scholarly journals Microarray Identification of Clostridium difficile Core Components and Divergent Regions Associated with Host Origin

2009 ◽  
Vol 191 (12) ◽  
pp. 3881-3891 ◽  
Author(s):  
Tavan Janvilisri ◽  
Joy Scaria ◽  
Angela D. Thompson ◽  
Ainsley Nicholson ◽  
Brandi M. Limbago ◽  
...  
Keyword(s):  
Clostridium Difficile ◽  
Gene List ◽  
Core Gene ◽  
Comparative Genomic ◽  
Functional Categories ◽  
Genomic Changes ◽  
Core Components ◽  
Host Origin ◽  
High Degree ◽  
Insight Into

ABSTRACT Clostridium difficile is a gram-positive, spore-forming enteric anaerobe which can infect humans and a wide variety of animal species. Recently, the incidence and severity of human C. difficile infection has markedly increased. In this study, we evaluated the genomic content of 73 C. difficile strains isolated from humans, horses, cattle, and pigs by comparative genomic hybridization with microarrays containing coding sequences from C. difficile strains 630 and QCD-32g58. The sequenced genome of C. difficile strain 630 was used as a reference to define a candidate core genome of C. difficile and to explore correlations between host origins and genetic diversity. Approximately 16% of the genes in strain 630 were highly conserved among all strains, representing the core complement of functional genes defining C. difficile. Absent or divergent genes in the tested strains were distributed across the entire C. difficile 630 genome and across all the predicted functional categories. Interestingly, certain genes were conserved among strains from a specific host species, but divergent in isolates with other host origins. This information provides insight into the genomic changes which might contribute to host adaptation. Due to a high degree of divergence among C. difficile strains, a core gene list from this study offers the first step toward the construction of diagnostic arrays for C. difficile.

scholarly journals Patterns of Sequence Conservation in the S-Layer Proteins and Related Sequences in Clostridium difficile

2002 ◽  
Vol 184 (14) ◽  
pp. 3886-3897 ◽  
Author(s):  
Emanuela Calabi ◽  
Neil Fairweather
Keyword(s):  
Clostridium Difficile ◽  
Open Reading Frames ◽  
C Terminus ◽  
Antibiotic Associated Diarrhea ◽  
Processing Site ◽  
Different Strains ◽  
Related Proteins ◽  
High Degree ◽  
Insight Into ◽  
Reading Frames

ABSTRACT Clostridium difficile is the etiological agent of antibiotic-associated diarrhea. Among the factors that may play a role in infection are S-layer proteins (SLPs). Previous work has shown these to consist mainly of two components, resulting from the cleavage of a precursor encoded by the slpA gene. The high-molecular-weight (MW) subunit is related both to amidases from B. subtilis and to at least another 28 gene products in C. difficile strain 630. To gain insight into the functions of the SLPs and related proteins, we have further investigated the pattern of variability both at the slpA locus and at six nearby paralogs. Sequencing of the slpA gene from an S-layer group II strain and a variant S-layer group strain confirms a high degree of divergence in the low-MW SLP, which may result from diversifying selection. A highly conserved motif, however, is found at the C terminus in all low-MW subunits and may be essential for SlpA precursor cleavage. In strain 167, a variant cleavage product is present, suggesting a secondary processing site. Southern blotting analysis shows slpA-like open reading frames (ORFs) 2 to 7 to be conserved in all nine strains tested, with one exception: ORF2, which encodes a 66-kDa polypeptide coextracted at low pH with the main SLPs in strain 630, may be partially deleted in strain 167. Polymorphism within the slpA-ORF7 cluster may be more pronounced in the region proximal to the slpA gene. Unexpectedly, a high-MW subunit probe cross hybridizes to sequences outside the slpA locus, which appear to vary in number in different strains.

scholarly journals The Distribution of Several Genomic Virulence Determinants Does Not Corroborate the Established Serotyping Classification of Bacillus thuringiensis

2021 ◽  
Vol 22 (5) ◽  
pp. 2244
Author(s):  
Anton E. Shikov ◽  
Yury V. Malovichko ◽  
Arseniy A. Lobov ◽  
Maria E. Belousova ◽  
Anton A. Nizhnikov ◽  
...  
Keyword(s):  
Bacillus Thuringiensis ◽  
Protein Identification ◽  
Core Gene ◽  
Comparative Genomic ◽  
Virulence Determinants ◽  
Strain Characterization ◽  
Proteomic Approach ◽  
Liquid Chromatography Tandem Mass ◽  
Identity Threshold ◽  
Genome Assemblies

