Which methods are the most effective in enabling novice users to participate in ontology creation? A usability study.

Producing findable, accessible, interoperable and reusable (FAIR) data cannot be accomplished solely by data curators in all disciplines. In biology, we have shown that phenotypic data curation is not only costly, but it is burdened with inter-curator variation. We intend to propose a software platform that would enable all data producers, including authors of scientific publications, to produce ontologized data at the time of publication. Working toward this goal, we need to identify ontology construction methods that are preferred by end users. Here, we employ two usability studies to evaluate effectiveness, efficiency and user satisfaction with a set of four methods that allow an end user to add terms and their relations to an ontology. Thirty-three participants took part in a controlled experiment where they evaluated the four methods (Quick Form, Wizard, WebProtégé and Wikidata) after watching demonstration videos and completing a hands-on task. Another think-aloud study was conducted with three professional botanists. The efficiency effectiveness and user confidence in the methods are clearly revealed through statistical and content analyses of participants' comments. Quick Form, Wizard and WebProtégé offer distinct strengths that would benefit our author-driven FAIR data generation system. Features preferred by the participants will guide the design of future iterations.

Incentivising use of structured language in biological descriptions: Author-driven phenotype data and ontology production.

Phenotypes are used for a multitude of purposes such as defining species, reconstructing phylogenies, diagnosing diseases or improving crop and animal productivity, but most of this phenotypic data is published in free-text narratives that are not computable. This means that the complex relationship between the genome, the environment and phenotypes is largely inaccessible to analysis and important questions related to the evolution of organisms, their diseases or their response to climate change cannot be fully addressed. It takes great effort to manually convert free-text narratives to a computable format before they can be used in large-scale analyses. We argue that this manual curation approach is not a sustainable solution to produce computable phenotypic data for three reasons: 1) it does not scale to all of biodiversity; 2) it does not stop the publication of free-text phenotypes that will continue to need manual curation in the future and, most importantly, 3) It does not solve the problem of inter-curator variation (curators interpret/convert a phenotype differently from each other). Our empirical studies have shown that inter-curator variation is as high as 40% even within a single project. With this level of variation, it is difficult to imagine that data integrated from multiple curation projects can be of high quality. The key causes of this variation have been identified as semantic vagueness in original phenotype descriptions and difficulties in using standardised vocabularies (ontologies). We argue that the authors describing phenotypes are the key to the solution. Given the right tools and appropriate attribution, the authors should be in charge of developing a project's semantics and ontology. This will speed up ontology development and improve the semantic clarity of phenotype descriptions from the moment of publication. A proof of concept project on this idea was funded by NSF ABI in July 2017. We seek readers input or critique of the proposed approaches to help achieve community-based computable phenotype data production in the near future. Results from this project will be accessible through https://biosemantics.github.io/author-driven-production.

Investigation of Free-Standing Plasmonic Mesoporous Ag/CMK-8-Nafion Composite Membrane for the Removal of Organic Pollutants with 254-nm UV Irradiation.

"Carbon-based material" has demonstrated a great potential on water purification due to its strong physical adsorption to organic pollutants in the water. Three-dimensional cubic ordered mesoporous carbon (CMK-8), one of the well-known ordered mesoporous carbons, was prepared by using nanocasting method with mesoporous silica (KIT-6) as the template. In this study, CMK-8 blended with Nafion polymer to form a free-standing mesoporous CMK-8-Nafion composite membrane. The synthesis of high crystallinity CMK-8 was characterized by X-ray diffraction (XRD) and transmission electron microscopy (TEM). More than 80% methyl orange (MO) removal efficiency was observed under 254-nm UV irradiation after 120 min. Ninety-two percent recycling performance was remained after four recycling tests, which indicated a reliable servicing lifetime for the water purification. Furthermore, an additional layer of plasmonic silver nanoparticles (Ag NPs) was integrated into this CMK-8-Nafion membrane for higher pollutant removal efficiency, attributing from the generation of plasmon-resonance hot electrons from Ag NPs. A 4-in. CMK-8-Nafion composite membrane was also fabricated for the demonstration of potential large-scale utilization.

