Generalization of a Suffix Tree for RNA Structural Pattern Matching

In molecular biology, it is said that two biological sequences tend to have similar properties if they have similar three-dimensional structures. Hence, it is very important to find not only similar sequences in the string sense, but also structurally similar sequences from databases. In this paper we propose a new data structure that is a generalization of a parameterized suffix tree (p-suffix tree for short) introduced by Baker. We call it the structural suffix tree or s-suffix tree for short. The s-suffix tree can be used for finding structurally related patterns of RNA or single-stranded DNA. Furthermore, we propose an O(n(log|| + log||)) on-line algorithm for constructing it, where n is the sequence length, || is the size of the normal alphabet, and || is that of the alphabet called parameter, which is related to the structure of the sequence. Our algorithm achieves linear time when it is used to analyze RNA and DNA sequences. Furthermore, as an algorithm for constructing the p-suffix tree, it is the first on-line algorithm, though the computing bound of our algorithm is the same as that of Kosarajus best-known algorithm. The results of computational experiments using actual RNA and DNA sequences are also given to demonstrate our algorithms practicality.     

基于奇异值分解的RNA二级结构相似度计算方法

针对传统的核糖核酸(RNA)分子结构相似度计算方法存在复杂度高、未能充分考虑二级结构全局信息的缺点,基于一种7维序列编码方法，提出了一种利用矩阵奇异值分解提取RNA二级结构数据分布特征的算法，利用提取出的奇异值向量,基于向量距离进行RNA二级结构相似度比对.通过对Yeast tRNA phe、PSTV、poliovirus mutant 3种RNA分子二级结构构象的实验分析，表明了该方法的可行性和高效性.并将这种方法推广至任意两个RNA分子之间二级结构的相似度衡量，同样取得了不错的效果.     

Iron‐Oxide‐Based Nanovector for Tumor Targeted siRNA Delivery in an Orthotopic Hepatocellular Carcinoma Xenograft Mouse Model

Hepatocellular carcinoma (HCC) is one of the deadliest cancers worldwide. Small interfering RNA (siRNA) holds promise as a new class of therapeutics for HCC, as it can achieve sequence‐specific gene knockdown with low cytotoxicity. However, the main challenge in the clinical application of siRNA lies in the lack of effective delivery approaches that need to be highly specific and thus incur low or no systemic toxicity. Here, a nonviral nanoparticle‐based gene carrier is presented that can specifically deliver siRNA to HCC. The nanovector (NP‐siRNA‐GPC3 Ab) is made of an iron oxide core coated with chitosan‐polyethylene glycol (PEG) grafted polyethyleneimine copolymer, which is further functionalized with siRNA and conjugated with a monoclonal antibody (Ab) against human glypican‐3 (GPC3) receptor highly expressed in HCC. A rat RH7777 HCC cell line that coexpresses human GPC3 and firefly luciferase (Luc) is established to evaluate the nanovector. The nanoparticle‐mediated delivery of siRNA against Luc effectively suppresses Luc expression in vitro without notable cytotoxicity. Significantly, NP‐siLuc‐GPC3 Ab administered intravenously in an orthotopic model of HCC is able to specifically bound to tumor and induce remarkable inhibition of Luc expression. The findings demonstrate the potential of using this nanovector for targeted delivery of therapeutic siRNA to HCC.     

Cooperative Treatment of Metastatic Breast Cancer Using Host–Guest Nanoplatform Coloaded with Docetaxel and siRNA

Conventional chemotherapy shows moderate efficiency against metastatic cancer since it targets only part of the mechanisms regulating tumor growth and metastasis. Here, gold nanorod (GNR)‐based host‐guest nanoplatforms loaded with docetaxel (DTX) and small interfering RNA (siRNA)‐p65 (referred to as DTX‐loaded GNR (GDTX)/p65) for chemo‐, RNA interference (RNAi), and photothermal ablation (PTA) cooperative treatment of metastatic breast cancer are reported. To prepare the nanoplatform, GNRs are first coated with cyclodextrin (CD)‐grafted polyethylenimine (PEI) and then loaded with DTX and siRNA through host–guest interaction with CD and electrostatic interaction with PEI, respectively. Upon near‐infrared laser irradiation, GNRs generate a significant hyperthermia effect to trigger siRNA and DTX release. DTX reduces tumor growth by inhibiting mitosis of cancer cells. Meanwhile, siRNA‐p65 suppresses lung metastasis and proliferation of cancer cells by blocking the nuclear factor kappa B (NF‐κB) pathway and downregulating the downstream genes matrix metalloproteinase‐9 (MMP‐9) and B cell lymphoma‐2 (Bcl‐2). It is demonstrated that GDTX/p65 in combination with laser irradiation significantly inhibits the growth and lung metastasis of 4T1 breast tumors. The antitumor results suggest promising potential of the host–guest nanoplatform for combinational treatment of metastatic cancer by using RNAi, chemotherapy, and PTA.     

