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Journal articles on the topic 'E. coli CcdB'

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Published: 6 September 2023

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1

Wang, Hailong, Xiaoying Bian, Liqiu Xia, Xuezhi Ding, Rolf Müller, Youming Zhang, Jun Fu, and A. Francis Stewart. "Improved seamless mutagenesis by recombineering using ccdB for counterselection." Nucleic Acids Research 42, no. 5 (December 24, 2013): e37-e37. http://dx.doi.org/10.1093/nar/gkt1339.

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Abstract Recombineering, which is the use of homologous recombination for DNA engineering in Escherichia coli, usually uses antibiotic selection to identify the intended recombinant. When combined in a second step with counterselection using a small molecule toxin, seamless products can be obtained. Here, we report the advantages of a genetic strategy using CcdB as the counterselectable agent. Expression of CcdB is toxic to E. coli in the absence of the CcdA antidote so counterselection is initiated by the removal of CcdA expression. CcdB counterselection is robust and does not require titrations or experiment-to-experiment optimization. Because counterselection strategies necessarily differ according to the copy number of the target, we describe two variations. For multi-copy targets, we use two E. coli hosts so that counterselection is exerted by the transformation step that is needed to separate the recombined and unrecombined plasmids. For single copy targets, we put the ccdA gene onto the temperature-sensitive pSC101 Red expression plasmid so that counterselection is exerted by the standard temperature shift to remove the expression plasmid. To reduce unwanted intramolecular recombination, we also combined CcdB counterselection with Redα omission. These options improve the use of counterselection in recombineering with BACs, plasmids and the E. coli chromosome.

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2

Allali, Noureddine, Hassan Afif, Martine Couturier, and Laurence Van Melderen. "The Highly Conserved TldD and TldE Proteins of Escherichia coli Are Involved in Microcin B17 Processing and in CcdA Degradation." Journal of Bacteriology 184, no. 12 (June 15, 2002): 3224–31. http://dx.doi.org/10.1128/jb.184.12.3224-3231.2002.

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ABSTRACT Microcin B17 (MccB17) is a peptide antibiotic produced by Escherichia coli strains carrying the pMccB17 plasmid. MccB17 is synthesized as a precursor containing an amino-terminal leader peptide that is cleaved during maturation. Maturation requires the product of the chromosomal tldE (pmbA) gene. Mature microcin is exported across the cytoplasmic membrane by a dedicated ABC transporter. In sensitive cells, MccB17 targets the essential topoisomerase II DNA gyrase. Independently, tldE as well as tldD mutants were isolated as being resistant to CcdB, another natural poison of gyrase encoded by the ccd poison-antidote system of plasmid F. This led to the idea that TldD and TldE could regulate gyrase function. We present in vivo evidence supporting the hypothesis that TldD and TldE have proteolytic activity. We show that in bacterial mutants devoid of either TldD or TldE activity, the MccB17 precursor accumulates and is not exported. Similarly, in the ccd system, we found that TldD and TldE are involved in CcdA and CcdA41 antidote degradation rather than being involved in the CcdB resistance mechanism. Interestingly, sequence database comparisons revealed that these two proteins have homologues in eubacteria and archaebacteria, suggesting a broader physiological role.

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3

Aguirre-Ramírez, Marisela, Jesús Ramírez-Santos, Laurence Van Melderen, and M. Carmen Gómez-Eichelmann. "Expression of the F plasmid ccd toxin–antitoxin system in Escherichia coli cells under nutritional stress." Canadian Journal of Microbiology 52, no. 1 (January 1, 2006): 24–30. http://dx.doi.org/10.1139/w05-107.

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The ccd system of the F plasmid encodes CcdB, a protein toxic to DNA-gyrase, and CcdA, its antitoxin. The function attributed to this system is to contribute to plasmid stability by killing bacteria that lose the plasmid during cell division. However, the function of ccd in resting bacteria is not clear. Results presented show that ccd transcription increases as bacteria enter stationary phase and that the amount of the Ccd proteins is higher in bacteria under nutritional stress than in growing bacteria. Moreover, an increase in the frequency of Lac+ "adaptive" mutations was observed in stationary-phase bacteria that over-express the Ccd proteins.Key words: ccd system, nutritional stress, adaptive mutation.

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4

Zhang, Qing, Zhenya Yan, Yan Xu, Jian Sun, and Guangdong Shang. "Characterization of Inducible ccdB Gene as a Counterselectable Marker in Escherichia coli Recombineering." Current Microbiology 74, no. 8 (June 1, 2017): 961–64. http://dx.doi.org/10.1007/s00284-017-1273-3.

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5

BAJAJ, Kanika, Ghadiyaram CHAKSHUSMATHI, Kiran BACHHAWAT-SIKDER, Avadhesha SUROLIA, and Raghavan VARADARAJAN. "Thermodynamic characterization of monomeric and dimeric forms of CcdB (controller of cell division or death B protein)." Biochemical Journal 380, no. 2 (June 1, 2004): 409–17. http://dx.doi.org/10.1042/bj20031528.

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The protein CcdB (controller of cell division or death B) is an F-plasmid-encoded toxin that acts as an inhibitor of Escherichia coli DNA gyrase. The stability and aggregation state of CcdB have been characterized as a function of pH and temperature. Size-exclusion chromatography revealed that the protein is a dimer at pH 7.0, but a monomer at pH 4.0. CD analysis and fluorescence spectroscopy showed that the monomer is well folded, and has similar tertiary structure to the dimer. Hence intersubunit interactions are not required for folding of individual subunits. The stability of both forms was characterized by isothermal denaturant unfolding and calorimetry. The free energies of unfolding were found to be 9.2 kcal·mol−1 (1 cal≈4.184 J) and 21 kcal·mol−1 at 298 K for the monomer and dimer respectively. The denaturant concentration at which one-half of the protein molecules are unfolded (Cm) of the dimer is dependent on protein concentration, whereas the Cm of the monomer is independent of protein concentration, as expected. Although thermal unfolding of the protein in aqueous solution is irreversible at neutral pH, it was found that thermal unfolding is reversible in the presence of GdmCl (guanidinium chloride). Differential scanning calorimetry in the presence of low concentrations of GdmCl in combination with isothermal denaturation melts as a function of temperature were used to derive the stability curve for the protein. The value of ΔCp (representing the change in excess heat capacity upon protein denaturation) is 2.8±0.2 kcal·mol−1·K−1 for unfolding of dimeric CcdB, and only has a weak dependence on denaturant concentration.

