Hands-on Laboratory Research Articles

Metabolomics for undergraduates: Identification and pathway assignment of mitochondrial metabolites.

Metabolomics is a key discipline in systems biology, together with genomics, transcriptomics, and proteomics. In this omics cascade, the metabolome represents the biochemical products that arise from cellular processes and is often regarded as the final response of a biological system to environmental or genetic changes. The overall screening approach to identify all the metabolites in a given biological system is called metabolic fingerprinting. Using high-resolution and high-mass accuracy mass spectrometry, large metabolome coverage, sensitivity, and specificity can be attained. Although the theoretical concepts of this methodology are usually provided in life-science programs, hands-on laboratory experiments are not usually accessible to undergraduate students. Even if the instruments are available, there are not simple laboratory protocols created specifically for teaching metabolomics. We designed a straightforward hands-on laboratory experiment to introduce students to this methodology, relating it to biochemical knowledge through metabolic pathway mapping of the identified metabolites. This study focuses on mitochondrial metabolomics since mitochondria have a well-known, medium-sized cellular sub-metabolome. These features facilitate both data processing and pathway mapping. In this experiment, students isolate mitochondria from potatoes, extract the metabolites, and analyze them by high-resolution mass spectrometry (using an FT-ICR mass spectrometer). The resulting mass list is submitted to an online program for metabolite identification, and compounds associated with mitochondrial pathways can be highlighted in a metabolic network map.

Improving Anatomical Knowledge Through Nested Interactive Modules on the Obstetrics and Gynecology Clinical Clerkship

BACKGROUND: Deficits in retention of anatomy knowledge from the preclinical years to clinical application on the wards have been well-documented in medical education literature. OBJECTIVE: This study aims to determine if interactive clinically-oriented basic anatomy modules nested longitudinally in the curriculum increase anatomy knowledge in medical students on the obstetrics and gynecology clinical clerkship. METHODS: A 20-question multiple-choice examination was administered to 143 consenting third-year medical students at the beginning and end of each obstetrics and gynecology rotation at a large, urban medical school. Students participated in a 2-hour hands-on skills laboratory with preparatory e-modules linking basic anatomy to clinical application during each rotation. Topics included perineal muscle anatomy (obstetric laceration repair), anterior abdominal wall anatomy (cesarean delivery), vulvovaginal and uterine anatomy (intrauterine device insertion), and pelvic organ, vasculature, and neural anatomy (hysterectomy). Data were analyzed using a univariate analysis of variance with post-hoc t tests. RESULTS: Mean anatomy knowledge scores improved significantly after nesting of interactive modules, increasing from 57% to 69% (P<.001). Knowledge retention was the lowest in the topics of embryology (45%), uterine anatomy (47%), pelvic vasculature (46%), and fallopian tube anatomy (54%). Mean postrotation scores for uterine, vasculature, and fallopian tube anatomy increased significantly to 78% (P<.001), 72% (P<.001) and 71% (P<.001) respectively. CONCLUSIONS: Medical students' baseline anatomical knowledge before entering the obstetrics and gynecology clerkship is poor. Nesting anatomical science into the clinical curriculum through preparatory e-modules and hands-on anatomy laboratory sessions may improve pelvic anatomy knowledge. These data may be used to increase longitudinal integration of the various disciplines across the undergraduate medical curriculum.

Fostering STEM literacy through a tabletop wind turbine environmental science laboratory activity

Increasingly, national education policy is focusing on improving science, technology, engineering, and math (STEM) literacy by using energy as a subject matter. In particular, The Next Generation Science Standards (NGSS 2014) identified energy as an issue that collectively relates the principles of science, technology, engineering, and math for students. Learning about energy, especially alternative energy, is much broader than STEM as it also connects a current issue to environmental impacts, the economy, and society—the three pillars of sustainability. In this paper, we present a hands-on laboratory activity developed for an introductory environmental science course that uses tabletop wind turbines designed to improve students’ STEM and energy literacy and to introduce them to the science and technology of wind energy and basic land use considerations of siting wind farms. In this lab, students conceptualize and calculate the basic physical properties of wind energy potential and production by measuring velocities and calculating optimal energy production through various modifications to turbine placement and blade manipulation. Students construct mini-wind farms with multiple turbines and manipulate the footprint and height to achieve the greatest energy production on the smallest footprint thus incorporating land use considerations. This lab engages students, most of whom are not STEM majors; supports their ability to solve a real, hands-on integrated STEM problem; and increases their understanding and ability to communicate about the scientific and technical aspects of energy, in particular wind energy.

