1,059 Matching Annotations
  1. Feb 2018
    1. net primary production

      The rate of photosynthesis of plants minus the rate of respiration plants conduct to survive.

      Plants convert light energy, from the sun, to sugar during photosynthesis. Plants then use the sugar they created as energy to survive and function in their environment, this is considered plant respiration. The total amount of sugar left over is considered the net primary productivity of a plant.

    2. grasslands, C4 grasses and legumes tend to promote greater soil carbon accumulation (8).

      In a research study, conducted by D. A. Fornara and other scientists, C4 grasses and legumes were found to promote the greatest amount of carbon accumulation in the soil. If these two plant species were to go extinct, the total amount of carbon storage would vastly decrease because they are the main contributors to carbon accumulation in the soil. The results of this previous research study support the conclusion that different plant species affect ecosystem services differently.

    3. Moreover, species identities influence ecosystem services (39), such that the order in which species are lost from ecosystems could influence the quantitative responses of ecosystem services, like carbon storage.

      A research paper, drafted by C. M. Tobner and others, states that specific characteristics of different plant species influences ecosystem service such as: climate regulations, the amount of atmospheric CO2 converted into biomass (carbon storage), and water purification. All plant species do not affect atmospheric CO2 reduction in the same capacity. The loss of certain plant species could have a greater impact on ecosystem services, like carbon storage, than others plant types.

    4. edaphic factors

      An abiotic element that affects an environment. The amount of precipitation, temperature, geography, etc. These elements affect a plant's ability to reproduce, function, and conduct photosynthesis.

    5. Although the pattern of increasing plant carbon storage (and thus value) with plant species richness may be general, reflecting the well-documented relationship between plant species richness and plant productivity (4), it is possible that biome-specific estimates of the value of species richness will reflect variation in the relationships between species richness and carbon storage.

      A previous research paper, written by B. J. Cardinale and others, showed that there may be a general relationship, in all environments, that increased plant diversity increases the amount of carbon storage. Different environments around the world could respond differently to the same level of species richness, but will have an overall increase in carbon uptake.

      The author suggests that the estimated values of the most effective amount of plant diversity, for different environments, could show variation in the relationship between species richness and carbon uptake. By conducting experiments, on a variety of different environments, we will be able to figure out the best level of plant diversity, in specific environments, for the highest level of carbon storage. These results could greatly help reduce the CO2 pollution in the atmosphere and help deter global warming.

    6. incorporating this information into the C storage valuation of conversion of marginal or abandoned agricultural land into forests (17) (where forests rather than grasslands are the typically native vegetation) would also advance our knowledge about economic consequences of management decisions.

      A research study, by K. Paustain and others, indicates that the increased uses of forest species, in stripped farmlands, rather than using grassland species could help advance the knowledge of what is the best way to benefit the human population. This gain of knowledge, about land management, would help find the most effective way to decrease the amount of CO2 pollution in the earth's atmosphere. At the very least, the increased awareness of different methods of restoration, for different land types, would determine the additional increase in carbon uptake and its economic worth to total carbon reduction.

    7. Similarly, assuming that higher forest species richness also enhances C storage (5, 6)

      In multiple research papers dictated, by leading scientists A. Paquette and L. Gamfeldt, that higher species diversity in forests correlates to increased carbon storage. This research gives insight into the possibility of using forest species, for restoration purposes, instead of grassland species to increase the total amount of carbon storage in a environment.

    8. It is also worth noting that converting marginal or recently abandoned agricultural land (with typically very low soil C and species richness) to diverse prairie (for example, 11 species) would result in even greater increases in C storage than increasing CRP grasslands from 6 to 11 species (38).

      A previous research study, conducted by C. Fissore and coworkers, proposed that increasing species richness in recently abandoned farmlands, with low levels of carbon in the soil, to become diverse prairies would result in a higher increase of carbon uptake when compared to increasing plant diversity from 6 to 7 in CRP grasslands. Meaning that the addition of species richness, in environments with low levels of carbon, has a greater affect on carbon storage than conservation grasslands. By turning recently abandoned farmlands into diverse prairies, through the introduction of plant diversity, the amount of carbon sequestered from the atmosphere increases and helps deter global warming faster than the use of CRP grasslands.

    9. seeding monocultures

      Growing only one type of plant species in an environment.

      The use of only one plant species reduces the total amount of carbon uptake in a farmer's field and strips valuable nutrients in an environment and faster than the addition of multiple plant species.

    10. Although this may be more expensive up front than seeding monocultures (37)

      In a previous work written by P. Torok and research team, concluded that the use of a diverse seed mixture is more expensive to farmers than growing only only type of seed. This is a drawback to the the benefit of increased species richness in farmlands, but the advantage of a diverse array of plant species far out weights the initial cost when considering carbon uptake in an environment.

    11. Practices as simple as using more diverse seed mixes can promote higher species richness in prairie restoration (35, 36).

      A previous research paper posted, by leading scientists E. Grman and D. L. Larson, reported that the practice of increasing plant diversity is simple. All farmers have to do is use a seed mixture with a more diverse array of plant species. The use of the diverse seed mixture will help increase the carbon uptake in the farmers fields and help decrease atmospheric CO2 levels.

    12. from the Minnesota grassland experiments, the marginal value of gaining one additional species over this entire CRP area (increasing species richness from S = 6 to S = 7), would amount to ~$722 million. Restoring species richness on CRP grasslands to levels observed for the remnant grasslands (from S = 6 to S = 11) would confer a value for the increased carbon storage of ~$2.350 billion

      In a previous Minnesota grassland experiment, the addition of species richness from 6 to 7, increased the carbon uptake, of the CRP grasslands, by about $722 million. The increase of species richness from 6 to 11 increased the total carbon uptake, of CRP grasslands, by $2.350 billion. The authors used the economic worth or carbon to calculate the numbers seen above. Overall the author is trying to convey that increased species richness, in CRP grasslands, vastly increases the amount of carbon sequestered by the plants and is a huge benefit to carbon reduction in the United States.

    13. We synthesized published estimates of species richness in CRP grasslands and paired reference native grasslands (16, 31–34) and found that species richness in CRP grasslands (S = 6.5 ± 1.1) was lower than in adjacent remnant grassland sites (S = 11.4 ± 1.8), indicating the potential for CRP restoration to achieve higher species richness and associated ecosystem services.

      J. L. O'Connell and coworkers published estimates of plant diversity in CRP grasslands compared to native grasslands. The author of this research paper found similar results that species richness in CRP grasslands was lower than the native grasslands.The lower recorded plant diversity means there is a higher potential, in conservation grasslands, for increased species richness and ecological benefit.The increased plant diversity, in CRP grasslands, will benefit the ecosystem by increased uptake of carbon from the atmosphere and contributions to nutrient cycles.

    14. Across the conterminous United States, approximately 12.34 million ha of land under cultivation have been converted to CRP grasslands, increasing land C uptake by approximately 6.54 teragrams C year−1 [area and C uptake estimates averaged from (17, 27–30)].

      The author of this research paper used the findings of K. Paustain and coworkers to estimate the carbon uptake of CRP grasslands over 12.34 million hectares. The conversion of previous farmlands to grasslands helps increase the amount of carbon taken from the atmosphere by 6.54 teragrams per year. This helps reduce the total pollution of CO2 in the earth's atmosphere and restore nutrients to the deprived farmlands.

    15. CRP

      The Conservation Reverse Program was a policy implemented by the U.S. Department of Agriculture (USDA), for sensitive agricultural lands to not be used for farming or ranching, but instead for conservation benefits. The conservation benefits the USDA wishes to advance are: plant species' ability to stabilize soil, filter water, purify air, and support local wildlife.

