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:

"Pneumococcal bacteria (Streptococcus pneumoniae) can cause several different serious infections including pneumonia, sinusitis, and meningitis. Studies to monitor the levels of pneumococcal bacteria ‘carried’ by individuals are called carriage studies and are used to inform vaccination programs. But most carriage study techniques distinguish between pneumococcal subtypes based on their outside structure, or serotype, rather than by genetic strain. Consequently, little is known about strain-specific carriage and interactions between strains. To close this gap, researchers trialed a new workflow using single-molecule real-time (SMRT) sequencing of the genetic marker plyNCR. Tests using mock bacterial communities found that this workflow was sensitive and highly specific to S. pneumoniae. Banked nasal swabs collected from infants during their first year of life were used for a real-world test..."

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:

"Antibiotic treatment affects the gut microbiomes of different individuals to varying degrees. Such personalized responses may arise from differences in pretreatment microbiomes among individuals, but this possibility hasn’t been directly assessed in humans. To test this hypothesis, a recent study used high-throughput 16S rRNA sequencing to analyze 260 stool samples from 39 patients with acute myeloid leukemia. Each patient received multiple antibiotics during an approximately 4-week hospital stay for chemotherapy, and the samples were collected twice weekly. The results revealed that the microbe communities were more similar among samples from the same patient than among samples from different patients, suggesting that the communities maintained some continuity despite the heavy antibiotic treatment. Statistical analyses showed that the antibiotic-induced microbiome changes were dependent on the pretreatment microbiome compositions and identified 6 taxa that predicted the extent of the changes..."

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:

"In laying hens, the cecal microbiota is important for digestion and metabolism. However, it also produces hydrogen sulfide gas, an odorous and harmful pollutant that is released in large amounts from poultry houses. Host microRNAs (miRNAs) can regulate the gut microbiota, but whether they affect hydrogen sulfide production in hens is unclear. To clarify this issue, a recent study analyzed the cecal content of two laying hen breeds, Hy-line Gray and Lohmann Pink, with naturally different hydrogen sulfide production. Differential expression of several microbial genes was related to the difference in hydrogen sulfide production between breeds, miRNA-containing exosomes were present in the cecal contents, and the differentially expressed host miRNA gga-miR-222a regulated two of the altered microbial genes encoding methionine synthases. During in vitro fermentation, gga-miR-222a upregulated the two methionine synthase genes..."

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:

"Environmental pollution can have harsh effects on many systems in the body, but in addition to well-appreciated internal effects, pollutants can also harm our body’s outer barrier – our skin. Polyaromatic hydrocarbons (PAHs), organic molecules found in air pollution, can damage the skin. accelerating aging, altering skin pigmentation, and affecting pathways underlying acne and skin cancer. Unfortunately, exactly how PAH pollution harms the skin remains poorly understood. In a new study, researchers evaluated the cheek and scalp microbiota of over 200 individuals from two cities in China: one with high pollution levels and one with less PAH pollution. They found that individuals from the city with heavier pollution had higher PAH contamination of their skin, and certain bacteria were more prevalent in the high-PAH city, including some that contribute to skin conditions..."

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:

"High-throughput sequencing of bacterial DNA samples allows for rapid analysis of bacterial communities from many samples at once. However, the utility of these methods is limited for samples with few bacteria, or a low bacterial load, or those with large amounts of DNA from non-bacterial sources, such as a host. Often, both limitations are a problem in analyzing clinical samples. A recent paper proposes a modified preparation protocol to increase sensitivity in samples with intermediate or low bacterial loads. To test a wide range of bacterial loads, the researchers used repeat tracheal aspirate samples from intubated pediatric patients. The modified protocol detected sequence data from over 30% more samples than the standard protocol. Where both protocols had results, they returned similar levels of community diversity, and the composition of those communities was also similar..."

