1,721,027 research outputs found
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Metagenomics Study of the Taxonomic and Functional Compositions of Microbial Communities in Fine Dust Particulate Matter
No full textAsian dust events or known as the Yellow dust events in South Korea is a seasonal phenomenon that usually occurs during spring time which also affecting the other East Asian countries (China and Japan) due to the global dust transportation. The dust particles are usually dispersed from the semi-arid or arid region such as the Gobi Desert and the Taklamakan Desert in Mongolia across the vast ocean to a more humid mainland. During these phenomenal events, the level of the dust particles increases significantly, increasing the levels of associated chemical components and microorganisms. In the great concerns of the elevated particulate matter (PM) level especially the fine fraction (PM with an aerodynamic diameter < 2.5 µm, PM2.5) known as the event days had raised the effort of understanding the microbial community abundance and composition shift in between the non-event days and event days. Depending on the sizes of the dust particles, it is usually the smaller particles that have higher risk and greater impact on human health. The inhalation of this PMs could lead to the increase of risk in respiratory disease problems, asthmatic patients, allergies, and reduced in lung functions.
By far, most studies have conducted the impact of the chemical components of the PM towards human health and yet there is still limited study in the biological components of the PM. Indeed, the various chemical and biological components in airborne PM can pose a threat to human health. Nevertheless, it is known that the microorganisms including bacteria and fungi are successful life forms because of their ability to reproduce rapidly, adaptability to new environments, and capacity to disperse globally, especially through wind or as bioaerosols. These bioaerosols may contains critical human or plant pathogenic species which can cause diseases and bring harms to the human health as well as agriculture economic growth. Furthermore, the bioaerosols can also contain the airborne components of microorganisms including secondary metabolites such as endotoxins and mycotoxins which some are carcinogenic and the toxins can have serious human health impacts.
Despite of these airborne microorganisms to be widely dispersed in the atmosphere, there are still lacking of knowledge about the airborne microorganisms. This is because most of the studied conducted on airborne microbes were based on the cultivation technique and slowly changes to the culture-independent method such as 16S rRNA targeted-gene sequencing analysis. 16S rRNA gene analysis or also known as polymerase chain reaction (PCR)-based analysis is one of the most commonly use molecular technique to characterize the microbial community because it can provide rapid information and able to use on a minute amount of genomic DNA. In addition to the culture-independent analysis, there is a more recent and advanced method which can study both microbial community as well as its metabolic potential that is the whole metagenomics shotgun sequencing (WMS). Therefore, the importance of knowing the key microbial genes of the sampled community can give better understanding of the microbes behavior in the atmosphere. More knowledge can be obtained on how these airborne microbes can survives in the harsh conditions (high levels of UV radiation, low water activity, and extreme temperatures). Therefore, in order to study the airborne microorganisms of the collected samples, this dissertation is divided into 4 main objectives as follows:
1. Selecting the appropriate aerosol samplers for maximum efficiency of bioaerosols collection
2. Characterization of the airborne bacterial and fungal community in the collected samples by culture-independent analysis
3. Increased the understanding of the characterized airborne bacterial and fungal community and composition shifts in between the non-event and event day samples by using whole metagenomics shotgun sequencing
4. To develop more optimize sampling and processing method for direct application of whole metagenomics shotgun sequencing
The presented thesis contributes to emphasize the importance of understanding the airborne microbial community especially during the elevated level of PMs during the event days. Among the significance findings from this dissertation were the bacterial community differed between the non-event and event days sample. In certain cases, the Proteobacteria was more prevalent during non-event day, while Bacteroidetes dominated during event day. Even though the bacteria were more dominant in the aerosol samples compared to the fungal community, based on the findings in this study, there is still a notable abundance of fungal community in the samples. Ascomycota group were highly abundant especially during the event day. This could lead to the assumptions that Ascomycota which mainly consists of spore-forming fungi, can attached to the dust particles and be carried away through wind dispersal. Furthermore, several pathogenic genera were identified and the proportion was higher during the event days. In related to the functional composition, it seems that the abundance of nitrogen-fixing bacteria is also associated with the abundance of functional genes related to nitrogen metabolism.
