In reference 20, Potapov and colleagues published a world map that outlines the "Intact Forest Landscapes" (i.e., large areas of undisturbed forest). You can view the map here.

"Carbon stocks" refers to the amount of carbon that is stored in forests. Trees, other plants, and even forest soils store organic carbon (e.g., think of photosynthesis).

In references 16–18, the authors describe baseline measurements for carbon emissions and stocks in tropical forests/regions.

Now, what is the difference between a carbon stock and a carbon emission?

A carbon stock is stored carbon. (Think of a tree trunk made of carbon-rich cellulose and lignin.)

A carbon emission, however, is carbon that has been released into the atmosphere. (Now, consider a tree trunk that has been burnt to ash, thereby releasing carbon.)

Why were agricultural lands abandoned in Eurasian coniferous forests?

The answer lies in changing political regimes. A large number of farms were abandoned in post-Soviet Russia (after socialism fell) because the economy and institutions of Russia where undergoing a radical change.

Hansen and colleagues reference work from Jonathan Foley and colleagues (2005), which details how harvesting natural resources can have negative effects through a decrease in ecosystem services.

For example, Foley and colleagues show that "forests in the Yangtze watershed help moderate" water flow, which then supplies a hydroelectric plant with energy (40 million kilowatt hours per year). This energy is valued at $610,000!

In comparison, this value is roughly 40% of the value of the trees in the forest that are then harvested for timber.

In comparison, this value is roughly 40% of the value of the trees in the forest that are then harvested for timber. Thus, harvesting resources (in this case timber) can negatively effect other ecosystem services (in this case water flow), which are also important (e.g., worth $610,000 in energy).

Which came first, the rain or the rainforest? Find out here and discover one of the many ways that forests affect our water supply.

In reference 40, Goetz and Dubayah summarize both aircraft and satellite imaging techniques. They also explain how tree canopy height is measured.

Tree canopy height is measured by light reflectance. First, a laser on a satellite (in this case, NASA's Geoscience Laser Allometry System, or GLAS) is emitted and pointed at the surface of Earth.

The light from the laser reflects off of Earth's surface and is then received by the satellite. The time that it takes for this to happen can determine the distance from the satellite to Earth's surface.

When the laser is emitted over a forest, the tree's leaves and branches reflect the energy, yet some of the laser's energy will still reach the ground and will be reflected from the surface of the soil.

Thus, the satellite receives two main light reflectance measurements: reflectance from the ground and reflectance from the tree canopy.

Then, the difference in the time it takes for the ground reflectance and canopy reflectance light to reach the satellite determines how tall the trees are.

For more information, check out Figure 2.

For Hansen and colleagues' study, they decided that any plant that had a canopy height of 5 m or taller was a tree (rather than a shrub or herbaceous plant).

Thus, determining canopy height is an important step in processing the satellite images to find where forests are distributed around the world.

In reference 36, Gong and colleagues describe the first study that uses Landsat satellite images that photograph Earth's surface at a 30 m by 30 m resolution.

With these photos, they characterized Earth's surface into different land types (e.g., agricultural land, forests, grasslands, ice).

They found that "forests, grasslands, and shrublands cover 28.35%, 13.37%, and 11.49% of the world, respectively. … Inland waterbodies, barren lands, and snow and ice cover 3.56%, 16.51%, and 12.81% of the world, respectively."

In reference 30, Hansen and colleagues look at tree cover using the Moderate Resolution Imaging Spectroradiometer (MODIS) instrument.

The calculations for tree cover were then used in this current paper to determine forest distribution, loss, and gain.

Also, note that technology is continuously advancing. Reference 30 was published in 2003. At this time MODIS was the most sophisticated satellite imaging instrument available. Yet, it could take images at a resolution of only 500 meters squared.

In this paper from 2013, Hansen and colleagues use Landsat data that has a resolution of 30 meters squared.

On page 7 of the supplemental material s Figure S2. On the x-axis are the countries with forestry programs, whereas countries on the y-axis have deforestation caused by factors other than forestry.

To normalize data in statistics refers to adjusting the values in a way that gets rid of confounding factors, in this case these factors are the large variation in sizes of different countries and sizes of forests that are being changed in each country.

By normalizing these data, Hansen and colleagues can directly compare the forest change in different countries.

Normalization is akin to the saying "comparing apples to oranges," and taking the apples and oranges and making them more similar to each other so that they can be directly compared, like comparing star fruit with star fruit. (Star fruits taste like the cross between an apple and an orange.)

Tree canopy density is an important concept in this study, because it determines whether an area of land is a "forest" or not a "forest."

To explain, Hansen and colleagues could analyze the satellite images of Earth at a resolution of 30 m by 30 m. For each of these 30 m by 30 m sections, they then calculated the proportion of that section that was covered in a tree canopy.

Using this map, forests can be defined as a user prefers by applying a threshold of tree cover density; for example, tree cover greater than 50% can be labeled as forest.

To discover more about boreal forest fires, click here.

In addition, this refers to previous work from Potapov and colleagues (including some of the authors from this study.) that identified the cause of forest loss around the globe.

They found that within the boreal climate domain "of the total forest cover loss identified, 58.9% is attributable to wildfires."

