Accessing NCBI data using the NCBI Sequence Viewer and Genome Data Viewer (GDV).

The National Center for Biotechnology Information (NCBI) is an archive providing free access to a wide range and large volume of biological sequence data and literature. Staff scientists at NCBI analyze user-submitted data in the archive, producing gene and SNP annotation and generating sequence alignment tools. NCBI's flagship genome browser, Genome Data Viewer (GDV), displays our in-house RefSeq annotation; is integrated with other NCBI resources such as Gene, dbGaP, and BLAST; and provides a platform for customized analysis and visualization. Here, we describe how members of the biomedical research community can use GDV and the related NCBI Sequence Viewer (SV) to access, analyze, and disseminate NCBI and custom biomedical sequence data. In addition, we report how users can add SV to their own web pages to create a custom graphical sequence display without the need for infrastructure investments or back-end deployments.

PLAZA 5.0: extending the scope and power of comparative and functional genomics in plants.

PLAZA is a platform for comparative, evolutionary, and functional plant genomics. It makes a broad set of genomes, data types and analysis tools available to researchers through a user-friendly website, an API, and bulk downloads. In this latest release of the PLAZA platform, we are integrating a record number of 134 high-quality plant genomes, split up over two instances: PLAZA Dicots 5.0 and PLAZA Monocots 5.0. This number of genomes corresponds with a massive expansion in the number of available species when compared to PLAZA 4.0, which offered access to 71 species, a 89% overall increase. The PLAZA 5.0 release contains information for 5 882 730 genes, and offers pre-computed gene families and phylogenetic trees for 5 274 684 protein-coding genes. This latest release also comes with a set of new and updated features: a new BED import functionality for the workbench, improved interactive visualizations for functional enrichments and genome-wide mapping of gene sets, and a fully redesigned and extended API. Taken together, this new version offers extended support for plant biologists working on different families within the green plant lineage and provides an efficient and versatile toolbox for plant genomics. All PLAZA releases are accessible from the portal website: https://bioinformatics.psb.ugent.be/plaza/.

Elucidation of intermediates and mechanisms in heterogeneous catalysis using infrared spectroscopy.

Infrared spectroscopy has a long history as a tool for the identification of chemical compounds. More recently, various implementations of infrared spectroscopy have been successfully applied to studies of heterogeneous catalytic reactions with the objective of identifying intermediates and determining catalytic reaction mechanisms. We discuss selective applications of these techniques with a focus on several heterogeneous catalytic reactions, including hydrogenation, deNOx, water-gas shift, and reverse-water-gas shift. The utility of using isotopic substitutions and other techniques in tandem with infrared spectroscopy is discussed. We comment on the modes of implementation and the advantages and disadvantages of the various infrared techniques. We also note future trends and the role of computational calculations in such studies. The infrared techniques considered are transmission Fourier transform infrared spectroscopy, infrared reflection-absorption spectroscopy, polarization-modulation infrared reflection-absorption spectroscopy, sum-frequency generation, diffuse reflectance infrared Fourier transform spectroscopy, attenuated total reflectance, infrared emission spectroscopy, photoacoustic infrared spectroscopy, and surface-enhanced infrared absorption spectroscopy.

Probing Water and CO2 Interactions at the Surface of Collapsed Titania Nanotubes Using IR Spectroscopy.

Collapsed titania nanotubes (cTiNT) were synthesized by the calcination of titania nanotubes (TiNT) at 650 °C, which leads to a collapse of their tubular morphology, a substantial reduction in surface area, and a partial transformation of anatase to the rutile phase. There are no significant changes in the position of the XPS responses for Ti and O on oxidation or reduction of the cTiNTs, but the responses are more symmetric than those observed for TiNTs, indicating fewer surface defects and no change in the oxidation state of titanium on oxidative and/or reductive pretreatment. The interaction of H2O and CO2 with the cTiNT surface was studied. The region corresponding to OH stretching absorptions extends below 3000 cm(-1), and thus is broader than is typically observed for absorptions of the OH stretches of water. The exchange of protons for deuterons on exposure to D2O leads to a depletion of this extended absorption and the appearance of new absorptions, which are compatible with deuterium exchange. We discuss the source of this extended low frequency OH stretching region and conclude that it is likely due to the hydrogen-bonded OH stretches. Interaction of the reduced cTiNTs with CO2 leads to a similar but smaller set of adsorbed carbonates and bicarbonates as reported for reduced TiNTs before collapse. Implications of these observations and the presence of proton sources leading to hydrogen bonding are discussed relative to potential chemical and photochemical activity of the TiNTs. These results point to the critical influence of defect structure on CO2 photoconversion.