Nevertheless, the techniques used in this dissertation can also be applied for other environmental samples such as bioreactor or other microbiomes. Depending on the research objectives, one can choose their own approach that is suitable to the study. The application of metagenomics studies can give more insight in related to the microbial community and its metabolic potential. Also, increasing the datasets of the studies for research feasibility as well as finding of novel genes or organisms especially for the uncultured organisms. In conclusion, the decrease in sequencing costs and improvements in sequencing technology has resulted in a dramatic increase in the availability of sequencing data over the past decade. Whole metagenomics shotgun sequencing is becoming a popular strategy for various analyses, and in one of these days, it might replace the PCR-based analysis.Docto
Development of Sensing Systems for Dissolved Carbon Monoxide Concentration Using a Mo–Cu Dependent Carbon Monoxide Dehydrogenase
No full textCarbon monoxide (CO) generated in notable amounts from industrial processes as well as gasification of carbon-containing compounds is widely used as feedstock in biological and chemical gas conversion to value-added platform chemicals. In a typical CO conversion process, CO is supplied in gaseous form and the CO in dissolved form (liquid-phase) can be subsequently converted into valuable products including alcohols, hydrocarbons, and organic acids via biological or chemical catalysis. For optimal performance of this CO conversion process, monitoring dissolved CO concentration, Cco is therefore integral because Cco determines the gas-liquid mass transfer coefficient, a key parameter for the biological and chemical gas conversion. CO in gaseous form can be directly determined by gas-chromatography. However, CO is sparingly soluble in water, making the dissolved CO concentration more challenging to determine. Typically, Cco is indirectly estimated by measuring the concentration of CO in the gas phase and then Cco is calculated employing Henry’s law (assuming thermodynamic equilibrium). Therefore, this indirect method is limited because the Cco during most biological and chemical CO conversions are dynamically changing, and often a single measurement and complete analysis generally take over 10 minutes. The work presented in this thesis was motivated by the need for a direct determination of Cco. The core of this thesis is focusing on exploiting the intrinsic specificity of enzymes capable of catalyzing CO reaction as the biorecognition element in an enzyme-based biosensor. The first element of the work described in this thesis is the selection of the enzyme that preserves biocatalytic CO oxidation activity upon immobilization on the electrode surface. Next, heterologous expression of the target gene encoding the enzyme Mo–Cu dependent carbon monoxide dehydrogenase (CODH) in E. coli was secured for the convenient production of enzymes to be used in the development of the enzyme-based biosensor. With the expression system secured in hand, two different architectures sensing systems for monitoring Cco were explored. The first design is the use of recombinant Mo–Cu CODH as the CO-catalyst unit (CO to CO2) in front of a CO2 transducer. The developed CO-biomicrosensor exhibited approximately 95% sensor response towards CO in 5 min with linear sensor response towards quite low CO concentrations (0–9 µM) and a LOD of 15 nM. The sensor was approximately retained activity and sensitivity of 80% for one-week continuous operation. The second architecture is the enzyme immobilized on the electrode surface, in which the electrons generated from the CO oxidation to CO2 by CODH are transferred and collected at the electrode surface can be quantified as current. The main challenge of this second enzyme biosensor architecture is establishing stable directed immobilization that retains the biocatalytic function of the enzyme and secured efficient electrical connection between the active site and the electrode surface. To address this challenge, genetic modification of Mo–Cu CODH to fuse solid-binding peptides at a specific site was attempted. The “wire-ready” synthetic CODH-Ls demonstrated bi-functional activities, of CO oxidation, and solid-binding activity, as confirmed via conventional enzyme solution assay, atomic force microscopy (AFM), and quartz crystal microbalance (QCM), respectively. The next research question that was investigated in this study is the effect of the distance between immobilization point(s) and the enzyme active site on the electron transfer kinetics at the enzyme-electrode interface. To address this specific question, three synthetic CODH-Ls having gbp fused at N- or/and C-terminus were specifically designed to control immobilization of the enzyme in different points or site, and therefore the distance between the active site and the immobilization point varies accordingly, hence resulting in different electron transfer kinetics at the enzyme-electrode interface. The electrochemical result confirmed that only gbp(N)-CODH-L-gbp(C) is capable of direct electron transfer because the presence of the gbp at both N- and C-terminus facilitate a shorter distance between the enzyme active site and the electrode surface. The results exemplify the effect of the distance between enzyme immobilization point and active site to the electron transfer kinetics at the enzyme-electrode interface which is integral to the DET-based biosensor. Overall, the studies presented in this thesis outline the development of sensing systems for dissolved CO concentration using the enzyme, CODH as the CO catalyst unit. Taken together, the approaches demonstrated here is applicable not only for use in the development of CO sensing system, but also other application not limited to the enzymatic-based biosensor, enzymatic fuel cell, enzymatic electrosynthesis which can be tailored by using different enzyme, protein, or other biomolecules.Docto
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Strain Development of Acetogen, Eubacterium limosum KIST612 for Carbon Monoxide-Based Ethanol Production
No full textAcetogens are capable of fixing inorganic gases to acetate via Wood-Ljungdahl pathway. Due to their potential to produce value-added metabolites, such as organic acids with/without bio-alcohols, acetogens have received attention in the field of biorefinery. Several efforts are being made to construct genetic toolbox in order to engineer acetogens with the final goal to manipulate a catabolic metabolism to enhance product yields. However, up to now, successful genetic engineering systems are limited to a few acetogens. Eubacterium limosum KIST612 is one of the promising acetogen of which the syngas-utilizing ability had been well studied as well as the genomic data are available. In this research, metabolic engineering was applied to develop the KIST612 that produces a non-native ethanol from carbon monoxide. For development of the strain, it is necessary to understand metabolic properties and bioenergetics and to construct appropriate genetic systems.
