Physiological state-specific models in estimation of recombinant Escherichia coli fermentation performance

Implementation of advanced control strategies in bioprocesses is often hindered by the lack of on-line measurements reflecting the physiological state of the culture. Although a number of techniques have been used to estimate key variables from data monitored on-line, these often do not explicitly take into account changes in physiological state and information on many aspects of physiological state that may not be present in on-line data. Here we demonstrate that data obtained from chemical fingerprinting methods, such as pyrolysis mass spectrometry, can be used to identify changes in the physiological state during cultivation. This information can be utilized for the estimation of the physiological state and can enable physiological state-specific-model development for on-line bioprocess control.     

Automatic on-line growth estimation method for outdoor algal biomass production

An on-line measuring procedure for estimating productivity in outdoor algal cultures was developed and tested experimentally. The procedure is based on a previously described method for on-line measuring net O(2) production rate (OPR). The data obtained by this method was found to correlate well with the conventional procedures for estimation productivity by measuring the changes in biomass concentration in the culture. The new procedure seems to be superior to the latter since it can be carried out in an almost continuous way and can give immediate indication on the productivity. OPR could be used to monitor on-line the photosynthetic and/or respiration activity in small research fermentors or in large-scale open systems outdoors.     

Publish and Perish?

The publishing of research has implications for the evaluation of research careers, research departments, and funding for research projects. Researchers' academic evaluation relies heavily on the status of the journals in which they publish. The inclusion of one's work in the Science Citation Index (SCI) and the Social Science Citation Index (SSCI) is often used as an indicator of academic quality. This is unfortunate for many environmental researchers, as their journals are not represented in the SCI and SSCI. Two investigations were carried out to determine the reasons for this. The first investigation identified 352 existing environmental academic journals, classified into seven categories (and several subcategories). Of these, two categories were not represented in the SCI or SSCI: environmental systems analysis journals and corporate environmental management journals. The second survey investigated the publishing patterns of interdisciplinary research groups and the characteristics of the journals in which they publish. In spite of acceptable citation levels, interdisciplinary environmental journals are excluded from the SCI and SSCI. A major reason seems to be that citations of their articles are uncounted by the Institute for Scientific Information (ISI), the organization producing the SCI and SSCI, because citations mostly take place in a group of journals completely unrepresented in ISI's database.     

Random drift versus selection in academic vocabulary: an evolutionary analysis of published keywords

The evolution of vocabulary in academic publishing is characterized via keyword frequencies recorded in the ISI Web of Science citations database. In four distinct case-studies, evolutionary analysis of keyword frequency change through time is compared to a model of random copying used as the null hypothesis, such that selection may be identified against it. The case studies from the physical sciences indicate greater selection in keyword choice than in the social sciences. Similar evolutionary analyses can be applied to a wide range of phenomena; wherever the popularity of multiple items through time has been recorded, as with web searches, or sales of popular music and books, for example.     

生态系统完整性在管理层面的体现方式: 以跨省国家公园统一管理的体制机制为例

生态系统完整性保护是国家公园的重要管理目标, 但学术上的完整性如何体现为管理上的完整性需要基于科学概念进行体制设计。从管理层面体现生态系统完整性需要突破原有的属地化要素管理模式, 把国家公园作为国土空间用途管制的独立单元, 将“山水林田湖草”统筹起来一体化管理, 但这种管理往往因为不同行政区不同的“权、钱”相关制度引发的激励不相容而难以实现, 尤其在国家公园跨省的情况下。可以首先实现跨省国家公园不同省的管理机构“权、钱”相关制度统一, 再构建协调机制或组建类似资产管理的协调机构, 以实现激励相容。在这样的体制机制下, 今后的国家公园划界也易于突破省界藩篱, 更好体现科学概念上的完整性。     