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:

"Soil and sediment microorganisms are remarkably diverse and are critical for ecosystem health. However, they are underrepresented in public databases, and assembling new metaproteomic datasets is challenging, which makes it difficult to characterize the microorganisms in specific soil samples. To increase the outputs of soil metaproteomic studies, a recent study compared various database construction strategies. Search strategies using either sample-specific metagenomic databases or public databases produced comparable peptide-spectrum matches for a floodplain soil core. However, a two-step cascaded search combining both types of databases led to greater peptide-spectrum matching. The combination strategy also improved functional annotation of the peptides, and the resulting metaproteome (MetaP) annotations correlated well with the metagenome (MetaG) annotations..."

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:

"Immunotherapy is one of the most powerful weapons for fighting cancer. This approach re-activates the anti-tumor activity of compromised immune cells, but one glaring weakness is that it can over-activate the immune system, leading to adverse events that can range from mild headache to anaphylaxis. That has some researchers turning to the gut for solutions. The intestinal microbiome is a complex ecosystem that regulates our physiology and psychology, both in health and in diseases such as cancer. Growing evidence suggests that certain microbes could be harnessed to boost anti-cancer immunotherapies. These microbes could secrete molecules that promote the spread of immune cells that target tumors or enhance immune cells’ ability to recognize cancer. Bolstered by recent advancements in sequencing techniques, microbiome research could be the perfect complement to cancer immunotherapy..."

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:

"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.

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:

"Advances in genomic laboratory and bioinformatics techniques have allowed us to infer microbial ecology information from genomes. This ability has led to great advances in microbiome science; however, there is not yet a standard comprehensive workflow for functional annotation. Some software tools annotate metabolic functions, but the new tool 'METABOLIC' improves upon this and expands into biogeochemical pathways like the carbon cycle. METABOLIC takes sequence inputs from isolates, metagenome-assembled genomes, or single-cell genomes. The data can be processed through two workflow scales: genome and/or community. The genome-scale workflow annotates the genomes and validates motifs of conserved protein residues. It also analyzes metabolic pathways and calculates the microbial contributions to individual biogeochemical processes and cycles. The community-scale workflow adds to this by first determining the genome abundance in the microbiome..."

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:

"Deep shale formations underlie most of North America and are typically inhospitable to microbial life. However, hydrologic fracturing of shale creates space and injects moisture and nutrients into the system, thus allowing new microbial communities to form. These communities can cause problems by corroding infrastructure and souring the hydrocarbon steam. Understanding the behavior of these microbial communities could lead to better management techniques. Recently, researchers examined the microbial genomes and metabolic capacity of fractured shale wells in Oklahoma, USA. Oklahoma shale is much hotter and has lower salinity than the previously characterized formations in the eastern USA. This study found that the Oklahoma formations had greater microbial taxonomic and metabolic diversity than the eastern formations. Sampling over time revealed that this microbial community broke down complex polymers from the fracturing process and used them for nutrients..."

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:

"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.

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:

"Phosphorus is essential for life to function. It is a critical component of the energy metabolism molecules, genetic materials, and cell structures of all life. Phosphorus only enters natural ecosystems through the slow weathering of stone. Then microbes help maintain and regulate phosphorus by cycling it between its organic and inorganic forms. Understanding microbial phosphorus cycling is critical to many fields of study, like ecology and agriculture. However, researchers lack a comprehensive understanding of the phosphorus cycling genes microbes use, but the recently developed curated phosphorus cycling database (PCycDB) could help close that gap. PCycDB covers 10 phosphorus metabolic processes and 139 gene families, including several that have been missed elsewhere. Testing PCycDB with simulated datasets revealed high annotation accuracy, positive predictive value, sensitivity, specificity, and negative predictive value..."

