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Science论文导读 1103

时间: 2017年11月14日 | 作者: admin | 来源: 未知
Science20171103 1 【生物】 Structure of the mitochondrial inner membrane AAA+ protease YME1 gives insight into substrate processing Cristina Puchades et.al 线粒体内膜 AAA + 蛋白酶 YME1 的结构解析揭示其底物处理机制

Science20171103

1【生物】Structure of the mitochondrial inner membrane AAA+ protease YME1 gives insight into substrate processing

 

Cristina Puchades et.al

 

线粒体内膜AAA +蛋白酶YME1的结构解析揭示其底物处理机制

 

http://science.sciencemag.org/content/358/6363/eaao0464

 

(导读 严冰)固定于酵母线粒体内膜的AAA+蛋白酶YME1负责线粒体内蛋白质的质量控制,含有ATPase域和蛋白酶域。本文通过冷冻电镜解析出其ATPase域的高分辨率结构,发现ATPase域呈闭合的非对称螺旋阶梯状,将未折叠的底物环绕其中,中央孔道内保守的酪氨酸残基与底物多肽接触,通过ATP水解循环改变酪氨酸位置,从而将底物转运至楼梯底部的环状蛋白酶域中。该转运机制很可能也适用于其他的AAA+ ATPase

图片2.png 

We present an atomic model of a substrate-bound inner mitochondrial membrane AAA+ quality control protease in yeast, YME1. Our ~3.4-angstrom cryo–electron microscopy structure reveals how the adenosine triphosphatases (ATPases) form a closed spiral staircase encircling an unfolded substrate, directing it toward the flat, symmetric protease ring. Three coexisting nucleotide states allosterically induce distinct positioning of tyrosines in the central channel, resulting in substrate engagement and translocation to the negatively charged proteolytic chamber. This tight coordination by a network of conserved residues defines a sequential, around-the-ring adenosine triphosphate hydrolysis cycle that results in stepwise substrate translocation. A hingelike linker accommodates the large-scale nucleotide-driven motions of the ATPase spiral relative to the planar proteolytic base. The translocation mechanism is likely conserved for other AAA+ ATPases.

 

2【生物】Lattice system of functionally distinct cell types in the neocortex

Hisato Maruoka et.al

 

新皮质中功能不同的细胞组成栅栏系统

 

http://science.sciencemag.org/content/358/6363/610

 

(导读 严冰)哺乳动物新皮质中不同类型的细胞是否会形成反复的结构模式还未研究清楚。本文报道位于新皮质第五层的不同类型细胞形成细胞类型特异性的放射状聚簇结构——微柱(microcolumn),大量的微柱形成六角形马赛克模式镶嵌在不同新皮质区域。位于同一微柱内的神经元有相似特征的视觉反应。早期产后发育时期,微柱由细胞类型特异性的缝隙链接相连,发育后期称为聚合性突触输入的中心。这为皮质信号处理研究提供模板。

 

The mammalian neocortex contains many cell types, but whether they organize into repeated structures has been unclear. We discovered that major cell types in neocortical layer 5 form a lattice structure in many brain areas. Large-scale three-dimensional imaging revealed that distinct types of excitatory and inhibitory neurons form cell type–specific radial clusters termed microcolumns. Thousands of microcolumns, in turn, are patterned into a hexagonal mosaic tessellating diverse regions of the neocortex. Microcolumn neurons demonstrate synchronized in vivo activity and visual responses with similar orientation preference and ocular dominance. In early postnatal development, microcolumns are coupled by cell type–specific gap junctions and later serve as hubs for convergent synaptic inputs. Thus, layer 5 neurons organize into a brainwide modular system, providing a template for cortical processing.

 

3 【神经】Topological and modality-specific representation of somatosensory information in the fly brain

Asako Tsubouchi and Tomoko Yano et.al

果蝇大脑体感信息的拓扑和特定模式表征

http://science.sciencemag.org/content/358/6363/615

 

(导读 阿金)本研究发现昆虫体感神经类型投射模式与脊髓与哺乳动物的脊髓神经节的类似。腹侧大脑支配的感觉神经直接形成特定模式和拓扑体感地图。了解基本模式和创立基因工具将为阐明躯体感觉产生机制提供基础。

 

Insects and mammals share similarities of neural organization underlying the perception of odors, taste, vision, sound, and gravity. We observed that insect somatosensation also corresponds to that of mammals. In Drosophila, the projections of all the somatosensory neuron types to the insect’s equivalent of the spinal cord segregated into modality-specific layers comparable to those in mammals. Some sensory neurons innervate the ventral brain directly to form modality-specific and topological somatosensory maps. Ascending interneurons with dendrites in matching layers of the nerve cord send axons that converge to respective brain regions. Pathways arising from leg somatosensory neurons encode distinct qualities of leg movement information and play different roles in ground detection. Establishment of the ground pattern and genetic tools for neuronal manipulation should provide the basis for elucidating the mechanisms underlying somatosensation.

