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https://www.readbyqxmd.com/read/28642636/nucleotide-composition-determines-the-role-of-translational-efficiency-in-human-genes
#1
Binata Halder, Arup Kumar Malakar, Supriyo Chakraborty
The basic sequence features were analysed that influence gene expression via codon usage bias of the selected forty coding sequences of Homo sapiens in a simple prokaryotic model i.e. E. coli K-12 genome. The prime objective was to elucidate the interrelationships among tRNA gene copy numbers, synonymous codons, amino acids and translational efficiency using tRNA adaptation index. It was evident from RSCU scores and principal component analysis, that only those preferred codons were used by the isoacceptor tRNAs that had G and C base at their third codon position...
2017: Bioinformation
https://www.readbyqxmd.com/read/28638626/effects-of-liposomal-curcumin-on-five-opportunistic-bacterial-strains-found-in-the-equine-hindgut-preliminary-study
#2
S D Bland, E B Venable, J L McPherson, R L Atkinson
BACKGROUND: The horse intestinal tract is sensitive and contains a highly complex microbial population. A shift in the microbial population can lead to various issues such as inflammation and colic. The use of nutraceuticals in the equine industry is on the rise and curcumin is thought to possess antimicrobial properties that may help to minimize the proliferation of opportunistic bacteria. METHODS: Four cecally-cannulated horses were utilized to determine the optimal dose of liposomal-curcumin (LIPC) on reducing Streptococcus bovis/equinus complex (SBEC), Escherichia coli K-12, Escherichia coli general, Clostridium difficile, and Clostridium perfringens in the equine hindgut without adversely affecting cecal characteristics...
2017: Journal of Animal Science and Technology
https://www.readbyqxmd.com/read/28607160/a-pria-mutant-expressed-in-two-pieces-has-almost-full-activity-in-e-coli-k-12
#3
Maxime Leroux, Niketa Jani, Steven J Sandler
The ability to restart broken DNA replication forks is essential across all domains of life. In Escherichia coli, the priA, priB, priC and dnaT genes encode the Replication Restart Proteins (RRPs) to accomplish this task. PriA plays a critical role in Replication Restart such that its absence reveals a dramatic phenotype: poor growth, high basal levels of SOS expression, poorly partitioned nucleoids (Par(-)), UV sensitivity and recombination deficiency. PriA has 733 amino acids and its structure is composed of six domains that enable it to bind to DNA replication fork-like structures, re-model the strands of DNA, interact with SSB (single-stranded DNA binding protein), PriB and DnaT, and display ATPase, helicase and translocase activities...
June 12, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28599915/multiplex-polymerase-chain-reaction-for-identification-of-escherichia-coli-escherichia-albertii-and-escherichia-fergusonii
#4
Rebecca L Lindsey, L Garcia-Toledo, D Fasulo, L M Gladney, N Strockbine
Escherichia coli, Escherichia albertii, and Escherichia fergusonii are closely related bacteria that can cause illness in humans, such as bacteremia, urinary tract infections and diarrhea. Current identification strategies for these three species vary in complexity and typically rely on the use of multiple phenotypic and genetic tests. To facilitate their rapid identification, we developed a multiplex PCR assay targeting conserved, species-specific genes. We used the Daydreamer™ (Pattern Genomics, USA) software platform to concurrently analyze whole genome sequence assemblies (WGS) from 150 Enterobacteriaceae genomes (107 E...
June 6, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28598040/doing-the-research-that-informs-practice-a-retrospective-view-of-one-group-s-attempt-to-study-the-teaching-and-learning-of-organic-chemistry
#5
George M Bodner, Rob Ferguson, Selçuk Çalimsiz
The idea that the focus of educational research should be on results that can inform the practice of teaching has been an implicit assumption for so many years that one would be hard-pressed to trace it back to an individual source. At one time, the people doing such research in STEM disciplines were faculty in schools or colleges of education who focused on K-12 classrooms and looked for ideas, concepts, and principles that would be valid across a range of STEM disciplines. Eventually, this research was done on college- or university-level students, as well, and there was a shift toward what has been called discipline-based educational research (DBER) that looks at the problems associated with the teaching and learning of a given discipline, such as chemistry...