    16. These scenarios are hypothetical because species richness is not uniformly distributed, because species loss does not occur independently of other shifts in community and ecosystem processes, and because the selection of the median range is arbitrary, given the large variation among species and the marked reduction in the ranges of grassland species due to extensive historical conversion of grasslands to agriculture

      The previous research (26) states that species richness is not uniform throughout an ecosystem since the amount of species throughout an ecosystem can vary due to different conditions.

      The paper also points out that other conditions besides carbon storage can affect biodiversity of an ecosystem. This paper takes that into consideration by comparing the results of the experiment to the historical levels of biodiversity recorded in the grasslands.

    17. Conservation Reserve Program

      The establishment of the Conservation Reserve Program was important in determining the results of this experiment. The program was created to encourage farmers to use some land to plant vegetative cover rather than crops to provide habitat for pollinators, reduce erosion, and improve water quality.

      The federal government pays farmers to make these land conversions, which places an economic value on species richness.

    18. social cost

      A social cost is an expense that must be payed by an entire society as a result of a particular event, action, or policy change. In this context, the event would be an increased species richness.

    19. grassland restoration

      The ability of an environment to restore itself after the ecosystem has been through devastating changes. From the growth of primary organisms and the accumulation of food and energy, an ecosystem can rebuild itself.

    20. Table 1. Marginal values of carbon stored by additional species to a grassland ecosystem for three carbon prices capturing the range summarized by the Interagency Working Group on the Social Cost of Carbon (25). Values are means and 95% confidence intervals in $ sp−1 ha−1 for ecosystem carbon (soil and plants) averaged across the BigBIO and BioCon grassland experiments. Values are in 2010 U.S. dollar (USD).

      An increased number of species in an environment decreases estimated social cost.

      The values are averaged between BioCon and BigBIO experiments, so this suggests that both of these experiments lead to the conclusion of a lower social cost being associated with increased species richness.

    21. ig. 3. Marginal present discounted economic value over 50 years from adding one species as a function of final species richness, using three estimates of the social cost of carbon: low (green), medium (blue), and high (purple) estimates described by the U.S. government (25) and in Materials and Methods. Marginal values were estimated from the two grassland experiments shown in Fig. 1 and are expressed here as USD (2010) per species per hectare, integrated over 50 years. (A) The marginal values for BigBio. (B) The marginal values for BioCON. Lines indicate means for each of the three estimates for the social cost of carbon. Shaded regions indicate 95% confidence intervals. For ease of visualization of values for BioCON, the confidence interval for the high estimate of the social cost of carbon is truncated at species richness of 15, and the confidence interval for the low estimate of the social cost of carbon begins at species richness of 3. For orientation, the position on the y axis (ordinate) corresponding to the x axis (abscissa) value of 5 shows the marginal value of adding the fifth species to a grassland initially containing four species.

      Marginal value changes in BigBio and BioCON with increasing species richness.

      For both instances, the amount of marginal value added per species decreases as species richness increases.

      This is likely due to competition between species. As the species have to compete with each other, they are not able to contribute as much to the ecosystem.

    22. Although the values declined with increasing diversity, at no point did the 95% confidence limit overlap zero: There was always a positive economic value for carbon storage to increasing species richness up to 16 species.

      Though the results show that carbon accumulation decreases at higher levels, at no point did carbon accumulation drop below what was accumulated in the control fields and this was thanks to the plant diversity.

    23. Fig. 1. Marginal carbon storage, which is the incremental change in cumulative carbon storage over 50 years caused by adding one additional species, as a function of final species richness, estimated from two grassland experiments (BioCON shown in gray; BigBio in blue). Means are shown in solid lines, with shaded regions indicating 95% confidence intervals estimated from bootstrapping for plant carbon (top), soil carbon (middle), and total ecosystem carbon (bottom).

      Marginal carbon storage changes in plants, soil, and entire ecosystems as species richness increases.

      For plants, soil, and ecosystems, the amount of carbon storage added per species decreases as species richness increases.

    24. Fig. 2. Marginal carbon accumulation over time at different levels of species richness. Each line shows the additional carbon accumulated over time caused by increasing species richness by one species. Numeric labels on each curve indicate the specific increment in species richness, with “2” indicating the marginal carbon accumulation caused by increasing S from 1 to 2, “3” indicating the marginal carbon accumulation caused by increasing S from 2 to 3, etc., up to 16.

      Carbon uptake increases significantly less per species at high levels of species richness than it does at low levels of species richness.

      It also shows that cumulative marginal carbon uptake rate declines over time.

    25. Carbon accumulation slowed during the 50-year simulation (Fig. 2). Annual marginal carbon accumulation and annual marginal value were highest early in the 50-year simulation and declined over time.

      The results state that the carbon intake decreased over a 50-year period as suggested in Figure 2. The annual marginal carbon uptake was higher earlier in the 50-year stimulation and declined as time went on. These results conclude that the highest amount of carbon accumulation occurs in more primitive environments.

    26. As a result, the largest marginal values of cumulative carbon storage occurred at low levels of species richness, and the smaller marginal values occurred at the high richness levels.

      The results show that the largest marginal values, of carbon accumulation, occurred at lower levels of plant diversity and marginal values decrease at higher levels of species richness.

      This occurred because of increased competition between plant species as species richness increased. This indicates that lower levels of plant diversity are the best situation for accumulating the most carbon, in plants and the soil, in an environment.

    27. For plants, we used observed changes in plant carbon content. For soils, we used data on soil carbon and plant productivity to model carbon accumulation as a function of increasing species richness over a 50-year period.

      The author used the observation of increased plant growth to measure the amount of carbon being sequestered by the plants.

      For soil, the author used data collected over a 50-year period, on soil carbon levels and plant productivity, to measure to total amount of carbon accumulated when introduced to increased species richness. The author was then able to create a fraction, used in later equation (1), of carbon content to estimate the amount of carbon in the soil during the experiment.

    28. We utilized these data to assess the marginal increase in carbon content with increasing species richness and estimated the economic value of the carbon storage conferred

      The author used data collected from the American grasslands, with increased plant diversity, to see if there was an increase in carbon uptake, in the environment, compared to the control group's carbon content.

      Using the valuation of carbon the author then estimated the economical worth of the carbon storage in the experimental fields in order to graph the results to show a correlation.

    29. despite some evidence that species richness also stimulates soil carbon turnover (23).

      A previous research paper, drafted by J. P. Reid and others, suggests that increased plant diversity, in a grassland environment, shows evidence of stimulating carbon turnover in the soil. The greater the number of plant species, the faster carbon cycles through the environment.

      The cycle is as follows: atmosphere -> plant (via photosynthesis) -> soil -> back to plant -> back to atmosphere due to plant respiration.

    30. We analyzed data from two experiments, performed in a North American grassland where species richness had been manipulated for over a decade periodic measurements of plant and soil carbon content in this site over time have suggested that both factors increase with species richness (8, 22),

      The author collected data, from two different American grassland fields with varying levels of plant species diversity for over ten years, on the amount of carbon in both the plants and the soil.

      In multiple research papers, written by leading scientists D. A. Fornara and P. B. Reich, the results show that increased plant diversity, in grassland environments, increased the carbon content in both plants and soil. The data in this research paper correlates with the past findings that an increase in species richness, in American grasslands, increases carbon storage in an ecosystem over time.

    31. Adding species increased cumulative carbon storage in plant, soil, and ecosystem carbon pools (Fig. 1):

      The results of the experiment show that an increase in plant diversity, in the American grassland fields, increased the amount of carbon accumulated in the plants and soil as shown in Figure 1. By increasing the amount of different plant species, in an environment, this increased the total amount of plant growth and also increased the amount of carbon stored in the soil.

