights the convergence of proteomics efforts in the two sectors. The completion of the genome sequences of a large number of prokaryotic and eukaryotic species has catalyzed new research approaches to study the structure, function and control of biological processes. They are characterized by the systematic and in many cases quantitative analysis of all the molecules of a particular type expressed by a cell or tissue. The systematic analysis of proteins has been terms ''proteomics''. In an initial phase, most of the proteomics efforts were focused on large-scale protein identification. More recently, the objectives and technologies of proteomics have been diversified and expanded. Current proteomics research attempts to systematically and, where applicable, quantitatively determine the many properties of proteins and their biological function, including: protein abundance, state of modification, specific activity, interaction with other biomolecules, half-life, subcelluar location, structure and more. Significant current challenges include the development of suitable technologies to determine these properties on a proteome-wide scale, the interpretation of the large amounts of data obtained, and the integration of different types of data into a coherent model describing a biological process. The scientific program of the meeting intended to provide an up-to-date overview of the breadth of proteomics research and of emerging and mature technologies. Special emphasis was placed on discussing how proteomics technologies intersect with biological and clinical research. This was accomplished by bringing together leading experts from the different areas ...
Date: March 25, 2003
Creator: Aebersold, Ruedi
Partner: UNT Libraries Government Documents Department

Feasibility of eddy current measurement of ferrite content in stainless steel welds

Description: A phase-sensitive eddy current system was used to measure the presence of ferrite in an austenitic stainless steel matrix. Measurements were made on pressed powder specimens and on a weld in Type 304L stainless steel. The data obtained showed that small amounts of ferrite, on the order of 1 to 3%, could easily be detected. Variation in ferrite with position within the weld was also detected with good reproducibility. Absolute values for the ferrite content were not obtained as accurate standards for calibration were not available. (auth)
Date: December 17, 1973
Creator: Lassahn, G. D. & Moment, R. L.
Partner: UNT Libraries Government Documents Department

Age estimates of stratospheric air

Description: It is shown that careful consideration of /sup 32/P//sup 7/Be ratios (both isotopes being generated in the atmosphere by cosmic radiation) not only yields information on the stratospheric or tropospheric origin of air masses. These ratios may also be used to determine the residence time in the stratosphere of tropospheric air that underwent upward transport through the tropopause and re-entered the troposphere at a later date. (auth)
Date: August 1, 1973
Creator: Reiter, E.R.
Partner: UNT Libraries Government Documents Department

Molecular uranates - laser synthesis of uranium oxide anions in the gas phase

Description: Laser ablation of solid UO{sub 3} or (NH{sub 4}){sub 2}U{sub 2}O{sub 7} yielded in the gas phase molecular uranium oxide anions with compositions ranging from [UO{sub n}]{sup -} (n = 2-4) to [U{sub 14}O{sub n}]{sup -} (n = 32-35), as detected by Fourier transform ion cyclotron resonance mass spectrometry. The cluster series [U{sub x}O{sub 3x}]{sup -} for x {le} 6 and various [U{sub x}O{sub 3x-y}]{sup -}, in which y increased with increasing x, could be identified. A few anions with H atoms were also present, and their abundance increased when hydrated UO{sub 3} was used in place of anhydrous UO{sub 3}. Collision-induced dissociation experiments with some of the lower m/z cluster anions supported extended structures in which neutral UO{sub 3} constitutes the building block. Cationic uranium oxide clusters [U{sub x}O{sub n}]{sup +} (x = 2-9; n = 3-24) could also be produced and are briefly discussed. Common trends in the O/U ratios for both negative and positive clusters could be unveiled.
Date: December 14, 2009
Creator: Marcalo, Joaquim; Santos, Marta; Pires de Matos, Antonio & Gibson, John K
Partner: UNT Libraries Government Documents Department

Supersymmetry with Small mu: Connections between Naturalness, DarkMatter, and (Possibly) Flavor

Description: Weak scale supersymmetric theories often suffer from several naturalness problems: the problems of reproducing the correct scale for electroweak symmetry breaking, the correct abundance for dark matter, and small rates for flavor violating processes. We argue that the first two problems point to particular regions of parameter space in models with weak scale supersymmetry: those with a small {mu} term. This has an interesting implication on direct dark matter detection experiments. We find that, if the signs of the three gaugino mass parameters are all equal, we can obtain a solid lower bound on the spin-independent neutralino-nucleon cross section, {sigma}{sub SI}. In the case that the gaugino masses satisfy the unified mass relations, we obtain {sigma}{sub SI} {approx}> 4 x 10{sup -46} cm{sup 2} (1 x 10{sup -46} cm{sup 2}) for fine-tuning in electroweak symmetry breaking no worse than 10% (5%). We also discuss a possibility that the three problems listed above are all connected to the hierarchy of fermion masses. This occurs if supersymmetry breaking and electroweak symmetry breaking (the Higgs fields) are coupled to matter fields with similar hierarchical structures. The discovery of {mu} {yields} e transition processes in near future experiments is predicted in such a framework.
Date: June 11, 2006
Creator: Kitano, Ryuichiro Kitano & Nomura, Yasunori
Partner: UNT Libraries Government Documents Department