June 9, 2017: Chemistry, An Asian Journal
https://www.readbyqxmd.com/read/28585781/interspecies-cross-talk-between-co-cultured-pseudomonas-putida-and-escherichia-coli
#6
Carlos Molina-Santiago, Zulema Udaondo, Baldo F Cordero, Juan L Ramos
Pseudomonas putida and Escherichia coli are ubiquitous microorganisms that can be isolated from soil rhizosphere, the surface of vegetables, fresh waters and wastewaters-environments in which they likely co-exist. Despite this, the potential interactions between these microbes have not been studied in detail. To analyze these interactions, we carried out RNA-seq transcriptomic analysis of these microbes as monocultures and as co-cultures. Our results show that co-culture of these microbes significantly alters transcriptional profiles...
June 6, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28570122/simufish-an-interactive-application-to-teach-k-12-students-about-zebrafish-behavior
#7
Violet Mwaffo, Veronika Korneyeva, Maurizio Porfiri
As the zebrafish is rapidly becoming a species of choice in preclinical research, several efforts are being placed toward creating educational programs for K-12 students based on this promising model organism. However, as any other model organisms, the use of zebrafish in classroom settings requires additional experimental resources and poses ethical challenges related to animal use. To mitigate these factors, we have developed an application (app), simUfish, which implements a mathematical model of zebrafish behavior for generating multiple fish trajectories and animating their body undulations...
June 1, 2017: Zebrafish
https://www.readbyqxmd.com/read/28560186/tracking-bioluminescent-etec-during-in-vivo-balb-c-mouse-colonization
#8
Gerardo E Rodea, Francisco X Montiel-Infante, Ariadnna Cruz-Córdova, Zeus Saldaña-Ahuactzi, Sara A Ochoa, Karina Espinosa-Mazariego, Rigoberto Hernández-Castro, Juan Xicohtencatl-Cortes
Enterotoxigenic Escherichia coli (ETEC) is a leading cause of diarrhea worldwide. Adhesion to the human intestinal tract is crucial for colonization. ETEC adhesive structures have been extensively studied; however, colonization dynamics remain uncharacterized. The aim of this study was to track bioluminescent ETEC during in vivo infection. The promoter region of dnaK was fused with the luc gene, resulting in the pRMkluc vector. E. coli K-12 and ETEC FMU073332 strains were electroporated with pRMkluc. E. coli K-12 pRMkluc was bioluminescent; in contrast, the E...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28552553/large-scale-chromosome-folding-versus-genomic-dna-sequences-a-discrete-double-fourier-transform-technique
#9
V R Chechetkin, V V Lobzin
Using state-of-the-art techniques combining imaging methods and high-throughput genomic mapping tools leaded to the significant progress in detailing chromosome architecture of various organisms. However, a gap still remains between the rapidly growing structural data on the chromosome folding and the large-scale genome organization. Could a part of information on the chromosome folding be obtained directly from underlying genomic DNA sequences abundantly stored in the databanks? To answer this question, we developed an original discrete double Fourier transform (DDFT)...
May 26, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28549374/metabolic-engineering-of-escherichia-coli-to-high-efficient-synthesis-phenylacetic-acid-from-phenylalanine
#10
Lihua Zhang, Qian Liu, Hong Pan, Xun Li, Daoyi Guo
Phenylacetic acid (PAA) is a fine chemical with a high industrial demand for its widespread uses. Whereas, microorganic synthesis of PAA is impeded by the formation of by-product phenethyl alcohol due to quick, endogenous, and superfluous conversion of aldehydes to their corresponding alcohols, which resulted in less conversation of PAA from aldehydes. In this study, an Escherichia coli K-12 MG1655 strain with reduced aromatic aldehyde reduction (RARE) that does duty for a platform for aromatic aldehyde biosynthesis was used to prompt more PAA biosynthesis...
December 2017: AMB Express
https://www.readbyqxmd.com/read/28533218/involvement-of-two-component-signaling-in-bacterial-motility-and-biofilm-development
#11
Birgit M Prüβ
Two-component signaling is a specialized mechanism that bacteria use to respond to changes in their environment. Non-pathogenic strains of E. coli K-12 harbor 30 histidine kinases and 32 response regulators, which form a network of regulation that integrates many other global regulators that do not follow the two-component signaling mechanism, as well as signals from central metabolism. The output of this network is a multitude of phenotypic changes in response to changes in the environment. Among these phenotypic changes, many two-component systems control motility and/or the formation of biofilm, sessile communities of bacteria that form on surfaces...
