oalib

Publish in OALib Journal

ISSN: 2333-9721

APC: Only $99

Submit

Any time

2019 ( 517 )

2018 ( 833 )

2017 ( 763 )

2016 ( 1118 )

Custom range...

Search Results: 1 - 10 of 465300 matches for " Nicholas A. Pudlo "
All listed articles are free for downloading (OA Articles)
Page 1 /465300
Display every page Item
Recognition and Degradation of Plant Cell Wall Polysaccharides by Two Human Gut Symbionts
Eric C. Martens,Elisabeth C. Lowe,Herbert Chiang,Nicholas A. Pudlo,Meng Wu,Nathan P. McNulty,D. Wade Abbott,Bernard Henrissat,Harry J. Gilbert,David N. Bolam,Jeffrey I. Gordon
PLOS Biology , 2012, DOI: 10.1371/journal.pbio.1001221
Abstract: Symbiotic bacteria inhabiting the human gut have evolved under intense pressure to utilize complex carbohydrates, primarily plant cell wall glycans in our diets. These polysaccharides are not digested by human enzymes, but are processed to absorbable short chain fatty acids by gut bacteria. The Bacteroidetes, one of two dominant bacterial phyla in the adult gut, possess broad glycan-degrading abilities. These species use a series of membrane protein complexes, termed Sus-like systems, for catabolism of many complex carbohydrates. However, the role of these systems in degrading the chemically diverse repertoire of plant cell wall glycans remains unknown. Here we show that two closely related human gut Bacteroides, B. thetaiotaomicron and B. ovatus, are capable of utilizing nearly all of the major plant and host glycans, including rhamnogalacturonan II, a highly complex polymer thought to be recalcitrant to microbial degradation. Transcriptional profiling and gene inactivation experiments revealed the identity and specificity of the polysaccharide utilization loci (PULs) that encode individual Sus-like systems that target various plant polysaccharides. Comparative genomic analysis indicated that B. ovatus possesses several unique PULs that enable degradation of hemicellulosic polysaccharides, a phenotype absent from B. thetaiotaomicron. In contrast, the B. thetaiotaomicron genome has been shaped by increased numbers of PULs involved in metabolism of host mucin O-glycans, a phenotype that is undetectable in B. ovatus. Binding studies of the purified sensor domains of PUL-associated hybrid two-component systems in conjunction with transcriptional analyses demonstrate that complex oligosaccharides provide the regulatory cues that induce PUL activation and that each PUL is highly specific for a defined cell wall polymer. These results provide a view of how these species have diverged into different carbohydrate niches by evolving genes that target unique suites of available polysaccharides, a theme that likely applies to disparate bacteria from the gut and other habitats.
Effects of Diet on Resource Utilization by a Model Human Gut Microbiota Containing Bacteroides cellulosilyticus WH2, a Symbiont with an Extensive Glycobiome
Nathan P. McNulty,Meng Wu,Alison R. Erickson,Chongle Pan,Brian K. Erickson,Eric C. Martens,Nicholas A. Pudlo,Brian D. Muegge,Bernard Henrissat,Robert L. Hettich,Jeffrey I. Gordon
PLOS Biology , 2013, DOI: 10.1371/journal.pbio.1001637
Abstract: The human gut microbiota is an important metabolic organ, yet little is known about how its individual species interact, establish dominant positions, and respond to changes in environmental factors such as diet. In this study, gnotobiotic mice were colonized with an artificial microbiota comprising 12 sequenced human gut bacterial species and fed oscillating diets of disparate composition. Rapid, reproducible, and reversible changes in the structure of this assemblage were observed. Time-series microbial RNA-Seq analyses revealed staggered functional responses to diet shifts throughout the assemblage that were heavily focused on carbohydrate and amino acid metabolism. High-resolution shotgun metaproteomics confirmed many of these responses at a protein level. One member, Bacteroides cellulosilyticus WH2, proved exceptionally fit regardless of diet. Its genome encoded more carbohydrate active enzymes than any previously sequenced member of the Bacteroidetes. Transcriptional profiling indicated that B. cellulosilyticus WH2 is an adaptive forager that tailors its versatile carbohydrate utilization strategy to available dietary polysaccharides, with a strong emphasis on plant-derived xylans abundant in dietary staples like cereal grains. Two highly expressed, diet-specific polysaccharide utilization loci (PULs) in B. cellulosilyticus WH2 were identified, one with characteristics of xylan utilization systems. Introduction of a B. cellulosilyticus WH2 library comprising >90,000 isogenic transposon mutants into gnotobiotic mice, along with the other artificial community members, confirmed that these loci represent critical diet-specific fitness determinants. Carbohydrates that trigger dramatic increases in expression of these two loci and many of the organism's 111 other predicted PULs were identified by RNA-Seq during in vitro growth on 31 distinct carbohydrate substrates, allowing us to better interpret in vivo RNA-Seq and proteomics data. These results offer insight into how gut microbes adapt to dietary perturbations at both a community level and from the perspective of a well-adapted symbiont with exceptional saccharolytic capabilities, and illustrate the value of artificial communities.
Recognition and Degradation of Plant Cell Wall Polysaccharides by Two Human Gut Symbionts
Eric C. Martens equal contributor ,Elisabeth C. Lowe equal contributor,Herbert Chiang,Nicholas A. Pudlo,Meng Wu,Nathan P. McNulty,D. Wade Abbott,Bernard Henrissat,Harry J. Gilbert,David N. Bolam ,Jeffrey I. Gordon
PLOS Biology , 2011, DOI: 10.1371/journal.pbio.1001221
