Engineering of zinc finger and MHC motifs to locked-in tertiary folds

Summary The assembly of helical and β-sheet peptide blocks containing reactive chain ends results in highly branched chain architectures (‘locked-in folds’) mimicking native tertiary structures. This molecular kit strategy allows to bypass the protein folding problem in protein de novo design and gives access to protein mimetics of high thermodynamic stability. The validity of this concept is exemplified for the design and synthesis of locked-in folds mimicking the zinc finger and MHC folding motifs.     

Environmentally Conscious Product Design: A Collaborative Internet-based Modeling Approach

This paper proposes a computer-based method for providing product designers with real-time environmental impact assessment. In this concurrent modeling approach, environmental experts build life-cycle models, define their interfaces, and publish them as distributed objects on the Internet. Traditional designers integrating these objects into their design models have access to the impact assessment methods provided by the environmental expert. In this paradigm, the focus shifts from providing techniques that let non-expert designers perform life-cycle impact assessments to tools that facilitate timely communication and information transfer between designers and appropriate environmental experts. Establishing real-time communication between the product design models and the environmental life-cycle models is the primary focus of this paper. Methods for establishing and maintaining the interaction between life-cycle and product design models are described. A beverage container design example illustrates how this collaborative approach can use environmental and traditional design goals to determine effective tradeoffs between design alternatives.     

A Regression Modeling Approach for Describing Patterns of HIV Genetic Variation

We introduce a novel approach for describing patterns of HIV genetic variation using regression modeling techniques. Parameters are defined for describing genetic variation within and between viral populations by generalizing Simpson's index of diversity. Regression models are specified for these variation parameters and the generalized estimating equation framework is used for estimating both the regression parameters and their corresponding variances. Conditions are described under which the usual asymptotic approximations to the distribution of the estimators are met. This approach provides a formal statistical framework for testing hypotheses regarding the changing patterns of HIV genetic variation over time within an infected patient. The application of these methods for testing biologically relevant hypotheses concerning HIV genetic variation is demonstrated in an example using sequence data from a subset of patients from the Multicenter AIDS Cohort Study.     

Critical Design Ethnography as Action Research

"Critical Design Ethnography: Designing for Change" is reviewed in terms of action research under five dimensions: knowledge in practice, participation and democracy, many ways of knowing, emergence, and worthwhile purposes. Particular attention is paid to the tensions between the design agenda and the empowerment agenda.     

Environmental Supply-Chain Management in the Computer Industry:A Transaction Cost Economics Perspective

Our article uses the theory of transaction cost economics as a conceptual basis for examining the contracting mechanisms by which firms in the computer industry structure programs to encourage their suppliers to improve their environmental management systems and/or the environmental quality of their products. We explore the economic transactions hazards associated with asking suppliers to invest in the specialized technologies required to improve environmental performance of products and management practices and the relational contracting mechanisms computer industry firms are using to protect themselves against these hazards. We also describe the importance the managers we interviewed attributed to various transactions hazards and their perceptions of how well their firms were coping with them. We conclude by discussing questions for future research. By using TCE to frame our analysis of how computer manufacturers are structuring their relationships with their suppliers in the environmental area, we hope to show how social science theory can be used to enrich and increase the practicality of the work done by engineers and others in the mainstream areas of the industrial ecology field.     

The Role of Voluntary Industry Standards in Environmental Supply-Chain Management

Our article uses a new institutional economics (NIE) framework to explore the role of voluntary industry standards in the development and implementation of environmental supplier-management programs in the computer industry. We examine two different voluntary standards, one for the management of design for environment (DfE) in the semiconductor fabrication equipment sector and the other for assessing the implementation and use of environmental management systems throughout the computer industry supply chain. We compare and contrast the two standards to explain why the former was widely adopted and has helped integrate DfE into buyer-supplier relations among adopters, whereas the latter failed to gain acceptance. In line with NIE logic, both standards aimed to lower transaction and customization costs by setting "rules of the game" for interfirm transactions that would help simplify and routinize novel environmental supply-chain programs and activities. Their differential success can be elucidated in terms of how well each met the NIE criteria for remediableness and legitimacy. We conclude that voluntary standards have the potential to play an important role in promoting DfE in industrial supply chains. We further conclude that NIE provides a conceptual framework of great value to industrial ecologists who analyze how industry standards and other institutions help firms move toward more sustainable supply-chain management practices.     