Bacillus thuringiensis, commonly referred to as Bt, is an object of the lasting interest of microbiologists due to its highly effective insecticidal properties, which make Bt a prominent source of biologicals. To categorize the exuberance of Bt strains discovered, serotyping assays are utilized in which flagellin serves as a primary seroreactive molecule. Despite its convenience, this approach is not indicative of Bt strains’ phenotypes, neither it reflects actual phylogenetic relationships within the species. In this respect, comparative genomic and proteomic techniques appear more informative, but their use in Bt strain classification remains limited. In the present work, we used a bottom-up proteomic approach based on fluorescent two-dimensional difference gel electrophoresis (2D-DIGE) coupled with liquid chromatography/tandem mass spectrometry(LC-MS/MS) protein identification to assess which stage of Bt culture, vegetative or spore, would be more informative for strain characterization. To this end, the proteomic differences for the israelensis-attributed strains were assessed to compare sporulating cultures of the virulent derivative to the avirulent one as well as to the vegetative stage virulent bacteria. Using the same approach, virulent spores of the israelensis strain were also compared to the spores of strains belonging to two other major Bt serovars, namely darmstadiensis and thuringiensis. The identified proteins were analyzed regarding the presence of the respective genes in the 104 Bt genome assemblies available at open access with serovar attributions specified. Of 21 proteins identified, 15 were found to be encoded in all the present assemblies at 67% identity threshold, including several virulence factors. Notable, individual phylogenies of these core genes conferred neither the serotyping nor the flagellin-based phylogeny but corroborated the reconstruction based on phylogenomics approaches in terms of tree topology similarity. In its turn, the distribution of accessory protein genes was not confined to the existing serovars. The obtained results indicate that neither gene presence nor the core gene sequence may serve as distinctive bases for the serovar attribution, undermining the notion that the serotyping system reflects strains’ phenotypic or genetic similarity. We also provide a set of loci, which fit in with the phylogenomics data plausibly and thus may serve for draft phylogeny estimation of the novel strains.

scholarly journals Structural insight into Wnt signaling inhibition by Clostridium difficile toxin B

FEBS Journal ◽  
2018 ◽  
Vol 286 (5) ◽  
pp. 874-881 ◽  
Author(s):  
Peng Chen ◽  
Liang Tao ◽  
Zheng Liu ◽  
Min Dong ◽  
Rongsheng Jin
Keyword(s):  
Clostridium Difficile ◽  
Wnt Signaling ◽  
Toxin B ◽  
Clostridium Difficile Toxin ◽  
Structural Insight ◽  
Clostridium Difficile Toxin B ◽  
Insight Into

Oil Companies and Climate Change: Inconsistencies between Strategy Formulation and Implementation?

2007 ◽  
Vol 7 (3) ◽  
pp. 42-62 ◽  
Author(s):  
Ingvild Andreassen Sæverud ◽  
Jon Birger Skjærseth
Keyword(s):  
Climate Change ◽  
Strategy Formulation ◽  
Oil Companies ◽  
Corporate Strategies ◽  
International Climate ◽  
Framework Conditions ◽  
High Degree ◽  
The Relationship ◽  
Level 2 ◽  
Insight Into

This article examines major oil companies in terms of climate strategies and their implementation. More specifıcally, it takes a critical look at Shell, BP, and ExxonMobil, and the relationship between rhetoric and action regarding investments in climate-friendly activities. Empirical evidence indicates a generally high degree of consistency between what these companies say and what they do, but interesting differences are also found: ExxonMobil has done somewhat more than its climate strategy formulations would suggest; Shell has done somewhat less; whereas BP's activities are mainly in line with its statements. Factors at three levels contribute to explaining these differences: (1) the company level, 2) the political framework conditions in the various regions where the companies operate, 3) international climate cooperation. The fındings and explanations, although restricted to the three oil companies with regard to climate change, provide insight into the relationship between corporate strategies and implementation more generally. They offer understanding and analytical categories for assessing how well and why such multinational entities put into practice stated objectives.