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:

"Cyanobacteria blooms in freshwater ecosystems are difficult to predict and can be harmful to humans and animals. Microcystis is a genus of cyanobacteria that can cause these toxic blooms. They form close associations with heterotrophic bacteria - their microbiome, but the details of these associations are not well understood. To examine this relationship, researchers characterized the genetic diversity of over 100 Microcystis colonies. They identified 18 distinct Microcystis genotypes. The genetic diversity was greater between colonies than within them, suggesting that Microcystis forms colonies via clonal expansion. Each Microcystis genotype had its own microbiome composition and related genotypes had similar microbiomes. Two of the nine most prevalent colony-associated bacteria genera, Roseomonas and Rhodobacter, showed strong signs of co-phylogeny with Microcystis. These closely associated bacteria may be expanding the metabolic capabilities of Microcystis..."

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

A rubric in student language written for elementary students to self-assess the retelling of a story.

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:

"Designer rootstocks enable fruit trees to thrive under otherwise unbearable conditions, providing strong anchorage and defending against biological and nonbiological stressors. But what role does the root microbiome play in this assistive act? To find out, researchers used 16S rRNA sequencing to examine the rootstocks of Valencia orange trees in Florida. Results showed that the genetic makeup of different rootstocks determined how the root microbiome responded to compost treatment. The aspects of the root microbiome that were rootstock- specific included bacterial abundance, diversity, and community composition. These findings suggest that specific bacteria drive changes in nutrient concentrations accessed by different rootstocks. Understanding this intimate relationship is important to supporting overall plant health and could inspire research into how root microbes might affect other parts of trees..."

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:

"A team at Stanford and Southampton Universities has discovered a new set of mutations that could explain why certain people have inflammatory bowel disease, or IBD. While the mutations are rare, they point to an important role for a family of so-called chaperone proteins, which help other proteins fold properly in cells, and offer new ways to treat the disease. IBD is an autoimmune disease characterized by inflammation of the gastrointestinal tract, and comes in two common forms: Crohn’s disease and ulcerative colitis. Patients usually suffer from abdominal pain and diarrhea. In severe cases, people can’t absorb enough nutrients, and the condition becomes life-threatening. While environmental factors play a role, so do genes. Scientists have identified more than 160 positions in the genome where variants can increase the risk of developing the disease. But they still explain just a fraction of the genetic contribution..."

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:

"Freshwater salinization, which can be caused by saltwater intrusion, urbanization, and climate change, is becoming an extensive global environmental problem. Microeukaryotic plankton are key components of aquatic ecosystems and play significant ecological roles. However, few studies have investigated the influences of small salinity shifts on microeukaryotic plankton community assembly and co-occurrence networks in inland freshwaters. In a recent study, researchers used high-throughput sequencing to analyze microeukaryotic plankton communities in a subtropical urban reservoir. They found that increasing salinity altered the community composition and led to a significant decrease in plankton diversity. The salinity changes influenced the microeukaryotic plankton community assembly primarily by regulating the deterministic-stochastic balance. The core plankton sub-network had greater robustness at low salinity levels, while the satellite sub-networks had greater robustness at medium/high salinity levels..."

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

These lesson plans and activities were purposed and designed by Paula Turon Loren for Kindergarden English teachers in the United Kingdom. The activity is designed and differentiated for different ability groups, thus teachers can adapt the lesson to their students levels and needs. Moreover, the materials may be used and adapted for any country's specific context. 

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:

"What constitutes a healthy genitourinary microbiome? We’re not exactly sure, which can make diagnosing UTIs difficult, especially when conventional tests reveal nontraditional pathogens or low bacteria levels in urine from patients experiencing symptoms. To learn more about healthy microbiome states, researchers recently used shotgun metagenomics to characterize the urinary microbial profiles of 30 asymptomatic volunteers. The microbial taxonomic groups and functions fluctuated over time, indicating the dynamic nature of the microbiome. The researchers also compared the asymptomatic profiles to urine samples from 122 patients with UTI symptoms. Interestingly, most of the suspected-UTI profiles overlapped with the asymptomatic profiles. In addition, suspected-UTI samples with insignificant or no culture growth had WBC counts indicating inflammation, suggesting that bacterial presence alone doesn’t explain the onset of clinical UTI symptoms..."

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.