From field to gel blot: teaching a holistic view of developmental phenomena to undergraduate biology students at the University of Tokyo

We present here an outline of the lectures and laboratory exercises for undergraduate developmental biology students at the University of Tokyo. The main aim of our course is to help students fill the gap between natural history, classical embryology and molecular developmental biology. To achieve this aim, we take up various topics in the lectures, from fertilization and early development to developmental engineering. Our laboratory exercises begin with an introduction to the natural history of the organism. The entire class and the instructors collect newts in the field and discuss features of their mating behavior and so on. In the laboratory, students are absorbed by exercises such as a lampbrush chromosome preparation and an in vitro beating heart induction. After that, students choose their own research projects for which they will employ both classical embryological and modern molecular biological techniques. At the end of our course, the connectivity principle from field to gel blot will be part of the students' understanding.     

An intensive hands-on course designed to teach molecular biology techniques to physiology graduate students

To address a growing need to make research trainees in physiology comfortable with the tools of molecular biology, we have developed a laboratory-intensive course designed for graduate students. This course is offered to a small group of students over a three-week period and is organized such that comprehensive background lectures are coupled with extensive hands-on experience. The course is divided into seven modules, each organized by a faculty member who has particular expertise in the area covered by that module. The modules focus on basic methods such as cDNA subcloning, sequencing, gene transfer, polymerase chain reaction, and protein and RNA expression analysis. Each module begins with a lecture that introduces the technique in detail by providing a historical perspective, describing both the uses and limitations of that technique, and comparing the method with others that yield similar information. Most of the lectures are followed by a laboratory session during which students follow protocols that were carefully designed to avoid pitfalls. Throughout these laboratory sessions, students are given an appreciation of the importance of proper technique and accuracy. Communication among the students, faculty, and the assistant coordinator is focused on when and why each procedure would be used, the importance of each step in the procedure, and approaches to troubleshooting. The course ends with an exam that is designed to test the students' general understanding of each module and their ability to apply the various techniques to physiological questions.     

Enhancing theoretical understanding of a practical biology course using active and self-directed learning strategies

Laboratories are recognised as central in science education, allowing students to consolidate knowledge and master practical skills, however, their effectiveness has been questioned. Whilst laboratory practicals are useful for students’ learning of basic procedures, they have been shown to be less effective for developing conceptual understanding of the subject. Interactive lectures and bespoke digital resources were utilised in order to enhance theoretical understanding of laboratory practical molecular sessions, thus enabling students to take responsibility for and direct their own learning, encouraging inquiry-based learning. Providing easy to access additional learning resources offered students an opportunity to better prepare themselves for the laboratory, and consolidate their knowledge through subsequent review and self-testing in their own time. Grades before and after implementation of these active learning strategies were analysed to look at the impact on student learning and this study demonstrates that integrating these into a challenging practical biology course improved grades significantly with a concomitant increase in the number of ‘A’ grades attained. Feedback to evaluate use and perceptions of both interactive lectures and digital resources were also analysed. It has been shown here that these activities enhanced student experience and understanding of the course.     

An intense half-semester developmental biology course,as taught at Uppsala University,Sweden

This intensive course, designed for advanced undergraduates and beginning graduate students, was first taught in 1995 at Uppsala University, Sweden, and consists of a half-semester (8-9 weeks) of daily lecture and laboratory sessions covering a broad range of topics and giving an overview of developmental biology and some of its applications. The labs introduce students to a diverse assortment of model systems. The course goals are to present a comparative view of animal development (gametogenesis, fertilization, gastrulation, neurulation, organogenesis), followed by lectures on cellular and molecular mechanisms that regulate development, such as induction mechanisms, cell adhesion and migration, cell-matrix interactions and genomic imprinting. The development of complex systems, such as the nervous system, limbs and flowers, is emphasized, including aspects such as malformations, homeosis and mutant analysis, reproduction and fertility problems, and the connection between development and cancer. Model organisms are emphasized, but evolutionary aspects receive due attention. Typically, during the first 5 weeks, a day begins with lectures in the morning and ends with labs or demonstrations and seminars in the afternoon. Wednesday afternoons are "free" to give time for reading. A theory test is taken at the end of this period. Then, students do supervised research for 3 weeks to give them a feel for what it is like to do "real science." Finally, students present oral and written reports on their projects. This is the only course students enroll in during this portion of the semester, so they are expected to devote full effort to it.     