The KIST612 is one of the few acetogens that can produce butyrate from carbon monoxide. The butyrate production is engaged in the energy conservation of the strain. A genome-guided analysis was used to delineate the pathway of butyrate formation, the enzymes involved and the potential coupling to ATP synthesis. Oxidation of CO is catalyzed by the CO dehydrogenase/acetyl-CoA synthase and coupled to the reduction of ferredoxin. Oxidation of reduced ferredoxin is catalyzed by the Rnf complex in a Na+-dependent manner. Consistent with the finding of a Na+-dependent Rnf complex is the presence of a conserved Na+-binding motif in the c subunit of the ATP synthase. As an activity of the butyryl-CoA dehydrogenase, it was confirmed that the reduction of crotonyl-CoA to butyryl-CoA by oxidation of NADH was coupled to reduction of ferredoxin. It can be postulated that the butyryl-CoA dehydrogenase uses flavin-based electron bifurcation to reduce ferredoxin, which is consistent with the finding of etfA and etfB genes next to it.
As a specific characteristic of KIST612, the strain exhibits metabolic versatility depending on the energy source. This metabolic versatility is well represented in the butyrate production of the strain. To assess the versatile regulation on the metabolism, the transcriptional dynamics of KIST612 was explored across different carbon/energy/electron sources and growth phases. A total of 4,579 genes were identified; among them, more than half were differentially transcribed under various growth conditions. These differentially expressed genes were classified into six categories based on their patterns of transcriptional regulation. Pathway enrichment analysis of the differentially expressed genes identified an unexpected feature for both energy metabolism and butyrate synthesis, in that KIST612 has two distinct butyrate formation routes: i) acetate-assimilatory butyrate formation, which dominates under autotrophic condition; and ii) dissimilatory butyrate formation with de-phosphorylation of butyryl phosphate, which dominates under heterotrophic condition.
The foreign gene introduction and expression system was developed, as a genetic toolbox for KIST612. The compacted size of shuttle vector backbone was constructed for the strain by modifying pJIR418 that the stable replication was confirmed. In addition, the transcriptomics-based candidate selection of native constitutive promoter and the β-glucuronidase (GUS) reporter gene assay enabled to sort one strong and constitutive native promoter H2 (Prbo) for the strain. Then, based on the genetic system of the strain, the recombinant vector (pECPH2::adhE), that the heterologous gene encoding bi-functional aldehyde/alcohol dehydrogenase (AdhE) with H2 (Prbo) promoter was inserted in the shuttle vector for KIST612, was constructed and it was introduced into the strain. The successful transformation and expression of heterologous AdhE gene enabled to produce non-native ethanol from the strain.
