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6.8: References - Biology

6.8: References - Biology


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Brachmann CB, Davies A, Cost GJ, Caputo E, Li J, Hieter P & Boeke JD (1998) Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruptions and other applications. Yeast 14: 115-132.

D’Andrea R, Surdin-Kerjan Y, Pure G, & Cherest H (1987) Molecular genetics of met17 and met 25 mutants of Saccharomyces cerevisiae: intragenic complementation between mutations of a single structural gene. Mol Gen Genet 207: 165-170.

Masselot M & DeRobichon-Szulmajster H (1975) Methionine biosynthesis in Saccharomyces cerevisiae. I. Genetical analysis of auxotrophic mutants. Mol Gen Genet 139: 121-132.

Sherman F (2002) Getting started with yeast. Method Enzymol 350: 3-41.
Thomas, D & Surdin-Kerjan Y (1997) Metabolism of sulfur amino acids in Saccharomyces

cerevisiae. Microbiol Mol Biol Rev 61: 503-532.
Winzeler EA, Shoemaker DD, Astromoff A et al. (1999) Functional characterization of the

Saccharomyces cerevisiae genome by gene deletion and parallel analysis. Science 285: 901-906.


A standardized citation metrics author database annotated for scientific field

Affiliation Departments of Medicine, Health Research and Policy, Biomedical Data Science, and Statistics and Meta-Research Innovation Center at Stanford (METRICS), Stanford University, Stanford, California, United States of America

Affiliation Research Intelligence, Elsevier B.V., Amsterdam, the Netherlands

Affiliation SciTech Strategies, Inc., Wayne, Pennsylvania, United States of America

Affiliation SciTech Strategies, Inc., Albuquerque, New Mexico, United States of America


Characteristic structural features

The structures of SET-domain proteins that are currently known include: the crystal structures of two members of the SUV39 family, Neurospora crassa Decrease in DNA methylation 5 (DIM-5) [15, 16] and S. pombe CLR4 [17] four structures of human SET7/9 in various configurations [18–21] a nuclear magnetic resonance (NMR) structure of a viral protein that contains only the SET domain [22] and a structure of the non-histone protein methyltransferase Rubisco LSMT, an unclassified member of the superfamily [23, 24]. These structures revealed that the SET domain forms a novel β fold not seen in any other previously characterized AdoMet-dependent methyltransferases (reviewed in [25]). The fold has a series of curved β strands forming several small sheets, packed together with pre-SET (or N-SET) and post-SET (or C-SET) domains or regions (Figure 3). The pre-SET domain of SUV39-family proteins (see Table 2) contains nine invariant cysteine residues that are grouped into two segments of five and four cysteines separated by various numbers of amino acids (CXCX5CX4CXC-XN-CX3CXCX3C, where N is 46 in DIM-5 and 28 in CLR4). The nine cysteines of the pre-SET domain of DIM-5 coordinate three zinc ions to form an equilateral triangular cluster, Zn3Cys9 (Figure 3a). The SET domain, which may have evolved through the duplication of a three-stranded unit [26], is folded in all the solved structures into several small β sheets surrounding a knot-like structure by threading of the carboxyl terminus through an opening of a short loop formed by a preceding stretch of the sequence (Figure 3). This remarkable 'pseudoknot' fold brings together the two most-conserved sequence motifs of the SET domain (RFINHXCXPN and ELXFDY see Figure 1) to form an active site in a location immediately next to the pocket where the methyl donor binds and to the peptide-binding cleft.

Representative examples of SET-domain-containing structures. (a) Neurospora crassa DIM-5 (Protein DataBank (PDB) code 1PEG.pdb) (b) human SET7/9 (1O9S.pdb). The pre-SET, SET, and post-SET domains in DIM-5 and the N-SET, SET, and C-SET domains in SET7/9 are indicated. The pseudoknot formed by two conserved SET motifs and the bound histone H3 peptide are also illustrated. The reaction byproduct AdoHcy is in stick representation and the zinc ions are shown as balls. N, amino terminus C, carboxyl terminus.

The post-SET region of DIM-5 contains three conserved cysteine residues, arranged CXCX4C, that are essential for its histone lysine methyltransferase activity [15]. The structure of DIM-5 in a ternary complex with an H3 K9 peptide and AdoHcy [16] reveals that, as expected from their arrangement, these three post-SET-domain cysteines coordinate a zinc ion tetrahedrally together with cysteine 244 of the SET-domain signature motif RFINHXCXPN in the pseudoknot near the active site (Figure 3a). Consequently, a narrow channel is formed to accommodate the side chain of the target lysine. Three ternary structures - SET7/9 in complex with a peptide containing histone H3 K4 [21], DIM-5 in complex with a histone H3 K9 peptide [16], and Rubisco LSMT in complex with a free lysine [24] - reveal that the target lysine is inserted into a narrow channel so that the target nitrogen would be in close proximity to the methyl donor AdoMet at the opposite end of the channel.

Close examination of the region carboxy-terminal to the SET domain in many proteins, including members of the SUV39, SET1, and SET2 families, suggests that the post-SET-domain metal center observed in DIM-5 is universal among all those members of the superfamily that have the cysteine-rich post-SET domain. For almost all SET-domain proteins, there appears to be an absolute correlation between the presence of the post-SET domain and a cysteine corresponding to Cys244 of DIM-5 near the active site. Comparison of DIM-5 with SET7/9 [19, 21] and the Rubisco LSMT [23, 24], two SET-domain proteins that do not have Cys-rich pre-SET and post-SET domains, reveals a remarkable example of convergent evolution. In particular, as in DIM-5, these two enzymes rely on residues carboxy-terminal to the SET domain for the formation of lysine channel, but they do so by packing of an α helix, rather than a metal center, onto the active site.


6.8: References - Biology

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6.8: References - Biology

This fact sheet was created to help biologists and resource managers understand emerging methods for detecting environmental DNA and their potential application for inventorying and monitoring aquatic species. It is a synthesis of published information.

Figure 1. This tadpole of the Rocky Mountain tailed frog secretes enough DNA into the surrounding water that it can be detected in a water sample collected downstream (see Goldberg and others, 2011). Photograph taken by Jason Jones, Nevada Department of Wildlife.

What is Environmental DNA?

DNA, short for deoxyribonucleic acid, is the hereditary material in organisms that contains the biological instructions for building and maintaining them. The chemical structure of DNA is the same for all organisms, but differences exist in the order of the DNA building blocks, known as base pairs. Unique sequences of base pairs, particularly repeating patterns, provide a means to identify species, populations, and even individuals.

Environmental DNA (eDNA) is nuclear or mitochondrial DNA that is released from an organism into the environment. Sources of eDNA include secreted feces, mucous, and gametes shed skin and hair and carcasses. eDNA can be detected in cellular or extracellular (dissolved DNA) form.

In aquatic environments, eDNA is diluted and distributed by currents and other hydrological processes (fig. 1), but it only lasts about 7–21 days, depending on environmental conditions (Dejean and others, 2011). Exposure to UVB radiation, acidity, heat, and endo- and exonucleases can degrade eDNA.

Use of eDNA for Inventory and Monitoring

Improved Detection of Native Species

Protocols using eDNA may allow for rapid, cost-effective, and standardized collection of data about species distribution and relative abundance. For small, rare, secretive, and other species that are difficult to detect, eDNA provides an attractive alternative for aquatic inventory and monitoring programs. Increasing evidence demonstrates improved species detection and catch-per-unit effort compared with electrofishing, snorkeling, and other current field methods. Thus, detection of species using eDNA may improve biodiversity assessments and provide information about status, distribution, and habitat requirements for lesser-known species.

Early Detection of Invasive Species

eDNA may also be an effective tool for early detection of aquatic invasive species. Recent studies have focused on Asian carp (Jerde and others, 2011) and American bullfrogs (Dejean and others, 2012), but protocols are being developed for New Zealand mudsnails, zebra mussels, quagga mussels, and others. Application of eDNA methods for invasive species monitoring may include periodically collecting water samples and screening them for several invasive species at once. Boat-ballast water, a source of introduction for many invasive species including mollusks, also could be sampled. Some intensive eradication programs for invasive species fail when a few surviving individuals recolonize the ecosystem. eDNA methods may provide a means of confirming eradication of all invaders.