 

4 【生物】ER-mitochondria tethering by PDZD8 regulates Ca2+ dynamics in mammalian neurons

Yusuke Hirabayashi and Seok-Kyu Kwon et.al

PDZD8介导的ER-线粒体耦合调控哺乳动物神经元胞质内Ca 2+动态变化

http://science.sciencemag.org/content/358/6363/623

(导读 严冰)在酵母中的ERMES复合物可连接内质网(ER)与线粒体,但后生动物中并未发现任何ERMES蛋白的直系同源物。本文报导,哺乳动物的ER-线粒体连接形成需要PDZD8蛋白,其SMP域与酵母Mmm1SMP域功能上同源。在神经细胞中,突触信号诱导ER释放Ca2+后,需要PDZD8来实现线粒体的Ca2+吸收,因此ER-线粒体耦合很可能与神经细胞树突的Ca2+动态变化有关。

Interfaces between organelles are emerging as critical platforms for many biological responses in eukaryotic cells. In yeast, the ERMES complex is an endoplasmic reticulum (ER)–mitochondria tether composed of four proteins, three of which contain a SMP (synaptotagmin-like mitochondrial-lipid binding protein) domain. No functional ortholog for any ERMES protein has been identified in metazoans. Here, we identified PDZD8 as an ER protein present at ER-mitochondria contacts. The SMP domain of PDZD8 is functionally orthologous to the SMP domain found in yeast Mmm1. PDZD8 was necessary for the formation of ER-mitochondria contacts in mammalian cells. In neurons, PDZD8 was required for calcium ion (Ca2+) uptake by mitochondria after synaptically induced Ca2+-release from ER and thereby regulated cytoplasmic Ca2+ dynamics. Thus, PDZD8 represents a critical ER-mitochondria tethering protein in metazoans. We suggest that ER-mitochondria coupling is involved in the regulation of dendritic Ca2+ dynamics in mammalian neurons.

 

5.【物理】 High-speed plasmonic modulator in a single metal layer

单层金属层中的高速等离子体调制器

Masafumi Ayata, Juerg Leuthold et al.

http://science.sciencemag.org/content/358/6363/630

 

Plasmonics provides a possible route to overcome both the speed limitations of electronics and the critical dimensions of photonics. We present an all-plasmonic 116–gigabits per second electro-optical modulator in which all the elements—the vertical grating couplers, splitters, polarization rotators, and active section with phase shifters—are included in a single metal layer. The device can be realized on any smooth substrate surface and operates with low energy consumption. Our results show that plasmonics is indeed a viable path to an ultracompact, highest-speed, and low-cost technology that might find many applications in a wide range of fields of sensing and communications because it is compatible with and can be placed on a wide variety of materials.

 

(导读 葛鹏)表面等离子体为克服电子器件的速度和尺寸限制提供了新的途径。本研究展示了一种速度达116千兆比特每秒的全等离子体电光调制器,其中包含的垂直光栅耦合器、分配器、偏振旋转器、移相器有效截面等所有元素均在单层金属层中。该器件可以基于多种衬底表面,且耗能低因此在传感和通信领域的用途非常广泛

 

 

6 【化学】Self-assembled three-dimensional chiral colloidal architecture

自组装的三维手性胶体结构

Matan Yah Ben Zion et.al

http://science.sciencemag.org/content/358/6363/633http://science.sciencemag.org/content/358/6360/206

 

(导读 魏甜甜)尽管立体化学处于分子科学的研究中心,但它的研究领域先前一直被限制在纳米尺度。本研究通过结合DNA纳米技术和胶体科学实现了微米级胶体团簇的自组装。利用DNA弯折的功能弹性与胶粒的结构刚性,作者展示了三维微构造的平行自组装,并显示出其高度具体的几何结构,包括控制位置、二面角和团簇手性。

 

Although stereochemistry has been a central focus of the molecular sciences since Pasteur, its province has previously been restricted to the nanometric scale. We have programmed the self-assembly of micron-sized colloidal clusters with structural information stemming from a nanometric arrangement. This was done by combining DNA nanotechnology with colloidal science. Using the functional flexibility of DNA origami in conjunction with the structural rigidity of colloidal particles, we demonstrate the parallel self-assembly of three-dimensional microconstructs, evincing highly specific geometry that includes control over position, dihedral angles, and cluster chirality.

