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Search Results: 1 - 10 of 462054 matches for " Dionysios A. Antonopoulos "
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Metagenomic Profiling of a Microbial Assemblage Associated with the California Mussel: A Node in Networks of Carbon and Nitrogen Cycling
Catherine A. Pfister,Folker Meyer,Dionysios A. Antonopoulos
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0010518
Abstract: Mussels are conspicuous and often abundant members of rocky shores and may constitute an important site for the nitrogen cycle due to their feeding and excretion activities. We used shotgun metagenomics of the microbial community associated with the surface of mussels (Mytilus californianus) on Tatoosh Island in Washington state to test whether there is a nitrogen-based microbial assemblage associated with mussels. Analyses of both tidepool mussels and those on emergent benches revealed a diverse community of Bacteria and Archaea with approximately 31 million bp from 6 mussels in each habitat. Using MG-RAST, between 22.5–25.6% were identifiable using the SEED non-redundant database for proteins. Of those fragments that were identifiable through MG-RAST, the composition was dominated by Cyanobacteria and Alpha- and Gamma-proteobacteria. Microbial composition was highly similar between the tidepool and emergent bench mussels, suggesting similar functions across these different microhabitats. One percent of the proteins identified in each sample were related to nitrogen cycling. When normalized to protein discovery rate, the high diversity and abundance of enzymes related to the nitrogen cycle in mussel-associated microbes is as great or greater than that described for other marine metagenomes. In some instances, the nitrogen-utilizing profile of this assemblage was more concordant with soil metagenomes in the Midwestern U.S. than for open ocean system. Carbon fixation and Calvin cycle enzymes further represented 0.65 and 1.26% of all proteins and their abundance was comparable to a number of open ocean marine metagenomes. In sum, the diversity and abundance of nitrogen and carbon cycle related enzymes in the microbes occupying the shells of Mytilus californianus suggest these mussels provide a node for microbial populations and thus biogeochemical processes.
BMP signaling components in embryonic transcriptomes of the hover fly Episyrphus balteatus (Syrphidae)
Steffen Lemke, Dionysios A Antonopoulos, Folker Meyer, Marc H Domanus, Urs Schmidt-Ott
BMC Genomics , 2011, DOI: 10.1186/1471-2164-12-278
Abstract: To search for BMP signaling components in E. balteatus, we generated and analyzed transcriptomes of freshly laid eggs (0-30 minutes) and late blastoderm to early germband extension stages (3-6 hours) using Roche/454 sequencing. We identified putative E. balteatus orthologues of 43% of all annotated D. melanogaster genes, including the genes of all BMP ligands and other BMP signaling components.The diversification of several BMP signaling components in the dipteran linage of D. melanogaster preceded the origin of the amnioserosa.[Transcriptome sequence data from this study have been deposited at the NCBI Sequence Read Archive (SRP005289); individually assembled sequences have been deposited at GenBank (JN006969-JN006986).]Across animals, the Bone Morphogenetic Protein (BMP) signaling pathway plays a major role in specifying the dorsoventral (DV) axis [1,2]. However, the components of the BMP pathway have been repeatedly modified through lineage specific gene duplications and gene losses [3,4]. Whether some of these genetic changes correlate with the origin of species-specific morphological traits that develop under the control of the BMP pathway is unknown. Flies (Diptera) provide an excellent opportunity to address this question firstly because the BMP signaling pathway of Drosophila melanogaster has been studied in great detail [5,6], and secondly because tissue specification presumably under the control of BMP signaling along the DV axis of dipterans has undergone significant change [7]. In D. melanogaster, dorsal blastoderm differentiates into a single extraembryonic epithelium, called amnioserosa, which closes the developing embryo dorsally [8]. This tissue is found in higher cyclorrhaphan flies (Schizophora), but in other dipterans, dorsal blastoderm gives rise to distinct serosal and amniotic epithelia [9-11]. Serosa and amnion develop from an amnioserosal fold at the margins of the gastrulating embryo. The outer cell layer of this fold becomes the serosa, whi
Regional Mucosa-Associated Microbiota Determine Physiological Expression of TLR2 and TLR4 in Murine Colon
Yunwei Wang,Suzanne Devkota,Mark W. Musch,Bana Jabri,Cathryn Nagler,Dionysios A. Antonopoulos,Alexander Chervonsky,Eugene B. Chang
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0013607
Abstract: Many colonic mucosal genes that are highly regulated by microbial signals are differentially expressed along the rostral-caudal axis. This would suggest that differences in regional microbiota exist, particularly mucosa-associated microbes that are less likely to be transient. We therefore explored this possibility by examining the bacterial populations associated with the normal proximal and distal colonic mucosa in context of host Toll-like receptors (TLR) expression in C57BL/6J mice housed in specific pathogen-free (SPF) and germ-free (GF) environments. 16S rRNA gene-based terminal restriction fragment length polymorphism (T-RFLP) and clone library analysis revealed significant differences in the community structure and diversity of the mucosa-associated microbiota located in the distal colon compared to proximal colon and stool, the latter two clustering closely. Differential expression of colonic TLR2 and TLR4 along the proximal-distal axis was also found in SPF mice, but not in GF mice, suggesting that enteric microbes are essential in maintaining the regional expression of these TLRs. TLR2 is more highly expressed in proximal colon and decreases in a gradient to distal while TLR4 expression is highest in distal colon and a gradient of decreased expression to proximal colon is observed. After transfaunation in GF mice, both regional colonization of mucosa-associated microbes and expression of TLRs in the mouse colon were reestablished. In addition, exposure of the distal colon to cecal (proximal) microbiota induced TLR2 expression. These results demonstrate that regional colonic mucosa-associated microbiota determine the region-specific expression of TLR2 and TLR4. Conversely, region-specific host assembly rules are essential in determining the structure and function of mucosa-associated microbial populations. We believe this type of host-microbial mutualism is pivotal to the maintenance of intestinal and immune homeostasis.
