ASER: Animal Sex Reversal Database

Sex reversal, representing extraordinary sexual plasticity during the life cycle, not only triggers reproduction in animals but also affects reproductive and endocrine system-related diseases and cancers in humans. Sex reversal has been broadly reported in animals; however, an integrated resource hub of sex reversal information is still lacking. Here, we constructed a comprehensive database named ASER (Animal Sex Reversal) by integrating sex reversal-related data of 18 species from teleostei to mammalia. We systematically collected 40,018 published papers and mined the sex reversal-associated genes (SRGs), including their regulatory networks, from 1611 core papers. We annotated homologous genes and computed conservation scores for whole genomes across the 18 species. Furthermore, we collected available RNA-seq datasets and investigated the expression dynamics of SRGs during sex reversal or sex determination processes. In addition, we manually annotated 550 in situ hybridization (ISH), fluorescence in situ hybridization (FISH), and immunohistochemistry (IHC) images of SRGs from the literature and described their spatial expression in the gonads. Collectively, ASER provides a unique and integrated resource for researchers to query and reuse organized data to explore the mechanisms and applications of SRGs in animal breeding and human health. The ASER database is publicly available at http://aser.ihb.ac.cn/.     

Sequence‐based analysis of protein degradation rates

Protein turnover is a key aspect of cellular homeostasis and proteome dynamics. However, there is little consensus on which properties of a protein determine its lifetime in the cell. In this work, we exploit two reliable datasets of experimental protein degradation rates to learn models and uncover determinants of protein degradation, with particular focus on properties that can be derived from the sequence. Our work shows that simple sequence features suffice to obtain predictive models of which the output correlates reasonably well with the experimentally measured values. We also show that intrinsic disorder may have a larger effect than previously reported, and that the effect of PEST regions, long thought to act as specific degradation signals, can be better explained by their disorder. We also find that determinants of protein degradation depend on the cell types or experimental conditions studied. This analysis serves as a first step towards the development of more complex, mature computational models of degradation of proteins and eventually of their full life cycle. Proteins 2017; 85:1593–1601. © 2017 Wiley Periodicals, Inc.     

Multi‐criteria manufacturability indices for ranking high‐concentration monoclonal antibody formulations

The need for high‐concentration formulations for subcutaneous delivery of therapeutic monoclonal antibodies (mAbs) can present manufacturability challenges for the final ultrafiltration/diafiltration (UF/DF) step. Viscosity levels and the propensity to aggregate are key considerations for high‐concentration formulations. This work presents novel frameworks for deriving a set of manufacturability indices related to viscosity and thermostability to rank high‐concentration mAb formulation conditions in terms of their ease of manufacture. This is illustrated by analyzing published high‐throughput biophysical screening data that explores the influence of different formulation conditions (pH, ions, and excipients) on the solution viscosity and product thermostability. A decision tree classification method, CART (Classification and Regression Tree) is used to identify the critical formulation conditions that influence the viscosity and thermostability. In this work, three different multi‐criteria data analysis frameworks were investigated to derive manufacturability indices from analysis of the stress maps and the process conditions experienced in the final UF/DF step. Polynomial regression techniques were used to transform the experimental data into a set of stress maps that show viscosity and thermostability as functions of the formulation conditions. A mathematical filtrate flux model was used to capture the time profiles of protein concentration and flux decay behavior during UF/DF. Multi‐criteria decision‐making analysis was used to identify the optimal formulation conditions that minimize the potential for both viscosity and aggregation issues during UF/DF. Biotechnol. Bioeng. 2017;114: 2043–2056. © 2017 The Authors. Biotechnology and Bioengineering Published by Wiley Perodicals, Inc.     

Developing manufactured soils from industrial by‐products for use as growth substrates in mine reclamation

Suitable soils for reclamation can be acquired through excavation and translocation of local soils, increasing the industrial footprint on previously undisturbed lands and causing negative environmental impacts. Manufactured soils (Technosols) could be a viable soil source when the availability of suitable natural soils is limited. The purpose of this study was to manufacture a Technosol from an admixture of woody residuals, primary paper sludge, and two subtypes of nonacid generating crushed mine rock, to function as a growth substrate for revegetation of mined land. Technosols manufactured with 0, 25, 50, and 75% organic materials (v/v) were assessed in a 10‐week growth study using annual ryegrass biomass production and allocation as a performance indicator. Technosols containing no organic materials had significantly lower plant nutrient concentrations than Technosols containing an organic constituent and, after 5 weeks of growth, ryegrass grown on nonorganic Technosols had greater root:shoot ratios than ryegrass grown on organic Technosols. Organics increase the water holding capacity and nutrient concentrations of Technosols and should be included in manufacturing Technosols for revegetation. Technosols manufactured with primary paper sludge produced lower shoot biomass than Technosols manufactured with woody residuals, which could be in part due to the higher pH of the paper sludge. Technosols can be manufactured for revegetation purposes and individual components should be assessed before and after mixing. Further development of Technosols should include field testing and amendment or fertilizer use to improve soil nutrient content.     