 

7 【物理】Nonreciprocal lasing in topological cavities of arbitrary geometries

Babak Bahari, et.al

在任意几何形状拓扑空腔中的非互易激光振荡器

http://science.sciencemag.org/content/358/6363/636

 

(导读 阿金)光学谐振腔因其几何形状和互易性限制了光学器件的集成。本研究研发出一种工作在通信波段的新型激光器,在几何独立的集成非互易拓扑腔内,将单向光子边缘态的受激辐射耦合到特定的波导输出,其隔离比例超过10dB。研究结果为开发任意形状的复杂拓扑电路开辟了新道路。

 

Resonant cavities are essential building blocks governing many wave-based phenomena, but their geometry and reciprocity fundamentally limit the integration of optical devices. We report, at telecommunication wavelengths, geometry-independent and integrated nonreciprocal topological cavities that couple stimulated emission from one-way photonic edge states to a selected waveguide output with an isolation ratio in excess of 10 decibels. Nonreciprocity originates from unidirectional edge states at the boundary between photonic structures with distinct topological invariants. Our experimental demonstration of lasing from topological cavities provides the opportunity to develop complex topological circuitry of arbitrary geometries for the integrated and robust generation and transport of photons in classical and quantum regimes.

 


8 【物理】Femtosecond laser reshaping yields gold nanorods with ultranarrow surface plasmon resonances

Guillermo González-Rubio et.al

飞秒激光重塑可产生具有超窄表面等离子体共振的金纳米棒

http://science.sciencemag.org/content/358/6363/640

 

(导读 阿金)本研究利用飞秒激光金纳米棒进行调控重塑,从而得到超窄局域化表面等离子体共振带这个过程需要在纳米棒表面活性剂的表面密度与照射能量之间实现巧妙的平衡,因为低冷却速率可产生剧烈的形态变化。研究结果为实现具有光学响应、接近理论极限的高品质金纳米棒提供了一个简单、快速、可重复操作的方法。

 

The irradiation of gold nanorod colloids with a femtosecond laser can be tuned to induce controlled nanorod reshaping, yielding colloids with exceptionally narrow localized surface plasmon resonance bands. The process relies on a regime characterized by a gentle multishot reduction of the aspect ratio, whereas the rod shape and volume are barely affected. Successful reshaping can only occur within a narrow window of the heat dissipation rate: Low cooling rates lead to drastic morphological changes, and fast cooling has nearly no effect. Hence, a delicate balance must be achieved between irradiation fluence and surface density of the surfactant on the nanorods. This perfection process is appealing because it provides a simple, fast, reproducible, and scalable route toward gold nanorods with an optical response of exceptional quality, near the theoretical limit.

 

 

9 【物理】A cryofuge for cold-collision experiments with slow polar molecules

Xing Wu et.al

可以进行低极性分子冷碰撞实验的冷冻离心机

http://science.sciencemag.org/content/358/6363/645

 

(导读 阿金)超冷分子作为前沿研究项目,在低速下制备其高密度样品仍具挑战。本研究通过使用非常规的冷冻离心机技术,将低温冷却的分子动能调控至1 K × kB (波尔兹曼常数),使氟代甲烷和氘代氨样品密度高于每立方厘米109,相互作用时间超过25毫秒,并观察到分子间的低温偶极碰撞,确定了它们的碰撞截面。

 

Ultracold molecules represent a fascinating research frontier in physics and chemistry, but it has proven challenging to prepare dense samples at low velocities. Here, we present a solution to this goal by means of a nonconventional approach dubbed cryofuge. It uses centrifugal force to bring cryogenically cooled molecules to kinetic energies below 1 K × kB in the laboratory frame, where kB is the Boltzmann constant, with corresponding fluxes exceeding 1010 per second at velocities below 20 meters per second. By attaining densities higher than 109 per cubic centimeter and interaction times longer than 25 milliseconds in samples of fluoromethane as well as deuterated ammonia, we observed cold dipolar collisions between molecules and determined their collision cross sections.

