A partial flip classroom exercise in a large introductory general biology course increases performance at multiple levels

Incorporation of active learning into large lecture classes is gaining popularity as a pedagogical method due to its known benefits in helping learning outcomes. A more recent active learning technique that has emerged is the flipped classroom. In this study, we investigated the effects of incorporating a ‘partial-flip’ into an introductory general biology course, where only a portion of the class time was spent in a flipped classroom format. This partial flip presented the classic biology experiment of Meselson and Stahl that discovered the mechanism of DNA replication. Performance on in-class formative assessments and subsequent summative assessments (eg out-of-class assignments and exams relating to this material) was compared between a class that had the partial flip and a control class that had a traditional lecture. The partial flip students scored higher on in-class formative questions, specific exam questions and final exam essay questions. We found that the partial flip had different effects in males versus females depending on the assessment. The partial flip manipulation appeared equally effective in aiding both below and above average students in formative assessments. Overall, this study shows that the partial flip classroom can be an effective technique to incorporate into existing courses and that it does provide some benefits compared to traditional lecture.     

Memory for Lectures: How Lecture Format Impacts the Learning Experience

The present study investigated what impact the presentation style of a classroom lecture has on memory, mind wandering, and the subjective factors of interest and motivation. We examined if having a professor lecturing live versus on video alters the learning experience of the students in the classroom. During the lectures, students were asked to report mind wandering and later complete a memory test. The lecture format was manipulated such that all the students received two lectures, one live and one a pre-recorded video. Results indicate that lecture format affected memory performance but not mind wandering, with enhanced memory in the live lectures. Additionally, students reported greater interest and motivation in the live lectures. Given that a single change to the classroom environment, professor presence, impacted memory performance, as well as motivation and interest, the present results have several key implications for technology-based integrations into higher education classrooms.     

Hybrid lecture-online format increases student grades in an undergraduate exercise physiology course at a large urban university

Hybrid courses allow students additional exposure to course content that is not possible in a traditional classroom environment. This exposure may lead to an improvement in academic performance. In this report, I describe the transition of a large undergraduate exercise physiology course from a traditional lecture format to a hybrid lecture-online format. A total of 658 final grades (traditional = 346, hybrid = 312) was used to evaluate the effect of course format on academic performance. The hybrid online portion was delivered using WebCT Vista, enhanced with various instructional technologies. The hybrid lecture portion was enhanced with an in-class response system. PowerPoint files were used to distribute in-class lectures in both formats of the course. Final student grades were 9.9% higher (83% of the increase due to an increase in the exam grade) when the course was administered in a hybrid format (P = 0.01), which translated to a one letter grade increase on a standard grading scale. Transition from a traditional lecture format to a hybrid format significantly enhanced student learning; presumably, this increase is due to the fact that students were able to increase their exposure to course content via access to material on WebCT.     

Molecular modeling of blood-brain barrier nutrient transporters: in silico basis for evaluation of potential drug delivery to the central nervous system

For drugs that act in the brain, the blood-brain barrier (BBB) is a considerable physical barrier which influences the distribution of drugs to the brain. The BBB is essentially impermeable for hydrophilic and/or charged compounds. Nutrient membrane transporters have an important physiological role in the transport of essential substances across the BBB required for normal brain function. We and others have shown that these transporters may have utility as drug delivery vectors, thereby increasing brain distribution of these compounds via these systems. In this review, we evaluate molecular (in silico) models of BBB transport proteins. Few BBB membrane transporters have been crystallized, but their crystal structures have a possibility for use in homology modeling. Other techniques commonly used are 2D quantitative structure-activity relationships (QSAR), as well as 3D-QSAR techniques including comparative molecular field analysis (CoMFA) and comparative similarity index analysis (CoMSIA). Each of these models provides valuable information for ascertaining their potential basis for BBB transport and brain drug delivery.     

