Confirmation bias in studies of fluctuating asymmetry

Fluctuating asymmetry (FA) represents small, non-directional deviations from perfect symmetry in morphological characters. FA is generally accepted to increase in response to stress; therefore, FA is frequently used in ecological studies as an index of stress experienced by an organism, in particular due to environmental pollution. We experimentally tested the hypothesis that the outcomes of studies based on FA measurements may have been influenced by confirmation bias, i.e. the tendency of humans to seek out evidence in a manner that confirms their hypotheses and beliefs. We collected 100 leaves of downy birch (Betula pubescens) from a single tree, grouped them haphazardly into ten samples, scanned every sample, and then asked each of 31 scientists (experienced in studying FA) to measure FA from the scanned images of all 100 leaves. Three groups of participants were provided with false information about the origin of each sample and about the hypothesis to be tested, and one group (control) was provided with true information. The participants who believed that the leaves originated from a heavily polluted site reported significantly higher values of FA when compared to the participants who believed that the leaves were collected from an unpolluted site. When the participants were told that half the samples originated from a polluted site and half from a clean site and were asked to attribute each sample to either of these sites based on leaf FA, the differences in FA between samples classified as ‘polluted’ and ‘unpolluted’ were much higher than the differences obtained from measurements of the same sets of samples made by the control group. We conclude that when scientists expected to find high FA in some samples, the results of their measurements confirmed their expectations. This effect, classified as confirmation bias, may considerably influence the outcomes of the research on FA. This confirmation bias can be avoided by using a blind method, where the person conducting measurements is not aware of the origin of samples being measured. We argue that the use of blind methods is critically important for any study addressing environmental or genetic impacts on FA.     

Assessment of occupational exposure to PAHs in an Estonian coke oven plant- correlation of total external exposure to internal dose measured as 1-hydroxypyrene concentration

The exposure of cokery workers to polynuclear aromatic hydrocarbons at an Estonian oil shale processing plant was assessed by using occupational hygiene and biomonitoring measurements which were carried out twice, in midwinter and in the autumn. To assess the external dose of polynuclear aromatic hydrocarbons, pyrene and benzo[a]pyrene concentrations were measured from the breathing zone of workers during a workshift. Skin contamination with pyrene and benzo[a]pyrene was assessed by skin wipe sampling before and after the workshift. As a biomarker of overall exposure to polynuclear aromatic hydrocarbons, and as an integral of all absorption routes of pyrene, 1-hydroxypyrene concentration was measured from post shift urine samples. Of the personal air samples, 18% exceeded the Finnish threshold limit value of benzo[a]pyrene (10 μg m^-3). Mean value (two separate measurements together) for benzo[a]pyrene was 5.7 μg m^-3 and for pyrene, 8.1 μg m^-3. Based on skin wipe sample analyses, the skin contamination was also obvious. The mean value of benzo[a]pyrene in the samples collected after the shift was 1.2 ng cm^-2. Benzo[a]pyrene was not found in control samples. The mean value of urinary 1-hydroxypyrene concentration was 6.0 μmol mol^-1 creatinine for the exposed workers and 0.5 μmol mol^-1 creatinine for the controls. This study undoubtedly shows the usefulness of 1-hydroxypyrene as an indicator of internal dose of polynuclear aromatic hydrocarbons. It can be concluded that the cokery workers at the Kohtla-Järve plant are exposed to high concentrations of polynuclear aromatic compounds, and the exposure level is considerably higher during the winter measurements.     