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6

Hashimi, Saeed M., Melisa K. Wall, Andrew B. Smith, Anthony Maxwell, and Robert G. Birch. "The Phytotoxin Albicidin is a Novel Inhibitor of DNA Gyrase." Antimicrobial Agents and Chemotherapy 51, no. 1 (January 2007): 181–87. http://dx.doi.org/10.1128/aac.00918-06.

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ABSTRACT Xanthomonas albilineans produces a family of polyketide-peptide compounds called albicidins which are highly potent antibiotics and phytotoxins as a result of their inhibition of prokaryotic DNA replication. Here we show that albicidin is a potent inhibitor of the supercoiling activity of bacterial and plant DNA gyrases, with 50% inhibitory concentrations (40 to 50 nM) less than those of most coumarins and quinolones. Albicidin blocks the religation of the cleaved DNA intermediate during the gyrase catalytic sequence and also inhibits the relaxation of supercoiled DNA by gyrase and topoisomerase IV. Unlike the coumarins, albicidin does not inhibit the ATPase activity of gyrase. In contrast to the quinolones, the albicidin concentration required to stabilize the gyrase cleavage complex increases 100-fold in the absence of ATP. The slow peptide poisons microcin B17 and CcdB also access ATP-dependent conformations of gyrase to block religation, but in contrast to albicidin, they do not inhibit supercoiling under routine assay conditions. Some mutations in gyrA, known to confer high-level resistance to quinolones or CcdB, confer low-level resistance or hypersensitivity to albicidin in Escherichia coli. Within the albicidin biosynthesis region in X. albilineans is a gene encoding a pentapeptide repeat protein designated AlbG that binds to E. coli DNA gyrase and that confers a sixfold increase in the level of resistance to albicidin in vitro and in vivo. These results demonstrate that DNA gyrase is the molecular target of albicidin and that X. albilineans encodes a gyrase-interacting protein for self-protection. The novel features of the gyrase-albicidin interaction indicate the potential for the development of new antibacterial drugs.

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7

Loris, Remy, Minh-Hoa Dao-Thi, El Mustapha Bahassi, Laurence Van Melderen, Freddy Poortmans, Robert Liddington, Martine Couturier, and Lode Wyns. "Crystal structure of CcdB, a topoisomerase poison from E. coli 1 1Edited by T. Richmond." Journal of Molecular Biology 285, no. 4 (January 1999): 1667–77. http://dx.doi.org/10.1006/jmbi.1998.2395.

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8

Maki, S., S. Takiguchi, T. Miki, and T. Horiuchi. "Modulation of DNA supercoiling activity of Escherichia coli DNA gyrase by F plasmid proteins. Antagonistic actions of LetA (CcdA) and LetD (CcdB) proteins." Journal of Biological Chemistry 267, no. 17 (June 1992): 12244–51. http://dx.doi.org/10.1016/s0021-9258(19)49831-1.

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9

Baishya, S., A. Das Talukdar, and M. Dutta Choudhury. "Secondary resistance gene ccdB and repA2 facilitates carbapenem resistance in Escherichia coli carrying New Delhi Metallo-beta-lactamase." International Journal of Infectious Diseases 101 (December 2020): 36–37. http://dx.doi.org/10.1016/j.ijid.2020.09.129.

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10

Sundararaj, S. "The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli." Nucleic Acids Research 32, no. 90001 (January 1, 2004): 293D—295. http://dx.doi.org/10.1093/nar/gkh108.

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11

Li, Qi, Bingbing Sun, Jun Chen, Yiwen Zhang, Yu Jiang, and Sheng Yang. "A modified pCas/pTargetF system for CRISPR-Cas9-assisted genome editing in Escherichia coli." Acta Biochimica et Biophysica Sinica 53, no. 5 (March 25, 2021): 620–27. http://dx.doi.org/10.1093/abbs/gmab036.

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Abstract The clustered regularly interspaced short palindromic repeats (CRISPR)-associated nuclease 9 (Cas9)-based genome editing tool pCas/pTargetF system that we established previously has been widely used in Escherichia coli MG1655. However, this system failed to manipulate the genome of E. coli BL21(DE3), owing to the potential higher leaky transcription of the gRNA-pMB1 specific to pTargetF in this strain. In this study, we modified the pCas/pTargetF system by replacing the promoter of gRNA-pMB1 with a tightly regulated promoter PrhaB, changing the replicon of pCas to a nontemperature-sensitive replicon, adding the sacB gene into pCas, and replacing the original N20-specific sequence of pTargetF with ccdB gene. We call this updated system as pEcCas/pEcgRNA. We found that gRNA-pMB1 indeed showed a slightly higher leaky expression in the pCas/pTargetF system compared with pEcCas/pEcgRNA. We also confirmed that genome editing can successfully be performed in BL21(DE3) by pEcCas/pEcgRNA with high efficiency. The application of pEcCas/pEcgRNA was then expanded to the E. coli B strain BL21 StarTM (DE3), K-12 strains MG1655, DH5α, CGMCC3705, Nissle1917, W strain ATCC9637, and also another species of Enterobacteriaceae, Tatumella citrea DSM13699, without any specific modifications. Finally, the plasmid curing process was optimized to shorten the time from $\sim$60 h to $\sim$32 h. The entire protocol (including plasmid construction, editing, electroporation and mutant verification, and plasmid elimination) took only $\sim$5.5 days per round in the pEcCas/pEcgRNA system, whereas it took $\sim$7.5 days in the pCas/pTargetF system. This study established a faster-acting genome editing tool that can be used in a wider range of E. coli strains and will also be useful for other Enterobacteriaceae species.

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12

Cheng, Chunzhen, Rui Yang, Lu Yin, Jianying Zhang, Limin Gao, Rong Lu, Yan Yang, et al. "Characterization of Carotenoid Cleavage Oxygenase Genes in Cerasus humilis and Functional Analysis of ChCCD1." Plants 12, no. 11 (May 26, 2023): 2114. http://dx.doi.org/10.3390/plants12112114.

