Lignocellulose digestion in Protaetia brevitarsis: a tightly designed microbial production line

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: "Domesticated edible insects are a sustainable protein source that has been gaining global attention. P. brevitarsis is one such species, and their larvae can also eat decaying organic waste and turn it into a plant-growth promoting mixture. But organic matter like this is high in lignocellulose, which is difficult to digest. In fact, these larvae lack the enzymes needed to break lignocellulose down on their own. So, researchers checked their microbiome for microbial genes able to fill in the gaps. The researchers established a comprehensive reference catalog of gut microbial and host genes. Between the two sets of genes, lignocellulose-degrading enzymes were abundant and highly diversified. P. brevitarsis larvae also selectively enriched their microbiome for lignocellulose-degrading microbes and had physiological adaptations that assisted in lignocellulose degradation..." The rest of the transcript, along with a link to the research itself, is available on the resource itself.

Material Type: Diagram/Illustration, Reading

Amping up the AMPK/SR-A1 pathway can reduce chemo-induced nerve pain

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: "Many patients undergoing chemotherapy for cancer develop a serious side effect called chemotherapy-induced peripheral neuropathy (CIPN). CIPN involves pain, tingling, burning, or numbness in the hands and feet and is caused by neuroinflammation triggered by the protein HMGB1, but the exact mechanisms aren’t clear. To learn more and help find a treatment, researchers recently examined the plasma of human patients and mice with oxaliplatin-induced CIPN. They found that the levels of HMGB1 and its target enzyme MMP-9 (a pain marker) were elevated in CIPN plasma and that a higher dose of oxaliplatin was associated with higher HMGB1 levels and worse pain. In cell experiments, HMGB1 was degraded—and inflammatory molecule expression was suppressed—when the enzyme AMPK was activated suggesting that AMPK activation might be beneficial for CIPN. These effects were dependent on the protein SR-A1..." The rest of the transcript, along with a link to the research itself, is available on the resource itself.

Material Type: Diagram/Illustration, Reading

Microbiome-produced lactic acid promotes cervical/vaginal epithelial barrier integrity

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: "Women with a Lactobacillus-dominated cervical/vaginal microbiome have a reduced risk of acquiring sexually transmitted infections (STIs). including HIV infection. However, the protective mechanisms of Lactobacillus species are unclear. To learn more, researchers recently bulk-analyzed the proteins in vaginal swabs from 113 young South African women. Compared to women with Lactobacillus-depleted microbiomes, women with Lactobacillus-dominated vaginal microbiomes had higher levels of bacterial lactate dehydrogenase an important lactic acid–producing enzyme. In addition, the abundance of this enzyme was associated with the abundance of epithelial barrier proteins suggesting that lactate dehydrogenase is directly related to the physical barrier function of cervicovaginal tissue. Similarly, in cultured cervicovaginal epithelial cells, physiologically relevant concentrations of lactic acid improved epithelial barrier integrity and increased the expression of molecules that “glue” barrier cells together..." The rest of the transcript, along with a link to the research itself, is available on the resource itself.

Material Type: Diagram/Illustration, Reading

Fungi decompose proteins in the world's oceans

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: "Terrestrial fungi are well known as decomposers, breaking down dead matter to return nutrients to the soil. However, the roles of fungi in the ocean are less well understood. Oceanic fungi occur with other microbes throughout the water column, where they break down carbohydrates. A recent study examined the role of these marine fungi in recycling proteins, which represent more than half of living and dead marine biomass. Researchers performed a multi-omics analysis of all oceanic fungal-affiliated enzymes that break down proteins (peptidases). They found that the abundance, diversity, and expression of fungal peptidases increased with ocean depth, similar to fungal carbohydrate-degrading enzymes (CAZymes). This indicates a strong link between the carbon and nitrogen cycles in the open ocean. In-depth analysis of the most widely utilised fungal proteases revealed that the majority of pelagic fungal communities are dominated by saprotrophy rather than parasitism..." The rest of the transcript, along with a link to the research itself, is available on the resource itself.

