Papers by Keyword: RNA

Abstract: This paper considers a novel approach for integration between molecular engineering of XNA-based structures and additive manufacturing of XNA-based devices based on multiparametric characterization of XNAs by different functional descriptors (such as physical properties of XNA-based materials and precursors of XNA-based molecular devices) and the possibility of thermal or electron-beam processing as a prerequisite of the industrial technical process development for such device implementation. This can be performed in the framework of additive manufacturing by connecting the output of the XNA synthesizer or nucleic acid synthesizer with 3D-printer nozzles in such a way that oligos / AGCTX products are supported into the nozzles separately.

Abstract: Detergents represent a unique class of chemical compounds. They can alter surface and interphase bonds, and form micellar systems. These detergent properties allow to alter wettability of surfaces, stabilize or destabilize dispersed systems, and modify the properties of liquid phases. Therefore, the use of detergents is virtually unlimited in chemical synthesis and processing, medicine, biological systems and agricultural biology. The article includes the studies of the feasibility of application of 1,1,1,3,5,5,5-heptamethyltrisiloxane modified by polyalkylene oxide in combination with allyloxypolyethyleneglycol in the ratio of 10:1 as a detergent for agrobacterial-mediated transformation. Tween 20 detergent was used as a means of control in the concentration of 5%. As a result of histochemical analysis of transformed tissues, a significant difference was determined in expression of beta-glucuronidase reporter gene. The study of gene expression by calculating the relative content of mRNA showed that the initial number of mRNA copies of genetic makers transfected by co-culturing in a liquid medium with addition of Tween 20 is on the average 32% lower than when using modified heptamethyltrisiloxane

Abstract: Mesophilic iron and sulfur-oxidizing acidophiles are commonly used for the extraction of base metals from low-grade sulfide ores in some copper Chilean mines. However, relatively little is known about their activities in cold environments. Some natural ecosystems present in the Andes Mountains, such as the Chilean Altiplano, meet environmental conditions for the growth of psychrotolerant leaching microorganisms. In this work, we obtained enrichment cultures of iron- and sulfur-oxidizing microorganisms from an acid river in the Chilean Altiplano. Molecular identification was performed using PCR products of bacterial 16S rRNA clone libraries, and the sequences analysis revealed the presence of a microorganism related to the recently described psychrotolerant Acidithiobacillus ferrivorans. The Acidithiobacillus strain was able to grow at temperatures ranging between 4 and 30°C, and pH values ranged between 1.7 and 2.5. According to the energy sources, this microorganism was able to grow using ferric iron, sulfur, thiosulfate and tetrathionate. Optimal growth was observed in presence of ferric ion, where the culture reached a potential redox value of 600 mV and a cellular number of 3×10⁷ cells/mL. Molecular analysis of variants of gene encoding for rusticyanin showed that rusB gene was amplified from A. ferrivorans strain and no PCR product was obtained for the rusA gene. Our description is consistent with data previously reported for A. ferrivorans strains. Finally, results of this study highlight the importance and potential of novel native bacterial species proficient in mineral oxidation under low-temperature conditions.

Abstract: DNA and RNA based analysis was a useful way to characterize microbial communities during biohydrometallurgical processes. However, feasible, affordable and efficient DNA and RNA separation methods are rarely reported although several simultaneous DNA and RNA extraction methods have been developed recently. In this study, various salts including NaCl, CaCl2 and LiCl were tested for separation of DNA and RNA. Salt concentration, nucleic acid concentration, precipitation temperature and time were optimized. The results showed that LiCl was more efficient to separate DNA and RNA than the other two salts. The optimized conditions were as follows: 1/4 volume saturated LiCl was used for precipitating RNA first at -20°C for 30 min for total nucleic acid concentration of approximately 200-400 ng/μL, and then centrifuged at 12,000×g at room temperature for 20 min to collect RNA. DNA in the supernatant was precipitated using 0.6 volume isopropanol and then collected by centrifugation at 12,000×g at room temperature for 20 min. The results indicated that DNA and RNA could be extracted from not only pure culture of Acidithiobacillus ferrooxidans(A.ferrooxidans), Acidithiobacillus caldus(A. caldus), Acidithiobacillus albertensis(A. albertensis), Leptospirillum ferrooxidans(L. ferrooxidans), Ferroplasma thermophilium(F. thermophilium), but also the acid mine drainage(AMD) water samples from Daye copper mine, Xiangxi gold mine, Axi gold mine. The resulted DNA and RNA could be amplified and A260/280 was 1.8-2.0, A260/230 was 1.8-2.2, which indicated high quality of DNA and RNA. This method could be widely used for separation of bioleaching bacteria DNA and RNA extracted simultaneously.