《广西植物》三十年发展回顾分析

介绍了《广西植物》的创办情况,并从八个角度,即:刊物取得各种标识码;办刊宗旨和方针、专业分工范围、读者对象;获奖、馆藏、收录及进入各类数据库情况;各项指标统计结果;植物新分类群的发表;国际发行与交换;出版育人;学术影响力等方面,对刊物三十年发展进行了回顾性分析。结果显示:《广西植物》三十年来在各方面都取得了较为明显的进步,质量不断提高,为植物学界发现人才、培养人才做出了积极的贡献。展望未来同时面临着困难、挑战、机遇与希望,期刊编辑部应以继续提高期刊质量,实现期刊数字化、网络化为发展方向,以立精品期刊,创一流刊物为持续发展的目标,努力走出去,学习名刊的办刊经验,使刊物融入世界学术信息大循环中。     

More topics from the tropics: additional thoughts to Mammides et al.

Most studies on tropical conservation questions are conducted by researchers of developed countries from the north. This geographic disconnection was recently criticised by Mammides et al. Here, we reflect on their findings and add further views from scientist’s and journal editor’s perspectives. We argue that journals are, a priori, most strongly interested in research questions and approaches that will likely increase their scientific impact and prestige. This is rarely compatible with publishing articles on questions with restricted global impact or based on single taxa. We question whether small changes in the editorial policy of international conservation journals will considerably improve the geographic diversity in key conservation publications. Rather, thematic scopes of the leading conservation journals should be modified, preferably in close collaboration with leading conservationists from the south. We are convinced that long-term investments in the tropics will create a stronger local scientific community, thus bolstering academic morale, and finally may lead to an increase in the submission and acceptance rate of articles written from scientists from these regions.     

COMMENTARY: SCIENCE SCANDAL OR ETHICS SCANDAL? OLIVIERI REDUX

Dr. Nancy Olivieri has become an icon of research integrity for her insistence on publishing adverse data about a drug she was investigating. She has been celebrated world-wide as a hero of biomedical ethics for her bravery in disclosing potential dangers to research subjects, in the face of both drug company threats and coercive pressures from her hospital and university. Like so many other 'whistle-blowers' however, she now faces both personal vilification and disturbing accusations of scientific error. The case against Olivieri is assessed and found to be baseless.     

Anatomy and physiology of a scientific paper

Writing and publishing a scientific paper in academic journals is a highly competitive, time-consuming stepwise process. The road to scientific writing and publication is rarely straightforward. Scientific writing has uniform format, which is perplexing for the novice science writers due to its inflexible anatomy (structure) and physiology (functions). Many obstacles are allied with the scientific writing path which can be minimized by applying some simple guidelines and practices. The scientific papers have an almost similar format but, original articles are divided into distinct sections and each segment contains a specific type of information. The basic anatomy of scientific papers is mainly comprised of the structure of the various components of a scientific paper, including title, abstract, introduction, methods, results, discussion, conclusion, acknowledgments and references. However, the physiology of a scientific paper is difficult to understand. Early career researchers and trainees may be less familiar with the various components of scientific papers. In this study, we applied an observational approach to describe the essential steps to facilitate the readers and writers to understand the basic characteristics, anatomy and physiology of writing the various sections of a scientific paper for an academic science journal.     

Nitrogenase activity in cyanobacteria measured by the acetylene reduction assay: a comparison between batch incubation and on-line monitoring

A new on-line method for measuring acetylene reduction is described. It consists of a gas-flow cell connected to an electronic gas-mixing system and an automatic sample loop in the gas chromatograph. Alternatively, ethylene can be determined by using laser-based trace gas detection. The laser-based trace gas detection technique achieves a detection limit that is three orders of magnitude better than gas chromatography. We have applied the on-line method to the measurement of nitrogen fixation in a culture of the heterocystous cyanobacterium Nodularia spumigena and compared it with conventional batch-type incubations. Incubation of N. spumigena in the gas-flow cell resulted in very short response times with a steady-state flux of ethylene obtained within 2 min. Nitrogenase was shown to respond immediately to changes in light and oxygen. Monitoring of nitrogenase activity could be continued for several hours without having a negative impact on nitrogen fixation rates in N. spumigena . This was not the case in batch incubations, in which changes in nitrogenase activities were recorded during incubations, probably as a result of varying oxygen concentrations. It was therefore concluded that the on-line method is superior to batch incubations when rates of nitrogenase activity are to be measured. The method is suitable for natural samples (water or sediment).     