Plasmon-Induced Hot Electrons on Mesoporous Carbon for Decomposition of Organic Pollutants under Outdoor Sunlight Irradiation.

In this study, a 4 in. CMK-8-Nafion membrane was fabricated using three-dimensional cubic ordered mesoporous carbon CMK-8 blended with a Nafion polymer. Plasmon-resonance hot electrons and holes from Au nanoparticles (NPs) combined with this CMK-8-Nafion membrane resulted in the effective decomposition of methyl orange (MO) due to the synergetic work of hot carriers with mesoporous carbon; a sample of Au/CMK-8-Nafion exposed to outdoor sunlight radiation for 150 min successfully removed 97% of MO. Fourier transform infrared spectroscopy (FTIR) was employed to examine the generation of hydroxyl groups (OH-) during decomposition. Finally, the spatial distribution of hydroxyl groups was also investigated across the different coverage densities of plasmonic Au NPs.

Systematic screening of glycosylation- and trafficking-associated gene knockouts in Saccharomyces cerevisiae identifies mutants with improved heterologous exocellulase activity and host secretion.

BACKGROUND: As a strong fermentator, Saccharomyces cerevisiae has the potential to be an excellent host for ethanol production by consolidated bioprocessing. For this purpose, it is necessary to transform cellulose genes into the yeast genome because it contains no cellulose genes. However, heterologous protein expression in S. cerevisiae often suffers from hyper-glycosylation and/or poor secretion. Thus, there is a need to genetically engineer the yeast to reduce its glycosylation strength and to increase its secretion ability. RESULTS: Saccharomyces cerevisiae gene-knockout strains were screened for improved extracellular activity of a recombinant exocellulase (PCX) from the cellulose digesting fungus Phanerochaete chrysosporium. Knockout mutants of 47 glycosylation-related genes and 10 protein-trafficking-related genes were transformed with a PCX expression construct and screened for extracellular cellulase activity. Twelve of the screened mutants were found to have a more than 2-fold increase in extracellular PCX activity in comparison with the wild type. The extracellular PCX activities in the glycosylation-related mnn10 and pmt5 null mutants were, respectively, 6 and 4 times higher than that of the wild type; and the extracellular PCX activities in 9 protein-trafficking-related mutants, especially in the chc1, clc1 and vps21 null mutants, were at least 1.5 times higher than the parental strains. Site-directed mutagenesis studies further revealed that the degree of N-glycosylation also plays an important role in heterologous cellulase activity in S. cerevisiae. CONCLUSIONS: Systematic screening of knockout mutants of glycosylation- and protein trafficking-associated genes in S. cerevisiae revealed that: (1) blocking Golgi-to-endosome transport may force S. cerevisiae to export cellulases; and (2) both over- and under-glycosylation may alter the enzyme activity of cellulases. This systematic gene-knockout screening approach may serve as a convenient means for increasing the extracellular activities of recombinant proteins expressed in S. cerevisiae.

The pharmacological activities of (-)-anonaine.

Several species of Magnoliaceae and Annonaceae are used in Traditional Chinese Medicine. (-)-Anonaine, isolated from several species of Magnoliaceae and Annonaceae, presents antiplasmodial, antibacterial, antifungal, antioxidation, anticancer, antidepression, and vasorelaxant activity. This article provides an overview of the pharmacological functions of (-)-anonaine.

Review on pharmacological activities of Cinnamomum subavenium.

This review describes the morphological, phytochemical and pharmacological properties of Cinnamomum subavenium (Lauraceae). The plant grows wild in southern Mainland China, Burma, Cambodia, Taiwan, Malaysia and Indonesia. This plant is recorded as having long been used to treat carcinomatous swelling, stomach ache, chest pain, abdominal pain, hernia, diarrhoea, rheumatism, nausea and vomiting. This article enumerates an overview of phytochemical and pharmacological aspects that is useful to researchers for further exploration for the necessary development of this potential herb.

Inhibitory effect of hexahydrocurcumin on human platelet aggregation.