Incorporation of adenosine into nucleotides of chromaffin cells maintained in primary cultures

Extracellular adenosine was incorporated into nucleotides of bovine chromaffin cells maintained in primary culture. In intact chromaffin tissue, a very low incorporation was found (0.8 pmol/10⁶ cells/h at an adenosine concentration of 11.45 μM), which increased 282 times in freshly isolated chromaffin cells. When maintained in primary culture, this value decreased to a value similar to that of chromaffin tissue, but later on, and in the presence of nerve growth factor (NGF), a time dependent increase of adenosine incorporation was observed which, in 84-h old cells reached up to 54 times more than that found in intact tissue. This incorporation might reflect changes in the adenosine transport at the cell membrane level, furthered by NGF effect. Incorporation, which was time-dependent, was weakly modified by stimulation of cells with 10^?4 M acetylcholine. However, acetylcholine-induced release of labelled nucleotides from chromaffin granules was observed, probably in relation to granule maturation.     

Simulated beetle defoliation on willow genotypes in mixture and monotype plantations

The effect of simulated beetle damage (0%, 25%, 50% and 75% mechanical defoliation) on 12 willow genotypes, grown in short‐rotation coppice, was studied in a modified criss‐cross experimental design. The design enabled the above‐ground effects of monoculture and mixed planting to be assessed. Repeated measurements were modelled to produce derived variables in terms of time or, more appropriately, in terms of accumulated day length (i.e. ‘developmental time’) units. These derived variables were then analysed using the REsidual Maximum Likelihood (REML) method implemented in GenStat? (2001) . No significant competition effect between the genotypes due to planting regime was detected. Genotypes Salix viminalis × Salix schwerinii‘Beagle’ and S. viminalis × S. schwerinii‘Torhild’ were found to have the greatest rate of increase in leaves regardless of defoliation and also the greatest height prior to defoliation. Genotype Salix dasyclados‘Loden’ showed the highest rate of growth under the stress of defoliation. When assessing height at the end of the growing season, S. viminalis × S. schwerinii‘Olof’ was the highest genotype for 25% and 75% levels of defoliation, but genotypes Salix aurita × Salix cinerea‘Delamere’, Loden and S. viminalis × Salix burjatica‘Ashton Parfitt’ appeared to be most tolerant by having consecutively lower base day lengths (i.e. increasing the accumulation of developmental units and the length of the growing season) for increasing defoliation. Shorter genotypes tended to be more tolerant, but of the higher genotypes reaching a control height of greater than 3 m by the end of the growing season, S. viminalis × S. schwerinii‘Tora’ and Beagle performed best to 50% defoliation.     

蛋白质组学中新蛋白质鉴定的研究方法和策略

当前,基于生物质谱进行蛋白质鉴定的技术已经成为蛋白质组学研究的支撑技术之一.产生的数据主要使用数据库搜索的方法进行处理,这种方法的一大缺陷是不能鉴定数据库中未包含的蛋白质,因此如何充分利用质谱数据对蛋白质组研究的意义很大,而新蛋白质鉴定更是其中一个重要的内容.新蛋白质鉴定是蛋白质鉴定的一个方面,新蛋白质的定义按照序列和功能的已知程度分为3个层次;以蛋白质鉴定的方法为基础,目前新蛋白质鉴定的方法可分为denovo测序和相似序列搜索结合的方法以及搜索EST、基因组等核酸数据库的方法2大类;两者各有利弊.存在各自的问题和相应处理的策略.不同的研究者可以根据具体目的应用和发展不同的鉴定方法,同时新蛋白质的鉴定也将随着蛋白质组学研究的发展而更加完善.