I-tee

We present an Intelligent Training Exercise Environment (i-tee), a fully automated Cyber Defense Competition platform. The main features of i-tee are: automated attacks, automated scoring with immediate feedback using a scoreboard, and background traffic generation. The main advantage of this platform is easy integration into existing curricula and suitability for continuous education as well as on-site training at companies. This platform implements a modular approach called learning spaces for implementing different competitions and hands-on labs. The platform is highly automated to enable execution with up to 30 teams by one person using a single server. The platform is publicly available under MIT license.

INTEGRATED HANDS-ON AND REMOTE PID TUNING LABORATORY

University control engineering coursesusually focus on Proportional Integral Derivative (PID)controllers. Moreover PID controllers are used in morethan 90% of the industrial control applications, becausethey are relatively cheap, easy to use, and robust enoughfor most industrial applications. However, universityteaching attaches most importance to the theoreticalknowledge of PID controllers, rather than the practicalskills required to support the use of these controllers inindustry. In addition, the cost and space challengesassociated with hands on laboratories make simulationbased laboratories a more attractive option for teachingPID controllers. Unfortunately, simulations do notcapture the complexity of control systems that areimportant to develop the practical skills of students. Inthis paper, we present a laboratory setup that is used toteach practical skills in PID tuning. The system controlsthe temperature of a small fictitious house whosetemperature is affected by an uncontrolled heating sourceand blow fan. The PID data is accessible to the systemuser through OLE( Object Linking &amp; Embedding) forProcess Control, also referred as Open ProcessControl(OPC) technology. This technology allows thesystem to be used as a hands-on or remote laboratory,which allows students to learn the complexity of PIDcontrollers, while removing the time and spaceconstraints imposed by purely hands on laboratories.Being accessible remotely, the setup enables andencourages instructors to include demonstrations of PIDtuning into their lectures

"See one, do one, teach one": inadequacies of current methods to train surgeons in hernia repair.

Residency/fellowship training in hernia repair is still too widely characterized by the "see one, do one, teach one" model. The goal of this study was to perform a needs assessment focused on surgical training to guide the creation of a curriculum by SAGES intended to improve the care of hernia patients. Using mixed methods (interviews and online survey), the SAGES hernia task force (HTF) conducted a study asking subjects about their perceived deficits in resident training to care for hernia patients, preferred training topics about hernias, ideal learning modalities, and education development. Participants included 18 of 24 HTF members, 27 chief residents and fellows, and 31 surgical residents. HTF members agreed that residency exposes trainees to a wide spectrum of hernia repairs by a variety of surgeons. They cited outdated materials, techniques, and paucity of feedback. Additionally, they identified the "see one, do one, teach one" method of training as prevalent and clearly inadequate. The topics least addressed were system-based approach to hernia care (46 %) and patient outcomes (62 %). Training topics residents considered well covered during residency were: preoperative and intraoperative decision-making (90 %), complications (94 %), and technical approach for repairs (98 %). Instructional methods used in residency include assisted/supervised surgery (96 %), Web-based learning (24 %), and simulation (30 %). Residents' preferred learning methods included simulation (82 %), Web-based training (61 %), hands-on laboratory (54 %), and videos (47 %), in addition to supervised surgery. Trainees reported their most desired training topics as basic techniques for inguinal and ventral hernia repairs (41 %) versus advanced technical training (68 %), which mirrored those reported by attending surgeons, 36 % and 71 %, respectively. There was a consensus among HTF members and surgical trainees that a comprehensive, dynamic, and flexible educational program employing various media to address contemporary key deficits in the care of hernia patients would be welcomed by surgeons.

Promoting Student Development of Models and Scientific Inquiry Skills in Acid–Base Chemistry: An Important Skill Development in Preparation for AP Chemistry

In this study, two groups of 11th grade chemistry students (n = 210) performed a sequence of hands-on and virtual laboratories that were progressively more inquiry-based. One-half of the students did the laboratory sequence with the addition of a teacher-led discussion connecting student data to student-generated visual representations of different acid–base models (Arrehenius and Bronsted–Lowry). Students were assessed for perceptions about their learning as well as their understanding of acid–base models. The results showed improvement in 79% of the students in understanding acid–base chemistry following the inquiry laboratories as well as improved mental models explaining acid–base chemistry in 72% of the students. The students also responded favorably to the addition of virtual laboratories, with 77% reporting improved understanding of the chemistry as a result of the addition of the technology.

The 114th Annual Scientific Meeting of the American Society of Colon and Rectal Surgeons.

