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Relevant bibliographies by topics / Bacterial translation

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Academic literature on the topic 'Bacterial translation'

Author: Grafiati

Published: 4 June 2021

Last updated: 13 June 2025

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Journal articles on the topic "Bacterial translation"

1

Manuell, A., M. V. Beligni, K. Yamaguchi, and S. P. Mayfield. "Regulation of chloroplast translation: interactions of RNA elements, RNA-binding proteins and the plastid ribosome." Biochemical Society Transactions 32, no. 4 (2004): 601–5. http://dx.doi.org/10.1042/bst0320601.

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Chloroplast gene expression is primarily controlled during the translation of plastid mRNAs into proteins, and genetic studies have identified cis-acting RNA elements and trans-acting protein factors required for chloroplast translation. Biochemical analysis has identified both general and specific mRNA-binding proteins as components of the regulation of chloroplast translation, and has revealed that chloroplast translation is related to bacterial translation but is more complex. Utilizing proteomic and bioinformatic analyses, we have identified the proteins that function in chloroplast translation, including a complete set of chloroplast ribosomal proteins, and homologues of the 70 S initiation, elongation and termination factors. These analyses show that the translational apparatus of chloroplasts is related to that of bacteria, but has adopted a number of eukaryotic mechanisms to facilitate and regulate chloroplast translation.

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Starosta, Agata L., Jürgen Lassak, Kirsten Jung, and Daniel N. Wilson. "The bacterial translation stress response." FEMS Microbiology Reviews 38, no. 6 (2014): 1172–201. http://dx.doi.org/10.1111/1574-6976.12083.

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Zhou, Yuefen, Vlad E. Gregor, Zhongxiang Sun, et al. "Structure-Guided Discovery of Novel Aminoglycoside Mimetics as Antibacterial Translation Inhibitors." Antimicrobial Agents and Chemotherapy 49, no. 12 (2005): 4942–49. http://dx.doi.org/10.1128/aac.49.12.4942-4949.2005.

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ABSTRACT We report the structure-guided discovery, synthesis, and initial characterization of 3,5-diamino-piperidinyl triazines (DAPT), a novel translation inhibitor class that targets bacterial rRNA and exhibits broad-spectrum antibacterial activity. DAPT compounds were designed as structural mimetics of aminoglycoside antibiotics which bind to the bacterial ribosomal decoding site and thereby interfere with translational fidelity. We found that DAPT compounds bind to oligonucleotide models of decoding-site RNA, inhibit translation in vitro, and induce translation misincorporation in vivo, in agreement with a mechanism of action at the ribosomal decoding site. The novel DAPT antibacterials inhibit growth of gram-positive and gram-negative bacteria, including the respiratory pathogen Pseudomonas aeruginosa, and display low toxicity to human cell lines. In a mouse protection model, an advanced DAPT compound demonstrated efficacy against an Escherichia coli infection at a 50% protective dose of 2.4 mg/kg of body weight by single-dose intravenous administration.

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Díaz-Orejas, Ramón, Elizabeth Diago-Navarro, Ana María Hernández Arriaga, et al. "Bacterial toxin-antitoxin systems targeting translation." Journal of Applied Biomedicine 8, no. 4 (2010): 179–88. http://dx.doi.org/10.2478/v10136-009-0021-9.

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Chen, Yu-Xiang, Zhi-yu Xu, Xueliang Ge, et al. "Selective translation by alternative bacterial ribosomes." Proceedings of the National Academy of Sciences 117, no. 32 (2020): 19487–96. http://dx.doi.org/10.1073/pnas.2009607117.

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Alternative ribosome subunit proteins are prevalent in the genomes of diverse bacterial species, but their functional significance is controversial. Attempts to study microbial ribosomal heterogeneity have mostly relied on comparing wild-type strains with mutants in which subunits have been deleted, but this approach does not allow direct comparison of alternate ribosome isoforms isolated from identical cellular contexts. Here, by simultaneously purifying canonical and alternative RpsR ribosomes fromMycobacterium smegmatis, we show that alternative ribosomes have distinct translational features compared with their canonical counterparts. Both alternative and canonical ribosomes actively take part in protein synthesis, although they translate a subset of genes with differential efficiency as measured by ribosome profiling. We also show that alternative ribosomes have a relative defect in initiation complex formation. Furthermore, a strain ofM. smegmatisin which the alternative ribosome protein operon is deleted grows poorly in iron-depleted medium, uncovering a role for alternative ribosomes in iron homeostasis. Our work confirms the distinct and nonredundant contribution of alternative bacterial ribosomes for adaptation to hostile environments.