May 22, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28526842/revealing-genome-scale-transcriptional-regulatory-landscape-of-ompr-highlights-its-expanded-regulatory-roles-under-osmotic-stress-in-escherichia-coli-k-12-mg1655
#12
Sang Woo Seo, Ye Gao, Donghyuk Kim, Richard Szubin, Jina Yang, Byung-Kwan Cho, Bernhard O Palsson
A transcription factor (TF), OmpR, plays a critical role in transcriptional regulation of the osmotic stress response in bacteria. Here, we reveal a genome-scale OmpR regulon in Escherichia coli K-12 MG1655. Integrative data analysis reveals that a total of 37 genes in 24 transcription units (TUs) belong to OmpR regulon. Among them, 26 genes show more than two-fold changes in expression level in an OmpR knock-out strain. Specifically, we find that: 1) OmpR regulates mostly membrane-located gene products involved in diverse fundamental biological processes, such as narU (encoding nitrate/nitrite transporter), ompX (encoding outer membrane protein X), and nuoN (encoding NADH:ubiquinone oxidoreductase); 2) by investigating co-regulation of entire sets of genes regulated by other stress-response TFs, stresses are surprisingly independently regulated among each other; and, 3) a detailed investigation of the physiological roles of the newly discovered OmpR regulon genes reveals that activation of narU represents a novel strategy to significantly improve osmotic stress tolerance of E...
May 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28522702/complete-genome-sequence-of-escherichia-coli-phage-vb_ecom_alf5
#13
Laurynas Alijošius, Eugenijus Šimoliūnas, Laura Kaliniene, Rolandas Meškys, Lidija Truncaitė
Here, we announce the complete genome sequence of the Escherichia coli myophage vB_EcoM_Alf5 belonging to the genus Felixo1virus, whose members have not been comprehensively studied at the molecular level. Phage vB_EcoM_Alf5 infects E. coli K-12-derived laboratory strains and therefore is well suited for functional studies.
May 18, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28510572/1-2-million-kids-and-counting-mobile-science-laboratories-drive-student-interest-in-stem
#14
Amanda L Jones, Mary K Stapleton
In today's increasingly technological society, a workforce proficient in science, technology, engineering, and mathematics (STEM) skills is essential. Research has shown that active engagement by K-12 students in hands-on science activities that use authentic science tools promotes student learning and retention. Mobile laboratory programs provide this type of learning in schools and communities across the United States and internationally. Many programs are members of the Mobile Lab Coalition (MLC), a nonprofit organization of mobile and other laboratory-based education programs built on scientist and educator collaborations...
May 2017: PLoS Biology
https://www.readbyqxmd.com/read/28507611/the-impact-of-extended-typing-on-red-blood-cell-alloimmunization-in-transfused-patients
#15
Tatjana Makarovska-Bojadzieva, Emilija Velkova, Milenka Blagoevska
BACKGROUND: Red blood cell (RBC) alloimmunization is still an actual problem in our transfusion practice. In 2011, in addition to the regular ABO/D blood group typing, phenotyping for Rh (C, c, E, e) and Kell antigens was introduced for blood donors and patients undergoing blood transfusion. Our aim was to evaluate the impact of the extended RBC typing and donor/recipient matching on the incidence of RBC alloimmunization. METHODS: A retrospective comparative study was conducted by reviewing RBC request records for about 36,000 patients transfused with RBC in the period from 2013 to 2015 in comparison to the similar study conducted on 47,000 transfused patients in the period from 2005 to 2008...
April 15, 2017: Open Access Macedonian Journal of Medical Sciences
https://www.readbyqxmd.com/read/28489862/novel-genes-associated-with-enhanced-motility-of-escherichia-coli-st131
#16
Asha Kakkanat, Minh-Duy Phan, Alvin W Lo, Scott A Beatson, Mark A Schembri
Uropathogenic Escherichia coli (UPEC) is the cause of ~75% of all urinary tract infections (UTIs) and is increasingly associated with multidrug resistance. This includes UPEC strains from the recently emerged and globally disseminated sequence type 131 (ST131), which is now the dominant fluoroquinolone-resistant UPEC clone worldwide. Most ST131 strains are motile and produce H4-type flagella. Here, we applied a combination of saturated Tn5 mutagenesis and transposon directed insertion site sequencing (TraDIS) as a high throughput genetic screen and identified 30 genes associated with enhanced motility of the reference ST131 strain EC958...