The 114th Annual Scientific Meeting of the American Society of Colon and Rectal Surgeons (ASCRS) took place in Boston, Massachusetts, from May 30 to June 3, 2015. Of the 3029 participants, there were 2080 physicians and healthcare providers including 759 attendees representing 75 countries outside of the USA. In addition to many workshops, symposia, hands-on laboratories and 98 podium/video presentations, there were 413 e-poster presentations (of 954 total abstracts received a record high). The meeting included workshops on how to write examination questions, transanal endoscopic surgery, anal intraepithelial neoplasia and high-resolution anoscopy, laparoscopic colectomy, optimal management of fecal incontinence and robotic colorectal surgery: tips, tricks and simulation. Symposia included laparoscopic and robotic surgery, advanced endoscopy and endoluminal surgery, managing complex surgical patients/complications, the genetics of colorectal cancer and an update on inflammatory bowel disease. There was a special emphasis on rectal cancer, including symposia addressing ‘‘Controversies in rectal cancer management’’ and ‘‘Optimizing outcomes through techniques.’’ Of the named lectureships, the ‘‘Masters in Colorectal Surgery Lectureship’’ (each year, a different senior surgeon who has made a considerable contribution to the specialty and ASCRS is honored) titled ‘‘The value of mentorship’’ was delivered by ASCRS President-Elect Patricia L. Roberts, MD, to honor ASCRS Past-President David J. Schoetz, Jr., MD (both of Lahey Hospital and Medical Center, Burlington, MA). Previous honorees include ASCRS Past-Presidents Eugene P. Salvati, MD (2014), Victor W. Fazio, MD (2013), Herand Abcarian, MD (2012), Philip H. Gordon, MD (2011), and the first recipient Stanley M. Goldberg, MD (2010). Another named lectureship, the Norman D. Nigro, MD Research Lectureship, was delivered by Professor Antonio Lacy, MD, PhD (Barcelona, Spain), on ‘‘The evolution of minimally invasive surgery for colorectal cancer: Past, Present, and Future.’’ A memorial lectureship honoring Fig. 1 Terry C. Hicks, MD (Oschner Clinic, New Orleans, LA), on the right (immediate Past-President ASCRS, 2014–2015) handing over the Presidential Medallion to Charles E. Littlejohn, MD (Stamford, Connecticut), on the left (current ASCRS President, 2015–2016) at the ASCRS Annual Business Meeting on June 3, 2015, in Boston, MA

Learning outcome achievement in non-traditional (virtual and remote) versus traditional (hands-on) laboratories: A review of the empirical research

This review presents the first attempt to synthesize recent (post-2005) empirical studies that focus on directly comparing learning outcome achievement using traditional lab (TL; hands-on) and non-traditional lab (NTL; virtual and remote) participants as experimental groups. Findings suggest that most studies reviewed (n = 50, 89%) demonstrate student learning outcome achievement is equal or higher in NTL versus TL across all learning outcome categories (knowledge and understanding, inquiry skills, practical skills, perception, analytical skills, and social and scientific communication), though the majority of studies (n = 53, 95%) focused on outcomes related to content knowledge, with most studies (n = 40, 71%) employing quizzes and tests as the assessment instrument. Scientific inquiry skills was the least assessed learning objective (n = 4, 7%), and lab reports/written assignments (n = 5, 9%) and practical exams (n = 5, 9%) were the least common assessment instrument. The results of this review raise several important concerns and questions to be addressed by future research.

Biomarker discovery: quantification of microRNAs and other small non-coding RNAs using next generation sequencing.

BackgroundSmall ncRNAs (sncRNAs) offer great hope as biomarkers of disease and response to treatment. This has been highlighted in the context of several medical conditions such as cancer, liver disease, cardiovascular disease, and central nervous system disorders, among many others. Here we assessed several steps involved in the development of an ncRNA biomarker discovery pipeline, ranging from sample preparation to bioinformatic processing of small RNA sequencing data.MethodsA total of 45 biological samples were included in the present study. All libraries were prepared using the Illumina TruSeq Small RNA protocol and sequenced using the HiSeq2500 or MiSeq Illumina sequencers. Small RNA sequencing data was validated using qRT-PCR. At each stage, we evaluated the pros and cons of different techniques that may be suitable for different experimental designs. Evaluation methods included quality of data output in relation to hands-on laboratory time, cost, and efficiency of processing.ResultsOur results show that good quality sequencing libraries can be prepared from small amounts of total RNA and that varying degradation levels in the samples do not have a significant effect on the overall quantification of sncRNAs via NGS. In addition, we describe the strengths and limitations of three commercially available library preparation methods: (1) Novex TBE PAGE gel; (2) Pippin Prep automated gel system; and (3) AMPure XP beads. We describe our bioinformatics pipeline, provide recommendations for sequencing coverage, and describe in detail the expression and distribution of all sncRNAs in four human tissues: whole-blood, brain, heart and liver.ConclusionsUltimately this study provides tools and outcome metrics that will aid researchers and clinicians in choosing an appropriate and effective high-throughput sequencing quantification method for various study designs, and overall generating valuable information that can contribute to our understanding of small ncRNAs as potential biomarkers and mediators of biological functions and disease.Electronic supplementary materialThe online version of this article (doi:10.1186/s12920-015-0109-x) contains supplementary material, which is available to authorized users.

