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 resistance is a growing problem worldwide—and in outer space. Spaceflight can promote biofilm formation and antimicrobial resistance development, and astronauts are especially vulnerable to infection due to the unique demands of spaceflight. To support future space travel, it is critical to understand exactly how spaceflight affects microbial diversity and virulence. To learn more, researchers recently used a machine learning algorithm to analyze sequencing data from the Microbial Tracking (MT)-1 mission, which sampled microbes at eight locations on the International Space Station during three flights. The model predicted the presence of hundreds of antibiotic resistance genes (ARGs) in the 226 bacterial strains isolated from the flights, including strains of the potentially very pathogenic bacterium Enterobacter bugandensis and the food poisoning-related bacterium Bacillus cereus..."

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:

"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.

Biology is designed for multi-semester biology courses for science majors. It is grounded on an evolutionary basis and includes exciting features that highlight careers in the biological sciences and everyday applications of the concepts at hand. To meet the needs of today’s instructors and students, some content has been strategically condensed while maintaining the overall scope and coverage of traditional texts for this course. Instructors can customize the book, adapting it to the approach that works best in their classroom. Biology also includes an innovative art program that incorporates critical thinking and clicker questions to help students understand—and apply—key concepts.

By the end of this section, you will be able to:Define genomicsDescribe genetic and physical mapsDescribe genomic mapping methods

By the end of this section, you will be able to:Describe three types of sequencingDefine whole-genome sequencing

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 skin is the interface between the human body and the environment, and the different features in distinct skin regions, such as different temperatures, humidity levels, gland densities, and pH values, create a variety of niches that can support a diverse skin microbiome. This microbiome includes bacteria, archaea, viruses, fungi, and even mites. A healthy skin microbiome helps maintain skin homeostasis, protects against pathogens, communicates with and trains the immune system, and affects wound healing. However, the skin microbiome can be influenced by many factors, including intrinsic factors like aging and extrinsic factors like cosmetic. Recent advances in molecular biology techniques and next-generation sequencing have drastically increased our understanding of the microorganisms that live on our skin, but the microbes are often still difficult to culture and study..."

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

This project-based laboratory course provides students with in-depth experience in experimental molecular genetics, using modern methods of molecular biology and genetics to conduct original research. The course is geared towards students (including sophomores) who have a strong interest in a future career in biomedical research. This semester will focus on chemical genetics using Caenorhabditis elegans as a model system. Students will gain experience in research rationale and methods, as well as training in the planning, execution, and communication of experimental biology.
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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:

"p53 is widely considered the most frequently mutated gene in human disease, including in cancer. Normally, p53 acts as a checkpoint for recognizing DNA damage and actually suppresses tumor formation. Alterations to p53 compromise this function and can make way for life-threatening tumor growth. A new study examined how abnormal p53 might create conditions favorable for one of the most aggressive forms of ovarian carcinoma. The authors of the study began by knocking the p53 gene out of ovarian carcinoma cells and monitoring the effects. Next-generation sequencing of the p53-less cells revealed significantly elevated expression of fibronectin, a structural protein linked to various carcinomas. Loss of p53 function also appeared to boost the cancer cells’ ability to migrate and spread. Data on actual patients with ovarian cancer confirmed the pattern observed in the lab..."

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:

"Cancer is a leading cause of mortality worldwide. Some types of cancer are linked to infection by viruses and bacteria, but many such links remain unexplored, indicating that other carcinogenic microbes are likely to exist. A recent study used a large, high-quality collection of 3025 whole-genome sequencing datasets to identify relationships between cancer, bacteria, and viruses. A custom-built pipeline based on the Kraken taxonomic sequence classification system software was used to identify bacterial and viral sequences in the datasets. A total of 3,534,707 read pairs matching 218 bacterial, viral, or phage species-level taxa were detected in tumor and matched healthy tissues. Of these, 27 taxa were identified to be linked to cancer. The findings support known associations between viruses, bacteria, and tumor and patient phenotypes and also reveal entirely new associations. For example, Pseudomonas spp..."

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 phylogeography is the study of diversification and distribution of microorganisms across space and time, offering unique insights into eco-evolutionary processes that influence the ubiquity and diversity of microbial populations in the environment. However, our understanding of microbes lags far behind that of macroorganisms, primarily because many dominant microorganisms are difficult to culture. A recent study evaluated the microbial phylogeography of one tiny inhabitant of freshwater ecosystems. Bacterioplankton are common to many freshwater ecosystems despite the fact that these habitats are geographically disconnected, and better understanding their microdiversity is key to uncovering the eco-evolutionary processes behind their dominance. Using long-read amplicon sequencing, researchers evaluated pelagic bacterioplankton assemblages in 11 deep freshwater lakes in Japan and Europe..."

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:

"Although the brain has always been viewed as a sterile organ, recent studies have suggested the existence of a ‘brain microbiome,’ perturbations of which could cause neuroinflammatory conditions. Unfortunately, experiments aimed at detecting a brain microbiome are limited by a low bacterial biomass. Bacteria must be detected through an overwhelming amount of host DNA, and the low biomass additionally raises the risk of amplifying exogenous contaminants. A recent study tested the hypothesis that there is a bacterial brain microbiome. Using 16S rRNA sequencing, researchers evaluated brain samples from healthy individuals and individuals suffering from Parkinson’s disease (PD), along with murine brains. They found that while amplicon sequencing detected bacterial signals in both human and murine brains, the estimated bacterial biomass was extremely low. Careful reanalysis suggested that bacterial signals were explained by exogenous DNA contamination and false-positive amplification of host DNA..."