The effects of hexahydrocurcumin on adenosine diphosphate (ADP)-induced human platelet aggregation were studied. Treatment of human platelet-rich plasma with hexahydrocurcumin resulted in an inhibitory effect on platelet aggregation, suggesting the potential of this compound as an anti-atherosclerogenic agent in humans.

PGASO: A synthetic biology tool for engineering a cellulolytic yeast.

BACKGROUND: To achieve an economical cellulosic ethanol production, a host that can do both cellulosic saccharification and ethanol fermentation is desirable. However, to engineer a non-cellulolytic yeast to be such a host requires synthetic biology techniques to transform multiple enzyme genes into its genome. RESULTS: A technique, named Promoter-based Gene Assembly and Simultaneous Overexpression (PGASO), that employs overlapping oligonucleotides for recombinatorial assembly of gene cassettes with individual promoters, was developed. PGASO was applied to engineer Kluyveromycesmarxianus KY3, which is a thermo- and toxin-tolerant yeast. We obtained a recombinant strain, called KR5, that is capable of simultaneously expressing exoglucanase and endoglucanase (both of Trichodermareesei), a beta-glucosidase (from a cow rumen fungus), a neomycin phosphotransferase, and a green fluorescent protein. High transformation efficiency and accuracy were achieved as ~63% of the transformants was confirmed to be correct. KR5 can utilize beta-glycan, cellobiose or CMC as the sole carbon source for growth and can directly convert cellobiose and beta-glycan to ethanol. CONCLUSIONS: This study provides the first example of multi-gene assembly in a single step in a yeast species other than Saccharomyces cerevisiae. We successfully engineered a yeast host with a five-gene cassette assembly and the new host is capable of co-expressing three types of cellulase genes. Our study shows that PGASO is an efficient tool for simultaneous expression of multiple enzymes in the kefir yeast KY3 and that KY3 can serve as a host for developing synthetic biology tools.

A highly efficient ß-glucosidase from the buffalo rumen fungus Neocallimastix patriciarum W5.

BACKGROUND: Cellulose, which is the most abundant renewable biomass on earth, is a potential bio-resource of alternative energy. The hydrolysis of plant polysaccharides is catalyzed by microbial cellulases, including endo-ß-1,4-glucanases, cellobiohydrolases, cellodextrinases, and ß-glucosidases. Converting cellobiose by ß-glucosidases is the key factor for reducing cellobiose inhibition and enhancing the efficiency of cellulolytic enzymes for cellulosic ethanol production. RESULTS: In this study, a cDNA encoding ß-glucosidase was isolated from the buffalo rumen fungus Neocallimastix patriciarum W5 and is named NpaBGS. It has a length of 2,331 bp with an open reading frame coding for a protein of 776 amino acid residues, corresponding to a theoretical molecular mass of 85.1 kDa and isoelectric point of 4.4. Two GH3 catalytic domains were found at the N and C terminals of NpaBGS by sequence analysis. The cDNA was expressed in Pichia pastoris and after protein purification, the enzyme displayed a specific activity of 34.5 U/mg against cellobiose as the substrate. Enzymatic assays showed that NpaBGS was active on short cello-oligosaccharides from various substrates. A weak activity in carboxymethyl cellulose (CMC) digestion indicated that the enzyme might also have the function of an endoglucanase. The optimal activity was detected at 40°C and pH 5 ~ 6, showing that the enzyme prefers a weak acid condition. Moreover, its activity could be enhanced at 50°C by adding Mg2+ or Mn2+ ions. Interestingly, in simultaneous saccharification and fermentation (SSF) experiments using Saccharomyces cerevisiae BY4741 or Kluyveromyces marxianus KY3 as the fermentation yeast, NpaBGS showed advantages in cell growth, glucose production, and ethanol production over the commercial enzyme Novo 188. Moreover, we showed that the KY3 strain engineered with the NpaNGS gene can utilize 2 % dry napiergrass as the sole carbon source to produce 3.32 mg/ml ethanol when Celluclast 1.5 L was added to the SSF system. CONCLUSION: Our characterizations of the novel ß-glucosidase NpaBGS revealed that it has a preference of weak acidity for optimal yeast fermentation and an optimal temperature of ~40°C. Since NpaBGS performs better than Novo 188 under the living conditions of fermentation yeasts, it has the potential to be a suitable enzyme for SSF.