Developing eDNA Protocols for Species Monitoring

Primer and Probe Design

Conventional Polymerase Chain Reaction (PCR) methods can be used for analyzing eDNA, but they may cross-amplify and provide false-positive results. Quantitative PCR (qPCR) methods are preferable to conventional PCR because they are likely more sensitive. In qPCR, primers are used to amplify a region of DNA that is specific to a target organism, and a probe is used to provide additional specificity and quantitative information. Several eDNA primer and probe sequences for individual species have been published. Other primer/probe sets must be designed for new species or specific needs.

Laboratory Optimization

The primer and probe design must be tested to ensure that the qPCR reaction always results in a positive detection in the presence of target-organism DNA and that amplification of non-target DNA does not occur. DNA from the target species should be screened prior to analyzing environmental samples to ensure test sensitivity. Preferably, this will involve 10 or more samples collected across the range of the species where the test will be applied. Closely related, co-occurring species also should be screened to ensure specificity prior to analyzing environmental samples, preferably involving five or more samples of each.

DNA can be extracted from preserved tissue samples using readily available kits. It is critical that no cross contamination occurs between species during the tissue-storage or extraction processes.

How to Design Species-Specific Primers and Probe for qPCR

  1. Create an inclusive consensus sequence that incorporates all within-species variability for a species in a well-known region of DNA. Mitochondrial DNA is preferred because it is more abundant than nuclear DNA, and more sequence data are available. Use sequences published in GenBank (National Center for Biotechnology Information, 2012), or sequence tissue samples of target species. It is important that the data incorporated include adequate sampling in the geographic area where the test will be applied.
  2. For the selected probe chemistry, set appropriate qPCR primer software to design short, unique sequences for use as forward- and reverse-primers and probe. Optimal probe length will differ by chemistry. These primers and probe will allow for amplification and detection of the target sequence (90–120 base-pair length is recommended).
  3. Compare the resulting design to sequences in GenBank to determine if the sequences are likely to cross-amplify with other species. Try to incorporate as many differences as possible (at least 2 on each primer and 2 on the probe, including 1 toward the 3’ end) between the primer/probe design for your target species and any other species in the database.

Figure 2. A water sample can be collected easily in the field in a sterile bottle and, if needed, stored temporarily in a cooler or refrigerator before eDNA is concentrated through filtration or centrifugation. Photograph taken by Matthew Laramie, U.S. Geological Survey.

Field Sampling

Four methods for field sampling have been developed to date: (1) collect 15 mL of water, preserve using ethanol and sodium acetate, and freeze immediately (Ficetola and others, 2008 Thomsen and others, 2012), (2) filter water through a cellulose nitrate filter (Goldberg and others, 2011), (3) filter water through a glass fiber filter (Jerde and others, 2011), and (4) filter water through carbonate filter (Takahara and others, 2012) (table 1 figs. 2–4). The latter three methods require pumps (either in-line, such as a peristaltic pump, or vacuum-line) and measurement of water filtered (volumes of 1–10 L are common). Filter methods also require either freezing of the filter paper (Jerde and others, 2011 Takahara and others, 2012) or dehydration of the filter paper in vials with molecular-grade ethanol (Goldberg and others, 2011). Although all these methods have been successful, ongoing testing, standardization, and optimization of field and laboratory protocols will continue to improve applications for inventory and monitoring programs.

DNA Extraction and Amplification

DNA extracted from the preserved samples is stable once it has been purified and preserved, and only a portion is used in each PCR reaction. This preserved DNA can be later tested for additional species if desired.

Following DNA extraction, qPCR analysis provides detection information about the target species’ DNA. Although the amount of target DNA present in field samples may be quantified (Thomsen and others, 2012 Takahara and others, 2012), this fact sheet is limited to presence/absence information.

Sources of Error

Identifying sources of error or uncertainty is a critical process in any study, especially for monitoring programs where results could influence future management decisions. Darling and Mahon (2011) provide an excellent overview of potential sources of uncertainty associated with DNA-based methods for monitoring aquatic species. The following points are important when using eDNA methods.

Design of Molecular Assay

Assay design must account for the variation within a species and the variation among species. Failure to incorporate the full range of genetic variation of a target species can lead to false negatives, whereas failure to incorporate the full range of genetic variation in closely related, co-occurring species can lead to false positives. Therefore, it is important to select a genetic region that maximizes the amount of genetic information available for target and related non-target species. For some species, this may require sequencing additional samples to ensure the assay is both sensitive and specific.

Table 1. Methods used to detect eDNA from aquatic organisms in freshwater environments.

[Abbreviations: L, liter ha, hectare mL, milliliter M, Molar °C, degrees Celsius μm, micrometer cm, centimeter m 3 , cubic meter km 3 , cubic kilometer]

Great crested newt (Triturus cristatus)

European weather loach (Misgurnus fossilis)

Eurasian otter (Lutra lutra)

White-faced darter (Leucorrhinia pectoralis)

Figure 3. An example of streamside water filtration using a peristaltic pump and sterile filter funnel. Photograph taken by Matthew Laramie, U.S. Geological Survey.

Figure 4. Filtration allows a specified quantity of water to be “tested” for eDNA. During filtration, DNA in the water is trapped on the filter paper, which is frozen or dehydrated. Photograph taken by Matthew Laramie, U.S. Geological Survey.

Quality Control

Positive and negative controls are necessary to ensure quality and reliability of results at each stage of the study. All DNA extractions should include a negative control, so that cross contamination between extracts can be detected. Each well of the PCR plate should include an internal positive control to ensure that the reaction is not inhibited. All eDNA extractions and qPCR setups should be conducted in a PCR-free laboratory space where concentrated (such as from tissue) DNA samples have not been handled. Thermocyclers and real-time PCR machines should be located outside of this space.

Detection Probability

Like other field-based sampling, results of eDNA detection may have some inaccuracy, and replicate samples are required to estimate occupancy while accounting for uncertainty. In other words, not detecting DNA of a species does not mean it is absent. The lower limits of detection for species are currently unknown and likely vary depending on the species and its density, size, behavior, and habitat.

Field Negative Controls

Two types of negative controls are often employed in the field to increase accuracy. First, samples from a few sites outside the range of a target species are used to confirm non-detection in locations where the species is not present. Second, samples are collected from distilled water using the field protocol at each site to ensure that cross contamination is not occurring between replicate samples within a site and between sites. Sterile gloves, filters, water collection bottles, and sample containers reduce risk of contamination. High-quality sample tubes placed individually inside plastic, sealable bags can reduce cross-contamination should leakage occur when samples are stored or shipped to laboratories.

Timing of Sampling

The timing of sampling may need to coincide with the life history or behavior of a target species. For example, during reproduction when young-of-year are present, eDNA may be abundant. The arrival of migratory species can be detected assuming no other life stages of the species remain in the system.

PCR Replication

Degraded, low-quantity DNA samples are often analyzed in triplicate to ensure detection of DNA (Waits and Paetkau, 2005) and to assess potential false-positives. Using this approach, additional analysis is required if results are not uniform. Standard curves should be developed based on DNA obtained from tissue samples of target species and span the range of sample results.

Future Directions

Although eDNA methods show great potential for inventory and monitoring aquatic species, there are still details to resolve. Thomsen and others (2012) point out that it is necessary to gain a better understanding of how field methods, laboratory protocols, and environmental conditions influence the detection of eDNA. Further, there is little information about factors that influence lower limits of detection, production of DNA, and persistence of DNA in different types of aquatic systems. These factors will likely vary among species and life stages. Before adoption of standard procedures for eDNA sampling and analysis, further development and comparative testing of protocols are necessary.

References Cited

Darling, J.A., and Mahon, A.R., 2011, From molecules to management—Adopting DNA-based methods for monitoring biological invasions in aquatic environments. Environmental Research, v. 111, iss. 7, p. 978–988, doi:10.1016/j.envres.2011.02.001.

Dejean, T., Valentini, A., Duparc, A., Pellier-Cuit, S., Pompanon, F., Taberlet, P., and Miaud, C., 2011, Persistence of environmental DNA in freshwater ecosystems: PLoS ONE, v. 6, no. 8, e23398, doi:10.1371/journal. pone,0023398.

