scholarly journals A Microcosm of the Biomedical Research Experience for Upper-level Undergraduates

2008 ◽  
Vol 7 (2) ◽  
pp. 210-219 ◽  
Author(s):  
Daryl D. Hurd
Keyword(s):  
Cell Biology ◽  
Focal Point ◽  
Model Organism ◽  
Persuasive Communication ◽  
Biological Research ◽  
Research Experience ◽  
Nematode Caenorhabditis Elegans ◽  
Use Of Time ◽  
Upper Level ◽  
Biology Laboratory

The skill set required of biomedical researchers continues to grow and evolve as biology matures as a natural science. Science necessitates creative yet critical thinking, persuasive communication skills, purposeful use of time, and adeptness at the laboratory bench. Teaching these skills can be effectively accomplished in an inquiry-based, active-learning environment at a primarily undergraduate institution. Cell Biology Techniques, an upper-level cell biology laboratory course at St. John Fisher College, features two independent projects that take advantage of the biology of the nematode Caenorhabditis elegans, a premier yet simple model organism. First, students perform a miniature epigenetic screen for novel phenotypes using RNA interference. The results of this screen combined with literature research direct students toward a singe gene that they attempt to subclone in the second project. The biology of the chosen gene/protein also becomes an individualized focal point with respect to the content of the laboratory. Progress toward course goals is evaluated using written, oral, and group-produced assignments, including a concept map. Pre- and postassessment indicates a significant increase in the understanding of broad concepts in cell biological research.

scholarly journals Mosses: Accessible Systems for Plant Development Studies

2021 ◽  
Author(s):  
Jordi Floriach-Clark ◽  
Han Tang ◽  
Viola Willemsen
Keyword(s):  
Plant Cell ◽  
Cell Biology ◽  
Vascular Plants ◽  
Asymmetric Cell Division ◽  
Apical Cell ◽  
Model Organism ◽  
Land Plant ◽  
Biological Research ◽  
Central System ◽  
Future Potential

Mosses are a cosmopolitan group of land plants, sister to vascular plants, with a high potential for molecular and cell biological research. The species Physcomitrium patens has helped gaining better understanding of the biological processes of the plant cell, and it has become a central system to understand water-to-land plant transition through 2D-to-3D growth transition, regulation of asymmetric cell division, shoot apical cell establishment and maintenance, phyllotaxis and regeneration. P. patens was the first fully sequenced moss in 2008, with the latest annotated release in 2018. It has been shown that many gene functions and networks are conserved in mosses when compared to angiosperms. Importantly, this model organism has a simplified and accessible body structure that facilitates close tracking in time and space with the support of live cell imaging set-ups and multiple reporter lines. This has become possible thanks to its fully established molecular toolkit, with highly efficient PEG-assisted, CRISPR/Cas9 and RNAi transformation and silencing protocols, among others. Here we provide examples on how mosses exhibit advantages over vascular plants to study several processes and their future potential to answer some other outstanding questions in plant cell biology.

scholarly journals Versatile CRISPR/Cas9 Systems for Genome Editing in Ustilago maydis

2021 ◽  
Vol 7 (2) ◽  
pp. 149
Author(s):  
Sarah-Maria Wege ◽  
Katharina Gejer ◽  
Fabienne Becker ◽  
Michael Bölker ◽  
Johannes Freitag ◽  
...  
Keyword(s):  
Genome Editing ◽  
Cell Biology ◽  
Gene Deletion ◽  
Fluorescent Protein ◽  
Point Mutations ◽  
Model Organism ◽  
Ustilago Maydis ◽  
Genomic Locus ◽  
Targeted Gene Deletion ◽  
Molecular Cell Biology

The phytopathogenic smut fungus Ustilago maydis is a versatile model organism to study plant pathology, fungal genetics, and molecular cell biology. Here, we report several strategies to manipulate the genome of U. maydis by the CRISPR/Cas9 technology. These include targeted gene deletion via homologous recombination of short double-stranded oligonucleotides, introduction of point mutations, heterologous complementation at the genomic locus, and endogenous N-terminal tagging with the fluorescent protein mCherry. All applications are independent of a permanent selectable marker and only require transient expression of the endonuclease Cas9hf and sgRNA. The techniques presented here are likely to accelerate research in the U. maydis community but can also act as a template for genome editing in other important fungi.

scholarly journals Mask R-CNN Based C. Elegans Detection with a DIY Microscope

Biosensors ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 257
Author(s):  
Sebastian Fudickar ◽  
Eike Jannik Nustede ◽  
Eike Dreyer ◽  
Julia Bornhorst
Keyword(s):  
Cell Biology ◽  
High Throughput Screening ◽  
Low Cost ◽  
Image Acquisition ◽  
Rapid Development ◽  
Model Organism ◽  
Large Data ◽  
Data Set ◽  
C Elegans ◽  
Do It Yourself