Find out more about mountain pine bark beetles on the U.S. Forest Service website.

Also, check out this figure from Kurz and colleagues on the extent of mountain pine beetle infestations (in red) in British Colombia, Canada.

W. A. Kurz, C. C. Dymond, G. Stinson, G. J. Rampley, E. T. Neilson, A. L. Carroll, T. Ebata, L. Safranyik, Mountain pine beetle and forest carbon feedback to climate change. Nature 452, 987–990 (2008).

In 2010 Indonesia and Norway signed the Oslo Pact, which gives Indonesia a $1 billion incentive to reduce their carbon emissions by conserving forests rather than clearing them for oil palm plantations, for example.

However, this pact isn't exactly perfect and has its own loopholes.

For instance, forests in the lowlands of Indonesia have been previously used for logging and thus do not qualify in the terms of the Oslo Pact. Therefore, logged forests that may still hold considerable carbon and be home to rich biodiversity are not protected.

Landsat is a a joint program between the U.S. Geological Service (USGS) and the National Aeronautics and Space Administration (NASA).

In this program, satellites orbit around Earth and take photos of Earth's surface.

The photos taken from the satellites are not the type of photos you would take with a typical smartphone. Instead, these images can show the energy that is both reflected and emitted from Earth in many different wavelengths, including blue, green, red, near-infrared, midinfrared, and thermal-infrared light.

For a look at energy wavelengths click here.

To distinguish forests from other land types (e.g., grasslands, water, etc.), one can look at a combination of different wavelengths in the Landsat data. For instance, looking at a combination of the red, near-infrared, and shortwave infrared wavelengths helps identify forests. Our eyes are similar to a satellite sensor, except we only see in the visible wavelengths, namely red, green, and blue. Forests, to our eyes, appear dark green, meaning low blue and red reflectance and brighter green reflectance. By using remote sensing technology, we can improve our identification of forest extent and change by adding other wavelengths of reflected and emitted energy not visible to the naked eye.

Find out more about how the different wavelengths can help identify different features, here.

You can view some Landsat photos here. Be sure to check out the photos of deforestation in Bolivia, which is particularly relevant to this study!

Also check out this Landsat image video.

Landsat images are online and available to the public. You can find data here.

Hansen and colleagues use Landsat data to evaluate changes in forest cover from 2000 to 2012. How do they communicate this information? Are these maps informative? Why or why not?

In reference 29, Hansen and colleagues detail the use of Landsat data to look at continent-scale images.

This initial study helped Hansen and colleagues to then scale up to look at global patterns in land change in the present study.

In reference 35, Achard and colleagues investigate deforestation in tropical humid forests. To do this, they surveyed 100 sites in Latin America, Africa, Southeast Asia, and India.

Hansen and colleagues build off of this study by looking at all forests worldwide and do not limit themselves to particular sites.

Before Hansen and colleagues could analyze the Landsat images, they had to preprocess them. This preprocessing included making corrections for clouds and shadows, assessing the quality of the images, and normalizing the images so that they can all be directly compared.

Nanofiltration can be used in water and wastewater treatment to remove ions and organic substances. The applications can include water softening, color removal, industrial wastewater treatment, water reuse, and desalination. Additional information can be found in this peer reviewed article.

Sulfate-reduction bacteria can use various electron donors including hydrogen, lactate, ethanol, and methanol.

For more detailed information:

A review of biological sulfate conversions in wastewater treatment (Review) Tian-wei Haoa, Peng-yu Xianga, Hamish R. Mackeya, Kun Chia, Hui Luc, Ho-kwong Chuia, Mark C.M. van Loosdrechtb, Guang-Hao Chena.

Sulfur cycle:

Real world image:

The paper connects to Vision and Change Core Competencies and Disciplinary Practice Competency 6 while showing students how science could be connected to society even in the process of data collection.

The paper connects to the English Language Arts Standards 11-12.6 as it analyzes the problem of sewer corrosion and explains the main sources of high sulfide concentrations with the designed experiments and modeling. Moreover, it identifies the importance of an integrated urban water management system as an issue that remains unresolved.

The total number of samples taken from a sample population.

Standard error of the mean = standard deviation/number of samples (Reference)

Gravity sewer systems are used to transport wastewater by means of gravity.

Mostly used in seawater desalination, which means removing salt from seawater to produce drinkable water. A more detailed explanation on how reverse-osmosis works can be found here.

This is a book reference that includes information on experiments and case studies done to compare ferric chloride and aluminum use in water treatment and their effects on concrete corrosion.

Water-sensitive urban design (WSUD) can be described as connecting the water cycle into urban design to try to eliminate the negative effects of stormwater. Examples of WSUD can be:

-Green roofs,

-Rainwater tanks for stormwater harvesting and reuse,

-Porous pavements,

-Undergroundwater recharge and reuse, etc.

For additional information, visit

The article connects to the Learning Standards, Common Core: Statistics and Probability (Construct viable arguments and critique the reasoning of others) :

The paper critiques the current division in drinking water production and sewer/wastewater management in the decision-making process and encourages the implementation of a water cycle approach that integrates these governmental subsystems.

Fair

Conditions in absence of oxygen.

Another common term in this context is anoxic conditions. It refers to the conditions without oxygen but with the presence of nitrate.