Dejean, T., Valentini, A., Miquel, C., Taberlet, P., Bellemain, E., and Miaud, C., 2012, Improved detection of an alien invasive species through environmental DNA barcoding—The example of the American bullfrog Lithobates catesbeianus: Journal of Applied Ecology, v. 49, iss. 4, p. 953–959, doi: 10.1111/j.1365-2664.2012.02171.x.

Ficetola, G.F., Miaud, Claude, Pompanon, François, and Taberlet, Pierre, 2008, Species detection using environmental DNA from water samples: Biology Letters, v. 4, p. 423–425, doi:10.1098/rsbl.2008.0118.

Goldberg, C.S., Pilliod, D.S., Arkle, R.S., and Waits, L.P., 2011, Molecular detection of vertebrates in stream water—A demonstration using Rocky Mountain tailed frogs and Idaho giant salamanders: PLoS ONE v. 6, no. 7, e22746, doi:10.1371/journal.pone.0022746.

Jerde, C.L., Mahon, A.R., Chadderton, W.L., and Lodge, D.M., 2011, “Sight-unseen” detection of rare aquatic species using environmental DNA: Conservation Letters, v. 4, iss. 2, p. 150–157, doi:10.1111/j.1755-263X.2010.00158.x.

National Center for Biotechnology Information, 2012, NCBI: U.S. National Laboratory of Medicine, National Center for Biotechnology Information database, accessed October 4, 2012, at http://www.ncbi.nlm.nih.gov/genbank/.

Takahara, T., Minamoto, T., Yamanaka, H., Doi, H., and Kawabata, Z., 2012, Estimation of fish biomass using environmental DNA: PLoS One, v. 7, iss. 4, e35868, doi:10.1371/journal.pone.0035868.

Thomsen, P.F., Kielgast, J., Iversen, L.L., Wiuf, C., Rasmussen, M., Gilbert, M.T.P., Orlando, L., and Willerslev, E., 2012, Monitoring endangered freshwater biodiversity using environmental DNA: Molecular Ecology, v. 21, iss. 11, p. 2565–2573, doi:10.1111/j.1365-294X.2011.05418.x.

Waits, L.P., and Paetkau, D., 2005, Noninvasive genetic sampling tools for wildlife biologists—Review of applications and recommendations for accurate data collection: Journal of Wildlife Management, v. 69, iss. 4, p. 1419–1433, doi:10.2193/0022-541X(2005)69[1419:NGSTFW]2.0.CO2.

Top bullfrog photograph: Environmental DNA has been used to detect non-native species, like this American bullfrog, in lakes and ponds in Europe (Dejean and others, 2012). Photograph taken by John Cossel, Department of Biology, Northwest Nazarene University.

First posted November 18, 2012

For additional information contact:
Director, Forest and Rangeland Ecosystem Science Center
U.S. Geological Survey
777 NW 9th Street, Suite 400,
Corvallis, Oregon 97330
http://fresc.usgs.gov/

Part or all of this report is presented in Portable Document Format (PDF) the latest version of Adobe Reader or similar software is required to view it. Download the latest version of Adobe Reader, free of charge.

Suggested citation:

Pilliod, D.S., Goldberg, C.S., Laramie, M.B., and Waits, L.P., 2013, Application of environmental DNA for inventory and monitoring of aquatic species: U.S. Geological Survey Fact Sheet 2012-3146, 4 p.

U.S. Department of the Interior | U.S. Geological Survey
URL: https://pubs.usgs.gov/fs/2012/3146/
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Page Last Modified: Tuesday, November 29, 2016, 06:33:38 PM


Lesson Plan & Activities 6-8

Here you can find lesson plans and activities that may be useful in classrooms 6-8.

USGS Kids- Activities
Activities, games, coloring pages, projects, and stories that teach younger children about animals, climate change, bee population declines, wild birds, and more.

Animal Coloring Sheets- Activities
Individual coloring pages of birds, bats, reptiles, amphibians, and otters from our friends at the Western Ecological Research Center.

Wildlife and Contaminants- Lessons
A series of lessons targeted to high school students that introduces the topic of ecotoxicology and guides students through the scientific process of gathering raw data and drawing conclusions about the impact of contaminants on wildlife.

Become a Phenology Observer- Activity
The National Phenology Network (sponsored by the USGS) is looking for volunteers to help monitor plant and animal species found across the United States. Learn how to monitor plant and animal phenology and sign up to contribute new observations to the national phenology database. Make this a classroom project!

Lessons on the Lake: An Educator's Guide to the Pontchartrain Basin- Lessons
Louisiana's Lake Pontchartrain Basin is home to 1.5 million people and an estuary ecosystem with enormous biodiversity. Activities in the educator's guide help students in grades 5-12 gain an understanding and appreciation of the Basin and teaches them the skills to identify environmental concerns, make changes, and solve problems.

Land and People- Activity
Students look at interactions between people and the environment in three regions of the United States: Cape Cod, Los Angeles, and the Everglades. Targeted to grades 7-12.

Interactive San Francisco Bay Data- Activity
Look at plots of data collected from the water of San Francisco Bay, then generate your own plots using real data. How does a change in light penetration compare to water temperature? Does a change in salinity correspond with a change in chlorophyll?

North American Amphibian Monitoring Program (NAAMP)- Activity
NAAMP is a collaborative effort that uses volunteers to monitor populations of vocal amphibians. Participants who meet minimum standards are assigned roadside routes where data is collected after dark. This program is currently only active in states in the central and eastern U.S.

Topographic Map Resources for Teachers - Lessons and Activities
This directory level site includes links to various resources on topographic maps, how to obtain them, read them, their history, and map projections and includes links to various teaching activities and modules. It is the one-stop shop for learning about, using, and teaching topographic map concepts.

Exploring Maps - Lesson
Exploring Maps is an interdisciplinary set of materials on mapping for grades 7-12. Students will learn basic mapmaking and map-reading skills and will see how maps can answer fundamental geographic questions. The map images and activities in this packet can be used in various courses, including geography, history, math, art, English, and the sciences.

Constructing a 3D Topographic Map- Activity
This exercise uses clear plastic take-out lids, each marked with a different elevation line, and stacked to produce a 3D topographic map. It includes a base map of Angel Island (San Francisco Bay) but can be adapted to any local topographic feature.

27 Ideas for Teaching with Topographic Maps- Activites
Contains 27 ideas for teaching with the approximately 57,000 topographic maps that the USGS offers.

Map Mysteries- Background Information and Activity
Sample questions to use with USGS topographic and thematic maps as starting points to uncover mysteries about the cultural and physical geography of the Earth.

Corn Maze Geography- Activites
Visit a corn maze and use these activities to learn about maps and geography.

How to Use a Compass with a USGS Topographic Map- Activity
Learn to navigate using a topographic map and a compass.

Topographic Maps Illustrating Physiographic Features- Activity
Topographic maps can be used to study a wide range of physical features in the United States. This helps students learn about the geologic evolution of the Nation's natural landscapes and shows how topographic maps reveal more about the land surface than just its shape and elevation. Roam your cursor across maps and images on this online viewer to learn about selected features of the American landscape.

Map-It: Form-based Simple Map Generator- Activity
Enter the longitude and latitude of points to plot on a simple map. Download a postscript version of the resulting map. Satellite Imagery

Tracking Change over Time- Activity
Enhance students' learning of geography, map reading, earth science, and problem solving through landscape changes recorded by satellites in space.

AmericaView- Lessons
USGS is a partner in AmericaView, which has lesson plans and other education resources for working with satellite imagery. Mostly targeted to grades 6-12.

Tracking Change over Time- Activity
Enhance students' learning of geography, map reading, earth science, and problem solving through landscape changes recorded by satellites in space.

AmericaView- Lessons
USGS is a partner in AmericaView, which has lesson plans and other education resources for working with satellite imagery. Mostly targeted to grades 6-12.

3D Paper Models- Activity
3-D paper models (with accompanying Educator Guides) are a fun and interactive way to teach geologic concepts. Although these models were created in the 1990s and have a somewhat low resolution, they’re still good! Animations mentioned in the Educator Guides are no longer available

Journey Along a Field Line- Activity
A sixteen-page comic book about the Earth's magnetic field. Travel down through the interior of the earth then back up into the ionosphere to learn how the magnetic field works.

