All resources in OER Fundamentals Fall 2024

Search

Exploring metabolite metabolism using the Enzyme Portal

(View Complete Item Description)

This webinar will provide a practical overview of how to use the Enzyme Portal to find enzyme-related information about metabolites. The Enzyme Portal is a freely available resource to find and explore enzyme features. It integrates relevant enzyme data for a wide range of species from various resources including UniProt, PDB, Reactome and CHEMBL. We will demonstrate how to use the Enzyme Portal to find relevant enzymes involved in a specific metabolite biosynthesis or catabolism. Who is this course for? This webinar is aimed at individuals who wish to learn more about enzymes and metabolites. No prior knowledge of bioinformatics is required, but an undergraduate level understanding of biology would be useful.

Material Type: Lecture

The enzyme HK2 is a potential regulator of osteoarthritis

(View Complete Item Description)

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview: "Patients with osteoarthritis typically experience progressive cartilage degeneration, joint inflammation, and bony growth around the joints. Treatment of this painful condition remains difficult because the underlying mechanisms aren’t clear, but recent evidence suggests that an increase in aerobic glycolysis, a form of glucose metabolism, may play a role. Aerobic glycolysis is regulated in part by the enzyme hexokinase 2 (HK2), which is upregulated in the joint tissues of patients with osteoarthritis . In addition to participating in glycolysis, HK2 affects cell growth, proliferation, survival, organelle recycling, and death under the influences of various other osteoarthritis-related proteins and pathways. For example, HK2 activity is promoted by the PI3K/Akt pathway, which is activated in osteoarthritis cartilage and HK2 might activate the transcription factor NF-κB to encourage downstream inflammatory processes in joints..." The rest of the transcript, along with a link to the research itself, is available on the resource itself.

Material Type: Diagram/Illustration, Reading

Artificial enzymes facilitate targeted cancer therapy

(View Complete Item Description)

This resource is a video abstract of a research paper created by Research Square on behalf of its authors. It provides a synopsis that's easy to understand, and can be used to introduce the topics it covers to students, researchers, and the general public. The video's transcript is also provided in full, with a portion provided below for preview: "Despite their known benefits, chemotherapy and other cancer treatments can take a toll on patients. Side effects such as hair loss, nausea, immune system suppression, fatigue, cognitive impairment, and infertility are common. The reason is that many cancer-fighting treatments target cells that quickly reproduce, which is true of cancer cells but also of other, healthy cells in the body, including blood cells and those lining the gastrointestinal tract. Is it possible to target only cancerous tissues with therapeutic drugs so that healthy organs remain unaffected? Researchers at the RIKEN Cluster for Pioneering Research in Japan are engineering molecules to do just that. The team showed that artificially designed gold-based enzymes (or metalloenzymes) can be used to guide drug delivery through a technique called selective cell tagging therapy. These metalloenzymes are studded with sugar molecules that can bind to specific proteins called lectins displayed on the surface of cancer cells..." The rest of the transcript, along with a link to the research itself, is available on the resource itself.

Material Type: Diagram/Illustration, Reading

Supplement for Standard Biochemistry Textbooks

(View Complete Item Description)

Dr. Bolander recently retired from the University of South Carolina, where he taught biochemistry at both the graduate and undergraduate levels for decades. He accumulated considerable figures and notes and is making them available to others involved with teaching biochemistry or related courses. These notes cover material with weaker coverage in standard biochemistry textbooks. This text is supplemental rather than primary.

Material Type: Lecture Notes, Reading

Author: Dr. Franklyn F. Bolander Jr.

Integrating knowledge of proteins and small molecules with UniProtKB

(View Complete Item Description)

A complete understanding of biological systems requires integration of knowledge of the regulation and function of small molecule metabolites – the metabolome – with that of genes, transcripts, and proteins (the genome, transcriptome, and metabolome). The UniProt knowledgebase UniProtKB supports biomedical research by providing a comprehensive, high quality and freely accessible resource of protein sequences and functional information. UniProtKB integrates, interprets and standardizes data from a range of sources including the scientific literature, tools for protein sequence analysis, other knowledge resources and databases, and automatic annotation systems, to provide a detailed overview of the available protein knowledge. This webinar will provide an introduction into how UniProtKB captures and represents knowledge of small molecule metabolites using the Rhea knowledgebase of biochemical reactions, based on the chemical ontology ChEBI, and how UniProt users can access and exploit that knowledge. Who is this course for? This webinar targets life scientists and bioinformaticians who study enzymes and small molecules, particularly those interested in linking or bridging the two domains. No prior knowledge of bioinformatics or cheminformatics is required, but an undergraduate level knowledge of biology/ biochemistry would be useful. Outcomes By the end of the webinar you will be able to: Describe how UniProt annotates enzyme and transporter function, and where the data comes from Find and retrieve information about specific enzymes, transporters and the metabolites on which they act, by searching UniProtKB using text, chemical structures, and chemical classifications Help us develop the representation of small molecule data in UniProtKB by providing valuable feedback

Material Type: Lecture

CRISPER Prokaryotic Antiviral Defense Mechanism

(View Complete Item Description)

Barrangou and a team of researchers at Danisco first experimentally demonstrated the technique of CRISPR (Clusters of Regularly Interspaced Short Palindromic Repeats). To fight off the infecting bacteriophages, the bacterial immume systems (CRISPR-Cas9) specifically target genomic sequences. Cas9 is an enzyme that cuts DNA which is associated with the specialized stretches of CRISPR DNA. This figure clearly depicts how the bacterium protects itself from the infecting viruses (bacteriophages).

