Computational Analysis of the Ligand Binding Site of the Extracellular ATP Receptor, DORN1
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60 APPLIED LIFE SCIENCES↗
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Results for “Sequence Alignment”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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SU-E-T-563: A Fast and Quantative Picket-Fence Test of a Submillimeter Patient Positioning System for Stereotactic Radiosurgery
Purpose: Picket-fence test is a qualitative TG142-recommended quality assurance (QA) test for multileaf collimators. In study, we adopted the same concept and developed a fast but quantatitive QA test for an automatic patient positioning system that requires submilleter accuracy for a radiosurgical treatment. Methods: A piece of radiochromic film was first placed inside a spherical solid water phantom and then irradiated with a sequenence of linearly placed shots of same collimator size (e.g. 4-mm) via the Leskell Gamma Knife Perfexion system (PFX). The shots were positioned with either equal or non-equal gaps of approximately 4 mm to 8 mm depending on the location of the region of interest. A pattern recognization program was developed and then applied to measure the gap spacing between two adjacent shots. The measured distance was then compared with the initial preset values for the test. Results: By introducing variable systematic and random shifts of 0.1 mm to 0.5 mm to the shot sequence, the maximum gap variation from the described test was found to be 0.35 mm or less. On average the positioning uncertainty for the PFX delivery system was found to be 0.1±0.2 mm. No significant difference in the positioning uncertainty was noted for the centrally aligned shot sequence locations versus the peripherally aligned shot sequence locations. Conclusion: A new quantitative picket-fence type test was developed and demonstrated for routine QA of the submillimeter PFX patient positioning sytem. This test also enables independent verification of any patient-specific shot positioning for a critical treatment such as a tumor in brainstem. Dr Ma is currently on the board of international society of stereotactic Radiosurgery.
60 APPLIED LIFE SCIENCES↗
Microbial Dark Matter: Unusual intervening sequences in 16S rRNA genes of candidate phyla from the deep subsurface
The Microbial Dark Matter project has sequenced genomes from over 200 single cells from candidate phyla, greatly expanding our knowledge of the ecology, inferred metabolism, and evolution of these widely distributed, yet poorly understood lineages. The second phase of this project aims to sequence an additional 800 single cells from known as well as potentially novel candidate phyla derived from a variety of environments. In order to identify whole genome amplified single cells, screening based on phylogenetic placement of 16S rRNA gene sequences is being conducted. Briefly, derived 16S rRNA gene sequences are aligned to a custom version of the Greengenes reference database and added to a reference tree in ARB using parsimony. In multiple samples from deep subsurface habitats but not from other habitats, a large number of sequences proved difficult to align and therefore to place in the tree. Based on comparisons to reference sequences and structural alignments using SSU-ALIGN, many of these ?difficult? sequences appear to originate from candidate phyla, and contain intervening sequences (IVSs) within the 16S rRNA genes. These IVSs are short (39 - 79 nt) and do not appear to be self-splicing or to contain open reading frames. IVSs were found in the loop regions of stem-loop structures in several different taxonomic groups. Phylogenetic placement of sequences is strongly affected by IVSs; two out of three groups investigated were classified as different phyla after their removal. Based on data from samples screened in this project, IVSs appear to be more common in microbes occurring in deep subsurface habitats, although the reasons for this remain elusive.
09 BIOMASS FUELS↗
Generate Optimized Genetic Rhythm for Enzyme Expression in Non-native systems
Most amino acids are represented by more than one codon, resulting in redundancy in the genetic code. Silent codon substitutions that do not alter the amino acid sequence still have an effect on protein expression. We have developed an algorithm, GoGREEN, to enhance the expression of foreign proteins in a host organism. GoGREEN selects codons according to frequency patterns seen in the gene of interest using the codon usage table from the host organism. GoGREEN is also designed to accommodate gaps in the sequence.This software takes for input (1) the aligned protein sequences for genes the user wishes to express, (2) the codon usage table for the host organism, (3) and the DNA sequence for the target protein found in the host organism. The program will select codons based on codon usage patterns for the target DNA sequence. The program will also select codons for “gaps” found in the aligned protein sequences using the codon usage table from the host organism.