scholarly journals Metabolic Diversity within the Globally Abundant Marine Group IIEuryarchaeaOffers Insight into Ecological Patterns

2018 ◽  
Author(s):  
Benjamin J Tully
Keyword(s):  
Organic Matter ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Metabolic Diversity ◽  
Metabolic Potential ◽  
Surface Ocean ◽  
Ecological Patterns ◽  
Reference Genomes ◽  
Insight Into

AbstractDespite their discovery over 25 years ago, the Marine Group IIEuryarchaea(MGII) have remained a difficult group of organisms to study, lacking cultured isolates and genome references. The MGII have been identified in marine samples from around the world and evidence supports a photoheterotrophic lifestyle combining phototrophy via proteorhodopsins with the remineralization of high molecular weight organic matter. Divided between two clades, the MGII have distinct ecological patterns that are not understood based on the limited number of available genomes. Here, I present the comparative genomic analysis of 250 MGII genomes, providing the most detailed view of these mesophilic archaea to-date. This analysis identified 17 distinct subclades including nine subclades that previously lacked reference genomes. The metabolic potential and distribution of the MGII genera revealed distinct roles in the environment, identifying algal-saccharide-degrading coastal subclades, protein-degrading oligotrophic surface ocean subclades, and mesopelagic subclades lacking proteorhodopsins common in all other subclades. This study redefines the MGII and provides an avenue for understanding the role these organisms play in the cycling of organic matter throughout the water column.

scholarly journals Transcriptomic-Based Quantification of the Epithelial-Hybrid-Mesenchymal Spectrum Across Biological Contexts

Biomolecules ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 29
Author(s):  
Susmita Mandal ◽  
Tanishq Tejaswi ◽  
Rohini Janivara ◽  
Syamanthak Srikrishnan ◽  
Pradipti Thakur ◽  
...  
Keyword(s):  
Cancer Cells ◽  
Cancer Metastasis ◽  
Expression Profiles ◽  
Gene List ◽  
Cellular Reprogramming ◽  
Induced Pluripotent ◽  
Patient Prognosis ◽  
High Degree

Epithelial-mesenchymal plasticity (EMP) underlies embryonic development, wound healing, and cancer metastasis and fibrosis. Cancer cells exhibiting EMP often have more aggressive behavior, characterized by drug resistance, and tumor-initiating and immuno-evasive traits. Thus, the EMP status of cancer cells can be a critical indicator of patient prognosis. Here, we compare three distinct transcriptomic-based metrics—each derived using a different gene list and algorithm—that quantify the EMP spectrum. Our results for over 80 cancer-related RNA-seq datasets reveal a high degree of concordance among these metrics in quantifying the extent of EMP. Moreover, each metric, despite being trained on cancer expression profiles, recapitulates the expected changes in EMP scores for non-cancer contexts such as lung fibrosis and cellular reprogramming into induced pluripotent stem cells. Thus, we offer a scoring platform to quantify the extent of EMP in vitro and in vivo for diverse biological applications including cancer.

scholarly journals Vies en Vlaams: de literaire contestatie uit de jaren zestig

1970 ◽  
Vol 64 ◽  
pp. 117-128
Author(s):  
Liesbeth Plateau
Keyword(s):  
Literary History ◽  
Systematic Investigation ◽  
Nineteen Sixties ◽  
Literary Field ◽  
Short Life ◽  
Short Life Span ◽  
Cultural Life ◽  
Key Players ◽  
High Degree ◽  
Insight Into

This contribution presents an introductory analysis of one of the key players of the socalled“stenciled revolution” in Flanders in the nineteen sixties. Before concepts likeprovo distressed the entire societal and cultural life in the Netherlands, certain phenomenain Flanders anticipated to this. From 1963, small stenciled magazines shot up likemushrooms in the Flemish literary field. Due to their aggressive stand against the literaryestablishment, the critics quickly caught sight of them and engaged in an energeticpolemic. Because of their involvement in the literary polemics, the stenciled magazinesshortly determined the literary life to a high degree. However, partly due to their complexhistory and short life span, a systematic investigation of this phenomenon has not yet beenconducted. Nevertheless, the underground- magazines of the “stenciled revolution” are invarious ways relevant to a renewed literary history, as they explore both the literary-criticaland the creative-literary boundaries of the traditional contrast between literature andnon-literature. In this article, I focus on one of the most creative-literary oriented of theseFlemish stenciled magazines, namely daele (1966-1968), to gain an insight into the identityof the “stenciled revolution”.