 

 

 

10 【物理】Even-denominator fractional quantum Hall states in bilayer graphene

J. I. A. Li et.al

双层石墨烯(BLG)中偶分母分数的量子霍尔态

http://science.sciencemag.org/content/358/6363/648

 

(导读 阿金)理论预测BLG的独特朗道能级谱支持非阿贝尔偶分母分数量子霍尔(FQH)态,类似于GaAs中鉴定出的5/2态,但其性质仍难确定。本研究报道了对双栅BLG器件中的偶分母FQH稳定序列的输运测量,确认其基态的自旋极化属性。研究结果表明BLG可作为调控由非阿贝尔激发的拓扑基态的有效平台。

 

The distinct Landau level spectrum of bilayer graphene (BLG) is predicted to support a non-abelian even-denominator fractional quantum Hall (FQH) state similar to the Embedded Image state first identified in GaAs. However, the nature of this state has remained difficult to characterize. Here, we report transport measurements of a robust sequence of even-denominator FQH in dual-gated BLG devices. Parallel field measurement confirms the spin-polarized nature of the ground state, which is consistent with the Pfaffian/anti-Pfaffian description. The sensitivity of the even-denominator states to both filling fraction and transverse displacement field provides new opportunities for tunability. Our results suggest that BLG is a platform in which topological ground states with possible non-abelian excitations can be manipulated and controlled.

 

 

11 【进化】Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago

Carina M. Schlebusch and Helena Malmström, et.al

 

非洲南部古老基因组显示现代智人出现于35万到26万年前

 

http://science.sciencemag.org/content/358/6363/652

 

 

Southern Africa is consistently placed as a potential region for the evolution of Homo sapiens. We present genome sequences, up to 13x coverage, from seven ancient individuals from KwaZulu-Natal, South Africa. The remains of three Stone Age hunter-gatherers (about 2000 years old) were genetically similar to current-day southern San groups, and those of four Iron Age farmers (300 to 500 years old) were genetically similar to present-day Bantu-language speakers. We estimate that all modern-day Khoe-San groups have been influenced by 9 to 30% genetic admixture from East Africans/Eurasians. Using traditional and new approaches, we estimate the first modern human population divergence time to between 350,000 and 260,000 years ago. This estimate increases the deepest divergence among modern humans, coinciding with anatomical developments of archaic humans into modern humans, as represented in the local fossil record.

 

导读 郭怿暄现代人类进化于非洲,但具体时间尚不清楚。本研究通过对非洲南部的7名古人类进行基因组测序,发现来自石器时代个体在遗传上与现代南部San部族更接近,而来自铁器时代个体更接近班图人。据此估计现代智人第一次分化时间在35万到26年前,这一结论也同样印证了化石记录中人类解剖结构的发展。

 

12 【进化】A high-coverage Neandertal genome from Vindija Cave in Croatia

Kay Prüfer et.al

来自克罗地亚Vindija洞穴的高覆盖率尼安德特人基因组

 

http://science.sciencemag.org/content/358/6363/655

 

(导读 陈月欣) 迄今为止,唯一一份高质量尼安德特人基因组样本来自于南西伯利亚。本研究对约50,000年前克罗地亚Vindija洞穴的一位女性尼安德特人进行了高质量基因组测序,发现他们的群体应该较小,并推测现代人可能拥有比此前估计更多的尼安德特人基因。

To date, the only Neandertal genome that has been sequenced to high quality is from an individual found in Southern Siberia. We sequenced the genome of a female Neandertal from ~50,000 years ago from Vindija Cave, Croatia, to ~30-fold genomic coverage. She carried 1.6 differences per 10,000 base pairs between the two copies of her genome, fewer than present-day humans, suggesting that Neandertal populations were of small size. Our analyses indicate that she was more closely related to the Neandertals that mixed with the ancestors of present-day humans living outside of sub-Saharan Africa than the previously sequenced Neandertal from Siberia, allowing 10 to 20% more Neandertal DNA to be identified in present-day humans, including variants involved in low-density lipoprotein cholesterol concentrations, schizophrenia, and other diseases.

 

13 【进化】Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers

Martin Sikora1  , et.al

 

古代基因组显示上旧石器时代早期采集者的社会和繁殖行为

 

http://science.sciencemag.org/content/358/6363/659

 

 

Present-day hunter-gatherers (HGs) live in multilevel social groups essential to sustain a population structure characterized by limited levels of within-band relatedness and inbreeding. When these wider social networks evolved among HGs is unknown. To investigate whether the contemporary HG strategy was already present in the Upper Paleolithic, we used complete genome sequences from Sunghir, a site dated to ~34,000 years before the present, containing multiple anatomically modern human individuals. We show that individuals at Sunghir derive from a population of small effective size, with limited kinship and levels of inbreeding similar to HG populations. Our findings suggest that Upper Paleolithic social organization was similar to that of living HGs, with limited relatedness within residential groups embedded in a larger mating network.