Material Type: Diagram/Illustration, Reading

Do not enter: TRIM protein prevents white spot syndrome virus from invading crayfish cells

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: "White spot syndrome virus (WSSV) is the most destructive virus in crustacean aquaculture, causing huge economic losses. Preventing the initial entry of the virus into host cells is likely the most economical way to control WSSV infection. However, the exact mechanism of virus invasion isn’t clear. To learn more, researchers recently investigated how WSSV evades the host immune system in the crayfish Procambrus clarkii. They found that the enzyme TRIM was significantly upregulated in WSSV-infected crayfish. A recombinant TRIM protein inhibited WSSV replication in the crayfish, while blocking TRIM promoted it, suggesting that this enzyme plays a protective role. Further experiments revealed that TRIM interacts with the viral protein VP26. This interaction keeps the host protein AP-1 from entering the nucleus and driving the expression of dynamin. Without dynamin, WSSV can’t enter the host cell via membrane vesicles..." The rest of the transcript, along with a link to the research itself, is available on the resource itself.

Material Type: Diagram/Illustration, Reading

Lab Manual: Introduction to Biotechnology

This well-organized lab manual is housed in LibreTexts and each of the 21 labs begins by listing goals and student learning outcomes. Each lab contains useful images and highlights important equations and examples. The laboratory topics include basic lab skills and topics such as safety, metrics & measurements, pipetting, microscopy, spectrophotometry, making buffers and measuring pH, DNA and protein gel electrophoresis, PCR, ELISA, performing restriction enzyme digests and transformation, and Good Manufacturing Practices (GMP). This lab manual provides specific directions as to how students should organize their corresponding laboratory notebook and each lab asks students specific conclusion questions that they are supposed to answer in their lab notebook.

Material Type: Activity/Lab, Textbook

Author: Orange County Biotechnology Education Collaborative

Microbial Megaproducers: Discovery, Biosynthesis, Engineering and Applications of Natural Products

The natural world is a mega-factory of small molecules, peptides, fatty acids, phospholipids, and a host of other compounds, known as natural products (NPs). Immensely diverse in structure and function, NPs have strongly influenced how we treat infectious disease, cancer, pain, and a host of other conditions. Roughly half of the drugs that have been approved in the past 30 years are NPs, derivatives of NPs or NP-inspired. In this discussion-based course, we will delve into research on discovering NPs from producing organisms, investigating the biochemistry of NP production, and using synthetic biology to create NP derivatives—all with a particular emphasis on how genomic data guides and informs all these studies. This course is one of many Advanced Undergraduate Seminars offered by the Biology Department at MIT. These seminars are tailored for students with an interest in using primary research literature to discuss and learn about current biological research in a highly interactive setting. Many instructors of the Advanced Undergraduate Seminars are postdoctoral scientists with a strong interest in teaching.

Material Type: Full Course

Authors: Hetrick, Kenton, Ulrich, Emily

Biological Chemistry I

This course examines the chemical and physical properties of the cell and its building blocks, with special emphasis on the structures of proteins and principles of catalysis, as well as the chemistry of organic / inorganic cofactors required for chemical transformations within the cell. Topics encompass the basic principles of metabolism and regulation in pathways, including glycolysis, gluconeogenesis, fatty acid synthesis / degradation, pentose phosphate pathway, Krebs cycle and oxidative phosphorylation. Course Format This OCW Scholar course, designed for independent study, is closely modeled on the course taught on the MIT campus. The on-campus course has two types of class sessions: Lectures and recitations. The lectures meet three times each week and recitations meet once a week. In recitations, an instructor or Teaching Assistant elaborates on concepts presented in lecture, working through new examples with student participation, and answers questions. MIT students who take the corresponding residential class typically report an average of 10–15 hours spent each week, including lectures, recitations, readings, homework, and exams. All students are encouraged to supplement the textbooks and readings with their own research. The Scholar course has three major learning units, called Modules. Each module has been divided into a sequence of lecture sessions that include: Textbook Readings Lecture Notes or Storyboards A video by Professor JoAnne Stubbe or Professor John Essigmann Problem Sets and solutions To help guide your learning, each of these problem sets are accompanied by Problem Solving Videos where Dr. Bogdan Fedeles solves one of the problems from the set.

