A Bayesian method for analysing spotted microarray data

In the decade since their invention, spotted microarrays have been undergoing technical advances that have increased the utility, scope and precision of their ability to measure gene expression. At the same time, more researchers are taking advantage of the fundamentally quantitative nature of these tools with refined experimental designs and sophisticated statistical analyses. These new approaches utilise the power of microarrays to estimate differences in gene expression levels, rather than just categorising genes as up- or down-regulated, and allow the comparison of expression data across multiple samples. In this review, some of the technical aspects of spotted microarrays that can affect statistical inference are highlighted, and a discussion is provided of how several methods for estimating gene expression level across multiple samples deal with these challenges. The focus is on a Bayesian analysis method, BAGEL, which is easy to implement and produces easily interpreted results.     

Alginate embedding and subsequent sporulation of in vitro-produced Conidiobolus thromboides hyphae using a pressurised air-extrusion method

Conidiobolus thromboides is an entomophthoralean fungus with potential as a biological control agent of aphids. However, its application in biological control is limited due to its formulation requirements. The objective of this study was to develop and optimise a novel air-extrusion method to embed C. thromboides hyphae at high density in alginate pellets. An orthogonal experimental design was used to investigate selected combinations of parameters known to affect hyphal density within pellets. The diameter of pellets produced, and the calculated density of hyphae within them, ranged from 0.18 ± 0.09 to 3.17 ± 0.06 mm and from 0.02 to 350.56 mg/mm³ respectively. These data were used to predict the optimal parameter combination to deliver the greatest density of hyphae of C. thromboides per pellet: 1% sodium alginate, a 1:2 ratio of hyphae to sodium alginate, an orifice diameter of 0.232 mm and an air pressure of 0.05 MPa. Pellets made under the optimal conditions predicted produced a mean total of 4.3 ± 0.6 × 10⁵ conidia per pellet at 100% relative humidity which was significantly greater than the mean total number of conidia produced from infected aphid cadavers of comparable size (9.35 ± 0.85 × 10⁴) (p < 0.001). In conclusion, air-extrusion embedding appears to be a promising method for formulating in vitro-produced hyphae of C. thromboides for use in biological control.     

β-Carboline alkaloids induce structural plasticity and inhibition of SARS-CoV-2 nsp3 macrodomain more potently than remdesivir metabolite GS-441524: computational approach

The nsp3 macrodomain is implicated in the viral replication, pathogenesis and host immune responses through the removal of ADP-ribosylation sites during infections of coronaviruses including the SARS-CoV-2. It has ever been modulated by macromolecules including the ADP-ribose until Ni and co-workers recently reported its inhibition and plasticity enhancement unprecedentedly by remdesivir metabolite, GS-441524, creating an opportunity for investigating other biodiverse small molecules such as β-Carboline (βC) alkaloids. In this study, 1497 βC analogues from the HiT2LEAD chemical database were screened, using computational approaches of Glide XP docking, molecular dynamics simulation and pk-CSM ADMET predictions. Selectively, βC ligands, 129, 584, 1303 and 1323 demonstrated higher binding affinities to the receptor, indicated by XP docking scores of –10.72, –10.01, –9.63 and –9.48 kcal/mol respectively than remdesivir and GS-441524 with –4.68 and –9.41 kcal/mol respectively. Consistently, their binding free energies were –36.07, –23.77, –24.07 and –17.76 kcal/mol respectively, while remdesivir and GS-441524 showed –21.22 and –24.20 kcal/mol respectively. Interestingly, the selected βC ligands displayed better stability and flexibility for enhancing the plasticity of the receptor than GS-441524, especially 129 and 1303. Their predicted ADMET parameters favour druggability and low expressions for toxicity. Thus, they are recommended as promising adjuvant/standalone anti-SARS-CoV-2 candidates for further study.Key words: SARS-CoV-2, nsp3 macrodomain, ADP-ribose, β-carboline, bioinformatics, drug design     

Identifying protein construct variants with increased crystallization propensity--a case study

This study describes an efficient multiparallel automated workflow of cloning, expression, purification, and crystallization of a large set of construct variants for isolated protein domains aimed at structure determination by X-ray crystallography. This methodology is applied to MAPKAP kinase 2, a key enzyme in the inflammation pathway and thus an attractive drug target. The study reveals a distinct subset of truncation variants with improved crystallization properties. These constructs distinguish themselves by increased solubility and stability during a parallel automated multistep purification process including removal of the recombinant tag. High-throughput protein melting point analysis characterizes this subset of constructs as particularly thermostable. Both parallel purification screening and melting point determination clearly identify residue 364 as the optimal C terminus for the kinase domain. Moreover, all three constructs that ultimately crystallized feature this C terminus. At the N terminus, only three amino acids differentiate a noncrystallizing from a crystallizing construct. This study addresses the very common issues associated with difficult to crystallize proteins, those of solubility and stability, and the crucial importance of particular residues in the formation of crystal contacts. A methodology is suggested that includes biophysical measurements to efficiently identify and produce construct variants of isolated protein domains which exhibit higher crystallization propensity.     

对6个国外城市街道规划设计导则的解析——“如何规划步行友好的城市街道开放空间？”

本文将“如何通过街道规划设计,营建步行友好的城市开放空间环境,提高居民生活质量？”作为研究视角,抽取了6个国外城市街道规划设计导则中与“如何规划设计步行友好的城市开放空间？”密切相关的内容,根据相关导则编制的逻辑将内容进行提炼、归纳和重组。针对中国通过改善街道步行环境建设高品质城市的诉求以及相关导则中缺少对使用者需求关注的现状,提出了将需求调查纳入规划规定环节、从环境特征角度出发进行街道分类与定位、关注地域特征与集约性生态设施的环境营造方法以及提升步行道功能多样性和空间相容性的建议。     

The 2009 Nobel Prize in Chemistry: Thomas A. Steitz and the structure of the ribosome

Over the past 200 years, there have been countless groundbreaking discoveries in biology and medicine at Yale University. However, one particularly noteworthy discovery with profoundly important and broad consequences happened here in just the past two decades. In 2009, Thomas Steitz, the Sterling Professor of Molecular Biophysics & Biochemistry, was awarded the Nobel Prize in Chemistry for "studies of the structure and function of the ribosome," along with Venkatraman Ramakrishnan of the MRC Laboratory of Molecular Biology and Ada E. Yonath of the Weizmann Institute of Science. This article covers the historical context of Steitz's important discovery, the techniques his laboratory used to study the ribosome, and the impact that this research has had, and will have, on the future of biological and medical research.     

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.