Infrastructure (e.g. roads, bridges, pipe lines, etc.): basic equipment and structures for proper functioning of a region or organization (Reference).

Coagulants are chemicals used to remove particulates by forming flocs and therefore increasing the weight and facilitating the gravity settling (Reference).

Diseases could be bacterial, viral, or parasitic. Examples: diarrhoea, hepatitis A, and giardiasis (Reference).

This paper connects to NGSS 8 practices for science and engineering Practice 1 and Science Practices for AP Biology Practice 3 by describing the problem that sulfide is the main reason for sewer corrosion globally.

The paper connects to Learning Standards Common Core:Statistics and Probability (Make inferences and justify conclusions from sample surveys, experiments, and observational studies) : Figures 1 and 2 demonstrate results from gathered data and surveys explaining that aluminum sulfate has a major role as a sulfate source in sewer corrosion.

This reference can be visited in order to get an idea of approaching water infrastructure replacement requirements.

They estimated that the budget requirement for the replacement of water infrastructures will be about $250 billion in the next 30 years.

Highly basic polyaluminum chloride (PAC) products can be used for water and wastewater treatment processes.

PAC is a type of aluminum product that is not as acidic as aluminum sulfate in the solutions. So during PAC addition, there is less risk of a shock acidic load in the treatment plants (Reference).

This reference investigates the use of an enhanced coagulation process in order to remove not only the particles, but also dissolved organic material in the water, which will help to increase the drinking water quality.

Mitigation can be defined as actions to prevent damage to the property (Reference).

Here is an informative and funny (close to the end) video describing coagulation/flocculation process.

Coagulation is a key process during drinking water purification. Aluminum sulfate is one of the most commonly used coagulants during drinking water treatment for removal of impurities such as suspended solids and natural organic matter.

While aluminum forms precipitates, sulfate remains dissolved in the drinking water and ultimately ends up in sewage, and thus increases the total sulfate load in sewage.

Figure 5 in Supplementary Materials shows differences in the cost of treatment in two cases: Average HRT and T=20C, Long HRT and T=25C (As mentioned before HRT describes the time necessary for particles to travel the system from the entrance till the outlet.)

Figure S5 shows the cost of treatment per m3 of water treated in the y-axis. The x-axis presents the two different scenarios: baseline (average HRT and T=20C) and long HRT and T=25C.

They looked at the effect of these two scenarios in two samples:

Source water sulfate with 15 mgS/L and Source water with no sulfate. In both scenarios, source water with sulfate had higher expenses compared with the condition with no sulfate in source water.

The long HRT condition is investigated to account for the conditions that could favor sulfide formation and corrosion in the sewer, in other words it is a representation of the worst-case scenario.

Particles ranging between 1 and 1000 nanometers in diameter (Reference)

In other words, when sulfate is not used as a coagulant, sulfate concentrations of the water coming into the treatment plants were similar to the sulfate concentrations of the water leaving the plants.

This reference is a technical report by the Environmental Protection Agency.

It consists of parts including: national assessment of corrosion; effects of industrial pretreatment, detection, prevention, and repair of hydrogen sulfide corrosion damage.

The reference can be reached by visiting this link

The time needed for a component to exit the system.

This study investigates the changes in the natural organic matter (NOM) concentration in raw and conventionally treated drinking waters in two hemispheres. They investigated the characteristics of NOM in Norwegian and Australian waters as well as the effect of coagulation treatment.

A statistical term. When you order the numbers in a sample from lowest to highest the number in the middle gives the median value.

Domestic watewaters are produced in our homes, whereas industrial wastewaters, as the name implies, are produced as a result of an industrial activity.

Inorganic anion (a negatively charged ion) of sulfur

Here is a fun video showing drinking water treatment.

FeCl3. This is a commonly used coagulant during water treatment, and also has wide-spread used during wastewater treatment for the removal of phosphate as well as sulfide.

Total chemical consumption is reported as 70% in wastewater treatment, 15% drinking water treatment, and 15% other (electronics, photography, and asphalt).

This paper looks in depth into the issue of seawater desalination. It is trying to answer questions such as energy requirements, how new materials/technologies can improve it, and sustainability. In this paper, the reference is used to convey the idea that these technologies still require improvement to compete with conventional drinking water treatment.

One of the important findings of the empirical literature on youth and jobs programs is that job programs are very costly to operate. Often the social benefits of a program do not justify its costs.

Violence is a social problem particularly troubling in Chicago. This is an issue that President Obama has discussed as important to address. This link shows you some trends:

http://crime.chicagotribune.com/

Previous research conducted by the author shows that social-emotional learning curriculum is capable of reducing violence even when a summer jobs program is not in place.

A proxy is a substitute. In the analysis of research, sometimes certain measurements or indicators are wanted but missing from the data set. If that is the case, a proxy measurement can be the solution.

In this case the researcher wants to have an indication of family poverty because poverty is an important piece for understanding the background of the students involved in the study. Because free or reduced price lunches are based on household income levels, they can serve as a proxy measurement.

Observational studies are those based only on the observation of interactions. There is no experimental intervention.

Because the previous observational studies do not prove that summer jobs cause a reduction in violence, the author proposes an experimental research design.