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Protein remote homology detection and structural alignment using deep learning
Exploiting sequence–structure–function relationships in biotechnology requires improved methods for aligning proteins that have low sequence similarity to previously annotated proteins. We develop two deep learning methods to address this gap, TM-Vec and DeepBLAST. TM-Vec allows searching for structure–structure similarities in large sequence databases. It is trained to accurately predict TM-scores as a metric of structural similarity directly from sequence pairs without the need for intermediate computation or solution of structures. Once structurally similar proteins have been identified, DeepBLAST can structurally align proteins using only sequence information by identifying structurally homologous regions between proteins. It outperforms traditional sequence alignment methods and performs similarly to structure-based alignment methods. We show the merits of TM-Vec and DeepBLAST on a variety of datasets, including better identification of remotely homologous proteins compared with state-of-the-art sequence alignment and structure prediction methods.
59 BASIC BIOLOGICAL SCIENCES↗
A General Framework to Learn Tertiary Structure for Protein Sequence Characterization
During the past five years, deep-learning algorithms have enabled ground-breaking progress towards the prediction of tertiary structure from a protein sequence. Very recently, we developed SAdLSA, a new computational algorithm for protein sequence comparison via deep-learning of protein structural alignments. SAdLSA shows significant improvement over established sequence alignment methods. In this contribution, we show that SAdLSA provides a general machine-learning framework for structurally characterizing protein sequences. By aligning a protein sequence against itself, SAdLSA generates a fold distogram for the input sequence, including challenging cases whose structural folds were not present in the training set. About 70% of the predicted distograms are statistically significant. Although at present the accuracy of the intra-sequence distogram predicted by SAdLSA self-alignment is not as good as deep-learning algorithms specifically trained for distogram prediction, it is remarkable that the prediction of single protein structures is encoded by an algorithm that learns ensembles of pairwise structural comparisons, without being explicitly trained to recognize individual structural folds. As such, SAdLSA can not only predict protein folds for individual sequences, but also detects subtle, yet significant, structural relationships between multiple protein sequences using the same deep-learning neural network. The former reduces to a special case in this general framework for protein sequence annotation.
59 BASIC BIOLOGICAL SCIENCES↗
ModBase, a database of annotated comparative protein structure models, and associated resources
ModBase is a database of annotated comparative protein structure models. The models are calculated by ModPipe, an automated modeling pipeline that relies primarily on Modeller for fold assignment, sequence–structure alignment, model building and model assessment. ModBase currently contains 10 355 444 reliable models for domains in 2 421 920 unique protein sequences. ModBase allows users to update comparative models on demand, and request modeling of additional sequences through an interface to the ModWeb modeling server. ModBase models are available through the ModBase interface as well as the Protein Model Portal. Recently developed associated resources include the SALIGN server for multiple sequence and structure alignment, the ModEval server for predicting the accuracy of protein structure models, the PCSS server for predicting which peptides bind to a given protein and the FoXS server for calculating and fitting Small Angle X-ray Scattering profiles.
59 BASIC BIOLOGICAL SCIENCES↗
Amplicon Sequencing Reveals Microbiological Signatures in Spent Nuclear Fuel Storage Basins
Water quality is an important determinant for the structural integrity of alloy cladded fuels and assemblies during long-term wet storage. Detailed characterization of a water filled storage basin for spent nuclear reactor fuel was performed following the formation and proliferation of an amorphous white flocculent. White precipitant was sampled throughout the storage basin for chemical and spectroscopic characterization, and eDNA was extracted for pyrosequencing of bacterial rRNA gene diversity. Accordingly, spectroscopic analyses indicated the precipitant to be primarily amorphous to crystalline aluminum (oxy) hydroxides with minor associated elemental components including Fe, Si, Ti, and U. High levels of dissolved carbon were co-localized with the precipitant relative to bulk water. Bacterial densities were highly variable between sampling locations and with depth; cell numbers (log scale) ranged from 5.6 to 4.89 cells / mL. Bacterial diversity that was physically associated with the aluminum (oxy) hydroxide complexes exceeded an estimated 4,000 OTUs / amplicon library (3% cutoff) and the greatest percent majority of sequences were aligned to the families Burkholderiales (23%), Nitrospiraceae (23%), Hyphomicrobiaceae (17%), and Comamonadaceae (6%). We surmise that episodic changes in the physical and chemical properties of the basin contribute to the polymerization of aluminum (oxy) hydroxides, which in turn can chemisorb nutrients, carbon ligands and bacterial cells from the surrounding bulk aqueous phase. As such, these precipitants should establish favorable microhabitats for bacterial colonization and growth. Comparative analyses of 16S rRNA gene amplicon libraries across diverse environmental landscapes were performed and microbiological signatures unique to the spent nuclear fuel storage basin environment were revealed. These insights could spur the development of tractable bioindicators that are specific of and diagnostic for water quality at discrete locations and finer scales of resolution, marking an important contribution for improved water quality and management of spent nuclear fuel storage facilities.