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Carotenoid cleavage oxygenases (CCOs) are key enzymes that function in degrading carotenoids into a variety of apocarotenoids and some other compounds. In this study, we performed genome-wide identification and characterization analysis of CCO genes in Cerasus humilis. Totally, nine CCO genes could be classified into six subfamilies, including carotenoid cleavage dioxygenase 1 (CCD1), CCD4, CCD7, CCD8, CCD-like and nine-cis-epoxycarotenoid dioxygenase (NCED), were identified. Results of gene expression analysis showed that ChCCOs exhibited diverse expression patterns in different organs and in fruits at different ripening stages. To investigate the roles of ChCCOs in carotenoids degradation, enzyme assays of the ChCCD1 and ChCCD4 were performed in Escerichia coli BL21(DE3) that can accumulate lycopene, β-carotene and zeaxanthin. The prokaryotic expressed ChCCD1 resulted in obvious degradation of lycopene, β-carotene and zeaxanthin, but ChCCD4 did not show similar functions. To further determine the cleaved volatile apocarotenoids of these two proteins, headspace gas chromatography/mass spectrometer analysis was performed. Results showed that ChCCD1 could cleave lycopene at 5, 6 and 5′, 6′ positions to produce 6-methy-5-hepten-2-one and could catalyze β-carotene at 9, 10 and 9′, 10′ positions to generate β-ionone. Our study will be helpful for clarifying the roles of CCO genes especially ChCCD1 in regulating carotenoid degradation and apocarotenoid production in C. humilis.

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13

Hu, Yongmei, Nan Peng, Wenyuan Han, Yuxia Mei, Zhengjun Chen, Xu Feng, Yun Xiang Liang, and Qunxin She. "An archaeal protein evolutionarily conserved in prokaryotes is a zinc-dependent metalloprotease." Bioscience Reports 32, no. 6 (October 15, 2012): 609–18. http://dx.doi.org/10.1042/bsr20120074.

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A putative protease gene (tldD) was previously identified from studying tolerance of letD encoding the CcdB toxin of a toxin–antidote system of the F plasmid in Escherichia coli. While this gene is evolutionarily conserved in archaea and bacteria, the proteolytic activity of encoded proteins remained to be demonstrated experimentally. Here we studied Sso0660, an archaeal TldD homologue encoded in Sulfolobus solfataricus by overexpression of the recombinant protein and characterization of the purified enzyme. We found that the enzyme is active in degrading azocasein and FITC–BSA substrates. Protease inhibitor studies showed that EDTA and o-phenanthroline, two well-known metalloprotease inhibitors, either abolished completely or strongly inhibited the enzyme activity, and flame spectrometric analysis showed that a zinc ion is a cofactor of the protease. Furthermore, the protein forms disulfide bond via the Cys416 residue, yielding protein dimer that is the active form of the enzyme. These results establish for the first time that tidD genes encode zinc-containing proteases, classifying them as a family in the metalloprotease class.

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14

Kaneko, Takao, Tohru Mizushima, Yoshihisa Ohtsuka, Kenji Kurokawa, Kazuhiro Kataoka, Takeyoshi Miki, and Kazuhisa Sekimizu. "Co-induction of DNA relaxation and synthesis of DnaK and GroEL proteins inEscherichia coli by expression of LetD (CcdB) protein, an inhibitor of DNA gyrase encoded by the F factor." Molecular and General Genetics MGG 250, no. 5 (March 1996): 593–600. http://dx.doi.org/10.1007/bf02174447.

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15

Weibel, Pascal, Miriam Ender, Jerzy Madon, Annelies S. Zinkernagel, and Reto A. Schuepbach. "Selection Vector for Direct Cloning of Proof Reading Polymerase Chain Reaction Products Based on the Lethal <i>ccdB</i> Gene in <i>Escherichia coli </i>." Advances in Microbiology 03, no. 01 (2013): 14–20. http://dx.doi.org/10.4236/aim.2013.31002.

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16

Miao, Huimin, Panyong Wang, Yingge Cong, Wenfei Dong, and Li Li. "Preparation of Ciprofloxacin-Based Carbon Dots with High Antibacterial Activity." International Journal of Molecular Sciences 24, no. 7 (April 6, 2023): 6814. http://dx.doi.org/10.3390/ijms24076814.

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Nowadays, bacterial infections are attracting great attention for the research and development of new antimicrobial agents. As one of the quinolones, ciprofloxacin (CI) has a broad-spectrum, strong antibacterial effect. However, the clinical use of ciprofloxacin is limited by drug resistance. Ciprofloxacin carbon dots (CCDs) with enhanced antibacterial activity and copper-doped ciprofloxacin carbon dots (Cu-CCDs) were synthesized by a simple hydrothermal method. The results of structural analysis and antibacterial experiments show that CCDs and Cu-CCDs have effective antibacterial properties by retaining the active groups of ciprofloxacin (-COOH, C-N, and C-F), and Cu-CCDs doped with copper have a better antibacterial effect. In addition, experiments have shown that Cu-CCDs show excellent antibacterial activity against E. coli and S. aureus and have good biocompatibility, which indicates that they have great prospects in clinical applications. Therefore, novel modified copper CCDs with broad-spectrum antibacterial activity, which can be used as antibacterial nanomaterials for potential applications in the field of antibacterial drugs, were synthesized in this study.

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17

Deshmukh, Meenal, Serdar Turkarslan, Donniel Astor, Maria Valkova-Valchanova, and Fevzi Daldal. "The Dithiol:Disulfide Oxidoreductases DsbA and DsbB of Rhodobacter capsulatus Are Not Directly Involved in Cytochrome c Biogenesis, but Their Inactivation Restores the Cytochrome c Biogenesis Defect of CcdA-Null Mutants." Journal of Bacteriology 185, no. 11 (June 1, 2003): 3361–72. http://dx.doi.org/10.1128/jb.185.11.3361-3372.2003.