Diversity and Strain Specificity of Plant Cell Wall Degrading Enzymes Revealed by the Draft Genome of Ruminococcus flavefaciens FD-1
Margret E. Berg Miller, Dionysios A. Antonopoulos, Marco T. Rincon, Mark Band, Albert Bari, Tatsiana Akraiko, Alvaro Hernandez, Jyothi Thimmapuram, Bernard Henrissat, Pedro M. Coutinho, Ilya Borovok, Sadanari Jindou, Raphael Lamed, Harry J. Flint, Edward A. Bayer, Bryan A. White
PLOS ONE , 2009, DOI: 10.1371/journal.pone.0006650
Abstract: Background Ruminococcus flavefaciens is a predominant cellulolytic rumen bacterium, which forms a multi-enzyme cellulosome complex that could play an integral role in the ability of this bacterium to degrade plant cell wall polysaccharides. Identifying the major enzyme types involved in plant cell wall degradation is essential for gaining a better understanding of the cellulolytic capabilities of this organism as well as highlighting potential enzymes for application in improvement of livestock nutrition and for conversion of cellulosic biomass to liquid fuels. Methodology/Principal Findings The R. flavefaciens FD-1 genome was sequenced to 29x-coverage, based on pulsed-field gel electrophoresis estimates (4.4 Mb), and assembled into 119 contigs providing 4,576,399 bp of unique sequence. As much as 87.1% of the genome encodes ORFs, tRNA, rRNAs, or repeats. The GC content was calculated at 45%. A total of 4,339 ORFs was detected with an average gene length of 918 bp. The cellulosome model for R. flavefaciens was further refined by sequence analysis, with at least 225 dockerin-containing ORFs, including previously characterized cohesin-containing scaffoldin molecules. These dockerin-containing ORFs encode a variety of catalytic modules including glycoside hydrolases (GHs), polysaccharide lyases, and carbohydrate esterases. Additionally, 56 ORFs encode proteins that contain carbohydrate-binding modules (CBMs). Functional microarray analysis of the genome revealed that 56 of the cellulosome-associated ORFs were up-regulated, 14 were down-regulated, 135 were unaffected, when R. flavefaciens FD-1 was grown on cellulose versus cellobiose. Three multi-modular xylanases (ORF01222, ORF03896, and ORF01315) exhibited the highest levels of up-regulation. Conclusions/Significance The genomic evidence indicates that R. flavefaciens FD-1 has the largest known number of fiber-degrading enzymes likely to be arranged in a cellulosome architecture. Functional analysis of the genome has revealed that the growth substrate drives expression of enzymes predicted to be involved in carbohydrate metabolism as well as expression and assembly of key cellulosomal enzyme components.
