The Role of RNA in Biological Phase Separations

Phase transitions that alter the physical state of ribonucleoprotein particles contribute to the spacial and temporal organization of the densely packed intracellular environment. This allows cells to organize biologically coupled processes as well as respond to environmental stimuli. RNA plays a key role in phase separation events that modulate various aspects of RNA metabolism. Here, we review the role that RNA plays in ribonucleoprotein phase separations.     

Corneal Dystrophy Mutations Drive Pathogenesis by Targeting TGFBIp Stability and Solubility in a Latent Amyloid-forming Domain

Numerous mutations in the corneal protein TGFBIp lead to opaque extracellular deposits and corneal dystrophies (CDs). Here we elucidate the molecular origins underlying TGFBIp's mutation-induced increase in aggregation propensity through comprehensive biophysical and bioinformatic analyses of mutations associated with every major subtype of TGFBIp-linked CDs including lattice corneal dystrophy (LCD) and three subtypes of granular corneal dystrophy (GCD 1–3). LCD mutations at buried positions in the C-terminal Fas1–4 domain lead to decreased stability. GCD variants show biophysical profiles distinct from those of LCD mutations. GCD 1 and 3 mutations reduce solubility rather than stability. Half of the 50 positions within Fas1–4 most sensitive to mutation are associated with at least one known disease-causing mutation, including 10 of the top 11 positions. Thus, TGFBIp aggregation is driven by mutations that despite their physico-chemical diversity target either the stability or solubility of Fas1–4 in predictable ways, suggesting straightforward general therapeutic strategies.     

基于FAHP-TOPSIS法的我国省域低碳发展水平评价

在区分低碳经济与低碳发展的基础上,构建了一套低碳发展指标体系,并采用整合的FAHP-TOPSIS法对我国30个省区进行评价研究。结果表明：①该指标体系是实用且有效的,可以成功的用来评价一个区域的低碳发展水平。②整合的FAHP-TOPSIS法引入了模糊数集,能有效处理专家评估过程中的模糊性,评估结果也符合实际。③2003年到2008年,上海低碳发展水平有所下降,下降率为1.91%;其余各省区均在增长,浙江增长最大,北京增长最小,两者增长率分别为29.73%和0.38%。④北京一直拥有相对最高的低碳发展水平,而辽宁和江西一直分别处于第6和10位。宁夏、青海、甘肃、贵州及河南则一直依次处于低碳发展水平的倒数前5位,且位次不变。最后,分析了评估结果的合理性及不确定性并提出了一些提高省域低碳发展水平的可行途径及未来可进一步研究的方向。     

番茄Sl_OASTL/LCD基因的克隆与表达及其对侧根生长的作用

硫化氢（H2S）是植物中最新发现的一种气体信号分子,高等植物中内源H2S主要由L-型半胱氨酸脱巯基酶（LCD）和D-型半胱氨酸脱巯基酶（DCD）两类蛋白产生。我们的前期研究结果表明外源H2S能够促进植物侧根发育。为了研究内源H2S的产生机制及H2S与一氧化氮（NO）在调控侧根发育中的作用,本实验以番茄幼苗为材料,克隆了编码H2S合成酶基因Sl_OASTL/LCD;研究抑制内源H2S对NO诱导侧根发育的影响;并研究了NO对Sl_OASTL/LCD表达的影响。结果显示：（1）番茄根中存在3个O-乙酰丝氨酸（硫醇）裂解酶基因（Sl_OASTL1、Sl_OASTL2、Sl_OASTL3）。比对和结构分析显示,Sl_OASTL1为编码H2S合成酶基因LCD,所以将Sl_OASTL1命名为Sl_OASTL/LCD;启动子区域分析显示,Sl_OASTL/LCD基因上游含有多个响应NO和植物激素信号的保守基序。（2）与对照相比,内源H2S合成酶抑制剂DL-炔丙基甘氨酸（PAG）和内源H2S清除剂亚牛磺酸（HT）处理均能抑制侧根生长。（3）外源NO供体硝普钠（SNP）显著诱导侧根生长。（4）PAG和HT处理均能够抑制NO对侧根生长的诱导作用。（5）RT-PCR分析显示,SNP处理能够显著诱导幼苗根中Sl_OASTL/LCD的表达。上述结果表明,NO可能通过调控Sl_OASTL/LCD的表达产生内源H2S诱导番茄幼苗侧根发育。     

Behavioural relevance of polarization sensitivity as a target detection mechanism in cephalopods and fishes

Aquatic habitats are rich in polarized patterns that could provide valuable information about the environment to an animal with a visual system sensitive to polarization of light. Both cephalopods and fishes have been shown to behaviourally respond to polarized light cues, suggesting that polarization sensitivity (PS) may play a role in improving target detection and/or navigation/orientation. However, while there is general agreement concerning the presence of PS in cephalopods and some fish species, its functional significance remains uncertain. Testing the role of PS in predator or prey detection seems an excellent paradigm with which to study the contribution of PS to the sensory assets of both groups, because such behaviours are critical to survival. We developed a novel experimental set-up to deliver computer-generated, controllable, polarized stimuli to free-swimming cephalopods and fishes with which we tested the behavioural relevance of PS using stimuli that evoke innate responses (such as an escape response from a looming stimulus and a pursuing behaviour of a small prey-like stimulus). We report consistent responses of cephalopods to looming stimuli presented in polarization and luminance contrast; however, none of the fishes tested responded to either the looming or the prey-like stimuli when presented in polarization contrast.     