Caenorhabditis elegans (C. elegans) is an important model organism for studying molecular genetics, developmental biology, neuroscience, and cell biology. Advantages of the model organism include its rapid development and aging, easy cultivation, and genetic tractability. C. elegans has been proven to be a well-suited model to study toxicity with identified toxic compounds closely matching those observed in mammals. For phenotypic screening, especially the worm number and the locomotion are of central importance. Traditional methods such as human counting or analyzing high-resolution microscope images are time-consuming and rather low throughput. The article explores the feasibility of low-cost, low-resolution do-it-yourself microscopes for image acquisition and automated evaluation by deep learning methods to reduce cost and allow high-throughput screening strategies. An image acquisition system is proposed within these constraints and used to create a large data-set of whole Petri dishes containing C. elegans. By utilizing the object detection framework Mask R-CNN, the nematodes are located, classified, and their contours predicted. The system has a precision of 0.96 and a recall of 0.956, resulting in an F1-Score of 0.958. Considering only correctly located C. elegans with an [email protected] IoU, the system achieved an average precision of 0.902 and a corresponding F1 Score of 0.906.

Cystic Fibrosis as a Theme to Incorporate Team-Based Learning in Cell Biology Courses

2018 ◽  
Vol 80 (1) ◽  
pp. 2-5
Author(s):  
Jennifer Hurst-Kennedy
Keyword(s):  
Cystic Fibrosis ◽  
High School Students ◽  
Cell Biology ◽  
Class Group ◽  
Teaching Strategy ◽  
School Students ◽  
Group Problem ◽  
Video Viewing ◽  
Team Based Learning ◽  
Upper Level

Team-based learning (TBL) is structured, cooperative learning teaching strategy used in a variety of disciplines. TBL uses a three-step approach for delivering content to students: out-of-class preparation, readiness assurance, and application. In this article, a method for incorporating TBL into an undergraduate cell biology course using cystic fibrosis (CF) as a theme is described. Class content is divided into modules. Each module consists of (1) out-of-class video viewing and reading assignments; (2) individual and team assessments, mini-lectures, and think-pair-share activities to assess understanding of the material; and (3) in-class, group problem sets related to the molecular pathogenesis of CF. Although originally designed for an introductory undergraduate cell biology course, this curriculum can be easily adapted for upper-level undergraduate and high school students.

scholarly journals The Road Less Traveled? Unconventional Protein Secretion at Parasite–Host Interfaces

2021 ◽  
Vol 9 ◽  
Author(s):  
Erina A. Balmer ◽  
Carmen Faso
Keyword(s):  
Protein Secretion ◽  
Cell Biology ◽  
Mammalian Cells ◽  
Cell Model ◽  
Signal Sequence ◽  
Model Organism ◽  
Secreted Proteins ◽  
Current Status ◽  
Secretory Proteins ◽  
Secretion Pathways

Protein secretion in eukaryotic cells is a well-studied process, which has been known for decades and is dealt with by any standard cell biology textbook. However, over the past 20 years, several studies led to the realization that protein secretion as a process might not be as uniform among different cargos as once thought. While in classic canonical secretion proteins carry a signal sequence, the secretory or surface proteome of several organisms demonstrated a lack of such signals in several secreted proteins. Other proteins were found to indeed carry a leader sequence, but simply circumvent the Golgi apparatus, which in canonical secretion is generally responsible for the modification and sorting of secretory proteins after their passage through the endoplasmic reticulum (ER). These alternative mechanisms of protein translocation to, or across, the plasma membrane were collectively termed “unconventional protein secretion” (UPS). To date, many research groups have studied UPS in their respective model organism of choice, with surprising reports on the proportion of unconventionally secreted proteins and their crucial roles for the cell and survival of the organism. Involved in processes such as immune responses and cell proliferation, and including far more different cargo proteins in different organisms than anyone had expected, unconventional secretion does not seem so unconventional after all. Alongside mammalian cells, much work on this topic has been done on protist parasites, including genera Leishmania, Trypanosoma, Plasmodium, Trichomonas, Giardia, and Entamoeba. Studies on protein secretion have mainly focused on parasite-derived virulence factors as a main source of pathogenicity for hosts. Given their need to secrete a variety of substrates, which may not be compatible with canonical secretion pathways, the study of mechanisms for alternative secretion pathways is particularly interesting in protist parasites. In this review, we provide an overview on the current status of knowledge on UPS in parasitic protists preceded by a brief overview of UPS in the mammalian cell model with a focus on IL-1β and FGF-2 as paradigmatic UPS substrates.

scholarly journals Phylogenetic Study of Bufonidae (Amphibia: Anura) from Sumatera and Asia Based on Cytochrome B Gene

2021 ◽  
Vol 11 (3) ◽  
pp. 383-387
Author(s):  
Djong Tjong ◽  
◽  
Dewi Roesma ◽  
Silvia Indra ◽  
◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Cytochrome B ◽  
Cell Biology ◽  
Sequence Divergence ◽  
Phylogenetic Study ◽  
Tissue Samples ◽  
Duttaphrynus Melanostictus ◽  
Level Increase ◽  
West Sumatra ◽  
Biology Laboratory