Science teachers’ perception and implementation of inquiry-based reform initiatives in relation to their beliefs and professional identity

The purpose of this study was to understand how early career science teachers perceive and interpret the calls for inquiry-based instruction (as suggested by National Science Education Standards) in relation to their emerging professional identity and beliefs. Further, this study explored how the school and classroom contexts influenced teachers’ implementation of the reform-based teaching practices. Using semi-structured interviews with twelve early career science teachers, this study revealed that teachers often showed limited understanding about inquiry-based instruction, such as hands-on lab activities, and devoted small amount of time for implementing inquiry teaching. However, interestingly, their beliefs about teaching science were aligned with the assumptions of inquiry-based instruction. The lack of inconsistency between beliefs and practices seem to result from the influence of contextual factors. School and classroom environments that limit teachers’ agency and sense of power lead teachers to experience unpleasant emotions, which may eventually threaten their identity as a teacher. This paper ends with implications for school administrators and policy makers.

A fun and effective self-learning approach to teaching microcontrollers and mobile robotics

This paper describes how students can be guided to become their own best teachers, able to test their newly acquired skills with only minimum or no direct assistance from an instructor or lecturer. ‘Closed-loop’ student-centred learning and problem-based learning approaches are described, involving weekly lectures and hands-on lab activities that keep students highly curious, motivated and engaged in self-regulated learning. Students are required to design and test their own original circuits and software code by modifying, extending or expanding the sample circuits and example code described in the lecture notes, in order to complete and demonstrate specific objectives or requirements for each weekly lab session. These ‘closed-loop’ student-centred learning labs ensure that all teams of students achieve a common or minimum acceptable level of practical skills, which adequately prepares them for a ‘design-and-build’ competition. This style of learning also helps develop generic life-long learning skills such as investigating and identifying problems (problem definition and analysis), independent research and experimentation, decision making, communication and teamwork. Even without any prior hands-on experience with electronic circuit design, programming and microcontrollers, each team of students was able to apply and demonstrate new knowledge and skills, devise and test original designs for circuits and software without any supervision, solve and fix complex problems successfully and confidently, and build an operational remote-controlled electric vehicle or mobile robot for a final competition. Some went even further and built sensor-guided fully autonomous mobile robots. Three different competitions described in this paper include a timed racing car competition, a multi-player box grabbing contest over a rocky obstacle course and a ‘robot wars’ competition that was televised on Channel 10 news in Australia.

Introducing NMR to a General Chemistry Audience: A Structural-Based Instrumental Laboratory Relating Lewis Structures, Molecular Models, and 13C NMR Data

This paper describes a first-year general chemistry laboratory that uses NMR spectroscopy and model building to emphasize molecular shape and structure. It is appropriate for either a traditional or an atoms-first curriculum. Students learn the basis of structure and the use of NMR data through a cooperative learning hands-on laboratory experience, and work in groups to assign names and structures to unknown compounds. This laboratory can be successfully run at a number of experimental levels, from students preparing their own NMR samples for analysis to running this as a dry laboratory with spectra provided by the instructor.

Platform for Teaching Mobile Robotics

This paper describes the development of a motivating and innovative multi-robot formation control platform for laboratory experiments with mobile robots. The platform is composed of two components: a simulator and an environment to experiment with low cost wheeled mobile robots. The environment constitutes a ready to use test tool that provides to engineering students the opportunity to simulate and test many different formation and cooperation control strategies with a real system. Currently the platform is used in the Systems and Control Engineering Master program offered by the National University of Distance Education (UNED) and the Complutense University of Madrid (UCM) in Spain. The use of the platform exposes students to hands-on laboratory sessions, contributing to their development as engineers.