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Jeong, Yujin, Hyeonseok Shin, Sang Woo Seo, Donghyuk Kim, Suhyung Cho, and Byung-Kwan Cho. "Elucidation of bacterial translation regulatory networks." Current Opinion in Systems Biology 2 (April 2017): 84–90. http://dx.doi.org/10.1016/j.coisb.2017.01.009.

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Salomon, Dor, and Kim Orth. "Lost after translation: post-translational modifications by bacterial type III effectors." Current Opinion in Microbiology 16, no. 2 (2013): 213–20. http://dx.doi.org/10.1016/j.mib.2013.01.013.

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Chatterjee, Surajit, Adrien Chauvier, Shiba S. Dandpat, Irina Artsimovitch, and Nils G. Walter. "A translational riboswitch coordinates nascent transcription–translation coupling." Proceedings of the National Academy of Sciences 118, no. 16 (2021): e2023426118. http://dx.doi.org/10.1073/pnas.2023426118.

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Bacterial messenger RNA (mRNA) synthesis by RNA polymerase (RNAP) and first-round translation by the ribosome are often coupled to regulate gene expression, yet how coupling is established and maintained is ill understood. Here, we develop biochemical and single-molecule fluorescence approaches to probe the dynamics of RNAP–ribosome interactions on an mRNA with a translational preQ1-sensing riboswitch in its 5′ untranslated region. Binding of preQ1 leads to the occlusion of the ribosome binding site (RBS), inhibiting translation initiation. We demonstrate that RNAP poised within the mRNA leader region promotes ribosomal 30S subunit binding, antagonizing preQ1-induced RBS occlusion, and that the RNAP–30S bridging transcription factors NusG and RfaH distinctly enhance 30S recruitment and retention, respectively. We further find that, while 30S–mRNA interaction significantly impedes RNAP in the absence of translation, an actively translating ribosome promotes productive transcription. A model emerges wherein mRNA structure and transcription factors coordinate to dynamically modulate the efficiency of transcription–translation coupling.

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Dethlefsen, Les, and Thomas M. Schmidt. "Performance of the Translational Apparatus Varies with the Ecological Strategies of Bacteria." Journal of Bacteriology 189, no. 8 (2007): 3237–45. http://dx.doi.org/10.1128/jb.01686-06.

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ABSTRACT Protein synthesis is the predominant activity of growing bacteria; the protein synthesis system accounts for more than one-half the cell's dry mass and consumes most of the cell's energy during rapid growth. Translation has been studied extensively using model organisms, and the translational apparatus is qualitatively similar in terms of structure and function across all known forms of life. However, little is known about variation between organisms in translational performance. Using measurements of macromolecular content in a phylogenetically diverse collection of bacteria with contrasting ecological strategies, we found that the translational power (the rate of protein synthesis normalized to the mass of the protein synthesis system) is three- to fourfold higher among bacteria that respond rapidly to nutrient availability than among bacteria that respond slowly. An analysis of codon use in completely sequenced bacterial genomes confirmed that the selective forces acting on translation vary with the ecological strategy. We propose that differences in translational power result from ecologically based variation among microbes in the relative importance of two competing benefits: reducing the biomass invested in the protein synthesis system and reducing the energetic expense of protein synthesis.

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Ude, Susanne, Jürgen Lassak, Agata L. Starosta, Tobias Kraxenberger, Daniel N. Wilson, and Kirsten Jung. "Translation Elongation Factor EF-P Alleviates Ribosome Stalling at Polyproline Stretches." Science 339, no. 6115 (2012): 82–85. http://dx.doi.org/10.1126/science.1228985.

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Translation elongation factor P (EF-P) is critical for virulence in bacteria. EF-P is present in all bacteria and orthologous to archaeal and eukaryotic initiation factor 5A, yet the biological function has so far remained enigmatic. Here, we demonstrate that EF-P is an elongation factor that enhances translation of polyproline-containing proteins: In the absence of EF-P, ribosomes stall at polyproline stretches, whereas the presence of EF-P alleviates the translational stalling. Moreover, we demonstrate the physiological relevance of EF-P to fine-tune the expression of the polyproline-containing pH receptor CadC to levels necessary for an appropriate stress response. Bacterial, archaeal, and eukaryotic cells have hundreds to thousands of polyproline-containing proteins of diverse function, suggesting that EF-P and a/eIF-5A are critical for copy-number adjustment of multiple pathways across all kingdoms of life.

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Dissertations / Theses on the topic "Bacterial translation"

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Zhang, Jingji. "Accuracy of mRNA Translation in Bacterial Protein Synthesis." Doctoral thesis, Uppsala universitet, Struktur- och molekylärbiologi, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-262901.

