Integrated cell biology/biochemistry/molecular genetics laboratories: the cytoplasmic genome projects

This paper describes an integrated laboratory project for intermediate to advanced undergraduate students. The project spans an entire academic quarter (10 weeks) and involves a series of operations that give students experience with fundamental techniques in cell biology, molecular biology, biochemistry, genomics, and bioinformatics. In the process, the student learning community is strengthened, students gain increasing confidence in their abilities in the laboratory, and data are collected toward the eventual sequencing of a cytoplasmic genome. The culmination of the project is the preparation by students of a paper written in the format of a particularly accessible online journal. Journal of Industrial Microbiology & Biotechnology (2000) 24, 339–344. Received 02 April 1999/ Accepted in revised form 22 November 1999     

Integrating biotechnology into a non-majors biology curriculum

A general education biology course entitled ‘Biotechnology Transforms Our World’ has been developed to illustrate biological concepts with advances from biotechnology. The contributions of molecular biology to understanding human genetics, evolution, plant and animal (including human) biology and ecology are illustrated with specific case studies. Journal of Industrial Microbiology & Biotechnology (2000) 24, 308–309. Received 02 April 1999/ Accepted in revised form 11 November 1999     

Biotechnology training at California State University, Hayward: a model program

The Biotechnology Certificate Program (BCP) at California State University, Hayward was initiated in 1986 in response to industry demands for qualified employees in the molecular life sciences. This 9-month post-baccalaureate program includes laboratory courses in recombinant DNA techniques, protein chemistry, PCR, DNA sequencing, animal cell culture as well as two lecture courses in molecular biology. Rigorous selection at both entry and exit stages of the program ensures knowledgeable graduates with a greater than 90% employment placement. Corporate participation has been a cornerstone of the BCP and we anticipate continued cooperation in the future as the program evolves to meet the expanding needs of the biotechnology industry. Journal of Industrial Microbiology & Biotechnology (2000) 24, 364–366. Received 19 April 1999/ Accepted in revised form 09 November 1999     

The Philosophical Dullness of Classical Ecology, and a Levinsian Alternative

Ecology has had a lower profile in Biology & Philosophy than one might expect on the basis of the attention ecology is given in public discussions in relation to environmental issues. Our tentative explanation is that ecology appears theoretically redundant within biology and, consequently, philosophically challenging problemsrelated to biology are commonly supposed to be somewhere else, particularly in the molecular sphere. Richard Levins has recognized the genuine challenges posed by ecology for theoretical and philosophical thinking in biology. This essay sets the stage for appreciating his work; it was preceded by four articles published in Biology & Philosophy 15(2),and is followed by a personal reminiscent.     

Integration of laboratory exercises in developmental biology and neurobiology courses using the Xenopus oocyte expression system

This collaborative laboratory exercise integrates two upper division laboratory courses (Developmental Biology and Neurobiology) offered to biology majors at Wake Forest University. The laboratory exercise involves the use of the Xenopus oocyte expression system to study the function of specific membrane receptors and ligand-activated channels. cDNA or mRNA for receptor proteins is injected into Xenopus oocytes. The oocytes are assayed for expression of receptor proteins and two-electrode voltage clamping is done to determine whether the expressed proteins are functional in the oocyte system. This series of laboratory exercises is innovative in its interdisciplinary and collaborative approach to undergraduate teaching, and in its use of sophisticated molecular biological and physiological techniques in the undergraduate teaching laboratory. Students learn first-hand how these techniques have been used to achieve a new level of understanding of both development and neurobiology. Journal of Industrial Microbiology & Biotechnology (2000) 24, 353–358. Received 02 April 1999/ Accepted in revised form 10 November 1999     

A series of laboratory exercises utilizing luxR gene of Vibrio fischeri and gfp gene of Aequoria victoria to teach the broad applications of polymerase chain reaction

Three experiments are described; directional cloning of the luxR gene from the bioluminescent marine bacterium, Vibrio fischeri, directional cloning of the gfpgene from the marine jelly fish, Aequoria victoria, and the construction of a LuxR-GFP fusion protein. Experiments are presented using lux and gfp in an undergraduate biology curriculum. Journal of Industrial Microbiology & Biotechnology (2000) 24, 345–352. Received 02 April 1999/ Accepted in revised form 19 November 1999     

Bioinformatics in the community college

Biotechnology is becoming an information-based field. In this article we describe some resources available to instructors, show how these resources are used in the biotechnology training program, and provide examples of activities used by non-science majors to increase their understanding of biology. We discuss some of the challenges we have encountered using these tools in the classroom. Journal of Industrial Microbiology & Biotechnology (2000) 24, 314–318. Received 08 April 1999/ Accepted in revised form 10 November 1999     

A simple and accurate method for generating co-dominant markers: an application of conformation-sensitive gel electrophoresis to linkage analysis in the silkworm