    32. We calculated the marginal change in carbon content with increased richness next, we calculated the economic value of species richness for carbon storage in grasslands, using a wide range of estimates of the social cost of carbon compiled by the Interagency Working Group in a recent synthesis used by U.S. federal agencies when estimating the benefits of carbon reductions from application of federal rules and regulations [mid-range estimate, $137.26 per metric ton C (MT C−1), ranging from a low estimate of 41.94toahighestimateof41.94toahighestimateof41.94 to a high estimate of 400.33 MT C−1; see Materials and Methods] (25).

      The author used the data collected to find the change in the amount of carbon, in the American grassland fields, when exposed to increased plant diversity. The author then used data on the cost of carbon, by the Interagency Working Group and a previous research study conducted by the United States Government, to calculate the economical worth of the carbon stored in the American grassland fields.The previous research study gave the author insight into the how to assign a dollar total amount to carbon in the American grassland fields.

    33. carbon pools

      Reservoirs of carbon that accumulate in plants, soil, ocean, and atmosphere. This paper specifically looks at the carbon reservoirs in the grassland ecosystems where the experiment is taking place.

    34. intrinsic value

      The base-line economical worth assigned to plants for just being plants.This paper explains that there are many different characteristics that can be used to calculate a plant's economic worth based on the plant species importance to an ecosystem.The economical worth of plant species increases as levels of CO2 in the atmosphere increases because of their ability to take CO2 out of the atmosphere and store it.

    35. Valuation also provides a quantitative foundation for assessing decisions about land use involving trade-offs (21),

      A research paper, composed by J.H. Goldstein and others, states that the price of carbon emissions (provided by the carbon market) influences the amount of land companies are allowed to obtain. If companies have a high rate of carbon emissions going into the the earth's atmosphere then the amount of land they can use decreases.

    36. Our approach to this question offers a quantitative monetized view of one of the values of biodiversity that contrasts with the typically qualitative nature of most other assessments of biodiversity value (18–20).

      In multiple research papers biodiversity was calculated using a number, rather then a qualitative assessment. This paper takes the same approach. Diversity is thus assigned a number instead of an observation for further calculations to determine the affects of biodiversity on carbon storage.

    37. valuation

      Companies have to pay for the amount of carbon dioxide they emit, so in the context of this paper it means the dollar amount assigned to carbon.

    38. Reduced carbon gain as species diversity declines reduces carbon input to soil and, in some longer-term experiments, reduces soil carbon stocks (8).

      In a previous research paper, written by D. A. Fornara and coworkers, it was described that as species diversity declines carbon gain is reduced and in long-term experiments the decline of species richness reduced the total amount of carbon in the soil. Meaning that as plant diversity decreases the amount of carbon taken up by plants decreases and in the long-term the amount of carbon stored in the soil also decreases. If the amount of carbon in the soil decreases that means that there is more carbon being stored in the atmosphere, which proves that plant species diversity is vital for climate regulation.

    39. Observations in forests also indicate that local species richness contributes to carbon gain across broad gradients of climate and soil conditions (5–7).

      In multiple research studies conducted by leading scientists, A. Paquette, L. Gamfeldt, and J. Liang, proposed that local species richness contributes to carbon gain across a variety of different climate and soil conditions. Meaning that plant diversity in an ecosystem, regardless of climate and soil conditions, causes an increase in carbon uptake by plants. Which can be seen through the increased growth of plants in an environment.

    40. Syntheses of experiments across different ecosystems indicate that biomass accumulation tends to decline as local species richness decreases (4)

      A previous research paper, by B. J. Cardinale and others, states that a decrease in species richness causes a decrease in biomass accumulation. This shows that carbon sequestration diminishes as ecosystem biodiversity decreases. This is driven by less competition among species which in turn increases carbon availability and decreases total carbon uptake.

    41. (3)

      Has the Earth's sixth mass extinction already arrived? A. D. Barnosky, N. Matzke, S. Tomiya, G. O. U. Wogan, B. Swartz, T. B. Quental, C. Marshall, J. L. McGuire, E. L. Lindsey, K. C. Maguire, B. Mersey, E. A. Ferrer

      This article suggests that the current rate of species extinction is higher than what has been expected in the past (compared against fossil records). The authors propose that this elevated rate of extinction may possibly be the beginning of the 6th known mass extinction event on earth.

      This extinction would drastically lower biodiversity by killing off many species that would otherwise function as carbon sinks. The release of such massive amounts of carbon might have dramatic effects upon the environment.

    42. photosynthetic biodiversity

      Different species that conduct photosynthesis to create energy. Different plant species that convert light energy into chemical energy. For this experiment, the author questions the impact of increased species richness on carbon storage in American grasslands.

    43. “the variety of living [photosynthetic] organisms, the genetic differences among them, and the communities and ecosystems in which they occur”

      A previous research paper, written by Keystone Center, states that genetic diversity in the plant life along with the way communities of plants interact in an ecosystem is vital for the carbon storage cycle on earth. Different species of plants are able to store different amount of carbon, if there was no diversity between plant species then the amount of carbon storage in an ecosystem would be altered. Without diversity in plant species, our oxygen-dependent existence and regulation of global climate might not be possible.

    44. twice the economic value of increasing species richness from 1 to 2.

      Each additional degree of species richness is worth less than the previous degree of richness in terms of economic value. Therefore, the economic value does not increase in direct proportion with the species richness, although they are correlated.

    45. proliferation

      A rapid increase in the amount of a quantifiable unit. In plant species, proliferation refers to the rapid increase in the number of plant species that now inhabit earth. The diverse array of species around the world is a valuable component to producing ecosystem services that benefit all organisms.

    46. aerobic life

      Organisms that require oxygen to produce energy and to survive. Plants help to maintain the earth's oxygen rich atmosphere through photosynthesis (CO2 is taken in and oxygen is released). Without the existence of plant life, other organisms that depend on oxygen to breathe would not exist.

    47. The rise of photosynthesis nearly 4 billion years ago initiated the transfer of carbon dioxide in the atmosphere to organic carbon, much of which is now contained in rocks (1)

      Past and present of sediment and carbon biogeochemical cycling models

      By: Mackenzie, FT (Mackenzie, FT); Lerman, A (Lerman, A); Andersson, AJ (Andersson, AJ)

      This is a secondary study of the history of the carbon cycle, with respect to the onset of industrialization as well as the dynamic role the ocean plays in carbon storage. Prior to industrialization, the ocean was a net source of CO2 emissions due to the net carbon differences between photosynthesis and respiration. However, the massive CO2 releases from the burning of fossil fuels have made the ocean into a net carbon sink.

      This citation is referring to the storage of carbon within calcium carbonate (CaCO3), or limescale within the ocean. This limescale comprises most of the 'rocks' in reference.

    48. biomass

      As plants conduct photosynthesis and gain energy, they grow. Plants accumulate biomass through the storage of carbon and uptake of other vital nutrients required for plant grow. By taking the dry-weight of plants, the scientist can see how much carbon is being taking up through the soil.

    49. marginal value

      Marginal value is the amount of economic growth received for each additional unit of species richness relative to the previous unit. The paper suggests that marginal value decreases with the addition of species, when considering biomass accumulation, due to competition. This implies the addition of each new species to an ecosystem causes diminishing returns on rate of growth for all plants because each plant is competing for limited resources.

    50. economic value

      The amount of energy the grasslands will be producing. If there is a greater degree of competition between the different species than there will be a higher output of growth and carbon storage.

    51. species richness

      The number of different collective groups of organisms that are in a habitat. The increasing number of varieties of organisms will be compared to the carbon storage throughout the habitat. The scientists expect that a higher number of variety will disclose an increase in economic value.

    52. Biodiversity

      A measure of the variety of life or different species in a specific environment. Increased biodiversity is associated with promoting competition which increases carbon storage.

