The pairwise approach to analysing species co‐occurrence

The analysis of species co‐occurrence patterns continues to be a main pursuit of ecologists, primarily because the coexistence of species is fundamentally important in evaluating various theories, principles and concepts. Examples include community assembly, equilibrium versus non‐equilibrium organization of communities, resource partitioning and ecological character displacement, the local–regional species diversity relationship, and the metacommunity concept. Traditionally, co‐occurrence has been measured and tested at the level of an entire species presence–absence matrix wherein various algorithms are used to randomize matrices and produce statistical null distributions of metrics that quantify structure in the matrix. This approach implicitly recognizes a presence–absence matrix as having some real ecological identity (e.g. a set of species exhibiting nestedness among a set of islands) in addition to being a unit of statistical analysis. An emerging alternative is to test for non‐random co‐occurrence between paired species. The pairwise approach does not analyse matrix‐level structure and thus views a species pair as the fundamental unit of co‐occurrence. Inferring process from pattern is very difficult in analyses of co‐occurrence; however, the pairwise approach may make this task easier by simplifying the analysis and resulting inferences to associations between paired species.     

Dissecting the transcriptional phenotype of ribosomal protein deficiency: implications for Diamond-Blackfan Anemia

Defects in genes encoding ribosomal proteins cause Diamond Blackfan Anemia (DBA), a red cell aplasia often associated with physical abnormalities. Other bone marrow failure syndromes have been attributed to defects in ribosomal components but the link between erythropoiesis and the ribosome remains to be fully defined. Several lines of evidence suggest that defects in ribosome synthesis lead to “ribosomal stress” with p53 activation and either cell cycle arrest or induction of apoptosis. Pathways independent of p53 have also been proposed to play a role in DBA pathogenesis.     

美国生物医药产业竞争力分析与启示

进入生物经济时代以来,以生物医药产业为代表的生物技术产业正在引领人类新一波技术产业革命。我国针对生物医药产业作出的战略部署已经取得了明显成效,但与美国等生物医药强国相比仍有较大的竞争差距。采用波特钻石模型构建了生物医药产业国际竞争力理论分析框架,以美国为例分析其生物医药产业在要素状况、企业结构和竞争、需求条件、相关及支持性产业、政府和发展机会六个方面的竞争优势,并基于此提出了我国发展生物医药产业的政策建议,从而为我国生物医药产业发展提供政策参考。     

Mechanism of cell contact-dependent glycolipid synthesis: further studies with glycolipid-glass complex

An initiation factor from rabbit reticulocytes can overcome the block in initiation of protein synthesis occurring in reticulocyte lysates when exogenous hemin is not present, or when double-stranded RNA is added. This factor has been identified with IF-MP, an initiation factor capable of forming ternary complexes with GTP and methionyl-tRNA_F. Initiation factor IF-M3 by itself is unable to overcome the block in initiation, but appears to stimulate this activity of IF-MP. IF-MP binds to single-stranded R17 RNA as well as to double-stranded RNA, while IF-M3 only binds to double-stranded RNA. The protein synthetic activity of IF-MP is sensitive to N-ethylmaleimide, but its ability to bind RNA is resistant.     

Using multiplex-staining to study changes in the maize leaf phosphoproteome in response to mechanical wounding

Mechanical wounding of 2-week-old maize (Zea mays L.) leaves, one of the first steps in both pathogen infection and herbivore attack, stimulates metabolism and activates signal transduction pathways dedicated to defense and recovery. The signaling pathways include reversible protein phosphorylation which can modulate protein activities, and transmit signals within cellular pathways and networks. We have used multiplex-staining of high-resolution 2D gels for protein (Sypro Ruby) and phosphorylation (Pro-Q Diamond) as a strategy for quantifying changes in the stoichiometry of phosphorylation after wounding for 270 protein spots. Rigorous statistical analysis of the time-index data allowed us to accept patterns of change in 125 of the spots as non-random, and these patterns were assigned to five clusters. A reliable identity was assigned to 21 selected proteins, most of which have been previously described as phospho-proteins. The results suggest that analysis of protein spots from high-resolution 2D gels by multiplex-staining for protein plus phosphorylation is a strategy that can be broadly useful for study of how the phospho-proteome responds to abiotic stress.     

