65 research outputs found
Importance of Glutamate Dehydrogenase (GDH) in Clostridium difficile Colonization In Vivo
No full textCitation: Girinathan, B. P., Braun, S., Sirigireddy, A. R., Lopez, J. E., & Govind, R. (2016). Importance of Glutamate Dehydrogenase (GDH) in Clostridium difficile Colonization In Vivo. Plos One, 11(7), 18. doi:10.1371/journal.pone.0160107Clostridium difficile is the principal cause of antibiotic-associated diarrhea. Major metabolic requirements for colonization and expansion of C. difficile after microbiota disturbance have not been fully determined. In this study, we show that glutamate utilization is important for C. difficile to establish itself in the animal gut. When the gluD gene, which codes for glutamate dehydrogenase (GDH), was disrupted, the mutant C. difficile was unable to colonize and cause disease in a hamster model. Further, from the complementation experiment it appears that extracellular GDH may be playing a role in promoting C. difficile colonization and disease progression. Quantification of free amino acids in the hamster gut during C. difficile infection showed that glutamate is among preferred amino acids utilized by C. difficile during its expansion. This study provides evidence of the importance of glutamate metabolism for C. difficile pathogenesis
Bacteriophage mediated toxin gene regulation in Clostridium difficle
No full textEmbargo status: Restricted to TTU community only. To view, login with your eRaider (top right). Others may request the author grant access exception by clicking on the PDF link to the left
Two-fluid Physical Modeling of Superconducting Resonators in the ARTEMIS Framework
No full textInput files, data files and scripts to replicate results in "Two-fluid Physical Modeling of Superconducting Resonators in the ARTEMIS Framework" (Jambunathan et el.)
Please direct any questions to the corresponding author, Revathi Jambunathan (rjambunathan [at] lbl.gov)
Artemis simulations were run using the development branch of artemis https://github.com/ECP-WarpX/artemis
Some simulations in this paper were performed with different commit hashes of artemis and amrex, however, the input files should still work with the most recent development branch of artemis.
In the attached tar file, the input files, data, and scripts used to analyse simulation results shown in Figures 1, 2, 3, 4, and 6 of the paper are provided. To run the simulations on perlmutter GPUs, the code is compiled with USE_GPU=TRUE and USE_LLG=FALS
Secretion of Clostridium difficile toxins A and B requires the holin-like protein TcdE.
No full textThe pathogenesis of Clostridium difficile, the major cause of antibiotic-associated diarrhea, is mainly associated with the production and activities of two major toxins. In many bacteria, toxins are released into the extracellular environment via the general secretion pathways. C. difficile toxins A and B have no export signature and their secretion is not explainable by cell lysis, suggesting that they might be secreted by an unusual mechanism. The TcdE protein encoded within the C. difficile pathogenicity locus (PaLoc) has predicted structural features similar to those of bacteriophage holin proteins. During many types of phage infection, host lysis is driven by an endolysin that crosses the cytoplasmic membrane through a pore formed by holin oligomerization. We demonstrated that TcdE has a holin-like activity by functionally complementing a λ phage deprived of its holin. Similar to λ holin, TcdE expressed in Escherichia coli and C. difficile formed oligomers in the cytoplamic membrane. A C. difficile tcdE mutant strain grew at the same rate as the wild-type strain, but accumulated a dramatically reduced amount of toxin proteins in the medium. However, the complemented tcdE mutant released the toxins efficiently. There was no difference in the abundance of tcdA and tcdB transcripts or of several cytoplasmic proteins in the mutant and the wild-type strains. In addition, TcdE did not overtly affect membrane integrity of C. difficile in the presence of TcdA/TcdB. Thus, TcdE acts as a holin-like protein to facilitate the release of C. difficile toxins to the extracellular environment, but, unlike the phage holins, does not cause the non-specific release of cytosolic contents. TcdE appears to be the first example of a bacterial protein that releases toxins into the environment by a phage-like system
Disruptive Technology: Do Robots Want Your Job?
No full textKeynote talk with Martin Ford, author of Rise of the Robots. Part of the “Deep Humanities,” One-Day Symposium: FrankenSTEM? Technology Ethics in Silicon Valley, organized by Dr. Revathi Krishnaswamy & Dr. Katherine D. Harris, Department of English and Comparative Literature, San Jose State University.