Impact of problem-based learning in a large classroom setting: student perception and problem-solving skills

Problem-based learning (PBL) can be described as a learning environment where the problem drives the learning. This technique usually involves learning in small groups, which are supervised by tutors. It is becoming evident that PBL in a small-group setting has a robust positive effect on student learning and skills, including better problem-solving skills and an increase in overall motivation. However, very little research has been done on the educational benefits of PBL in a large classroom setting. Here, we describe a PBL approach (using tutorless groups) that was introduced as a supplement to standard didactic lectures in University of British Columbia Okanagan undergraduate biochemistry classes consisting of 45-85 students. PBL was chosen as an effective method to assist students in learning biochemical and physiological processes. By monitoring student attendance and using informal and formal surveys, we demonstrated that PBL has a significant positive impact on student motivation to attend and participate in the course work. Student responses indicated that PBL is superior to traditional lecture format with regard to the understanding of course content and retention of information. We also demonstrated that student problem-solving skills are significantly improved, but additional controlled studies are needed to determine how much PBL exercises contribute to this improvement. These preliminary data indicated several positive outcomes of using PBL in a large classroom setting, although further studies aimed at assessing student learning are needed to further justify implementation of this technique in courses delivered to large undergraduate classes.     

Homology modeling: an important tool for the drug discovery

In the last decades, homology modeling has become a popular tool to access theoretical three-dimensional (3D) structures of molecular targets. So far several 3D models of proteins have been built by this technique and used in a great diversity of structural biology studies. But are those models consistent enough with experimental structures to make this technique an effective and reliable tool for drug discovery? Here we present, briefly, the fundamentals and current state-of-the-art of the homology modeling techniques used to build 3D structures of molecular targets, which experimental structures are not available in databases, and list some of the more important works, using this technique, available in literature today. In many cases those studies have afforded successful models for the drug design of more selective agonists/antagonists to the molecular targets in focus and guided promising experimental works, proving that, when the appropriate templates are available, useful models can be built using some of the several software available today for this purpose. Limitations of the experimental techniques used to solve 3D structures allied to constant improvements in the homology modeling software will maintain the need for theoretical models, establishing the homology modeling as a fundamental tool for the drug discovery.     

A new addition to the structural bioinformatics toolbox: 3D models of short bioactive peptides from multiple sequences using feedback restrained molecular dynamics (FRMD).

Modem molecular biology techniques allow the use of new approaches for the 3D mapping of 1D information. Molecular biology techniques are capable of producing large amounts of 1D information (sequences) from a number of different sources (phage displays, ESTs, etc.). In this work, we present a technique that takes advantage of large sets of 1D information and increasingly available computer power to create 3D models. For the purpose of validation the technique is first applied to the modeling of an erythropoietin analog of known 3D structure from 1D information only. The technique is then used to model the immunoreactive region of echinococcus granulosus AgB based on phage raised mimotopes for which there is no previous structural information.The technique here presented is of general application to similar problems where 1D information is available and structure activity relationships (SAR) is needed.     

Multiple-format sessions for teaching endocrine physiology

The University of Kentucky medical curriculum was revised in 1994 to implement a more interactive approach. The Endocrine Physiology section of the new physiology course, Human Function, was modified from its former daily lecture and weekly laboratory format to eight daily 3 1/2-h sessions. Each session is composed of four components: a didactic lecture, a whole class discussion session, a quiz, and a patient presentation. These components are presented in a staggered format over the course of 2 days, i.e., the lecture is presented on the first day, and the remaining three components take place on the second day. This allows students to assimilate the new lecture material before participating in the discussion session, quiz, and patient presentation, which are more interactive. This format has been received favorably by the students because of its variety, and it is easier to keep up with the material.     

Structure‐based barcoding of proteins

A reduced representation in the format of a barcode has been developed to provide an overview of the topological nature of a given protein structure from 3D coordinate file. The molecular structure of a protein coordinate file from Protein Data Bank is first expressed in terms of an alpha‐numero code and further converted to a barcode image. The barcode representation can be used to compare and contrast different proteins based on their structure. The utility of this method has been exemplified by comparing structural barcodes of proteins that belong to same fold family, and across different folds. In addition to this, we have attempted to provide an illustration to (i) the structural changes often seen in a given protein molecule upon interaction with ligands and (ii) Modifications in overall topology of a given protein during evolution. The program is fully downloadable from the website http://www.iitg.ac.in/probar/ .     