Single Cell Portal: an interactive home for single-cell genomics data.

Single-cell omics research has the power to leave a deep impact on modern healthcare. Sharing data widely and freely advances this progress in both the academic and clinical spheres. We developed the Single Cell Portal (SCP) to maximize the impact of this work. SCP enables data sharing, supports dynamic results visualization, and facilitates scientific exploration across a large repository of single-cell datasets. SCP's data contributors maintain full control over how their data are shared and presented, without requiring web development expertise. Finally, SCP supports the entire lifecycle of a research project, from sparking an idea, to fine-tuning the data with collaborators, to sharing results in an accessible and interactive way. This paper highlights the most valuable ways in which SCP helps to advance single-cell research.

GeMo: a web-based platform for the visualization and curation of genome ancestry mosaics.

In silico chromosome painting is a technique by which contributions of distinct genetic groups are represented along chromosomes of hybrid individuals. This type of analysis is used to study the mechanisms by which these individuals were formed. Such techniques are well adapted to identify genetic groups contributing to these individuals as well as hybridization events. It can also be used to follow chromosomal recombinations that occurred naturally or were generated by selective breeding. Here, we present GeMo, a novel interactive web-based and user-oriented interface to visualize in a linear-based fashion results of in silico chromosome painting. To facilitate data input generation, a script to execute analytical commands is provided and an interactive data curation mode is supported to ensure consistency of the automated procedure. GeMo contains preloaded datasets from published studies on crop domestication but can be applied to other purposes, such as breeding programs Although only applied so far on plants, GeMo can handle data from animals as well. Database URL: https://gemo.southgreen.fr/.

Interfacial Unit-Dependent Catalytic Activity for CO Oxidation over Cerium Oxysulfate Cluster Assemblies.

Atomically precise cerium oxo clusters offer a platform to investigate structure-property relationships that are much more complex in the ill-defined bulk material cerium dioxide. We investigated the activity of the MCe70 torus family (M = Cd, Ce, Co, Cu, Fe, Ni, and Zn), a family of discrete oxysulfate-based Ce70 rings linked by monomeric cation units, for CO oxidation. CuCe70 emerged as the best performing MCe70 catalyst among those tested, prompting our exploration of the role of the interfacial unit on catalytic activity. Temperature-programmed reduction (TPR) studies of the catalysts indicated a lower temperature reduction in CuCe70 as compared to CeCe70. In situ diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) indicated that CuCe70 exhibited a faster formation of Ce3+ and contained CO bridging sites absent in CeCe70. Isothermal CO adsorption measurements demonstrated a greater uptake of CO by CuCe70 as compared to CeCe70. The calculated energies for the formation of a single oxygen defect in the structure significantly decreased with the presence of Cu at the linkage site as opposed to Ce. This study revealed that atomic-level changes in the interfacial unit can change the reducibility, CO binding/uptake, and oxygen vacancy defect formation energetics in the MCe70 family to thus tune their catalytic activity.

Displacement of hexanol by the hexanoic acid overoxidation product in alcohol oxidation on a model supported palladium nanoparticle catalyst.

