A Web Application for Generation of Random DNA Sequences with a Single Open Reading Frame: Exemplars for Genetics and Bioinformatics Education

A standard genetic/bioinformatic activity in the genomics era is the identification within DNA sequences of an "open reading frame" (ORF) that encodes a polypeptide sequence. As an educational introduction to such a search, we provide a webapp that composes, displays for solution, and then solves short DNA exemplars with a single ORFTo the Editor: We wish to bring a new Web resource to the attention of CBE—Life Sciences Education readers.When being introduced to the central dogma of nucleic acid transactions, students are often required to identify the 5′→3′ DNA template strand in a double-stranded DNA (dsDNA) molecule; transcribe an antiparallel, complementary 5′→3′ mRNA; and then translate the mRNA codons 5′→3′ into an amino acid polypeptide by means of the genetic code table. Although this algorithm replicates the molecular genetic process of protein synthesis, experience shows that the series of left/right, antiparallel, and/or 5′→3′ reversals is confusing to many students when worked by hand. Students may also obtain the “right” answer for the “wrong” reasons, as when the “wrong” DNA strand is transcribed in the “wrong” 3′→5′ direction, so as to produce a string of letters that “translates correctly.”In genetics and bioinformatics education, we have found it more intuitively appealing to demonstrate and emphasize the equivalence of the mRNA to the DNA sense strand complement of the template strand. The sense strand is oriented in the same 5′→3′ direction and has a sequence identical to the mRNA, except for substitution of thymidine in the DNA for uracil in the mRNA. It is thus more computationally efficient to “read” the polypeptide sequence directly from this strand, with mental substitution of thymidine in the triplets of the genetic code table. (By definition, “codons” occur only in mRNA: the equivalent three-letter words in the DNA sense strand may be designated “triplets.”) This is the same logic used in DNA “translation” software programs.A further constraint often imposed on dsDNA teaching exemplars is that five of the six possible reading frames are “closed” by the occurrence of one or more “stop” triplets, and only one is an open reading frame (ORF) that encodes an uninterrupted polypeptide. We designate this the “5&1” condition. The task for the student is to identify the ORF and “translate” it correctly. Other considerations include correct labeling of the sense and template DNA strands, their 5′ and 3′ ends (and of the mRNA as required), and the amino (N) and carboxyl (C) termini of the polypeptide.Thus, instructors face the logistical challenge of creating dsDNA sequences that satisfy the “5&1” condition for homework and exam questions. Instructors must compose sequences with one or more “stops” in the three overlapping read frames of one strand, while simultaneously creating two “stopped” frames and one ORF in the other. We have explored these constraints as an algorithmic and computational challenge (Carr et al., 2014 ). There are no “5&1” exemplars of length L ≤ 10, and the proportion of exemplars of length L ≥ 11 is very small relative to the 4^L possible sequences (e.g., 0.0023% for L = 11, 0.048% for L = 15, 0.89% for L = 25). This makes random exploration for such exemplars inefficient.We therefore developed a two-stage recursive search algorithm that samples 4^L space randomly to generate “5&1” exemplars of any specified length L from 11 ≤ L ≤ 100. The algorithm has been implemented as a Web application (“RandomORF,” available at www.ucs.mun.ca/~donald/orf/randomorf). Figure 1 shows a screen capture of the successive stages of the presentation. The application requires JavaScript on the computer used to run the Web browser.Open in a separate windowFigure 1.Successive screen captures of the webapp RandomORF. First panel: the Length parameter is the desired number of base pairs. Second panel: Clicking the “Generate dsDNA” button shows the dsDNA sequence to be solved, with labeled 5′ and 3′ ends. The button changes to “Show ORF.” Third panel: A second click shows the six reading frames, with the ORF highlighted. Here, the ORF is in the sixth reading frame on the bottom (sense) strand. The polypeptide sequence, read right to left, is N–EITHLRL–C, where N and C are the amino and carboxyl termini, respectively. The conventional IUPAC single-letter abbreviations for amino acids are centered over the middle base of the triplet; stop triplets are indicated by asterisks (*).The webapp provides a means for students to practice identifying ORFs by efficiently generating many examples with unique solutions (Supplemental Material); this can take the place of the more standard offering of a small number of set examples with an answer key. The two-stage display makes it possible for problems to be worked “cold,” with the correct ORF identified only afterward. For examinations, any exemplar may be presented in any of four ways, by transposing the top and bottom strands and/or reversing the direction of the strands left to right. Presentation of the 5′ end of the sense strand at the lower left or upper or lower right tests student recognition that sense strands are always read in the 5′→3′ direction, irrespective of the “natural” left-to-right and/or top-then-bottom order. We intend to modify the webapp to include other features of pedagogical value, including constraints on [G+C] composition and the type, number, and distribution of stop triplets. We welcome suggestions from readers.     

Attachment dimensions as predictors of mental health and psychosocial well-being in the transition to university

This study sought to investigate the predictive relationship that dimensions of attachment shared with an array of indicators of psychosocial well-being and mental health in a sample of students making the transition to higher education. One hundred and thirty-one students completed the Vulnerable Attachment Styles Questionnaire (VASQ) prior to enrolment in their first semester of university education. Subsequently, the students completed measures related to perceived loneliness, institutional integration, psychological need satisfaction, depressive symptoms and ways of coping during their first semester. Results suggested that higher scores in relation to the insecurity dimension of the VASQ were instrumental in predicting negative psychosocial well-being and mental health. The results discussed the key vulnerability dimensions of attachment when seeking to predict indices of psychosocial well-being and mental health.     

