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Benzonase pre-digest successfully reduces DNA from dead bacteria and the host
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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:

"Next-generation sequencing (NGS) studies have led to dramatic improvements in our understanding of human microbiomes. However, this method is based on the presence of DNA and cannot distinguish between living and dead microbes on its own. Environments like our skin are hostile and have high microbe turnover, which leads to significant amounts of DNA from dead microbes, which can lead to inaccurate community estimations in NGS studies. To overcome this, researchers tested the feasibility of pre-treatment with Benzonase to digest unprotected DNA. They used both mock bacterial communities and skin microbiome samples with inactivated bacteria or bacteria-free DNA spiked-in. Benzonase (BDA) pre-treatment reduced the levels of DNA from dead bacteria in both mock and natural communities. It also reduced the amount of host DNA in samples with high human-to-microbial DNA ratios without obvious impact on the microbial profile..."

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:
10/14/2021
Best-practice evaluation and guidance for human metagenomic studies
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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:

"Metagenomic analysis frequently plays an important role in development pipelines for human fecal microbiome-related products, but validation and standardization of the methods used to extract DNA and assemble sequence libraries for these studies is currently lacking. To close this gap, researchers recently characterized existing protocols for accuracy and precision. First, they tested the quantification accuracy by using a defined mock community of bacteria. Then, the protocols that performed as expected were evaluated for both within- and inter-laboratory precision metrics. The protocols were also tested against the MOSAIC Standards Challenge samples. Lastly, they defined performance metrics for the recommended protocols to provide best-practice guidance. The uptake of the recommendations generated here should improve reproducibility in human metagenomic research and therefore facilitate development and commercialization of human microbiome-related products..."

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:
10/14/2021
CREATES
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CREATES is a set of 6 steps that help learners read and critically analyze scientific papers. The CREATES method, pioneered by Dr. Sally Hoskins, has a demonstrated positive impact on undergraduate students' self-confidence in scientific reading, as well as in their general perceptions of and beliefs about science and scientific thinking (Hoskins, et. al, 2017).

The new CREATES site, created in collaboration with Jordan Moberg Parker, UCLA's Director of Undergraduate Laboratory Curriculum and Assessment in Microbiology, Immunology, and Molecular Genetics, uses interactive media, step-by-step directions, and detailed annotation of authentic examples to guide students through the process.

Subject:
Applied Science
Life Science
Physical Science
Material Type:
Full Course
Interactive
Author:
Doug Worsham
Kian Ravaei
Xinyi(Alex) Yan
Dr. Jordan Moberg Parker
Date Added:
07/20/2020
Charting the complexity of the activated sludge microbiome with a hybrid sequencing strategy
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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:

"The development of long-read sequencing has allowed for the generation of more complete and contiguous genomes in metagenomics studies. However, long-reads are more prone to sequencing errors than short-reads, and these errors can end up incorporated in the draft genomes. Combining short- and long-reads can overcome such errors, but is computationally taxing. To avoid this, researchers developed the ‘Hierarchical Clustering Based Hybrid Assembly (HCBHA) approach.’ This approach first groups the long- and short-reads into candidate bacterial haplotypes and then assembles each group separately, which reduces the computational demand . Researchers tested this framework on a microbiome from activated sludge, an important part of wastewater treatment. The highly complex microbiomes found in activated sludge remove pollutants from wastewater..."

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:
01/11/2022
Combining single-cell genomics and metagenomics to improve assembly in complex microbial communities
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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:

"High-quality reference genomes are needed to understand the physiology and function of uncultured microbes in complex ecosystems. Metagenomics has been an incredibly useful tool for studying microbial communities, but assigning sequence assemblies accurately to genomes is difficult in microbial species or strains that lack a reference genome. These 'consensus genomes' have lower resolution than those generated from cultured isolates. Combining single-cell genomics with metagenomics may allow us to overcome these methodological weaknesses. Thus, researchers recently developed a framework called SMAGLinker, which integrates single-cell genomes from microfluidic droplets and uses them as guides for metagenome assembly. Compared to metagenomics alone, SMAGLinker showed more precise contig binning and higher recovery rates of rRNA and plasmids in a mock microbial community. In human gut and skin microbiota samples, SMAGLinker returned more genomes than the conventional metagenomics frameworks..."

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:
10/13/2021
Delft Design Approach
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In our daily lives we use hundreds or even thousands of products and services. They are all designed, some with more success than others. The ‘Delft Design Approach’ is a structured approach that helps designers to tackle complex design challenges: from formulating a strategic vision, to mapping user behaviors, their needs and their environment, to developing and selecting meaningful proposals for products and services.

DDA691x offers a college-level introduction to the Delft Design Approach through lectures and exercises on design fundamentals and 6 methods. You will understand basic models and concepts that underlie the Delft approach. You will also develop the capability to use 6 basic methods in a design context. You will do so by applying the methods to realistic design challenges and by reflecting on your own performance by comparing it to that of expert designers as well as through peer discussion.