This work characterizes the adsorption, structure, and binding mechanism of oxygenated organic species from cyclohexane solution at the liquid/solid interface of optically flat alumina-supported palladium nanoparticle surfaces prepared by atomic layer deposition (ALD). The surface-specific nonlinear optical vibrational spectroscopy, sum-frequency generation (SFG), was used as a probe for adsorption and interfacial molecular structure. 1-Hexanoic acid is an overoxidation product and possible catalyst poison for the aerobic heterogeneous oxidation of 1-hexanol at the liquid/solid interface of Pd/Al(2)O(3) catalysts. Single component and competitive adsorption experiments show that 1-hexanoic acid adsorbs to both ALD-prepared alumina surfaces and alumina surfaces with palladium nanoparticles, that were also prepared by ALD, more strongly than does 1-hexanol. Furthermore, 1-hexanoic acid adsorbs with conformational order on ALD-prepared alumina surfaces, but on surfaces with palladium particles the adsorbates exhibit relative disorder at low surface coverage and become more ordered, on average, at higher surface coverage. Although significant differences in binding constant were not observed between surfaces with and without palladium nanoparticles, the palladium particles play an apparent role in controlling adsorbate structures. The disordered adsorption of 1-hexanoic acid most likely occurs on the alumina support, and probably results from modification of binding sites on the alumina, adjacent to the particles. In addition to providing insight on the possibility of catalyst poisoning by the overoxidation product and characterizing changes in its structure that result in only small adsorption energy changes, this work represents a step toward using surface science techniques that bridge the complexity gap between fundamental studies and realistic catalyst models.

Identification of binding sites for acetaldehyde adsorption on titania nanorod surfaces using CIMS.

The interaction of acetaldehyde with TiO(2) nanorods has been studied under low pressures (acetaldehyde partial pressure range 10(-4)-10(-8) Torr) using chemical ionization mass spectrometry (CIMS). We quantitatively separate irreversible adsorption, reversible adsorption, and an uptake of acetaldehyde assigned to a thermally activated surface reaction. We find that, at room temperature and 1.2 Torr total pressure, 2.1 ± 0.4 molecules/nm(2) adsorb irreversibly, but this value exhibits a sharp decrease as the analyte partial pressure is lowered below 4 × 10(-4) Torr, regardless of exposure time. The number of reversible binding sites at saturation amounts to 0.09 ± 0.02 molecules/nm(2) with a free energy of adsorption of 43.8 ± 0.2 kJ/mol. We complement our measurements with FTIR spectroscopy and identify the thermal dark reaction as a combination of an aldol condensation and an oxidative adsorption that converts acetaldehyde to acetate or formate and CO, at a measured combined initial rate of 7 ± 1 × 10(-4) molecules/nm(2) s. By characterizing binding to different types of sites under dark conditions in the absence of oxygen and gas phase water, we set the stage to analyze site-specific photoefficiencies involved in the light-assisted mineralization of acetaldehyde to CO(2).

A novel CO2 utilization technology for the synergistic co-production of multi-walled carbon nanotubes and syngas.

Dry reforming of methane (DRM) is a well-known process in which CH4 and CO2 catalytically react to produce syngas. Solid carbon is a well-known byproduct of the DRM but is undesirable as it leads to catalyst deactivation. However, converting CO2 and CH4 into solid carbon serves as a promising carbon capture and sequestration technique that has been demonstrated in this study by two patented processes. In the first process, known as CARGEN technology (CARbon GENerator), a novel concept of two reactors in series is developed that separately convert the greenhouse gases (GHGs) into multi-walled carbon nanotubes (MWCNTs) and syngas. CARGEN enables at least a 50% reduction in energy requirement with at least 65% CO2 conversion compared to the DRM process. The second process presents an alternative pathway for the regeneration/reactivation of the spent DRM/CARGEN catalyst using CO2. Provided herein is the first report on an experimental demonstration of a 'switching' technology in which CO2 is utilized in both the operation and the regeneration cycles and thus, finally contributing to the overall goal of CO2 fixation. The following studies support all the results in this work: physisorption, chemisorption, XRD, XPS, SEM, TEM, TGA, ICP, and Raman analysis.

When the solute becomes the solvent: orientation, ordering, and structure of binary mixtures of 1-hexanol and cyclohexane over the (0001) α-Al2O3 surface.

