Effect of temperature on the CO2 splitting rate in a DBD microreactor.

A novel plate-to-plate dielectric barrier discharge microreactor (micro DBD) has been demonstrated in CO2 splitting. In this design, the ground electrode has a cooling microchannel to maintain the electrode temperature in the 263-298 K range during plasma operation. A small gap size between the electrodes of 0.50 mm allowed efficient heat transfer from the surrounding plasma to the ground electrode surface to compensate for heat released in the reaction zone and maintain a constant temperature. The effect of temperature on CO2 conversion and energy efficiency was studied at a voltage of 6-9 kV, a frequency of 60 kHz and a constant CO2 flow rate of 20 ml min-1. The CO2 decomposition rate first increased and then decreased as the electrode temperature decreased from 298 to 263 K with a maximum rate observed at 273 K. Operation at lower temperatures enhanced the vibrational dissociation of the CO2 molecule as opposed to electronic excitation which is the main mechanism at room temperature in conventional DBD reactors, however it also reduced the rate of elementary reaction steps. The counterplay between these two effects leads to a maximum in the reaction rate. The power consumption monotonously increased as the temperature decreased. The effective capacitance of the reactor increased by 1.5 times at 263 K as compared to that at 298 K changing the electric field distribution inside the plasma zone.

Pygenomics: manipulating genomic intervals and data files in Python.

SUMMARY: We present pygenomics, a Python package for working with genomic intervals and bioinformatic data files. The package implements interval operations, provides both API and CLI, and supports reading and writing data in widely used bioinformatic formats, including BAM, BED, GFF3, and VCF. The source code of pygenomics is provided with in-source documentation and type annotations and adheres to the functional programming paradigm. These features facilitate seamless integration of pygenomics routines into scripts and pipelines. The package is implemented in pure Python using its standard library only and contains the property-based testing framework. Comparison of pygenomics with other Python bioinformatic packages with relation to features and performance is presented. The performance comparison covers operations with genomic intervals, read alignments, and genomic variants and demonstrates that pygenomics is suitable for computationally effective analysis. AVAILABILITY AND IMPLEMENTATION: The source code is available at https://gitlab.com/gtamazian/pygenomics.

A collection of read depth profiles at structural variant breakpoints.

SWaveform, a newly created open genome-wide resource for read depth signal in the vicinity of structural variant (SV) breakpoints, aims to boost development of computational tools and algorithms for discovery of genomic rearrangement events from sequencing data. SVs are a dominant force shaping genomes and substantially contributing to genetic diversity. Still, there are challenges in reliable and efficient genotyping of SVs from whole genome sequencing data, thus delaying translation into clinical applications and wasting valuable resources. SWaveform includes a database containing ~7 M of read depth profiles at SV breakpoints extracted from 911 sequencing samples generated by the Human Genome Diversity Project, generalised patterns of the signal at breakpoints, an interface for navigation and download, as well as a toolbox for local deployment with user's data. The dataset can be of immense value to bioinformatics and engineering communities as it empowers smooth application of intelligent signal processing and machine learning techniques for discovery of genomic rearrangement events and thus opens the floodgates for development of innovative algorithms and software.

Chromosome-Length Assembly of the Baikal Seal (Pusa sibirica) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal.

Pusa sibirica, the Baikal seal, is the only extant, exclusively freshwater, pinniped species. The pending issue is, how and when they reached their current habitat-the rift lake Baikal, more than three thousand kilometers away from the Arctic Ocean. To explore the demographic history and genetic diversity of this species, we generated a de novo chromosome-length assembly, and compared it with three closely related marine pinniped species. Multiple whole genome alignment of the four species compared with their karyotypes showed high conservation of chromosomal features, except for three large inversions on chromosome VI. We found the mean heterozygosity of the studied Baikal seal individuals was relatively low (0.61 SNPs/kbp), but comparable to other analyzed pinniped samples. Demographic reconstruction of seals revealed differing trajectories, yet remarkable variations in Ne occurred during approximately the same time periods. The Baikal seal showed a significantly more severe decline relative to other species. This could be due to the difference in environmental conditions encountered by the earlier populations of Baikal seals, as ice sheets changed during glacial-interglacial cycles. We connect this period to the time of migration to Lake Baikal, which occurred ~3-0.3 Mya, after which the population stabilized, indicating balanced habitat conditions.

A Genome-Wide Association Study Reveals a BDNF-Centered Molecular Network Associated with Alcohol Dependence and Related Clinical Measures.