Subject:
Applied Science
Engineering
Material Type:
Full Course
Provider:
Delft University of Technology
Provider Set:
Delft University OpenCourseWare
Author:
Dr. Jaap Daalhuizen
Date Added:
08/01/2018
Holo-omics: a powerful tool investigating plant-microbiome interactions
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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:

"Host-microbiome interactions are a critical component of host health, and plants have a particularly complex relationship with their microbiomes. Understanding these functional relationships will allow us to predict, and even influence, host fitness. Many ‘-omics’ techniques have been developed, and each is a powerful tool solo, but combining them opens the door to a more holistic, systems-level understanding. This strategy, called holo-omics, requires careful experimental design and faces several challenges as a field. First, it currently lacks well-tested analytical frameworks. Second, there is a need for freely available, specialized bioinformatics tools, as most focus on just one data source and don't integrate host and microbe data. Lastly, the heterogeneous nature of holo-omics data requires a wide range of expertise - including plant biologists, microbe experts, statisticians, and computational biologists..."

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:
10/15/2021
IDIS 302: Cases and Theories
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Word Count: 6872

(Note: This resource's metadata has been created automatically by reformatting and/or combining the information that the author initially provided as part of a bulk import process.)

Subject:
Anthropology
Arts and Humanities
Philosophy
Social Science
Material Type:
Textbook
Date Added:
01/26/2024
Ion-Exchange Chromatography
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We now know how to analyze pure compounds, but what if we have a mixture? Spectrophometry becomes quite complex when dealing with multiple species of compounds at once. In order to purify a compound we can separate if from a mixture based on its intrinsic chemical properties. Remember that fluorescein is negatively charged at a pH above pKa of the carboxyl group. We can take advantage of this fact and use its attraction to positive charges to separate it from other molecules. In ion-exchange chromatography, we will use a stationary phase with a positive charge, allowing negatively charged molecules to bind and positively charged species to flow through. We can then disrupt this interaction and retrieve our now-purified molecule, and use spectrophotometric analysis of our purified fractions to determine how well we were able to separate our molecules.

Material Type:
Activity/Lab
Lecture Notes
Student Guide
Textbook
Date Added:
02/06/2015
Isolation of new ureolytic bacteria from the rumen of cattle
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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:

"Ruminants are the only animals not dependent on dietary amino acids as a source of nitrogen. They have ureolytic bacteria in their rumen that hydrolyze urea into ammonia and use it as a nitrogen source. However, very few ureolytic bacteria have been isolated and studied in pure culture to date. To close this gap, researchers established and used a new integrated approach on bacteria from cattle rumens. They started with urease gene (ureC) guided enrichment and then embedded single cells in agarose microspheres for in situ cultivation. This allowed them to isolate and characterize diverse ureolytic bacteria with demonstrated urease activity. The researchers sequenced a subset of the isolated bacteria and found 28 strains from 12 species with urease genes. These bacterial species had not previously been found in the rumen, but this team detected them in metagenomes from 6 ruminant species. The new strains contained unique genes compared to known related strains, indicating new metabolic functions..."

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:
04/24/2023
Linking to Data - Effect on Citation Rates in Astronomy
Read the Fine Print
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Is there a difference in citation rates between articles that were published with links to data and articles that were not? Besides being interesting from a purely academic point of view, this question is also highly relevant for the process of furthering science. Data sharing not only helps the process of verification of claims, but also the discovery of new findings in archival data. However, linking to data still is a far cry away from being a "practice", especially where it comes to authors providing these links during the writing and submission process. You need to have both a willingness and a publication mechanism in order to create such a practice. Showing that articles with links to data get higher citation rates might increase the willingness of scientists to take the extra steps of linking data sources to their publications. In this presentation we will show this is indeed the case: articles with links to data result in higher citation rates than articles without such links. The ADS is funded by NASA Grant NNX09AB39G.

Subject:
Physical Science
Material Type:
Reading
Provider:
arXiv:1111.3618 [astro-ph]
Author:
Alberto Accomazzi
Edwin A. Henneken
Date Added:
08/07/2020
OptoNotch: Using light to activate Notch signaling
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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:

"NOTCH1 is a protein implicated in various diseases, including breast cancer. In order to control Notch signaling, researchers have developed a light-activated tool called OptoNotch. OptoNotch is an engineered form of NOTCH1 that is activated under blue light. This mimics NOTCH1’s natural activation program: activation, release from the plasma membrane, translocation to the nucleus, and initiation of potentially harmful expression of different genes. The ability to activate NOTCH1 using only light makes OptoNotch highly targeted and easier to implement than chemical- or genetic-based systems. When deployed in two lines of breast cancer cells, OptoNotch could track how NOTCH1 contributed to accelerated cell proliferation, as well as cell migration, the phenotype of cancer cells in 3D cultures, mimicking patients' tumors, and resistance to common chemotherapy drugs. OptoNotch could help scientists to understand the roles of NOTCH1 in normal and disease conditions, and help screen for promising drug candidates..."

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:
01/30/2023
The Polar Express Delivers Equity in the Kindergarten Classroom
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This free, online article, developed for elementary teachers, describes a Kindergarten polar science, standards aligned, unit centered on The Polar Express developing literacy, math, and science skills.