Connects to Essential knowledge 3.A.1 in AP Biology Course Description.

http://apcentral.collegeboard.com/apc/public/courses/teachers_corner/2117.html

Covered with fibrotic tissue.

A scar on human skin is an example of fibrosis. Instead of skin cells replacing the injury, fibrotic connective tissue takes it place.

Discusses models of skeletal patterning.

Review of pattern formation in vertebrates, but more under the sense of development rather than regeneration.

A "textbook" that provides a basic foundation in regenerative biology. Discusses the dependence of skeletal muscle regeneration on nerves.

A hormone that acts as a signal for growth in an organism. Can either be a sterol or protein.

At the cellular level, growth factors often promote synthesis of new DNA and cell division.

A type of cell that is closely affiliated with cells making up the peripheral nervous system. Briefly, these cells provide support for the nerve cells.

They are also thought to be important in promoting the regeneration of peripheral nerves after transection

A wrist level stump is made by transecting the "hand" of the salamander off.

That blastema is then grafted on the shoulder stump of another salamander. The shoulder stump of that salamander is made by amputating the whole limb.

A textbook/reference book that provides readers a basic foundation of regenerative biology.

Review article. Describes how Neuregulin-1 is the likely signaling molecule that causes myelin formation.

Review article. Discusses the field of limb regeneration in vertebrates and its possible contribution to medicine.

When abnormal blastemas are formed via changing direction of the brachial nerve, fibroblasts from the dermis of the skin must be grafted to produce the full limb.

Those fibroblasts are likely providing some sort of instructions telling the blastema how to form the rest of the limb as well as contributing directly to the new tissue.

An increase in how often the cells divide.

Another way of saying low magnification, zoomed far out.

A GPI-anchored protein important in tissue reorganization events.

A protein that has gone through the secretory pathway and been released into the outside environment.

For a video on protein trafficking and secretion please see: https://www.youtube.com/watch?v=rvfvRgk0MfA

The nerves that extend into the limb were cut at the brachial plexus. This is essentially the region where the limb meets body. In humans, roughly around the shoulder area.

For an image see here

The authors don't believe that nAG has any effect on specifying tissues. In other words, it does not tell a stem cell to become bone or neurons or skin.

Instead, nAG has its effect simply by increasing the number of dividing cells.

Deformed, wasted, smaller in size.

A gland or glands or related to them.

The authors rename the homolog of this protein as nAG in their studies. The "n" stands for newt.

This is a stage in early limb regeneration where the blastema is still present, but you are starting to see growth of the new limb.

Breaking tissue or a clump of cells down into single, individual cells.

Save or reverse. To put another way, "can nAG restore limb regeneration in denervated animals?"

The movement of cancer from one location to another.

For example, lung cancer can metastasize and spread to the lymph nodes.

BrdU was added to medium for a period of time and then removed.

Pulse labeling, in general, is the addition of substance and then its subsequent removal.

This is much like the pulse button of a blender where you press it for a few seconds to blend and then release it shortly after to stop.

Describes a step-wise procedure for examining limb regeneration. However, this paper is referenced in regard to the fact that they demonstrate deviation of the nerve can cause an ectopic blastema.

A diagram of their protocol can be found here

Stands for Human Natural Killer-1. Based on this naming what organism was originally discovered in?

African clawed frogs (scientific name Xenopus laevis or shortened to Xenopus) is a common model organism in biology.

Development of a pattern.

In the case of biology, this usually refers to how a structure such as the limb becomes patterned. That is, how muscle cells are specified, how the digits are made, how the cells know to become skin cells, etc.

The evidence from this figure suggests that nAG is able to cause more blastemal cells to divide. The authors propose that this is how nAG works in the salamander.

This gets at a possible mechanism for nAG's effect in the living organism and provides potential avenues for further study.

The regeneration stage where digits (fingers) are clearly visible and present.

The limb on the other side of the body. For example, your left arm is contralateral to your right arm.

Tubulin is a major protein of the cytoskeleton and makes up microtubules.

Acetylated tubulin is very similar, but has an acetyl group (COCH\(_3\)) added to it.

Proteins that are part of the same family as nAG.

Artificially changing direction or "deflecting" the brachial nerve to another part of the salamander can cause an abnormal limb blastema to form.

Remember, the brachial nerve is where they denervated the salamander at in many of their experiments.

This suggests that something from the brachial nerve, likely nAG, is stimulating division and growth of these cells.

That is, for a limb to regenerate it depends on, or needs the nerve.

Without the nerve supply to the limb, it fails to regenerate.

test

test

Author's Hypothesis: 4

The estimated duration of immune suppression in hypothesis 3 must be biologically relevant. We have years of data from other scientists who have measured the amount of mortality following measles infections. Thus, to strengthen the reliability of this paper's findings, then the duration of immune-amnesia that this paper determines should agree with the time frame during which previous studies have found children to be at increased risk of mortality following measles.

Additionally, a basic hypothesis underlying this paper is that children recover from immune-amnesia by rebuilding their immune response through re-exposure to pathogens. This process is similar to how children first build up their immune response after birth - through exposure to pathogens. Thus, if the hypothesis put forth in this paper is correct, then the time it takes to recover from measles induced immune-amnesia (i.e. the duration of immune-amnesia) should be similar to the amount of time it takes children to build an immune response in the first place.