Photogrammetry: a useful tool for three‐dimensional morphometric analysis of small mammals

Recently, the improvement of methods for shape analysis has revolutionized the field of morphometrics. While three‐dimensional (3D) imaging technology is increasingly available, many studies of 3D structures still use two‐dimensional (2D) data, even when this may result in the loss of important information. This is particularly conspicuous in the study of small mammals, as devices precise enough for 3D digitization of small objects are the most expensive. Thus, the development of low‐cost methods aimed to recover 3D shape from small mammals would be of wide interest. Photogrammetry allows for obtaining 3D data with a lower cost than other 3D techniques, but it has not been previously applied to the study of small mammals. Accordingly, here we test the suitability of photogrammetric techniques to obtain 3D landmarks on mouse skulls as a model for small mammals. Shape and size of 3D models obtained with photogrammetric techniques were consistent among replicates, even when different sets of photographs were used. The linear measurements obtained from 3D models produced here were highly correlated with measurements obtained with callipers on actual crania, and differences among both sets of measures were smaller than those among individuals in most of the tested measures. These results show for the first time that photogrammetry is a precise technique for 3D shape analysis of small mammals. Photogrammetry also proved to be accurate for obtaining linear measurements between 3D landmarks; however, further studies are needed to demonstrate that this technique is also accurate to recreate 3D shapes.     

Teaching more by lecturing less

We carried out an experiment to determine whether student learning gains in a large, traditionally taught, upper-division lecture course in developmental biology could be increased by partially changing to a more interactive classroom format. In two successive semesters, we presented the same course syllabus using different teaching styles: in fall 2003, the traditional lecture format; and in spring 2004, decreased lecturing and addition of student participation and cooperative problem solving during class time, including frequent in-class assessment of understanding. We used performance on pretests and posttests, and on homework problems to estimate and compare student learning gains between the two semesters. Our results indicated significantly higher learning gains and better conceptual understanding in the more interactive course. To assess reproducibility of these effects, we repeated the interactive course in spring 2005 with similar results. Our findings parallel results of similar teaching-style comparisons made in other disciplines. On the basis of this evidence, we propose a general model for teaching large biology courses that incorporates interactive engagement and cooperative work in place of some lecturing, while retaining course content by demanding greater student responsibility for learning outside of class.     

Grasping molecular structures through publication-integrated 3D models

Although the need for communicating 3D data using simple and intuitive means extends to disciplines as diverse as biology, engineering sciences and the visual arts, none of the currently available molecular-visualization programs depicting potentially highly complex structures are compatible with the portable document format (PDF), the current gold standard of electronic publishing. Therefore, it is highly desirable for authors to be able to provide their readers with a basic 3D display of structures that can be accessed without the need for specialized visualization software. Here, we describe how an interactive 3D model of a molecular complex can be embedded directly into a PDF, thus providing readers with important and educational visual information that would otherwise be more difficult to disseminate.     

Heteronuclear three-dimensional NMR spectroscopy applied to CMP-KDO synthetase (27.5 kD)

A heteronuclear three-dimensional NMR experiment has been applied to uniformly 15N-labeled CMP-KDO synthetase (CTP:3-deoxy-D-manno-octulosonate cytidylyl transferase; E.C. 2.7.7.38) complexed with an inhibitor and CTP. Using this 3D technique, the 2D NOE spectrum of the ternary complex was dramatically simplified by editing with respect to the 15N frequencies of the labeled enzyme. This 3D NMR method is a useful tool for resolving spectral overlap and is particularly well-suited for NMR studies of large molecules which are difficult to study by conventional 2D NMR techniques.     

Shedding light on the puzzle of drug-membrane interactions: Experimental techniques and molecular dynamics simulations

Lipid membranes work as barriers, which leads to inevitable drug-membrane interactions in vivo. These interactions affect the pharmacokinetic properties of drugs, such as their diffusion, transport, distribution, and accumulation inside the membrane. Furthermore, these interactions also affect their pharmacodynamic properties with respect to both therapeutic and toxic effects. Experimental membrane models have been used to perform in vitro assessment of the effects of drugs on the biophysical properties of membranes by employing different experimental techniques. In in silico studies, molecular dynamics simulations have been used to provide new insights at an atomistic level, which enables the study of properties that are difficult or even impossible to measure experimentally. Each model and technique has its advantages and disadvantages. Hence, combining different models and techniques is necessary for a more reliable study. In this review, the theoretical backgrounds of these (in vitro and in silico) approaches are presented, followed by a discussion of the pharmacokinetic and pharmacodynamic properties of drugs that are related to their interactions with membranes. All approaches are discussed in parallel to present for a better connection between experimental and simulation studies. Finally, an overview of the molecular dynamics simulation studies used for drug-membrane interactions is provided.     