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ABSTRACT The cytoplasmic membrane protein CcdA and its homologues in other species, such as DsbD of Escherichia coli, are thought to supply the reducing equivalents required for the biogenesis of c-type cytochromes that occurs in the periplasm of gram-negative bacteria. CcdA-null mutants of the facultative phototroph Rhodobacter capsulatus are unable to grow under photosynthetic conditions (Ps−) and do not produce any active cytochrome c oxidase (Nadi−) due to a pleiotropic cytochrome c deficiency. However, under photosynthetic or respiratory growth conditions, these mutants revert frequently to yield Ps+ Nadi+ colonies that produce c-type cytochromes despite the absence of CcdA. Complementation of a CcdA-null mutant for the Ps+ growth phenotype was attempted by using a genomic library constructed with chromosomal DNA from a revertant. No complementation was observed, but plasmids that rescued a CcdA-null mutant for photosynthetic growth by homologous recombination were recovered. Analysis of one such plasmid revealed that the rescue ability was mediated by open reading frame 3149, encoding the dithiol:disulfide oxidoreductase DsbA. DNA sequence data revealed that the dsbA allele on the rescuing plasmid contained a frameshift mutation expected to produce a truncated, nonfunctional DsbA. Indeed, a dsbA ccdA double mutant was shown to be Ps+ Nadi+, establishing that in R. capsulatus the inactivation of dsbA suppresses the c-type cytochrome deficiency due to the absence of ccdA. Next, the ability of the wild-type dsbA allele to suppress the Ps+ growth phenotype of the dsbA ccdA double mutant was exploited to isolate dsbA-independent ccdA revertants. Sequence analysis revealed that these revertants carried mutations in dsbB and that their Ps+ phenotypes could be suppressed by the wild-type allele of dsbB. As with dsbA, a dsbB ccdA double mutant was also Ps+ Nadi+ and produced c-type cytochromes. Therefore, the absence of either DsbA or DsbB restores c-type cytochrome biogenesis in the absence of CcdA. Finally, it was also found that the DsbA-null and DsbB-null single mutants of R. capsulatus are Ps+ and produce c-type cytochromes, unlike their E. coli counterparts, but are impaired for growth under respiratory conditions. This finding demonstrates that in R. capsulatus the dithiol:disulfide oxidoreductases DsbA and DsbB are not essential for cytochrome c biogenesis even though they are important for respiration under certain conditions.

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18

Huang, Bo-Chin, Kai-Chieh Chang, and Fei-Yi Hung. "Study on Microstructure, Mechanical Properties and Erosion Characteristics of Al-Si Alloy Manufactured by Continuous Casting Direct Rolling Process." Applied Sciences 11, no. 18 (September 9, 2021): 8351. http://dx.doi.org/10.3390/app11188351.

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Al-Si alloys exhibit promising wear resistance, thus being mainly employed to weld Al alloy parts and processed into components of equipment. During the new continuous casting direct rolling (CCDR) process, the raw material gradually cools and solidifies, simultaneously plastically deformed. Hence, the materials manufactured through the CCDR process presented an unparalleled microstructure. The experimental results indicated that the strength of the CCDR Al-Si alloy can be increased through cold rolling. A two-stage heat treatment (solid solution and aging treatment) was introduced to improve the ductility and satisfy the industrial application. Furthermore, the erosion wear characteristics and fracture mechanism of the CCDR Al-Si alloy dominated by the ductility were confirmed. Both cold rolling specimens (FR) and those with heat treatment (FRH) showed greater wear resistance than as-manufactured (F). The FR specimens exhibited greater wear resistance owing to a higher Al matrix strength at a lower impact angle; on the other hand, at a higher impact angle, the FRH specimens with a softer Al matrix presented better wear resistance due to the formation of a lip structure to reduce material removal. The TEM results confirmed that the nanoscale grains formation was induced in the erosion-affected region and affected the Si concentration. Conclusively, the heat-treated CCDR Al-Si alloy possessed excellent erosion resistance and workability, which can serve as a reference processed as wear-resistant mechanical parts.

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19

Erlendsson, Lýđur S., and Lars Hederstedt. "Mutations in the Thiol-Disulfide Oxidoreductases BdbC and BdbD Can Suppress Cytochrome c Deficiency of CcdA-Defective Bacillus subtilis Cells." Journal of Bacteriology 184, no. 5 (March 1, 2002): 1423–29. http://dx.doi.org/10.1128/jb.184.5.1423-1429.2002.

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ABSTRACT Cytochromes of the c type in the gram-positive bacterium Bacillus subtilis are all membrane anchored, with their heme domains exposed on the outer side of the cytoplasmic membrane. They are distinguished from other cytochromes by having heme covalently attached by two thioether bonds. The cysteinyls in the heme-binding site (CXXCH) in apocytochrome c must be reduced in order for the covalent attachment of the heme to occur. It has been proposed that CcdA, a membrane protein, transfers reducing equivalents from thioredoxin in the cytoplasm to proteins on the outer side of the cytoplasmic membrane. Strains deficient in the CcdA protein are defective in cytochrome c and spore synthesis. We have discovered that mutations in the bdbC and bdbD genes can suppress the defects caused by lack of CcdA. BdbC and BdbD are thiol-disulfide oxidoreductases. Our experimental findings indicate that these B. subtilis proteins functionally correspond to the well-characterized Escherichia coli DsbB and DsbA proteins, which catalyze the formation of disulfide bonds in proteins in the periplasmic space.

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20

Bialasová, Kristina, Irena Němečková, Jan Kyselka, Jiří Štětina, Kateřina Solichová, and Šárka Horáčková. "Influence of flaxseed components on fermented dairy product properties." Czech Journal of Food Sciences 36, No. 1 (February 28, 2018): 51–56. http://dx.doi.org/10.17221/411/2017-cjfs.

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The addition of flaxseed meal and flaxseed oil on the growth and viability of Lactobacillus acidophilus CCDM 151 and yoghurt culture CCDM 21 during cold storage in fermented milk was tested. It was found that the oil addition in the amount of 0.6% w/w in milk did not influence the growth and acid production of Lactobacillus acidophilus CCDM 151, while the acidification activity of yoghurt culture was slightly lower compared to pure milk and connected with lower growth of Streptococcus thermophilus. On the contrary the addition of meal in amount of 7.6% w/w into milk stimulated the growth and acid production of Lactobacillus acidophilus CCDM 151. The viability of both tested cultures during one month storage of fermented milks at 5 ± 1°C was not influenced by the oil supplementation but the addition of meal decreased their viability significantly. The unusual volatile compounds acetone and butane-2-on were detected by SPME-GC in yoghurt with meal. Unlike oil, the addition of flaxseed meal increased the yoghurt firmness and influenced negatively yoghurt taste and flavour.