aluminum↗
A high-density SNP genetic map consisting of a complete set of homologous groups in autohexaploid sweetpotato (Ipomoea batatas)
Sweetpotato (Ipomoea batatas) is an autohexaploid species with 90 chromosomes (2n = 6x = 90) and a basic chromosome number of 15, and is therefore regarded as one of the most challenging species for high-density genetic map construction. Here, we used single nucleotide polymorphisms (SNPs) identified by double-digest restriction site-associated DNA sequencing based on next-generation sequencing technology to construct a map for sweetpotato. We then aligned the sequence reads onto the reference genome sequence of I. trifida, a likely diploid ancestor of sweetpotato, to detect SNPs. In addition, to simplify analysis of the complex genetic mode of autohexaploidy, we used an S1 mapping population derived from self-pollination of a single parent. As a result, 28,087 double-simplex SNPs showing a Mendelian segregation ratio in the S1 progeny could be mapped onto 96 linkage groups (LGs), covering a total distance of 33,020.4 cM. Based on the positions of the SNPs on the I. trifida genome, the LGs were classified into 15 groups, each with roughly six LGs and six small extra groups. The molecular genetic techniques used in this study are applicable to high-density mapping of other polyploid plant species, including important crops.
59 BASIC BIOLOGICAL SCIENCES↗
The LANL hemorrhagic fever virus database, a new platform for analyzing biothreat viruses
Hemorrhagic fever viruses (HFVs) are a diverse set of over 80 viral species, found in 10 different genera comprising five different families: arena-, bunya-, flavi-, filo- and togaviridae. All these viruses are highly variable and evolve rapidly, making them elusive targets for the immune system and for vaccine and drug design. About 55 000 HFV sequences exist in the public domain today. A central website that provides annotated sequences and analysis tools will be helpful to HFV researchers worldwide. The HFV sequence database collects and stores sequence data and provides a user-friendly search interface and a large number of sequence analysis tools, following the model of the highly regarded and widely used Los Alamos HIV database [Kuiken, C., B. Korber, and R.W. Shafer, HIV sequence databases. AIDS Rev, 2003. 5: p. 52–61]. The database uses an algorithm that aligns each sequence to a species-wide reference sequence. The NCBI RefSeq database [Sayers et al. (2011) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 39, D38–D51.] is used for this; if a reference sequence is not available, a Blast search finds the best candidate. Using this method, sequences in each genus can be retrieved pre-aligned. The HFV website can be accessed via http://hfv.lanl.gov.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Sequence Impedance Measurement of Utility-Scale Wind Turbines and Inverters – Reference Frame, Frequency Coupling, and MIMO/SISO Forms
Sequence impedance responses with or without considering frequency coupling in both MIMO and SISO forms are increasingly used for the stability analysis of three-phase power electronic systems; however, many aspects of sequence impedance measurement are not fully explored. It is not clear if the sequence impedance has a reference frame similar to the dq impedance. If so, the role of the grid voltage angle estimation in aligning the sequence impedance reference frame has not been discussed. Additionally, existing methods for measuring the sequence impedance with frequency coupling are complicated, are not feasible for large wind turbines and inverters, and provide the sequence impedance responses in only either MIMO or SISO form. This paper presents a sequence impedance measurement method that considers the frequency coupling, performs reference frame alignment, demonstrates the impact of the grid voltage angle estimation, and obtains the sequence impedance response in both MIMO and SISO forms. This paper demonstrates the proposed method and practical problems associated with the sequence impedance measurement of utility-scale wind turbines and inverters on a 1.9-MW Type III wind turbine and a 2.2-MVA inverter using an impedance measurement system built around a 7-MW/13.8-kV grid simulator and a 5-MW dynamometer.
