Ein mikrorechnersystem für fermentationseinrichtungen

For several years now, we can notice efforts in increasing the efficiency of microbial processes by means of more intensive scientific investigation of such processes. Essential prerequisites to it are improved possibilities for process monitoring (available sensors) as well as facilities for realtime processing of process information. In this paper a microcomputer system is represented, which has been constructed on the base of computing needs for fermentation. The computing needs for fermentation experiments are outlined and the structure of the microcomputer is described. As an example it is illustrated what tasks can be solved by this microcomputer in coupled operation with a laboratory fermentor.     

Ten simple rules for designing and running a computing minor for bio/chem students

Science students increasingly need programming and data science skills to be competitive in the modern workforce. However, at our university (San Francisco State University), until recently, almost no biology, biochemistry, and chemistry students (from here bio/chem students) completed a minor in computer science. To change this, a new minor in computing applications, which is informally known as the Promoting Inclusivity in Computing (PINC) minor, was established in 2016. Here, we present the lessons we learned from our experience in a set of 10 rules. The first 3 rules focus on setting up the program so that it interests students in biology, chemistry, and biochemistry. Rules 4 through 8 focus on how the classes of the program are taught to make them interesting for our students and to provide the students with the support they need. The last 2 rules are about what happens “behind the scenes” of running a program with many people from several departments involved.     

Analysis of data from incomplete block designs

This paper presents an organized solution to the problem of computing inter- and intrablock analyses of incomplete block designs, based on the modified maximum likelihood principle proposed by Patterson and Thompson (1971, Biometrika 58, 545-554). The calculations are set out to be easily programmed on a microcomputer. The method is attractive because it is simple, yet sufficiently general to handle a wide class of designs, including partially balanced incomplete block designs, designs with unequal block sizes, designs with missing values, and generally unbalanced split-plot experiments.     

The future of education in the molecular life sciences

The changing landscape of education in biochemistry and molecular biology presents many challenges for the future, for students and educators alike. The exponential increase in knowledge, the genomics, proteomics and computing revolutions, and the merging of once separate fields in biology, chemistry, physics and mathematics, mean that we need to rethink how we should be preparing today's science undergraduates for the future. What do we need to change, and how will we implement it?     

运用《生物化学》歌曲，辅助《生物化学》教学

《生物化学》以生物体为对象,研究其生命的化学本质,是生命科学领域的核心课程。长期以来,由于生物化学课程知识点多、范围广和内容抽象,在一定程度上会影响学生学习的自信心,压抑其学习过程中的兴趣,致使学习的积极性不高。最近10～20年里,国外将科学（science）、技术学（technology）、工程学（engineering）及数学（mathematics）的教育与艺术学（arts）,特别是与艺术学中的音乐结合实施教学,形成一种所谓的STEAM (STEM + Arts) 策略,对STEM教育进行辅助,取得了不错的效果。基于以上情况,结合国内生物化学教学实际,笔者尝试将生物化学歌曲应用于课堂教学过程中,辅助教学。生物化学歌曲可以将抽象难懂的生物化学知识转变成悦耳动听的歌曲,在教学过程中能激发学生的学习兴趣,活跃课堂气氛,使学生在学习过程中爱上生物化学;在生物化学歌曲的创作过程中,能促进学生的思考创新,内化重点难点,使深奥的问题形象化;在学习过程中用歌声展现生物化学的魅力,让知识成为有趣的知识,让其成为有趣的学习者。本文介绍了国内生物化学歌曲发展壮大历程,结合具体实例从利用生物化学歌曲引入教学、理解生物化学内容、密切联系生活三方面评论了生物化学歌曲在辅助生物化学教学中的应用,并从歌词的改编、旋律的选择、歌曲的传唱、教学的设计等方面需要注意的问题进行讨论。     

A low-cost chromatograph data-collection system

A data collection system has been constructed, based on the low-cost BBC microcomputer, which provides for the digitization and storage of the data from one or more g.l.c. or h.p.l.c. instruments, or from other data sources with similar data rates. The data can be observed during collection on the graphics screen, and are then stored on disk for subsequent processing. This processing is designed to be interactive, so that the operator can influence decisions about base-line drifts, peak separations, etc. when integrating the peaks, and can decide which peaks are to be stored in a time/intensity record, on the basis of a visual display of the trace. A low cost multi-channel precision ADC, using isolated voltage-to-frequency transducers sited at the sources of data, and multiple counters at the computer, may be used to measure several signals simultaneously even when they originate at some distance from the computer, and extra memory can also be added to the BBC microcomputer to allow temporary storage of data. The software is written in machine code (for the data collection) and BASIC (for the analysis routines) so that modifications to the latter routines can be made easily. The user interface is suitable for routine users who have no computing experience.     

基于CiteSpace生物化学实验教学动态与热点可视化分析

生物化学是生物学和医学学科非常重要的基础课程,是进入21世纪以来发展最为迅速和最具活力的学科之一.生物化学理论教学极具抽象性,所以其实验教学是理解相关理论与掌握实际技能的重要环节.在生物化学实验教学过程中,及时掌握新的教学理念,新的教学方法,新的教学热点,紧跟教学发展趋势一直是教师们关注的重点问题.本文以中国学术期刊网...     

