De novo discovery of antibody drugs – great promise demands scrutiny

ABSTRACT

We live in an era of rapidly advancing computing capacity and algorithmic sophistication. “Big data” and “artificial intelligence”find progressively wider use in all spheres of human activity, including healthcare. A diverse array of computational technologies is being applied with increasing frequency to antibody drug research and development (R&D). Their successful applications are met with great interest due to the potential for accelerating and streamlining the antibody R&D process. While this excitement is very likely justified in the long term, it is less likely that the transition from the first use to routine practice will escape challenges that other new technologies had experienced before they began to blossom. This transition typically requires many cycles of iterative learning that rely on the deconstruction of the technology to understand its pitfalls and define vectors for optimization. The study by Vasquez et al. identifies a key obstacle to such learning: the lack of transparency regarding methodology in computational antibody design reports, which has the potential to mislead the community efforts     

Embodied Resource Flows in a Global Economy

This article presents a methodology for identifying critical links in global resource supply chains by tracking resources from their extraction in one region of the world economy through their embodiment in intermediate products in the same and other regions to eventual embodiment in final goods. We build on previous work that applied an absorbing Markov chain (AMC) to results obtained using an input‐output (IO) model of a single region to define a resource‐specific network within that economy. In the absence of model calculations, the AMC can also be applied to standard IO data for a past year. This article first generalizes the analytic framework from a single region to the important case of the global resource‐specific network. This network typically includes cycling of embodied resources between sectors not only within each economy, but also among regions, as subsequent rounds of intermediate products are traded. Next, we refine that analysis to exhibit a crucial subnetwork, the resource end‐use network, which only tracks the portion of the resource that ends up embodied in a specific final product in a given region. Finally, we develop techniques to distinguish key branches of these networks and provide detailed insights about the structure of global resource dependence. A numerical example is applied to results of scenario analysis using an IO model of the world economy. Two alternative scenarios are compared. In each scenario, embodied resources are carried over specific branches of a global network in three regions using three resources to produce four goods.     

Purification and Characterization op a 31-Kilodalton Iron-Regulated Periplasmic Protein from Pasteurella Haenolytica A1

ABSTRACT

A prominent iron-regulated periplasmic protein was purified from Pasteurella haemolytica grown in an iron-deficient chemically defined medium. The protein was purified by anion exchange chromatography and appeared as a single band by SDS-PAGE with a molecular weight of 32,000. A yield of five mg was obtained from 91 mg of protein extract. The iron-regulated protein existed as a monomer in the native state with an average molecular weight of 29,877 as determined by analytical ultracentrifugation. The protein had a molecular weight of 30,880 as determined by matrix-assisted laser desorption mass spectrometry, hence the protein is referred to as the 31 kDa protein. Isoelectric focusing showed four bands with pIs of 7.15, 6.8, 6.6, and 5.9, The secondary structure of the protein was determined by circular dichroism and contained 16% α-helical structure. The N-terminal sequence, EPFKVVTTFTVIQDIAQNVAGDKAT, showed a 95% identity with the 31 kDa iron-binding protein from Haemophilus influenzae. Isolation and characterization of iron-regulated proteins are of particular interest because of their potential roles in iron assimilation and microbial virulence.     

Acidophytic shrublands in the north-west of the Italian peninsula: Ecology,chorology and syntaxonomy

Abstract

The shrublands growing on siliceous and/or calcium-poor substrata of the hilly and mountainous areas of north-western and central Italy were studied. This secondary vegetation is dominated by several acidophilous shrubs like Ulex europaeus, Cytisus scoparius, Erica arborea, E. scoparia and Calluna vulgaris. The synecology, synchorology and syntaxonomy of this vegetation was studied using multivariate methods, and discussed in comparison with similar types described in other zones of the Italian peninsula. Two new subassociations are proposed here: Erico arboreae-Arbutetum unedonis genistetosum germanicae and Calluno-Sarothamnetum ericetosum scopariae. Calluno-Sarothamnetum is typified; the Sarothamnion alliance is discussed and referred to Cytisetea scopario-striati. The presence of Calluno-Ulicetea and Cytisetea scopario-striati classes is discussed, and a syntaxonomical scheme is proposed.     

The Effect of Formaldehyde on Tissue Lipids and on Histochemical Reactions for Carbonyl Groups

Histcchemical and chemical evidence indicates that formaldehyde combines with unsaturated lipids at the double bond. The resulting complex contains a free carbonyl group which probably originates from the formaldehyde. The reaction occurs over a wide pH range, and takes place in the absence of oxygen or moisture. The reaction product is visualized by the Schiff reagent, and by the Ashbel-Seligman procedure. In the plasmal procedure, when performed on formalin-treated material, the reaction has the same significance as the pseudo-plasmal reaction, i.e. it denotes the presence of double bonds. The Ashbel-Seligman technic seems to be more sensitive to this complex than the Schiff reagent and shows it more markedly than it does the true plasmals and the atmospherically oxidized unsaturated compounds.     