17 WIND ENERGY↗
Evolution of high cellulolytic activity in symbiotic Streptomyces through selection of expanded gene content and coordinated gene expression
In this study, the evolution of cellulose degradation was a defining event in the history of life. Without efficient decomposition and recycling, dead plant biomass would quickly accumulate and become inaccessible to terrestrial food webs and the global carbon cycle. On land, the primary drivers of plant biomass deconstruction are fungi and bacteria in the soil or associated with herbivorous eukaryotes. While the ecological importance of plant-decomposing microbes is well established, little is known about the distribution or evolution of cellulolytic activity in any bacterial genus. Here we show that in Streptomyces , a genus of Actinobacteria abundant in soil and symbiotic niches, the ability to rapidly degrade cellulose is largely restricted to two clades of host-associated strains and is not a conserved characteristic of the Streptomyces genus or host-associated strains. Our comparative genomics identify that while plant biomass degrading genes (CAZy) are widespread in Streptomyces , key enzyme families are enriched in highly cellulolytic strains. Transcriptomic analyses demonstrate that cellulolytic strains express a suite of multi-domain CAZy enzymes that are coregulated by the CebR transcriptional regulator. Using targeted gene deletions, we verify the importance of a highly expressed cellulase (GH6 family cellobiohydrolase) and the CebR transcriptional repressor to the cellulolytic phenotype. Evolutionary analyses identify complex genomic modifications that drive plant biomass deconstruction in Streptomyces , including acquisition and selective retention of CAZy genes and transcriptional regulators. Our results suggest that host-associated niches have selected some symbiotic Streptomyces for increased cellulose degrading activity and that symbiotic bacteria are a rich biochemical and enzymatic resource for biotechnology.
59 BASIC BIOLOGICAL SCIENCES↗
LoVoCCS. II. Weak Lensing Mass Distributions, Red-sequence Galaxy Distributions, and Their Alignment with the Brightest Cluster Galaxy in 58 Nearby X-Ray-luminous Galaxy Clusters
The Local Volume Complete Cluster Survey is an ongoing program to observe nearly a hundred low-redshift X-ray-luminous galaxy clusters (redshifts 0.03 < z < 0.12 and X-ray luminosities in the 0.1–2.4 keV band L X500c > 10 44 erg s −1 ) with the Dark Energy Camera, capturing data in the u, g, r, i, z bands with a 5σ point source depth of approximately 25th–26th AB magnitudes. Here, we map the aperture masses in 58 galaxy cluster fields using weak gravitational lensing. These clusters span a variety of dynamical states, from nearly relaxed to merging systems, and approximately half of them have not been subject to detailed weak lensing analysis before. In each cluster field, we analyze the alignment between the 2D mass distribution described by the aperture mass map, the 2D red-sequence (RS) galaxy distribution, and the brightest cluster galaxy (BCG). We find that the orientations of the BCG and the RS distribution are strongly aligned throughout the interiors of the clusters: the median misalignment angle is 19° within 2 Mpc. We also observe the alignment between the orientations of the RS distribution and the overall cluster mass distribution (by a median difference of 32° within 1 Mpc), although this is constrained by galaxy shape noise and the limitations of our cluster sample size. These types of alignment suggest long-term dynamical evolution within the clusters over cosmic timescales.
79 ASTRONOMY AND ASTROPHYSICS↗
Identification of a p-Coumarate Degradation Regulon in Rhodopseudomonas palustris by Xpression, an Integrated Tool for Prokaryotic RNA-Seq Data Processing
High-throughput sequencing of cDNA prepared from RNA, an approach known as RNA-seq, is coming into increasing use as a method for transcriptome analysis. Despite its many advantages, widespread adoption of the technique has been hampered by a lack of easy-to-use, integrated, open-source tools for analyzing the nucleotide sequence data that are generated. Here we describe Xpression, an integrated tool for processing prokaryotic RNA-seq data. The tool is easy to use and is fully automated. It performs all essential processing tasks, including nucleotide sequence extraction, alignment, quantification, normalization, and visualization. Importantly, Xpression processes multiplexed and strand-specific nucleotide sequence data. It extracts and trims specific sequences from files and separately quantifies sense and antisense reads in the final results. Outputs from the tool can also be conveniently used in downstream analysis. In this paper, we show the utility of Xpression to process strand-specific RNA-seq data to identify genes regulated by CouR, a transcription factor that controls p -coumarate degradation by the bacterium Rhodopseudomonas palustris.
59 BASIC BIOLOGICAL SCIENCES↗
FOAM (Functional Ontology Assignments for Metagenomes): A Hidden Markov Model (HMM) database with environmental focus
A new functional gene database, FOAM (Functional Ontology Assignments for Metagenomes), was developed to screen environmental metagenomic sequence datasets. FOAM provides a new functional ontology dedicated to classify gene functions relevant to environmental microorganisms based on Hidden Markov Models (HMMs). Sets of aligned protein sequences (i.e. ‘profiles’) were tailored to a large group of target KEGG Orthologs (KOs) from which HMMs were trained. The alignments were checked and curated to make them specific to the targeted KO. Within this process, sequence profiles were enriched with the most abundant sequences available to maximize the yield of accurate classifier models. An associated functional ontology was built to describe the functional groups and hierarchy. FOAM allows the user to select the target search space before HMM-based comparison steps and to easily organize the results into different functional categories and subcategories. FOAM is publicly available at http://portal.nersc.gov/project/m1317/FOAM/.