Bufonidae is widely distributed amphibian family around the world, including Indonesia (Sumatra) and Asia. Sumatra is an island which has separated because of sea level increase and create gene flows barrier for amphibian in Sumatra and Asia. The purpose of this research is to analyse Bufonidae phylogenetic which exist in several locations in Sumatra and Asia based on gene cytochrome b analysis. Samples were collected from six localities in West Sumatra. DNA extraction and amplification has been done in Genetics and Cell Biology Laboratory, Andalas University, whereas DNA sequencing were analyzed at MacroGen USA DNA Sequencing Laboratory, South Korea. About 14 tissue samples of Bufonidae from West Sumatra has been analyzed. The relationship of Bufonidae phylogenetics in Sumatra and Asia were divided into three main clusters. Duttaphrynus melanostictus in Sumatra is closer to Duttaphrynus melanostictus from India with 0,3-0,5% sequence divergence and it is a group of paraphyletic with Duttaphrynus melanostictus from Vietnam, Taiwan, and China.

A CURE Using Cell Culture–Based Research Enhances Career-Ready Skills in Undergraduates

2021 ◽  
Vol 4 (2) ◽  
pp. 49-61
Author(s):  
Jacqueline S. McLaughlin ◽  
◽  
Mit Patel ◽  
Joshua B. Slee ◽  
◽  
...  
Keyword(s):  
Cell Culture ◽  
Cell Biology ◽  
College Graduates ◽  
Undergraduate Research ◽  
Student Assessment ◽  
Future Research ◽  
Survey Analysis ◽  
Research Experience ◽  
Skill Sets ◽  
Host Inflammatory Response

A course-based undergraduate research experience (CURE) using cell culture–based research was developed to allow students to test potential molecules for their ability to prevent the host inflammatory response to implantable biomaterials. This CURE was utilized for lab instruction in cell biology courses over a three-year period at two institutions and was assessed using a modified student assessment of learning gains (SALG) survey and a rubric from the Association of American Colleges and Universities (AAC&U). The SALG survey analysis showed enhanced essential “hard” skill sets and attitudes important to a future research career using cell culture post–CURE participation. The results from both SALG and AAC&U assessments revealed gains in four of the six most highly valued “soft” skills rated by US employers as essential in their hiring of recent college graduates.

The Pathway to Bacterial Genetics

2021 ◽  
pp. 15-30
Author(s):  
Thomas E. Schindler
Keyword(s):  
Graduate School ◽  
Research Laboratory ◽  
Genetic Research ◽  
Model Organism ◽  
Biochemical Genetics ◽  
Research Experience ◽  
Induced Mutations ◽  
New Paradigm ◽  
Career Pathway ◽  
Early Training

This chapter reviews Esther Zimmer’s early training, as she set out on a parallel career pathway, from Neurospora to bacteria, to her future husband Joshua Lederberg. While still a junior at Hunter College, Zimmer found the best possible mentor in Bernard Ogilvie Dodge, the foremost expert in Neurospora, the new model organism of genetic research. After graduation, Dodge helped her gain further research experience at the Industrial Hygiene Research Laboratory in Bethesda, Maryland, where she worked with Alexander Hollaender, an expert in radiation biology. After two years of training in the procedures for developing X-ray and UV induced mutations, Zimmer acquired her bona fides for graduate school. She was accepted to graduate school at Stanford University because of Dodge’s association with George Beadle, who, with Edward Tatum, had developed a new paradigm for biochemical genetics: “one gene: one enzyme.” In 1946, their similar experiences in Neurospora research brought Joshua and Esther together.

scholarly journals Teaching a biology laboratory course using Dictyostelium

2019 ◽  
Vol 63 (8-9-10) ◽  
pp. 551-561
Author(s):  
David A. Knecht ◽  
Kate M. Cooper ◽  
Jonathan E. Moore
Keyword(s):  
Dictyostelium Discoideum ◽  
Cell Biology ◽  
Room Temperature ◽  
Model System ◽  
Educational Settings ◽  
Biology Teaching ◽  
Laboratory Course ◽  
Cellular Processes ◽  
Laboratory Courses ◽  
Biology Laboratory

The Dictyostelium discoideum model system is a powerful tool for undergraduate cell biology teaching laboratories. The cells are biologically safe, grow at room temperature and it is easy to experimentally induce, observe, and perturb a breadth of cellular processes making the system amenable to many teaching lab situations and goals. Here we outline the advantages of Dictyostelium, discuss laboratory courses we teach in three very different educational settings, and provide tips for both the novice and experienced Dictyostelium researcher. With this article and the extensive sets of protocols and tools referenced here, implementing these labs, or parts of them, will be relatively straightforward for any instructor.

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