This is a control experiment preformed by the authors.

To test that their analysis doesn't result in falsely positive results another childhood disease, Pertussis, which is preventable by vaccination but does not cause immunomodulation was also analyzed. It was found that data did not demonstrate immunomodulation like measles disease.

Sequelae simply means a negative after-effect.

In this case, it is the long-term negative impact on the bodies defense system (immune system) following a measles infection. This negative impact is also known as immunosuppression.

Typified means "characteristic of", as in basically all measles virus infections will behave this way.

Unmet vaccination targets mean that countries are failing to vaccinate enough of their populations to achieve herd immunity and provide adequate protection to prevent the spread of the measles disease.

Polymicrobial

Poly = many, like how a polyhedron is a shape with many sides

Microbial = having to do with microorganisms, or living things that are too small to see with the naked eye. Like viruses, bacteria and fungi, some of which can make you sick, and some which can be beneficial (like yogurt!)

All-cause infectious disease in this paper aims to describes infectious diseases other than measles. In other words, diseases caused by all infectious agents.

B and T lymphocytes are important cell types that make up the long-term response of your immune system.

When the body fights off disease it uses some generic, built-in responses to be able to start controlling an infection right away, but this innate response is rarely able to cure you. After about a week, your body learns the specific pathogen that is making you sick and makes B and T lymphocytes to effectively fight off that specific pathogen, and importantly, to remember it in case you get sick with the same thing again. Using this learning response (called an adaptive immune response because it adapts to the infection you have) is how vaccines work.

If the B and T lymphocytes you made against a specific pathogen are killed then you loose that specific response, the "memory" you built to defend yourself.

If the number of B and T lymphocytes you have is reduced, this can also impair your ability to fight off a pathogen no matter if you have done so before.

To learn more about how the immune system works to fight off infection you can read this free Chapter from the textbook "Molecular Biology of the Cell"

Interannual fluctuations in nonmeasles deaths is another way to say "the yearly change in the numbers of nonmeasles deaths." In other words, the number of children who die from diseases other than measles changes from year to year.

The authors in this paper will use these changes in the number of deaths, correlated to the number of measles cases, to demonstrate the long-term effect of measles caused immunosuppression.

The pre-vaccine era is before the measles vaccine became available for the public for use in the 1960's.

The post-vaccine era continues today, when the measles vaccine (MMR) is available to those who wish to receive it.

Disease mortality is the scientific term used for the amount of death a disease causes. The flu, which kills many people every year, has a HIGHER mortality than the common cold.

A more prolonged effect simply means a change which lasts longer. In this case it is a longer effect on host resistance (see next annotation).

Predispose means to make something easier to happen, in this case easier to get sick. For example, if you do not exercise and eat right you are predisposed to (or more likely to become) obese.

Population-level data is a term that is used in statistics to describe including the entire population in your analysis. This is in contrast to using a smaller sample population to infer (make an educated guess) things about the whole population.

For example, imagine that your entire school is the population you wish to study. If you want to collect population-level data you will need to ask everyone if they like chocolate ice cream. Sometimes this isn't possible so scientists collect the data from a smaller sample, like just your class. They learn that 75% of your class likes chocolate ice cream and so they infer that 75% of the entire school likes chocolate ice cream. This approach is easier, but it is still more accurate to survey the entire class.

In this study, the use of full population-level data, not inferences from sample data, makes their conclusions stronger.

Food for thought: What is the population that is really important to study in this research? In other worlds, the population of a single country is really a sample of what even larger population?

Ref 13. is a review from a conference where researchers met to better understand how factors about our lives can influence responses to vaccines. They propose that what vaccines we have received in the past, our childhood exposures, gender, and even our genes can affect our responses to vaccines.

Ref 11. WHO and other researchers have found that the Measles vaccine, and other live vaccines, can have effects of childhood mortality not associated with the vaccine target. This reference is a review of some of the studies done in the past to try and better understand this off target effect.

Ref 12. Scientists use a sample from Bangladesh to look at data similar to the results of this paper. They also find that Measles vaccinating reduces childhood mortality not due to Measles, specifically from diarrhea and oedema. However, the data used in their analysis is only one sample of a population and is confounded by some study control issues.

Ref 13. Researchers have also noted that there are differences in the gender of the child that can change how protective the Measles vaccine is at protecting against other illnesses.

The World Health Organization (WHO) is an important world-wide organization that measures human health, makes important recommendations to countries to help maintain the health of its citizens, and provides support during epidemics, outbreaks, and other human crisis.

They report on the importance and impact of measles disease, even with an available vaccine.

• Measles is one of the leading causes of death among young children even though a safe and cost-effective vaccine is available.
• In 2013, there were 145 700 measles deaths globally – about 400 deaths every day or 16 deaths every hour.
• Measles vaccination resulted in a 75% drop in measles deaths between 2000 and 2013 worldwide.
• In 2013, about 84% of the world's children received one dose of measles vaccine by their first birthday through routine health services – up from 73% in 2000.
• During 2000-2013, measles vaccination prevented an estimated 15.6 million deaths making measles vaccine one of the best buys in public health.