Abstract: Symbiotic bacteria inhabiting the human gut have evolved under intense pressure to utilize complex carbohydrates, primarily plant cell wall glycans in our diets. These polysaccharides are not digested by human enzymes, but are processed to absorbable short chain fatty acids by gut bacteria. The Bacteroidetes, one of two dominant bacterial phyla in the adult gut, possess broad glycan-degrading abilities. These species use a series of membrane protein complexes, termed Sus-like systems, for catabolism of many complex carbohydrates. However, the role of these systems in degrading the chemically diverse repertoire of plant cell wall glycans remains unknown. Here we show that two closely related human gut Bacteroides, B. thetaiotaomicron and B. ovatus, are capable of utilizing nearly all of the major plant and host glycans, including rhamnogalacturonan II, a highly complex polymer thought to be recalcitrant to microbial degradation. Transcriptional profiling and gene inactivation experiments revealed the identity and specificity of the polysaccharide utilization loci (PULs) that encode individual Sus-like systems that target various plant polysaccharides. Comparative genomic analysis indicated that B. ovatus possesses several unique PULs that enable degradation of hemicellulosic polysaccharides, a phenotype absent from B. thetaiotaomicron. In contrast, the B. thetaiotaomicron genome has been shaped by increased numbers of PULs involved in metabolism of host mucin O-glycans, a phenotype that is undetectable in B. ovatus. Binding studies of the purified sensor domains of PUL-associated hybrid two-component systems in conjunction with transcriptional analyses demonstrate that complex oligosaccharides provide the regulatory cues that induce PUL activation and that each PUL is highly specific for a defined cell wall polymer. These results provide a view of how these species have diverged into different carbohydrate niches by evolving genes that target unique suites of available polysaccharides, a theme that likely applies to disparate bacteria from the gut and other habitats.
On the intrinsic sterility of 3D printing
Russell Y Neches,Kaitlin J. Flynn,Luis Zaman,Emily Tung,Nicholas Pudlo
PeerJ , 2015, DOI: 10.7287/peerj.preprints.542v1
Abstract: 3D printers that build objects using extruded thermoplastic are quickly becoming common place tools in laboratories. We demonstrate that with appropriate handling, these devices are capable of producing sterile components from a non-sterile feedstock of thermoplastic without any treatment after fabrication. The fabrication process itself results in sterilization of the material. The resulting 3D printed components are suitable for a wide variety of applications, including experiments with bacteria and cell culture.
Operator norm convergence of spectral clustering on level sets
Bruno Pelletier,Pierre Pudlo
Statistics , 2010,
Abstract: Following Hartigan, a cluster is defined as a connected component of the t-level set of the underlying density, i.e., the set of points for which the density is greater than t. A clustering algorithm which combines a density estimate with spectral clustering techniques is proposed. Our algorithm is composed of two steps. First, a nonparametric density estimate is used to extract the data points for which the estimated density takes a value greater than t. Next, the extracted points are clustered based on the eigenvectors of a graph Laplacian matrix. Under mild assumptions, we prove the almost sure convergence in operator norm of the empirical graph Laplacian operator associated with the algorithm. Furthermore, we give the typical behavior of the representation of the dataset into the feature space, which establishes the strong consistency of our proposed algorithm.
Accurately Measuring Inspection Time with Computers  [PDF]
A. Kym Preiss, Nicholas R. Burns
International Journal of Intelligence Science (IJIS) , 2012, DOI: 10.4236/ijis.2012.24013
Abstract: Accurately measuring inspection time (IT) with computers requires several considerations. They are: 1) Screen redraw period; 2) Synchronous and timely image presentation; 3) Stimulus duration timing; 4) Image scale invariance; 5) Stan dardized presentation format (of which image scale invariance is a part). The first consideration dictates a minimum duration available for measuring IT. The second and third are necessary for accurate stimulus duration. The fourth is necessary to provide scale invariant images, that is, images with the same visual angle at a given viewing distance on any computer. And the fifth ensures that participants everywhere respond to the same task. Our computer program em bodies these elements and we make it freely available to any interested party. Data to establish validity and reliability are presented, and normative data on 2518 participants aged 6 to 92 years are available.
Disinfection of the hospital water supply: a hidden risk to dialysis patients
Nicholas A Hoenich
Critical Care , 2009, DOI: 10.1186/cc8158
