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Aseptic Technique in Environmental Science

JoVE 10040

Source: Laboratories of Dr. Ian Pepper and Dr. Charles Gerba - Arizona University
Demonstrating Author: Luisa Ikner


Aseptic technique is a fundamental skill widely practiced in the field of environmental microbiology that requires a balance of mindfulness and practice in the laboratory. Proper use of this technique reduces the…

 Environmental Microbiology

Recombineering and Gene Targeting

JoVE 5553

One of the most widely used tools in modern biology is molecular cloning with restriction enzymes, which create compatible ends between DNA fragments that allow them to be joined together. However, this technique has certain restrictions that limit its applicability for large or complex DNA construct generation. A newer technique that addresses some of these shortcomings…

 Genetics

Molecular Cloning

JoVE 5074

Molecular cloning is a set of methods, which are used to insert recombinant DNA into a vector - a carrier of DNA molecules that will replicate recombinant DNA fragments in host organisms. The DNA fragment, which may be a gene, can be isolated from a prokaryotic or eukaryotic specimen. Following isolation of the fragment of interest, or insert, both the vector and insert must be cut with…

 Basic Methods in Cellular and Molecular Biology

Decontamination for Laboratory Biosafety

JoVE 10399

Robert M. Rioux and Zhifeng Chen, Pennsylvania State University, University Park, PA


Decontamination is essential for laboratory biosafety, as the accumulation of microbial contamination in the laboratory can lead to the transmission of disease. The degree of decontamination can be classified as either disinfection or sterilization.…

 Lab Safety

What is the Immune System?

JoVE 10895

The immune system comprises diverse biological structures and processes that protect the body from disease. These processes can be classified into innate and adaptive immunity. To work effectively, the immune system needs to detect pathogens by distinguishing the body’s own structures from foreign elements. If this determination fails, autoimmune diseases occur in which the immune system reacts against the body’s own tissue. The innate immune system is the first line of defense against infection. It comprises physical barriers and a variety of cells that act quickly and non-specifically against elements that are foreign to the host (i.e., non-self). Examples of physical barriers in mammals are skin, the lining of the gastrointestinal tract, and secretions, such as mucus or saliva. Once an invader overcomes physical barriers, cells of the inflammatory response are recruited to the entry site: mast cells release a plethora of chemicals that attract other cells of the innate immune system and activates the adaptive immune system. Phagocytic cells, such as neutrophils and macrophages, ingest and destroy pathogens. Natural killer cells, a special type of white blood cell, destroy virus-infected cells. Together, cells of the innate immune system eradicate the invader or hinder its spread, and activate the adaptive immune system. How can an organism

 Core: Biology

Complementary DNA

JoVE 10818

Only genes that are transcribed into messenger RNA (mRNA) are active, or expressed. Scientists can, therefore, extract the mRNA from cells to study gene expression in different cells and tissues. The scientist converts mRNA into complementary DNA (cDNA) via reverse transcription. Because mRNA does not contain introns (non-coding regions) and other regulatory sequences, cDNA—unlike genomic DNA—also allows researchers to directly determine the amino acid sequence of the peptide encoded by the gene. cDNA can be generated by several methods, but a common way is to first extract total RNA from cells, and then isolate the mRNA from the more predominant types—transfer RNA (tRNA) and ribosomal (rRNA). Mature eukaryotic mRNA has a poly(A) tail—a string of adenine nucleotides—added to its 3’ end, while other types of RNA do not. Therefore, a string of thymine nucleotides (oligo-dTs) can be attached to a substrate such as a column or magnetic beads, to specifically base-pair with the poly(A) tails of mRNA. While mRNA with a poly(A) tail is captured, the other types of RNA are washed away. Next, reverse transcriptase—a DNA polymerase enzyme from retroviruses—is used to generate cDNA from the mRNA. Since, like most DNA polymerases, reverse transcriptase can add nucleotides only to the 3’ end of a chain, a pol

 Core: Biology

The Roles of Bacteria and Fungi in Plant Nutrition

JoVE 11104

Plants have the impressive ability to create their own food through photosynthesis. However, plants often require assistance from organisms in the soil to acquire the nutrients they need to function correctly. Both bacteria and fungi have evolved symbiotic relationships with plants that help the species to thrive in a wide variety of environments.

