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 laboratory and computational tools available to microbiome researchers have greatly improved in recent years, especially in assembling genomes from complex communities. Most of the research to date has focused on macrodiversity, which is classical ecology metrics like population abundance, α-diversity, and β-diversity. But microdiversity — population genetics metrics like single nucleotide polymorphisms (SNPs) and selective pressures — is important to consider. There are several technical and accessibility issues that hinder widespread analysis of microdiversity in metagenomic datasets, but the recently developed open-access software tool MetaPop is designed to close this gap. MetaPop provides a user-friendly interface to analyze both the macro- and microdiversity of microbial and viral community metagenomes. For small datasets, MetaPop can be run on a laptop, making it a practical choice for non-bioinformaticians or labs without access to high-powered computing..."

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

Welcome to the Teachers' Corner of Small Things Considered. In this section, we include the posts we deem most adequate for teaching purposes. We have reorganized them into subject areas geared for a typical microbiology course. To date, this material has been used for various forms of intellectual enrichment, e.g., suggested readings, class presentations, a source of topics for term papers. You can also find here our Talmudic Questions, which we characterize as those whose answers cannot be found in Google. We are told that some of these questions have been used in exams ranging from tests for undergraduate courses to qualifying/prelims for graduate students.

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:

"Amphibians are one of the most vulnerable animal groups on the planet, with over 40% of their species threatened with extinction. A major driver of that vulnerability is the fungal pathogen _Batrachochytrium dendrobatidis_ (Bd). Bd is linked to the decline of at least 500 amphibian species, the greatest loss in biodiversity due to a pathogen ever recorded. The amphibian skin microbiome community structure has been linked to health outcomes of Bd infection, but the functional importance of the microbiota is not yet fully understood. To close this gap and potentially discover biomarkers or disease control methods, researchers investigated the microbiome of midwife toads. They examined both wild populations with naturally occurring Bd infection and controlled laboratory exposure. Infection with Bd led to changes in the microbial community structure, gene profile, and metabolic function in laboratory and wild toad populations..."

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

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:

"Wastewater treatment plants are a critical piece of infrastructure that depend on microbes, both resident and incoming. Incoming microbes can be beneficial but may include parasites that need to be removed. Resident microbes, meanwhile, help break down organic waste. While much is known about bacteria in wastewater treatment plants, eukaryotes are frequently overlooked. Recently, researchers examined the whole microbiome of 10 wastewater treatment plants in Switzerland. They utilized metagenomics to measure which microbes were present and metatranscriptomics to analyze their activity. Bacteria were the most numerous— but eukaryotes, particularly protists, showed the most activity, and there was a surprising number and range of active parasites, which were particularly prevalent in the inflow. Network analysis suggested predation by resident microbes likely helped remove parasites..."

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

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:

"Viruses might be small, but they drive ecological change across the planet. That includes helping lock otherwise harmful carbon away in soil. Unfortunately, little is known about soil viruses worldwide. A recent study extensively examined the viral microbiome of a Minnesotan peatland from the experimental site SPRUCE. Peatlands are the largest natural terrestrial reservoirs of carbon on earth and, as such, are a critical component of the carbon cycle. The makeup of viral communities in the SPRUCE peat varied with sample depth, water content, and carbon chemistry factors. Of the 4,326 distinct virus types identified from SPRUCE, only 164 had been previously detected in other soils and those matches were almost exclusively from other peatlands. Peatlands are a very wet, but otherwise terrestrial, ecosystem. However, none of the previously detected aquatic viruses matched SPRUCE viruses, which suggests a terrestrial and aquatic ‘species’ divide..."

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

Small molecules are chemicals that can interact with proteins to affect their functions. Learn about the structure and biological functions of various small molecules like sugar and caffeine. Also featured on the HHMI DVD, Scanning Life's Matrix: Genes, Proteins, and Small Molecules. Available free from HHMI.