Exercise Prevents Weight Gain and Alters the Gut Microbiota in a Mouse Model of High Fat Diet-Induced Obesity
Christian C. Evans, Kathy J. LePard, Jeff W. Kwak, Mary C. Stancukas, Samantha Laskowski, Joseph Dougherty, Laura Moulton, Adam Glawe, Yunwei Wang, Vanessa Leone, Dionysios A. Antonopoulos, Dan Smith, Eugene B. Chang, Mae J. Ciancio
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0092193
Abstract: Background Diet-induced obesity (DIO) is a significant health concern which has been linked to structural and functional changes in the gut microbiota. Exercise (Ex) is effective in preventing obesity, but whether Ex alters the gut microbiota during development with high fat (HF) feeding is unknown. Objective Determine the effects of voluntary Ex on the gastrointestinal microbiota in LF-fed mice and in HF-DIO. Methods Male C57BL/6 littermates (5 weeks) were distributed equally into 4 groups: low fat (LF) sedentary (Sed) LF/Sed, LF/Ex, HF/Sed and HF/Ex. Mice were individually housed and LF/Ex and HF/Ex cages were equipped with a wheel and odometer to record Ex. Fecal samples were collected at baseline, 6 weeks and 12 weeks and used for bacterial DNA isolation. DNA was subjected both to quantitative PCR using primers specific to the 16S rRNA encoding genes for Bacteroidetes and Firmicutes and to sequencing for lower taxonomic identification using the Illumina MiSeq platform. Data were analyzed using a one or two-way ANOVA or Pearson correlation. Results HF diet resulted in significantly greater body weight and adiposity as well as decreased glucose tolerance that were prevented by voluntary Ex (p<0.05). Visualization of Unifrac distance data with principal coordinates analysis indicated clustering by both diet and Ex at week 12. Sequencing demonstrated Ex-induced changes in the percentage of major bacterial phyla at 12 weeks. A correlation between total Ex distance and the ΔCt Bacteroidetes: ΔCt Firmicutes ratio from qPCR demonstrated a significant inverse correlation (r2 = 0.35, p = 0.043). Conclusion Ex induces a unique shift in the gut microbiota that is different from dietary effects. Microbiota changes may play a role in Ex prevention of HF-DIO.
Standard Colonic Lavage Alters the Natural State of Mucosal-Associated Microbiota in the Human Colon
Laura Harrell, Yunwei Wang, Dionysios Antonopoulos, Vincent Young, Lev Lichtenstein, Yong Huang, Stephen Hanauer, Eugene Chang
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0032545
Abstract: Background & Aims Past studies of the human intestinal microbiota are potentially confounded by the common practice of using bowel-cleansing preparations. We examined if colonic lavage changes the natural state of enteric mucosal-adherent microbes in healthy human subjects. Methods Twelve healthy individuals were divided into three groups; experimental group, control group one, and control group two. Subjects in the experimental group underwent an un-prepped flexible sigmoidoscopy with biopsies. Within two weeks, subjects were given a standard polyethylene glycol-based bowel cleansing preparation followed by a second flexible sigmoidoscopy. Subjects in control group one underwent two un-prepped flexible sigmoidoscopies within one week. Subjects in the second control group underwent an un-prepped flexible sigmoidoscopy followed by a second flexible sigmoidoscopy after a 24-hour clear liquid diet within one week. The mucosa-associated microbial communities from the two procedures in each subject were compared using 16S rRNA gene based terminal restriction fragment length polymorphism (T-RFLP), and library cloning and sequencing. Results Clone library sequencing analysis showed that there were changes in the composition of the mucosa-associated microbiota in subjects after colonic lavage. These changes were not observed in our control groups. Standard bowel preparation altered the diversity of mucosa-associated microbiota. Taxonomic classification did not reveal significant changes at the phylum level, but there were differences observed at the genus level. Conclusion Standard bowel cleansing preparation altered the mucosal-adherent microbiota in all of our subjects, although the degree of change was variable. These findings underscore the importance of considering the confounding effects of bowel preparation when designing experiments exploring the gut microbiota.
Passive Knowledge: How to Make Sense of Kant’s A Priori——Or How Not to Be “Too Busily Subsuming”  [PDF]
Constantin Antonopoulos
Open Journal of Philosophy (OJPP) , 2011, DOI: 10.4236/ojpp.2011.12008
Abstract: Subjectivists, taking the “collapse” of the observation-interpretation contrast much too seriously, are led to imagine that even perceptual knowledge is active. And therefore subject dependent. Turning the tables on this popular trend, I argue that even conceptual knowledge is passive. Kant’s epistemology is conceptual. But if also active, then incoherent. If synthetic a priori truths are to follow upon our mental activity, they were neither true nor, far less, a priori before that activity. “A priori” and “active” are contradictory attributes of knowledge. As, indeed, are “a priori” and “subject-dependent” to begin with. Nothing a priori can be dependent on anything except itself, and least of all on the human subject. Kant does consider the active aspect of thought. The difference is that for him the more active it becomes, the less it is to be trusted. For we are no longer in the province of the Understanding, and its necessary truths, but in the realm of Pure Reason and its dialectical antinomies. Cognition activists who take a liking to Kant have simply mistaken Reason for the Understanding. And Reason is to Kant “the seat of all transcendental illusion”.