    53. Carbon storage

      The ability of plants to uptake carbon from the environment and convert it into biomass. Plants decrease CO2 levels by absorbing carbon from the atmosphere to use for photosynthesis.

    1. To dissect the transcriptional regulatory circuitry of the insulin signaling cascade in the CA in response to starvation, transcript levels for 4 key genes were analyzed in the CA of 4 days old adult females fed sugar or water (Fig. 3).Transcript levels for the insulin receptor (INSr), the Forkhead-box-binding protein (FOXO) and the translation initiation inhibitor eIF4E-binding protein (4EBP) were significantly increased in the CA of starved females. Transcripts for the target of rapamycin (TOR) protein were significantly decreased in the CA of starved females.

      Transcript levels are the rate that transcription is occurring, this can be important to determine what is affecting the starving females within the 4 key genes that were tested.

    2. JH and insulin are involved in a complex regulatory network, in which they influence each other and in which the insect's nutritional status is a crucial determinant of the network's output [5].

      Typically, insulin is obtained from the food we eat, if the mosquito does not have enough nutrition and food the insulin levels will be low. If the mosquito's nutrition improves than the insulin will be obtained from the food she eats.

      When insulin or the juvenile hormone binds to a receptor it carries out a process so it can send a message to the nucleus of the cell, this allows for activation of regulation. When insulin binds to the insulin receptor that stimulates development and growth. In this case, the juvenile hormone regulates metabolism, reproduction, and nutrition within the cells of mosquitoes. This way insulin and the juvenile hormone are working together in keeping the insects healthy.

    3. oogenesis

      The process in female reproduction where the eggs or ova (female gametes) are produced.

    4. 12.Noriega FG (2004) Nutritional regulation of JH synthesis: a mechanism to control reproductive maturation in mosquitoes? Insect Biochem Molec Biol 34: 687–693.

      The juvenile hormone is the most important hormone to all insects, especially in adult female Aedes aegypti. This mosquito uses nutrients to boost JH levels which increases reproduction.

    5. 1.Boggs CL (2009) Understanding insect life histories and senescence through a resource allocation lens. Functional Ecology 23: 27–37.

      Mosquitoes carrying Zika can contaminate and spread the disease in the human population in a second. Zika is a yellow fever. This 2017 news relates to the article because if mosquito populations are controlled by hormone regulation, then genetically modifying a suppressor can develop a method to prevent the disease from spreading.

    6. FOXO knockdown in starved cockroaches elicited an increase of JH biosynthesis; implying that FOXO plays an inhibitory role on JH biosynthesis during starvation

      Since FOXO is a protein that regulates gene expression and is not nutritionally regulated. When the mosquitoes are given water with no sucrose the FOXO stops the role of the JH biosynthesis. This happens because the FOXO is not being transcriptionally regulated when the mosquito is being deprived of nutrients.

    7. assay

      The process of testing a material to determine its composition and quality.

    8. transduction

      The transfer of DNA from a virus into a cell.

    9. fluorescent

      Shows radiation from somewhere else by allowing the wavelength to become shorter with a x-rays or ultraviolet waves.

    10. derivatization

      This is a technique used in chemistry. It is important because it allows for the development of chemical compound of a desired chemical structure based on a similar product.

    11. To determine the effect of starvation on lipid reserves, the total lipid contents of mosquitoes were quantified in either sugar-fed or starved females

      Starvation is a state in which the body responds to long periods of fasting. The body then burns fatty acids and lipid reserves, along with small amounts of muscle tissue to provide the brain with an energy source of glucose.

    12. Forkhead-box-binding protein

      Proteins that bind to DNA and regulate gene expression.

    13. µl

      Microliter; there are 1,000,000µl in one liter (L)

    14. Corpora allata-corpora cardiaca complexes (CA-CC)

      The corpora allata (CA) is responsible for the production and release of juvenile hormones. The corpora cardiaca (CC) complexes are responsible for regulating reproduction and metamorphosis. The CC send out messages for the body to produce hormones that mature ovaries and hormones to produce insulin.

    15. Here diet restriction, in vivo depletion of INSr and FOXO using RNA interference (RNAi) and insulin treatments were used to modify insulin signaling and study the cross-talk between insulin and JH in response to starvation.

      INSr is a gene that encodes for a cell surface receptor, also known as tyrosine kinase. Binding of insulin initiates the insulin signaling pathway, which regulates how glucose is absorbed by muscle and fat cells. FOXO is a series of transcription factors, which are proteins that control transcription of genetic information from DNA to messenger RNA. FOXO transcription factors are responsible for regulating which genes are expressed, and these transcription factors are also responsible for signaling apoptosis, or cellular suicide, when a cell is damaged beyond repair.

    16. PI3K

      This involves an intracellular signaling pathway, which occurs within the cell membrane of a cell, and is important in regulating the cell cycle. Also, it is directly related to how cancer forms and the length of an organism's lifespan.

    17. bovine insulin

      This type of insulin is also known as beef insulin because it is extracted from the pancreas of cattle. Bovine insulin differs from human insulin because it is less soluble and absorbed by the body more slowly. Like human insulin, bovine insulin regulates how much glucose is administered to muscle and fat cells.

    18. corpora allata

      The glands that are attached to the brain of insects that produce juvenile hormones that help to promote gene expression in larva development.

    19. diapause,

      The pause that occurs in an insect during development.

    20. metamorphosis

      Transformation from juvenile to adult where the adult will have similar hormone levels before and after metamorphosis.

    21. versatile

      Able to adapt or be adapted to different functions. In this case, the juvenile hormone is a molecule that adjust to different environments.

    22. insulin-TOR (target of rapamacyn) signaling pathway

      The insulin/TOR pathway regulates a cell's and an organism's metabolism, and serves an essential function in controlling tissue growth and responses to starvation.

    1. white muscle

      Type of skeletal muscle that takes up most of the muscle of a fish.

    2. lateral

      From the side.

    3. dorsal

      The back of a body; posterior.

    4. hypodermic

      Relating to the region immediately beneath the skin.

    5. Grass stimulator

      A device that gives off electric impulses.

    6. electrical stimulus

      Using electric impulses (to contract muscles).

    7. Wardle, C. S.​​​​​​​ (1975). Limit of fish swimming speed. Nature 255, 725-727.doi:10.1038/255725a0

      This paper considers the various characteristics that limit the swimming speed of fish. For one, it analyzes how smaller fish are capable of higher tail beat frequencies than larger fish. Also, that the stride length of a fish is not longer than the fish's size. Furthermore, swimming speed is limited by the contraction time of swimming muscle so maximum swimming speeds are determined by muscle contraction time and stride length.

    8. Iosilevskii, G. and Weihs, D. (2008). Speed limits on swimming of fishes and cetaceans. J. R. Soc. Interface 20, 329-338. doi:10.1098/rsif.2007.1073

      The paper analyzes the limitations that stop fish from swimming faster. Small fish are held back by the power available, and larger fish are limited by cavitation.

    9. Brill, R. W. (1996). Selective advantages conferred by the high performance physiology of tunas, billfishes, and dolphin Fish. Comp. Biochem. Physiol. A Comp. Physiol. 13A, 3-15.doi:10.1016/0300-9629(95)02064-0

      In this review the author talks about the characteristics that give tuna fish high performance. These characteristics include 3 things: high rates of somatic and gonadal growth, rates of digestion, and rates of recovery from exhaustive exercise. This study uses these findings to defy the myth that sailfish and other pelagic fish just have high maximum swimming speeds that allows them to avoid cavitation.

    10. burst speed-length relationship

      To account for an initial burst of energy, that gives an initial burst of speed.

    11. post hoc

      Occurs after the event.

    12. ensonified area

      An area filled with sound.