Read more here: WHO Measles Key Facts

Vaccine hesitancy refers to the choice of some individuals to not have their children vaccinated against measles.

The debate surrounding vaccination began with a now discredited paper in 1998 that falsely claimed a component of the MMR vaccine was linked to autism. This paper was based on false patient data, but it got a lot of press and scared many parents. Read more about the history of this debate and it's impact on public health in this BBC article.

Watch a short CNN video here about why the MMR vaccine is safe.

Vision and Change Core Competencies and Disciplinary Practice. Competency 4: Ability to tap into the interdisciplinary nature of science

This paper relies heavily on the data collected by national public health organizations, previous observations and research, and the ability of biostatisticians and mathematicians to analyze the data in new and creative ways.

Common Core: Statistics & Probability: Calculate expected values and use them to solve problems

The authors have calculated the length of immunomodulation in this paper and used it as a model to understand the impact of measles on childhood infectious disease mortality, students have been able to follow that process in this paper.

Vision and Change Core Competencies and Disciplinary Practice. Competency 1: Ability to apply the process of science Students who read this article are being shown how scientists gather and analyze data to test a hypothesis and come to conclusions. They are then asked new questions based on those conclusions and evaluating the results.

NGSS 8 practices for science and engineering/Science practices for AP biology. Practice #6 The student can work with scientific explanations and theories

This paper deals with a topic which has been well researched in the past, in order to understand this work students must understand the previous theories and how the authors theory of using high-income country data provides a new explanation on previous observed phenomenon

English Language and Standards (Science & Technical Subjects) 11-12.3: Follow precisely a complex multistep procedure when carrying out experiments, taking measurements, or preforming technical tasks; analyze the specific results based on explanations in the text.

This article requires students to follow a process which analyzes data based on 4 stages of testing to evaluate a conclusion

Conclusion 4: When the analyses in this paper were repeated using non-measles deaths due to specific infectious diseases (i.e. pneumonia, bronchitis, diarrheal disease, etc...) the results were consistent with the primary analyses, which were performed by pooling all of the non-measles infectious disease death counts together.

Conclusion 2 and 3: When the authors take into account that there is some extended duration to the measles induced immune-amnesia, they find that their math reveals an average 28.3 months duration. As explained above, this is because the prevalence of immune-amnesia had the strongest correlation with non-measles infectious disease mortality under the assumption that the immune-amnesia lasted for 28.3 months on average.

Conclusion 1 The authors observe a correlation in Europe and the United States between measles infections and overall mortality (death). These results meet their first hypothesis.

The Facial Action Coding System (FACS) is a system for identifying and categorizing changes in facial expression.

Even minute anatomical changes in facial muscles (i.e., contraction or relaxation of specific muscles in the face) can be coded as distinct "action units," and there is extensive training involved in being able to identify and code these facial movements.

The head scientist involved in designing the FACS system, Paul Ekman, is known for using FACS to detect microexpressions—brief, involuntary facial movements that can be used, among other things, in the detection of deception.

The television show Lie To Me was loosely based on Ekman and his work.

Named after 19th century French physician Guillaume Duchenne, a "Duchenne smile" is one that involves both the mouth and the eyes; it is considered to be a more "genuine" display of happiness, compared with a smile that only involves the mouth.

Here's an example, modeled by psychologist Paul Ekman, who is an expert on facial expressions and emotion.

Can you tell which one is which?

Test yourself with this short video!

The Linguistic Inquiry Word Count (LIWC, pronounced "Luke") software is text analysis software that can analyze linguistic content for specific words and/or categories of words.

This is the muscle that circles around the eye. It controls blinking, squinting, and the movement at the corners of the eyes that relates to Duchenne smiles.

Hedonic well-being is characterized by the achievement/fulfillment of pleasure. It is often considered to be a relatively short-term form of happiness.

This is the muscle that controls the corners of the mouth.

"Ego defensiveness" is very similar to self-protection. The idea is that people have psychological mechanisms that are commonly used to protect/defend the "ego," or the self.

"Political ideology" refers to how people identify themselves on the spectrum between liberalism and conservatism.

"Self-report measures" involve responses to basic survey questions. For example, asking participants how happy they are, on a scale from 1 to 10, would be a self-report measure.

By looking at the difference in violent behavior between youth who are involved in a summer jobs program and those who are not involved in a summer jobs program, this study finds that summer jobs do help reduce youth violence. Importantly, the reduction occurs after the summer jobs program ends.

Another consideration for the interpretation of these data is that analysis relies on arrest rates. Arrest rates only reflect a fraction of actual violent acts since many such acts are not reported and many do not result in an arrest.

One of the possible explanations for why violent crime arrests drop consistently after the end of the jobs program is that time spent in school increases. Testing for this effect, however, shows that this is not likely.

Because of the way this study is designed, it is not possible to make the claim that arrest rates decline even more for youth who can be categorized as at higher risk for violent activity. However, findings from this study show that this might be likely. This would make for interesting future research.

Even though there was a reduction in the arrest rates for violent crimes, there are no statistically significant changes in the arrest rates for property, drug, or other kinds of crimes. This indicates that there is something unique about the relationship between the summer jobs program and violent crime.

This is a significant finding of the study. When comparing violent crime arrests between the treatment group (summer jobs) and the control group (no summer jobs), there were 43% fewer arrests for the treatment group after they participated in this summer job program.