At least 50% of factors predisposing to alcohol dependence (AD) are genetic and women affected with this disorder present with more psychiatric comorbidities, probably indicating different genetic factors involved. We aimed to run a genome-wide association study (GWAS) followed by a bioinformatic functional annotation of associated genomic regions in patients with AD and eight related clinical measures. A genome-wide significant association of rs220677 with AD (p-value = 1.33 × 10-8 calculated with the Yates-corrected χ2 test under the assumption of dominant inheritance) was discovered in female patients. Associations of AD and related clinical measures with seven other single nucleotide polymorphisms listed in previous GWASs of psychiatric and addiction traits were differently replicated in male and female patients. The bioinformatic analysis showed that regulatory elements in the eight associated linkage disequilibrium blocks define the expression of 80 protein-coding genes. Nearly 68% of these and of 120 previously published coding genes associated with alcohol phenotypes directly interact in a single network, where BDNF is the most significant hub gene. This study indicates that several genes behind the pathogenesis of AD are different in male and female patients, but implicated molecular mechanisms are functionally connected. The study also reveals a central role of BDNF in the pathogenesis of AD.

Genome-wide association study reveals genetic variants associated with HIV-1C infection in a Botswana study population.

Although there have been many studies of gene variant association with different stages of HIV/AIDS progression in United States and European cohorts, few gene-association studies have assessed genic determinants in sub-Saharan African populations, which have the highest density of HIV infections worldwide. We carried out genome-wide association studies on 766 study participants at risk for HIV-1 subtype C (HIV-1C) infection in Botswana. Three gene associations (AP3B1, PTPRA, and NEO1) were shown to have significant association with HIV-1C acquisition. Each gene association was replicated within Botswana or in the United States-African American or United States-European American AIDS cohorts or in both. Each associated gene has a prior reported influence on HIV/AIDS pathogenesis. Thirteen previously discovered AIDS restriction genes were further replicated in the Botswana cohorts, extending our confidence in these prior AIDS restriction gene reports. This work presents an early step toward the identification of genetic variants associated with and affecting HIV acquisition or AIDS progression in the understudied HIV-1C afflicted Botswana population.

Draft de novo Genome Assembly of the Elusive Jaguarundi, Puma yagouaroundi.

The Puma lineage within the family Felidae consists of 3 species that last shared a common ancestor around 4.9 million years ago. Whole-genome sequences of 2 species from the lineage were previously reported: the cheetah (Acinonyx jubatus) and the mountain lion (Puma concolor). The present report describes a whole-genome assembly of the remaining species, the jaguarundi (Puma yagouaroundi). We sequenced the genome of a male jaguarundi with 10X Genomics linked reads and assembled the whole-genome sequence. The assembled genome contains a series of scaffolds that reach the length of chromosome arms and is similar in scaffold contiguity to the genome assemblies of cheetah and puma, with a contig N50 = 100.2 kbp and a scaffold N50 = 49.27 Mbp. We assessed the assembled sequence of the jaguarundi genome using BUSCO, aligned reads of the sequenced individual and another published female jaguarundi to the assembled genome, annotated protein-coding genes, repeats, genomic variants and their effects with respect to the protein-coding genes, and analyzed differences of the 2 jaguarundis from the reference mitochondrial genome. The jaguarundi genome assembly and its annotation were compared in quality, variants, and features to the previously reported genome assemblies of puma and cheetah. Computational analyzes used in the study were implemented in transparent and reproducible way to allow their further reuse and modification.

Monitoring Chemistry In Situ with a Smart Stirrer: A Magnetic Stirrer Bar with an Integrated Process Monitoring System.

Inspired by the miniaturization and efficiency of the sensors for telemetry, we have developed a device that provides the functionalities of laboratory magnetic stirring and integrated multisensor monitoring of various chemical reaction parameters. The device, called "Smart Stirrer", when immersed in a solution, can in situ monitor physical properties of the chemical reaction such as the temperature, conductivity, visible spectrum, opaqueness, stirring rate, and viscosity. This data is transmitted real-time over a wireless connection to an external system, such as a PC or smartphone. The flexible open-source software architecture allows effortless programming of the operation parameters of the Smart Stirrer in accordance with the end-user needs. The concept of the Smart Stirrer device with an integrated process monitoring system has been demonstrated in a series of experiments showing its capability for many hours of continuous telemetry with fine accuracy and a high data rate. Such a device can be used in conventional research laboratories, industrial production lines, flow reactors, and others where it can log the state of the process to ensure repeatability and operational consistency.

Contactless mass transfer for intra-droplet extraction.