Inhibition of TGFbeta1 Signaling Attenutates ATM Activity inResponse to Genotoxic Stress

Description: Ionizing radiation causes DNA damage that elicits a cellular program of damage control coordinated by the kinase activity of ataxia telangiectasia mutated protein (ATM). Transforming growth factor {beta}1 (TGF{beta}), which is activated by radiation, is a potent and pleiotropic mediator of physiological and pathological processes. Here we show that TGF{beta} inhibition impedes the canonical cellular DNA damage stress response. Irradiated Tgf{beta}1 null murine epithelial cells or human epithelial cells treated with a small molecule inhibitor of TGF{beta} type I receptor kinase exhibit decreased phosphorylation of Chk2, Rad17 and p53, reduced {gamma}H2AX radiation-induced foci, and increased radiosensitivity compared to TGF{beta} competent cells. We determined that loss of TGF{beta} signaling in epithelial cells truncated ATM autophosphorylation and significantly reduced its kinase activity, without affecting protein abundance. Addition of TGF{beta} restored functional ATM and downstream DNA damage responses. These data reveal a heretofore undetected critical link between the microenvironment and ATM that directs epithelial cell stress responses, cell fate and tissue integrity. Thus, TGF{beta}1, in addition to its role in homoeostatic growth control, plays a complex role in regulating responses to genotoxic stress, the failure of which would contribute to the development of cancer; conversely, inhibiting TGF{beta} may be used to advantage in cancer therapy.
Date: September 15, 2006
Creator: Kirshner, Julia; Jobling, Michael F.; Pajares, Maria Jose; Ravani, Shraddha A.; Glick, Adam B.; Lavin, Martin J. et al.
Partner: UNT Libraries Government Documents Department


Description: The International Organization for Standardization (ISO) has published a Guide to the expression of Uncertainty in Measurement (GUM). The IUPAC Commission on Isotopic Abundance and Atomic Weight (CIAAW) began attaching uncertainty limits to their recommended values about forty years ago. CIAAW's method for determining and assigning uncertainties has evolved over time. We trace this evolution to their present method and their effort to incorporate the basic ISO/GUM procedures into evaluations of these uncertainties. We discuss some dilemma the CIAAW faces in their present method and whether it is consistent with the application of the ISO/GUM rules. We discuss the attempt to incorporate variations in measured isotope ratios, due to natural fractionation, into the ISO/GUM system. We make some observations about the inconsistent treatment in the incorporation of natural variations into recommended data and uncertainties. A recommendation for expressing atomic weight values using a tabulated range of values for various chemical elements is discussed.
Date: July 23, 2007
Creator: Holden, N. E.
Partner: UNT Libraries Government Documents Department


Description: In response to a recommendation to the Commission on Isotopic Abundances and Atomic Weights (CIAAW) that abridged versions of the Table on Standard Atomic Weights be prepared and published, this report has been prepared. A brief history is presented of such Atomic Weight tables that have been abridged to four significant figures and to five significant figures are noted. Tables of Standard Atomic Weight values abridged to four places and five places from the official 2007 Table of Atomic Weights approved by CIAAW are included.
Date: August 1, 2007
Creator: HOLDEN,N.E.
Partner: UNT Libraries Government Documents Department

Validation of two ribosomal RNA removal methods for microbial metatranscriptomics

Description: The predominance of rRNAs in the transcriptome is a major technical challenge in sequence-based analysis of cDNAs from microbial isolates and communities. Several approaches have been applied to deplete rRNAs from (meta)transcriptomes, but no systematic investigation of potential biases introduced by any of these approaches has been reported. Here we validated the effectiveness and fidelity of the two most commonly used approaches, subtractive hybridization and exonuclease digestion, as well as combinations of these treatments, on two synthetic five-microorganism metatranscriptomes using massively parallel sequencing. We found that the effectiveness of rRNA removal was a function of community composition and RNA integrity for these treatments. Subtractive hybridization alone introduced the least bias in relative transcript abundance, whereas exonuclease and in particular combined treatments greatly compromised mRNA abundance fidelity. Illumina sequencing itself also can compromise quantitative data analysis by introducing a G+C bias between runs.
Date: October 1, 2010
Creator: He, Shaomei; Wurtzel, Omri; Singh, Kanwar; Froula, Jeff L; Yilmaz, Suzan; Tringe, Susannah G et al.
Partner: UNT Libraries Government Documents Department