Material Type: Full Course

Authors: Essigmann, John, Fedeles, Bogdan, Stubbe, Joanne

Single-Molecule Imaging: Capturing Nanoscale Cellular Machines in Action

Did you know that we have approximately 2 meters of DNA packed in our cells, which are less than 10 μm diameter? Or that to replicate DNA it is copied at a rate of 70,000 basepairs per second by a cellular apparatus that coordinates at least six different enzymes? Or that microtubules form greater than 1 meter long “railways” upon which molecular machines transport cargo within nerve cells? In this course, we will explore how single-molecule imaging techniques capture the mega-cellular machines working in real-time. This course is one of many Advanced Undergraduate Seminars offered by the Biology Department at MIT. These seminars are tailored for students with an interest in using primary research literature to discuss and learn about current biological research in a highly interactive setting. Many instructors of the Advanced Undergraduate Seminars are postdoctoral scientists with a strong interest in teaching.

Material Type: Full Course

Author: Kose, Hazal

Improved assay for quantifying citrullinated histones as markers of disease

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: "Neutrophil extracellular traps, or NETs, are stringy chromatin networks that are ejected from immune cells to capture and neutralize harmful pathogens. But over-casting NETs can be indicative of disease, including cancer and thrombosis. As a result, NETs have become a promising non-invasive biomarker, and one way to quantify these networks is by detecting a critical component of NETs— histones whose arginine residues have been converted to citrulline, or H3Cit. These assays use antibodies to measure H3Cit in patient plasma, but a recent study shows that existing assays are limited by two important factors: Part of the problem is that available antibodies to H3Cit display low specificity, poor signal-to-noise, and lot variability. The second issue is that these assays are calibrated using enzymatically citrullinated, free histone peptides, which are unstable in human plasma and produce variable performance between batches..." The rest of the transcript, along with a link to the research itself, is available on the resource itself.

Material Type: Diagram/Illustration, Reading

Biochemistry Laboratory

The course, which spans two thirds of a semester, provides students with a research-inspired laboratory experience that introduces standard biochemical techniques in the context of investigating a current and exciting research topic, acquired resistance to the cancer drug Gleevec. Techniques include protein expression, purification, and gel analysis, PCR, site-directed mutagenesis, kinase activity assays, and protein structure viewing. This class is part of the new laboratory curriculum in the MIT Department of Chemistry. Undergraduate Research-Inspired Experimental Chemistry Alternatives (URIECA) introduces students to cutting edge research topics in a modular format. Acknowledgments Development of this course was funded through an HHMI Professors grant to Professor Catherine L. Drennan.

Material Type: Full Course

Author: Taylor, Elizabeth

Turning Evolutionary Dials: Directed Evolution Techniques for Climate Change and Beyond

This course will cover the many ways in which we have realized evolution in the laboratory toward functional biomolecules, such as protein and nucleic-acid-based therapeutics, enzymes that catalyze production of synthetic drugs, and carbon-dioxide capture molecules to lessen the impact of climate change. Students will both become familiar with the field of directed molecular evolution and learn how to critically analyze primary research papers, design research experiments, and present data relating to molecular biology and evolution. The importance of directed evolution in biomedical and biotechnological careers, both academic and industrial, will be highlighted. This course is one of many Advanced Undergraduate Seminars offered by the Biology Department at MIT. These seminars are tailored for students with an interest in using primary research literature to discuss and learn about current biological research in a highly interactive setting. Many instructors of the Advanced Undergraduate Seminars are postdoctoral scientists with a strong interest in teaching.

