Photoregulation of Gene Expression with Ligand-Modified Caged siRNAs through Host/Guest Interaction

Small interfering RNA (siRNA) can effectively silence target genes through Argonate 2 (Ago2)-induced RNA interference (RNAi). It is very important to control siRNA activity in both spatial and temporal modes. Among different masking strategies, photocaging can be used to regulate gene expression through light irradiation with spatiotemporal and dose-dependent resolution. Many different caging strategies and caging groups have been reported for light-activated siRNA gene silencing. Herein, we describe a novel caging strategy that increases the blocking effect of RISC complex formation/process through host/guest (including ligand/receptor) interactions, thereby enhancing the inhibition of caged siRNA activity until light activation. This strategy can be used as a general approach to design caged siRNAs for the photomodulation of gene silencing of exogenous and endogenous genes.     

用于厚屏蔽小探测器的蒙特卡罗模拟减方差方法研究

反应堆屏蔽计算中经常出现厚屏蔽、小探测器问题，常规蒙特卡罗方法难以有效解决。基于自动重要抽样（AIS）方法，本文提出了小探测器自动重要抽样(SDAIS)方法，并针对小探测器问题，优化了AIS方法的虚粒子赌分裂算法。该方法在自主开发的蒙特卡罗屏蔽程序MCShield上进行了实现。使用NUREG/CR-6115 PWR基准题验证该方法的正确性和计算效率。结果表明，SDAIS方法可有效地解决厚屏蔽小探测器问题，相比AIS方法及传统的重要性方法，计算效率提升1~2个量级。     

Regulatory RNAs: A Universal Language for Inter-Domain Communication

In eukaryotes, microRNAs (miRNAs) have roles in development, homeostasis, disease and the immune response. Recent work has shown that plant and mammalian miRNAs also mediate cross-kingdom and cross-domain communications. However, these studies remain controversial and are lacking critical mechanistic explanations. Bacteria do not produce miRNAs themselves, and therefore it is unclear how these eukaryotic RNA molecules could function in the bacterial recipient. In this review, we compare and contrast the biogenesis and functions of regulatory RNAs in eukaryotes and bacteria. As a result, we discovered several conserved features and homologous components in these distinct pathways. These findings enabled us to propose novel mechanisms to explain how eukaryotic miRNAs could function in bacteria. Further understanding in this area is necessary to validate the findings of existing studies and could facilitate the use of miRNAs as novel tools for the directed remodelling of the human microbiota.     

一种基于小字典不对等语料的跨语言词嵌入方法

双语词嵌入通常采用从源语言空间到目标语言空间映射,通过源语言映射嵌入到目标语言空间的最小距离线性变换实现跨语言词嵌入。然而大型的平行语料难以获得,词嵌入的准确率难以提高。针对语料数量不对等、双语语料稀缺情况下的跨语言词嵌入问题,该文提出一种基于小字典不对等语料的跨语言词嵌入方法,首先对单语词向量进行归一化,对小字典词对正交最优线性变换求得梯度下降初始值,然后通过对大型源语言(英语)语料进行聚类,借助小字典找到与每一聚类簇相对应的源语言词,取聚类得到的每一簇词向量均值和源语言与目标语言对应的词向量均值,建立新的双语词向量对应关系,将新建立的双语词向量扩展到小字典中,使得小字典得以泛化和扩展。最后,利用泛化扩展后的字典对跨语言词嵌入映射模型进行梯度下降求得最优值。在英语—意大利语、德语和芬兰语上进行了实验验证,实验结果证明该文方法可以在跨语言词嵌入中减少梯度下降迭代次数,减少训练时间,同时在跨语言词嵌入上表现出较好的正确率。     

Epigenetic Targets for Oligonucleotide Therapies of Pulmonary Arterial Hypertension

Arterial wall remodeling underlies increased pulmonary vascular resistance and right heart failure in pulmonary arterial hypertension (PAH). None of the established vasodilator drug therapies for PAH prevents or reverse established arterial wall thickening, stiffening, and hypercontractility. Therefore, new approaches are needed to achieve long-acting prevention and reversal of occlusive pulmonary vascular remodeling. Several promising new drug classes are emerging from a better understanding of pulmonary vascular gene expression programs. In this review, potential epigenetic targets for small molecules and oligonucleotides will be described. Most are in preclinical studies aimed at modifying the growth of vascular wall cells in vitro or normalizing vascular remodeling in PAH animal models. Initial success with lung-directed delivery of oligonucleotides targeting microRNAs suggests other epigenetic mechanisms might also be suitable drug targets. Those targets include DNA methylation, proteins of the chromatin remodeling machinery, and long noncoding RNAs, all of which act as epigenetic regulators of vascular wall structure and function. The progress in testing small molecules and oligonucleotide-based drugs in PAH models is summarized.     

The organization of biological sequences into constrained and unconstrained parts determines fundamental properties of genotype–phenotype maps

Biological information is stored in DNA, RNA and protein sequences, which can be understood as genotypes that are translated into phenotypes. The properties of genotype–phenotype (GP) maps have been studied in great detail for RNA secondary structure. These include a highly biased distribution of genotypes per phenotype, negative correlation of genotypic robustness and evolvability, positive correlation of phenotypic robustness and evolvability, shape-space covering, and a roughly logarithmic scaling of phenotypic robustness with phenotypic frequency. More recently similar properties have been discovered in other GP maps, suggesting that they may be fundamental to biological GP maps, in general, rather than specific to the RNA secondary structure map. Here we propose that the above properties arise from the fundamental organization of biological information into ‘constrained'' and ‘unconstrained'' sequences, in the broadest possible sense. As ‘constrained'' we describe sequences that affect the phenotype more immediately, and are therefore more sensitive to mutations, such as, e.g. protein-coding DNA or the stems in RNA secondary structure. ‘Unconstrained'' sequences, on the other hand, can mutate more freely without affecting the phenotype, such as, e.g. intronic or intergenic DNA or the loops in RNA secondary structure. To test our hypothesis we consider a highly simplified GP map that has genotypes with ‘coding'' and ‘non-coding'' parts. We term this the Fibonacci GP map, as it is equivalent to the Fibonacci code in information theory. Despite its simplicity the Fibonacci GP map exhibits all the above properties of much more complex and biologically realistic GP maps. These properties are therefore likely to be fundamental to many biological GP maps.