Clustering biomolecular complexes by residue contacts similarity

Inaccuracies in computational molecular modeling methods are often counterweighed by brute-force generation of a plethora of putative solutions. These are then typically sieved via structural clustering based on similarity measures such as the root mean square deviation (RMSD) of atomic positions. Albeit widely used, these measures suffer from several theoretical and technical limitations (e.g., choice of regions for fitting) that impair their application in multicomponent systems (N > 2), large-scale studies (e.g., interactomes), and other time-critical scenarios. We present here a simple similarity measure for structural clustering based on atomic contacts--the fraction of common contacts--and compare it with the most used similarity measure of the protein docking community--interface backbone RMSD. We show that this method produces very compact clusters in remarkably short time when applied to a collection of binary and multicomponent protein-protein and protein-DNA complexes. Furthermore, it allows easy clustering of similar conformations of multicomponent symmetrical assemblies in which chain permutations can occur. Simple contact-based metrics should be applicable to other structural biology clustering problems, in particular for time-critical or large-scale endeavors.     

Lessons Learned from Implementing a Wet Laboratory Molecular Training Workshop for Beach Water Quality Monitoring

Rapid molecular testing methods are poised to replace many of the conventional, culture-based tests currently used in fields such as water quality and food science. Rapid qPCR methods have the benefit of being faster than conventional methods and provide a means to more accurately protect public health. However, many scientists and technicians in water and food quality microbiology laboratories have limited experience using these molecular tests. To ensure that practitioners can use and implement qPCR techniques successfully, we developed a week long workshop to provide hands-on training and exposure to rapid molecular methods for water quality management. This workshop trained academic professors, government employees, private industry representatives, and graduate students in rapid qPCR methods for monitoring recreational water quality. Attendees were immersed in these new methods with hands-on laboratory sessions, lectures, and one-on-one training. Upon completion, the attendees gained sufficient knowledge and practice to teach and share these new molecular techniques with colleagues at their respective laboratories. Key findings from this workshop demonstrated: 1) participants with no prior experience could be effectively trained to conduct highly repeatable qPCR analysis in one week; 2) participants with different desirable outcomes required exposure to a range of different platforms and sample processing approaches; and 3) the collaborative interaction amongst newly trained practitioners, workshop leaders, and members of the water quality community helped foster a cohesive cohort of individuals which can advocate powerful cohort for proper implementation of molecular methods.     

Understanding protein flexibility through dimensionality reduction.

This work shows how to decrease the complexity of modeling flexibility in proteins by reducing the number of dimensions necessary to model important macromolecular motions such as the induced-fit process. Induced fit occurs during the binding of a protein to other proteins, nucleic acids, or small molecules (ligands) and is a critical part of protein function. It is now widely accepted that conformational changes of proteins can affect their ability to bind other molecules and that any progress in modeling protein motion and flexibility will contribute to the understanding of key biological functions. However, modeling protein flexibility has proven a very difficult task. Experimental laboratory methods, such as x-ray crystallography, produce rather limited information, while computational methods such as molecular dynamics are too slow for routine use with large systems. In this work, we show how to use the principal component analysis method, a dimensionality reduction technique, to transform the original high-dimensional representation of protein motion into a lower dimensional representation that captures the dominant modes of motions of proteins. For a medium-sized protein, this corresponds to reducing a problem with a few thousand degrees of freedom to one with less than fifty. Although there is inevitably some loss in accuracy, we show that we can obtain conformations that have been observed in laboratory experiments, starting from different initial conformations and working in a drastically reduced search space.     