The AdhE transformants were cultivated on both heterotrophic glucose- and autotrophic CO- substrate conditions, repectively. As a result of product profiling, KIST612 transformants produced non-native ethanol without any butyrate production in the both conditions. The native butyrate production of KIST612 was inhibited by competition with ethanol production through the heterotrophic expression of AdhE, even without any genome editing. In addition, the transformants produced ethanol with clear re-assimilation of acetate in only autotrophic CO condition, similar to the feature of butyrate production in wild-type KIST612. Interestingly, the AdhE1 transformants produced 27 mM of ethanol consuming 12.9 mmols of CO with complete re-assimilation of acetate, in CO fed-batch condition. In conclusion, the KIST612 was successfully engineered to ethanol producer, as well it was confirmed the possibility of product unification into ethanol by CO fermentation of the strain.Docto
Carbon Monoxide Sensitivity to Hydrogen Consumption in Eubacterium limosum KIST612
No full textSyngas, a mixture of mostly hydrogen (H2), carbon monoxide (CO), and carbon dioxide (CO2), is used as a carbon and energy source by certain anaerobic microorganisms, called acetogens. Acetogens are strictly anaerobic bacteria which are able to utilize syngas components (H2, CO, and CO2) through the Wood-Ljungdahl pathway (WLP). In this study, we have tested substrate utilization and selectivity of Eubacterium limosum KIST612 when the strain was cultivated in the medium containing H2, CO2, and CO, respectively. The result showed that H2 consumption was completely inhibited when the dissolved CO concentration is over 0.05 ± 0.01. To reveal the reason, the biochemical properties of [FeFe]-hydrogenase would be investigated. We conducted hydrogenase activity and CO inhibition test on whole crude extract of Eubacterium limosum KIST612 that cultivated different type of substrate such as 20mM glucose, 1 atm of CO, and 1 atm of H2CO2. Also the subunits of Hyd were successfully expressed in Escherichia coli DH5α This study suggests the guideline for enhanced productivity by optimizing to consume co-substrate in syngas fermentation.Maste
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
Solid Binding Peptide-Guided Enzyme Immobilization for Enzymatic Cascade-based Direct Bioelectrocatalytic System
No full textIn this study, enzyme cascade-based direct bioelectrocatalytic system has been constructed using genetic fusion methodology of solid binding peptide (SBP) tag and purposed to prove the feasibility of SBP linker to control 1) cofactor-surface orientation and 2) inter-enzyme relative orientation, as well as 3) position-selective adsorption on electrode.
In the first part of the study, the interfacial DET of gold binding peptide (GBP)-fused oxidoreductase on electrode was focused and evaluated depending on fused GBP types that were varied in the respect of amino acid sequence and length, though possessing identical gold binding specificity. The four types of GBP have been fused to DET-capable enzyme, GDHγα, producing 4 different fusion GDHγα. The significant alternation in oxidative current from fusion GDHγα on electrode was observed according to introduced GBP type. Through concomitant analysis with predictive docking model, it was found that cofactor-surface interface could be obstructed or open even by slight change in surface conformation of fusion enzymes which has induced by gold-binding conformation of fused GBPs. Then, INV as the upstream enzyme of GDHγα, was incorporated at previously established DET-based fusion GDHγα electrode, for investigate inter-enzyme orientation dependent cascade reaction in direct bioelectrocatalytic system. With altering inter-enzyme relative orientation by fusion of GBP at various ends of enzymatic structure of cascadic bienzyme, intermediate delivery between active sites of coupling enzymes was validated. As two different enzymes are co-immobilized, it was observed that not only intermediate delivery route could be variable depending on relative orientation of coupling enzymes, but also different type of co-bound enzyme could exhibit unfavorable steric effect that obstruct cofactor-surface interface, interfering interfacial DET. Thus, necessity of exquisite design of bienzymatic electrode was emphasized for construction of efficient enzyme cascade-induced direct bioelectrocatalytic system. Furthermore, the viability of SBP-fusion technology for enabling regioselective enzyme binding on predetermined surface has been demonstrated, which is a critical feature for further elaborate inter-enzyme distance modulation and binding distribution in enzyme electrodes. To optimize the selective gold binding characteristics of the fusion enzyme, the GBP tandem repeats were tuned considering genetic modification-dependent biocatalytic and gold-binding activity changes. Along with qualitative evidence for the fusion enzyme's selective binding properties toward gold versus the SiO2 surface, position-specific binding of GBP-fused enzyme on micro/nano-patterned Au/SiO2 surfaces was demonstrated, indicating that SBP fusion technology is promising for highly selective surface-templated assembly of enzymes.
Taken together, this work showed the efficacy of SBP fusion technology as a generic tool for developing cascade-induced direct bioelectrocatalytic system. The genetic fusion of GBP to the enzymatic structure enables surface-oriented immobilization of enzymes as well as inter-enzyme orientation when cascadic multienzymes are incorporated on single electrode. Additionally, precise arrangement of the enzyme on the electrode could be accomplished as a micro- and nanometer-scale predetermined surface is introduced as carrier.Docto
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