Bio-functional constituents from the stems of Liriodendron tulipifera.

Four known compounds have been isolated from the stems of Liriodendron tulipifera, and the structures of these pure constituents were determined using spectroscopic analysis. Isolated compounds were screened for free radical scavenging ability, metal chelating power assay and ferric reducing antioxidant power assay (FRAP). The anti-tyrosinase effects of L. tulipifera compounds were calculated the inhibition of hydroxylation of L-tyrosine to L-dopa according to an in vitro mushroom tyrosinase assay. The study also examined the bio-effects of the four compounds on the human melanoma A375.S2, and showed that liriodenine (1) and (-)-norglaucine (4) significantly inhibited the proliferation of melanoma cells in the cell viability assay. Wound healing results indicated that liriodenine (1), (-)-glaucine (3) and (-)-norglaucine (4) exerted anti-migration potential. Interestingly, (-)-glaucine (3), neither liriodenine (1) nor (-)-norglaucine (4) showed promising anti-migration potential without inducing significant cytotoxicity. Furthermore, a dramatically increased level of intracellular reactive oxygen species (ROS) was detected from (-)-glaucine (3). The cell cycle assessment demonstrated a moderate G2/M accumulation by (-)-glaucine (3). The above results revealed the anti-cancer effects of L. tulipifera compounds, especially on the anti-migration ability indicating the promising chemopreventive agents to human skin melanoma cells.

Observation of protein folding/unfolding dynamics of ubiquitin trapped in agarose gel by single-molecule FRET.

A ubiquitin mutant with two Cys mutations, m[C]q/S65C, was site-specifically labeled with two dye molecules, Alexa Fluor 488 (donor) and Alexa Fluor 594 (acceptor), due to the different reactivity of these two Cys residues. This doubly dye-labeled ubiquitin has lower structural stability than wild-type ubiquitin. Taking advantage of this decreased stability, conformational heterogeneity of this protein under nondenaturing condition was observed at the single-molecule level using single-paired Förster resonance energy transfer (FRET) by trapping the protein in agarose gel. Three conformational populations corresponding to folded (E (ET) ≈ 0.95), loosely packed (E (ET) ≈ 0.72), and unfolded (E (ET) ≈ 0.22) structures, and the structural transitions between them were observed. Our results suggest that agarose immobilization is good for observing structural dynamics of proteins under native condition.

A new benzodioxocinone from the leaves of Cinnamomum tenuifolium.

Investigation of the leaves' extract of Cinnamomum tenuifolium (Lauraceae) led to the isolation of one novel benzodioxocinone, 2,3-dihydro-6,6-dimethylbenzo-[b][1,5]dioxocin-4(6 H)-one (1). The structure was determined through in-depth spectroscopic and mass-spectrometric analyses. The antioxidant potential was evaluated using the following in vitro method: scavenging of 1,1-diphenyl-2-picrylhydrazyl radical. We also detected the anti-proliferative effect of 1 on human oral cancer cells and its IC(50) is 107.7 µM.

Functional characterization of cellulases identified from the cow rumen fungus Neocallimastix patriciarum W5 by transcriptomic and secretomic analyses.