Material Type: Full Course

Authors: Kizer, Megan, Wilson, Robbie

BIO181 General Biology I (4 Credit Hours)

Biological principles emphasizing structure and function at the molecular, cellular, and organismal levels of biological systems. Secondary school chemistry is strongly recommended. Primarily for biology majors and pre professional students in health-related fields.Required Text:    Biology 2nd Edition - OpenStax.orgLinks to an external site. - The textbook is free to download and is always available in the left navigation of your Canvas course.  Please see the getting started module for more information on how the textbook will be used in the course.    ISBN-10: 1-947172-52-2    ISBN-13: 978-1-947172-52-4BIO 181 Course Content:    Scientific Method    Basic chemistry and biological macromolecules    Organization of cells    Energy and Enzymes    Photosynthesis    Cellular respiration    Cell division    Genetics    Gene expression and regulation    Gene technology    Data collection and analysis

Material Type: Full Course

Author: Micah Weedman

Understanding the many functions of wood-degrading bacteria in the termite gut

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 termite gut is the world’s smallest bioreactor and the most efficient system for breaking down biomass. To learn how this mini-digester might one day be scaled up to a technologically meaningful level, researchers examined the structure and function of the gut microbiomes from 11 termite genera which were grouped by diet into plant-fiber feeders and soil feeders. Both groups had similar bacterial flora. But subtle differences did emerge, with each termite species harbouring a unique set of genes encoding for breaking down plant biomass. Future metagenomics studies could help refine the specific functions of different bacterial genes within the termite gut, allowing for better insight into the termite–bacteria relationship and teasing out capabilities that could help bring these microscopic reactors to the macroscale..." The rest of the transcript, along with a link to the research itself, is available on the resource itself.

Material Type: Diagram/Illustration, Reading

Parabacteroides-derived acetate alleviates heparanase-exacerbated pancreatitis

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: "Acute pancreatitis, which affects more than 34 out of every 100,000 people, is usually mild. However, some cases worsen rapidly, leading to hospitalization and even death. Acute pancreatitis is promoted by the enzyme heparanase and appears to be regulated by the gut microbiota, but the mechanisms and potential interplay of these factors are unknown. A recent study investigated these issues in mice with caerulein (Cn)-induced acute pancreatitis. Compared with wild-type (WT) mice, heparanase-overexpressing (Hpa-Tg) mice exhibited worse disease with neutrophil infiltration and had a different gut microbiota composition, but microbiota depletion and microbiota transfer between the groups attenuated heparanase’s aggravating effect, indicating that the effect was gut microbiome-dependent..." The rest of the transcript, along with a link to the research itself, is available on the resource itself.

Material Type: Diagram/Illustration, Reading

Distribution of bacterial genes driving dimethyl sulfide cycling in the polar oceans

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: "Dimethyl sulfide (DMS) is a gas produced by bacteria and algae that gives the ocean its distinctive scent. It also plays an important role in cloud formation, leading scientists to think its production may be instrumental in regulating climate change. But sea ice melt in the polar oceans under global warming has led to a reduction in DMS production, which may further intensify climate warming. To gain a better understanding of how bacteria contribute to DMS production, scientists recently investigated the distribution of bacterial genes involved in DMS cycling in seawater samples collected from around the world. They found evidence that intense DMS cycling facilitated predominantly by Alphaproteobacteria and Gammaproteobacteria occurs in the Arctic and Antarctic oceans, with high involvement of the enzymes DMSP demethylase, DMSP lyases, and trimethylamine monooxygenase..." The rest of the transcript, along with a link to the research itself, is available on the resource itself.