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21

Kamyshanskaya, I. G., and V. M. Cheremisin. "Results of clinical application of the color contrasting method of digitalx-rays." Diagnostic radiology and radiotherapy 12, no. 4 (January 20, 2022): 83–98. http://dx.doi.org/10.22328/2079-5343-2021-12-4-83-98.

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Introduction. Color processing of X-ray images has a long history and initially was directed for improvement of analysis of medical diagnostic images. Purpose — to evaluate the results of clinical application of the method for color contrast enhancement of digital radiographs.Material and methods. The study was carried out in the X-ray department of the city Mariinsky hospital in St. Petersburg, having installed a computer program on the workstations of the radiologists for carrying out color contrasting of digital radiographs (CCDR). The CCDR program allowed the radiologist to select one of 63 trajectories in 8 colors. Choosing options for coloring, we settled on a warm, cold, full scale, as well as 4 combinations of one color from cold and warm scales with a saturation from 0 to 100%. The CCDR performed 100 digital radiographs of various anatomical areas.We analyzed a variety of colors and their percentage of saturation in terms of optimal transmission of pathological signs of anatomical areas. 27 radiologists assessed the possibilities of CCDR in X-ray diagnostics.Results. Clinical application of CCDR showed that thanks to this method, tissues of different densities were distinguished in more detail on the X-ray image, since their contours were more expressively emphasized. Pathological symptoms, indistinctly expressed on a black-and-white radiograph, were convincingly reflected in the colorized image, which increased the sensitivity and specificity of the diagnosis. Thanks to color post-processing, it was possible to optimize subtle radiological signs of structural bone changes, traumatic injuries of the ribs, impaired pneumatization of the lungs (infiltration, hypoventilation), pneumo-, hydrothorax, and others. Of the radiologists, 77% considered it important to use CCDR in X-ray diagnostics.Conclusion. A digital radiograph, contrasted with a color of optimal saturation, has distinct advantages over a traditional blackand-white X-ray image, since it reveals hidden or subtle diagnostic information. The diagnostic efficiency of the method of color contrasting of radiographs is higher than the analysis of black-and-white images up to 13%.To increase the diagnostic capabilities of X-ray diagnostics, it is advisable to include the method of color contrasting in the package of computer post-processing of images, using at least three gamuts in the standard, the saturation of which is 25–50%.The colorized image does not replace black and white, but complements it, resolving the diagnostic doubts of the radiologist.

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22

Xu, Jun, Kai Xia, Pinyi Li, Chenggong Qian, Yudong Li, and Xinle Liang. "Functional investigation of the chromosomal ccdAB and hipAB operon in Escherichia coli Nissle 1917." Applied Microbiology and Biotechnology 104, no. 15 (June 13, 2020): 6731–47. http://dx.doi.org/10.1007/s00253-020-10733-6.

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23

Carballo-Uicab, Victor Manuel, Yair Cárdenas-Conejo, Alba Adriana Vallejo-Cardona, Margarita Aguilar-Espinosa, Jacobo Rodríguez-Campos, Hugo Serrano-Posada, José Alberto Narváez-Zapata, Felipe Vázquez-Flota, and Renata Rivera-Madrid. "Isolation and functional characterization of two dioxygenasese putatively involved in bixin biosynthesis in annatto (Bixa orellana L.)." PeerJ 7 (June 21, 2019): e7064. http://dx.doi.org/10.7717/peerj.7064.

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Carotenoid cleavage dioxygenases (CCDs) are enzymes that have been implicated in the biosynthesis of a wide diversity of secondary metabolites with important economic value, including bixin. Bixin is the second most used pigment in the world’s food industry worldwide, and its main source is the aril of achiote (Bixa orellana L.) seeds. A recent transcriptome analysis of B. orellana identified a new set of eight CCD members (BoCCD4s and BoCCD1s) potentially involved in bixin synthesis. We used several approaches in order to discriminate the best candidates with CCDs genes. A reverse transcription-PCR (RT-qPCR) expression analysis was carried out in five developmental stages of two accessions of B. orellana seeds with different bixin contents: (P13W, low bixin producer and N4P, high bixin producer). The results showed that three BoCCDs (BoCCD4-1, BoCCD4-3, and BoCCD1-1) had an expression pattern consistent with bixin accumulation during seed development. Additionally, an alignment of the CCD enzyme family and homology models of proteins were generated to verify whether the newly proposed CCD enzymes were bona fide CCDs. The study confirmed that these three enzymes were well-preserved and belonged to the CCD family. In a second selection round, the three CCD genes were analyzed by in situ RT-qPCR in seed tissue. Results indicated that BoCCD4-3 and BoCCD1-1 exhibited tissue-specific expressions in the seed aril. To test whether the two selected CCDs had enzymatic activity, they were expressed in Escherichia coli; activity was determined by identifying their products in the crude extract using UHPLC-ESI-QTOF-MS/MS. The cleavage product (bixin aldehyde) was also analyzed by Fourier transform infrared. The results indicated that both BoCCD4-3 and BoCCD1-1 cleave lycopene in vitro at 5,6-5′,6′.

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Xie, Ruhe, Hong Huang, Yuan Zhang, and Peiyun Yu. "Coupling relationship between cold chain logistics and economic development: A investigation from China." PLOS ONE 17, no. 2 (February 25, 2022): e0264561. http://dx.doi.org/10.1371/journal.pone.0264561.

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This paper builds an evaluation index system, uses the entropy weight method (EWM) to decide the weights and, based on the coupling coordination degree model (CCDM), it systematically studies the coupling relationship between Chinese cold chain logistics and the Chinese economy from 2010 to 2019. It performs a grey relational analysis (GRE) to explore the main factors influencing the coordinated development of the two. The results show that the coupling coordination degree between the two presents a steady upward trend, and their coupling relationship has been upgraded from ‘coordination’ to ‘good coordination’. They also indicate that the added value in the tertiary industry, the per capita gross domestic product (GDP), and household consumption levels are the main factors affecting the development of cold chain logistics, while the per capita cold storage capacity, the turnover of road cold chain freight, and the volume of human-power employed in cold chain logistics are the main factors affecting economic development. This study makes suggestions to support the coordinated development of cold chain logistics and economy, and provides a scientific basis for further research.

