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CORRAL: a new automated tool to detect eukaryotes in large-scale metagenomic datasets
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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:

"Microbiomes are more than just prokaryotes and viruses; they also contain important eukaryotes, including fungi and protists. However, eukaryotes are difficult to study using ‘shotgun’ metagenomics, as their signal is often overwhelmed by the prokaryotes. Some methods use eukaryote-specific marker genes, but they can’t detect eukaryotes that aren’t in the reference marker gene set, and such methods are not compatible with web-based tools for downstream analysis. But CORRAL (Clustering Of Related Reference ALignments) is designed to close those gaps. CORRAL identifies eukaryotes in metagenomic data based on alignments to eukaryote-specific marker genes and Markov clustering. It can detect microbial eukaryotes that are not included in the marker gene reference set. The process is even automated and can be carried out at scale. A recent paper demonstrates CORRAL’s sensitivity and accuracy with simulated datasets, mock community standards, and human microbiome datasets..."

The rest of the transcript, along with a link to the research itself, is available on the resource itself.

Subject:
Biology
Life Science
Material Type:
Diagram/Illustration
Reading
Provider:
Research Square
Provider Set:
Video Bytes
Date Added:
04/17/2023
CRISPER Prokaryotic Antiviral Defense Mechanism
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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).

Subject:
Genetics
Life Science
Material Type:
Diagram/Illustration
Author:
Theroid
Date Added:
09/13/2020
Cell Biology: Structure and Functions of the Nucleus
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CC BY-NC-SA
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The goal of this course is to teach both the fundamentals of nuclear cell biology as well as the methodological and experimental approaches upon which they are based. Lectures and class discussions will cover the background and fundamental findings in a particular area of nuclear cell biology. The assigned readings will provide concrete examples of the experimental approaches and logic used to establish these findings. Some examples of topics include genome and systems biology, transcription, and gene expression.

Subject:
Biology
Life Science
Physical Science
Material Type:
Full Course
Provider:
MIT
Provider Set:
MIT OpenCourseWare
Author:
Sharp, Phillip
Young, Richard
Date Added:
02/01/2010
Classifying Animals by Appearance Versus DNA Sequence
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CC BY-NC-SA
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The topic of this video module is how to classify animals based on how closely related they are. The main learning objective is that students will learn how to make phylogenetic trees based on both physical characteristics and on DNA sequence. Students will also learn why the objective and quantitative nature of DNA sequencing is preferable when it come to classifying animals based on how closely related they are. Knowledge prerequisites to this lesson include that students have some understanding of what DNA is and that they have a familiarity with the base-pairing rules and with writing a DNA sequence.

Subject:
Biology
Genetics
Life Science
Material Type:
Lecture
Provider:
MIT
Provider Set:
MIT Blossoms
Author:
Megan E. Rokop
Date Added:
06/11/2012
Community Genomes: using the example of Bauhinia Genome for genomics education. What is a genome project, and why are they important?
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CC BY
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This genomics education lesson plan was formulated and tested on some year 6 students with the help of their teacher Michelle Pardini at the Hong Kong ICS School. Using the example of the ongoing citizen science Bahinia Genome project from Hong Kong it hopes to serve as a model to inspire and inform other national genome projects, and aid the development of crucial genomic literacy and skills across the globe. Inspiring and training a new generation of scientists to use these tools to tackle the biggest threats to mankind: climate change, disease, and food security. It is released under a CC-BY SA 4.0 license, and utilised the following slide deck and final quiz. Promoting open science, all of the data and resources produced from the project is immediately put into the public domain. Please feel free to utilise, adapt and build upon any of these as you wish. The open licence makes these open education resources usable just with attribution and posting of modified resources under a similar manner. Contact BauhiniaGenome if you have any questions or feedback.Bauhinia Genome overviewFor a slidedeck for the lesson plan laid out here you can use the set in slideshare here.

Subject:
Biology
Computer Science
Genetics
Life Science
Material Type:
Lesson Plan
Author:
Scott Edmunds
Michelle Pardini
Rob Davidson
Date Added:
05/12/2016
Computational Functional Genomics
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CC BY-NC-SA
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The course focuses on casting contemporary problems in systems biology and functional genomics in computational terms and providing appropriate tools and methods to solve them. Topics include genome structure and function, transcriptional regulation, and stem cell biology in particular; measurement technologies such as microarrays (expression, protein-DNA interactions, chromatin structure); statistical data analysis, predictive and causal inference, and experiment design. The emphasis is on coupling problem structures (biological questions) with appropriate computational approaches.

Subject:
Applied Science
Biology
Health, Medicine and Nursing
Life Science
Physical Science
Material Type:
Full Course
Provider:
MIT
Provider Set:
MIT OpenCourseWare
Author:
Gifford, David
Jaakkola, Tommi
Date Added:
02/01/2005
Concepts of Biology by Rice University Textbook Resources for Biology I
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CC BY-NC-SA
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This is information to be used for a General Biology I (or Introduction to Biology) course for non-science majors.