    13. stationary dual frequency identification sonar (DIDSON)

      A multi-beam sonar used to detect fish up to 164 feet away from where the beam is being produced.

    14. echograms

      A test that uses high frequency sound waves (ultrasound) to detect a living thing.

    15. Maximum swimming speed was measured following (Wardle, 1975):

      The following formula was used to determine the maximum swimming speed for each of the fish. The measurements needed are the fork length of a fish, its stride length, and its tail-beat frequency.

    16. Pilot tests on euthanized rainbow trout (Oncorhynchus mykiss) (10°C) performed at the University of Copenhagen revealed no difference in peak contraction time with increasing stimulus voltage.

      This shows that having more or less voltage wouldn't affect the peak muscle contraction time, so having different fish be stimulated at different voltages wouldn't have affected the minimum contraction time that the authors were looking for during their experiment.

    17. We first applied 10V to a fish, doubling this amount in case of no contraction, using a maximum of 100V

      A small amount of voltage was used at first (10V), and this was then increased by doubling the initial voltage, until contraction occurred. However, a voltage above 100V was never used. To put this amount into perspective, the standard voltage for electrical outlets in the United States is 120V.

    18. amplifier

      An electronic device that increase the power of a signal.

    19. apparatus

      Equipment being used.

    20. strain gauges

      A device used to measure strain on an object.

    21. thermocouple

      Sensor used to measure temperature.

    22. elongated

      Stretched out or extended.

    23. From an evolutionary perspective, it is tempting to suggest that fish may not have evolved a muscular system capable of minimum contraction times such that they would be able to swim at speeds exceeding 10-15 m s−1(depending on fish size), given that it would result in costly damage to the fins.

      This statement explains why fish most likely cannot swim faster. Their muscular systems do not evolve because swimming any faster than the current rate would result in damage to their fins.

    24. acceleration specialist

      Barracudas' swimming mode is accelerator specialists: they swim with moderate drag but maximized thrust when they almost "jump" out at their prey, which is locally available. Because of this, they are considered by fishermen to be like "lazy fish" for mostly sitting still in shady areas, waiting for prey to swim near them and pounce, rather than going to hunt.

    25. Based on the estimated absolute speeds, sailfish appear to be the fastest of the four species investigated here, however, they were also 50-80 cm longer than the other three species and maximum speed is known to increase with fish length (Wardle, 1975). Using a length-speed relationship based on burst swimming performance of various species (Videler, 1993), we found that the size-corrected speed performance is highest in little tunny and barracuda, followed by dorado and sailfish (Fig. 2D).

      The goal of this study was to determine whether earlier studies were correct in their determination of maximum swimming speeds in sailfish as well as comparing sailfish speeds to other large marine predators. Here the author explains that compared to the other predators, the speed performance in sailfish based on size was the lowest. This is supported with Figure 2D

    26. anterior

      Frontal; on the front.

    27. unloaded muscle

      Remodeling of muscle (atrophic response) as an adaptation to the reduced loads placed upon it; decrements occur in skeletal muscle strength, fatigue resistance, motor performance, and connective tissue integrity.

    28. i.e. fish are taken out of the water and do not consider additional effects of drag.

      Their estimated swimming speeds are slightly higher than what is observed during predator-prey interactions because taking the fish out of the water and measuring its muscle would have not been limited by the real-life environment the fish normally swim in when chasing their prey, especially as they swim back and forth. So, their estimates can only give the theoretical maximum speed the fish can swim at without cavitation occurring, even if the fish don't actually swim at that speed.

    29. deviation

      The amount by which a single measurement differs from a fixed value such as the mean.

    30. full curves represent an estimate of maximum swimming speed caused by the cavitation limit at shallow depth

      Full curves in the graph represent the estimated maximum swimming speed which is limited by cavitation occuring in a shallow depth. It is important to mention "at shallow depth" because that would imply the fish are near the surface in warmer water, which would allow them to reach higher speeds before cavitation occurs than if they were in colder water.

    31. The calculated maximum attainable swimming speeds for the four species expressed in m s−1 (A) and in Lf s−1

      From graph A it can be seen that the sailfish had the highest maximum swimming speed. Next was the Barracuda, then the Little tunny. The Dorado had the lowest maximum swimming speed.

    32. Sailfish had significantly higher maximum swimming speeds (m s−1) than the other species (post hoc Tukey test, P<0.05); however, when considering size-corrected performance (i.e. residuals), sailfish had the lowest values

      Using certain statistical tests, the authors were able to find the differences they could properly analyze between the maximum swimming speed of the sailfish and the other 3 marine species. From here, they found that sailfish could reach higher swimming speeds than the other fish (shown in graph A). However, (in graph C) the maximum swimming speeds they OBSERVED in the barracudas, little tunny, and dorados were closer to the corresponding swimming speed they PREDICTED than for the sailfish (residuals = observed - predicted).

    33. post hoc Tukey test

      A statistical test used to confirm where the differences between groups occurred when it's known that there is a statistically significant difference between the means/averages of the groups.

    34. ANOVA

      A statistical method used to measure the variance in data between different groups.

    35. The body temperature at the stimulus location [15, 30, 45, 60, 75% along the fish fork length (Lf) with 0% representing the tip of the head and 100% the fork of the tail] was

      They also measured the muscle temperatures of each fish at the 5 different areas (along the length of the fish from head to tail) where they measured muscle contraction times. The temperature of the muscle would affect whether it contracts faster or slower (warmer is faster).

    36. Sea surface temperature

      The temperature at which fish live in also affects their swimming speed because warmer water generally enables them to propel through water more efficiently. That's why is it was especially important to record the temperatures of the waters from where the fish were collected.

    37. for swimming animals longer than ∼1 m, the speed at which cavitation occurs, with destructive consequences for the tissues

      Longer fish would be affected by limits in their water environment more than smaller fish because their length and greater ability to swim faster makes them more likely to have cavitation occur in their bodies. The increase of cavitation bubbles in their bodies would injure them and ultimately lead to their death.

    38. propulsive

      Creating enough force to result in movement.

    39. high-speed video are usually confined to relatively short time intervals, reducing the chance of detection of high speed events, which are thought to occur only rarely during an animal's lifetime

      The researchers tried to understand more about the maximum speeds of these fishes but unfortunately the technique of videotaping the fish in action were not able to provide enough information because they could never catch the fish swimming at their true maximum speed.

    40. hydrodynamic

      Relating to the study of hydrodynamics: a branch of physics that deals with the motion of fluids and the forces acting on solid bodies immersed in fluids and in motion relative to them.

    41. Estimates based on minimum muscle contraction times thus yield the theoretical maximum values attainable by fish

      Measuring the muscle contraction times of the fish after taking them out of the water enabled the researchers to know what the highest potential speed a fish can reach is without real-life factors of the fish's environment, like water current, affecting their data. Representative of data as if they had observed the fish in action with high-speed cameras.

    42. accelerometers

      An electromechanical device that measures acceleration forces affecting something. These forces can be all sorts of things such as the force of gravity pulling you down at your feet.

    43. theoretically, fish swimming speeds are physiologically limited by the tail-beat frequency attainable in a given environment

      In reality, even if you could see a fish swimming at its maximum speed, what that speed is would differ based on the environment of the fish. One variable in a fish's environment that affects its speed is the strength of the water current. If the current is great, then a fish swimming against it at its maximum ability would have a lower tail-beat frequency compared to the same fish swimming at its maximum ability in the direction of the current. You can think of how water current affects underwater organisms the same way how strong winds affect land organisms.

    44. to measure their minimum muscle contraction times

      It's too difficult to observe maximum speed as it's happening in the wild so the best method would be to observe the physiology of the fish. The faster the muscle of an organism contracts, the faster it can move. As a result, the lower the time it takes for fish muscle to make one contraction, the faster the fish.