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Reading of messenger RNA (mRNA) by aminoacyl-tRNAs (aa-tRNAs) on the ribosomes in the bacterial cell occurs with high accuracy. It follows from the physical chemistry of enzymatic reactions that there must be a trade-off between rate and accuracy of initial tRNA selection in protein synthesis: when the current accuracy, the A-value, approaches its maximal possible value, the d-value, the kinetic efficiency of the reaction approaches zero. We have used an in vitro system for mRNA translation with purified E. coli components to estimate the d- and A-values by which aa-tRNAs discriminate between their cognate and near cognate codons displayed in the ribosomal A site. In the case of tRNALys, we verified the prediction of a linear trade-off between kinetic efficiency of cognate codon reading and the accuracy of codon selection. These experiments have been extended to a larger set of tRNAs, including tRNAPhe, tRNAGlu, tRNAHis, tRNACys, tRNAAsp and tRNATyr, and linear efficiency-accuracy trade-off was observed in all cases. Similar to tRNALys, tRNAPhe discriminated with higher accuracy against a particular mismatch in the second than in the first codon position. Remarkably high d-values were observed for tRNAGlu discrimination against a C-C mismatch in the first codon position (70 000) and for tRNAPhe discrimination against an A-G mismatch in the second codon position (79 000). At the same time, we have found a remarkably small d-value (200) for tRNAGlu misreading G in the middle position of the codon (U-G mismatch). Aminoglycoside antibiotics induce large codon reading errors by tRNAs. We have studied the mechanism of aminoglycoside action and found that the drug stabilized aminoacyl-tRNA in a codon selective in relation to a codon non-selective state. This greatly enhanced the probability of near cognate aminoacyl-tRNAs to successfully transcend the initial selection step of the translating ribosome. We showed that Mg2+ ions, in contrast, favour codon non-selective states and thus induce errors in a principally different way than aminoglycosides. We also designed experiments to estimate the overall accuracy of peptide bond formation with, including initial selection accuracy and proofreading of tRNAs after GTP hydrolysis on EF-Tu. Our experiments have now made it possible to calibrate the accuracy of tRNA selection in the test tube to that in the living cells. We will now also be able to investigate the degree to which the accuracy of tRNA selection has been optimized for maximal fitness.

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Goyal, Akanksha, Riccardo Belardinelli, Cristina Maracci, Pohl Milon, and Marina V. Rodnina. "Directional transition from initiation to elongation in bacterial translation." Oxford University Press, 2015. http://hdl.handle.net/10757/579679.

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The transition of the 30S initiation complex (IC) to the translating 70S ribosome after 50S subunit joining provides an important checkpoint for mRNA selection during translation in bacteria. Here, we study the timing and control of reactions that occur during 70S IC formation by rapid kinetic techniques, using a toolbox of fluorescence-labeled translation components. We present a kinetic model based on global fitting of time courses obtained with eight different reporters at increasing concentrations of 50S subunits. IF1 and IF3 together affect the kinetics of subunit joining, but do not alter the elemental rates of subsequent steps of 70S IC maturation. After 50S subunit joining, IF2-dependent reactions take place independent of the presence of IF1 or IF3. GTP hydrolysis triggers the efficient dissociation of fMet-tRNAfMet from IF2 and promotes the dissociation of IF2 and IF1 from the 70S IC, but does not affect IF3. The presence of non-hydrolyzable GTP analogs shifts the equilibrium towards a stable 70S–mRNA–IF1–IF2–fMet-tRNAfMet complex. Our kinetic analysis reveals the molecular choreography of the late stages in translation initiation.<br>Boehringen Ingelheim Fonds and the G¨ottingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences (to A.G.); Max Planck Society and grants of the Deutsche Forschungsgemeinschaft (to M.V.R.); Peruvian Programa Nacional de Innovaci ´on para la Competitividad y Productividad [382-PNICP-PIBA-2014 (to P.M.)]. Funding for open access charge: Max Planck Society.<br>Revisión por pares

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Maksimova, Elena M., Daria S. Vinogradova, Ilya A. Osterman, et al. "Multifaceted Mechanism of Amicoumacin A Inhibition of Bacterial Translation." Frontiers Media S.A, 2021. http://hdl.handle.net/10757/655822.