Subject:
Biology
Life Science
Material Type:
Diagram/Illustration
Full Course
Homework/Assignment
Lecture
Lecture Notes
Lesson Plan
Module
Reading
Student Guide
Syllabus
Teaching/Learning Strategy
Unit of Study
Date Added:
08/10/2019
Concepts of Biology instructional videos - Camosun College
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CC BY
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This series of instructional videos was created by Camosun College for a Canadian edition of the OpenStax "Concepts of Biology" open textbook as part of the BC Open Textbook Project. The lectures are taught by Charles Molnar, a Biology instructor at Camosun College. The videos are accompanied by transcripts.

Subject:
Life Science
Material Type:
Lecture
Date Added:
08/15/2016
DNA
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CC BY-NC-SA
DNA
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Learn about DNA (deoxyribonucleic acid). Overview of DNA bases, complementary base pairing, and the structure of the double helix.

Subject:
Biology
Genetics
Life Science
Material Type:
Lesson
Provider:
Khan Academy
Provider Set:
Khan Academy
Author:
Sal Khan
Date Added:
09/22/2009
DNA Build
Read the Fine Print
Educational Use
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Students reinforce their knowledge that DNA is the genetic material for all living things by modeling it using toothpicks and gumdrops that represent the four biochemicals (adenine, thiamine, guanine, and cytosine) that pair with each other in a specific pattern, making a double helix. They investigate specific DNA sequences that code for certain physical characteristics such as eye and hair color. Student teams trade DNA "strands" and de-code the genetic sequences to determine the physical characteristics (phenotype) displayed by the strands (genotype) from other groups. Students extend their knowledge to learn about DNA fingerprinting and recognizing DNA alterations that may result in genetic disorders.

Subject:
Applied Science
Engineering
Genetics
Life Science
Material Type:
Activity/Lab
Provider:
TeachEngineering
Provider Set:
TeachEngineering
Author:
Denise W. Carlson
Janet Yowell
Malinda Schaefer Zarske
Megan Schroeder
Date Added:
09/18/2014
DNA Forensics and Color Pigments
Read the Fine Print
Educational Use
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Students perform DNA forensics using food coloring to enhance their understanding of DNA fingerprinting, restriction enzymes, genotyping and DNA gel electrophoresis. They place small drops of different food coloring ("water-based paint") on strips of filter paper and then place one paper strip end in water. As water travels along the paper strips, students observe the pigments that compose the paint decompose into their color components. This is an example of the chromatography concept applied to DNA forensics, with the pigments in the paint that define the color being analogous to DNA fragments of different lengths.

Subject:
Applied Science
Engineering
Genetics
History
History, Law, Politics
Life Science
Physical Science
Physics
Material Type:
Activity/Lab
Provider:
TeachEngineering
Provider Set:
TeachEngineering
Author:
Mircea Ionescu
Myla Van Duyn
Date Added:
09/18/2014
DNA Model
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 DNA Model Grade Level: 10thSubject: ALS:AnimalsDuration: 100 minutesDOK Level:4SAMR Level: Substitution Indiana Standard: ALSA-2.23 Explain the importance of DNA and differentiate the following terms, genome, gene, chromatin, chromosome, and chromatids.Objective: Students will be able to design and construct a DNA model with 100% accuracy.Essential Question: What is DNA?Procedure: Have students write down everything they know about DNAShow the video DNA Chalk Talk Present the lecture DNA BasicsDivide the students into pairsExplain the expectations of the DNA modelBrainstorming sheetWritten out planParagraph explaining the model and relating it the real DNA. The paragraph also needs to explain why the pieces of the model were used.Allow the students the rest of the time to create a brainstorming sheet and plan for building the next class timeAllow one class period for building and presentingProduct or Assessment: Students will be evaluated on their models and written paragraph. 

Subject:
Applied Science
Material Type:
Lesson Plan
Author:
Macon Beck
Date Added:
07/13/2017
DNA Origami
Unrestricted Use
Public Domain
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This short lesson is a modeling exercise to understand the structure of DNA and its relationship to nanoscale.

Subject:
Biology
Material Type:
Activity/Lab
Author:
Integrated Nanosystems Development Institute (INDI)
Date Added:
06/22/2021
DNA Replication
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CC BY-NC-SA
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Many biotechnology applications rely on the DNA replication process.  Through this lesson, students will better understand the DNA replication process and connect it to other biotechnology processes.

Subject:
Agriculture
Biology
Material Type:
Activity/Lab
Lesson
Author:
Abby Hitchler
Date Added:
07/07/2023
DNA Structure and Function
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CC BY
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This resource explains the structure and function of DNA using PowerPoint.  Videos and practice are linked into the presentation.  

Subject:
Life Science
Material Type:
Lecture
Author:
Despina Mitsos
Date Added:
07/13/2023
DNA:  The Book of You
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CC BY-NC-ND
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Your body is made of cells -- but how does a single cell know to become part of your nose, instead of your toes? The answer is in your body's instruction book: DNA. Joe Hanson compares DNA to detailed manual for building a person out of cells -- with 46 chapters (chromosomes) and hundreds of thousands of pages covering every part of you.

Subject:
Biology
Genetics
Life Science
Material Type:
Assessment
Lecture
Lecture Notes
Lesson Plan
Simulation
Provider:
TED
Provider Set:
TED-Ed
Author:
Joe Hanson
Nipun Sharma
Date Added:
07/02/2013