    45. attainable

      Possible to have or achieve.

    46. unequivocally

      Without a doubt.

    47. accelerometry

      Use of a accelerometer to quantify movement

    48. More recently, work on billfishes using data storage tags has shown that blue marlin (Makaira nigricans) rarely exceed speeds of 2 m s−1, with a maximum of 2.25 m s−1 (Block et al., 1992) and a study of sailfish hunting schooling sardines reported an upper speed limit of 8.19 m s−1

      Recent studies have shown that billfishes often prefer slower, more accurate swimming rather than fast swimming. This is said to be preferred due to their prey's maneuverability which is achieved by swimming unsteadily. Unsteady swimming refers to the sharp turns and quick changes in acceleration that smaller fish often use to escape larger predators.

    49. Animal maximum speeds play a significant ecological role, particularly in the context of predator-prey interactions

      The speed an animal can achieve when chasing prey is one factor that determines what type of prey they can or cannot eat. In terms of this, the more different types of speeds a fish can achieve, the more varieties of smaller fish it can successfully chase and eat. For the fishes studied, none of them swim at their maximum speed because it is not required to swim that fast to consume their prey.

    50. anaerobic

      Relating to, involving, or requiring an absence of free oxygen.

    51. pelagic

      Of or relating to the open sea.

    52. cavitation

      The rapid formation and collapse of vapor pockets in a flowing liquid in regions of very low pressure.

    53. predicts that such extreme speed is unlikely

      Using calculations, it should not be possible for sailfish and marlin to swim as fast as previously thought because swimming that fast would cause cavitation bubbles in the fish leading to death.

    1. DeGennaro M, McBride CS, Seeholzer L, Nakagawa T, Dennis EJ, Goldman C, Jasinskiene N, James AA, Vosshall LB.. orco mutant mosquitoes lose strong preference for humans and are not repelled by volatile DEET. Nature 2013; 498:487-91;

      Dr. DeGennaro established techniques to edit the genome of mosquitoes. He created the first mosquito mutant using zinc-finger nucleases to initiate the molecular genetic analysis of olfactory receptor function in Aedes aegypti mosquitoes. His work revealed new knowledge about the integration of host cues, mosquito host-preferences, mosquito nectar-seeking, and the mechanism of DEET repellency.

      Dr. DeGennaro demonstrated that the mosquitoes use the OR/ORCO olfactory receptor pathway to respond to human odors and DEET as well as nectar volatile. His work implicated the Ionotropic Receptor family of olfactory receptors in host-seeking mosquitoes. Additionally, he showed that DEET repels mosquitoes through ORCO-dependent olfaction and an unidentified taste receptor.

    2. An additional model for DEET repellency was based purely on its molecular structure.

      The hypothesis that DEET repellency is due to its non-polar molecular structure is rejected as studies of the insect sensilla show that DEET does not have any long term effect on the membrane or disrupt the odor detection.

    1. Caragata, E. P., Rancès, E., Hedges, L. M., Gofton, A. W., Johnson, K. N., O'Neill, S. L. and McGraw, E. A. (2013).Dietary cholesterol modulates pathogen blocking by Wolbachia. PLoS Pathog. 9, e1003459.

      Camacho, Oliva, and Serbus reviewed articles that explored how cholesterol affects Wolbachia, while further questioning how this may improve the overall pathogenic blocking capabilities of their host.

    2. Bordenstein, S. R. and Bordenstein, S. R. (2011). Temperature affects the tripartite interactions between bacteriophage WO, Wolbachia, and cytoplasmic incompatibility. PLoS ONE 6, e29106. Boyle, L., O'Neill, S. L., Robertson, H. M. and Karr, T. L. (1993). Interspecific and intraspecific horizontal transfer of Wolbachia in Drosophila. Science 260, 1796-1799.

      Camacho, Oliva, and Serbus review the contributions made by authors regarding the transfer and survival/ compatibility of Wolbachia in various environments.

      Camacho, Oliva, and Serbus further investigate the effects of Wolbachia on Drosophila in a high or low sucrose concentrated environment.

    3. Christensen, S., Pérez Dulzaides, R., Hedrick, V. E., Momtaz, A. J. M. Z., Nakayasu, E. S., Paul, L. N. and Serbus, L. R. (2016). Wolbachia endosymbionts modify Drosophila ovary protein levels in a context-dependent manner. Appl. Environ. Microbiol. 82, 5354-5363.

      Camacho, Oliva, and Serbus further explore a topic primarily researched by Serbus on how Drosophila ovaries are modified by Wolbachia.

    4. Dale, C. and Moran, N. A. (2006). Molecular interactions between bacterial symbionts and their hosts. Cell 126, 453-465.

      While Camacho, Oliva, and Serbus specified which interactions between bacterial symbionts and their hosts. The mechanism by which this interaction occurs is still unclear.

    5. Mouton, L., Henri, H., Charif, D., Bouletreau, M. and Vavre, F. (2007). Interaction between host genotype and environmental conditions affects bacterial density in Wolbachia symbiosis. Biol. Lett. 3, 210-213. Musselman, L. P., Fink, J. L., Narzinski, K., Ramachandran, P. V., Hathiramani, S. S., Cagan, R. L. and Baranski, T. J. (2011). A high-sugar diet produces obesity and insulin resistance in wild-type Drosophila. Dis. Model. Mech. 4, 842-849.

      Camacho, Oliva, and Serbus further explored how the Wolbachia titer increased depending on the type of sugar product fed to the Drosophila.

    6. Teixeira, L., Ferreira, A. and Ashburner, M. (2008). The bacterial symbiont Wolbachia induces resistance to RNA viral infections in Drosophila melanogaster. PLoS Biol. 6, e2.

      The information presented in this paper explores how the information presented by Camacho, Oliva, and Serbus is relevant. It states that according to the endosymbitic behavior of Wolbachia, the susceptibility of the host organism to viral RNA infections may be diminished due to the resistance of Wolbachia to those viral RNA infections.

    7. Wang, M. and Wang, C. (1993). Characterization of glucose transport system in Drosophila Kc cells. FEBS Lett. 317,241-244.

      Camacho, Oliva, and Serbus used the knowledge presented in this article to maximize the efficacy of the consumption of the varied glucose by Drosophila.

    8. Serbus, L. R., White, P. M., Silva, J. P., Rabe, A., Teixeira, L., Albertson, R. and Sullivan, W. (2015). The impact of host diet on Wolbachia titer in Drosophila. PLoS Pathog. 11, e1004777.

      Camacho, Oliva, and Serbus used a previously published article from Serbus to delve into the specifics of how the host diet impacts Wolbachia titer.

    9. Ponton, F., Wilson, K., Holmes, A., Raubenheimer, D., Robinson, K. L. and Simpson, S. J. (2015). Macronutrients mediate the functional relationship between Drosophila and Wolbachia. Proc. Biol. Sci. 282, 20142029.

      Camacho, Oliva, and Serbus demonstrate how macronutrients mediate the functional relationship between Drosophila and Wolbachia, by using sucrose and its dietary variants to create an environment allowing the Drosophila to thrive and the Wolbachia to proliferate within the Drosophila.

    10. Min, K.-T. and Benzer, S. (1997). Wolbachia, normally a symbiont of Drosophila, can be virulent, causing degeneration and early death. Proc. Natl. Acad. Sci. USA 94, 10792-10796.

      Camacho, Oliva, and Serbus explain the relevance of parasitic Wolbachia being detrimental to the growth and oocyte growth of the Drosophila.

    11. Post hoc data presented here were generated by SPSS as standard outputs of the analysis, including the adjusted P-values reported throughout the manuscript.

      The authors of this experiment used the SPSS statistical software system to create the graphs presented in the article, showing the descriptive statistic analysis.