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25

LAWSON, A. J., M. S. SHAFI, K. PATHAK, and J. STANLEY. "Detection of campylobacter in gastroenteritis: comparison of direct PCR assay of faecal samples with selective culture." Epidemiology and Infection 121, no. 3 (December 1998): 547–53. http://dx.doi.org/10.1017/s0950268898001630.

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The prevalence of campylobacter gastroenteritis has been estimated by bacterial isolation using selective culture. However, there is evidence that certain species and strains are not recovered on selective agars. We have therefore compared direct PCR assays of faecal samples with campylobacter culture, and explored the potential of PCR for simultaneous detection and identification to the species level. Two hundred unselected faecal samples from cases of acute gastroenteritis were cultured on modified charcoal cefoperazone deoxycholate agar and subjected to DNA extraction and PCR assay. Culture on CCDA indicated that 16 of the 200 samples contained ‘Campylobacter spp.’. By contrast, PCR assays detected campylobacters in 19 of the 200 samples, including 15 of the culture-positive samples, and further identified them as: C. jejuni (16), C. coli (2) and C. hyointestinalis (1). These results show that PCR offers a different perspective on the incidence and identity of campylobacters in human gastroenteritis.

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KWIATEK, KRZYSTOF, BOLESLAW WOJTON, and NORMAN J. STERN. "Prevalence and Distribution of Campylobacter spp. on Poultry and Selected Red Meat Carcasses in Poland." Journal of Food Protection 53, no. 2 (February 1, 1990): 127–30. http://dx.doi.org/10.4315/0362-028x-53.2.127.

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Campylobacter jejuni, Campylobacter coli, and Campylobacter laridis are recognized causes of alimentary infections in humans. These infections are most often transmitted by foods of animal origin, with undercooked poultry or unpasteurized milk most frequently implicated as vehicles. There are no data on the prevalence and distribution of Campylobacter spp. on meats in Poland. We assessed 839 poultry, 105 porcine, and 114 bovine carcasses for the qualitative presence of the organism on the freshly processed product. The organisms were found on 80.3% of the chicken, 48.0% of the duck, 38.0% of the goose, and 3.0% of the turkey carcasses examined. The contamination on porcine and bovine carcasses was 2.9 and 0.9%, respectively. In addition, we assessed and determined that modified Campylobacter charcoal differential agar (CCDA) medium was more sensitive and selective than Campylobacter brucella agar plate (Campy-BAP) medium for the isolation of Campylobacter spp. from poultry carcasses.

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27

Liu, Shuo Qian, Na Tian, Zhong Hua Liu, Jia Nan Huang, and Juan Li. "Cloning and Characterization of a Carotenoid Cleavage Dioxygenase from Artemisia Annua L." Applied Mechanics and Materials 108 (October 2011): 274–81. http://dx.doi.org/10.4028/www.scientific.net/amm.108.274.

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In order to discover the formation mechanism of carotenoid derived aroma, which has been wildly used on protection of crop against insect attacks, the full-length cDNA of an Artemisia annua carotenoid cleavage dioxygenase (AaCCD1) was cloned by rapid amplification of cDNA ends. The function of AaCCD1 was characterized by expression of AaCCD1 in a strain of E. coli accumulating carotenoids and enzyme assay in vitro. The completed open read frame of AaCCD1 was 1629 bp and it encoded a 542-amino acid protein with a 77% amino acid identity to Arabidopsis thaliana CCD1, a predicted molecular mass of 61.04 kDa and a pI of 5.8. AaCCD1 efficiently cleaves carotenoids and regulate the formation of terpenoid compounds. This is the first time to report the cloning and identification of carotenoid cleavage dioxygenase from Atemisia annua, which will play a great role on understanding the regulation of volatile compounds.

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Micari, Antonio, and Giuseppe Vadalà. "Tibioperoneal trunk pseudoaneurysm coil embolization." Catheterization and Cardiovascular Interventions 75, no. 2 (February 1, 2010): 276–78. http://dx.doi.org/10.1002/ccd.22256.

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29

Avila, Luisa Bataglin, Milena Ramos Vaz Fontes, Elessandra da Rosa Zavareze, Caroline Costa Moraes, Marcilio Machado Morais, and Gabriela Silveira da Rosa. "Recovery of Bioactive Compounds from Jaboticaba Peels and Application into Zein Ultrafine Fibers Produced by Electrospinning." Polymers 12, no. 12 (December 5, 2020): 2916. http://dx.doi.org/10.3390/polym12122916.

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This work focused on the recovery bioactive compounds from jaboticaba peels and to develop ultrafine fibers from zein incorporated with the jaboticaba extract by electrospinning technique. Jaboticaba peel extracts (JPE) were obtained by maceration according a central composite rotational design (CCDR) and characterized with respect to total phenolic content (TP), antioxidant activity (AA) and total anthocyanin (TA). The optimal condition for the extraction was obtained using a desirability function in order to maximize the presence of bioactive compounds. Under these conditions the amount of cyanidin-3-glucoside (Cn-3-Glu) and the antimicrobial inhibition (AI) of E. coli were evaluated. Ultrafine fibers were obtained by electrospinning technique using zein in an aqueous ethanol as solvent and freeze-dried JPE at different concentrations (1.7% and 3.3%) to produce a composite membrane. The apparent viscosity and electrical conductivity of the polymer solutions, as well as the morphology, thermal stability and functional groups of the ultrafine fibers, were evaluated. The optimal conditions for extraction were 88 °C and pH 1. Under these conditions, a high amount of Cn-3-Glu was obtained (718.12 mg 100 g−1), along with 22.2% antimicrobial inhibition against E. coli. The addition of JPE into composite membranes did not affect the morphology of fibers, which presented a homogeneous and continuous format. Therefore, fibers containing JPE showed interesting characteristics for the food packaging industry.

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Soma, Katsunori, Kensuke Shiomi, Kazuko Keino-Masu, and Masayuki Masu. "Expression of mouse Coiled-coil-DIX1 (Ccd1), a positive regulator of Wnt signaling, during embryonic development." Gene Expression Patterns 6, no. 3 (March 2006): 325–30. http://dx.doi.org/10.1016/j.modgep.2005.06.013.