This paper uses a new approach to look at an old problem--the problem of youth violence. The new approach involves testing whether summer jobs programs result in reduced youth violence.

The authors also crossed the yellow F1 males to wildtype females to generate F2 offspring. A diagram of this cross is shown in Figure 2A.

After they had determined which of the F1 progeny expressed the mutagenic chain reaction allele (yMCR), they crossed the yMCR F1 females back to wildtype males to obtain the F2 progeny.

The authors injected their construct into fly embryos so that the germline cells in the embryo would incorporate the construct into their nuclei. Once these flies (called the F0 generation) were adults, they crossed them back to wildtype flies to obtain the F1 progeny.

Connects to Essential Knowledge 3.A.1 of AP Biology Course Description.

http://apcentral.collegeboard.com/apc/public/courses/teachers_corner/2117.html

Connects to Essential Knowledge 3.A.3 of AP Biology Course Description.

http://apcentral.collegeboard.com/apc/public/courses/teachers_corner/2117.html

Esvelt et al. bring up several additional precautions to consider before use of gene drive on native populations, such as determining if gene drives could incorporate into related species and performing field trials of both the gene drive and the gene drive reversal.

The DiCarlo et al. study describes a method that can help prevent accidental release of mutagenic chain reaction organisms into the environment.

In this reference, the authors designed the gRNA targeting the fly yellow locus that Gantz and Bier used in the current paper. They chose to use this gRNA sequence because the authors in the reference here showed that this gRNA sequence resulted in the highest percentage (88%) of yellow mosaic flies of the 4 gRNAs tested.

In this paper, the authors use homology-directed repair (the same technique used in the current paper to generate the MCR allele) to introduce foreign DNA sequences at specific genome sites in the fly. This was an important advancement because most other studies have used CRISPR/Cas technology to create insertion or deletion mutations in target genes. The Gratz et al. paper showed that CRISPR/Cas9 could also be used to introduce large DNA sequences into specific sites of the fly genome.

In this article, the authors design two transgenic Drosophila melanogaster lines expressing Cas9 protein and guide RNAs that target either the ebony or yellow genes. The gRNAs guide Cas9 to these genes and induce mutations. They determined that their strategy for targeting these genes was highly efficient and specific.

In this extensive review, Feng Zhang discusses in detail the original use of CRIPSR/Cas in bacteria, the timeline for its use in research, and how it has been used for genome editing.

The Feng Zhang lab has been instrumental in the development of CRISPR/Cas technology for use in genome engineering. In this review, Zhang summarizes how the tool works, how it can be used for genome editing, regulating gene expression, and for gene therapy as well as some of the limitations/weaknesses that are associated with the technology.

Intravital microscopy is a technique used to image live animals. It is a live video of processes occurring in the animal while it is still alive. It gives information on different cellular interactions and activities in real time.

In this experiment, the authors inject tumor necrosis factor-α, an inflammatory cytokine within the scrotum of mice, and, via IVM, study local inflammatory response in the cremaster (that covers the testis and speramtic cord) muscles.

For more information on how neutrophils migrate, see:

http://www.urmc.rochester.edu/labs/Kim-Lab/projects/mac-1_cd11bcd18_in_neutrophil_migration

https://www.youtube.com/watch?v=_gSsVrrUtrw

This would be a good place for a previous work annotation

This is a review of clinical findings that explain the cellular responses in TRALI. They also talk about how the interaction between neutrophils and platelets is essential to trigger TRALI.

This paper is a good read to see time-lapse videos of intravital imaging and confocal microscopy. It explains how neutrophils require distinct mechanisms to first bind and then crawl out of the vasculature.

They next determined the receptor on the cell surface that allows these cells to interact with each other during these collisions.

Blocking PSGL-1 did not affect the ability of neutrophils to adhere firmly to the blood vessels, but it affected the crawling.

Thus, the authors take a guess that indirectly the PSGL-1 on the uropod, although not interacting with the endothelium, is somehow helping the neutrophils crawl.

The authors were able to see the neutrophils and platelets interacting with each other (in close proximity of these cells). Having labeled the CD62L with blue color, they were able to distinguish between the leading edge and the uropod.

Leukocytes are also called white blood cells. The vast majority of immune cells are leukocytes, neutrophils being one of them.

Integrins are another class of cell adhesion molecules. These receptors are known to interact with the extracellular matrix or surface proteins on endothelial cells, and help in the process of leukocyte extravasation, a process that involves the movement of leukocytes (white blood cells) through the walls of the blood vessels into the site of infection.

Chemokines are proteins released by cells that can recruit other cells by forming a chemical gradient (similar to a trail of scent).

Chemokines and selectins become alert/activated during an infection and, in turn, activate/trigger the integrins to initiate cellular recruitment.

In case of cellular responses, activation involves biochemical changes in the structure of molecules, which now allow it to bind/release from certain other molecules.

A series of such activation events is what induces a signaling cascade in cells.

Selectins are carbohydrate-binding molecules present on cell surfaces. Endothelial cells line the the walls of blood vessels.

E-selectins are produced by endothelial cells. During an infection, selectins serve to recruit immune cells to the site of inflammation.