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Amicoumacin A (Ami) halts bacterial growth by inhibiting the ribosome during translation. The Ami binding site locates in the vicinity of the E-site codon of mRNA. However, Ami does not clash with mRNA, rather stabilizes it, which is relatively unusual and implies a unique way of translation inhibition. In this work, we performed a kinetic and thermodynamic investigation of Ami influence on the main steps of polypeptide synthesis. We show that Ami reduces the rate of the functional canonical 70S initiation complex (IC) formation by 30-fold. Additionally, our results indicate that Ami promotes the formation of erroneous 30S ICs; however, IF3 prevents them from progressing towards translation initiation. During early elongation steps, Ami does not compromise EF-Tu-dependent A-site binding or peptide bond formation. On the other hand, Ami reduces the rate of peptidyl-tRNA movement from the A to the P site and significantly decreases the amount of the ribosomes capable of polypeptide synthesis. Our data indicate that Ami progressively decreases the activity of translating ribosomes that may appear to be the main inhibitory mechanism of Ami. Indeed, the use of EF-G mutants that confer resistance to Ami (G542V, G581A, or ins544V) leads to a complete restoration of the ribosome functionality. It is possible that the changes in translocation induced by EF-G mutants compensate for the activity loss caused by Ami.<br>Russian Foundation for Basic Research<br>Revisión por pares

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Lovmar, Martin. "Macrolide Antibiotics in Bacterial Protein Synthesis." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-6009.

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Catchpole, Ryan Joseph. "Evolution Of The Unnecessary : Investigating How fMet Became Central In Bacterial Translation Initiation." Thesis, University of Canterbury. School of Biological Sciences, 2015. http://hdl.handle.net/10092/10334.

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All bacteria initiate translation using formylated methionine, yet directly after translation, the formyl-group is removed. This sequence of addition and removal appears futile, yet every sequenced bacterial genome encodes the enzymes for formylation and deformylation, suggesting this process is essential. Puzzlingly, the process is absent from both Archaea and Eukaryotes, and moreover, bacterial mutants lacking both the formylase and deformylase activities are viable, albeit with a diminished growth rate. We created an Escherichia coli strain devoid of formylase and deformylase activity. This strain was then allowed to evolve over 1500 generations whereupon it reached wild-type growth rate, demonstrating that formylation can be completely dispensed with. This raises an additional question: if the formylation cycle is unnecessary, how did it emerge and why has it persisted? Our results show that the formylation-deformylation cycle could have evolved as a toxin-antitoxin pair (TA) with post-segregational killing (PSK) activity. TAs ‘addict’ cells to the plasmids that carry them by inducing PSK. We measured the stability of formylase-deformylase encoding plasmids and their ability to elicit PSK in our evolved E. coli strain. We report several lines of evidence consistent with the formylation-cycle having evolved from a plasmid-borne PSK element: 1) in the absence of deformylation, formyl-methionine on proteins is cytotoxic in bacteria 2) deformylation relieves the cytotoxicity of formyl-methionine, 3) the loss of a plasmid containing formylase and deformylase genes from evolved cells results in cessation of growth – a standard PSK phenotype. In addition, we introduced the E. coli formylase and deformylase genes into yeast and demonstrate that Met-tRNA formylation is not lethal, even in the absence of deformylation. This suggests PSK would be ineffectual in yeast, accounting for the absence of formylation from eukaryotic cytoplasmic translation. We also report the presence of formylase and deformylase genes in the two representative members of the archaeal Methanocopusculum genus. Moreover, we demonstrate that these genes have been acquired by a recent horizontal gene transfer from bacteria. Our results indicate that formylmethionine use in bacteria evolved, not through a direct functional benefit to cells, but through competition between infectious genetic elements.

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Gibbs, Michelle. "Roles of conserved translational GTPases in bacterial ribosome assembly." The Ohio State University, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=osu158645942027837.

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Fleming, Keiran Paul. "Liquid crystal NMR : application to a bacterial adhesin and a eukaryotic translation initiation factor." Thesis, Imperial College London, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.409641.

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Wei, Yulong. "The Roles of Stop Codons and 3’ Flanking Base in Bacterial Translation Termination Efficiency." Thesis, Université d'Ottawa / University of Ottawa, 2016. http://hdl.handle.net/10393/35529.