New techniques for three-dimensional data analysis in histopathology.

This paper describes two three-dimensional (3D) analytical techniques based on 3D mathematical morphology that have been found useful in quantifying the 3D spatial distribution of S-phase cells in a tubular tumor of the human breast. One technique is based on determining the normalized radial distribution of the S-phase cells with respect to the central axis of the tumor. The other technique is a novel extension of the polyhedra of Voronoi to quantify the distribution. The Voronoi polyhedron of a given S-phase cell nucleus is that polyhedron of minimal volume defined by planes all of which are perpendicular bisectors of the vectors extending from the given cell to all other S-phase cells in the tumor. Methods are demonstrated for generating these polyhedra and for histogramming their volumes. An illustration is given of using the histogram to sort the S-phase cells according to their 3D positional relationships. Displays showing the sorted cells in 3D and their associated Voronoi polyhedra are provided.     

种子休眠与破眠机理研究进展

种子休眠机理主要围绕透性、抑制剂作用和光敏素转化等方面的研究而建立。种皮的阻碍作用可能是由于种皮的物理或化学特性引起．可导致对水、光、气体或溶质的透性改变。抑制剂作用机理是抑制物质可抵消促进细胞分裂和生长发育的激素的作用。光敏素转化机理来源于与休眠有关的生物活性化学物质的合成、活化或破坏受光诱导的观点,由于发现了光敏素蓝色蛋白的活化型（Pfr）和钝化型（Pr）而得到强有力的支持,种子光休眠取决于光敏素蓝色蛋白的活化型（Pfr）含量和Pfr／（Pr＋Pfr）比值。目前,打破休眠的方法一般有机械破皮法、激素处理法、分子生物学技术法、物理处理法（如激光、烟、热等处理技术）、CO2处理法等。激素的平衡由抑制剂占优势向促进物占优势的变化是打破休眠的决定因素。研究破眠机理的分子生物学技术有多种,包括ABA突变体的利用、分子标记、转基因技术、用反义RAN阻止基因的表达、cDNA克隆技术等。用激光照射种子,把适宜的光射入细胞,可增加细胞生物能,促进种子发育,从而可能打破休眠。热处理的机理是由于加热可以增加种皮的透气性。CO2之所以能提高某些物种的萌发率,在于其影响了种子内部乙烯的敏感性。     

KING (Kinemage,Next Generation): A versatile interactive molecular and scientific visualization program

Proper visualization of scientific data is important for understanding spatial relationships. Particularly in the field of structural biology, where researchers seek to gain an understanding of the structure and function of biological macromolecules, it is important to have access to visualization programs which are fast, flexible, and customizable. We present KiNG, a Java program for visualizing scientific data, with a focus on macromolecular visualization. KiNG uses the kinemage graphics format, which is tuned for macromolecular structures, but is also ideal for many other kinds of spatially embedded information. KiNG is written in cross‐platform, open‐source Java code, and can be extended by end users through simple or elaborate “plug‐in” modules. Here, we present three such applications of KiNG to problems in structural biology (protein backbone rebuilding), bioinformatics of high‐dimensional data (e.g., protein sidechain chi angles), and classroom education (molecular illustration). KiNG is a mature platform for rapidly creating and capitalizing on scientific visualizations. As a research tool, it is invaluable as a test bed for new methods of visualizing scientific data and information. It is also a powerful presentation tool, whether for structure browsing, teaching, direct 3D display on the web, or as a method for creating pictures and videos for publications. KiNG is freely available for download at http://kinemage.biochem.duke.edu .     

Increasing student involvement in lectures: (very) low tech innovations in a biochemistry lecture class

The inherent passivity of the traditional lecture format makes this a poor mode for learning. In this paper I outline a simple but effective approach for eliciting student participation in the intermediate size lecture course (50–100 students). Two types of question are employed to increase student involvement. Each lecture ends with a set of questions directly related to concepts that will be covered in the next session. At the following lecture, specific students, chosen at random from the class list, are called on to answer these questions. Classroom participation is also elicited by calling on students to answer questions which focus on the major points during each lecture. Finally, students are invited to submit questions for inclusion on each exam. These devices make the lecture a more active and participatory experience.