Exploration of nano-surface chemistry for spectral analysis

The applications of nano-surface chemistry in the field of spectral analysis have attracted growing interest in recent years.In this article,we reviewed the applications of nanomaterials-based chemical reactions for spectral analysis,including the development in plasma-catalysis,surface-enhanced spectroscopy,separation and preconcentration,chemical vapor generation,labeling and signal amplification.Introduction of nano-surface chemistry to spectral analysis not only improves the sensitivity and selectivity,broadens the application range of spectral analysis,but also affords analytical community special characterization tools.     

Inverse computation and the Universal Resolving Algorithm

We survey fundamental concepts for inverse programming and then present the Universal Resolving Algorithm, an algorithm for inverse computation in a first-order, functional programming language. We discuss the key concepts of the algorithm, including a three-step approach based on the notion of a perfect process tree, and demonstrate our implementation with several examples of inverse computation.     

Spin-orbit coupling and zero-field splitting of the high-spin ferric enzyme-substrate complex: Protocatechuate 3,4-dioxygenase complexed with 3,4-dihydroxyphenylacetate

We used density functional calculations to investigate the electronic origins of the magnetic properties of the high-spin ferric enzyme-substrate complex protocatechuate 3,4-dioxygenase(3,4-PCD).The calculated g-tensors show that ligand-to-metal charge transfer transitions are from the protocatechuate(PCA) and Tyr408 orbitals to the Fe d orbitals,which lead to x-and y-polarized transitions.These polarized transitions require a spin-orbit coupling(SOC) matrix element in the z-direction,Lz(z=z’),resulting in a g z value of 2.0158,significantly deviating from 2.0023.A large zero-field splitting parameter value of+1.147cm-1 is due to △S =-1 spin-orbit mixing with the quartet states for the sextet ground state,accounting for around 73% of the SOC contribution.The SOC matrix elements indicate that the high-spin d 5 system Fe(Ⅲ),3,4-PCD-PCA is a weak spin-crossover compound with an SOC of 31.56 cm-1.     

基于高光谱指数的林农复合系统小麦冠层氮含量估算研究

以杨树-小麦间作系统为研究对象,采用Field Spec Pro FR2500地物光谱仪采集的小麦叶层光谱180份,选取基于单作麦田冠层氮含量估测模型中精度较高的9个指数用于估测林农复合系统中小麦冠层氮的含量,探讨不同水平枯落物覆盖量、林分密度、施肥量条件下小麦叶层氮含量的光谱特征。随机选取116份样本作为训练集基以9个指数分别建立估测模型,其余48份样本作为预测集对估测模型进行适应性检验。结果表明:FDNDNI、SDr-SDb两种指数的P-R2与C-R2达到了0.839、0.777与0.844、0.758,此系统预测杨麦间作系统中小麦叶片冠层的氮含量的精度较高,其余7个指数预测精度不理想。以9个指数所建立的估测模型的精度均低于其对单作麦田氮含量的估测精度。     

Gout-associated uric acid crystals activate the NALP3 inflammasome

Development of the acute and chronic inflammatory responses known as gout and pseudogout are associated with the deposition of monosodium urate (MSU) or calcium pyrophosphate dihydrate (CPPD) crystals, respectively, in joints and periarticular tissues. Although MSU crystals were first identified as the aetiological agent of gout in the eighteenth century and more recently as a 'danger signal' released from dying cells, little is known about the molecular mechanisms underlying MSU- or CPPD-induced inflammation. Here we show that MSU and CPPD engage the caspase-1-activating NALP3 (also called cryopyrin) inflammasome, resulting in the production of active interleukin (IL)-1beta and IL-18. Macrophages from mice deficient in various components of the inflammasome such as caspase-1, ASC and NALP3 are defective in crystal-induced IL-1beta activation. Moreover, an impaired neutrophil influx is found in an in vivo model of crystal-induced peritonitis in inflammasome-deficient mice or mice deficient in the IL-1beta receptor (IL-1R). These findings provide insight into the molecular processes underlying the inflammatory conditions of gout and pseudogout, and further support a pivotal role of the inflammasome in several autoinflammatory diseases.     

Structure of the Sec13/31 COPII coat cage

Endomembranes of eukaryotic cells are dynamic structures that are in continuous communication through the activity of specialized cellular machineries, such as the coat protein complex II (COPII), which mediates cargo export from the endoplasmic reticulum (ER). COPII consists of the Sar1 GTPase, Sec23 and Sec24 (Sec23/24), where Sec23 is a Sar1-specific GTPase-activating protein and Sec24 functions in cargo selection, and Sec13 and Sec31 (Sec13/31), which has a structural role. Whereas recent results have shown that Sec23/24 and Sec13/31 can self-assemble to form COPII cage-like particles, we now show that Sec13/31 can self-assemble to form minimal cages in the absence of Sec23/24. We present a three-dimensional reconstruction of these Sec13/31 cages at 30 A resolution using cryo-electron microscopy and single particle analysis. These results reveal a novel cuboctahedron geometry with the potential to form a flexible lattice and to generate a diverse range of containers. Our data are consistent with a model for COPII coat complex assembly in which Sec23/24 has a non-structural role as a multivalent ligand localizing the self-assembly of Sec13/31 to form a cage lattice driving ER cargo export.     