(导读 郭怿暄)多层级的社会群体对现代的狩猎采集者(HGs)有限的亲缘关系和近亲交配的水平人口结构是必须的。本研究通过对上旧石器时代早期Sunghir的多个晚期智人进行基因组测序。发现这些个体来源于一个拥有很小有效群体大小,其亲缘水平和近亲交配水平与现代狩猎采集者接近的群体。提示旧石器时代晚期的社会组织与当前存在HGs非常接近。

 

14 【生物】A glycerophospholipid-specific pocket in the RVFV class II fusion protein drives target membrane insertion

P. Guardado-Calvo et.al

 

RVF病毒 II类融合蛋白中的甘油磷脂特异性口袋驱使靶向膜插入

 

http://science.sciencemag.org/content/358/6363/663

 

(导读 陈月欣) 在非洲,RVF病毒通过蚊子叮咬在人类和畜类间传播疾病。本研究通过分析RVF病毒 II类融合蛋白Gc融合后的结构,发现蛋白内置的模块将数个融合环同时插入细胞膜改变膜结构并与甘油磷脂(GPL)结合。这样的融合蛋白结构在虫媒病毒中高度保守。

The Rift Valley fever virus (RVFV) is transmitted by infected mosquitoes, causing severe disease in humans and livestock across Africa. We determined the x-ray structure of the RVFV class II fusion protein Gc in its postfusion form and in complex with a glycerophospholipid (GPL) bound in a conserved cavity next to the fusion loop. Site-directed mutagenesis and molecular dynamics simulations further revealed a built-in motif allowing en bloc insertion of the fusion loop into membranes, making few nonpolar side-chain interactions with the aliphatic moiety and multiple polar interactions with lipid head groups upon membrane restructuring. The GPL head-group recognition pocket is conserved in the fusion proteins of other arthropod-borne viruses, such as Zika and chikungunya viruses, which have recently caused major epidemics worldwide.

 

15 【生物】Spindle asymmetry drives non-Mendelian chromosome segregation

Takashi Akera   et.al

 

纺锤体不对称驱动非孟德尔染色体分离

 

http://science.sciencemag.org/content/358/6363/668

 

 

Genetic elements compete for transmission through meiosis, when haploid gametes are created from a diploid parent. Selfish elements can enhance their transmission through a process known as meiotic drive. In female meiosis, selfish elements drive by preferentially attaching to the egg side of the spindle. This implies some asymmetry between the two sides of the spindle, but the molecular mechanisms underlying spindle asymmetry are unknown. Here we found that CDC42 signaling from the cell cortex regulated microtubule tyrosination to induce spindle asymmetry and that non-Mendelian segregation depended on this asymmetry. Cortical CDC42 depends on polarization directed by chromosomes, which are positioned near the cortex to allow the asymmetric cell division. Thus, selfish meiotic drivers exploit the asymmetry inherent in female meiosis to bias their transmission.

 

(导读 郭怿暄)女性减数分裂中,一些自私因子通过结合在卵细胞一侧的纺锤体,利用纺锤体的不对称来增强自身传递 。本研究发现位于细胞皮层的CDC42信号通过调节微管酪氨酸化诱导纺锤体的不对称,进而导致染色体的非孟德尔分离,而皮层CDC42依赖由染色体引起的极化。这一发现揭示自私因子利用女性减数分裂过程中内在不对称性增强自身传递的机制。

 

16 【生物】The condensin complex is a mechanochemical motor that translocates along DNA

Tsuyoshi Terakawa Shveta Bisht, Jorine M. Eeftens   et.al

凝集蛋白复合物是沿DNA转位的机械化学马达

http://science.sciencemag.org/content/358/6363/672

 

(导读 阿金)凝集蛋白是生物染色体组织和压缩的关键因素但机制不明。本研究使用单分子成像技术,展示酵母菌中的凝集蛋白依靠ATP水解,以每秒约60个碱基对的速度沿DNA双链移动超过1万个碱基对的距离。表明凝集蛋白的马达功能可为染色体压缩和维持结构提供重要驱动力。

 

Condensin plays crucial roles in chromosome organization and compaction, but the mechanistic basis for its functions remains obscure. We used single-molecule imaging to demonstrate that Saccharomyces cerevisiae condensin is a molecular motor capable of adenosine triphosphate hydrolysis–dependent translocation along double-stranded DNA. Condensin’s translocation activity is rapid and highly processive, with individual complexes traveling an average distance of ≥10 kilobases at a velocity of ~60 base pairs per second. Our results suggest that condensin may take steps comparable in length to its ~50-nanometer coiled-coil subunits, indicative of a translocation mechanism that is distinct from any reported for a DNA motor protein. The finding that condensin is a mechanochemical motor has important implications for understanding the mechanisms of chromosome organization and condensation.