Evolutionary rate variation and RNA secondary structure prediction

Predicting RNA secondary structure using evolutionary history can be carried out by using an alignment of related RNA sequences with conserved structure. Accurately determining evolutionary substitution rates for base pairs and single stranded nucleotides is a concern for methods based on this type of approach. Determining these rates can be hard to do reliably without a large and accurate initial alignment, which ideally also has structural annotation. Hence, one must often apply rates extracted from other RNA families with trusted alignments and structures. Here, we investigate this problem by applying rates derived from tRNA and rRNA to the prediction of the much more rapidly evolving 5'-region of HIV-1. We find that the HIV-1 prediction is in agreement with experimental data, even though the relative evolutionary rate between A and G is significantly increased, both in stem and loop regions. In addition we obtained an alignment of the 5' HIV-1 region that is more consistent with the structure than that currently in the database. We added randomized noise to the original values of the rates to investigate the stability of predictions to rate matrix deviations. We find that changes within a fairly large range still produce reliable predictions and conclude that using rates from a limited set of RNA sequences is valid over a broader range of sequences.     

气相分子吸收光谱法测定地下水中亚硝酸盐氮、氨氮、硝酸盐氮

采用气相分子吸收光谱法测定地下水中的亚硝酸盐氮(NO2^-)、氨氮(NH4^+)、硝酸盐氮(NO3^-)。考察NO2^-,NH4^+和NO3^-测定时的相互干扰,并给出了相应的消除方法。研究结果表明,测定NO2^-时,NH4^+和NO3^-无干扰;NO2^-对测定NH4^+和NO3^-产生干扰,可分别采用分段法和加入2滴10%氨基磺酸溶液的方法消除干扰;对于不含NO2^-或NO2-含量不高的地下水样品,可简化操作步骤直接测定NO3^-。该方法测定结果的相对标准偏差为0.73%~2.74%(n=12),样品加标回收率为97.67%~100.28%。所用检测仪器具有流动注射、自动进样及在线绘制标准曲线的功能,简化了标准方法中的样品前处理过程,减少了样品的损失,实现了自动化分析,大幅提高了检测结果的准确度和工作效率。     

Electromagnetic interference shielding and radiation absorption in thin polypyrrole films

Results of permittivity measurements, electromagnetic interference shielding effectiveness, and heat generation due to microwave absorption in conducting polymer coated textiles are reported and discussed. The intrinsically conducting polymer, polypyrrole, doped with anthraquinone-2-sulfonic acid (AQSA) or para-toluene-2-sulfonic acid (pTSA) was applied on textile substrates and the resulting materials were investigated in the frequency range 1-18 GHz. The 0.54 mm thick conducting textile/polypyrrole composites absorbed up to 49.5% of the incident 30-35 W microwave radiation. A thermography station was used to monitor the temperature of these composites during the irradiation process, where absorption was confirmed via visible heat losses. Samples with lower conductivity showed larger temperature increases caused by microwave absorption compared to samples with higher conductivity. A sample with an average sheet resistivity of 150 Ω/sq. showed a maximum temperature increase of 5.27 °C, whilst a sample with a lower resistivity (105 Ω/sq.) rose by 3.85 °C.     

Targeting of Single‐Stranded Oligonucleotides through Metal‐Induced Cyclization of Short Complementary Strands

A new strategy to cyclize short synthetic oligonucleotides on DNA or RNA target strands is described. The approach is based on metal‐templated cyclization of short synthetic oligonucleotides conjugated with two chelating 2,2′ : 6′,2′′‐terpyridine (Tpy) moieties at their 3′‐ and 5′‐ends. Cyclization after metal addition (Zn²⁺, Fe²⁺) was demonstrated by means of thermal‐denaturation experiments, MALDI‐Q‐TOF‐MS, and gel electrophoresis (PAGE). 1D‐ and 2D‐NMR Experiments were performed to analyze the association of complementary strands after metal‐mediated cyclization. Our protocol allows the efficient circularization of synthetic oligonucleotides. Thereby, the hybridization on a complementary strand was more efficient with an RNA target strand and a 2′‐O‐methylated circularized oligomer.     

Potential Achilles heels of SARS-CoV-2 are best displayed by the base order-dependent component of RNA folding energy

The base order-dependent component of folding energy has revealed a highly conserved region in HIV-1 genomes that associates with RNA structure. This corresponds to a packaging signal that is recognized by the nucleocapsid domain of the Gag polyprotein. Long viewed as a potential HIV-1 "Achilles heel," the signal can be targeted by a new antiviral compound. Although SARS-CoV-2 differs in many respects from HIV-1, the same technology displays regions with a high base order-dependent folding energy component, which are also highly conserved. This indicates structural invariance (SI) sustained by natural selection. While the regions are often also protein-encoding (e. g. NSP3, ORF3a), we suggest that their nucleic acid level functions can be considered potential "Achilles heels" for SARS-CoV-2, perhaps susceptible to therapies like those envisaged for AIDS. The ribosomal frameshifting element scored well, but higher SI scores were obtained in other regions, including those encoding NSP13 and the nucleocapsid (N) protein.     