Material Type: Diagram/Illustration

Author: Theroid

Adventures in Antibody Identification: Enzymes and Dara

(View Complete Item Description)

Only around 0.2-2.0% of the patient population will have detectable RBC antibodies -- fewer still will have multiplePatients more frequently exposed to RBC antigens are more likely to have antibodies (multiply transfused sickle cell adult patients ~47%)So you've mastered the type & screen and antibody panels... but what do you do if an antibody panel is inconclusive?Selected Cell Panels - select cells with minimal overlap of antigens; helpful for patients with a known history of an antibodyEnzyme-treated panels - destroy certain antigens and enhance expression of others; modify RBC surface by removing sialic acid residues and by denaturing or removing glycoproteinsExamples: ficin, papain, bromelin, trypsinOne-step enzyme method: enzymes utilized in place of enhancement media (instead of LISS or PEG)Two-step enzyme method: panel RBCs are treated with an enzyme first, then the antibody ID panel is done with treated cells; should compare reactivity to antibody ID panel of same cells without enzyme treatmentA special case seen in blood banking: Daratumumab ("Dara") patientsDaratumumab is a drug used in treatment of Multiple MyelomaPlasmacytoma or plasma cell cancer - plasma cells express CD 38~30k new cases, ~12.5k deaths per yearAnemia is a key symptom (with calcium levels, renal insufficiency, bone lesions)CD 38 is a cyclic ADP ribose hydrolase - with roles in calcium signalling & NAD metabolismExpressed on all cell types: notably Plasma cells and RBCsOne option for treating Multiple Myeloma is the drug Daratumumab: a monoclonal antibody IgG1K anti-CD 38; kills myeloma cells through patient's own immune responseWhat does this have to do with blood bank?CD38 is found on RBCs -- including screen and panel cells, in crossmatchesDara patients show PANAGGLUTINATION in all AHG testing - positive screen, panel, crossmatch, variable/weak positive DAT (at IgG)Multiple myeloma patients need frequent transfusions - increased chance of developing alloAbEnzyme treated panel case studyDara patient case study

Material Type: Module

Author: Ann Barrett

Enzyme Portal: Quick tour

(View Complete Item Description)

This quick tour provides a brief introduction to Enzyme Portal - a data resource that provides access to information from several enzyme-related databases, many of which are based at EMBL-EBI. By the end of the course you will be able to: Navigate Enzyme Portal to access enzyme-related data Identify the various possibilities to search Enzyme Portal Describe what type of enzyme-related data Enzyme Portal provides

Material Type: Full Course

Enzymes Help Us Digest Food

(View Complete Item Description)

Students learn about enzyme function, enzyme specificity, and the molecular basis of lactose intolerance through experiments with the enzyme lactase and analysis and discussion questions. Students engage in the scientific practices of designing and carrying out experiments and interpreting data. This activity is aligned with the Next Generation Science Standards.

Material Type: Activity/Lab, Lesson Plan

Authors: Ingrid Waldron, Jennifer Doherty

Lessons 1: Qualitative Kinetics: Examining the effect of an enzyme on a reaction

(View Complete Item Description)

Chemical kinetics and buffers are two topics that are extremely difficult for students to understand. Combining the two topics will allow for a staggered, repetitive approach to teaching students to understand of how these two topics in chemistry actually work. Students will both qualitatively and quantitatively track the effect and enzyme has on a reaction, calculate the reaction rate and buffer capacity. Students will use a variety of lab techniques including calculations using Beer’s Law and spectrophotometry.

Material Type: Lesson Plan

Author: Chris England

Clinical Hematology Atlas: A Pictorial Guide for the Hematology Laboratory (Taylor and Doty)

(View Complete Item Description)

In Medical Laboratory Science (MLS) Hematology courses, students learn to evaluate normal and abnormal blood cell morphology through microscopic examination of blood smears. They learn to interpret results and correlate with other laboratory data to identify hematologic disorders. Access to quality atlases are a vital tool in the students’ learning process. Because the cost of printing pictures is so great, the price of printed atlases is high. The number of images included is limited. And many excellent atlases are now out of print. This project seeks to eliminate those challenges for students by giving access to an Open Educational Resource (OER) atlas for hematology. This format is easily accessed during students’ time on campus and will continue into their careers as medical laboratory scientists. There are currently not many medical subject resources available as open resources. It is our hope that other healthcare professionals will find these resources beneficial. This project is unique in that students are the main contributors of the images used. While not entirely comprehensive at this point, the OER platform will allow for continual updating as new images and information become available.

Material Type: Textbook

Authors: Caroline Doty, Dawn Taylor

Load more