Material Type: Diagram/Illustration, Reading

Actinobacteria play a key role in plant residue decomposition

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: "Actinobacteria are some of the most widely distributed bacteria in soils and are well known for their ability to degrade plant residues in pure culture in the laboratory. Yet, despite the importance of microbe-driven decomposition to carbon sequestration in terrestrial systems, their importance and specific activity across diverse environments in the field are unknown. Researchers recently evaluated the ecophysiological roles of Actinobacteria in rice straw residue decomposition in a series of field and microcosm experiments. They found that although Actinobacteria represented only 4.6% of the total bacterial abundance, they encoded 16% of the total carbohydrate-active enzymes (CAZymes) involved in the breakdown of carbohydrates. The researchers also found that Actinobacteria taxonomic and functional compositions were relatively stable during straw decomposition and that the importance of Actinobacteria in decomposition increased as soil fertility decreased..." The rest of the transcript, along with a link to the research itself, is available on the resource itself.

Material Type: Diagram/Illustration, Reading

SOD1 protects neurons from a cycad neurotoxin via the Na⁺/Ca²⁺ exchanger protein NCX1

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: "Amyotrophic lateral sclerosis (ALS) is a devastating, fatal neurodegenerative disease. One of the likely mechanisms of ALS degeneration is a calcium (Ca²⁺) imbalance in neurons. The neurotoxin L-BMAA causes ALS-like symptoms, likely by causing a Ca²⁺ ‘leak’ in the endoplasmic reticulum (ER) leading to cell stress and death. The enzyme SOD1 and its non-metallated form ApoSOD1 can prevent cell death from L-BMAA. Both forms of SOD1 do this by rapidly increasing the concentration of Ca²⁺ in the ER, but the intermediary mechanism is not yet understood. However, a recent study suggested that the sodium/calcium ion (Na⁺/Ca²⁺) exchanger protein, NCX1, mediates this increase in Ca²⁺ concentration. Both forms of SOD1 activated NCX1 in its ‘reverse mode’ where it pumps Ca²⁺ back into the ER, counteracting the leak. This was likely achieved by a prior SOD1-induced increase in the Na⁺ concentration..." The rest of the transcript, along with a link to the research itself, is available on the resource itself.

Material Type: Diagram/Illustration, Reading

Protein phosphatases in TLR signaling

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 activation of toll-like receptors (TLRs) is critical to detecting potentially harmful microbes, but overactivation can be life-threatening, leading to autoimmune and inflammatory diseases. While much research has been dedicated to positive regulators of TLR signaling, such as protein serine/threonine kinases, much less has focused on phosphatases, which counterbalance and limit TLR signaling. Fortunately, a growing number of studies are exploring the roles of these enzymes and how they might be harnessed to prevent excessive immune activation. Two important families of protein phosphatases are phospho-protein phosphatases (PPPs) and metal-dependent protein phosphatases (PPMs). PPPs contain a highly conserved catalytic core domain, which can combine with regulatory subunits to home in on specific enzymatic targets. PPMs, on the other hand, rely on magnesium or manganese ions and do not form multi-subunit complexes..." The rest of the transcript, along with a link to the research itself, is available on the resource itself.

Material Type: Diagram/Illustration, Reading

Role of tyrosine kinases in bladder cancer progression

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: "Bladder cancer is the 10th most frequent malignancy in the world. Despite the availability of several treatment options, including surgery, chemotherapy, and radiotherapy, outcomes for patients with bladder cancer remain poor. Fortunately, a growing understanding of the molecular origins of the disease is revealing new targets for treatment. Among the most promising are a family of enzymes called tyrosine kinases. Tyrosine kinases modify the structure and function of tyrosine-containing proteins. This action helps regulate cellular processes such as growth, migration, differentiation, and metabolism. Dysregulation of tyrosine kinases is part of the pathway that leads to signs and symptoms of bladder cancer. Abnormal tyrosine kinase function can be caused by mutations, amplification, and chromosomal abnormalities. Ongoing studies are discovering how tyrosine kinases can serve as early markers of bladder cancer and how they might be manipulated to stop the progression of bladder tumors..." The rest of the transcript, along with a link to the research itself, is available on the resource itself.

Material Type: Diagram/Illustration, Reading