Mixtures of 1-hexanol in cyclohexane over the (0001) α-Al(2)O(3) surface were probed in the CH stretching region using vibrational broadband sum frequency generation (SFG). Below 10 mol % 1-hexanol, the alcohol adsorbs to the surface through interactions that result in observed free adsorption energies of around 14-15 kJ/mol obtained from the Langmuir adsorption model. Polarization-resolved SFG spectra indicate ordering of the alkyl tails with increasing surface coverage. Highly correlated with the ordering of 1-hexanol is an orientational change of the cyclohexane solvent from flat to most likely tilted, suggesting that cyclohexane mediates the adsorption of 1-hexanol via intercalation. Above 10 mol %, the SFG signals for 1-hexanol and cyclohexane decrease with increasing concentration of 1-hexanol, consistent with the notion that cyclohexane is excluded from the interfacial region while 1-hexanol becomes increasingly disordered. At the interface, the alcohol solute becomes the solvent at a mole fraction of only 10%, i.e., five times below what is considered the solute-to-solvent mole fraction transition in the bulk. These results provide an important benchmark for theory, inform reaction design, and demonstrate that bulk thermodynamic properties of binary mixtures are not directly transferable to interfacial environments.

Photo-Initiated Reduction of CO2 by H2 on Silica Surface.

The reduction of CO2 is a promising route to produce valuable chemicals or fuels and create C-neutral resource cycles. Many different approaches to CO2 reduction have been investigated, but the ability of vacuum UV (VUV) irradiation to cleave C-O bonds has remained largely unexplored for use in processes that convert CO2 into useful products. Compared with other photo-driven CO2 conversion processes, VUV-initiated CO2 reduction can achieve much greater conversion under common photochemical reaction conditions when H2 and non-reducible oxides are present. Infrared spectroscopy provides evidence for a chain reaction initiated by VUV-induced CO2 splitting, which is enhanced in the presence of H2 and silica. When the reaction is carried out in the presence of silica or alumina surfaces, CO yields are increased and CH4 is formed as the only other detected product. CH4 production is not promoted by traditional photocatalysts such as TiO2 under these conditions. Assuming improvements in lamp and reactor efficiencies with scale up, or coupling with other available CO/CO2 hydrogenation techniques, these results reveal a potential, simple strategy by which CO2 could be valorized.

Viewing RNA-seq data on the entire human genome.

RNA-Seq Viewer is a web application that enables users to visualize genome-wide expression data from NCBI's Sequence Read Archive (SRA) and Gene Expression Omnibus (GEO) databases. The application prototype was created by a small team during a three-day hackathon facilitated by NCBI at Brandeis University. The backend data pipeline was developed and deployed on a shared AWS EC2 instance. Source code is available at https://github.com/NCBI-Hackathons/rnaseqview.

TPD of nitric acid from BaNa-Y: evidence that a nanoscale environment can alter a reaction mechanism.

The mechanism of temperature-programmed desorption (TPD) of nitric acid chemisorbed on BaNa-Y was studied over the temperature range from 200 to 400 degrees C, in the presence and absence of CO. Nitric acid dissociates to form H(+) and NO(3)(-) when chemisorbed on BaNa-Y. The results of these experiments are consistent with H(+) and NO(3)(-) either reacting directly to produce OH and NO(2) or recombining to produce HNO(3), which is desorbed and rapidly decomposes within the zeolite pores to OH and NO(2). The kinetics and stoichiometry suggest that the hydroxyl radicals produced react with CO and NO(2) to form CO(2) + H and NO + HO(2), respectively. The H atoms thus formed react with OH in preference to NO(2), a change in mechanism consistent with literature rate constants and the expectation that the zeolite pore walls act as a third body for the reaction of H with OH. Finally, OH may react with NO(2) to form HO(2), which can undergo further reactions to form O(2), H(2)O, and/or H(2). No reaction between CO and NO(3) or CO and surface-bound NO(3)(-) was observed.