BACKGROUND: Neocallimastix patriciarum is one of the common anaerobic fungi in the digestive tracts of ruminants that can actively digest cellulosic materials, and its cellulases have great potential for hydrolyzing cellulosic feedstocks. Due to the difficulty in culture and lack of a genome database, it is not easy to gain a global understanding of the glycosyl hydrolases (GHs) produced by this anaerobic fungus. RESULTS: We have developed an efficient platform that uses a combination of transcriptomic and proteomic approaches to N. patriciarum to accelerate gene identification, enzyme classification and application in rice straw degradation. By conducting complementary studies of transcriptome (Roche 454 GS and Illumina GA IIx) and secretome (ESI-Trap LC-MS/MS), we identified 219 putative GH contigs and classified them into 25 GH families. The secretome analysis identified four major enzymes involved in rice straw degradation: ß-glucosidase, endo-1,4-ß-xylanase, xylanase B and Cel48A exoglucanase. From the sequences of assembled contigs, we cloned 19 putative cellulase genes, including the GH1, GH3, GH5, GH6, GH9, GH18, GH43 and GH48 gene families, which were highly expressed in N. patriciarum cultures grown on different feedstocks. CONCLUSIONS: These GH genes were expressed in Pichia pastoris and/or Saccharomyces cerevisiae for functional characterization. At least five novel cellulases displayed cellulytic activity for glucose production. One ß-glucosidase (W5-16143) and one exocellulase (W5-CAT26) showed strong activities and could potentially be developed into commercial enzymes.

Studying submicrosecond protein folding kinetics using a photolabile caging strategy and time-resolved photoacoustic calorimetry.

Kinetic measurement of protein folding is limited by the method used to trigger folding. Traditional methods, such as stopped flow, have a long mixing dead time and cannot be used to monitor fast folding processes. Here, we report a compound, 4-(bromomethyl)-6,7-dimethoxycoumarin, that can be used as a "photolabile cage" to study the early stages of protein folding. The folding process of a protein, RD1, including kinetics, enthalpy, and volume change, was studied by the combined use of a phototriggered caging strategy and time-resolved photoacoustic calorimetry. The cage caused unfolding of the photolabile protein, and then a pulse UV laser (∼10(-9) s) was used to break the cage, leaving the protein free to refold and allowing the resolving of two folding events on a nanosecond time scale. This strategy is especially good for monitoring fast folding proteins that cannot be studied by traditional methods.

Ultrasound-assisted plasma: a novel technique for inactivation of aquatic microorganisms.

Nonthermal plasma and ultrasound are two techniques capable of microorganism inactivation in a liquid phase. However, the interaction between the two techniques is not yet understood. In this study, an ultrasound-assisted plasma (USaP) technique by combining the two means is proposed. A lab-scale USaP system was designed and experimentally tested. The inactivation experiments were conducted with various conditions of two types of electrode layout (submerged and hybrid reactors), aeration or not, and two microorganism species E. coli and yeast. For a 30-min treatment, the inactivation efficiencies with no aeration were 2-, 2-, and 6-log reductions for ultrasound, plasma, and ultrasound-assisted plasma, respectively; and with aeration were 2-, 6-, and 6-log reductions, respectively. The aeration greatly enhanced the inactivation efficiency for the plasma but not for the ultrasound or the ultrasound-assisted plasma. The influences of electrode layout and microorganism species were insignificant on the inactivation efficiency. On the other hand, for a submerged reactor without aeration, the inactivation efficiency achieved with ultrasound-assisted plasma (eta(USaP)) was not only greater than eta(ultasound) or eta(plasma), but also greater than the summation of eta(ultrasound and eta(plasma). Namely, a synergistic effect of ultrasound-plasma combination on the inactivation was observed. No such synergistic effect was observed in a hybrid reactor or in aeration cases. The synergism is speculatively a virtue of the ultrasonic-generated bubbles that easily induce plasma discharges, and thus enhance microorganism inactivation in water.

White-light emission from an upconverted emission with an organic triplet sensitizer.

An energy upconversion system based on triplet-triplet annihilation exploiting an organic triplet sensitizer is devised and has achieved a white-light emission with a low power laser excitation.

Removal of volatile organic compounds by single-stage and two-stage plasma catalysis systems: a review of the performance enhancement mechanisms, current status, and suitable applications.