Abstract: The article by Bek and colleagues [1] in the previous issue of Critical Care raises an important and frequently unrecognised issue concerned with haemodialysis in a hospital setting. Renal services in hospitals frequently derive their water supply from the hospital water distribution network. Such networks are complex, can contain regions of low flow or stagnation, and frequently incorporate a storage tank to ensure adequate water pressure and availability of supply in times of peak demand. In common with any water distribution network, those in the hospital are subject to biofilm formation. A number of pathogens (for example, Legionella, pseudomonas, and mycobacteria) thrive in the biofilm and may be up to 3,000 times more resistant to bacteriostats added to the public water supply than their free-floating counterparts [2,3].To minimise risk from nosocomial infections, hospitals employ a range of preventive strategies to control the formation of biofilm, including the use of chemical agents such as silver-stabilised hydrogen peroxide [4,5]. Hydrogen peroxide is an oxidising agent, which at concentrations used for disinfection is considered safe to drink, enabling it to be used in 'live' buildings, and is eco-friendly since it breaks down to water and oxygen. Its effectiveness and stability can be enhanced by the addition of trace amounts of silver (silver-stabilized hydrogen peroxide).For dialysis applications, the unsuitability of drinking water has long been recognised and water for use in dialysis units undergoes additional treatment to reduce contaminant levels to below that specified in national or international standards dealing with water for use in dialysis [6]. Although the design of the water treatment plants used in dialysis units is dependent upon the quality of the feed or raw water and the uses that the treated water is put to within the dialysis unit (conventional haemodialysis, reprocessing of dialysers, or the production of infusate for 'on-line' t
Guest Foreword by Lord Phillips KG PC
Nicholas A. Phillips
International Review of Law , 2012, DOI: 10.5339/irl.2012.3
Abstract: The Rt Hon The Lord Phillips of Worth Matravers KG PC, President of the Supreme Court of the United Kingdom of Great Britain and Northern Ireland Ambition and excellence. Those two words epitomize Qatar. Under the leadership of his Highness the Emir, this small State has set out to make an impact on the world that belies its size. Ambitious was the plan to have an international broadcasting station. Ambitious was the plan to build from scratch a Museum of Islamic Art. Ambitious was the bid – the successful bid to host the World Cup in 2022. Ambitious is the bid to stage the Olympic Games in 2020. Qatar not merely has ambitions, it realizes its ambitions. And when it does so it is not enough to say that the result is ‘world class’, for Qatar sets out to be a world leader in whatever it puts its hand to. Excellence is the norm. Al Jazeera has established itself as the broadcasting station of choice for many throughout the world. The Doha Museum of Islamic Art is recognized as being second to none. In addition, the scale and standard of development in Doha itself is setting new standards of excellence in the fields of architecture and civil engineering. Thus when Qatar focuses its energies on education and the law, high achievements are expected. I shall have the honour of helping to achieve those expectations when I succeed Lord Woolf as President of Qatar’s new and impressive Civil and Commercial Court. The College of Law at Qatar University is already achieving excellence in the field of legal education. So, naturally, all expect great things of this new International Review of Law and I am delighted to have been invited to welcome it by this foreword. The range of the first edition is both international and topical. Those countries that have experienced the turbulence of the Arab Spring are settling new constitutions, and other countries are bent on constitutional reform designed to avoid such turbulence. So an erudite article on constitution-making could not come at a better time. For a country about to embark on a $200 billion construction program, an article on identifying and managing risk in international construction projects is tailor made. Cross-border sales and the corporate opportunity doctrine are two further topics that will be of interest to a wide range of commercial lawyers. All these are weighty articles of obvious contemporary relevance. For those who seek a little light relief, Carol Tan’s article on Colonial Cleansing is a delightful and fascinating historical excursion into the efforts of British colonial rule to clean up a holiday
Two New American Aradidae (Hemiptera-Heteroptera)
Nicholas A. Kormilev
Psyche , 1966, DOI: 10.1155/1966/42601
Abstract:
Theory and modeling of particles with DNA-mediated interactions
Nicholas A. Licata
Physics , 2008,
Abstract: In recent years significant attention has been attracted to proposals which utilize DNA for nanotechnological applications. Potential applications of these ideas range from the programmable self-assembly of colloidal crystals, to biosensors and nanoparticle based drug delivery platforms. In Chapter I we introduce the system, which generically consists of colloidal particles functionalized with specially designed DNA markers. The sequence of bases on the DNA markers determines the particle type. Due to the hybridization between complementary single-stranded DNA, specific, type-dependent interactions can be introduced between particles by choosing the appropriate DNA marker sequences. In Chapter II we develop a statistical mechanical description of the aggregation and melting behavior of particles with DNA-mediated interactions. In Chapter III a model is proposed to describe the dynamical departure and diffusion of particles which form reversible key-lock connections. In Chapter IV we propose a method to self-assemble nanoparticle clusters using DNA scaffolds. A natural extension is discussed in Chapter V, the programmable self-assembly of nanoparticle clusters where the desired cluster geometry is encoded using DNA-mediated interactions. In Chapter VI we consider a nanoparticle based drug delivery platform for targeted, cell specific chemotherapy. In Chapter VII we present prospects for future research: the connection between DNA-mediated colloidal crystallization and jamming, and the inverse problem in self-assembly.
Page 1 /465300
Display every page Item


Home
Copyright © 2008-2017 Open Access Library. All rights reserved.