苏州工业园区湖泊后生浮游动物群落结构及影响因子

苏州工业园区地处长江流域下游,随着城市化进程的不断推进,园区水生态系统结构与功能的稳定面临严峻考验。浮游动物作为水生态系统的重要组成部分,探究其群落结构的形成机制对生物多样性保护及生态系统健康发展具有重要意义。为深入了解苏州工业园区五个主要湖泊后生浮游动物群落结构的动态变化及影响因子,于2018年7月至2019年6月进行4次调查。研究共检出后生浮游动物112种（轮虫65种、枝角类29种、桡足类18种）,其中优势种12种（轮虫10种、枝角类和桡足类各1种）。Jaccard相似性分析表明,湖泊间后生浮游动物物种组成整体处于中等相似水平。后生浮游动物密度呈现出显著的季节和湖泊差异,而生物量、Shannon-Wiener多样性指数、Pielou均匀度指数以及Margalef丰富度指数仅存在显著的季节差异。聚类分析结果表明,夏季和秋季后生浮游动物群落结构最为相似。RDA分析表明,水温、溶解氧和pH是影响园区湖泊后生浮游动物群落结构的主要环境因子。Pearson相关性分析表明,湖泊面积与后生浮游动物群落结构无显著相关关系,样点近岸距离与生物量具有显著的正相关关系。基于水质评价标准和物种多样性指数可知,园区湖泊水质整体处于轻-中度污染水平。研究表明苏州工业园区五大湖泊后生浮游动物群落结构表现出同质化趋势;季节变化、环境因子以及样点近岸距离是调控群落结构形成的主要因素。     

A simple and convenient synthetic route to Ulipristal acetate

We set out to describe a new and efficient route for preparing Ulipristal acetate with a good yield. The selected epoxidization conditions gave out 80% of 5α,10α-epoxide 2a in the two diastereoisomers which greatly improved the yield of 11β-substituted isomer 4a. And phenyl–sulfinyl compound 6 was synthesized from ketone 5 directly treated with phenylsulfenyl chloride in the presence of triethylamine. These synthetic procedures is only 8 steps, less than currently reported in the literature, but more suitable for industrial process.     

Comprehensive study on Escherichia coli genomic expression: Does position really matter?

As a biorefinery platform host, Escherichia coli has been used extensively to produce metabolites of commercial interest. Integration of foreign DNA onto the bacterial genome allows for stable expression overcoming the need for plasmid expression and its associated instability. Despite the development of numerous tools and genome editing technologies, the question of where to incorporate a synthetic pathway remains unanswered. To address this issue, we studied the genomic expression in E. coli and linked it not only to 26 rationally selected genomic locations, but also to the gene direction in relation to the DNA replication fork, to the carbon and nitrogen source, to DNA folding and supercoiling, and to metabolic burden. To enable these experiments, we have designed a fluorescent expression cassette to eliminate specific local effects on gene expression. Overall it can be concluded that although the expression range obtained by changing the genomic location of a pathway is small compared to the range typically seen in promoter-RBS libraries, the effect of culture medium, environmental stress and metabolic burden can be substantial. The characterization of multiple effects on genomic expression, and the associated libraries of well-characterized strains, will only stimulate and improve the creation of stable production hosts fit for industrial settings.     

工业微生物解脂耶氏酵母及其应用研究*

解脂耶氏酵母是一种可利用多种底物发酵生产多种产品的非常规酵母,环境适应性强、易培养、安全性高。因此,该物种作为一种新型的生物工程菌株引起了科学界的广泛关注。近年来,工业生物技术因绿色、循环、低碳等优势成为新兴工业技术,在国内外得到了快速发展。介绍了解脂耶氏酵母的特征及其代谢生产各类化合物的方法,并通过对工业生物技术与传统化学化工技术的比较分析,阐述了工业生物技术的特点、研究现状及应用前景。     

工业微生物发酵过程中pH调控研究进展

pH是影响微生物生长的重要因素。工业发酵过程中,p H调控波动产生酸/碱胁迫,进而影响到微生物细胞的生长及目标产物的积累。阐述了工业微生物在发酵体系pH波动时所发生的生理变化,总结了目前工业发酵中pH调控的主要策略及各自的优缺点,并指出了未来p H调控的发展方向,以期为发酵工业pH调控提供新的思路。     