May 1, 2018, 7pm, The Tech Museum of Innovation, San Jose.https://scholarworks.sjsu.edu/frankenstein200_flyers/1003/thumbnail.jp
Urban Asymmetries Ciudad Juarez, Mexico: Designing A Transferium ...... A point of Exchange
No full textThe MSc. graduation project dealt with understanding the implications of Neo liberal policies on the city of Juarez which lies on the US - Mexico border. In 2009 Ciudad Juarez was rated as “the most violent zone in the world outside of declared war zones” due to high crime rates, femisides, homicides, corruption, drug trafficking and multiple other problems. The city is also presently facing massive exodus and the abandoning of large portions of its housing stock due to the increase in violence and a prevailing low intensity war between the state and the drug cartels. The reasons for this asymmetrical development are multiple and point towards a complex mesh of forces that transgress the scope of the built environment. They encompass entangled dimensions of political economy and socio-economic developments, which eventually affect the built environment. With this background a six month intense research was carried out and a counter proposal group strategy was proposed on a prototype site Riberas Del bravo and eventually an Urban & architectural intervention was designed. Thus as part of my graduation project I designed a collective transport system comprising of three design elements the Transferium hub, the bus stops and the routes on the prototype site. The core design idea dealt with developing a time based concept, that allowed hybridization of the programme and hence catered to both peak and anti-peak hour differently. Firstly a strong east west axis was developed to regulate and accentuate the flow of people along the canal & public promenade proposed as part of the group strategy. These east west axis were flanged by three pavilions serving the Transferium and Community center on the two edges and a multipurpose market space at the center. The central multipurpose market space manifested itself further as Hawking zone courtyard, Mobile Market courtyard and Permanent Market. During the peak hour the Transferium expanded into the central multipurpose space and during the anti-peak hour the community market/activities expanded into the multipurpose space. Thus depending on the flow of vehicles the central multipurpose space grew or condensed in size catering to different activities.Urban AsymmetriesDelft School of DesignArchitectur
FACS analysis of <i>C. difficile</i> cells for membrane permeability through propidium iodide (PI) and SYTO staining.
No full text<p><b>A.</b> The viability standard samples containing the heat killed and actively growing <i>C. difficile</i> cells at 1/100, 50/50 and 100/1 ratio, respectively. <b>B.</b> The <i>tcdE</i> mutant and the parent JIR8094 cells collected from the overnight (16 h) cultures, were subjected to FACS analysis following propidium iodide (PI) and SYTO staining.</p
Testing holin function of TcdE in <i>E. coli</i>.
No full text<p>Lysis curves of lysogenic cultures carrying λcI<sub>857</sub><i>Sam7</i> (<b>A</b>) or λCmrΔ(SR) (<b>B</b>) and plasmids expressing in trans λ<i>S</i>, <i>S<sup>105</sup></i>,TcdEM1, TcdEM25, and TcdEM27, respectively. A lysogenic strain carrying pBR322 was used as negative control. <b>C.</b> Lysis curve of <i>E. coli</i> λcI<sub>857</sub><i>Sam7</i> lysogen carrying plasmids expressing TcdEM1 in pCD463, TcdEMet1, TcdEMet1', TcdEMet25' and TcdEMet27' respectively. <b>D.</b> FACS analysis of <i>E. coli</i> λCmrΔ(SR) lysogens expressing either S<sup>105</sup> or TcdEM1 through propidium idodide (PI) and SYTO9 staining.</p
The holin like TcdE.
No full text<p><b>A.</b> Constructs used for holin expression under the control of the late transcription regulatory (LTR) elements of phage λ. The promoter <i>p<sub>R′</sub></i> and the transcriptional terminator <i>t<sub>R′</sub></i> of the λ LTR region are depicted as a bent arrow and a hairpin structure, respectively. <b>B.</b> TcdE sequence: all possible translational starts are indicated as Met<sub>1</sub>, Met<sub>25</sub> and Met<sub>27</sub>, the potential Shine-Dalgarno sequences are underlined and mutated nucleotides in the specified constructs are highlighted in bold.</p
Quantification of toxins and lactate dehydrogenase (LDH) activity in parent JIR8094 and <i>tcdE</i> mutant strains.
No full text<p>Toxin titers in the culture supernatants (<b>A</b>) and in cytoplasmic proteins (<b>B</b>) were determined by ELISA and the signal from the test was recorded as absorbance at 450 nm. The data shown are the mean +/− standard error of three replicative samples. Student's <i>t</i>-test was used for statistical analysis. (*) <i>P</i>-value is < to 0.05. Dot blots with monoclonal anti-TcdA and anti-TcdB are shown in the lower panels. Purified TcdA and TcdB were used as controls. <b>C.</b> LDH activity in the cytoplasmic fraction was determined using Promega CytoTox 96 and was measured as micro units calculated in comparison with standards provided in the kit. <b>D.</b> Cytoplasmic proteins collected from a 16 hours old cultures of parental and <i>tcdE</i> mutant strains were analyzed in dot blots using monoclonal antibodies against L7/L12 ribosomal subunits and the RNA polymerase beta subunit.</p
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