The pentose phosphate pathway in the yeasts Saccharomyces cerevisiae and Kloeckera apiculata,an exercise in comparative metabolism for food and wine science students

Comparative cellular metabolism can be a difficult area of biochemistry to teach in the undergraduate laboratory class. Student practicals involving animal tissues generally require approval from animal ethic committees, and the relevance for students whose primary interest in biochemistry is in the area of food and wine sciences, is often questioned. In this report, we present an undergraduate practical exercise in which glucose catabolism via the pentose phosphate pathway is compared in two types of yeast with direct relevance to the wine and food industries, Saccharomyces cerevisiae and Kloeckera apiculata. The exercise is carried out as a demonstration to second year undergraduate students, studying metabolic biochemistry. It is of some value in that it illustrates comparative cellular metabolism in wine yeasts and introduces the students to the safe use of radioisotopes.     

The methodological problems of the correlation of biochemistry and physiology in current research

An attempt to treat critically the key methodological positions of modern biochemistry, primarily, the medical biochemistry with reference to the physiologic, pathophysiologic and clinical tasks is made. The author puts forward questions: 1) if it is possible to apply traditional approaches (principles) of biochemical investigation developed on purified systems to the whole organism systems in situ and etc.; 2) if it coincides the methodical approaches of biochemistry on the one hand and physiology (pathophysiology)--on the other one, considering the mechanisms of disease development and correspondingly the assessment and choice of therapeutic methods; 3) if there exists a necessity to create a unite methodology of biochemical and physiologic knowledge as a basis of modern medical science as a whole. Some examples showing the possible ways of new methodic consideration of traditional conceptions of in vitro biochemistry are given.     

Proteomic tools for biomedicine

Proteomic tools measure gene expression, protein activity and interactions of biological events at the protein level. Proteins are the major catalysts of biological functions and contain several dimensions of information that collectively indicate the actual rather than the potential functional state as indicated by mRNA analysis. Measurements can be made in terms of protein quantity, location, and time-point. For the future we see a further integration of existing and new technologies for proteomics from a wide range of areas of biochemistry, chemistry, physics, computing science and molecular biology. This will further advance our knowledge of how biological systems are built up and what mechanisms control these systems. However, the potential of proteomics to comprehensively answer all biological questions is limited as only protein activity is measured. A unification of genomics, proteomics, and other technologies is needed if we are to start to understand the complexity of biological function in the context of disease and health.     

Essential Bioinformatics * Jin Xiong * Cambridge University Press; ISBN: 0-521-60082-0; 339pp.; 2006; * {pound}65.00 (hardcover); {pound}29.00 (paperback).

Few would argue the need for today's college biology majorsto have basic skills in bioinformatics. Yet, their undergraduatefaculty faces several challenges in providing these skills,particularly at smaller colleges. First, faculty members whoteach bioinformatics have usually been trained in molecularbiology, genetics or biochemistry. Therefore, most do not haveextensive applied mathematics experience beyond statistics.Second, bioinformatics textbooks for undergraduate biology majorsare rare. Most bioinformatics books are geared to researchers,computer programmers or graduate students. Others are simpleuser manuals, with little coverage of critical evaluation ofthe output. Third, most students today have great ‘point-and-click’computing skills, but minimal understanding or patience forcommand-line computing or programming. In light of these challenges to introducing undergraduate studentsto bioinformatics, it was quite a joy to read and review ProfessorJin Xiong's recent book, Essential Bioinformatics. This compact,economical, first edition of     

How does the ratio of ATP yield from the complete oxidation of palmitic acid to that of glucose compare with the relative energy contents of fat and carbohydrate?

The authors of many recent popular textbooks of biochemistry quote values for the ‘energy content’ of triacylglcyerol and dry carbohydrate on a weight basis as well as presenting calculations for the yield of ATP obtained when a molecule of glucose, or palmitic acid, is completely oxidised to CO₂ and H₂O. By extending these calculations and computing the yield of ATP in terms of the weight of glucose or palmitic acid oxidised to CO₂ and H₂O, it can be shown that the value for the ratio of the energy content of fat to that of carbohydrate is almost identical to the ratio of the yield of ATP per gram of palmitic acid oxidised, compared with that of glucose. Therefore, the efficiency (on a per gram basis) by which energy is made available as ATP is comparable for both the oxidation of fat and carbohydrate, thus underscoring the fact that the catabolic pathways for both fat and carbohydrate ultimately use the same means of generating ATP, namely, oxidative phosphorylation.     

A tribute to sulfur.

Recent progress in a number of areas of biochemistry and biology has drawn attention to the critical importance of sulfur in the biosynthesis of vital cofactors and active sites in proteins, and in the complex reaction mechanisms often involved. This brief review is intended as a broad overview of this currently rapidly moving field of sulfur biochemistry, for those who are interested or are involved in one or the other aspect of it, a synopsis by one who has stumbled into this field from several directions in the course of time. Only for iron are metal-sulfur relationships discussed in detail, as the iron-sulfur subfield is one of the most active areas.     