Antarctic Ice Sheet- Lessons and Activities
This report illustrates, through a paper model, why there are changes on the ice sheet that covers the Antarctica continent. By studying the paper model, students will better understand the evolution of the Antarctic ice sheet. Animations mentioned in the Educator Guides are no longer available.

Chicxulub Impact Event- Lessons and Activities
This report illustrates, by means of two paper models, how dinosaurs may have become extinct as a result of an asteroid impact. By studying the paper models, students will better understand the mass extinctions that have been part of the Earth's history. Animations mentioned in the Educator Guides are no longer available.

Crinoids- Lessons and Activities
This report illustrates, through the use of a paper model, how crinoids lived and became fossilized. By studying the paper model, students will better understand the flower-like animal that is referred to as a "sea lily" and its ocean-floor environment. Animations mentioned in the Educator Guides are no longer available.

How to Construct Four Paper Models that Describe Island Coral Reefs- Activity
This report contains instructions and patterns for preparing a set of four, three-dimensional paper models that schematically illustrate the development of island coral.

Make Your Own Paper Fossils- Lessons and Activities
This report illustrates, by means of paper models, how two organisms, a trilobite and a nautiloid, became fossils. The report is intended to help students and others visualize the size and shape of a trilobite and a nautiloid, the environment in which they lived, and the circumstances of their fossilization and subsequent discovery. Animations mentioned in the Educator Guides are no longer available.

Make Your Own Paper Model of a Volcano- Lessons and Activities
This report contains instructions and a pattern for making a three-dimensional paper model of a volcano. This model is intended to help students and others to visualize a stratovolcano (inside and out) and to learn some of the terms used by geologists in describing it.

Paper Model Showing Motion on the San Andreas Fault- Activity
This report contains instructions and patterns for preparing a three-dimensional model that schematically illustrates the fault motion that occurred during the Loma Prieta earthquake of October 17, 1989, in California. The model is intended to help students and others visualize the process of fault slip during earthquakes.

Sand Dunes- Lessons and Activities
This report illustrates, through computer animations and paper models, why sand dunes can develop different forms. By studying the animations and the paper models, students will better understand the evolution of sand dunes.

How to construct 7 paper models that describe faulting of the Earth- Activity
This report contains instructions and patterns for preparing seven three-dimensional paper models that schematically illustrate common earth faults and associated landforms.

2 Paper Models Showing the Effects of Glacial Ice on a Mountain Valley- Activity
This report contains instructions and templates for preparing three-dimensional paper models of two features a mountain valley partly filled by a glacier and the same valley after the glacier has melted. Included are brief descriptions of how such glaciers form, how they erode the landscape, and what kinds of physiographic features they produce.

Earthquake Effects- Lessons and Activities
The report is intended to help students and others visualize what causes earthquake shaking and some of the possible results of the shaking. Animations mentioned in the Educator Guides are no longer available.

Landslide Effects- Lessons and Activities
This report illustrates how four different types of landslides (slide, slump, flow, and rockfall) occur and what type of damage may result. The report is intended to help students and others visualize what causes landslides and some of the possible result of the landslides. Animations mentioned in the Educator Guides are no longer available.

Lifecycle of a Mineral Deposit- Lessons and Activities
This teacher’s guide includes are 10 activity-based learning exercises that educate students on basic geologic concepts the processes of finding, identifying, and extracting the resources from a mineral deposit and the uses of minerals. The guide is intended for grades 5 through 8 science teachers and students.

Plate Tectonics Tennis Ball Globe- Activity
Create a mini globe that shows the major plate boundaries of the world (scroll to page 15).

This Dynamic Planet Teaching Companion Packet- Lessons and Activities
This Teaching Companion is intended to assist teachers to teach plate tectonics, primarily for grades 6–14.

Schoolyard Geology- Activities
Structured activities use man-made features that are found in a typical schoolyard to demonstrate geologic principles.

Collecting Rocks- Activity
Learn about different types of rocks and how to identify and collect them.

What's in My Soil?- Activity
Students separate, examine and identify the major components of soil to better understand how these components give soil its unique physical characteristics.

Introduction to Soils- Lesson
This complete lesson plan teaches students how soils develop and provides links between soils, climate, vegetation, and geology. Includes materials for both teachers and students (handout, puzzle, field and lab sheets).

Graded Bedding- Activity
This activity introduces students to the concept of sorting materials in different mediums and the sedimentary feature called graded bedding. Students will discover that water is a good medium to separate and sort particles, and that particles behave differently in water than in air.

Geologic Age- Activity
Students investigate radioactivity as a tool for measuring geologic time.

Global Change- Activities
Includes introduction, activities, and teaching guide for topics relating to global change, time, and earth systems. Targeted to grades 4-6.

Tracking Change over Time- Activity
Enhance students' learning of geography, map reading, earth science, and problem solving through landscape changes recorded by satellites in space.

Greenhouse Gases- Activity
Students observe and contrast thermal properties of three major greenhouse changes over time for dry air, water saturated air, carbon dioxide, and methane.

Evaluating Glacier and Landscape Change- Lesson
In this lesson students interpret USGS data in multiple formats and draw conclusions based on the data presented.

Tabletop Earthquakes- Activity
Construct a simple earthquake machine to demonstrate the principles of seismology. Includes supporting instructional material.

Size and Occurrence of Floods- Activity
Students use macaroni or beans to calculate the statistics of floor recurrence (see back side of poster).

Living with a Volcano in your Backyard- Lesson
A three-unit guide that provides science content and inquiry-based activities about volcanoes of the Cascade Range for middle-school students, with an emphasis on Mount Ranier. Includes more than 30 activities, a field guide, glossary, and supplementary information.

Predict an Eruption!- Activities
This highly interactive site uses animations, illustrations, activities, and quizzes to show how eruptions at Mount St. Helens were accurately predicted by USGS scientists, then allows students to predict an actual eruption using real data.

The Fragile Fringe: A Guide for Teaching about Coastal Wetlands- Background Information and Activites
Material to use for developing a comprehensive study of coastal wetlands. Includes background information, suggested activities, glossary, references, and reading list. Activities can be demonstrated by the teacher or performed by students. Emphasis is on Gulf Coast wetlands.

Wise Wetland Ways- Activity
Teachers use wetland "artifacts" to stimulate a discussion about how we benefit from wetlands (see back of poster).

USGS Water Science School- Activities and Photos
The best starting point for a wealth of general information about water science. What is water? What are its properties and how are they measured? How is water used? How does the USGS measure streamflow and collect water samples? A glossary, picture gallery, and activity center are among the many additional features.

Hands-on Experiments to Test for Acid Mine Drainage- Activity
Fourteen very basic exercises use home-made litmus paper and household items to test creek water for acid mine drainage and to look at plants, bacteria, and insects living in the water.

Water Education Posters- Lessons and Activities
Water-resources topics of all completed posters are drawn in a cartoon format by the same cartoonist. Posters are available in color or B&W. The back sides of the color poster PDF files contain educational activities: one version for children in grades 3-5 and the other with activities for children in grades 6-8. The B&W posters are intended for coloring by children in grades K-5.

Outreach Notebook for Groundwater- Lessons
Five groundwater-related lesson plans for grades 6-8, complete with forms, diagrams, and supporting information. Although these were designed to be taught by an instructor and a water professional working together, a thoughtful educator could easily handle the lessons on their own.

Size and Occurrence of Floods- Activity
Students use macaroni or beans to calculate the statistics of floor recurrence (see back side of poster).


6.8: References - Biology

Didn't find it here? Try a Google search:

Collections of Biology Lesson Plans and Resources
SMILE Biology Index
A collection of nearly 200 lesson plans organized by topic!

Biology Lesson Plans
A long list from The Teacher's Guide.

Biology Lesson Plans
Several lessons from the Science Spot.

The Biology Corner
Many lesson plans, worksheets, WebQuests, and quizzes.

Free Biology Lesson Plans
Biology labs/experiments, activities, worksheets, projects, assessments, and multimedia from NGSS Life Science.

Biology Lesson Plan Menu
Many lesson plans from the Columbia University Summer Research Program for Science Teachers.