Photochemistry of the indoor air pollutant acetone on Degussa P25 TiO2 studied by chemical ionization mass spectrometry.

We have used chemical ionization mass spectrometry (CIMS) to study the adsorption and photochemistry of several oxygenated organic species adsorbed to Degussa P25 TiO2, an inexpensive catalyst that can be used to mineralize volatile organic compounds. The molecules examined in this work include the common indoor air pollutant acetone and several of its homologs and possible oxidation and condensation products that may be formed during the adsorption and/or photocatalytic degradation of acetone on titanium dioxide catalysts. We report nonreactive uptake coefficients for acetone, formic acid, acetic acid, mesityl oxide, and diacetone alcohol, and results from photochemical studies that quantify, on a per-molecule basis, the room-temperature photocatalytic conversion of the species under investigation to CO2 and related oxidation products. The data presented here imply that catalytic surfaces that enhance formate and acetate production from acetone precursors will facilitate the photocatalytic remediation of acetone in indoor environments, even at room temperature.

Interaction of the indoor air pollutant acetone with Degussa P25 TiO2 studied by chemical ionization mass spectrometry.

Preventing a build-up of indoor pollutant concentrations has emerged as a major goal in environmental chemistry. Here, we have applied chemical ionization mass spectrometry to study the interaction of acetone, a common indoor air pollutant, with Degussa P25 TiO2, an inexpensive catalyst that is widely used for the degradation of volatile organic compounds into CO2 and water. To better understand the adsorption of acetone onto Degussa P25, the necessary first step for its degradation, the experiments were carried out at room temperature in the absence of UV light. This allowed for the deconvolution of the nonreactive and reactive thermal binding processes on Degussa P25 at acetone partial pressures (10(-7)-10(-4) Torr) commonly found in indoor environments. On average, 30% of the adsorbed acetone is bound irreversibly, resulting in a surface coverage of irreversibly bound acetone of approximately 1 x 10(12) molecules/cm2 at 3-4 x 10(-5) Torr. Equilibrium and dynamic experiments yield a sticking coefficient of approximately 1 x 10(-4) that is independent of the acetone partial pressures examined here. Equilibrium binding constants and free energies of adsorption are reported.

Narrow-band irradiation of a homologous series of chlorophenols on TiO2: charge-transfer complex formation and reactivity.

The goal of this research was to investigate the formation and reactivity of charge-transfer complexes (CTCs) among a homologous series of chlorophenols on TiO2. We previously showed that 2,4,5-trichlorophenol (245TCP) forms a CTC with Degussa P25, a commercial preparation of TiO2. Here, we probe how light energy influences reactivity and product formation. Slurries of P25 containing 245TCP were irradiated at 360, 400, 430, 480, and 550 nm. At each wavelength, the amount of transformation of 245TCP correlates to the diffuse-reflectance absorbance of a 245TCP/P25 system, supporting the CTC as the cause of reaction. In addition, polymeric products are formed only under wavelengths that excite the CTC, indicating a different reaction mechanism for the CTC than for bandgap excitation of TiO2. We also found a higher quantum efficiency for CTC reactivity than for bandgap activation of the catalyst, suggesting that the photocatalytic efficiency and selectivity can be improved for certain compounds by designing catalytic materials that form CTCs with them. Furthermore, to determine how chlorine substitution patterns affected adsorption and sub-bandgap reactivity, P25 slurries containing phenol, 4-chlorophenol, 2,4-dichlorophenol, or 2,4,6-trichlorophenol were probed following dark contact or irradiation at 360, 430, or 550 nm. With respect to the extent of adsorption, complexation, reaction, and polymerization on P25, the behavior of 245TCP far exceeded that of the other chlorophenols. Among these chlorophenols, only 2,4-dichlorophenol produced a polymeric product. 245TCP is unique among this family of chlorophenols, which we attribute to a chlorine arrangement that leads to a favorable orbital overlap with TiO2 and sterically permits coupling reactions. Our results demonstrate the critical role that charge-transfer complexation can play in determining the rates and products of photocatalytic reactions.