A simple and sensitive method for linkage analysis is described, which is based on conformation-sensitive gel electrophoresis (CSGE). Using urea-containing agarose gels or a commercially available polyacrylamide-derived matrix, 13 polymorphic markers were newly identified for known genes of the silkworm, Bombyx mori, which had been scored as monomorphic by PCR-RFLP analysis. This method for detecting polymorphisms is quite sensitive, and can be performed with inexpensive reagents and apparatus that is available in most molecular biology laboratories. Received: 19 November 1998 / Accepted: 2 March 1999     

Challenges in understanding meiosis: fostering metaconceptual awareness among university biology students

ABSTRACT

In this study, firstly, university biology students’ conceptual understanding and potential misconceptions concerning meiosis were studied. Secondly, an easily applicable drawing task was used to foster students’ metaconceptual awareness which would help them to reach conceptual change. A quasi-experimental design with a non-equivalent control group was conducted. The students (N = 82) were divided into experimental and control groups. The control groups attended traditional teaching, i.e. lectures with practicals, whilst the experimental groups had an additional activating task before practicals. In the activating task, the students drew the selected phases of meiosis and marked given concepts of meiosis in the drawing. The drawings were scored and the solutions were discussed in detail with the students. After the activating task, the traditional practicals were held for both groups. After a week, both experimental and control groups were given the same task. The results show that students in the experimental group understood meiosis significantly better than the control group, who had more misconceptions after the instruction compared to the experimental group. Thus, fostering students’ metaconceptual awareness is crucial and relatively easy to apply, also in higher education.     

[PSI+] turns 50

abstract

The year 2015 sees the fiftieth anniversary of the publication of a research paper that underpins much of our understanding of fungal prion biology, namely “ψ, a cytoplasmic suppressor of super-suppressor in yeast” by Brian Cox. Here we show how our understanding of the molecular nature of the [PSI⁺] determinant evolved from an ‘occult’ determinant to a transmissible amyloid form of a translation termination factor. We also consider the impact studies on [PSI] have had – and continue to have - on prion research. To demonstrate this, leading investigators in the yeast prion field who have made extensive use of the [PSI⁺] trait in their research, provide their own commentaries on the discovery and significance of [PSI].     

Sweet home actinomycetes: The 1999 MDS Panlabs Lecture

For the past 25 years, I have devoted most of my research efforts to the application of molecular genetics to yield improvement and production of novel secondary metabolites in actinomycetes. My group at Lilly Research Laboratories worked with a variety of Streptomyces species and with strains of Amycolatopsis and Saccharopolyspora. We developed molecular genetic tools to manipulate actinomycete genes, and applied them to important secondary metabolites, including tylosin, daptomycin, vancomycin, chloroeremomycin, and spinosyns. In the early years, I helped establish recombinant DNA technology to manufacture mammalian proteins, and more recently, helped implement microbial genomics as a research tool for antibiotic discovery. In this paper, I review some highlights, primarily from the actinomycete work. Journal of Industrial Microbiology & Biotechnology (2000) 24, 79–88. Received 25 October 1999/ Accepted in revised form 12 November 1999     

一株花椒根腐病拮抗菌的分离鉴定及全基因组序列分析

【背景】花椒根腐病的防治一直是生产中难以解决的问题,优良生防菌的筛选是微生物菌剂研发的重要方向。【目的】解析花椒根腐病拮抗菌T-1的遗传信息,深入挖掘其拮抗基因簇资源,揭示该菌的拮抗机制。【方法】采用平板对峙法、形态观察、生理生化测定结合分子生物学等方法进行拮抗菌的分离鉴定,同时对菌株进行全基因组测序,并对其序列进行分析及比较基因组学分析。【结果】分离获得的菌株经鉴定为贝莱斯芽孢杆菌,编号T-1,该菌对花椒根腐病的抑制率可达72%,可使菌丝前端的生长严重受阻,抑菌谱检测和花椒根片的离体拮抗试验结果表明,拮抗菌T-1具有较广的抑菌活性且离体状态下对花椒根片具有一定的拮抗作用。其全基因组序列数据提交到NCBI的SRA数据库中获得登录号为SRX11086663,基因组总长为3 886 726 bp,GC含量为46.42%,全基因组中有4015个编码基因,占总基因组的89.74%,比较基因组学分析结果显示,菌株T-1与贝莱斯芽孢杆菌模式菌株FZB42相似性高,拮抗基因簇预测结果发现B. velezensis T-1基因组序列中有12个编码次级代谢产物基因合成簇,其中8个与已知功能基因簇高度相似...     