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Understanding translation efficiency is crucial to pharmaceutical companies that have invested substantial time and effort in engineering bacteria to produce recombinant proteins. While translation initiation and elongation have been studied intensively, much remains obscure in the subprocess of translation termination. We aim to understand how stop codons and the first 3’ flanking (+4) base affect translation termination efficiency. In chapter two, we hypothesized that stop codon usage of UAG and UGA is dependent on the abundance of their respective decoders, RF1 and RF2. We predicted and observed that bacterial species with high relative proportions of RF1 uses UAG more, and vice versa for UGA. In addition, the usage of UGA, not UAG, is always avoided in highly expressed genes. Thus, we argued against the claim made by a recent study that UAG is a minor stop codon in bacteria. The claim is incorrect because UAG does not meet the two criteria of a minor codon: i) it is most avoided in highly expressed genes, and ii) it corresponds to the least abundant decoder. Interestingly, we found that the proportion of RF2 decreases rapidly towards zero in species with high AT contents; this explains why UGA is reassigned to a sense codon in bacterial lineages with high AT content. In chapter three, we examined the role of the first downstream (+4) base Uracil in bacterial translation termination. The +4U is associated with a decrease in stop codon read-through in bacteria and yeast. We hypothesized that i) +4U enhances the termination efficiency of stop signals, and ii) +4U may serve to prevent stop codon misreading by near cognate tRNAs (nc_tRNAs). We predicted that i) +4U is preferred in highly expressed genes (HEGs) than lowly expressed genes (LEGs), and ii) +4U usage increases with the frequency of stop codon nc_tRNAs. We found +4U consistently over-represented in HEGs in contrast to LEGs; however, +4U usage in HEGs decreases in GC-rich species where most stop codons are UGA and UAG. In addition, +4U usage increases significantly with UAA usage in the known highly expressed ribosomal protein genes. These results suggest that +4U is a strong stop signal enhancer for UAA, not UAG or UGA. Furthermore, in HEGs, +4U usage also increases significantly with the abundance of UAA nc_tRNAs, suggesting that +4U increases UAA termination efficiency presumably by reducing misreading of UAA by nc_tRNAs.

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Oberholzer, Anselm Erich. "Structural studies on eukaryotic translation initiation factors and enzyme I of the bacterial phosphotransferase system /." [S.l.] : [s.n.], 2004. http://www.zb.unibe.ch/download/eldiss/04oberholzer_ae.pdf.

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Chow, I.-Ting. "Functional study of ClpB95 and ClpB80, the alternative translation products of the E. coli clpB transcript /." Thesis, Connect to this title online; UW restricted, 2005. http://hdl.handle.net/1773/9842.

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Books on the topic "Bacterial translation"

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A, Hodgson D., Thomas Christopher M, and Society for General Microbiology, eds. Signals, switches, regulons, and cascades: Control of bacterial gene expression. Cambridge University Press, 2002.

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Måns, Ehrenberg, ed. Structural aspects of protein synthesis. 2nd ed. World Scientific, 2013.

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Structural aspects of protein synthesis. World Scientific, 2005.

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(Editor), David A. Hodgson, and C. M. Thomas (Editor), eds. Signals, Switches, Regulons, and Cascades: Control of Bacterial Gene Expression (Society for General Microbiology Symposia). Cambridge University Press, 2002.

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Mijakovic, Ivan, Christophe Grangeasse, and Jörg Stülke, eds. Regulatory Potential of Post-translational Modifications in Bacteria. Frontiers Media SA, 2015. http://dx.doi.org/10.3389/978-2-88919-610-4.

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Mendelson, Marc. Antimicrobial stewardship in a resource-poor setting. Oxford University Press, 2016. http://dx.doi.org/10.1093/med/9780198758792.003.0018.

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Low- and middle-income countries (LMICs) face a high burden of infection and, commonly, colliding epidemics of HIV, malaria, tuberculosis, and other bacterial diseases. The resulting high usage of antimicrobials, inappropriate prescribing, and use of falsified or counterfeit medicines drives antimicrobial resistance. Stewardship programmes need to be developed within the social and cultural norms of the country, and take cognizance of competing health needs, which may prove important barriers. A situational analysis of the country’s resources and challenges with respect to antimicrobial resistance and the need for regional and international collaboration to effect change are important first steps to establishing a programme. Identifying, developing, and unifying stewardship champions aids in the translation of policy into practice. Leadership at the highest level is required in partnership with national government. While resource limitations are a significant barrier to stewardship programmes, concentrating on low-hanging fruit allows LMICs to develop meaningful programmes to combat antimicrobial resistance.

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Li, Yanyan, Sylvie Rebuffat, and Séverine Zirah. Lasso Peptides: Bacterial Strategies to Make and Maintain Bioactive Entangled Scaffolds. Springer, 2014.

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Wilson, Van G. Sumoylation: Molecular Biology and Biochemistry (Horizonbioscience). Taylor & Francis, 2004.

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Structural Aspects Of Protein Synthesis. World Scientific Publishing Company, 2004.

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Liljas, Anders. Structural Aspects Of Protein Synthesis. World Scientific Publishing Company, 2004.

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Book chapters on the topic "Bacterial translation"

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Kurita, Daisuke, Akira Muto, and Hyouta Himeno. "In Vitro Trans-Translation Assays." In Bacterial Regulatory RNA. Humana Press, 2012. http://dx.doi.org/10.1007/978-1-61779-949-5_20.

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Birge, Edward A. "Transcription and Translation: Processes and Basic Regulation." In Bacterial and Bacteriophage Genetics. Springer New York, 1994. http://dx.doi.org/10.1007/978-1-4757-2328-1_4.