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:

"Microbial life can be found in nearly every environment on earth. These tiny organisms can significantly impact their surroundings, be it deep-sea microbes influencing the ecology of the ocean floor or the human gut microbiome affecting health. Metagenomics, or the analysis of microbial DNA in different environments, has dramatically increased what is known about microbial life. These sequencing-based techniques are not dependent on culturing microbes, which can be an incredibly difficult undertaking. However, isolating and cultivating microbes remains important to both confirm and expand upon those results. Moreover, cultivated microbes could potentially be used as probiotics or biocontrol agents or for industrial purposes. To date, most environmental microbes remain uncultured, but metagenomic data can be leveraged to help researchers isolate and cultivate new ones..."

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

Our Patterns Biology development team of teacher leaders has been working hard through the spring and summer of 2020 to develop distance learning versions of the Patterns Biology units. Between March and May they released Distance Learning versions of units 4 and 5, as well as paper packets that can be printed for students who do not have access to technology at home. In preparation for fall of the 2020-21 school year, the team has just published Distance Learning versions of units 1 and 2 (see below links for each unit's page). Our Distance Learning units can be used in either a fully online or hybrid school model. A Distance Learning version of Unit 3 will be released by the end of September.

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:

"Microbiome sequencing data are very complex. In order to simplify analyses, researchers often perform unsupervised clustering to identify naturally occurring clusters and then investigate the clusters’ associations with various characteristics of interest. However, clustering performance and related conclusions can vary depending on the algorithm or beta diversity metric used. To improve microbiome analysis methods, a new study tested the performance of several metrics on four datasets with well-separated groups and a clinical dataset with less-clear group separation. None of the metrics was universally superior, but certain metrics underperformed under certain conditions. For example, the Bray-Curtis metric performed poorly in a dataset with rare high-abundance OTUs (groups of related bacteria), while the unweighted UniFrac metric performed poorly in a dataset with prevalent low-abundance OTUs..."

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

How do organisms survive the extreme pressures and temperatures of the ocean abyss? Join Dr. Doug Bartlett as he describes genomics research to understand how deep sea Bacteria have adapted to these extremes, and how this may lay the groundwork for biotechnology using deep sea Bacterial genes. (59 minutes)

Data Carpentry Genomics workshop lesson to learn how to structure your metadata, organize and document your genomics data and bioinformatics workflow, and access data on the NCBI sequence read archive (SRA) database. Good data organization is the foundation of any research project. It not only sets you up well for an analysis, but it also makes it easier to come back to the project later and share with collaborators, including your most important collaborator - future you. Organizing a project that includes sequencing involves many components. There’s the experimental setup and conditions metadata, measurements of experimental parameters, sequencing preparation and sample information, the sequences themselves and the files and workflow of any bioinformatics analysis. So much of the information of a sequencing project is digital, and we need to keep track of our digital records in the same way we have a lab notebook and sample freezer. In this lesson, we’ll go through the project organization and documentation that will make an efficient bioinformatics workflow possible. Not only will this make you a more effective bioinformatics researcher, it also prepares your data and project for publication, as grant agencies and publishers increasingly require this information. In this lesson, we’ll be using data from a study of experimental evolution using E. coli. More information about this dataset is available here. In this study there are several types of files: Spreadsheet data from the experiment that tracks the strains and their phenotype over time Spreadsheet data with information on the samples that were sequenced - the names of the samples, how they were prepared and the sequencing conditions The sequence data Throughout the analysis, we’ll also generate files from the steps in the bioinformatics pipeline and documentation on the tools and parameters that we used. In this lesson you will learn: How to structure your metadata, tabular data and information about the experiment. The metadata is the information about the experiment and the samples you’re sequencing. How to prepare for, understand, organize and store the sequencing data that comes back from the sequencing center How to access and download publicly available data that may need to be used in your bioinformatics analysis The concepts of organizing the files and documenting the workflow of your bioinformatics analysis

This course provides a foundation in the following four areas: evolutionary and population genetics; comparative genomics; structural genomics and proteomics; and functional genomics and regulation.

This fun Web site is part of OLogy, where kids can collect virtual trading cards and create projects with them. Here, they learn about the human genome project by clicking through an online slide show, hosted by kids, that answers these questions: What's a genome, anyway?What is the human genome project? What does it mean to me?