寺河矿大采高工作面通风系统优化

为了防治由于煤层开采强度、深度及瓦斯涌出量的增大而造成工作面瓦斯浓度的超限情况已成为煤矿开采中的重大安全隐患.文章通过对寺河矿大采高工作面多巷道布置进行相似材料模拟和现场试验,提出了三进两回的通风方式,使工作面通风系统得到优化,一定程度上解决了工作面瓦斯超限问题.多巷布置对高产高效工作面瓦斯治理技术研究具有重要意义,文章初步建立了工作面瓦斯治理的框架,为今后类似条件的工作面瓦斯治理提供了参考依据.     

Recovery of Bird Species in Minimally Restored Indonesian Tin Strip Mines

Bird species richness and individual abundances were recorded in old, unrestored tin strip mine plots, in mined plots restored 1, 2, and 3 years before the study, and in adjacent, unmined, natural secondary forest plots on the 11,340‐km² Indonesian island of Bangka (2°S, 106°E). The objective was to assess the ecological recovery of unrestored and minimally restored mine plots compared with surrounding reference forest. Unrestored mines had not been mined or used for any other purpose for 14–30 years; plots in their first, second, and third year since restoration were old mines planted with Acacia mangium (Leguminosae) at a density of 400 trees/ha. Natural secondary forest plots 20 or more years since the last disturbance were immediately adjacent to both unrestored and restored plots. Bird surveys on 4‐ha plots were performed during the 1995 breeding season. A comparison of data from unrestored plots of widely varying ages showed no significant differences among them for species richness, diversity (Shannon–Wiener index, H′), or individual abundance, indicating that little natural bird community recovery had occurred over time in the plots. However, increases did occur in restored sites over only 3 years for both species richness (r ² = 0.29, p = 0.04) and diversity (r ² = 0.45, p = 0.009). All values for third‐year restored plots, however, were still significantly lower than corresponding values for adjacent natural secondary forest plots. The quick return of bird activity on the plots after minimal efforts at restoration supports the idea that simple, inexpensive restoration can be effective for “jump starting” degraded systems at large scales. Such a restoration strategy might be of particular value for degraded land in developing nations, where scientific, professional, and financial resources might be in short supply. Using this strategy, a small number of restoration professionals could mobilize the labor of many local people in many areas, serving to both improve ecological systems and to educate and engage local populations in restoration and conservation projects.     

Q-omics: Smart Software for Assisting Oncology and Cancer Research

The rapid increase in collateral omics and phenotypic data has enabled data-driven studies for the fast discovery of cancer targets and biomarkers. Thus, it is necessary to develop convenient tools for general oncologists and cancer scientists to carry out customized data mining without computational expertise. For this purpose, we developed innovative software that enables user-driven analyses assisted by knowledge-based smart systems. Publicly available data on mutations, gene expression, patient survival, immune score, drug screening and RNAi screening were integrated from the TCGA, GDSC, CCLE, NCI, and DepMap databases. The optimal selection of samples and other filtering options were guided by the smart function of the software for data mining and visualization on Kaplan-Meier plots, box plots and scatter plots of publication quality. We implemented unique algorithms for both data mining and visualization, thus simplifying and accelerating user-driven discovery activities on large multiomics datasets. The present Q-omics software program (v0.95) is available at http://qomics.sookmyung.ac.kr.     

生物催化剂发现与改造的研究进展

生物催化是指将酶或生物有机体用于有用的化学转化的过程,在人们对传统化学催化的环境影响抱有忧虑的情况下,生物催化提供了一种有吸引力的选择。在过去的几十年里,对生物催化剂的研究每出现一次大的进步,生物催化的发展就会出现一次高潮。因此,生物催化剂的发现与改造已成为当今研究的热点。宏基因组文库技术的出现克服了许多微生物不可培养的障碍,人们能够从自然资源中获得丰富的潜在的生物催化剂。而基于理性设计的分子改造技术的发展,可以使得人们对潜在的生物催化剂进行快速而有效的改造以满足工业化生产的需求。随着生物催化剂发现与改造的手段不断进步,更多的优良生物催化剂得到了广泛的应用,生物催化在工业生产中也得到了更深入的应用。结合作者的研究工作,总结了生物催化剂发现与改良的一些研究进展,以为获得更多优良的、能够实现工业应用的生物催化剂奠定理论基础。     

Genome Mining and Molecular Networking Guided Isolation of Antimycin Analogs with Antifeedant Activities from the Deep-Sea-Derived Streptomyces sp. NA13

Polyphagous insects could affect agricultural production, which leads to serious economic losses. Due to the negative effects of synthesized insecticides, finding eco-friendly and new biopesticides is emergent. To develop natural origin insecticides, an integrative approach combining antifeedant activity screening, genome mining, and molecular networking has been applied to discover antifeedant secondary metabolites from Streptomyces sp. NA13, which leads to the isolation of a novel antimycin Q ( 1 ) and six known antimycin analogs (antimycins A1a, A2a, A3a, A4a, A7a, and N-formylantimycic acid methyl ester, 2 – 7 ). Their structures were identified by high-resolution mass spectrometry (HR-MS) and nuclear magnetic resonance (NMR) spectroscopic. The absolute configuration of 1 was elucidated by the comparison of coupling constant, electronic circular dichroism (ECD) analysis, and NMR calculations. 1 – 6 exhibited different levels of antifeedant activities against Helicoverpa armigera, especially 1– 4 . At the same time, the antifeedant activity of antimycin was reported firstly.