54 ENVIRONMENTAL SCIENCES↗
Sequencing and De Novo Transcriptome Assembly of Brachypodium sylvaticum (Poaceae)
Premise of the study: We report the de novo assembly and characterization of the transcriptomes of Brachypodium sylvaticum (slender false-brome) accessions from native populations of Spain and Greece, and an invasive population west of Corvallis, Oregon, USA. Methods and Results: More than 350 million sequence reads from the mRNA libraries prepared from three B. sylvaticum genotypes were assembled into 120,091 (Corvallis), 104,950 (Spain), and 177,682 (Greece) transcript contigs. In comparison with the B. distachyon Bd21 reference genome and GenBank protein sequences, we estimate >90% exome coverage for B. sylvaticum . The transcripts were assigned Gene Ontology and InterPro annotations. Brachypodium sylvaticum sequence reads aligned against the Bd21 genome revealed 394,654 single-nucleotide polymorphisms (SNPs) and >20,000 simple sequence repeat (SSR) DNA sites. Conclusions: To our knowledge, this is the first report of transcriptome sequencing of invasive plant species with a closely related sequenced reference genome. The sequences and identified SNP variant and SSR sites will provide tools for developing novel genetic markers for use in genotyping and characterization of invasive behavior of B. sylvaticum.
59 BASIC BIOLOGICAL SCIENCES↗
Extracting flat-field images from scene-based image sequences using phase correlation
Flat-field image processing is an essential step in producing high-quality and radiometrically calibrated images. Flat-fielding corrects for variations in the gain of focal plane array electronics and unequal illumination from the system optics. Typically, a flat-field image is captured by imaging a radiometrically uniform surface. The flat-field image is normalized and removed from the images. There are circumstances, such as with remote sensing, where a flat-field image cannot be acquired in this manner. For these cases, we developed a phase-correlation method that allows the extraction of an effective flat-field image from a sequence of scene-based displaced images. The method uses sub-pixel phase correlation image registration to align the sequence to estimate the static scene. The scene is removed from sequence producing a sequence of misaligned flat-field images. An average flat-field image is derived from the realigned flat-field sequence.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Cytochrome P450 20A1 in zebrafish: Cloning, regulation and potential involvement in hyperactivity disorders
Cytochrome P450 (CYP) enzymes for which there is no functional information are considered “orphan” CYPs. Previous studies showed that CYP20A1, an orphan, is expressed in human hippocampus and substantia nigra, and in zebrafish (Danio rerio) CYP20A1 maternal transcript occurs in eggs, suggesting involvement in brain and in early development. Moreover, hyperactivity is reported in humans with chromosome 2 microdeletions including CYP20A1. We examined CYP20A1 in zebrafish, including impacts of chemical exposure on expression. Zebrafish CYP20A1 cDNA was cloned, sequenced, and aligned with cloned human CYP20A1 and predicted vertebrate orthologs. CYP20A1s share a highly conserved N-terminal region and unusual sequences in the I-helix and the heme-binding CYP signature motifs. CYP20A1 mRNA expression was observed in adult zebrafish organs including the liver, heart, gonads, spleen and brain, as well as the eye and optic nerve. Putative binding sites in proximal promoter regions of CYP20A1s, and response of zebrafish CYP20A1 to selected nuclear and xenobiotic receptor agonists, point to up-regulation by agents involved in steroid hormone response, cholesterol and lipid metabolism. There also was a dose-dependent reduction of CYP20A1 expression in embryos exposed to environmentally relevant levels of methylmercury. Morpholino knockdown of CYP20A1 in developing zebrafish resulted in behavioral effects, including hyperactivity and a slowing of the optomotor response in larvae. The results suggest that altered expression of CYP20A1 might be part of a mechanism linking methylmercury exposure to neurobehavioral deficits. The expanded information on CYP20A1 brings us closer to “deorphanization”, that is, identifying CYP20A1 functions and its roles in health and disease. - Highlights: • The “orphan” CYP20A1 was cloned from zebrafish and its sequence analyzed. • Knockdown of CYP20A1 reduced an optomotor response and elicited bursts of activity. • Effects of knockdown resemble some features of a microdeletion of CYP20A1 in human. • Expression of CYP20A1 was downregulated by the neurotoxicant methylmercury. • CYP20A1 may be involved in neurobehavioral processes and effects of some chemicals.
60 APPLIED LIFE SCIENCES↗