scholarly journals Complex Minisatellite Rearrangements Generated in the Total or Partial Absence of Rad27/hFEN1 Activity Occur in a Single Generation and Are Rad51 and Rad52 Dependent

2006 ◽  
Vol 26 (17) ◽  
pp. 6675-6689 ◽  
Author(s):  
Judith Lopes ◽  
Cyril Ribeyre ◽  
Alain Nicolas
Keyword(s):  
Pedigree Analysis ◽  
Model System ◽  
Yeast Cells ◽  
Single Generation ◽  
Daughter Cells ◽  
Double Deletion ◽  
Mother And Daughter ◽  
Complex Events ◽  
High Degree ◽  
Insight Into

ABSTRACT Genomes contain tandem repeat blocks that are at risk of expansion or contraction. The mechanisms of destabilization of the human minisatellite CEB1 (arrays of 36- to 43-bp repeats) were investigated in a previously developed model system, in which CEB1-0.6 (14 repeats) and CEB1-1.8 (42 repeats) alleles were inserted into the genome of Saccharomyces cerevisiae. As in human cells, CEB1 is stable in mitotically growing yeast cells but is frequently rearranged in the absence of the Rad27/hFEN1 protein involved in Okazaki fragments maturation. To gain insight into this mode of destabilization, the CEB1-1.8 and CEB1-0.6 human alleles and 47 rearrangements derived from a CEB1-1.8 progenitor in rad27Δ cells were sequenced. A high degree of polymorphism of CEB1 internal repeats was observed, attesting to a large variety of homology-driven rearrangements. Simple deletion, double deletion, and highly complex events were observed. Pedigree analysis showed that all rearrangements, even the most complex, occurred in a single generation and were inherited equally by mother and daughter cells. Finally, the rearrangement frequency was found to increase with array size, and partial complementation of the rad27Δ mutation by hFEN1 demonstrated that the production of novel CEB1 alleles is Rad52 and Rad51 dependent. Instability can be explained by an accumulation of unresolved flap structures during replication, leading to the formation of recombinogenic lesions and faulty repair, best understood by homology-dependent synthesis-strand displacement and annealing.

Molecular interactions shaping the tetraspanin web

2017 ◽  
Vol 45 (3) ◽  
pp. 741-750 ◽  
Author(s):  
Sjoerd J. van Deventer ◽  
Vera-Marie E. Dunlock ◽  
Annemiek B. van Spriel
Keyword(s):  
Molecular Interactions ◽  
Intracellular Signaling ◽  
Spatial Organization ◽  
Complex Mixture ◽  
Point Of View ◽  
Intramolecular Interactions ◽  
Fundamental Understanding ◽  
High Degree ◽  
Partner Proteins ◽  
Insight Into

To facilitate the myriad of different (signaling) processes that take place at the plasma membrane, cells depend on a high degree of membrane protein organization. Important mediators of this organization are tetraspanin proteins. Tetraspanins interact laterally among themselves and with partner proteins to control the spatial organization of membrane proteins in large networks called the tetraspanin web. The molecular interactions underlying the formation of the tetraspanin web were hitherto mainly described based on their resistance to different detergents, a classification which does not necessarily correlate with functionality in the living cell. To look at these interactions from a more physiological point of view, this review discusses tetraspanin interactions based on their function in the tetraspanin web: (1) intramolecular interactions supporting tetraspanin structure, (2) tetraspanin–tetraspanin interactions supporting web formation, (3) tetraspanin–partner interactions adding functional partners to the web and (4) cytosolic tetraspanin interactions regulating intracellular signaling. The recent publication of the first full-length tetraspanin crystal structure sheds new light on both the intra- and intermolecular tetraspanin interactions that shape the tetraspanin web. Furthermore, recent molecular dynamic modeling studies indicate that the binding strength between tetraspanins and between tetraspanins and their partners is the complex sum of both promiscuous and specific interactions. A deeper insight into this complex mixture of interactions is essential to our fundamental understanding of the tetraspanin web and its dynamics which constitute a basic building block of the cell surface.

Sign in / Sign up

Export Citation Format

Share Document