Online Biology Book
Just what the title suggests!

NIH Curriculum Supplement Series
Curriculum supplements consistent with National Science Education Standards from the U.S. Department of Health and Human Services Science Education.

Biology Lessons
A large collection of lesson plans for all grade levels. See also Hands-on Science Lessons.

Cells/Meiosis/Mitosis Lesson Plans
Jello Cells
A "Cell Unit" with a lesson titled Jello Cells.

Cells
Several lesson plans from the Biology Corner.

How Do Cells Reproduce?
A lesson plan for grades 9-10.

Mitosis/Meiosis Flip Book
A high school lesson plan. See also How Cells Divide: Mitsis and Meiosis for a slide show from NOVA's "18 Ways to Make a Baby."

Phases of Meiosis
A worksheet complete with diagrams from the Biology Corner.

Cell Division and Mitosis
A lesson plan for high school biology.

Mitosis
A lesson plan for grades 6-8 from Science Net Links.

Genes/Genetics Lesson Plans
From Cell to DNA
A high school lesson plan from Science Netlinks.

Genetics
More lesson plans from the Biology Corner.

Genetics
A middle school lesson plan from Discovery Education.

Genetics Lesson Plan
A lesson plan for 5th grade.

Building a Model DNA
Another middle grade lesson plan from Discovery Education.

Beans to Genes: Genetic Probability
A secondary lesson plan.

The Future's in the Genes
A lesson plan for grades 3-5 from Education World.

From Jeans to Genes
A middle school lesson plan introducing students to the structure of chromosomes.

Our Genes/Our Choices
Five lesson plans for grades 6-8 or 9-12 from PBS.

Population Genetics
An simulation and explanation.

Genetics Education Center
Genetics lesson plans, resources, and links.

The Genome: Controversy for All Times
A secondary unit examining the ethical and moral issues surrounding research into mapping the human genome.

Whose Life Is It?
A high school lesson plan that uses a fictional story to examine some of the ethical and values issues related to human cloning.

The Clone Age
A lesson plan for grades 6-8 from Discovery Education.

Evolution Lesson Plans
Understanding Evolution
From the Evolution Wing, this site provides information about and links to other sites related to the history of evolution. See also The Ultimate Creation vs. Evolution Resource.

Evolution Lessons
A collection of high school lesson plans from Evolution and the Nature of Science Institutes.

The Evolution of Plants
Information and sample lesson plans from a high school unit.

Hominid Evolution
Another unit for high school biology or advanced biology.

Human Evolution
A high school lesson plan from Discovery Education integrating the study of human evolution and history.

Evolution
Also from Discovery, a lesson plan for grades 9-12 in which students learn about Darwin, his theory of evolution, and some of the controversies related to it.

Darwin's Evolution
A high school lesson plan in which students learn about Charles Darwin.

Origin of the Species vs. Zoological Philosophy
A middle or junior high school lesson plan in which students debate the theories of Darwin and Lamarck.

Historical Thinking Matters: Scopes Trial
A 5-day lesson plan. See also Whose ‘Truth’ Is Out There? for a lesson plan from the N.Y. Times. For background information, see The Antievolution Crusade of the 1920s, Clash of Cultures: The Scopes Trial.

Online Lessons for Students: Learning Evolution
Seven lesson plans providing " multimedia pathways to help students understand evolution and the nature of science
."

Evolution Project
A lesson plan from The Biology Corner.

Tree of Life
Information about phylogeny and biodiversity. "The information is linked together in the form of the evolutionary tree that connects all organisms to each other."

Botany/Plants Lesson Plans an d Resources ( Including Lessons on Farms)
Botany Activities and Lesson Plans
About 20 lesson plans from the Illinois State Museum.

Botany
Many lesson plans from SMILE.

Plants
Lesson plans from the Biology Corner.

Plant Science Lesson Plans
Plant tissue systems, angiosperm, and gymnosperm lesson plans from NGSS Life Science.

All About Plants
An elementary lesson plan from Discovery Education.

Botany and Art and their Roles in Conservation
An interesting lesson plan from the Smithsonian.

The Importance of Photosynthesis and Respiration
A lesson plan from the New Mexico AgriScience Lesson Plan Library

Plant Cycles: Photosynthesis and Transpiration
A lesson plan for grades 3-5.

Parts of a Flower
An K-1 lesson plan. See also Friendly Flowers for a K-2 lesson.

Wildflower Garden
A lesson plan in which students design about a wildflower garden. For information on wildflowers, go to The Wildflower Center and Wildflowers.

Gems from the Garden - Digging Up Activities for All Ages
Many for gardening-related activities from Education World.

What's in a Garden?
An elementary lesson plan. See also Sharing the Joy of a Garden.

The Great Plant Escape
An interdisciplinary program for students in grades 4-5 designed to introduce them to plant science and increase their understanding of how foods grow. available in either Spanish or English.

Let It Grow: An Inquiry-Based Organic Gardening Research Project
An excellent lesson plan for grades 6-8 from Read Write Think.

Plants and Animals: Partners in Pollination
Three lesson plans for grades 3-8 from the Smithsonian Institute.

AppleQuest
An elaborate WebQuest for grades 5+ about growing apples!

Apples & More
From the University of Illinois Extension, this website offers suggestions for accessible and stimulating activities for a series of lessons about apples. The unit encompasses many areas of the curriculum: math, science, writing, literature, art and social studies. See also Apple Fast Facts.

Johny Appleseed Day Research Activity
An elementary-grade lesson plan.. See also Johnny Appleseed or John Chapman: Which Character is Your Favorite? and Apples, Apples, Apples for other lesson plans.

Farms and Agriculture Lesson Plans
On the Farm Theme Unit
A kindergarten unit.

Farm
Links to worksheets, unit, lesson plans, and other resources from ProTeacher.com.

Wheat Lesson Ideas
For grades K-2. See also Growing Wheat in the Classroom.

From Seed to Plant
A primary-grade lesson plan.

National Agriculture in the Classroom
Search the new Curriculum Matrix for lesson plans from the USDA. See also Ag Lesson Plans in Power Point Format
.

California Foundation for Agriculture in the Classroom
Select Teaching Resources in the top menu to find lesson plans for a variety of grade levels.

AppleQuest
An elaborate WebQuest for grades 5+ about growing apples!

Apples & More
From the University of Illinois Extension, this website offers suggestions for accessible and stimulating activities for a series of lessons about apples. The unit encompasses many areas of the curriculum: math, science, writing, literature, art and social studies. See also Apple Fast Facts for information and teaching ideas from the Wisconsin Apple Growers Association.

Johny Appleseed Day Research Activity
An elementary-grade lesson plan.. See also Johnny Appleseed, Johnny Appleseed or John Chapman: Which Character is Your Favorite? and Apples, Apples, Apples for other lesson plans.

Pumpkin Themes
Links to many lesson plans and units on pumpkins. See also Pump up the Curriculum with Pumpkins. Go to Fall Holiday Lesson Plans for Halloween ideas.

Hot Seeds
An inquiry-based lesson for grades 5-12 complete with assessment rubrics.


Forestry/Trees Lesson Plans - Click on a topic: forestry, trees, leaves, tree rings

Forestry
Sustainable Forestry
A lesson plan from the Penn State School of Forest Resources. See their
From the Woods Series.

Lesson Plans for Forest-Minded Teachers
Many lesson plans in pdf format for a variety of grade levels from the Idaho Forest Products Commission. This site takes a a while to load!

Forestry/Natural Resources Lesson Plans
Many lesson plans organized by grade level.

Forestry Lesson Plans
Many lesson plans for all grade levels from Forestinfo.org.

LEAF Wisconsin K-12 Forestry Lesson Guides
Lesson plans for all grade levels from University of Wisconsin Stevens Point.

If a Tree Falls in the Forest
A lesson plan for grade 5 Learn NC.

Biomes: Forests and Seeds
A middle-grade lesson plan from Discovery Education in which students learn how seasonal changes affect life in a temperate forest.

Parts of a Tree
A kindergarten lesson plan.
See also Trees and Their Parts.

Seasons of Trees
An elementary-grade lesson plan from the above site.

Is that Tree Safe?
A lesson plan for grades 6-8.

Uses of Trees
A kindergarten lesson plan in which students identify three or four ways trees are used.