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Birge, Edward A. "Transcription and Translation: Processes and Basic Regulation." In Bacterial and Bacteriophage Genetics. Springer New York, 2000. http://dx.doi.org/10.1007/978-1-4757-3258-0_4.

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Schlessinger, David. "Integration of the Ribosome Cycle in Bacterial Cell Physiology." In Genetics of Translation. Springer Berlin Heidelberg, 1988. http://dx.doi.org/10.1007/978-3-642-73139-6_1.

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Oh, Eugene. "Monitoring Bacterial Translation Rates Genome-Wide." In Methods in Molecular Biology. Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1150-0_1.

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Kim, Dong-Myung, and James R. Swartz. "Improved Composition and Energy Supply for Bacterial Batch Systems." In Cell-Free Translation Systems. Springer Berlin Heidelberg, 2002. http://dx.doi.org/10.1007/978-3-642-59379-6_3.

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Hershey, John W. B., Helen S. Cummings, John F. Sands, Vinay Pathak, and Heidemarie Ernst. "The Structure and Expression of DNAs Encoding Initiation Factors from Bacterial and Mammalian Cells." In Genetics of Translation. Springer Berlin Heidelberg, 1988. http://dx.doi.org/10.1007/978-3-642-73139-6_19.

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Ehrenberg, Måns, Vildan Dincbas, David Freistroffer, et al. "Mechanism of Bacterial Translation Termination and Ribosome Recycling." In The Ribosome. ASM Press, 2014. http://dx.doi.org/10.1128/9781555818142.ch44.

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Meydan, Sezen, Dorota Klepacki, Alexander S. Mankin, and Nora Vázquez-Laslop. "Identification of Translation Start Sites in Bacterial Genomes." In Methods in Molecular Biology. Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1150-0_2.

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Kuttler, Céline. "Simulating Bacterial Transcription and Translation in a Stochastic π Calculus." In Transactions on Computational Systems Biology VI. Springer Berlin Heidelberg, 2006. http://dx.doi.org/10.1007/11880646_6.

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Conference papers on the topic "Bacterial translation"

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Sano, Michael B., Rafael V. Davalos, and Paul Gatenholm. "Dielectrophoretic Microweaving: Biofabrication of Aligned Bacterial Nanocellulose for Regenerative Medicine." In ASME 2009 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2009. http://dx.doi.org/10.1115/sbc2009-206787.

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The use of natural and synthetic polymers as scaffolding material for regenerative medicine is far from clinical translation for most tissue applications. This is due primarily to lack of manufacturing control over mechanical properties and 3D architecture which promote cell attachment and proliferation. Cellulose, a natural polymer produced by the majority of plants, can be assembled into nanofibrils by bacteria. The advantage of bacterial cellulose is that it has unique biocompatibility, mechanical integrity, hydroexpansivity, and is stable under a wide range of conditions [1]. It is thus ideal as a scaffolding material on which to seed cells for regenerative medicine applications. The bacteria Acetobacter Xylinum produces nanoscale cellulose ribbons at an average rate of 2μm/min [2].

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Ou, Fang, Julia Robertson, Cushla McGoverin, Simon Swift, and Frédérique Vanholsbeeck. "Near-real time monitoring of bacterial viability using the optrode: a portable fluorimeter." In Translation of Lasers and Biophotonics Technologies and Procedures: Toward the Clinic, edited by Lothar D. Lilge and Carsten M. Philipp. SPIE, 2019. http://dx.doi.org/10.1117/12.2525558.

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Kim, Chang-Beom, Edward Steager, and Min Jun Kim. "Non-Labeled Cell Tracking Velocimetry for Biological Flows." In ASME 2007 International Mechanical Engineering Congress and Exposition. ASMEDC, 2007. http://dx.doi.org/10.1115/imece2007-41200.

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A tracking algorithm was developed to study the velocity field of flagellated bacteria, Serratia marcescens, swarming on a soft agar plate. Average velocities for local regions regularly arranged over the entire flow field were investigated rather than those for individual bacterium. The velocity field of the bacteria typically featured the combination of curvilinear translation and vortex modes. They repeated these patterns for a short time period, forming several groups and dissipating. To further investigate the flow patterns generated by the collective motion of the swarming bacteria, the velocity field on the swarm was spatially correlated.

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Steager, Edward, M. Selman Sakar, Dalhyung Kim, Vijay Kumar, George J. Pappas, and Min Jun Kim. "Hybrid Control and Transport Using Bacteria-Driven Microbiorobots." In ASME 2009 International Mechanical Engineering Congress and Exposition. ASMEDC, 2009. http://dx.doi.org/10.1115/imece2009-11327.