Studies of lysine cyclodeaminase from Streptomyces pristinaespiralis: Insights into the complex transition NAD+ state

Lysine cyclodeaminase (LCD) catalyzes the piperidine ring formation in macrolide-pipecolate natural products metabolic pathways from a lysine substrate through a combination of cyclization and deamination. This enzyme belongs to a unique enzyme class, which uses NAD⁺ as the catalytic prosthetic group instead of as the co-substrate. To understand the molecular details of NAD⁺ functions in lysine cyclodeaminase, we have determined four ternary crystal structure complexes of LCD-NAD⁺ with pipecolic acid (LCD-PA), lysine (LCD-LYS), and an intermediate (LCD-INT) as ligands at 2.26-, 2.00-, 2.17- and 1.80 Å resolutions, respectively. By combining computational studies, a NAD⁺-mediated “gate keeper” function involving NAD⁺/NADH and Arg49 that control the binding and entry of the ligand lysine was revealed, confirming the critical roles of NAD⁺ in the substrate access process. Further, in the gate opening form, a substrate delivery tunnel between ε-carboxyl moiety of Glu264 and the α-carboxyl moiety of Asp236 was observed through a comparison of four structure complexes. The LCD structure details including NAD⁺-mediated “gate keeper” and substrate tunnel may assist in the exploration the NAD⁺ function in this unique enzyme class, and in regulation of macrolide-pipecolate natural product synthesis.     

Synergistic contribution of SMAD signaling blockade and high localized cell density in the differentiation of neuroectoderm from H9 cells

Directed neural differentiation of human embryonic stem cells (ESCs) enables researchers to generate diverse neuronal populations for human neural development study and cell replacement therapy. To realize this potential, it is critical to precisely understand the role of various endogenous and exogenous factors involved in neural differentiation. Cell density, one of the endogenous factors, is involved in the differentiation of human ESCs. Seeding cell density can result in variable terminal cell densities or localized cell densities (LCDs), giving rise to various outcomes of differentiation. Thus, understanding how LCD determines the differentiation potential of human ESCs is important. The aim of this study is to highlight the role of LCD in the differentiation of H9 human ESCs into neuroectoderm (NE), the primordium of the nervous system. We found the initially seeded cells form derived cells with variable LCDs and subsequently affect the NE differentiation. Using a newly established method for the quantitative examination of LCD, we demonstrated that in the presence of induction medium supplemented with or without SMAD signaling blockers, high LCD promotes the differentiation of NE. Moreover, SMAD signaling blockade promotes the differentiation of NE but not non-NE germ layers, which is dependent on high LCDs. Taken together, this study highlights the need to develop innovative strategies or techniques based on LCDs for generating neural progenies from human ESCs.     

Similarities and differences between frozen-hydrated, rigor acto-S1 complexes of insect flight and chicken skeletal muscles

The structure and function of myosin crossbridges in asynchronous insect flight muscle (IFM) have been elucidated in situ using multiple approaches. These include generating “atomic” models of myosin in multiple contractile states by rebuilding the crystal structure of chicken subfragment 1 (S1) to fit IFM crossbridges in lower-resolution electron microscopy tomograms and by “mapping” the functional effects of genetically substituted, isoform-specific domains, including the converter domain, in chimeric IFM myosin to sequences in the crystal structure of chicken S1.We prepared helical reconstructions (∼ 25 Å resolution) to compare the structural characteristics of nucleotide-free myosin0 S1 bound to actin (acto-S1) isolated from chicken skeletal muscle (CSk) and the flight muscles of Lethocerus (Leth) wild-type Drosophila (wt Dros) and a Drosophila chimera (IFI-EC) wherein the converter domain of the indirect flight muscle myosin isoform has been replaced by the embryonic skeletal myosin converter domain. Superimposition of the maps of the frozen-hydrated acto-S1 complexes shows that differences between CSk and IFM S1 are limited to the azimuthal curvature of the lever arm: the regulatory light-chain (RLC) region of chicken skeletal S1 bends clockwise (as seen from the pointed end of actin) while those of IFM S1 project in a straight radial direction. All the IFM S1s are essentially identical other than some variation in the azimuthal spread of density in the RLC region. This spread is most pronounced in the IFI-EC S1, consistent with proposals that the embryonic converter domain increases the compliance of the IFM lever arm affecting the function of the myosin motor. These are the first unconstrained models of IFM S1 bound to actin and the first direct comparison of the vertebrate and invertebrate skeletal myosin II classes, the latter for which, data on the structure of discrete acto-S1 complexes, are not readily available.