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31

Wang, Chaohua, and Xiaodong Xie. "Treatment of an unraveled intracerebral coil." Catheterization and Cardiovascular Interventions 76, no. 5 (October 6, 2010): 746–50. http://dx.doi.org/10.1002/ccd.22643.

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32

Kuhn, Micheal A., and Larry A. Latson. "Transcatheter embolization coil closure of patent ductus arteriosus -modified delivery for enhanced control during coil positioning." Catheterization and Cardiovascular Diagnosis 36, no. 3 (November 1995): 288–90. http://dx.doi.org/10.1002/ccd.1810360325.

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Soga, Yoshimitsu, Koyu Sakai, and Masakiyo Nobuyoshi. "Renal artery aneurysm treatment with coil embolization." Catheterization and Cardiovascular Interventions 69, no. 5 (2007): 697–700. http://dx.doi.org/10.1002/ccd.21090.

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34

Dobrolet, Nancy C., and Jos� A. Ettedgui. "Changes in coil morphology following transcatheter coil occlusion of the patent ductus arteriosus using a modified snare technique." Catheterization and Cardiovascular Interventions 52, no. 4 (2001): 504–9. http://dx.doi.org/10.1002/ccd.1113.

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35

Nogi, Shunji, Noriyuki Haneda, Hideshi Tomita, and Kenji Yasuda. "Transcatheter coil occlusion of perimembranous ventricular septal defects." Catheterization and Cardiovascular Interventions 72, no. 5 (November 1, 2008): 683–90. http://dx.doi.org/10.1002/ccd.21703.

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36

Linnemeier, Thomas J. "The hot and cold issues of laser angioplasty." Catheterization and Cardiovascular Diagnosis 27, no. 1 (September 1992): 1–4. http://dx.doi.org/10.1002/ccd.1810270102.

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37

Ho, David S. W., Ming W. Liu, Sriram Iyer, James M. Parks, and Gary S. Roubin. "Sizing the gianturco-roubin coronary flexible coil stent." Catheterization and Cardiovascular Diagnosis 32, no. 3 (July 1994): 242–48. http://dx.doi.org/10.1002/ccd.1810320309.

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38

Wang, Lei, and Gordon L. Archer. "Roles of CcrA and CcrB in Excision and Integration of Staphylococcal Cassette Chromosome mec, a Staphylococcus aureus Genomic Island." Journal of Bacteriology 192, no. 12 (April 9, 2010): 3204–12. http://dx.doi.org/10.1128/jb.01520-09.

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ABSTRACT The gene encoding resistance to methicillin and other β-lactam antibiotics in staphylococci, mecA, is carried on a genomic island, SCCmec (for staphylococcal cassette chromosome mec). The chromosomal excision and integration of types I to IV SCCmec are catalyzed by the site-specific recombinases CcrA and CcrB, the genes for which are encoded on each element. We sought to identify the relative contributions of CcrA and CcrB in the excision and integration of SCCmec. Purified CcrB but not CcrA was shown to mediate the gel shift of chromosomal target integration sequences (attB) in electrophoretic mobility shift assays. However, preincubation of CcrB-DNA complexes with increasing concentrations of CcrA blocked gel shift. The interaction of CcrB and CcrA was confirmed by Escherichia coli two-hybrid analysis. SCCmec excision mediated by plasmid-encoded and inducible ccrA, ccrB, or both genes was assessed by PCR in Staphylococcus aureus. CcrB alone could mediate excision but excision was at an alternate att site (attR2) within the right extremity of SCCmec. In contrast, both CcrB and CcrA were required to mediate excision at the chromosomal attB site (called attR when SCCmec is integrated). Insertion of a plasmid containing the SCCmec att site (attS) into the chromosome required both CcrA and CcrB, but CcrA overexpression lowered integration frequency. Thus, while CcrB binds DNA, interaction between CcrA and CcrB, in a precise ratio, is required for attB site-specific excision and SCCmec chromosomal insertion.

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39

Alder, Adrian, Iris Holdermann, Peter Beyer, and Salim Al-Babili. "Carotenoid oxygenases involved in plant branching catalyse a highly specific conserved apocarotenoid cleavage reaction." Biochemical Journal 416, no. 2 (November 12, 2008): 289–96. http://dx.doi.org/10.1042/bj20080568.

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Recent studies with the high-tillering mutants in rice (Oryza sativa), the max (more axillary growth) mutants in Arabidopsis thaliana and the rms (ramosus) mutants in pea (Pisum sativum) have indicated the presence of a novel plant hormone that inhibits branching in an auxin-dependent manner. The synthesis of this inhibitor is initiated by the two CCDs [carotenoid-cleaving (di)oxygenases] OsCCD7/OsCCD8b, MAX3/MAX4 and RMS5/RMS1 in rice, Arabidopsis and pea respectively. MAX3 and MAX4 are thought to catalyse the successive cleavage of a carotenoid substrate yielding an apocarotenoid that, possibly after further modification, inhibits the outgrowth of axillary buds. To elucidate the substrate specificity of OsCCD8b, MAX4 and RMS1, we investigated their activities in vitro using naturally accumulated carotenoids and synthetic apocarotenoid substrates, and in vivo using carotenoid-accumulating Escherichia coli strains. The results obtained suggest that these enzymes are highly specific, converting the C27 compounds β-apo-10′-carotenal and its alcohol into β-apo-13-carotenone in vitro. Our data suggest that the second cleavage step in the biosynthesis of the plant branching inhibitor is conserved in monocotyledonous and dicotyledonous species.

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40

Meier, Bernhard. "Coil closure of residual shunt after amplatzer pfo occlusion." Catheterization and Cardiovascular Interventions 77, no. 5 (March 17, 2011): 720–21. http://dx.doi.org/10.1002/ccd.22845.

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41

Butman, Samuel M. "Does the “cold” laser simply need a cover up?" Catheterization and Cardiovascular Interventions 80, no. 5 (October 24, 2012): 860. http://dx.doi.org/10.1002/ccd.24665.