Learning About Genetic Engineering in an Outreach Laboratory: Influence of Motivation and Gender on Students’ Cognitive Achievement

During the last 10 years, outreach science laboratories have become increasingly popular due to resource and time limitations in schools. Outreach laboratories offer hands-on projects in a situated and authentic learning setting, thereby promoting the development of students’ scientific literacy. However, students’ cognitive achievement within this context is still a subject of study. The aim of our outreach-lab study was twofold: first, we investigated the influence of students’ motivation to learn science on their cognitive achievement. Second, we examined possible gender differences with respect to achievement, cognitive load, and instructional efficiency. We conducted an educational intervention on plant genetic engineering with Bavarian 10th graders (N = 197) in an outreach laboratory. We applied a pre–post design with a follow-up test monitoring students’ motivation to learn science, their cognitive achievement, and cognitive load. The last two variables were combined in the calculation of instructional efficiency. Our results indicated a substantial knowledge increase both in the short term and in the long term (medium to large effect), while highly motivated students achieved higher scores. Furthermore, we found significant gender differences in cognitive achievement and instructional efficiency, revealing that the females had a higher knowledge increase, resulting in a higher instructional efficiency (small to medium effect). Our findings suggest that active engagement in hands-on laboratory activities is especially beneficial for females. Therefore, we recommend improving the quality and quantity of laboratory experiences in science education to overcome gender differences. We discuss some potential implications for teaching.

Application of the Mirrorball High-Sensitivity Cytometer to Multiplexed Assays for Antibody Drug Discovery

Highly sensitive, high-throughput assay technologies are required for the identification of antibody therapeutics. Multiplexed assay systems are particularly advantageous because they allow evaluation of several parameters within 1 well, increasing throughput and reducing hands-on laboratory time.The mirrorball (TTP Labtech), using high-throughput fluorometric microvolume assay technology, offers simultaneous scanning with up to 3 lasers as well as laser scatter detection. This makes the mirrorball especially suitable for the development of highly sensitive and multiplexed assays.We have developed bead- and cell-based binding assays that demonstrate how the multilaser capability of the mirrorball can be exploited to enhance assay sensitivity. In addition, using the multilaser simultaneous scanning capability, we have established multiplexed cytokine quantitation assays and antibody–cell binding assays.Our results demonstrate the potential utility of this technology to improve the sensitivity and efficiency of biologics screening, resulting in streamlining of the lead antibody selection process.

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.

BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge.

The binding energy distribution analysis method (BEDAM) protocol has been employed as part of the SAMPL4 blind challenge to predict the binding free energies of a set of octa-acid host-guest complexes. The resulting predictions were consistently judged as some of the most accurate predictions in this category of the SAMPL4 challenge in terms of quantitative accuracy and statistical correlation relative to the experimental values, which were not known at the time the predictions were made. The work has been conducted as part of a hands-on graduate class laboratory session. Collectively the students, aided by automated setup and analysis tools, performed the bulk of the calculations and the numerical and structural analysis. The success of the experiment confirms the reliability of the BEDAM methodology and it shows that physics-based atomistic binding free energy estimation models, when properly streamlined and automated, can be successfully employed by non-specialists.

Collaboration and Near-Peer Mentoring as a Platform for Sustainable Science Education Outreach

Decreased funding for middle and high school education has resulted in reduced classroom time, which, when coupled with an increased focus on standardized testing, has decreased the exposure of many middle school students to hands-on science education. To help address these challenges, we developed an integrated outreach program, spanning grades 6–12, designed to engage students by bringing students to the University of Oregon to perform hands-on laboratory experiments. Initially developed to supplement science education lost to state-mandated furlough days, the programmatic design can be applied readily in other contexts including afterschool, weekend, or summer programs. The outreach activities and scaffolding rely heavily on near-peer mentoring, which provides a visible pathway for younger students to envision themselves as future scientists while also providing mentoring and leadership opportunities for high school, undergraduate, and graduate students. The use of near-peer mentoring is also critically important for the program’s sustainability because it enables a more efficient allocation of graduate student and faculty time. In the first 2.5 years, over 450 middle school students have participated in the program and student feedback shows that students are engaged and excited about the outreach activities.

Assessing the Remote Engineering Lab VISIR at Al-Quds University in Palestine

Engineering labs play a vital role in engineering education, make science come alive, and supply students with better understanding of theories. As a result, they contribute to the improvement of their knowledge and skills. Remote labs not enable sharing of teaching resources such as devices, equipment and instrumentation between universities, but also relax time and space constraints; yet they are considered as a complementary asset to the traditional hands-on labs. This paper is concerned with a two-stage assessment of the engineering remote lab VISIR. In the first stage, the assessment investigated if the students accept to use VISIR in their future lab courses at the Faculty of Engineering at Al-Quds University in Palestine. In the second stage, a deeper analysis will be performed to compare VISIR to hands-on and simulators based on the evaluation criteria: performance, students’ retention rate and satisfaction survey.