How Does Your Tree Measure Up?
See also Forest Measurements.



Leaves
H ow are Leaves Alike and Different?
A lesson plan that can be adapted to various grade levels. See also What Tree Is That? for a tree identification field guide.

Fall Leaves Fall!
A lesson plan for grades K-2 using the book by this title.

Leaf ID and Leaf Bingo
Another 3rd-grade lesson plan from the above source. See also What Can a Leaf Be?

Tree Rings
I t's All in the Rings
A lesson plan for grades 7-12. See also Tree Rings as Records of the Past for a lesson plan adaptable to grades 1-8 and About Tree Rings for an excellent resource.

Tree Rings
A lesson plan for grades 3-5 from the National Park Service. See also What Can We Learn from Old Trees?

Tree Ring Dating
A grade 5 lesson plan from Learn NC.

Rain Forest Lesson Plans
Rain Bird Rain Forest Teaching Curriculum
Curriculum materials and activities for all grade levels.

Rainforest Alliance Curriculum
Click on the grade level you teach on the left side to find the lesson plans.

Rain Forest Animals
A teacher's guide from Newton's Apple.

Rainforest
An elementary-grade lesson plan from A to Z Teacher Stuff.

The Layers of the Rain Forest
An elementary lesson plan. See Virtual Rainforest for an online tour.

It's Goin' Down The Rain Forest
A 4-lesson unit from Learning to Give.
|
Amazon deforestation
A lesson plan from the BBC.

Amazon Rainforest WebQuest
See also Let's Explore the Rainforest
for another WebQuest.




Invasive Species Lesson Plans - Animals and Plants
Invasive Species Educational Resources
Activities and lesson plans from the Wisconsin DNR.

Battlefield Earth
Learning activities about the dangers of invasive species from the National Teacher Training Institute.

Introduction to Invasive Species
An activity form grades 6-8 from National Geographic.

Invasive Species Lesson Plan
Students learn the basics about invasive species. See also Invasive Species for a similar 8th-grade lesson plan.

Invasive Species Lesson Plan: The Invasion Game
From BrainPop, this activity can be sued with grades 3-12.

Invasive Plants
High school lesson plans based on Kentucky Core Content.

Invasive Species Integrated Curriculum Unit
A middles school unit about Phragmites, an invasive wetland plant.

Invasive Species Game
A high school lesson plan from the University of Toledo.

Real-Life Aliens: Introduced Species
A lesson plan for high school and above.

Introduced Animals and Invaders in Hawaii
An instructor's guide from the Honolulu Zoo Society.

Zoology/Animals Lesson Plans
Zoology Activities and Lessons Plans
More than 20 lesson plans from the Illinois State Museum.

Zoology
Many lesson plans from the SMILE.

Animal Lesson plans
Lesson plans on animal classification, animal behavior, invertebrates, and vertebrates.

National Wildlife Federation
Many lesson plans organized by topic.

Lesson plans for Teachers
Several lesson plans from the Humane Society.

Right Whale Curriculum
Many 4th-grade lesson plans.

In the Company of Whales
A lesson plan for grades 6-8. See also Whales for another lesson plan for grades 6-8. For more information on whales, go to The Whale Centre.

Whales
A Teacher's Guide with lesson plans for grades 4-8 from Sea World.

Tale of a Whale
A lesson plan adaptable to many grade levels from Smithsonian Education.

Shark!
A teacher's guide for grades 4-8. See also the K-3 Teacher's Guide.

Exploring Our Oceans
A unit from the Yale New Haven Teachers Institute.

Animal Adaptations in the Ocean
An activity for grades 6-8 from National Geographic.

Coral Cam Lesson Plans
Fifteen lesson plans on topics related to coral reefs. Most are adaptable to a variety of grade levels. See also Coral Reef WebQuest.

Sea Shells
A K-2 lesson plan. See also Shells.

Biomes: Freshwater and Seawater
A lesson plan for grades 6-8 from Discovery Education. See also Aquatic Habitats for another middle-grade lesson plan from Discovery Education.

Fun with Fish
An outdoor education lesson plan in which students learn about fish and fishing.

The Minnesota Fish Quiz
Not a lesson plan, but this interactive, online quiz is a fun way to learn about Minnesota fish species and may be just what you need to motivate the boys in your classroom this spring!

How Many Fish Are in that Pond?
A high school lesson plan in which students learn about sampling and statistical methods used in estimating wildlife populations.

Fish and Ladders
A lesson plan for grades 5-8 about the spawning migration of Chinook Salmon. See the high school version of this lesson.

Creative Writing: I am a Fish
A lesson plan integrating science and creative writing.

Something Fishy
This lesson plan for grades for grades 6-9. For an incredible amount of information on fish, go to Fishbase.

Science - Fish Knowledge
Lesson plans from the Wisconsin DNR.

Fish Information Service (FINS)
An elaborate site providing information for aquarists. See also Fish Channel.

Animals: Mammals Lesson Plans
(Lesson plans for fish/marine animals are listed above. Scroll past mammals for lesson plans on farm animals, reptiles/amphibians, birds, dinosaurs, or insects/spiders. For information and resources on zoos and/or specific animals, go to the Zoos and Museums Page.

Animal Classification
A K-5 lesson from Discovery Education.

What's a Mammal
A K-5 lesson plan. See also Magnificent Mammals.

Oh Deer
A lesson plan for grades 4-5.

Wildlife Lesson Plans
Many lesson plans for all grade levels from Penn State.

Wildlife Management Activity Guide Index
Lesson plans from the National park Service.

Bat Unit Study
Teaching ideas using the book Stellaluna.

North American Bear Center
Many lesson plans and activities. See also Bears/Hibernation for a Pre-K activity.

How Polar Bears Stay Warm
A literature-based primary-grade lesson plan. See also Why Polar Bears Are White?

What Bear Goes Where?
A lesson plan in which students construct posters of three different bear habitats. See Bears for many similar activities.

The North American Bison Lesson Plan
For grades 3-5.

Tracking the Buffalo
Background information and classroom materials.

Big Cats
A lesson plan for grades 6-8.

Dogs
A lesson plan for grades 6-8 in which students learn about characteristics of dogs and dog breeds. See also Breeds of Dogs and Dogs at Work.

Dogs and More Dogs
A classroom activity fro NOVA/PBS.

Endangered Species Theme Page
Links to lesson plans and resources.

ABC of Endangered Species
A lesson plan for grades K-6 from Education World. See also Illustrating Endangered Species.

Endangered Species of PA
A high school lesson plan from Penn State University.

Schoolyard Habitats
A "How-To Guide" National Wildlife Federation.

Farm Animals
Farm Animal Sounds: Pen Pals
A kindergarten lesson plan emphasizing animal sounds, listening, and movement.

On the Farm or in the Zoo?
An elementary lesson plan in which students
categorize animals into two groups, farm animals and zoo animals.

Animal Babies on the Farm
A kindergarten or primary-grade lesson plan in which children learn the names of farm animals and match them to their offspring's names.

Farm Animal Immigrants
A 5th-grade lesson plan in which students will identify a rare or endangered farm animal, locate its country of origin on a world map, and determine why it was an imported.

Fun at the Farm
Elementary-level activities.

Sheep to Sweaters
An idea for an activity from Crayola.

The Perfect Cow?
A high school lesson plan

Reptiles and Amphibians
Reviled and Revered
Reptiles and amphibians from the Smithsonian Institution. Scroll down the page for 5 lesson plans and resources. Take a look at the Reptile Data Base for information about snakes and other reptiles.

Reptiles Alive
Lesson plans, teacher's guide, reference materials. crafts.

Reptile Adaptation
A K-5 lesson plan from Discovery Education.

All About Reptiles
An elementary lesson plan.

Herp Care Collection
Advice for keeping a reptile in your home or classroom.

Snakes
A middle school lesson plan from Discovery Education. See also Basic facts about Snakes.

Lesson Plans for Sea Turtles
A literature-based lesson.

A Thousand Friends of Frogs
A good source of basic frog information.

Frogs and Toads Are Different (But Still Friends)
A 2nd-grade lesson plan using the book, Frog and Toad Are Friends. See also Comparing and Contrasting with Frog and Toad.