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42

Lacombe, P., P. Rocha, X. Marchand, R. Mulot, M. Rigaud, G. Jondeau, J. M. Weber, and J. C. Kahn. "High flow coronary fistula closure by percutaneous coil packing." Catheterization and Cardiovascular Diagnosis 28, no. 4 (April 1993): 342–46. http://dx.doi.org/10.1002/ccd.1810280415.

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43

Horáčková, Šárka, Blanka Vrchotová, Daniel Koval, Akkenzhe Omarova, Marcela Sluková, and Jiří Štětina. "Use of Lactiplantibacillus plantarum for dairy and non-dairy fermented products." Czech Journal of Food Sciences 40, No. 5 (October 26, 2022): 392–99. http://dx.doi.org/10.17221/132/2022-cjfs.

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In this study, two strains of Lactiplantibacillus plantarum 299v and CCDM 181 were tested for their ability to grow in milk and soy beverage, for stability during cold storage of fermented beverages, compatibility with yoghurt culture and activity against yeasts. Both strains grew better in soy drink compared to milk. During co-culturing with the yoghurt culture, sufficient acidification of milk and soy beverage necessary for the production of fermented products was achieved. The stability of tested strains in media at pH 4.5 for 28 days at 5 °C was good. L. plantarum was effective in the inhibition of undesirable yeast growth, but the ability was strain-specific. Tested strains demonstrated also a strain-specific ability to suppress the growth of yoghurt culture bacteria. For a possible application of co-culturing L. plantarum with the yoghurt culture, verification of the mutual compatibility of specific strains is necessary.

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Lee, Candice Y., Peter A. Knight, and Frederick S. Ling. "Coil embolization of a symptomatic left internal mammary arteriovenous fistula." Catheterization and Cardiovascular Interventions 83, no. 5 (July 2, 2013): E174—E177. http://dx.doi.org/10.1002/ccd.25024.

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45

Johnson, Walter H., Robyn K. Peterson, Donna F. Howland, and James E. Lock. "Systemic heparinization does not prevent clot formation in coil embolization." Catheterization and Cardiovascular Diagnosis 20, no. 4 (August 1990): 267–70. http://dx.doi.org/10.1002/ccd.1810200412.

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46

Van Den Brand, M., H. Pieterman, H. Suryapranata, and A. J. J. C. Bogers. "Closure of a coronary fistula with a transcatheter implantable coil." Catheterization and Cardiovascular Diagnosis 25, no. 3 (March 1992): 223–26. http://dx.doi.org/10.1002/ccd.1810250310.

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47

Shiomi, Kensuke, Mizuki Kanemoto, Kazuko Keino-Masu, Sachine Yoshida, Katsunori Soma, and Masayuki Masu. "Identification and differential expression of multiple isoforms of mouse Coiled-coil-DIX1 (Ccd1), a positive regulator of Wnt signaling." Molecular Brain Research 135, no. 1-2 (April 2005): 169–80. http://dx.doi.org/10.1016/j.molbrainres.2004.12.002.

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48

Pasek, Raymond C., Erik Malarkey, Nicolas F. Berbari, Neeraj Sharma, Robert A. Kesterson, Laura L. Tres, Abraham L. Kierszenbaum, and Bradley K. Yoder. "Coiled-coil domain containing 42 ( Ccdc 42) is necessary for proper sperm development and male fertility in the mouse." Developmental Biology 412, no. 2 (April 2016): 208–18. http://dx.doi.org/10.1016/j.ydbio.2016.01.042.

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49

Chen, Xiao-Hong, Ellen B. Geller, and Martin W. Adler. "CCKB receptors in the periaqueductal grey are involved in electroacupuncture antinociception in the rat cold water tail-flick test." Neuropharmacology 37, no. 6 (June 1998): 751–57. http://dx.doi.org/10.1016/s0028-3908(98)00028-8.

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50

Krausova, Gabriela, Iveta Hynstova, Roman Svejstil, Iva Mrvikova, and Robert Kadlec. "Identification of Synbiotics Conducive to Probiotics Adherence to Intestinal Mucosa Using an In Vitro Caco-2 and HT29-MTX Cell Model." Processes 9, no. 4 (March 24, 2021): 569. http://dx.doi.org/10.3390/pr9040569.

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The ability of bacteria to adhere to the intestinal mucosa is a critical property necessary for the long-term colonization of the intestinal tract. This ability can be highly sensitive to the presence of prebiotics. However, limited data are available in this respect for beneficial bacteria such as probiotics or resident gut microbiota. We previously demonstrated that the presence of prebiotics may decrease adherence in several pre- and probiotic combinations. Thus, characterizing the interactions between numerous combinations involving different classes of pre- and probiotics can be crucial in identifying new synbiotics. Accordingly, here, we extend our prior analyses to evaluate the adhesion of five lactobacilli, six bifidobacteria, and one probiotic Escherichia coli strains, as commercial probiotics or promising probiotic candidates, together with the cariogenic Bifidobacterium dentium strain. As an in vitro intestinal mucosa model, Caco-2 and mucin-secreting HT29-MTX cells were co-cultured at 9:1 in the presence or absence of prebiotics. Commercial inulin-type fructooligosaccharide prebiotics Orafti® GR, Orafti® P95, and galactooligosaccharide-based prebiotic formula Vivinal®, including purified human milk oligosaccharides (HMOs) were added into the cultivation media as the sole sugar source (2.5% each). Adherence was tested using microtiter plates and was evaluated as the percentage of fluorescently labeled bacteria present in the wells after three washes. Consistent prebiotics-mediated enhanced adherence was observed only for the commercial probiotic strain E. coli O83. For the remaining strains, the presence of HMO or prebiotics Orafti® P95 or Orafti® GR decreased adherence, reaching statistical significance (p < 0.05) for three of out of eight (HMO) or five of out of 11 strains tested, respectively. Conversely, Vivinal® enhanced adhesion in six out of the 12 strains tested, and notably, it significantly attenuated the adherence of the cariogenic Bifidobacterium dentium Culture Collection of Dairy Microorganisms (CCDM) 318. To our knowledge, this represents the first report on the influence of commercial prebiotics and HMOs on the adhesion of the cariogenic Bifidobacterium sp. Vivinal® seems to be a promising prebiotic to be used in the formulation of synbiotics, supporting the adhesion of a wide range of probiotics, especially the strains B. bifidum BBV and BBM and the probiotic Escherichia coli O83.

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