    12. kurtosis

      A measure of peak sharpness for a distribution.

    13. skewedness

      A measure of asymmetry, primarily describing some distribution by reference to the tails of the dataset. Left skewed data has a tail that leans to the left and right skewed data has a tail that leans to the right.

    14. The descriptive statistics function was used to analyze the distribution of the data.

      Author used descriptive statistics (mean, median, mode, etc) to compare data collected on the oocyte Wobalchia titer and those collected on oocyte size.

    15. data

      A set of numbers or observations.

    16. For measurement of ovary volume, tissues were dissected from adult flies and imaged using an AmScope MD500 5.0 megapixel digital Camera mounted upon a Jenco ST-F803 dissection microscope set at 1× magnification.

      Using the AmScope digital camera, the authors were able to improve the visualization of the ovaries by having the field of view appear on a computer screen and analyze from there.

    17. Screen shots of these ovary fill diagrams were then imported into Fiji (Image J version 2.0.0-rc-43/1.51d, NIH) for conversion into 8-bit, thresholded black and white images. The area of the ovary fill diagrams was determined in terms of pixels2 by the Analyze Particles function in Fiji. A scale bar was also used to calculate a pixel2 to micron2ratio (9.3025:1) that was applied to all oocyte area data, for presentation and discussion purposes only. Statistical differences were determined through analysis of the primary data in terms of pixel2 units.

      In this experiment, the authors used the Fiji Image J processing software in order to calculate the size and area of the oocytes, providing more insight into how the oocytes were affected.

    18. Three or more experimental replicates were performed for all treatment conditions examined. Significance of differences between conditions was determined by ANOVA analysis of the raw data.

      The authors involved compared the oocyte titer raw data for each experimental replicate using the ANOVA analysis system by testing the differences of the means present.

    19. Images were manually processed in Photoshop to remove extraneous signal outside the oocyte, and remaining oocyte puncta were quantified using the Analyze Particles feature in Image J version 2.0.0-rc-43/1.51d (NIH).

      The authors used photoshop, an image editing software, in order to remove and unnecessary signaling outside the oocyte, making it easier to analyze and interpret the data.

      Full tutorial and introduction to processing scientific images in photoshop: https://www.youtube.com/watch?v=SbsDtPouggs

    20. confocal images

      The authors collected confocal images though confocal laser scanning microscopy which is an optical imaging technique to increase the optical resolution and contrast of a micrograph by using a spatial pinhole to block out-of-focus light during image formation.

    21. All replicates were imaged by laser scanning confocal microscopy on either Leica SP2 or an Olympus FV1200 confocal microscope at 63× magnification with 1.5× zoom.

      Laser scanning was used to magnify the cells and staining enhanced the detail of the structures, shown in black and white for differentiation purposes as well as measurement.

    22. This stock carries the wMel Wolbachia strain as confirmed previously (Christensen et al., 2016). 0−24-hour-old adult flies were selected at random and transferred into new bottles of standard food and aged for 2 days. Then flies were transferred to vials of nutrient-altered food and incubated for 3 days. Controls were run in parallel with all treatment conditions in all experiments.

      The authors of this experiment used flies this young in order to ensure the flies had not developed any Wolbachia yet, meaning it would be easier to extract the oocytes without shredding the tissue.

    23. All feeding experiments were done using flies of the genotype w; Sp/Cyo; Sb/Tm6B, reared on standard food and in a controlled, 25°C environment.

      Specific genotypes allowed for less error or genetic disruption of results.

    24. To ensure homogeneous suspensions of nutrient-altered diet preparations, all food vials were immediately transferred to an ice bucket to be cooled with additional stirring every 10 min until the food completely solidified. Kimwipe strips were inserted into the food to wick away excess moisture.

      The authors placed the vials in an ice bath (placed in bucket of ice) in order to ensure a homogenous suspension, meaning that the substances in the vials were equally suspended from each other.

    25. This standard food was used as a base for all nutrient-altered foods that were prepared in this study (Table S3). The sugar-enriched foods were prepared by first making a stock sugar solution of 20 g sugar in 10 ml ddH2O, solubilized with rounds of 15 s in the microwave and then stirring, repeated until the sugar dissolved. 1.5 ml amounts of these sugar solutions were immediately mixed with 3.5 ml of melted standard food. As aspartame, erythritol, saccharin, and xylitol were not uniformly soluble, the sweetener-enriched foods were generated through direct addition of powder equivalents directly into 5 ml of melted standard food to a final concentration of 1 M (Table S3). Yeast-enriched food was prepared by mixing 1.5 ml of heat-killed yeast paste into 3.5 ml melted standard food. Dually enriched food was prepared through addition of 1.5 ml sugar solution and 1.5 ml heat-killed yeast to 2 ml standard food. Desiccated food was prepared by addition of 2.5 g silica gel (roughly 2.5 ml volume) to vials containing 5 ml standard food (Table S3).

      The recipes for the substance-enriched foods given to the flies.

    26. Integrated quantitative analyses will play an important role going forward in elucidating the mechanisms of oocyte colonization by Wolbachia.

      Uncovering the mechanism of Wolbachia invasion may open doors to eradicating viral diseases like Zika and dengue virus.

      Read more on the world mosquito program: http://www.eliminatedengue.com/program

    27. The impact of dietary sugars on oocyte Wolbachia titer is currently best explained through nutritional impacts on the host.

      Female mosquitoes with sugar-fed diets survive longer than those without sugar-diets. Wolbachia titer size is affected by levels of sugar in the host's diet, which may show correlation between mosquito life expectancy and Wolbachia titer size from dietary sugars.

      Read more on Oxford Academic: https://academic.oup.com/jme/article/12/2/220/2219171

    28. dietary desiccation tests showed reduction of oocyte Wolbachia titer rather than an increase, suggesting that sugar-based titer responses are unrelated to hydration.

      What was hypothesized to be a player in the mechanism of Wolbachia colonization of the germ line cells ended up being a dead end. The processes of hydrating the cell were not related to concentration of Wolbachia.

    29. From the perspective of Wolbachia endosymbiosis, this study suggests that dietary sugars induce different classes of mechanistic responses.

      This could be a new mechanism affecting Wolbachia interaction with host, similar to recently discovered mechanism affecting sperm in flies using Wolbachia.

      Read more on BIOmed central: https://parasitesandvectors.biomedcentral.com/articles/10.1186/1756-3305-6-36

    30. The impact of diverse dietary sugars on insulin signaling has not been fully defined in D. melanogaster. From the perspective of Wolbachia endosymbiosis, this study suggests that dietary sugars induce different classes of mechanistic responses.

      The researcher's reasoning for executing this experiment was to uncover the frontier that is the mechanism that act in Wolbachia concentration, as there is very little information on it.

    31. Thus, ovary volume reduction associated with sweet tastants parallels that induced by sugar-enriched diets. However, as sugar-enriched diets elevate oocyte Wolbachia titer and sweet tastants do not, this indicates that oocyte Wolbachia titer is not specified exclusively by ovary size.

      In order to test taste perception as a mechanism, sweet tastants were used as well. What was found was that although these tastants did impact ovary size similarly to sugar, there was no significant difference with Wolbachia concentration.

    32. Through apparent impacts on systemic insulin signaling, sucrose-rich diets have been shown to reduce ovary size, whereas yeast-rich diets increase it (Fig. 3A) (Geminard et al., 2009; LaFever and Drummond-Barbosa, 2005; Morris et al., 2012). Direct measurement of ovary volume in response to these diets confirms that the size changes are substantial (Fig. 3B).

      Referencing the control, there was significant difference when comparing this group to the substance-enriched environments when observing ovary size. For yeast-fed cells, the ovary size would size would increase while sucrose-fed cells would decrease in ovary size.