Frogs: Fact and Folklore
A middle school lesson plan from Discovery Education.|

Life Cycle of a Frog
An elementary lesson plan.

The Mysterious Tadpole
Activities for using the book by this title with your 4th-graders.

How Far Can a Frog Jump?
A 4th-grade lesson plan introducing the metric system by simulating a jumping frog contest like that described in Mark Twain's "The Notorious Jumping Frog of Calaveras County." It may provide an interesting way to integrate science, math, and literature.

Frog Dissection
See also Dissecting a Virtual Frog.

Birds
Raptor Center
Great site from the Minnesota Raptor Center.

Birds by Inquiry
A kindergarten lesson plan from Learn NC.

Illinois Prairies Research Institute - Educational Materials
Twelve excellent bird-related lesson plans for grades 3-6.

Birds through the Seasons
A 2nd-grade unit from Core Knowledge.

All About Birds WebQuest

Hummingbird Projects and Activities
Several Activities from Operation Ruby Throat.

Watch the Birdie
A 6-week unit for grades 5-6 in which students develop language arts skills while studying North American birds.

Bird Migration
A lesson plan from the U.S. Fish and Wildlife Service. See also On the Fly: Studying Bird Migration and Behavior.

Lesson Plans About Migration
Several lesson plans from Migration Science and Mystery.

Birds
A high school lesson plan from Discovery Education.

Birding Basics
A lesson plan for grade 4 from the Wisconsin DNR. See also Birding Basics for grades 5-8 and Avian Adaptations for other lesson plans from this source.

Make Way for the Ducklings Art Lesson
A lesson plan for grades 1-3 for this classic book by Robert McCloskey. See also Make Way for the Ducklings: A Bird's Eyeview of Geography.

Mr. Popper's Penguins
A discussion guide for this book by Richard and Florence Atwater. See also Demonstrating Comprehension through Journal Writing for another lesson plan using this book.

Tacky the Penguin
This primary-grade lesson plan titled "What Makes Us Different?" uses Helen Lester's Tacky the Penguin to explore individual differences.

Meet the Penguins!
Lesson plans and a book list from Scholastic..

Winter Animals
A primary-grade lesson plan about penguins from Scholastic.

Dinosaurs (Scroll down past the lessons for links to sites with dinosaur information, pictures, and a dinosaur dictionary)
Dinosaur Lesson Plan
For the elementary grades.

Dinosaurs
A 2nd-grade unit.

Discovering Dinosaurs
A K-5 lesson plan from the Discovery Education. See also Dinosaurs in Argentina for grades 6-8 lesson.

Dinosaurs! Teaching Guide
For grades k-8 from Scholastic. See also Dinosaurs Before Dark.

Fossils 1: Fossils and DinosaurA
A lesson plan from Science Net Links. See also Fossils 2 , Dinosaurs 1: Where Are the Dinosaurs, and Dinosaurs 2: What Were Dinosaurs Like?


A Fossil's Journey
A Lesson plan for grades 3-5 from the National Parks Service.

Dinosaurs: Meat-Asaurus or Vegie-Asaurus?
An activity for grades 3-5 using The Magic School Bus: The Busasaurus.

Dinosaur Detective
A lesson plan for grades 6-8.

Zoom Dinosaurs
An on-line book with fact sheets, printouts, lists of dinosaurs, a dino dictionary, and more.

New Illustrations
Excellent site for locating illustrations of and information about many species of dinosaurs.

Iowa State Entomology Index of Internet Resources
A
directory and search engine of insect-related resources on the Internet.

What's Bugging You?
Ideas for lesson plans and activities from Education World.

Using Live Insects in the Classroom
Information from the University of Kentucky. See also
Insect Models for an Internet-based K-2 lesson plan.

Crickets in the Classroom Page
A unit involving the use of crickets to teach skills of observation and measurement. The page also provides information on crickets and sources for obtaining them.

Insect Mania
An elaborate 2nd-grade unit from Core Knowledge. See also Investigating Insects for another 2nd-grade unit.

Life in a Pine Cone
Another middle-grade activity.

Inventing Insects
A "creative lesson plan" from Scholastic.

Insects
An elementary-level WebQuest.

Insect Anatomy
A discovery-based lesson plan for grades 6-9.

Insects of the World
A WebQuest complete with an evaluation rubric. See also Creepy Crawly Insect Collection.

Plants and Animals: Partners in Pollination
Three lesson plans for grades 3-8 from the Smithsonian Institute.

Canadian Honey Council
Curriculum activities for grades 1-3.

Bee Lesson Plans
Five elementary lesson plans from the Honeybee Conservancy.

Bee Unit Study
Information and activities for a primary-grade unit.

Become a Bee: Bee Anatomy
A lesson plan for grades 1-5.

Buzzy, Buzzy Bee
A lesson plan for grades 2-7

Bees
A lesson plan for grades 6-8 from Discovery Education. See also Pollination Parties.

Butterfly Website: Butterfly Teaching Tools
Scroll down the page to find many lesson plans. Click on gallery to see butterfly images.

Monarch Butterflies
Eight days of primary-grade activities.

The Life Cycle of a Butterfly
A lesson plan that uses Eric Carle's The Very Hungry Caterpillar .

Butterflies
A 2nd-grade WebQuest.

A Butterfly's Home
A lesson plan for grades K-2 on creating a butterfly garden. See also Observing the Lifecycle of a Butterfly.

Symmetry in Butterflies
Kindergarten and PreK activities from the MN Science Museum.

Insectlopedia
Information about biting insects.

Orkin Science Education
Educator resources, games and coloring, as well as lesson plans.

Iowa State University Entomology Image Gallery
More great insect pictures!

Spiders
Be Nice to Spiders
A primary-grade lesson plan from Scholastic.

Project-Based STEM for Kids - Spiders
A lesson plan for grades K-2.

Spiders
An elementary unit with seven lesson plans.

Now We Know Spiders
One lesson plan from the above unit using the book Anansi the Spider by G. McDermott.

Senses Lesson Plans
The Five Senses
A lesson plan using My Five Senses by Aliki.

The Five Senses
A first-grade lesson plan from Teachers.net.

Five Senses
A WebQuest for grades K-2.

The Eye: Structure and Function
A lesson plan for grades 6-8. See also Sight and Light.

Virtual Cow Eye’s Dissection
Almost as good as the real thing! It could be used as a high school level pre-lab or an alternative to an actual dissection.

Hearing
Twelve lesson plans for grades K-8. Also, see the Virtual Tour of the Ear.

The Science of Sound
Information from Scholastic.

The Phenomenon of Sound: Waves
A K-5 lesson plan from Discovery Education. See also Sound Vibrations.

Good Senses
A middle school lesson plan from The Discovery Education. See also Sight and Sound.

The Phenomenon Of Sound: Waves
A lesson plan for grades K-5 from Discovery Education.

A Unit on Sound: Ideas for Interdisciplinary Lessons
Ideas for integrating science and music from the Virtual Museum of Musical Instruments. See also Make Your Own Musical Instrument.

Senses- Smell
A lesson plan for grades K-2.

Physiology/Anatomy Lesson Plans
Inner Body
Human anatomy online.

Cells Alive!
See images of cells

Visible Human Body
A guided tour!

Body Systems
An elementary-grade lesson plan from Discovery Education.

Building a Baby
Lesson plans from the The Discovery Education.

Give Me a Break
An elementary-grade lesson plan in which students develop a survey and collect data on broken bones.

The Musculoskeletal System
A lesson plan for grades 6-8 from Discovery Education. See also Muscles in Motion.

The Heart: The Engine of Life
Information from the Franklin Institute.

Here's to Your Healthy Heart!
A middle-grade lesson plan from Discovery Education.

The Heart
A high school lesson plan.

An Insight Into the Hormones of Life
A middle-grade unit on hormones.

The Brain: Understanding Neurobiology through the Study of Addiction
A Teacher's Guide with five lesson plans for grades 9-12 from the National Institutes of Health Curriculum Supplement Series.

Brain Power
A lesson plan for grades 6-8 in which students learn about the human brain and memory functions. See also Brain Watching for a high school lesson plan.

Neuroscience for Kids
Incredible online information about the human nervous system. Go to Brain Awareness Week Lessons for several lesson plans on the brain and nervous system.


