基于词汇化随机文法模型的RNA二级结构预测

针对经典的随机文法模型预测RNA二级结构存在精度不高的问题,本文给出了一种词汇化随机文法模型预测RNA二级结构的方法。首先,用最大熵模型获取RNA序列中的词条信息,通过Viterbi算法搜索每个词条被标注为某种二级结构类型的最大概率;然后,将这些词条信息作为先验信息在随机文法模型训练过程中引入,从而加快对二级结构的搜索过程,提高准确率。     

基于快速动态权重匹配的RNA二级结构预测算法

在动态权重匹配算法的基础上提出了基于快速动态权重匹配的RNA二级结构预测算法。通过引入最大动态权重茎区搜索算法降低时间复杂度和扩大搜索假结的区域提高预测假结的能力,使得快速动态权重匹配算法与动态权重匹配算法相比,不仅具有O(n3)的更加理想的时间复杂度,而且还能预测更多可能存在的假结。     

Next‐Generation Sequencing Reveals Differential Responses to Acute versus Long‐Term Exposures to Graphene Oxide in Human Lung Cells

Numerous studies have addressed the biological impact of graphene‐based materials including graphene oxide (GO), yet few have focused on long‐term effects. Here, RNA sequencing is utilized to unearth responses of human lung cells to GO. To this end, the BEAS‐2B cell line derived from normal human bronchial epithelium is subjected to repeated, low‐dose exposures of GO (1 or 5 µg mL^?1) for 28 days or to the equivalent, cumulative amount of GO for 48 h. Then, samples are analyzed by using the NovaSeq 6000 sequencing system followed by pathway analysis and gene ontology enrichment analysis of the differentially expressed genes. Significant differences are seen between the low‐dose, long‐term exposures and the high‐dose, short‐term exposures. Hence, exposure to GO for 48 h results in mitochondrial dysfunction. In contrast, exposure to GO for 28 days is characterized by engagement of apoptosis pathways with downregulation of genes belonging to the inhibitor of apoptosis protein (IAP) family. Validation experiments confirm that long‐term exposure to GO affects the apoptosis threshold in lung cells, accompanied by a loss of IAPs. These studies reveal the sensitivity of RNA‐sequencing approaches and show that acute exposure to GO is not a good predictor of the long‐term effects of GO.     

Rekindling RNAi Therapy: Materials Design Requirements for In Vivo siRNA Delivery

With the recent FDA approval of the first siRNA‐derived therapeutic, RNA interference (RNAi)‐mediated gene therapy is undergoing a transition from research to the clinical space. The primary obstacle to realization of RNAi therapy has been the delivery of oligonucleotide payloads. Therefore, the main aims is to identify and describe key design features needed for nanoscale vehicles to achieve effective delivery of siRNA‐mediated gene silencing agents in vivo. The problem is broken into three elements: 1) protection of siRNA from degradation and clearance; 2) selective homing to target cell types; and 3) cytoplasmic release of the siRNA payload by escaping or bypassing endocytic uptake. The in vitro and in vivo gene silencing efficiency values that have been reported in publications over the past decade are quantitatively summarized by material type (lipid, polymer, metal, mesoporous silica, and porous silicon), and the overall trends in research publication and in clinical translation are discussed to reflect on the direction of the RNAi therapeutics field.     

HPLC法测定酵母RNA降解的4种核苷酸

采用反相高效液相色谱 (HPL C)分离了酵母 RNA降解的 4种核苷酸。检测波长为 2 5 4 nm,流动相为2 0 mm ol· L- 1 (NH4 ) H2 PO4 。方法精密度分别为 RSDCMP=1.79% ,RSDUMP=0 .36 % ,RSDGMP=0 .79% ,RSDAMP=0 .5 7% ,测得的 4种核苷酸的回收率分别为 98.9% ,99.1% ,10 0 .8%和 99.9%。     

Photocrosslinking of RNA and PhotoMet‐Containing Amphiphilic α‐Helical Peptides

Discovering RNA–protein interactions : A library of photoMet‐containing peptides was synthesized by using an Arg‐ and Leu‐rich α‐helical amphiphilic peptide. Irradiation of mixtures of these peptides and Rev‐responsive element (RRE) hairpin RNA promoted formation of covalent adducts. Analysis of one adduct showed that U26 in the bulged stem is responsible for covalent bond formation with the carbene intermediate. This strategy can provide important structural information about RNA–peptide interactions.

     

Bacterial Alarmone,Guanosine 5′‐Diphosphate 3′‐Diphosphate (ppGpp), Predominantly Binds the β′ Subunit of Plastid‐Encoded Plastid RNA Polymerase in Chloroplasts

It's alarming : Bacterial alarmone guanosine 5′‐diphosphate 3′‐diphosphate (ppGpp), which is a key regulatory molecule that controls the stringent response, also exists in chloroplasts of plant cells. Cross‐linking experiments with 6‐thioguanosine 5′‐diphosphate 3′‐diphosphate (6‐thioppGpp) and chloroplast RNA polymerase indicate that ppGpp binds the β′ subunit of plastid‐encoded plastid RNA polymerase that corresponds to the Escherichia coli β′ subunit.