Inflammation, meaning swelling with redness and pain, is one of the major consequences of an immune response. However, sometimes excessive inflammation can be harmful to the host, hence referred to as inflammatory injury (injury inflicted upon the host by the body's immune system).

In general, when the mammalian body encounters a foreign object, be it a pathogen causing disease or an allergic nonpathogenic molecule, the immune cells in the system are triggered and begin a cascade of reactions in an attempt to contain and eventually eliminate the foreign entity.

There are also reasons why summer jobs might not have any effect or have the opposite effect by actually increasing violent activity. This is why this study is important to do.

Somatic refers to all the cells of the body that are not germline cells (eggs or sperm).

Germline cells are the sex cells in the body (sperm in males and eggs in females).

A genus of flies that are often used as model organisms in research. They are commonly called "fruit flies."

A chimeric fly has two distinct cell populations. In this case, a mutagenic event occurred early in the development of the female chimera, causing it to have one genotype on one half of its body, and a different genotype on the other half.

Refers to the phenotype of an organism as it was found in nature. In contrast to a mutant allele, the wildtype phenotype is the product of the "normal" allele for a particular gene.

In addition to the PCR genotyping, the authors performed DNA sequencing using DNA from F1 flies that were yellow (y-). DNA sequencing is a tool that allows you to determine the exact nucleotide sequence of a region of DNA. The goal of the sequencing was to confirm that the expected MCR construct had been inserted into the y locus.

Overall, the authors can conclude that their mutagenic chain reaction strategy is very efficient at driving mutations in both chromosomes simultaneously, creating a homozygous mutant.

As the authors discuss, there are so many ways in which this MCR strategy could be used to speed up the creation of animal models for research or for potential therapeutic uses. It is certainly an exciting new tool for biomedical research and for clinical applications!

Gantz and Bier used the gRNA sequence targeting the fly yellow locus that was originally described by Bassett et al.

This previous study by Gratz et al. demonstrated that homology-directed insertion of large foreign DNA sequences could efficiently be inserted into the fly genome by CRISPR/Cas9.

Gantz and Bier used the Cas9 transgene described in Gratz et al. (vasa-Cas9) as the source of Cas9 in their MCR construct because this gene (vasa) is expressed in all cells of the fly.

These two reviews by the Feng Zhang lab summarize much of the previous work done to lay the ground work of developing the CRISPR/Cas9 technology and its use in genome editing and making the mutagenic chain reaction performed in the current study possible.

Among the F1 progeny (offspring from flies injected with the Mutagenic Chain Reaction construct mated to wildtype flies), the authors obtained females that were yellow (y-), meaning that they expressed two copies of the recessive yellow allele. This is not possible according to the Mendelian rules of inheritance, which predict that all females of this cross should be brown (they would inherit a y+ allele from the wildtype parent and since the y- allele is recessive, one is not sufficient to create the yellow color).

The fact that the authors obtained yellow female flies means that their mutagenic chain reaction worked! The mutant allele these females inherited from the F0 parent subsequently mutated the wildtype allele they inherited from the wildtype parent, giving them two copies of the mutated allele.

Their DNA sequencing experiment confirmed that all yellow flies from the F2 generation had insertion of the expected MCR construct, again confirming the success of the MCR targeting. The authors also DNA sequenced the y locus from flies that did not have the predicted yellow color. They found that these events likely resulted from failure of homology-directed repair to occur. Instead, it seems that the Cas9 cut the DNA, but non-homologous end joining occurred to repair the break, so the MCR construct could not be inserted.

This YouTube video (starting at 3:18) describes the difference between homology-directed repair and non-homologous end-joining.

https://www.youtube.com/watch?v=vP8-5Bhd2ag

A genetic element is autocatalytic if it converts the companion chromosome to its own state.

Homology arms are DNA sequences in a plasmid that are identical to a specific genomic DNA sequence. The homology arms are used to direct homologous recombination of a plasmid into the genome.

Mosaic organisms have multiple cells populations with different genotypes. In this case, the mosaic flies had small patches of brown color but were mostly yellow.

Lakes, rivers, streams, etc. (NOT the ocean)

Lakes, rivers, streams

In other words, up to 40% of the carbon moving from the land to the atmosphere gets there via passing through surface water.

susceptible

Amount of time a molecule exists before it is broken down

Light travels from place to place in the form of a wave. All types of light have a characteristic wavelength. In the visible spectrum, red light has the longest wavelengths and purple has the shortest. UV light has shorter wavelengths than visible light.

Headwater streams are small, shallow streams that carry water from the surrounding land area into a main river.

Indicates that the water in this river came from melting glaciers

The amount of time that water stays in a lake before evaporating or flowing into another body of water.

Benthic is a word used to describe things that take place in the sediments at the bottom of a body of water.

Alaska is already experiencing the effects of climate change. See this article and this video for more information.

This article and this video describe the effects that climate change is already having on native Alaskans. Understanding how climate change will progress is important for maintaining these peoples' ability to live.

Bacterial respiration is when microbes “eat” organic carbon, causing it to break down into smaller molecules. In most cases, bacteria require oxygen to break down organic carbon.

Photochemical oxidation is when sunlight and oxygen react with organic carbon, causing it to break down into smaller molecules