Abstract: The distribution and diversity of bacterial community in Zijinshan commercial non-aeration copper bioheapleaching system operated at pH 0.8 for three years were investigated. The 24 meters high heap was cut off by mechanical digger. On the trapezoidal cross-section of the heap, 9 ore samples were taken from different vertical and horizontal locations and investigated by 16S rRNA gene clone library. Another 3 liquid samples from raffinate solution pond, spray solution pond and pregnant solution pond were also applied to 16S rRNA gene clone library analysis. The retrieved 1166 clone sequences from 12 samples were mainly related to genus Acidithiobacillus (42.36%), genus Leptospirillum (37.73%) and genus Sulfobacillus (6.52%). Relative high amount of heterotrophic bacteria were distributed at the ore surface in the internal part of the heap and in the liquid samples respectively. The retrieved heterotrophic bacterial sequences were mainly related to genus Acidiphilium (accounting 11.11% to 32.00% percent in the liquid samples), genus Acidovorax (accounting 12.37% in A1 sample), genus Pelomonas (accounting 4.17% to 10.31% in several ore samples) and genus Aquabacterium (accounting 10.31% in C2 sample). Bacterial diversity in the heap was increased from the surfcae layer to the interior of the heap. The proportion of genus Leptospirillum horizontally increased from the inner to the outer part while vertically decreased from lower depth (2-3 years leaching time) to higher depth(3-6 month leaching time), and reverse correlation of genus Acidithiobacillus was found in the heap. Our finding indicated that heterotrophic bacteria may play very important roles in the commercial bioheapleaching system, and revealed high distribution of genus Leptospirillum in the outer part of this non-aerated heap.

Abstract: In this paper, we present an improved BPSO to predict RNA secondary structure to improve the performance with two new strategies. First one is to reduce the searching space of PSO through super stem set construction. Second is to modify the general BPSO updating process to settle stem permutation and combination problems. The experimental results show that the new method is effective for RNA structure prediction in terms of sensitivity and specificity by different sequence datasets including simple pseudoknot.

Abstract: . Aloe, an important folk herbal drug, includes abundant polysaccharides and secondary metabolites which bringing about the difficulty of isolating high-quality DNA or RNA. In this paper, one and two improved methods were used to isolate the genomic DNA and RNA from the leaf of Aloe, respectively. The obtained samples presented good quality and integrality, and thus, they could be further used for many downstream molecular experiments. This reported protocols on extraction of DNA and RNA offered a valuable reference for other related studies.

Abstract: In order to investigate the relationship between the RNA structure and thermal stability, we used real-time PCR method to survey the degradation information of Bombyx mori larvae inter reference gene RNA treated with 70 °C to 90 °C. The results showed that there were some relativities between the whole thermal stability RNA and the GC contents. The whole RNA displayed prominent degradation above 70 °C. The amplification length of the two inner reference genes were 147 bp and 150 bp, respectively, and the GC content were 59.184% and 44.667%, respectively. The risdual ratio was 67.712% and 50.849%, respectively. These results explained that there were negative correlation between the degradation rate and the GC contents. This study reported the correlation between the degradation rate and the GC contents of inner reference gene, providing the references for studying the RNA thermal stability and related molecular biology research.

Abstract: Microfluidic devices are of considerable interest, since such technology offers great promise for the development of powerful and versatile miniaturized analyzers. Accordingly, the present work describes a microfluidic screening system that is composed of a microchip, hydrodynamic pumping unit and fluorescence detectors. To develop an assay for RNA-aminoglycoside interactions, microchips are designed and fabricated on a glass substrate, then flow simulations are performed in the microchannels. After optimizing the flow control and buffer composition for fluorescence-based biochemical assays, a fluorescently labeled aminoglycoside probe and RNA are allowed to flow continuously to the main micro-channel based on hydrodynamic pumping and their interactions monitored by fluorescence quenching, which is reversed upon competition with other aminoglycosides. Consequently, the proposed device can serve as an integrated microfluidic platform for the high-throughput screening of high affinity antibiotics for RNA targets.

Abstract: Autocatalytic chemical reactions may lead to spatio-temporal patterns if processed under non-equilibrium conditions. The patterns disappear when the conditions change and information stored in these non-equilibrium structures is lost since precise reconstructions are impossible. Replication of molecules, in particular of polynucleotides RNA or DNA, is an autocatalytic process too. The storage of information in polynucleotide sequences, however, allows for reconstruction of the molecules under suitable conditions. Conservation of information in polymer sequences constitutes the basic difference between chemical and biological self-organization. Evolution of RNA molecules is considered as pattern formation in sequence space, which manifests itself as another pattern in the space of minimum-free-energy structures. In addition, optimization of RNA structures and properties is visualized as an evolutionary trial-and-error process. This process can be interpreted as a simple form of learning at the level of ensembles or populations of molecules. Evolutionary optimization of RNA molecules occurs in steps: Short adaptive periods are interrupted by long epochs of quasi-stationarity during which the mean replication rate of the populations is essentially constant. Understanding of evolution is largely facilitated through consideration of sequence-structure relation as a many-to-one or non-invertible mapping from sequence space into structure space. Neutrality of sequences with respect to structure formation is highly relevant for evolutionary optimization on rugged fitness landscapes.