The collective bacteria residing in and around plant roots are termed the rhizosphere. These soil-dwelling bacterial species are incredibly diverse. Though some may be pathogenic, most have roles in promoting plant health. In exchange, the bacteria receive nutrition from plants in the form of carbohydrates, amino acids, and nucleic acids. The bacteria called rhizobacteria can protect plants by producing antibiotics or absorbing toxic metals in the soil. Additionally, bacteria help plants by accessing otherwise unusable stores of nutrients in the soil. For example, plants lack the molecular machinery to utilize nitrogen from the atmosphere directly. Instead, they take up nitrogen in the form of ammonium (NH4+) and nitrate (NO3- ), which is generated by soil-residing bacteria. During a process called nitrogen fixation, soil-dwelling bacteria convert atmospheric nitrogen to ammonia. Nitrogen-fixation requires large amounts of ATP that bacteria derive from plant-provided carbohydrates. Other groups of bacter

 Core: Biology

What is an Ecosystem?

JoVE 10926

An ecosystem is the interaction between all abiotic and biotic factors in an environment and can be classified as terrestrial or aquatic. Terrestrial ecosystems are categorized based on the climate, including annual temperature, rainfall, and seasonality. Aquatic ecosystems are separated further into freshwater and marine, and then by depth, which influences water temperature and the amount of sunlight that penetrates the water. Terrestrial ecosystems are classified into biomes, characterized by both the climate of the environment and the types of organisms that live there. Areas near the Earth’s equator that exhibit high, aseasonal temperatures and high quantities of annual rainfall are rainforests and house some of the most diverse habitats in the world. Ecosystems with high temperatures but deficient annual rainfall are deserts. Although desert ecosystems share these characteristics, their biodiversity can vary vastly. On the other side of the spectrum, the ecosystem with very low annual temperatures and low annual rainfall is the arctic biome. This ecosystem has the lowest biodiversity. Between these three major biomes are the seasonal tundra, temperate grassland and savanna ecosystems. These ecosystems exhibit oscillatory annual changes in both temperature and rainfall and harbor animals and plants specifically adapted to those seasonal changes.<

 Core: Biology

Cross-reactivity

JoVE 10900

The ability of a single antibody to recognize multiple structurally similar epitopes is an important immune defense strategy that enables the host to efficiently defend against many potentially threatening pathogens. However, cross-reactivity also elicits allergy symptoms against related allergens. It is increasingly important to understand the principles of cross-reactivity, as antibodies are actively being developed as therapeutic modalities for diverse diseases, including cancer. Antibodies can initiate an immune response by binding to specific structures on the surface of pathogens or other foreign elements. By definition, anything that is bound by an antibody, and subsequently elicits an immune response, is called an antigen. Often, antigens are proteins on the surface of viruses, bacteria, fungi, and protozoan invaders. The specific sequence of amino acids that is recognized by the antibody is called an epitope. Most epitopes are only 5-6 amino acids long. As such, a single antigen may present several distinct epitopes. Cross-reactivity occurs when two distinct epitopes are structurally similar, and hence are recognized by the same antibody. A major benefit of antibody cross-reactivity is that it provides cross-protective immunity to related pathogens. When a circulating antibody recognizes a viral or bacterial pathogen that it has encountered previ

 Core: Biology

What are Viruses?

JoVE 10821

A virus is a microscopic infectious particle that consists of an RNA or DNA genome enclosed in a protein shell. It is not able to reproduce on its own: it can only make more viruses by entering a cell and using its cellular machinery. When a virus infects a host cell, it removes its protein coat and directs the host’s machinery to transcribe and translate its genetic material. The hijacked cell assembles the replicated components into thousands of viral progeny, which can rupture and kill the host cell. The new viruses then go on to infect more host cells. Viruses can infect different types of cells: bacteria, plants, and animals. Viruses that target bacteria, called bacteriophages (or phages), are very abundant. Current research focuses on phage therapy to treat multidrug-resistant bacterial infections in humans. Viruses that infect cultivated plants are also highly studied since epidemics lead to huge crop and economic losses. Viruses were first discovered in the 19th century when an economically-important crop, the tobacco plant, was plagued by a mysterious disease—later identified as Tobacco mosaic virus. Animal viruses are of great importance both in veterinary research and in medical research. Moreover, viruses underlie many human diseases, ranging from the common cold, chickenpox, and herpes, to more dangerous infection

 Core: Biology
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