区域生物医药产业基于钻石模型的竞争力研究——以石家庄为例

以波特的钻石模型为基础,根据生物医药产业的特点形成了六因素钻石模型的分析框架。以石家庄为例,对影响产业竞争力的生产要素、需求要素、相关和支持性产业要素、企业战略结构和竞争要素、政府、创新这六个要素进行了分析。并对提升产业竞争力的路径进行了阐释,通过发挥比较优势,因地制宜选择合适的产业集群发展模式,积极推进"政产学研医"结合,多种手段搞好创新,积极承接生物制药产业外包服务,加强中介、信息等产业支撑建设,搞好社会文化对生物医药产业的支撑等,保证石家庄生物医药产业的可持续发展。     

Synthesis and Microdiffraction at Extreme Pressures and Temperatures

High pressure compounds and polymorphs are investigated for a broad range of purposes such as determine structures and processes of deep planetary interiors, design materials with novel properties, understand the mechanical behavior of materials exposed to very high stresses as in explosions or impacts. Synthesis and structural analysis of materials at extreme conditions of pressure and temperature entails remarkable technical challenges. In the laser heated diamond anvil cell (LH-DAC), very high pressure is generated between the tips of two opposing diamond anvils forced against each other; focused infrared laser beams, shined through the diamonds, allow to reach very high temperatures on samples absorbing the laser radiation. When the LH-DAC is installed in a synchrotron beamline that provides extremely brilliant x-ray radiation, the structure of materials under extreme conditions can be probed in situ. LH-DAC samples, although very small, can show highly variable grain size, phase and chemical composition. In order to obtain the high resolution structural analysis and the most comprehensive characterization of a sample, we collect diffraction data in 2D grids and combine powder, single crystal and multigrain diffraction techniques. Representative results obtained in the synthesis of a new iron oxide, Fe₄O₅ ¹ will be shown.     

Assortative Pairings in Diamond Firetails (Stagonopleura guttata) are not the Result of Mutual Mate Choice for an Ornament

Positive assortative mating occurs when individuals with similar phenotypes mate more frequently with each other than is expected by chance. In species in which both the males and females are ornamented, assortative pairings could arise from mutual mate choice on the same trait. We test this mechanism of mate choice and assortative pairing in the Diamond Firetail (Stagonopleura guttata), an Australian estrildid finch in which both sexes are ornamented with red bills, red rumps and white flank spots. We have previously shown sex differences in the degree of ornamentation as females have more flank spots than males. These white flank spots are used during sexual display, being fully displayed by courting males and by females when approaching a displaying male. Here, we experimentally test whether mutual mate preference is based on the number of flank spots. There was no evidence for a direct mutual preference for spot number. Given a choice of potential mates with a natural or experimentally manipulated number of flank spots, males preferred females with more spots, while female preference was not solely based on flank spots. Intriguingly, in both wild and captive Diamond Firetails, we found the number of flank spots in pairs was correlated suggesting a basis for positive assortative pairing. Nevertheless, we conclude that assortative pairing in Diamond Firetails is not due to mutual choice of mates based on the number of flank spots. We discuss different selection pathways for this trait in each sex.     

Analysis of the dynamic Bacillus subtilis Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes

The physiological role of proteins phosphorylated on serine/threonine/tyrosine (Ser/Thr/Tyr) residues or the identity of the corresponding kinases and phosphatases is generally poorly understood in bacteria. As a first step in analysing the importance of such phosphorylation, we sought to establish the nature of the Ser/Thr/Tyr phosphoproteome in Bacillus subtilis, using in vivo labelling with [(32)P]-orthophosphate, one-unit pH 2-DE, combined with MS. Highly reproducible 2-D profiles of phosphoproteins were obtained with early stationary-phase cells. The 2-D profiles contained at least 80 clearly labelled spots in the pH range 4-7. Forty-six spots were analysed by MS (confirmed in most cases by LC-MS/MS), identifying a total of 29 different proteins, with 19 identified for the first time as bacterial phosphoproteins. These phosphoproteins are implicated in a wide variety of cellular processes, including carbon and energy metabolism, transport, stress and development. Significant changes to the profiles were obtained as a result of cold, heat or osmotic shock, demonstrating that, in stationary-phase cells, the phosphoproteome is dynamic. An initial comparative study indicated that at least 25 [(32)P]-labelled spots were also stained by Pro-Q Diamond, with apparently six additional phosphoproteins uniquely detected by Pro-Q.