Molecular modeling and biocatalysis: explanations, predictions, limitations, and opportunities

Rapid advances in structural biology have revealed the three-dimensional structures of many biocatalysts. Molecular modeling is the tool that links these structures with experimental observations. As a qualitative tool, current modeling methods are extremely useful. They can explain, on a molecular level, unusual features of reactions. They can predict how to increase the selectivity either by substrate modification or by site-directed mutagenesis. Quantitative predictions, for example the degree of enantioselectivity, are still not reliable, however. Modeling is limited also by the availability of three-dimensional structures. Most current modeling involves hydrolases, especially proteases and lipases, but structures for other types of enzymes are starting to appear.     

The FEATURE framework for protein function annotation: modeling new functions,improving performance,and extending to novel applications

Structural genomics efforts contribute new protein structures that often lack significant sequence and fold similarity to known proteins. Traditional sequence and structure-based methods may not be sufficient to annotate the molecular functions of these structures. Techniques that combine structural and functional modeling can be valuable for functional annotation. FEATURE is a flexible framework for modeling and recognition of functional sites in macromolecular structures. Here, we present an overview of the main components of the FEATURE framework, and describe the recent developments in its use. These include automating training sets selection to increase functional coverage, coupling FEATURE to structural diversity generating methods such as molecular dynamics simulations and loop modeling methods to improve performance, and using FEATURE in large-scale modeling and structure determination efforts.     

Structural characterization of peptide hormone/receptor interactions by NMR spectroscopy.

The structural characterization of peptide hormones and their interaction with G-protein (guanine nucleotide-binding regulatory protein) coupled receptors by high-resolution nmr is described. The general approaches utilized can be categorized into three different classes based on their target: the ligand, the receptor, and the ligand/receptor complex. Examples of these different approaches, aimed at facilitating the rational design of peptides and peptidomimetics with improved pharmacological profiles, based on work carried out in our own laboratory, are given. In the ligand-based approach, the high-resolution structures of bradykinin analogues allowing for the development of a structure-activity relationship for activation of the B1 receptor are described. Studies targeting the receptor are to a large extent theoretical, based on computational molecular modeling. However, experimentally based structural features provided by high-resolution nmr can be used to great advantage, providing insight into the mechanism of receptor function, as illustrated here with results from parathyroid hormone. A similar combination of theoretical methods, supplemented by high-resolution structures from nmr has been utilized to probe the formation and stabilization of the ligand/receptor complex both for parathyroid hormone and cholecystokinin. In each of these three approaches, the importance of well-designed peptide mimetics and accurate structural analysis by high-resolution nmr, will be highlighted.     

A Web-based course of lectures in respiratory physiology

A complete course of respiratory physiology suitable for first-year medical and graduate students has been placed on the Web for our own students and for other educational institutions. There are several reasons for doing this. The first is that the modern-day student uses a variety of options for acquiring knowledge. These include attending lectures, reading texts, iPod downloads, and surfing the internet. This Web-based course is another option that may be preferable for some students. A second reason is that it is becoming increasingly difficult for some medical schools to find faculty members who are willing and able to teach the principles of respiratory physiology. This is a potentially serious problem because a sound knowledge of respiratory physiology will always be necessary for the intelligent practice of medicine. Schools with limited faculty may find it useful to use these Web-based lectures followed by a discussion session with students. Another reason is that some schools have moved away from systematic lectures to case-based discussions, with the possibility that students will not be exposed to some of the principles of respiratory physiology. The hope is that this comprehensive course of lectures will help students to assimilate this important material as the medical school curriculum continues to expand at a rapid rate.     

Transient state kinetics tutorial using the kinetics simulation program, KINSIM.

This article provides an introduction to a computer tutorial on transient state kinetics. The tutorial uses our Macintosh version of the computer program, KINSIM, that calculates the time course of reactions. KINSIM is also available for other popular computers. This program allows even those investigators not mathematically inclined to evaluate the rate constants for the transitions between the intermediates in any reaction mechanism. These rate constants are one of the insights that are essential for understanding how biochemical processes work at the molecular level. The approach is applicable not only to enzyme reactions but also to any other type of process of interest to biophysicists, cell biologists, and molecular biologists in which concentrations change with time. In principle, the same methods could be used to characterize time-dependent, large-scale processes in ecology and evolution. Completion of the tutorial takes students 6-10 h. This investment is rewarded by a deep understanding of the principles of chemical kinetics and familiarity with the tools of kinetics simulation as an approach to solve everyday problems in the laboratory.     