This study demonstrates the possibility of "contactless" mass transfer between two aqueous slugs (droplets) separated by an oil slug in Taylor flow inside milli-channels. Separation of the alternating aqueous slugs at the outlet was performed by switching a couple of solenoid valves at branched outlets according to signals obtained by an optical sensor at the branch. Transfer of bromothymol blue (BTB) from acidic to basic aqueous slugs was performed for demonstration. In some cases, aqueous slugs separated by oil, merged catching on each other due to the velocity difference. Interfacial tension which was affected by the solute concentration was responsible for the velocity difference. Position-specific mass transfer activity at the rear end of the aqueous slugs was found on the course of the experiment. A meandering channel decreased the velocity difference and enhanced mass transfer. Almost complete (93%) transfer of BTB was achieved within a short residence time of several minutes under optimized conditions. The presented system opens a way for advanced separation using minimum amounts of the oil phase and allows concentrating the solute by altering relative lengths of the sender and receiver slugs.

Genome-wide sequence analyses of ethnic populations across Russia.

The Russian Federation is the largest and one of the most ethnically diverse countries in the world, however no centralized reference database of genetic variation exists to date. Such data are crucial for medical genetics and essential for studying population history. The Genome Russia Project aims at filling this gap by performing whole genome sequencing and analysis of peoples of the Russian Federation. Here we report the characterization of genome-wide variation of 264 healthy adults, including 60 newly sequenced samples. People of Russia carry known and novel genetic variants of adaptive, clinical and functional consequence that in many cases show allele frequency divergence from neighboring populations. Population genetics analyses revealed six phylogeographic partitions among indigenous ethnicities corresponding to their geographic locales. This study presents a characterization of population-specific genomic variation in Russia with results important for medical genetics and for understanding the dynamic population history of the world's largest country.

A hydrothermally stable ytterbium metal-organic framework as a bifunctional solid-acid catalyst for glucose conversion.

Yb6(BDC)7(OH)4(H2O)4 contains both bridging hydroxyls and metal-coordinated waters, possessing Brønsted and Lewis acid sites. The material crystallises from water at 200 °C. Using the solid as a heterogenous catalyst, glucose is converted into 5-hydroxymethylfurfural, via fructose, with a total selectivity of ∼70% after 24 hours at 140 °C in water alone: the material is recyclable with no loss of crystallinity.

Acid and base catalysed reactions in one pot with site-isolated polyHIPE catalysts.

The polyHIPE catalysts based on styrene, vinyl benzyl chloride, and divinylbenzene co-polymerisation were functionalised with carboxylic and tertiary amine groups. Catalyst characterisation showed covalent bonding of the graft polymers. The macroporous and highly interconnected structure of polyHIPEs allows isolation of the acid and base functional groups and allows the presence of these otherwise incompatible functionalities on the same catalyst. The functionalised polyHIPE catalysts were shown to perform two reactions; (i) acid-catalysed acetal hydrolysis and (ii) base-catalysed Knoevenagel condensation in one-pot with 97% yield. The yield obtained is substantially higher than that observed with the homogeneous or resin polymer type catalysts due to the compartmentalisation of the active sites and improved mass transfer through the open porous polyHIPE structure.

Analytical "bake-off" of whole genome sequencing quality for the Genome Russia project using a small cohort for autoimmune hepatitis.

A comparative analysis of whole genome sequencing (WGS) and genotype calling was initiated for ten human genome samples sequenced by St. Petersburg State University Peterhof Sequencing Center and by three commercial sequencing centers outside of Russia. The sequence quality, efficiency of DNA variant and genotype calling were compared with each other and with DNA microarrays for each of ten study subjects. We assessed calling of SNPs, indels, copy number variation, and the speed of WGS throughput promised. Twenty separate QC analyses showed high similarities among the sequence quality and called genotypes. The ten genomes tested by the centers included eight American patients afflicted with autoimmune hepatitis (AIH), plus one case's unaffected parents, in a prelude to discovering genetic influences in this rare disease of unknown etiology. The detailed internal replication and parallel analyses allowed the observation of two of eight AIH cases carrying a rare allele genotype for a previously described AIH-associated gene (FTCD), plus multiple occurrences of known HLA-DRB1 alleles associated with AIH (HLA-DRB1-03:01:01, 13:01:01 and 7:01:01). We also list putative SNVs in other genes as suggestive in AIH influence.

Genome-Wide Analyses Reveal Gene Influence on HIV Disease Progression and HIV-1C Acquisition in Southern Africa.