Subject:
Applied Science
Environmental Science
Geoscience
Physical Science
Material Type:
Reading
Provider:
Ohio State University College of Education and Human Ecology
Provider Set:
Beyond Penguins and Polar Bears: An Online Magazine for K-5 Teachers
Author:
Mary LeFever
Date Added:
10/17/2014
Pre-implantation culture conditions may influence stem cells used in arthritis treatment
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CC BY
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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:

"Osteoarthritis is a painful degradation of joint cartilage. Therapies that boost cartilage's limited ability to repair using adipose tissue-derived stem cells (ASCs) have shown promise in cell culture and animal studies, but that success has not carried over to clinical trials. This variability in clinical trials may come down to how the cells are cultured prior to implantation. To test this, a recent study examined a co-culture system combining ASCs taken from the fat pad behind the patella and cartilage cells (chondrocytes). Co-cultured ASCs and chondrocytes had higher expression of cartilage-associated genes than expected, and the effect was larger in cultures with a lower ratio of ASCs to chondrocytes. This gene expression change likely reflects changes in the ASCs and would suggest that the ASCs are starting to make the molecular changes needed to repair damaged cartilage, but increased expression in the chondrocytes, rather than the ASCs, cannot be ruled out without further experiments..."

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:
05/18/2022
Principles of Microeconomics
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Principles of Microeconomics is an adaptation of the textbook, Microeconomics: Markets, Methods, and Models by D. Curtis and I. Irvine, which provides concise yet complete coverage of introductory microeconomic theory, application and policy in a Canadian and global environment.

Subject:
Economics
Social Science
Material Type:
Textbook
Provider:
Lyryx Learning
Author:
Doug Curtis
Ian Irvine
Date Added:
03/31/2017
Research Methods in Psychology
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Research Methods in Psychology is intended to provide a fundamental understanding of the basics of experimental research in the psychological sciences.

Research Methods in Psychology adapted by Michael G. Dudley is licensed under Creative Commons Attribution-NonCommercial-ShareAlike 4.0 license.
Research Methods in Psychology is adapted from a work produced and distributed under a Creative Commons license (CC BY-NC-SA) in 2010 by a publisher who has requested that they and the original author not receive attribution. This adapted edition is based on an adaptation produced by the University of Minnesota Libraries Publishing through the eLearning Support Initiative. This adapted edition was created by Michael G. Dudley with support from the Palomar College Foundation.
This adaptation has significantly altered the original 2010 text and removed images. This work is made available under the terms of a Creative Commons Attribution-NonCommercial-ShareAlike license.

Subject:
Psychology
Social Science
Material Type:
Textbook
Date Added:
01/19/2019
Survey of Educational Research Methods syllabus
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Syllabus for Survey of Educational Research Methods course that uses the open textbook Social Science Research: Principles, Methods, and Practices: https://scholarcommons.usf.edu/oa_textbooks/3/

Course description:
This course provides students with a survey of methods used in educational research, including qualitative, survey, quantitative group, correlational, single case, and action research. The role of systematic approaches to research in education is considered, and an overview of multiple ways of conducting research in education is provided. Emphasis will be placed on developing students’ competence in locating, evaluating and using published research to inform decision making in educational, clinical, and social settings. Guidelines for evaluating educational research that use the various methodologies are provided. Students will evaluate and critique published research articles.

Subject:
Education
Material Type:
Syllabus
Author:
Julie Alonzo
Date Added:
03/09/2020
Using mechanobiology and materials methods in epithelial-mesenchymal transition research
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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:

"Cancer-related mortality, a leading cause of death in the US, is driven by tumor invasion and metastasis. Implicated in these processes is epithelial-to-mesenchymal transition, or EMT. EMT drives invasion through a dramatic reorganization of a cell's cytoskeleton and the extracellular matrix. Because EMT is a rare event, undergone by a few abnormal cells, it is difficult to view directly in a patient. But new research methods are providing a lens into this critical process. Culturing cells on planar surfaces is revealing how their EMT behavior is coordinated and driven by leader cells. Research on the protein vimentin highlights its role in enabling cells to contort during migration or proliferation. Other studies examine how topographically patterning culture surfaces changes the behaviors of cells as they slip into and out of EMT. And 3D matrices are being used to examine the dissemination and disorganization of multicellular clusters..."

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:
03/11/2021
pKa of Fluorescein
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Previously, we showed how different compounds absorb light. The chemical structure of a molecule determines exactly how much light it absorbs, as well as which wavelengths are absorbed. It stands to reason then, that by removing an atom from a molecule, we can change the way it absorbs light. In this experiment, we will relate these two concepts by measuring the absorbance of a molecule under acidic and basic conditions. The changing pH will allow us to find how strongly a specific hydrogen is attached to our molecule, and we will observe how the changing chemical structure affects the observed absorbance. Afterwards, using mathematical analysis, we can experimentally determine the pKa, or affinity of our hydrogen to our parent molecule.

Material Type:
Activity/Lab
Student Guide
Date Added:
02/06/2015