This paper provides a comprehensive review regarding the application of plasma catalysis, the integration of nonthermal plasma and catalysis, on VOC removal. This novel technique combinesthe advantages of fast ignition/response from nonthermal plasma and high selectivity from catalysis. It has been successfully demonstrated that plasma catalysis could serve as an effective solution to the major bottlenecks encountered by nonthermal plasma, i.e., the reduction of energy consumption and unwanted/hazardous byproducts. Instead of working independently, the combination could induce extra performance enhancement mechanisms either in a single-stage or a two-stage configuration, in which the catalyst is located inside and downstream from the nonthermal plasma reactor, respectively. These mechanisms are believed to be responsible for the higher energy efficiency and better CO2 selectivity achieved with plasma catalysis. A comprehensive discussion on the performance enhancement mechanisms is provided in this review paper. Moreover, the current status of the applications of two different plasma catalysis systems on VOC abatement are also given and compared. The catalyst plays an important role in both configurations. Especially for the single-stage type, depositing an inappropriate active component on catalytic support would decrease the VOC removal efficiency instead. To date, no definite conclusion on catalyst selection forthe single-stage plasma catalysis is available. However, MnO2 seems to be the best catalyst for two-stage configuration because it could effectively decompose ozone and generate active species toward VOC destruction. On the other hand, although the single-stage plasma catalysis has been proved to be superior to the two-stage configuration, it does not mean that the former is always the best choice. Considering the typical VOC concentrations from different sources and the characteristics of different plasma catalysis systems, the single-stage and two-stage configurations are suggested to be more suitable for industrial and indoor air applications, respectively.

Identification and analysis of ancestral hominoid transcriptome inferred from cross-species transcript and processed pseudogene comparisons.

Comparative transcriptomics studies in hominoids are difficult because of lack of EST information in the great apes. Nevertheless, processed pseudogenes (PPGs), which are reverse-transcribed ancient transcripts present in the current genome, can be regarded as a virtual transcript resource that may compensate for the paucity of ESTs in non-human hominoids. Here we show that chimpanzee PPGs can be applied to identification of novel human exons/alternatively spliced variants (ASVs) and inference of the ancestral hominoid transcriptome and chimpanzee exon loss events. We develop a method for comparatively extracting novel transcripts from PPGs (designated "CENTP") and identify 643 novel human exons/ASVs. RT-PCR-sequencing experiments confirmed >50% of the tested exons/ASVs, supporting the effectiveness of the CENTP pipeline. With reference to the ancestral transcriptome inferred by CENTP, 47 chimpanzee exon loss events are identified. Furthermore, by combining out-group and PPG information, we identify 20 chimpanzee-specific exon loss and 10 human-specific exon gain events. We also demonstrate that the ancestral transcriptome and exon loss/gain events inferred based on comparisons of current transcripts may be incomplete (or occasionally inappropriate) because ancestral transcripts may not be represented in the ESTs of existing species. Finally, functional analysis reveals that the novel exons identified based on chimpanzee transcripts are significantly enriched in genes related to translation regulatory activity and viral life cycle, suggesting different expression levels of the associated transcripts, and thus divergent splicing isoform composition between human and chimpanzee in these functional categories.

CONDITIONAL PRODUCTION OF A FUNCTIONAL FISH GROWTH HORMONE IN THE TRANSGENIC LINE OF NANNOCHLOROPSIS OCULATA (EUSTIGMATOPHYCEAE)(1).

Plasmid phr-YPGHc, containing the fish growth hormone (GH) cDNA driven by a heat shock protein 70A promoter and a RUBISCO SSU 2 promoter, was transferred into the protoplast of marine microalga Nannochloropsis oculata (Droop) D. J. Hibberd by electroporation. Four transgenic clones were obtained in which the transferred phr-YPGHc was integrated into the genome and existed stably at least until the 50th generation. When we treated these transgenic microalgae by heat shock, the heterologous fish GH was produced in the amount of 0.42 to 0.27 µg · mL(-1) from the 50 mL of medium. We incubated artemia with the wildtype and transgenic N. oculata for 6 h and then fed these microalgae-treated artemia to red-tilapia larvae. After feeding, the growth of larvae that were fed artemia incubated with transgenic microalgae was greater (i.e., statistically significant: P < 0.05) than that of larvae that were fed artemia incubated with nontransgenic microalgae: 316% versus 104% in weight gain, and 217% versus 146% in body length increase, respectively. Therefore, the N. oculata enables production of functional GH, and we propose that it might be an excellent bioreactor material.