Sub-Saharan Africans infected with HIV-1C make up the largest AIDS patient population in the world and exhibit large heterogeneity in disease progression before initiating antiretroviral therapy. To identify host variants associated with HIV disease progression, we performed genome-wide association studies on a total of 556 treatment-naive HIV-infected individuals in Botswana. We characterized the pattern of HIV disease progression using a novel functional principal component analysis, which can better capture longitudinal CD4 and viral load (VL) trajectories. Two single-nucleotide polymorphisms (SNPs) near HCG22 (chr6, peak variant rs2535307, combined p = 3.72 × 10-7, minor allele as risky allele) and CCNG1 (chr5, peak variant kgp22385164, combined p = 1.88 × 10-6, minor allele as risky allele) were significantly associated with CD4 and VL dynamics. Inspection of SNPs in these gene regions in a third Botswana cohort (using GWATCH) also revealed a strong association of HCG22 with HIV-1C acquisition, suggesting that this region is associated with infection as well as disease progression. Our study uncovered two genetic regions that are significant and have specific effects on HIV-1C acquisition or progression in sub-Saharan Africans, and the result suggested new potential targets for AIDS prevention and treatment. In addition, our results also indicate the possibility of using genetic markers as HIV disease progression indicators in sub-Saharan Africans to prioritize fast progressors for antiretroviral treatment.

Novel synthesis of thick wall coatings of titania supported Bi poisoned Pd catalysts and application in selective hydrogenation of acetylene alcohols in capillary microreactors.

Catalysis in microreactors allows reactions to be performed in a very small volume, reducing the environmental problems and greatly intensifying the processes through easy pressure control and the elimination of heat- and mass-transfer limitations. In this study, we report a novel method for the controlled synthesis of micrometre-thick mesoporous TiO2 catalytic coatings on the walls of long channels (>1 m) of capillary microreactors in a single deposition step. The method uses elevated temperature and introduces a convenient control parameter of the deposition rate (displacement speed controlled by a stepper motor), which allows deposition from concentrated and viscous sols without channel clogging. A capillary microreactor wall-coated with titania supported Bi-poisoned Pd catalyst was obtained using the method and used for the semihydrogenation of 2-methyl-3-butyn-2-ol providing 93 ± 1.5% alkene yield for 100 h without deactivation. Although the coating method was applied only for TiO2 deposition, it is nonetheless suitable for the deposition of volatile sols.

GWATCH: a web platform for automated gene association discovery analysis.

BACKGROUND: As genome-wide sequence analyses for complex human disease determinants are expanding, it is increasingly necessary to develop strategies to promote discovery and validation of potential disease-gene associations. FINDINGS: Here we present a dynamic web-based platform - GWATCH - that automates and facilitates four steps in genetic epidemiological discovery: 1) Rapid gene association search and discovery analysis of large genome-wide datasets; 2) Expanded visual display of gene associations for genome-wide variants (SNPs, indels, CNVs), including Manhattan plots, 2D and 3D snapshots of any gene region, and a dynamic genome browser illustrating gene association chromosomal regions; 3) Real-time validation/replication of candidate or putative genes suggested from other sources, limiting Bonferroni genome-wide association study (GWAS) penalties; 4) Open data release and sharing by eliminating privacy constraints (The National Human Genome Research Institute (NHGRI) Institutional Review Board (IRB), informed consent, The Health Insurance Portability and Accountability Act (HIPAA) of 1996 etc.) on unabridged results, which allows for open access comparative and meta-analysis. CONCLUSIONS: GWATCH is suitable for both GWAS and whole genome sequence association datasets. We illustrate the utility of GWATCH with three large genome-wide association studies for HIV-AIDS resistance genes screened in large multicenter cohorts; however, association datasets from any study can be uploaded and analyzed by GWATCH.

Annotated features of domestic cat - Felis catus genome.

BACKGROUND: Domestic cats enjoy an extensive veterinary medical surveillance which has described nearly 250 genetic diseases analogous to human disorders. Feline infectious agents offer powerful natural models of deadly human diseases, which include feline immunodeficiency virus, feline sarcoma virus and feline leukemia virus. A rich veterinary literature of feline disease pathogenesis and the demonstration of a highly conserved ancestral mammal genome organization make the cat genome annotation a highly informative resource that facilitates multifaceted research endeavors. FINDINGS: Here we report a preliminary annotation of the whole genome sequence of Cinnamon, a domestic cat living in Columbia (MO, USA), bisulfite sequencing of Boris, a male cat from St. Petersburg (Russia), and light 30× sequencing of Sylvester, a European wildcat progenitor of cat domestication. The annotation includes 21,865 protein-coding genes identified by a comparative approach, 217 loci of endogenous retrovirus-like elements, repetitive elements which comprise about 55.7% of the whole genome, 99,494 new SNVs, 8,355 new indels, 743,326 evolutionary constrained elements, and 3,182 microRNA homologues. The methylation sites study shows that 10.5% of cat genome cytosines are methylated. An assisted assembly of a European wildcat, Felis silvestris silvestris, was performed; variants between F. silvestris and F. catus genomes were derived and compared to F. catus. CONCLUSIONS: The presented genome annotation extends beyond earlier ones by closing gaps of sequence that were unavoidable with previous low-coverage shotgun genome sequencing. The assembly and its annotation offer an important resource for connecting the rich veterinary and natural history of cats to genome discovery.