An Antidote to Use—From Semantics to Human Rights and Back  [PDF]
Constantin Antonopoulos
Open Journal of Philosophy (OJPP) , 2012, DOI: 10.4236/ojpp.2012.21008
Abstract: I unpack the contents of the motto that “meaning is use” in fivefold fashion and point to the elements it contains, which are open to an ideological exploitation, the main reason for its strong appeal among intellectual circles. I indicate how the sense of it, “where there is use, there is meaning”, has encouraged equalitarian accounts of meaning and truth (In this case, of truth as coherence). I then present and discuss Austin’s distinction between the Sentence and the Statement, which entails the presence of meaning preceding the use, and directing it, and offer a new proof that Sentences are impossible to eliminate in any semantic scheme of things. Austin’s distinction, as explained and defended, refutes the contention that “meaning is (just) use”. I proceed to his doctrine of Locution and Illocution, reflecting the previous, indicating by a series of examples, that illocutionary varieties, which are varieties but not variances (i.e. se- mantic mutations), can never extend beyond the se-mantic scope generically contained in the original, content; that is to say, the Sentence. Those that do, and they are several, violate the rules of sense. I enumerate his vast differences with Wittgenstein, and proceed to defend Austin’s noted conservatism against the novelties endorsed by the former and his disciples. Charging Wittgenstein’s private language attack as circular, I conclude by marking their further contrast on the actual foundations of meaning and truth.
The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes
Florent E. Angly ,Dana Willner,Alejandra Prieto-Davó,Robert A. Edwards,Robert Schmieder,Rebecca Vega-Thurber,Dionysios A. Antonopoulos,Katie Barott,Matthew T. Cottrell,Christelle Desnues,Elizabeth A. Dinsdale,Mike Furlan,Matthew Haynes,Matthew R. Henn,Yongfei Hu,David L. Kirchman,Tracey McDole,John D. McPherson,Folker Meyer,R. Michael Miller,Egbert Mundt,Robert K. Naviaux,Beltran Rodriguez-Mueller,Rick Stevens,Linda Wegley,Lixin Zhang,Baoli Zhu,Forest Rohwer
PLOS Computational Biology , 2009, DOI: 10.1371/journal.pcbi.1000593
Abstract: Metagenomic studies characterize both the composition and diversity of uncultured viral and microbial communities. BLAST-based comparisons have typically been used for such analyses; however, sampling biases, high percentages of unknown sequences, and the use of arbitrary thresholds to find significant similarities can decrease the accuracy and validity of estimates. Here, we present Genome relative Abundance and Average Size (GAAS), a complete software package that provides improved estimates of community composition and average genome length for metagenomes in both textual and graphical formats. GAAS implements a novel methodology to control for sampling bias via length normalization, to adjust for multiple BLAST similarities by similarity weighting, and to select significant similarities using relative alignment lengths. In benchmark tests, the GAAS method was robust to both high percentages of unknown sequences and to variations in metagenomic sequence read lengths. Re-analysis of the Sargasso Sea virome using GAAS indicated that standard methodologies for metagenomic analysis may dramatically underestimate the abundance and importance of organisms with small genomes in environmental systems. Using GAAS, we conducted a meta-analysis of microbial and viral average genome lengths in over 150 metagenomes from four biomes to determine whether genome lengths vary consistently between and within biomes, and between microbial and viral communities from the same environment. Significant differences between biomes and within aquatic sub-biomes (oceans, hypersaline systems, freshwater, and microbialites) suggested that average genome length is a fundamental property of environments driven by factors at the sub-biome level. The behavior of paired viral and microbial metagenomes from the same environment indicated that microbial and viral average genome sizes are independent of each other, but indicative of community responses to stressors and environmental conditions.
Globalization, Regional Productivity, Taste Bias and Internal Spatial Distribution  [PDF]
Dionysios Karavidas
Theoretical Economics Letters (TEL) , 2018, DOI: 10.4236/tel.2018.83043
Abstract: I consider an integrated model consisting of a system of two symmetric regions and the rest of the world that features 1) globalization, 2) regional heterogeneity in productivity, and 3) taste bias over domestic and foreign goods as key determinants of spatial agglomeration. I show that falling external trade barriers favor internal agglomeration. Moreover, a reduction in relative productivity compensates for the trade barriers between the two symmetric regions and the rest of the world; this also favors internal agglomeration of the mobile factor. In addition, I consider two cases of taste bias namely ethnocentrism and xenocentrism. I find that a shift of consumer preferences in the two symmetric regions with respect to goods that are made in the rest of the world results in internal agglomeration, too. Finally, a shift of consumer preferences in a region with respect to goods that are made in the other region results 1) in internal agglomeration under ethnocentrism, and 2) in internal dispersion under xenocentrism.
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