Bioremediation of Heavy Metals in Liquid Media Through Fungi Isolated from Contaminated Sources

Wastewater particularly from electroplating, paint, leather, metal and tanning industries contain enormous amount of heavy metals. Microorganisms including fungi have been reported to exclude heavy metals from wastewater through bioaccumulation and biosorption at low cost and in eco-friendly way. An attempt was, therefore, made to isolate fungi from sites contaminated with heavy metals for higher tolerance and removal of heavy metals from wastewater. Seventy-six fungal isolates tolerant to heavy metals like Pb, Cd, Cr and Ni were isolated from sewage, sludge and industrial effluents containing heavy metals. Four fungi (Phanerochaete chrysosporium, Aspegillus awamori, Aspergillus flavus, Trichoderma viride) also were included in this study. The majority of the fungal isolates were able to tolerate up to 400 ppm concentration of Pb, Cd, Cr and Ni. The most heavy metal tolerant fungi were studied for removal of heavy metals from liquid media at 50 ppm concentration. Results indicated removal of substantial amount of heavy metals by some of the fungi. With respect to Pb, Cd, Cr and Ni, maximum uptake of 59.67, 16.25, 0.55, and 0.55 mg/g was observed by fungi Pb3 (Aspergillus terreus), Trichoderma viride, Cr8 (Trichoderma longibrachiatum), and isolate Ni27 (A. niger) respectively. This indicated the potential of these fungi as biosorbent for removal of heavy metals from wastewater and industrial effluents containing higher concentration of heavy metals.     

Sustainability in the biopharmaceutical industry: Seeking a holistic perspective

Biopharmaceuticals manufacturing is a critical component of the modern healthcare system, with emerging new treatments composed of increasingly complex biomolecules offering solutions to chronic and debilitating disorders. While this sector continues to grow, it strongly exhibits “boom-to-bust” performance which threatens its long-term viability. Future trends within the industry indicate a shift towards continuous production systems using single use technologies that raises sustainability issues, yet research in this area is sparse and lacks consideration of the complex interactions between environmental, social and economic concerns. The authors outline a sustainability-focused vision and propose opportunities for research to aid the development of a more integrated approach that would enhance the sustainability of the industry.     

Structural Analysis of a Glycoside Hydrolase Family 11 Xylanase from Neocallimastix patriciarum: INSIGHTS INTO THE MOLECULAR BASIS OF A THERMOPHILIC ENZYME*

The catalytic domain of XynCDBFV, a glycoside hydrolase family 11 (GH11) xylanase from ruminal fungus Neocallimastix patriciarum previously engineered to exhibit higher specific activity and broader pH adaptability, holds great potential in commercial applications. Here, the crystal structures of XynCDBFV and its complex with substrate were determined to 1.27–1.43 Å resolution. These structures revealed a typical GH11 β-jelly-roll fold and detailed interaction networks between the enzyme and ligands. Notably, an extended N-terminal region (NTR) consisting of 11 amino acids was identified in the XynCDBFV structure, which is found unique among GH11 xylanases. The NTR is attached to the catalytic core by hydrogen bonds and stacking forces along with a disulfide bond between Cys-4 and Cys-172. Interestingly, the NTR deletion mutant retained 61.5% and 19.5% enzymatic activity at 55 °C and 75 °C, respectively, compared with the wild-type enzyme, whereas the C4A/C172A mutant showed 86.8% and 23.3% activity. These results suggest that NTR plays a role in XynCDBFV thermostability, and the Cys-4/Cys-172 disulfide bond is critical to the NTR-mediated interactions. Furthermore, we also demonstrated that Pichia pastoris produces XynCDBFV with higher catalytic activity at higher temperature than Escherichia coli, in which incorrect NTR folding and inefficient disulfide bond formation might have occurred. In conclusion, these structural and functional analyses of the industrially favored XynCDBFV provide a molecular basis of NTR contribution to its thermostability.