On-line stoichiometry and identification of metabolic state under dynamic process conditions

A method for the on-line calculation of conversion rates and yield coefficients under dynamic process conditions was developed. The method is based on cumulated mass balances using a moving average method. Elemental balances were used to test the measured cumulated quantities for gross errors and inappropriate stoichiometry definition followed by data reconciliation and estimation of non-measured conversion rates, using a bioprocess set-up including multiple on-line analysis techniques. The quantitative potential of the proposed method is demonstrated by executing transient experiments in aerobic cultures of Saccharomyces cerevisiae on glucose. Rates and yield coefficients could be consistently quantified in shift-up, shift-down, and accelerostat experiments. The method shows the capability to describe quantitatively transient changes in metabolism including uncoupling of catabolism and anabolism, also for the case when multiple components of metabolism are not measured. The validity of the experiment can be evaluated on-line. Additionally, the method detects with high sensitivity inappropriate stoichiometry definition, such as a change in state of metabolism. It was shown that concentration values can be misleading for the identification of the metabolic state. In contrast, the proposed method provides a clear picture of the metabolic state and new physiological regulations could be revealed. Hence, the novelty of the proposed method is the on-line availability of consistent stoichiometric coefficients allowing a significant speed up in strain characterization and bioprocess development using minimal knowledge of the metabolism. Additionally, it opens up the use of transient experiments for physiological studies.     

Combining on-line spectroscopy with synchrotron and X-ray free electron laser crystallography

With the recent advances in serial crystallography methods at both synchrotron and X-ray free electron laser sources, more details of intermediate or transient states of the catalytic reactions are being revealed structurally. These structural studies of reaction dynamics drive the need for on-line in crystallo spectroscopy methods to complement the crystallography experiment. The recent applications of combined spectroscopy and crystallography methods enable on-line determination of in crystallo reaction kinetics and structures of catalytic intermediates, sample integrity, and radiation-induced sample modifications, if any, as well as heterogeneity of crystals from different preparations or sample batches. This review describes different modes of spectroscopy that are combined with the crystallography experiment at both synchrotron and X-ray free-electron laser facilities, and the complementary information that each method can provide to facilitate the structural study of enzyme catalysis and protein dynamics.     

努力打造一流学术期刊,积极推动植物科学发展——庆祝《广西植物》创刊40周年

在庆祝《广西植物》创刊40周年之际,回顾了《广西植物》的发展历程,可分为4个阶段:初创内部刊物,萌芽起步; 国内外公开发行,期刊影响力提升; 抓住机遇,实现期刊跨越式发展; 打造期刊品牌特色,以特色栏目带动期刊整体发展。以创刊以来发表的学术论文为研究对象,基于中国知网和CNKI中国引文数据库的数据,使用引证分析法,从发文信息量、报道对象、稿源及作者队伍特点、论文资助项目、被国内期刊引用情况、发表文章下载量等方面分析了期刊的学术影响力。总结了期刊在以下方面所取得的成绩:发现人才和培养人才,为人才的成长提供优良平台; 期刊评价的各项指标提升,期刊影响力扩大; 围绕国家战略和重大社会需求,策划研究热点,打造学科特色栏目; 扩大作者群和读者群,加强编委会建设等。展望未来,面临巨大挑战。对此,笔者提出以下设想:第一,围绕创新型国家和科技强国建设任务,提升期刊的学术引领能力和品牌影响力; 第二,聚焦国家重大战略需求,围绕重大主题打造重点专栏、组织专题和专刊,服务经济社会发展主战场。第三,顺应媒体融合发展趋势,适应移动化、智能化的发展方向,探索全媒体出版等新型出版模式,加快期刊融合发展。第四,适度增加国际编委比例,提供论文英文长摘要,加强双语学术网站建设,提升开放办刊水平和国际传播能力,努力打造国内一流并具有国际影响力的学术期刊。     