Learning and teaching virtuous gratitude

Gratitude has been widely regarded by philosophers, psychologists and educational theorists as a personal and/or pro-social response of some moral significance. Indeed, beyond its more obvious value as a basic form of social association and reciprocation, gratitude has also been conceived as a moral virtue—if not, more grandly, as a ‘parent of the virtues’. Insofar, one might also expect the promotion of gratitude to be a matter of some educational importance. Despite this, and notwithstanding recent psychological attempts to develop practical interventions designed to promote gratitude, this paper argues not just that the educational role of such interventions is open to serious question, but also that—beyond any requirement of the young to express thanks as a matter of routine social reciprocation—the status of gratitude as an educable virtue is more complex and problematic than has often been previously supposed.     

CHARACTER IN TEACHING

ABSTRACT:  Qualities of personal character would appear to play a significant role in the professional conduct of teachers. It is often said that we remember teachers as much for the kinds of people they were than for anything they may have taught us, and some kinds of professional expertise may best be understood as qualities of character. After (roughly) distinguishing qualities of character from those of personality, the present paper draws on the resources of virtue ethics to try to make sense of the former. In the course of this, it is argued that while the key virtue ethical concept of phronesis or practical wisdom has been widely deployed to account for aspects of professional teacher expertise, it has also been subject to rather un-Aristotelian interpretation as a kind of situation-specific productive reasoning. The present paper seeks to show that it is better employed for understanding character in general and character in teaching in particular. The paper concludes with some observations about the professional education or cultivation of character.     

High-speed observations of football-boot-surface interactions of players in their natural environment

A protocol has been developed to obtain two-dimensional kinematic shoe data of football players in their training environment through high-speed video analysis. Such kinematic data can provide an understanding of how to better replicate the boundary conditions of football movements when simulated using mechanical traction and penetration test devices. As part of a pilot study, 11 youth academy players from a Premiership football club performed football-specific movements which were filmed at 1000 frames s^-1. The protocol required minimal set-up time and the area of the pitch to be filmed could be positioned in any part of the playing area, causing low disruption to the players. This aimed to ensure that the movements performed were representative of those carried out during competitive play. Results in this study are concerned with the kinematics of the shoe during contact with the ground for movements identified to be important in terms of injury risk and loss of performance (slipping). Shoe velocities and orientations were measured for subjects wearing shoes of different stud types (traditional round studs versus contemporary bladed studs) on two surfaces (artificial turf, in-filled with rubber and sand, versus a natural surface). All the parameters measured from the relatively small population of subjects had high variances and therefore few significant effects of studs and surface could be found. The data does however provide insight into the appropriate boundary conditions to be used in mechanical test devices. For example, in the forefoot push-off movement it can be seen that test devices should measure the traction forces when the shoe first starts to move, as this is when the player would lose performance, as opposed to the maximum traction which can occur after significant displacement of the shoe through the surface. Analysis of the orientation and velocity path of the studs just before contact with the ground shows that the studs could be aligned to enhance their penetration into the surface and optimise the traction properties of the studs. In order to determine the orientation and velocity of the shoes at crucial phases in movements force-plate data obtained in the laboratory should be utilised in future studies.     

Professing Education in a Postmodern Age

Although this paper is a written version of an inaugural lecture given at the University of Sheffield in December 1995, its central thesis is that, in a postmodern age, the practice of professors of education giving inaugural lectures is incoherent. To advance this thesis in an inaugural lecture entails an obvious contradiction which, it is proposed, can only be resolved by examining the historical origins of the inaugural lecture in the early medieval university. What emerges from this examination is not only that there is a pre-modern version of the inaugural lecture but that the virtue-based understanding of education which it presupposed can be revised and advanced in the postmodern world.     

Predicting the playing character of cricket pitches

A cricket pitch is a prepared strip of compacted soil and closely mown turf onto which the bowler projects the ball. The surface is of fundamental importance to the game and groundstaff seek to ensure that the ball rebound is of sufficient pace, bounce and consistency to promote skill in both the batsman and bowler. The scientific understanding of the factors that influence the playing quality of a pitch is incomplete and groundstaff often rely on experience and ‘rules of thumb’. A major programme of research was undertaken to determine the effectiveness of a range of pitch measurement apparatus that are perceived to provide indications of playing character. Over three seasons, 18 fieldwork visits were completed at 11 different first-class county grounds. Pitches were tested at the end of each match and direct assessments of pace, bounce and consistency were achieved by employing an artificial bowler and high speed video arrangement. Measurements of surface friction, hardness and restitution were also recorded. It was found that no single pitch measurement was able to provide a reliable indication of pace or bounce, but, when the measurements were combined in a simple Newtonian model, good predictions of pace were achieved. The study revealed a simple method by which groundstaff can predict pace during crucial stages in pitch preparation. However, the study also showed that bounce is affected by levels of pitch deformation and that development of impact models and bespoke measurement tools is needed to reliably predict variation in bounce.