Structural sensitivity of biological models revisited

Enhancing the predictive power of models in biology is a challenging issue. Among the major difficulties impeding model development and implementation are the sensitivity of outcomes to variations in model parameters, the problem of choosing of particular expressions for the parametrization of functional relations, and difficulties in validating models using laboratory data and/or field observations. In this paper, we revisit the phenomenon which is referred to as structural sensitivity of a model. Structural sensitivity arises as a result of the interplay between sensitivity of model outcomes to variations in parameters and sensitivity to the choice of model functions, and this can be somewhat of a bottleneck in improving the models predictive power. We provide a rigorous definition of structural sensitivity and we show how we can quantify the degree of sensitivity of a model based on the Hausdorff distance concept. We propose a simple semi-analytical test of structural sensitivity in an ODE modeling framework. Furthermore, we emphasize the importance of directly linking the variability of field/experimental data and model predictions, and we demonstrate a way of assessing the robustness of modeling predictions with respect to data sampling variability. As an insightful illustrative example, we test our sensitivity analysis methods on a chemostat predator-prey model, where we use laboratory data on the feeding of protozoa to parameterize the predator functional response.     

Identification of related proteins with weak sequence identity using secondary structure information

Molecular modeling of proteins is confronted with the problem of finding homologous proteins, especially when few identities remain after the process of molecular evolution. Using even the most recent methods based on sequence identity detection, structural relationships are still difficult to establish with high reliability. As protein structures are more conserved than sequences, we investigated the possibility of using protein secondary structure comparison (observed or predicted structures) to discriminate between related and unrelated proteins sequences in the range of 10%-30% sequence identity. Pairwise comparison of secondary structures have been measured using the structural overlap (Sov) parameter. In this article, we show that if the secondary structures likeness is >50%, most of the pairs are structurally related. Taking into account the secondary structures of proteins that have been detected by BLAST, FASTA, or SSEARCH in the noisy region (with high E: value), we show that distantly related protein sequences (even with <20% identity) can be still identified. This strategy can be used to identify three-dimensional templates in homology modeling by finding unexpected related proteins and to select proteins for experimental investigation in a structural genomic approach, as well as for genome annotation.     

Undergraduate structural biology education: A shift from users to developers of computation and simulation tools

The use of theory and simulation in undergraduate education in biochemistry, molecular biology, and structural biology is now common, but the skills students need and the curriculum instructors have to train their students are evolving. The global pandemic and the immediate switch to remote instruction forced instructors to reconsider how they can use computation to teach concepts previously approached with other instructional methods. In this review, we survey some of the curricula, materials, and resources for instructors who want to include theory, simulation, and computation in the undergraduate curriculum. There has been a notable progression from teaching students to use discipline-specific computational tools to developing interactive computational tools that promote active learning to having students write code themselves, such that they view computation as another tool for solving problems. We are moving toward a future where computational skills, including programming, data analysis, visualization, and simulation, will no longer be considered an optional bonus for students but a required skill for the 21st century STEM (Science, Technology, Engineering, and Mathematics) workforce; therefore, all physical and life science students should learn to program in the undergraduate curriculum.     

人类血型性状综合遗传大实验的设计与教学实践

综合大实验能够训练学生灵活应用理论知识并掌握实验技能,成为当前实验课教学改革的重要方式。本文以人类的ABO血型性状为实验对象,设计了“人类ABO血型分子基因分型与群体遗传平衡分析”大实验。实验中提取同学唾液中黏膜细胞的DNA,经过PCR扩增目的片段、酶切及电泳分离一系列分子遗传技术分析,鉴定出每位同学的基因型;然后以全班同学为一个类似孟德尔群体调查ABO血型的各种基因型频数,用Popgene软件分析各种群体遗传参数。通过开放教学不仅让学生掌握了分子遗传实验技术和群体遗传分析技术及软件应用,还让学生自主设计方案优化分子技术环节,提高学生驾驭知识的能力。通过5年的教学探索与实践,建立了稳定的分子遗传实验体系,能够清楚地检测出ABO血型的6种基因型：I^AI^A、I^Ai、I^BI^B、I^Bi、I^AI^B、ii;综合了分子遗传与群体遗传的实验教学,统计全班同学6种基因型的频数,直接计算3个复等位基因的频率,进而应用软件分析群体遗传各种参数;实现了学生自主设计并完成实验的开放式实验教学;大实验教学获得了学生的好评,取得了很好的教学效果。该大实验可直接应用于生物类专业的遗传学实验教学,其中的教学理念和方法还可推广应用于其他生物学实验教学。     