电感耦合等离子体原子发射光谱法测定镍基单晶高温合金中Mo、W、Ta、Re、Ru时元素之间相互干扰的消除与校正的研究

称取镍基单晶高温合金0.100 0g于聚四氟乙烯烧杯中,先令其与盐酸9mL和硝酸1mL加热反应,待反应缓慢时滴加氢氟酸2mL并继续加热使样品完全溶解。加入500g·L^-1酒石酸溶液2mL,冷却至室温,在塑料容量瓶中加水定容至100.0mL。按仪器工作条件采用电感耦合等离子体原子发射光谱法测定其中5种合金元素(Mo、W、Ta、Re、Ru)的含量,选择分析谱线依次为204.598,207.911,240.063,197.312,240.272nm。结果发现:除了Re外,其余4种元素的测定中均受共存元素的光谱干扰,严重影响了测定结果的准确性。为克服其干扰,除了采用基体匹配法消除镍的基体干扰外,试验采用混合校正系数矩阵法对测定结果进行校准。通过一系列试验计算得到混合校准系数矩阵K,并应用于模拟样品的分析。结果表明:经过矩阵K的校准,所测定的5种元素的准确度显著提高,达到了消除共存元素之间光谱干扰的目的。通过精密度试验,测得上述5种元素测定值的相对标准偏差(n=11)均在1.5%以下,并通过标准加入法进行回收试验,测得5种元素的回收率为97.0%~105%。     

Synthesis of novel analogs of aromatic peptide nucleic acids (APNAs) with modified conformational and electrostatic properties

Aromatic peptide nucleic acid analogs having an N-(2-aminobenzyl)glycine backbone (APNA 1) were previously identified as promising new leads for the design of polyaromatic DNA mimics. Structural modifications of 1, which lock the aromatic backbone into a unique conformation, while maintaining the same space distribution between the nucleobases as in 1, were investigated. The electrostatic potential of the aromatic backbone was also modified in an attempt to improve the solubility of these compounds in aqueous media and to evaluate how the quadrapole of the aromatic backbone may influence the biophysical properties of the APNA oligomers. PNA hexamers containing a single monomer insert of each new APNA monomer were used to explore the hybridization properties of these analogs with poly rA and poly dA. Preliminary results indicated that these modifications do not seriously alter the molecular recognition properties of APNAs towards DNA and RNA.     

Antistatic applications of conducting polyaniline

A method is described to impart flexibility and mechanical strength to conducting polyaniline by polymerizing aniline on fabrics and on cellulose papers. The study indicates that these conducting fabrics offer 16–18 dB of shielding effectiveness for the control of electromagnetic interference (EMI) up to a frequency of 10³ MHz.     

Chromatography of plasmid DNA

Liquid chromatography plays a central role in process-scale manufacturing of therapeutic plasmid DNA (pDNA) for gene therapy and DNA vaccination. Apart from its use as a preparative purification step, it is also very useful as an analytical tool to monitor and control pDNA quality during processing and in final formulations. This paper gives an overview of the use of pDNA chromatography. The specificity of pDNA purification and the consequent limitations to the performance of chromatography are described. Strategies currently used to overcome those limitations, as well as other possible solutions are presented. Applications of the different types of chromatography to the purification of therapeutic pDNA are reviewed, and the main advantages and disadvantages behind each technique highlighted.     

Fast folding and comparison of RNA secondary structures

Summary Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minimum free energies as well as at computations of the equilibrium partition functions and base pairing probabilities.An efficient heuristic for the inverse folding problem of RNA is introduced. In addition we present compact and efficient programs for the comparison of RNA secondary structures based on tree editing and alignment.All computer codes are written in ANSI C. They include implementations of modified algorithms on parallel computers with distributed memory. Performance analysis carried out on an Intel Hypercube shows that parallel computing becomes gradually more and more efficient the longer the sequences are.

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Schnelle Faltung und Vergleich von Sekundärstrukturen von RNA

Zusammenfassung Die im Vienna RNA package enthaltenen Computer Programme für die Berechnung und den Vergleich von RNA Sekundärstrukturen werden präsentiert. Ihren Kern bilden Algorithmen zur Vorhersage von Strukturen minimaler Energie sowie zur Berechnung von Zustandssumme und Basenpaarungswahrscheinlichkeiten mittels dynamischer Programmierung.Ein effizienter heuristischer Algorithmus für das inverse Faltungsproblem wird vorgestellt. Darüberhinaus präsentieren wir kompakte und effiziente Programme zum Vergleich von RNA Sekundärstrukturen durch Baum-Editierung und Alignierung.Alle Programme sind in ANSI C geschrieben, darunter auch eine Implementation des Faltungs-algorithmus für Parallelrechner mit verteiltem Speicher. Wie Tests auf einem Intel Hypercube zeigen, wird das Parallelrechnen umso effizienter je länger die Sequenzen sind.