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 candidate phyla radiation (CPR) is a lineage of bacteria with unusual ribosomal structures, reduced metabolic capacities, small genomes, and small cell sizes. Due to these traits, this phylum — also called Patescibacteria — is thought to be host-associated, and there are only a few cultivated representatives. Most CPR genomes originated from groundwater, but they also can be found in surface freshwater, where they remain largely understudied. To close this gap, a recent study examined CPRs from freshwater lakes in Europe and Asia with deep metagenomic sequencing, as well as the first use of Fluorescence in situ Hybridization followed by Catalyzed Reporter Deposition (CARD-FISH) to view CPRs in freshwater. Like previously described CPR members, the lineages in this study had reduced genome sizes, low abundance, and slow estimated replication rates..."

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

This is a seminar based on research literature. Papers covered are selected to illustrate important problems and approaches in the field of computational and systems biology, and provide students a framework from which to evaluate new developments.
The MIT Initiative in Computational and Systems Biology (CSBi) is a campus-wide research and education program that links biology, engineering, and computer science in a multidisciplinary approach to the systematic analysis and modeling of complex biological phenomena. This course is one of a series of core subjects offered through the CSB Ph.D. program, for students with an interest in interdisciplinary training and research in the area of computational and systems biology.

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 interactions between viruses and prokaryotes play a key role in shaping microbiomes. However, little is known about the factors influencing host-virus interaction networks, especially when it comes to host factors. To close this gap, researchers constructed a host-provirus network out of over 7,000 species-level prokaryote genomes from many environments. Proviruses are virus genomes that have been integrated into the host genome, allowing researchers to detect them from available genomic datasets. Using this host-provirus network, the researchers then calculated the host interaction specialization, which quantifies how specialized a given host is in relation to the available interacting virus partners. Broadly, fast growing prokaryotes showed less virus specificity than slow growers. This negative growth rate-specialization relationship was widespread across the Earth’s microbiomes..."

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

Anchoring Phenomenon: Identical twins have the same DNA yet one was diagnosed with breast cancer and the other was not?? One about diabetes? Unit Essential Question: Why are some people diagnosed with diabetes and breast cancer while others are not?

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:

"Viruses are a critical component of biosphere and human ecosystems, directly influencing human health and disease and controlling the output of engineered ecosystems. Unfortunately for scientists studying them, most viral signals remain hidden in sequence datasets due to a lack of optimal identification tools. A new tool aims to make virus identification easier. VirSorter2 is a DNA and RNA virus identification tool that leverages genome-informed database advances to improve the accuracy and range of virus sequence detection. Compared with other tools, VirSorter2 performs more consistently with high accuracy across diverse viruses and minimized errors associated with atypical cellular sequences, including eukaryotic genomes and plasmids. VirSorter2 is also modular, allowing it to expand to newly discovered viruses through the design of new viral classifiers..."

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

In 2004, the Ansari X PRIZE for suborbital spaceflight captured the public's imagination and revolutionized an industry, leveraging a $10M prize purse into over $100M in innovation. Building from that success, the X PRIZE Foundation is now developing new prizes to focus innovation around "Grand Challenge" themes, including genomics, energy, healthcare, and education.
This course will examine the intersection of incentives and innovation, drawing on economic models, historic examples, and recent experience of the X PRIZE Foundation to help develop a future prize in Energy Storage Technologies.

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:

"Genetic testing companies hold data for tens of millions of consumers who have paid, online, for genetic information, without consulting a doctor. This information encodes more than just ancestry; it also captures aspects of wellbeing as well as traits or predispositions for which test quality is often poor. These private companies are strictly prohibited in France. But that hasn’t stopped French research teams from working with them, or French people from paying for illegal tests over the Internet. So how can France keep control over its own genetic data? Our solution is e-CohortE. Designed to achieve the same ends sought by genetic testing companies, but legally and more effectively, e-CohortEs would correspond to a specific and legal French research protocol of RIPH. RIPH sponsors currently address only a few questions on a single topic and then terminate a cohort..."

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