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We are examining techniques for manipulation of microfabricated elements using arrays of bacteria as microactuators. Flagellated Serratia marcescens bacteria are attached to microstructures using a blotting technique that creates a bacterial monolayer carpet. These bacterial carpets naturally self-coordinate to propel the microstructures. We refer to these constructs as microbiorobots (MBR). Generally, the motion pattern of the MBRs is largely rotational in nature, and the center of mass deviates no more than several hundred microns from its original position. However, the angular velocity and orientation of the MBRs may be controlled using ultraviolet light stimulus, and the translational position may be adjusted using electrokinetic stimulus. Here, we demonstrate precision positional adjustment of a microbiorobotic transporter that is used to engage and transport cube-shaped particles 10 μm on each side.

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"Predicting elongation efficiency of gene translation for annotation of bacterial genomes: a case study for biosynthetic gene clusters of nonribosomal peptides." In Bioinformatics of Genome Regulation and Structure/ Systems Biology. institute of cytology and genetics siberian branch of the russian academy of science, Novosibirsk State University, 2020. http://dx.doi.org/10.18699/bgrs/sb-2020-020.

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Fu, Henry C., Vivek Shenoy, Thomas Powers, and Charles W. Wolgemuth. "Swimming Microorganisms in Complex Media." In ASME 2010 First Global Congress on NanoEngineering for Medicine and Biology. ASMEDC, 2010. http://dx.doi.org/10.1115/nemb2010-13155.

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Microogranisms such as sperm and E. coli swim in a low-Reynolds number environment. In the zero-Reynolds-number Stokes limit, their kinematics are completely controlled by viscous forces and inertia is unimportant. This swimming environment is quite different from our usual (high Reynolds number) intuition about swimming. For example, due to the kinematic reversibility of Stokes flow, motions that look the same going forward and backward in time, such as the linear motion of an oar-like appendage, do not lead to net translation. Thus microorganisms in Newtonian fluids use swimming motions with a clear time-direction, such as the traveling waves or rotating corkscrew shapes of eukaryotic and bacterial flagella, respectively. While there has been much investigation of microorganism swimming in Newtonian fluids such as water, much less attention has been paid to swimming in complex materials, such as non-Newtonian, viscoelastic fluids and gels. However, in many cases microorganisms do in fact swim through such complex materials in their natural biological environments. For example, mammalian sperm swim through viscoelastic cervical mucus in the female reproductive tract, while H. pylori swim through the gastric mucus lining the inside of the stomach. In this talk I discuss two ways in which swimming through complex media differs from swimming in Newtonian fluids. First, the forces exerted by a viscoelastic medium are different from those exerted by a Newtonian fluid. I address how this affects swimming shapes and speeds of flexible swimmers such as sperm. Second, I discuss swimming through solids such as gels, where compressibility and heterogeneity become important.

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Heflin, James R., Kelly McCutcheon, Aloka Bandara, et al. "Optical Fiber Long-Period Grating with Nanoscale Coatings for Rapid Identification of Bacterial Infections." In Clinical and Translational Biophotonics. OSA, 2018. http://dx.doi.org/10.1364/translational.2018.cth4b.6.

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Ehrlich, K., S. Duncan, T. R. Choudhary, et al. "Time-resolved single photon spectroscopy for optical fibre-based sensing of bacterial infections in the distal lung." In Clinical and Translational Biophotonics. OSA, 2020. http://dx.doi.org/10.1364/translational.2020.ttu2b.3.

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9

Wong, Denise, Edward B. Steager, and Vijay Kumar. "Near-Wall Dynamics and Photoresponse of Swimming Microbiorobots." In ASME 2012 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2012. http://dx.doi.org/10.1115/detc2012-71033.

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At the microscale, the ability to precisely move objects on the scale of microns is a challenge. One method is to use microbiorobots (MBRs), constructed of a neutrally-buoyant microstructure powered by a monolayer of swarmer flagellated bacteria adhered to the surface. The bacteria swim to propel the microstructure in a fluidic environment in the absence of external forces. The trajectory is a combination of translation and rotation, with the rotation generally observed to be clockwise when viewed from above. In order to create a dynamic model of the inherent motion of MBRs, we use UV light to immobilize the bacteria on different regions of an MBR and characterize the resultant motion. We show that the bacteria on the edge of the structure have different force contributions than those in the center of the microstructure where the flagella cannot interact with the surface under that MBR. This is a step towards improved accuracy in the control of MBRs when external forces are applied for manipulation.