Dynamics of alternative modes of RNA replication for positive-sense RNA viruses

We propose and study nonlinear mathematical models describing the intracellular time dynamics of viral RNA accumulation for positive-sense single-stranded RNA viruses. Our models consider different replication modes ranging between two extremes represented by the geometric replication (GR) and the linear stamping machine replication (SMR). We first analyse a model that quantitatively reproduced experimental data for the accumulation dynamics of both polarities of turnip mosaic potyvirus RNAs. We identify a non-degenerate transcritical bifurcation governing the extinction of both strands depending on three key parameters: the mode of replication (α), the replication rate (r) and the degradation rate (δ) of viral strands. Our results indicate that the bifurcation associated with α generically takes place when the replication mode is closer to the SMR, thus suggesting that GR may provide viral strands with an increased robustness against degradation. This transcritical bifurcation, which is responsible for the switching from an active to an absorbing regime, suggests a smooth (i.e. second-order), absorbing-state phase transition. Finally, we also analyse a simplified model that only incorporates asymmetry in replication tied to differential replication modes.     

Characterization of microbial communities in a fluidized-pellet-bed bioreactor for wastewater treatment

In order to make clear the microbiological characteristics of the fluidized-pellet-bed bioreactor (FPB) which is a newly developed wastewater treatment device to perform coagulation, particle pelletization, biological degradation and solid-liquid separation in a single unit, the method of denaturing gradient gel electrophoresis (DGGE) was applied in this study paying attention to the microbial diversity of the granular sludge. Spread plate method was also used for enumeration of aerobic bacteria in unit weight of granular sludge. As a result, slight difference was found between the total aerobic bacteria at the bottom, middle, and top sections though the dissolved oxygen (DO) concentration decreased from about 3.5 mg/L at the bottom inlet to 0.23 mg/L at the top of the FPB bioreactor. From the DGGE finger printing, 17 common species were identified from all these sections, and certain specific species were also identified from each section. The comparability of the microbial communities in the three sections was 83.1%, indicating a very stable structure of the microbial communities. The 16 S rRNA sequence analysis results revealed that the 18 operational taxonomic units (OTUs) obtained all belong to Eubacteria. Among them 11 are Proteobacteria, 3 are Actinobacteria, 2 are low G + C gram-positive bacteria and the remaining 2 belong to other bacteria branches. The dominant microbial communities are typical aerobes or facultative anaerobes commonly encountered in conventional activated sludge.     

An Algorithm for Predicting RNA Secondary Structure Including Pseudoknots

A new model and corresponding dynamic programming algorithm are presented to predict RNA secondary structure including pseudoknots in this paper. This algorithm can compute arbitrary planar pseudoknots and one non-planar pseudoknots in O（n5） time and O（n4） space.     

Transmission electron microscopy and scanning force microscopy of poly r(A-U) and poly r(A-U)-ethidium bromide

Transmission electron microscopy and scanning force microscopy of negative-stained, carbon-coated replica and mica-adsorbed preparations of 200 μM poly r(A-U) and 50 μM ethidium bromide/200 μM poly r(A-U) have been employed to evaluate ethidium-induced changes in poly r(A-U) topology. Poly r(A-U) alone exhibits elongated conformations 85–115 nm in length that possess a number of hairpin loops as well as single-stranded domains. While the double-stranded domains are found predominately at the base of the hairpin loops (diameter = 5–30 nm), other rod-like (presumably double-stranded) regions ranging from 25–80 nm in length are present in other portions of the poly r(A-U). In contrast with the poly r(A-U) alone, the EB/poly r(A-U) combination appears as a heterogeneous population of condensed structures whose lengths and widths vary from 12–88 nm and 15–45 nm, respectively. These conformational changes are due to a number of factors, including the displacement of ordered water surrounding the poly r(A-U) and charge shielding of the phosphate groups of the poly r(A-U) upon the binding of the ethidium.     

RNA Relics and Origin of Life

A number of small RNA sequences, located in different non-coding sequences and highly preserved across the tree of life, have been suggested to be molecular fossils, of ancient (and possibly primordial) origin. On the other hand, recent years have revealed the existence of ubiquitous roles for small RNA sequences in modern organisms, in functions ranging from cell regulation to antiviral activity. We propose that a single thread can be followed from the beginning of life in RNA structures selected only for stability reasons through the RNA relics and up to the current coevolution of RNA sequences; such an understanding would shed light both on the history and on the present development of the RNA machinery and interactions. After presenting the evidence (by comparing their sequences) that points toward a common thread, we discuss a scenario of genome coevolution (with emphasis on viral infectious processes) and finally propose a plan for the reevaluation of the stereochemical theory of the genetic code; we claim that it may still be relevant, and not only for understanding the origin of life, but also for a comprehensive picture of regulation in present-day cells.