Use of the green fluorescent protein as an educational tool

The green fluorescent protein (GFP) is a bioluminescent protein that can be expressed and easily detected as a fully fluorescent protein in both bacterial and eukaryotic cells. These properties, along with its ability to withstand exposure to denaturants, organic solvents, high temperature and a wide pH range, make GFP an ideal educational tool. To that end, two GFP-based laboratory modules are described that can be used to teach recombinant DNA and protein purification techniques to high school and undergraduate college students. Journal of Industrial Microbiology & Biotechnology (2000) 24, 323–326. Received 02 April 1999/ Accepted in revised form 20 November 1999     

Molecular studies on isopenicillin N synthases

The isopenicillin N synthases isolated thus far are related to oxidases from other microorganisms and plants. These enzymes maintain a non-heme monoferrous-dependent catalytic centre comprising a HisXAsp(53–57)XHis motif and a crucial substrate-binding pocket with an ArgXSer motif for their functionality. The elucidation of these motifs was dependent on information collated from studies on structural chemistry, structural biology, site-directed engineered mutations and biochemical experiments. It is envisaged that these enzymes can potentially be improved through molecular breeding and protein engineering. Received: 15 December 1999 / Received revision: 26 January 2000 / Accepted: 27 January 2000     

A new xylanase from a Trichoderma harzianum strain

A new xylanase (XYL2) was purified from solid-state cultures of Trichoderma harzianum strain C by ultrafiltration and gel filtration. SDS-PAGE of the xylanase showed an apparent homogeneity and molecular weight of 18 kDa. It had the highest activity at pH 5.0 and 45°C and was stable at 50°C and pH 5.0 up to 4 h xylanase. XYL2 had a low K _m with insoluble oat spelt xylan as substrate. Compared to the amino acid composition of xylanases from Trichoderma spp, xylanase XYL2 presented a high content of glutamate/glutamine, phenylalanine and cysteine, and a low content of serine. Xylanase XYL2 improved the delignification and selectivity of unbleached hardwood kraft pulp. Received 02 February 1999/ Accepted in revised form 17 April 1999     

Biology-specific vocabulary: students’ understanding and lecturers’ expectations of student understanding

Abstract

The current A-level biology curriculum includes a broad coverage of all the biosciences which demands knowledge of a wide range of biological vocabulary. Students (n = 184) from two UK universities were presented with a list of vocabulary, associated with a ‘Revise Biology’ text which highlighted key terms that students should know. Lecturers (n = 26) were asked which of these terms they expected students to know, or be aware of. Findings revealed that students’ claimed knowledge of vocabulary exceeded lecturer expectations. In addition, there were a number of terms which students did not understand and lecturers did not expect them to know, which could be removed from A-level biology courses. This is discussed in relation to whether A-level curricula need to be so content heavy and whether lecturers would benefit from knowing more about their students’ knowledge of discipline-specific terms.     

Teaching biology students to think divergently

A group of first-year biology students (N = 16) at a tertiary institution was instructed in techniques designed to increase their divergent thinking skills and thus their ability to generate ideas about issues in biology. A comparison was made between the performance of this group and a control group (N = 15) who had not received any training. The experimental group obtained significantly higher scores than the controls on post-test measures of divergent thinking for both general and biological topics. These differences in the biology measures were maintained in a delayed post-test. Results were interpreted as supporting the need for, and effectiveness of, simple techniques designed to improve thinking skills, specifically in biology.     

The auto-orientation in high magnetic fields of oxidized cytochrome b562 as source of constraints for solution structure determination

¹⁵N-¹H ¹J couplings were measured at 500 MHz and 800 MHz for ¹⁵N enriched oxidized cytochrome b ₅₆₂ from E. coli. The magnetic field dependence of 70 ¹J values, which could be measured without signal overlap, shows that there is a molecular magnetic anisotropy which provides partial molecular orientation in the magnetic field and, consequently, residual dipolar couplings (rdc). The rdc were used as further constraints to improve the existing structure [Arnesano et al. (1999) Biochemistry, 38, 8657–8670] with a protocol which uses the rhombic anisotropy [Banci et al. (1998) J. Am. Chem. Soc., 120, 12903–12909]. The overall large molecular magnetic anisotropy has been found to be determined by both the low spin iron (III) and the four helix bundle structure magnetic susceptibility anisotropy contributions.     

Stories,fun and games: Teaching genetics in primary school

Nuggets are suggestions with practical advice to help in communicating biology to students. They are shorter than the formal papers and have not been peer-reviewed, but may provide ideas for the classroom. Please send contributions to the editor at: jbe@iob.org     

A fast way to generate recombinant adenoviruses: a high-frequency-recombination system

The use of adenovirus for gene transfer has increased dramatically. One of the most time-consuming steps in any project involving adenovirus is to generate a unique recombinant adenovirus. This report provides a way to generate recombinant adenoviruses with significant reduced time and labor and a high rate of success. Journal of Industrial Microbiology & Biotechnology (2000) 24, 198–202. Received 12 August 1999/ Accepted in revised form 04 December 1999