Specific features of mental work capacity in 11-to 13-year-old schoolchildren during puberty

Experimental physiological, psychological, and hygienic studies were conducted for three years in the same fifth to seventh grade schoolchildren from 11 to 13 years of age. The findings made it possible to evaluate health status, the intensity of daily academic and out-of-school loads, changes in mental work capacity (MWC), and the relationship between the MWC and other indices of body function in the schoolchildren under study. The highest functional tension was experienced by the fifth grade schoolchildren and can be explained by the onset of puberty and changes in both the academic load and study conditions as compared to those at the previous stage of school education.     

“Reproducible” Research in Mathematical Sciences Requires Changes in our Peer Review Culture and Modernization of our Current Publication Approach

The nature of scientific research in mathematical and computational biology allows editors and reviewers to evaluate the findings of a scientific paper. Replication of a research study should be the minimum standard for judging its scientific claims and considering it for publication. This requires changes in the current peer review practice and a strict adoption of a replication policy similar to those adopted in experimental fields such as organic synthesis. In the future, the culture of replication can be easily adopted by publishing papers through dynamic computational notebooks combining formatted text, equations, computer algebra and computer code.     

Diet,inflammation and the gut microbiome: Mechanisms for obesity-associated cognitive impairment

Poor diet and obesity are associated with cognitive impairment throughout adulthood, and increased dementia risk in aging. Here we review the current literature interrogating the mechanisms by which diets high in fat, or fat and sugar lead to cognitive impairment, focusing on changes to gut microbiome composition, inflammatory signalling and blood-brain barrier integrity. Preclinical studies indicate weight gain is not necessary for diet-induced cognitive impairment. Rather, gut microbiome composition, and systemic and central inflammatory processes appear to contribute to diet-induced cognitive impairment. While both obese humans and rodents exhibit reduced blood-brain barrier integrity, cognitive impairments precede these changes, suggesting other mechanisms may underly diet-induced cognitive changes. Other potential candidates include hormone, glucoregulatory and cardiovascular changes. Poor diet and obesity act through multiple mechanisms to affect cognitive health and the challenge for future research is to identify key processes that can be reversed to improve cognition and quality of life.     

PUBLISHING IN THE GEOLOGICAL SCIENCES

A principal method of mastering the 'publication explosion' should be a more consistent structural differentiation of publishing, thus enabling a better channelling of information. Besides subject specialization, this can be achieved by clearer distinction between local, national, and international spheres of interest and between idiographic and nomothetic aspects of papers. The 'publication explosion' is a consequence of a corresponding increase in research, and quantitative curbing of publication should not be applied to such an extent that it affects the universal availability of scientific results. More stringent selection, however, would reduce the volume of primary publishing considerably. Training of authors in publishing techniques would greatly ease the burden of routine labour for editors. This, and the organization of scientific serials and articles to meet modern bibliographic-documentalistic needs, present problems calling for urgent solution at an international level.     

Ecological integrity of supraspecific taxa and the arctic biota

Some specific features of the development of concepts about integrity (systemic organization) of supraspecific taxa are considered. Several forms of integrity can be distinguished: taxonomic, or genealogical; evolutionary (considering a taxon as a developing system); ecological, or eco-adaptive (manifestation of the properties of a united system in the course of exploring the various conditions and types of environment by the phyletically specified biota). Taxa of different level “behave” as whole units or blocks, forming structural parts of the cenotic and biotic forms of life. The properties of integrity, systemic organization of supraspecific taxa can be displayed by analysis of changes in the structural parameters of the biota related to latitudinal gradients of climatic factors, in phenomena of individualistic distribution, ecological substitution (vicariance) of taxa, and preservation of their ecological functions (adaptive zone) despite the reduced species diversity. The variants of adaptive exploration of high-latitude landscape-zonal conditions are considered using examples from the Arctic flora and fauna.