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:

"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.

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:

"Much like the organisms that flood its instruments the microbiome research community is thriving. But researchers from the UK’s National Institute for Biological Standards and Control (NIBSC) say that it could be doing even better. They’ve developed the first reference reagents for microbiome DNA analysis, Gut-Mix-RR and Gut-HiLo-RR. It’s a move designed to promote standardization and reproducibility across the field of microbiome research as tests revealed drastic variations across shotgun sequencing taxonomic profilers, which could alter conclusions about interactions between different microbes . If researchers can reach a consensus on acceptable levels of errors and begin using the materials in their labs the reference reagents could help standardize downstream gut microbiome analyses. A large open-invite collaborative study for multiple laboratories is slated for later in 2020..."

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:

"Aquaculture is a critical industry for human food production, and strategies to improve fish nutrition while protecting the environment can help maximize aquaculture output and sustainability. However, the roles of the gut microbiome in fish nutrition are not well understood. To support further research, scientists recently developed SalmoSim, an in vitro model of the Atlantic salmon gut and microbiome. The researchers linked three bioreactors seeded with gut material from adult farmed salmon to simulate the stomach (S), pyloric caecum (PC), and midgut (MG). When a fishmeal “diet” (FMD) was supplied, SalmoSim’s microbial community stabilized in approximately 20 days and was ecologically indistinguishable from the real fish microbiome used to inoculate the system. Switching from the FMD to a fishmeal-free diet (FMF) for 20 days did not affect most microbes (operational taxonomic units, OTUs) in either SalmoSim or real salmon..."

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:

"The human microbiome is now known to play important roles in health and disease, but while microbiome research on European and North American populations has increased exponentially, African populations may be underrepresented. The relative lack of data could impair medical progress for Africans and obscure important treatment targets. To characterize the knowledge gaps, researchers recently searched the literature for next-generation sequencing studies published through April 1, 2020, that included African samples. Thirty-three out of 54 African countries were represented in the 168 studies found, primarily South Africa, Kenya, and Uganda. Only 26.8% of studies focused on diseases of significant public health concern in Africa. Among studies with intercontinental collaboration, the USA was the most common collaborator, and the first and last authors of most studies were not affiliated with African institutions. In addition, the primary funders were American or European institutions..."

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:

"When new viruses emerge, early detection is critical, but the detection of pathogens in clinical and environmental samples using high-throughput sequencing is often hampered by large amounts of background material. Enormous sequencing depth can be necessary to gain sufficient information to identify a certain pathogen. Now, a study demonstrates a new method to improve the sensitivity of viral diagnosis. Combining high-throughput sequencing with in-solution virus capture, researchers compiled a virus genome dataset for the design of a RNA-baits panel. The panel, called VirBaits, consists of about 178,000 RNA-baits based on over 18,000 complete viral genomes, targeting 35 epizootic and zoonotic viruses, including SARS-CoV-2. In a test of complex samples, viruses with both DNA and RNA genomes were enriched by anywhere from 10-fold to 10,000-fold, with enriched viruses having at least 72% overall identity shared with the viruses in the bait set..."

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:

"The rapid expansion of microbiome science has revealed much about the roles of microbes in health and disease. But the diversity of experimental tools available has made the reproducibility of microbiome studies a serious issue. To minimize bias during DNA extraction, researchers recently developed and tested WC-Gut RR—a whole-cell reference reagent specific to the gut microbiome. Built using 20 strains commonly found in the human gut, WC-Gut RR was designed to evaluate DNA extraction protocols used in microbiome pipelines. Researchers tested WC-Gut RR using 8 commercial DNA extraction kits, which revealed significant differences in, among other things, DNA yield, integrity, and purity. In addition, findings revealed that less complex reagents that do not feature anaerobic and hard-to-lyse strains can inflate the performance of microbiome DNA extraction kits..."

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:

"Colonic stem cells maintain a delicate balance with their surrounding microenvironment. This homeostasis is increasingly disturbed during colon cancer progression, which perpetuates the expansion and invasion of cancerous tissue. To decipher the interactions between colonic stem cells or tumor cells and their microenvironment, researchers examined Wnt signaling in cancer cell lines and patient-derived organoids. Wnt signaling is a major driver of stemness in epithelial cells in the colon and of colorectal cancer. Findings revealed that Wnt activity triggered the expression of the gene LARGE2, which in turn mediates the laminin-adhesive O-glycosylation of α-DG. The result was abnormally increased cellular adhesion to laminin during Wnt-driven cancer progression. While in vivo studies are needed to understand the disease relevance of this Wnt/LARGE2/α-DG axis, the observations could help researchers better understand colorectal cancer invasion and metastasis..."

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:

"Linked-read sequencing is helping microbiome researchers remove some of the ambiguities produced by short-read metagenomic sequencing, but how the parameters of linked-read sequencing affect metagenome assembly quality has remained unclear. Using simulated data, a mock community and real metagenomic data, a new study recommends best practices for linked-read sequencing of microbial genomes. Results showed that assemblies of medium-abundance microbes could be substantially improved by choosing a deep read depth. Indeed, selecting a read depth between 120X and 140X is recommended to optimize assembly quality. A tradeoff was observed between read depth per fragment and DNA fragment physical depth, with a deep read depth per fragment generating more high-quality bins. and DNA fragment physical depth controlling total assembly length..."

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