A critical assessment of comparative molecular modeling of tertiary structures of proteins*

In spite of the tremendous increase in the rate at which protein structures are being determined, there is still an enormous gap between the numbers of known DNA-derived sequences and the numbers of three-dimensional structures. In order to shed light on the biological functions of the molecules, researchers often resort to comparative molecular modeling. Earlier work has shown that when the sequence alignment is in error, then the comparative model is guaranteed to be wrong. In addition, loops, the sites of insertions and deletions in families of homologous proteins, are exceedingly difficult to model. Thus, many of the current problems in comparative molecular modeling are minor versions of the global protein folding problem. In order to assess objectively the current state of comparative molecular modeling, 13 groups submitted blind predictions of seven different proteins of undisclosed tertiary structure. This assessment shows that where sequence identity between the target and the template structure is high (> 70%), comparative molecular modeling is highly successful. On the other hand, automated modeling techniques and sophisticated energy minimization methods fail to improve upon the starting structures when the sequence identity is low (～30%). Based on these results it appears that insertions and deletions are still major problems. Successfully deducing the correct sequence alignment when the local similarity is low is still difficult. We suggest some minimal testing of submitted coordinates that should be required of authors before papers on comparative molecular modeling are accepted for publication in journals. © 1995 Wiley-Liss, Inc.     

The Laboratory of Photosynthesis and its successors at Gif-sur-Yvette,France*

This article is not a survey of all the research made during the last half century at the ‘Laboratoire de Photosynthèse’ of the ‘Centre National de la Recherche Scientifique’ (CNRS) in Gif-sur-Yvette, but rather some personal recollections, as faithful as possible. Not all people could be mentioned and the scientists named here are mainly those who, at different stages of the laboratory's evolution, created their research teams, within or outside the laboratory. The laboratory, closed now as an administrative entity, was founded in 1953 by the CNRS in Gif-sur-Yvette, near Paris. Besides the emerging research groups in Paris and at Saclay, it was then the only one in France to be entirely dedicated to photosynthesis. Initially, the focus was on metabolic biochemistry of photosynthesis in whole plants and unicellular algae. In 1959, biophysics of primary and associated processes was added and in 1966, the laboratory was enlarged to include molecular genetics and, somewhat later, structural biology. Most of the early members of the laboratory have now gone offstage, but the research goes on, in Gif and elsewhere, thanks to the numerous high-level scientists that have been trained there. Most of the basic questions have now been answered, and interest has shifted in two directions, atomic and integrated, while many other facets of research are no longer specific to photosynthesis but part of more general biological problems, a normal situation for an area that has reached its maturity. This paper is dedicated to the scientists, technicians, students and visitors who could not all be cited here, but who contributed so much to the life of the laboratory. This revised version was published online in June 2006 with corrections to the Cover Date.     

Can a tablet device alter undergraduate science students' study behavior and use of technology?

This article reports findings from a study investigating undergraduate biological sciences students' use of technology and computer devices for learning and the effect of providing students with a tablet device. A controlled study was conducted to collect quantitative and qualitative data on the impact of a tablet device on students' use of devices and technology for learning. Overall, we found that students made extensive use of the tablet device for learning, using it in preference to laptop computers to retrieve information, record lectures, and access learning resources. In line with other studies, we found that undergraduate students only use familiar Web 2.0 technologies and that the tablet device did not alter this behavior for the majority of tools. We conclude that undergraduate science students can make extensive use of a tablet device to enhance their learning opportunities without institutions changing their teaching methods or computer systems, but that institutional intervention may be needed to drive changes in student behavior toward the use of novel Web 2.0 technologies.