2017: PloS One
https://www.readbyqxmd.com/read/28483713/safety-assessment-of-astaxanthin-derived-from-engineered-escherichia-coli-k-12-using-a-13-week-repeated-dose-oral-toxicity-study-and-a-prenatal-developmental-toxicity-study-in-rats
#17
Yin-Ju Lin, Jian-Yu Lin, Di-Sheng Wang, Chien-Hao Chen, Ming-Hsi Chiou
Astaxanthin is a natural carotenoid with strong antioxidant activity that has been used for decades as a nutrient/color additive and it has recently been marketed as a health supplement. Astaxanthin can be synthesized in a wide range of microalgae, yeast, and bacteria. As genes directing astaxanthin biosynthesis in various organisms have been cloned, this study assessed the safety of astaxanthin crystal produced by Escherichia coli K-12 harboring plasmids carrying astaxanthin biosynthetic genes. The astaxanthin crystal contains a total carotenoid content of 950 mg/g and an astaxanthin content of 795 mg/g...
May 5, 2017: Regulatory Toxicology and Pharmacology: RTP
https://www.readbyqxmd.com/read/28482909/characteristics-of-primary-rat-microglia-isolated-from-mixed-cultures-using-two-different-methods
#18
Li Lin, Rakhi Desai, Xiaoying Wang, Eng H Lo, Changhong Xing
BACKGROUND: Microglial cultures comprise a critically important model system for investigating inflammatory mechanisms in almost all CNS disorders. Mild trypsinization and shaking are the two most commonly used methods to isolate primary microglia from mixed glial cultures. In this study, we characterized and compared microglia obtained using these two methods. METHODS: Primary rat microglia cultures were prepared from cerebral cortices of 1-2-day-old neonatal Sprague-Dawley rats...
May 8, 2017: Journal of Neuroinflammation
https://www.readbyqxmd.com/read/28479746/cloning-and-over-expression-of-non-coding-rna-rpra-in-e-coli-and-its-resistance-to-kanamycin-without-osmotic-shock
#19
Azita Sahni, Mohammadreza Hajjari, Jamshid Raheb, Ali Mohammad Foroughmand, Morteza Asgari
Recent reports have indicated that small RNAs have key roles in the response of the E.coli to stress and also in the regulating of virulence factors. It seems that some small non-coding RNAs are involved in multidrug resistance. Previous studies have indicated that rprA can increase the tolerance to Kanamycin in RcsB-deficient Escherichia coli K-12 following osmotic shock. The current study aims to clone and over-express the non-coding RNA rprA in E.coli and investigate its effect on the bacterial resistance to Kanamycin without any osmotic shock...
2017: Bioinformation
https://www.readbyqxmd.com/read/28468259/thielavins-w-z%C3%A2-new-antifouling-thielavins-from-the-marine-derived-fungus-thielavia-sp-ust030930-004
#20
Zhuang Han, Yong-Xin Li, Ling-Li Liu, Liang Lu, Xian-Rong Guo, Xi-Xiang Zhang, Xiao-Yong Zhang, Shu-Hua Qi, Ying Xu, Pei-Yuan Qian
Eleven new depsides-thielavins W-Z (1-4) and thielavins Z₁-Z₇ (5-11)-and also four known thielavins-A, H, J, and K (12-15)-were isolated from the ethyl acetate extract of a marine-derived fungal strain Thielavia sp UST030930-004. All of these compounds were evaluated for antifouling activity against cyprids of the barnacle Balanus (=Amphibalanus) amphitrite. The results showed that compounds 1-3 and 6-13 were active, with EC50 values ranging from 2.95 ± 0.59 to 69.19 ± 9.51 μM, respectively. The inhibitive effect of compounds 1-3 and 7 was reversible...
April 29, 2017: Marine Drugs
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