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Arora, Rahul D. "Definition, etiopathogenesis, management and role of flouroquinolone prophylaxis in prevention of spontaneous bacterial peritonitis complicating malignant ascites." In 16th Annual International Conference RGCON. Thieme Medical and Scientific Publishers Private Ltd., 2016. http://dx.doi.org/10.1055/s-0039-1685345.

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Background: Malignancy related ascites encompasses multiple etiologies which include peritoneal carcinomatosis, hepatic synthetic dysfunction due to parenchymal involvement by the tumour, transcoeloemic metastasis and chylous ascites due to lymphatic obstruction. Primary Cancer type, liver metastasis and serum albumin have been listed as independent prognostic markers in malignant ascites. Spontaneous Bacterial Peritonitis is usually seen as a complication of decompensated chronic liver disease due to translocation of bacteria or haematogenous dissemination from a distant focus of infection. The combination of a positive peritoneal fluid culture and an ascitic fluid neutrophil count >250 cells/mm3 and no evidence of intra-abdominal source of infection; or 2) culture negative neutrocytic ascites: the combination of negative peritoneal fluid bacterial culture and neutrophil count >500 cells/mm3, without antibiotics within 7 days with no obvious source of infection are used to define spontaneous bacterialperitonitis. Ciprofloxacin prophylaxis has been proposed as a prophylaxis to reduce the incidence and prevent the recurrence of spontaneous bacterial peritonitis. Materials and Methods: A web search of indexed literature was carried out articles containing information on spontaneous bacterial peritonitis in the setting of malignancy or malignancy related ascites or malignant ascites. Articles that carried relevant information about etiopathogenesis, management and translational research in the context of malignant ascites were also included. Results: A total of 32 articles were analysed and about half of them included in the discussion to answer the research question. Discussion: Inflammatory cytokines released by tumor and immune cells compromise the mesothelial cell layer that lines the peritoneal cavity, exposing the underlying extracellular matrix to which cancer cells readily attach leading to formation of spheroids which imparts resistance to anoikis, apoptosis and chemotherapeutics leading to efficient feed forward progressive cycle of seeding and growth of peritoneal metastasis. Intraperitoneal metastasis can cause peritoneal dysfunction, adhesions and malignant ascites. Epithelial mesenchymal transistion and myofibroblastic transformation occur in the mesothelial cells in response to pathological stimuli. Vascular endothelial growth factor is an important mitogen for endothelial cells and plays an important role in increasing capillary vascular permeability. In preclinical studies systemic administration of VEGF Trap which acts as a decoy receptor for VEGF has shown to decrease the formation of ascites fluid and prevent tumour dissemination. Epithelial ovarian cancer cells have developed various mechanisms to evade immune surveillance like development of surface microvesicles which contain CD 95 ligand leading to apoptosis of immune cells. Higher levels of osteoproteogerin, IL 10 and leptin in the ascitic fluid have been associated with a poor prognosis in malignant ascites. Tethered bowel sign and presence of fluid in the omental bursa on CT have been shown to distinguish between malignant ascites and Cirrhotic ascites with accuracy. Immunological approaches to management of malignant ascites include use of intraperitoneal triamcinolone, interferon, long acting synthetic corticosteroids and the trifoliate antibody catumaxomab. VEGF Inhihibitors like octreotide and long acting depot preparations of lanreotide have also been shown to be feasible therapeutic options. Anti androgenic agents and PARP inhibitors have also been proposed as management options. Spontaneous bacterial peritonitis in the setting of malignancy in the absence of hepatic dysfunction has been reported to have a poorer prognosis than SBP in the setting of decompensated liver disease. Monomicrobial and polymicrobial bacterascites have been proposed in the absence of an elevated neutrophil ascitic fluid count that does not meet the diagnostic criteria. Extensive liver metastasis where the diseased liver can be expected to behave like a cirrhotic liver and gastrointestinal bleeding (on the basis of an isolated case report) have been considered as risk factors for the development of SBP in malignant ascites. In a case series of 8 patients with malignancy related ascites Patients with total ascitic fluid concentration of less than 1 gm per litre were found to be at risk for Spontaneous bacterial peritonitis and warrant flouroquinolone prophylaxis. Conclusion: Spontaneous Bacterial Peritonitis complicating malignant ascites is questionable entity. Good quality Audits and Randomised control trials are warranted to in this domain to enable the definition of incidence, antecedent complications, management and prophylaxis to ensure applicability of translational research to the clinical domain.

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Reports on the topic "Bacterial translation"

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Eckdahl, Anthony J., Rachel Neal, A. Malcolm Campbell, and Todd T. Eckdahl. rClone: A Synthetic Biology Tool That Enables the Research of Bacterial Translation. Journal of Young Investigators, 2017. http://dx.doi.org/10.22186/jyi.32.3.7-12-19.

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