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Fai Mok SW, Thelen KM, Riemer C, Bamme T, Gultner S, Lutjohann D, Baier M: Simvastatin prolongs survival times in prion infections of the central nervous system. Biochemical and Biophysical Research Communications. 2006, 348 (2): 697-702. 10.1016/j.bbrc.2006.07.123.

Prusiner SB: Prions. Proc Natl Acad Sci USA. 1998, 95 (23): 13363-13383. 10.1073/pnas.95.23.13363.

Cunningham C, Deacon R, Wells H, Boche D, Waters S, Diniz CP, Scott H, Rawlins JN, Perry VH: Synaptic changes characterize early behavioural signs in the ME7 model of murine prion disease. Eur J Neurosci. 2003, 17 (10): 2147-2155. 10.1046/j.1460-9568.2003.02662.x.

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Pike LJ: Lipid rafts: heterogeneity on the high seas. Biochem J. 2004, 378 (Pt 2): 281-292. 10.1042/BJ20031672.

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Discussion

The use of synthetic biology to re-engineer complex systems has transformed our understanding of fundamental mechanisms and has driven a variety of applications, e.g., materials construction, chemical processing, and energy production (30 ⇓ ⇓ –33). However, the ability to reliably engineer complex biological systems that behave as expected remains limited due to their intrinsic complexity. Thankfully, biology itself provides natural resources that can be exploited to help satisfy the requirements for re-engineering. In the current study, by employing a posttranslational splicing strategy prevalent in RNA viruses, we have established a method for re-engineering CBS using a polyprotein-based strategy. Although others have used TEVp-based posttranslational cleavage to codeliver a small number of proteins into eukaryotic cells (e.g., refs. 34 and 35), to our knowledge, this strategy has not been used to date to engineer complex biological systems such as BNF. This strategy provides an important approach for efficient adaptation from an operon-based system into a polyprotein-based assembly. Balanced expression of CBS components can be achieved by organizing genes with similar expression levels into giant genes expressed as polyproteins, followed by subsequent cleavage to release single components. The advantages of this strategy are particularly useful for transforming complex systems from prokaryotes into eukaryotes. Eukaryotic promoters and terminators often span hundreds of base pairs, nearly 10 times the amount of their bacterial counterparts (36). Monocistronic expression of large numbers of heterologous genes in eukaryotes requires complex combinatorial design and the screening of many gene expression parts to surmount difficulties in coordinating the expression level of each component (14). Taken together, translation of genes into polyproteins reduces the number of translational units and maintains stoichiometric expression, thus simplifying the approach for adapting prokaryotic CBS for expression in eukaryotic cells. Although other approaches are available for coordinating expression of multiple genes in eukaryotes in an operon-like format—for example, using internal ribosome entry sites to direct translational initiation within the mRNA—this may result in substantially lower expression levels in comparison with normal Cap-dependent translation (37). Another possibility is to introduce the viral polyprotein self-cleavage peptide 2A to generate discrete translation products, although this results in an 18-aa tail, which may influence protein functionality (38).

We have successfully applied the TEV-based posttranslational slicing method for re-engineering the classical molybdenum nitrogenase system. Surprisingly, however, this strategy is less amenable to the minimal iron-only nitrogenase system (39) since the structural AnfH, AnfG, and AnfK proteins are relatively intolerant to the presence of the C-terminal ENLYFQ-tail (SI Appendix, Table S3). For the molybdenum system, the polyprotein strategy has the obvious advantage of maintaining the stoichiometry of the NifDK and NifEN protein complexes, although it cannot alleviate stability issues arising after polyprotein cleavage. Nevertheless, it appears to be remarkably robust to gene rearrangements that result in cotranslation of other nif components, even though this can significantly alter expression levels from those observed in the native system. Tolerance to protein-level changes was particularly notable when we tested the functionality of individual polyproteins in complementing nitrogenase activity in E. coli. For example, decreased levels of NifJ when cotranslated with NifV, or increased levels of NifY when cotranslated with NifM, did not greatly influence nitrogenase activity (SI Appendix, Fig. S4).

However, some protein combinations did not give rise to the expected stoichiometry when assembled as polyproteins. For example, cotranslation of NifU and NifS with NifV, or with NifZ, led to severe decreases in NifUS levels. In both cases, this had a detrimental effect on nitrogenase activity, emphasizing the crucial role played by NifU and NifS in [Fe-S] cluster biosynthesis for the three metalloclusters present in the nitrogenase component proteins (40 ⇓ –42). We also observed some spontaneous processing of NifJ and NifU when cotranslated as polyproteins independent from TEVp cleavage (SI Appendix, Fig. S4). We reason that this may result either from ribosome drop-off (43) or polyprotein instability.

We examined the potential advantages of incorporating fusion proteins into our polyprotein designs as an alternative to splicing and release of each individual component. In accordance with previous studies (25, 44, 45), significant activities were obtained with NifD∼NifK, NifE∼NifN, and NifN∼NifB protein fusions after optimization of linker lengths. However, among the polyprotein combinations that we tested, the only advantage conferred by this strategy was provided by the NifN∼B fusion when located in a polyprotein with NifE (nifEǒN∼B), which exhibited increased activity compared with NifENB spliced into single components (nifEǒNǒB). This enhancement may result from more efficient transfer of the NifB-co cluster from NifB to NifEN as reported previously (25). Interestingly, some polyproteins exhibited activity even in the absence of TEV protease cleavage. These functional polyproteins may provide initiatives for directed evolution of proteins with multiple functions, thus reducing the number of components required to re-engineer a CBS. Previous reports have suggested that NifW and NifZ function in MoFe protein maturation (28, 29), with NifZ acting as a chaperone in the assembly of P clusters (28, 29, 46). However, in our hands, in the heterologous E. coli background, single or double mutants of nifW and nifZ had negligible effects on the activity of the reconstituted operon-based nitrogenase system. In contrast, the polyprotein-based nitrogenase system was more fragile in this respect, with decreased activity being observed in the absence of NifW. It is possible that this represents a kinetic effect since nifW and nifZ mutants delay the induction of nitrogenase activity in K. oxytoca (29). Recently, it has been demonstrated that NifW and NifZ bind to immature forms of apo-NifDK and are likely to function as assembly factors required for P-cluster maturation (47). Since diazotrophic growth is slower in nifW mutants, it has been suggested that either the function of this gene can be partially complemented by another gene or nifW plays a kinetic role in MoFe protein maturation. These observations imply that the operon-based system in E. coli enables optimal maturation of the MoFe protein in the absence of NifW, whereas the requirement for this protein in the polyprotein-based system may reflect a slower rate of P-cluster formation or maturation. Thus, although our polyprotein combination appears to faithfully reproduce the protein stoichiometry observed with native nif operons, further iterations of this approach may be necessary to fully optimize nitrogenase biosynthesis and activity.

In recent studies, we and others have demonstrated that homologs of the [Fe-S] cluster biosynthesis machinery and electron transport modules present in eukaryotes are compatible with the nitrogenase system (10 ⇓ –12). If the Nif-specific components encoding iron-sulfur cluster biosynthesis (nifU, nifS) and electron transfer (nifJ, nifF) can be functionally replaced by their eukaryotic counterparts, the number of components required, for example, to assemble active nitrogenase in plant organelles could be significantly reduced (8, 10 ⇓ –12). One of our polyprotein-based nitrogenase systems, consisting of three giant genes (nifHǒDǒK, nifEǒN∼B, and nifVǒWǒMǒY) with nifU, nifS and nifJ, nifF expressed as separate components, exhibits 50% nitrogenase activity and permits slow growth of E. coli with N2 as the sole nitrogen source (assembly XII in Fig. 3). Our results therefore imply that only three giant genes might be required to engineer diazotrophy in eukaryotic organelles, with components for iron-sulfur cluster assembly and electron donation being supplied by the host.

In addition to complex biological systems such as nitrogen fixation, there is considerable interest in engineering bacterial metabolic pathways in plants, for example, to produce antifungal and antibacterial secondary metabolites that provide resistance against pathogens and for effective degradation of xenobiotics. The polyprotein strategy thus may provide a useful approach to engineering complex bacterial pathways for agronomic, ecological, and economic purposes.


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