An excitable gene regulatory circuit induces transient cellular differentiation

Certain types of cellular differentiation are probabilistic and transient. In such systems individual cells can switch to an alternative state and, after some time, switch back again. In Bacillus subtilis, competence is an example of such a transiently differentiated state associated with the capability for DNA uptake from the environment. Individual genes and proteins underlying differentiation into the competent state have been identified, but it has been unclear how these genes interact dynamically in individual cells to control both spontaneous entry into competence and return to vegetative growth. Here we show that this behaviour can be understood in terms of excitability in the underlying genetic circuit. Using quantitative fluorescence time-lapse microscopy, we directly observed the activities of multiple circuit components simultaneously in individual cells, and analysed the resulting data in terms of a mathematical model. We find that an excitable core module containing positive and negative feedback loops can explain both entry into, and exit from, the competent state. We further tested this model by analysing initiation in sister cells, and by re-engineering the gene circuit to specifically block exit. Excitable dynamics driven by noise naturally generate stochastic and transient responses, thereby providing an ideal mechanism for competence regulation.     

Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis

Ustilago maydis is a ubiquitous pathogen of maize and a well-established model organism for the study of plant-microbe interactions. This basidiomycete fungus does not use aggressive virulence strategies to kill its host. U. maydis belongs to the group of biotrophic parasites (the smuts) that depend on living tissue for proliferation and development. Here we report the genome sequence for a member of this economically important group of biotrophic fungi. The 20.5-million-base U. maydis genome assembly contains 6,902 predicted protein-encoding genes and lacks pathogenicity signatures found in the genomes of aggressive pathogenic fungi, for example a battery of cell-wall-degrading enzymes. However, we detected unexpected genomic features responsible for the pathogenicity of this organism. Specifically, we found 12 clusters of genes encoding small secreted proteins with unknown function. A significant fraction of these genes exists in small gene families. Expression analysis showed that most of the genes contained in these clusters are regulated together and induced in infected tissue. Deletion of individual clusters altered the virulence of U. maydis in five cases, ranging from a complete lack of symptoms to hypervirulence. Despite years of research into the mechanism of pathogenicity in U. maydis, no 'true' virulence factors had been previously identified. Thus, the discovery of the secreted protein gene clusters and the functional demonstration of their decisive role in the infection process illuminate previously unknown mechanisms of pathogenicity operating in biotrophic fungi. Genomic analysis is, similarly, likely to open up new avenues for the discovery of virulence determinants in other pathogens.     

Berezinskii-Kosterlitz-Thouless crossover in a trapped atomic gas

Any state of matter is classified according to its order, and the type of order that a physical system can possess is profoundly affected by its dimensionality. Conventional long-range order, as in a ferromagnet or a crystal, is common in three-dimensional systems at low temperature. However, in two-dimensional systems with a continuous symmetry, true long-range order is destroyed by thermal fluctuations at any finite temperature. Consequently, for the case of identical bosons, a uniform two-dimensional fluid cannot undergo Bose-Einstein condensation, in contrast to the three-dimensional case. However, the two-dimensional system can form a 'quasi-condensate' and become superfluid below a finite critical temperature. The Berezinskii-Kosterlitz-Thouless (BKT) theory associates this phase transition with the emergence of a topological order, resulting from the pairing of vortices with opposite circulation. Above the critical temperature, proliferation of unbound vortices is expected. Here we report the observation of a BKT-type crossover in a trapped quantum degenerate gas of rubidium atoms. Using a matter wave heterodyning technique, we observe both the long-wavelength fluctuations of the quasi-condensate phase and the free vortices. At low temperatures, the gas is quasi-coherent on the length scale set by the system size. As the temperature is increased, the loss of long-range coherence coincides with the onset of proliferation of free vortices. Our results provide direct experimental evidence for the microscopic mechanism underlying the BKT theory, and raise new questions regarding coherence and superfluidity in mesoscopic systems.     

Proteome survey reveals modularity of the yeast cell machinery

Protein complexes are key molecular entities that integrate multiple gene products to perform cellular functions. Here we report the first genome-wide screen for complexes in an organism, budding yeast, using affinity purification and mass spectrometry. Through systematic tagging of open reading frames (ORFs), the majority of complexes were purified several times, suggesting screen saturation. The richness of the data set enabled a de novo characterization of the composition and organization of the cellular machinery. The ensemble of cellular proteins partitions into 491 complexes, of which 257 are novel, that differentially combine with additional attachment proteins or protein modules to enable a diversification of potential functions. Support for this modular organization of the proteome comes from integration with available data on expression, localization, function, evolutionary conservation, protein structure and binary interactions. This study provides the largest collection of physically determined eukaryotic cellular machines so far and a platform for biological data integration and modelling.