Isolation of Avian Trypanosomes by Selective Centrifugation and Subsequent Processing for Electron Microscopy

Paraffin sections are usually rehydrated before staining. It is possible to apply aqueous dye solutions without first removing the wax. Staining then occurs more slowly, and only if the embedding medium has not melted or become unduly soft after catting. To avoid this problem, sections are flattened on water no hotter than 45 C and dried overnight at 40 C. Minor technical modifications to the staining procedures are needed. Mercury deposits are removed by iodine, and a 3% solution of sodium thiosnlfate in 60% ethanol is used to remove the iodine from paraffin sections. At room temperature, progressive staining takes 10–20 tunes longer for sections in paraffin than for hydrated sections; at 45 C, this can be shortened to about three times the regular staining time. After staining, the slides are rinsed in water, air dried, dewaxed with xylene, and coverslipped in the usual way. Nuclear staining in the presence of wax was achieved with toluidine blue, O, alum-hematoxylin and Weigert's iron-hematoxylin. Eosin and van Gieson's picric acid-acid fuchsine were effective anionic counterstains. A one-step trichrome mixture containing 3 anionic dyes and phosphomolybdic acid was unsuitable for sections in wax because it Imparted colors that were nninformative and quite different from those obtained with hydrated sections. Advantages of staining in the presence of wax include economy of solvents, reduced risk of overstaining and strong adhesion of sections to slides.     

Discriminating the effects of phylogenetic hypothesis,tree resolution and clade age estimates on phylogenetic signal measurements

Understanding how species traits evolved over time is the central question to comprehend assembly rules that govern the phylogenetic structure of communities. The measurement of phylogenetic signal (PS) in ecologically relevant traits is a first step to understand phylogenetically structured community patterns. The different methods available to estimate PS make it difficult to choose which is most appropriate. Furthermore, alternative phylogenetic tree hypotheses, node resolution and clade age estimates might influence PS measurements. In this study, we evaluated to what extent these parameters affect different methods of PS analysis, and discuss advantages and disadvantages when selecting which method to use. We measured fruit/seed traits and flowering/fruiting phenology of endozoochoric species occurring in Southern Brazilian Araucaria forests and evaluated their PS using Mantel regressions, phylogenetic eigenvector regressions (PVR) and K statistic. Mantel regressions always gave less significant results compared to PVR and K statistic in all combinations of phylogenetic trees constructed. Moreover, a better phylogenetic resolution affected PS, independently of the method used to estimate it. Morphological seed traits tended to show higher PS than diaspores traits, while PS in flowering/fruiting phenology depended mostly on the method used to estimate it. This study demonstrates that different PS estimates are obtained depending on the chosen method and the phylogenetic tree resolution. This finding has implications for inferences on phylogenetic niche conservatism or ecological processes determining phylogenetic community structure.     

lncRNA与miRNA相互调控作用及其与肿瘤的关系研究

长链非编码RNA (long non-coding RNA,lncRNA)是一类转录本长度大于200 bp的非编码RNA,可作为人类基因组中一类重要的调控分子通过多种方式发挥其生物学功能.近年来的研究表明,lncRNA也可以作为一种竞争性内源性RNA (competing endogenous RNA, ceRNA) 与miRNA相互作用,参与靶基因的表达调控,并在肿瘤的发生发展中发挥重要的作用.本综述在简要介绍lncRNA功能研究现状和主要研究方法的基础上,进一步分析了lncRNA与miRNA之间的互相调控关系及其在肿瘤发生发展中的作用,以便为后续的研究提供新的思路.     

Adaptive morphological shifts to novel habitats in marine sculpin fishes

Sculpin fishes of the North American Pacific Coast provide an ideal opportunity to examine whether adaptive morphological character shifts have facilitated occupation of novel habitat types because of their well‐described phylogeny and ecology. In this group, the basal‐rooted species primarily occupy the subtidal habitat, whereas the species in the most distal clades are found in the intertidal. We tested multiple evolutionary models to determine whether changes in body size and changes in number of scales are adaptive for habitat use in sculpins. Based on a statistically robust, highly resolved molecular phylogeny of 26 species of sculpins, in combination with morphometric and habitat affinity data, our analyses show that an adaptive model based on habitat use best explains changes in body size and number of scales. The habitat model was statistically supported over models of neutral evolution, stabilizing selection across all habitats, and three clade‐based models. We suggest that loss of scales and reduction of body size in the intertidal may facilitate cutaneous breathing in air when tidepools become hypoxic during low tides. This study demonstrates how the combined use of phylogenetic, ecological and statistical approaches helps to identify traits that are likely adaptive to novel habitats.