生物化学教学实用技巧和策略

生物化学是生命科学中最重要的基础专业课程之一。欲使教师讲好它,学生学好并非易事。在学生中经常流传着一句“生理生化,必有一挂”的口头禅,足见学生学习生物化学的难度。本文结合笔者在南京大学讲授生物化学25年多的实践及成功经验,与同行们分享生物化学的教学技巧和策略,如何上好第一次课,如何激发学生学习生物化学的兴趣,如何在教学中培养学生的科学思维,如何把传统课堂教学的手段与其他新型的教学方式结合,如何开展和组织“第二课堂”活动等,希望它们对同行们的生物化学教学有所启发和帮助。     

Computational models of molecular self-organization in cellular environments

The cellular environment creates numerous obstacles to efficient chemistry, as molecular components must navigate through a complex, densely crowded, heterogeneous, and constantly changing landscape in order to function at the appropriate times and places. Such obstacles are especially challenging to self-organizing or self-assembling molecular systems, which often need to build large structures in confined environments and typically have high-order kinetics that should make them exquisitely sensitive to concentration gradients, stochastic noise, and other non-ideal reaction conditions. Yet cells nonetheless manage to maintain a finely tuned network of countless molecular assemblies constantly forming and dissolving with a robustness and efficiency generally beyond what human engineers currently can achieve under even carefully controlled conditions. Significant advances in high-throughput biochemistry and genetics have made it possible to identify many of the components and interactions of this network, but its scale and complexity will likely make it impossible to understand at a global, systems level without predictive computational models. It is thus necessary to develop a clear understanding of how the reality of cellular biochemistry differs from the ideal models classically assumed by simulation approaches and how simulation methods can be adapted to accurately reflect biochemistry in the cell, particularly for the self-organizing systems that are most sensitive to these factors. In this review, we present approaches that have been undertaken from the modeling perspective to address various ways in which self-organization in the cell differs from idealized models.     

生物化学教学实用技巧和策略

生物化学是生命科学中最重要的基础专业课程之一。欲使教师讲好它,学生学好并非易事。在学生中经常流传着一句“生理生化,必有一挂”的口头禅,足见学生学习生物化学的难度。本文结合笔者在南京大学讲授生物化学25年多的实践及成功经验,与同行们分享生物化学的教学技巧和策略,如何上好第一次课,如何激发学生学习生物化学的兴趣,如何在教学中培养学生的科学思维,如何把传统课堂教学的手段与其他新型的教学方式结合,如何开展和组织“第二课堂”活动等,希望它们对同行们的生物化学教学有所启发和帮助。     

中国生物化学课程教学改革的历程(1985~2021)与成绩——基于NVivo 11 Plus软件的系统分析

课程是人才培养的核心要素,是学生从大学里受益最直接、最核心和最显效的途径。生物化学是生命科学中重要的核心课程。梳理我国生物化学课程教学改革的变迁对促进全国生物化学教育事业的发展具有实践意义。本文收集了自1985年以来,生物化学教学改革研究的文献5 871篇。按照国家主要教育方针政策和策略转变文件,将文献按其年份划分为1985~2006,2007~2012,2013~2016和2017~2021四个阶段。运用软件NVivo 11 Plus对文献题录文本和关键词进行相似性分析表明,生物化学课程教学研究与国家教育发展策略相适应,具有鲜明的时代特征。依据扎根理论,通过编码处理和客观分析,将生物化学教学研究划分为“教学策略”、“教学方向”、“教学对象”和“教学评价”四个范畴。详细阐述了“以学生为中心”的生物化学教学改革研究取得的成效:整合包括结构性思维、问题导向、团队合作、翻转课堂和线上线下混合的多种教学方法;结合包括多媒体、虚拟仿真和互联网的先进教学技术;发掘思政元素并将思政教育贯穿到生物化学教学全过程。从强化学生学习能力,关注学习效果和促进学生发展的多元角度促进我国生物化学教学事业的全面发展。     

Enhanced resolution of sedimentation coefficient distribution profiles by extrapolation to infinite time

Sedimentation velocity experiments can be used to identify two or more independent non-interacting macromolecules, which differ in their size by only a few percent. The procedure requires the extrapolation of differential apparent sedimentation coefficient distributions obtained at different running time to t → ∞ and works because it eliminates or greatly reduces diffusion effects. Here, we present an improved time extrapolation function of sedimentation distribution profiles originally presented by Stafford (In: Harding, Rowe, Horton (eds.) Analytical ultracentrifugation in biochemistry and polymer science, 1992). We describe a computing procedure with the program lamm to analyze concentration profiles obtained by absorbance or interference optics that utilizes suitable smoothing methods for noisy data sets and present examples which include time invariant noises.     

The genetic code and its optimization for kinetic energy conservation in polypeptide chains

Why is the genetic code the way it is? Concepts from fields as diverse as molecular evolution, classical chemistry, biochemistry and metabolism have been used to define selection pressures most likely to be involved in the shaping of the genetic code.