    33. Ovary

      A female organ that produces eggs.

    34. According to this analysis, no significant differences in oocyte area were identified between control and sucrose-enriched conditions [χ2(2)=12.2, P=0.085], nor control and yeast-enriched conditions [χ2(2)=6.6, P=0.811] (Fig. 2G). Significance was detected when comparing oocyte area values between sucrose- and yeast-enriched conditions [χ2(2)=18.7, P=0.004].

      Comparing yeast-enriched to sucrose-enriched, there was a significant difference in oocyte size, but not any significance when comparing either to the control. Therefore, oocyte size was not necessarily responsive either to control or substance-enriched regions.

    35. Oocyte

      An oocyte is an immature egg cell.

    36. disaccharide

      A disaccharide is two monosaccharides chemically linked together

    37. According to these criteria, oocyte Wolbachia titer in the yeast-enriched condition was significantly lower than the control [χ2(2)=27.3, P<0.001] (Fig. 2D). Though higher oocyte Wolbachia titers were detected in the sucrose-enriched condition, the values did not differ significantly from the control [χ2(2)=15.6, P=0.056]. Significant oocyte titer differences were detected between the yeast and sucrose conditions

      Although the presence of sucrose was not significantly increasing the concentration of bacteria compared to the control cells, it definitely was significantly higher than that of the yeast-fed cells.

    38. The molecular mechanisms that regulate Wolbachia titer are not well understood. Body-wide Wolbachiatiter has been reported to vary up to 180,000-fold in lab-reared offspring of mosquitoes collected from nature (Ahantarig et al., 2008), and 20,000-fold between wild-caught Drosophila innubila individuals (Unckless et al., 2009). This titer variation may be due in part to sensitivity to host temperature (Bordenstein and Bordenstein, 2011; Mouton et al., 2006, 2007; Wiwatanaratanabutr and Kittayapong, 2009, 2006), host crowding (Hoffmann et al., 1998; Wiwatanaratanabutr and Kittayapong, 2009), host genetic background (Boyle et al., 1993; Poinsot et al., 1998; Veneti et al., 2004; Serbus et al., 2011) and host age (Tortosa et al., 2010; Unckless et al., 2009).

      Background information on Wolbachia colonization mechanisms in germ line cells is not well known. Concentration variation may be due to multiple factors.

    39. mass action

      Parasite moves through a homogeneous host population (of fruit fly cells in this case), attempting to occupy as many cells as possible.

    40. Thus, persistence of Wolbachia in maternal germline cells is of critical importance for transmission to progeny. In the Drosophila melanogaster model system that naturally carries wMel Wolbachia (O'Neill et al., 1992; Riegler et al., 2005), the GSC are infected with these bacteria. This ensures that differentiating daughter cells (cystoblasts) inherit Wolbachia during mitosis (Ferree et al., 2005; King, 1970; Serbus et al., 2008). While the cystoblast undergoes mitosis to generate an interconnected cyst of 16 germline cells, Wolbachia exiting the nearby somatic cell niche also invade the germline cyst (Toomey et al., 2013). After the cyst is coated with a blanket of somatic follicle cells, creating a unit referred to as an egg chamber (King, 1970), additional horizontal invasion events may also occur (Casper-Lindley et al., 2011). Wolbachia also replicate to populate the germline cells of the egg chamber, including the oocyte cell that ultimately takes over to form a completed egg (King, 1970; Serbus et al., 2011). Similar germline loading mechanisms are expected to apply to other Wolbachia-Drosophila combinations, with differential contributions to germline colonization by GSC loading and horizontal invasion in each case (Toomey et al., 2013).

      Wolbachia enter several different types of cells with the ultimate goal of infecting eggs and passing on to the next generation.

    41. Though Wolbachia occupy the germline stem cells (GSC) of male and female hosts, removal of the bacteria during spermatogenesis creates a ‘dead end’ with respect to transmission (Bressac and Rousset, 1993;

      Wolbachia ensures maternal transmission by leading to the death of eggs fertilized by infected male flies. This does not occur, however, when an infected female and her eggs mate with an infected male fly. Wolbachia modify sperm in infected male flies, but do not reside within the sperm.

    42. Conversely, the wMelPop Wolbachia variant lyses brain cells and shortens insect lifespan (Min and Benzer, 1997)

      wMelPop Wolbachia variant is unique in being more pathogenic than symbiotic (as with most other strains of Wolbachia). It is not harmful to developing flies, but divides quite vigorously in adult flies, damaging several tissues, and ultimately prematurely killing the adult fly.

    43. protect the host from lethal RNA viruses (Chrostek et al., 2013; Hedges et al., 2008; Martinez et al., 2014; Teixeira et al., 2008)

      Wolbachia is known to confer resistance to viruses in hosts it infects.

    44. promote host reproduction (Dedeine et al., 2001; Landmann et al., 2011; Starr and Cline, 2002)

      Wolbachia have been found to be essential for proper production of offspring by certain organisms.

    45. Of those, some are reported to provide essential cofactors to the host (Ghedin et al., 2007; Hosokawa et al., 2010; Nikoh et al., 2014)

      Hosokawa et al. found that Wolbachia bacteria are essential for proper development of the bedbug, Cimex lectularius, through provisioning of vitamin B, an essential cofactor. Cofactors ensure that enzymes function correctly.

    46. At least 470 distinct Wolbachia strains have been reported to date (Baldo et al., 2006)

      Genus Wolbachia is quite diverse.

    47. loci

      Plural for locus, a particular place or point.

    48. 52% of all insect species

      It was found that about 52% of all insect species are infected with Wolbachia endosymbiotic bacteria.

    49. Wolbachia are Alphaproteobacteria that reside within the cells of mites, crustaceans, filarial nematodes (Werren et al., 2008)

      Wolbachia are found in various nematodes (e.g. roundworm) and arthropods (e.g. insect, spider, crustacean).

    50. Symbiotic interactions within the collective unit of an organism range from mutualistic to parasitic (Dale and Moran, 2006).

      Although a symbiont is typically understood to be helpful for the host organism, the line between endosymbionts and parasites is not well delineated. This is especially the case, for example with Wolbachia. This bacterium is capable of ensuring its transmission by favoring the survival of fly egg cells that are infected, and leads to the death of uninfected fly eggs. On the other hand, Wolbachia is also known for making infected fruit flies resistant to certain viruses that would otherwise afflict the flies.

    51. control

      A baseline or standard that allows scientists to ensure that their manipulation of some variable, such as a food type in this experiment, actually has an observable effect that deviates from the baseline or standard.

    52. To further investigate how oocyte Wolbachia titer is controlled, this study analyzed the response of wMel Wolbachia to diets enriched in an array of natural sugars and other sweet tastants. Confocal imaging of D. melanogaster oocytes showed that food enriched in dietary galactose, lactose, maltose and trehalose elevated Wolbachia titer.

      The paper attempts to find the mechanism responsible for Wolbachia concentration increase in germ line cells through tests of natural/artificial sugars and yeast.

    53. titer

      The concentration of a solution, in this case, the concentration of Wolbachia bacteria in maternal germline cells.

    1. Steel, M., and D. Penny. 2000. Parsimony, likelihood, and the role of models in molecular phylogenetics. Mol. Biol. Evol. 17:839–850.

      Throughout their research, Steel and Penny explicate the connection between maximum parsimony (MP) and maximum likelihood (ML). According to the paper, they state that there can be a link between both methods when there is no common mechanism between sites. Moreover, throughout this process, Steel and Penny clarify disputed points between the two methods. It was concluded that neither models outperform the other when it comes to recovering the tree.

      This paper utilizes this source to support which method would more accurately perform the recovery of the tree. Furthermore, the authors wanted to assure those interested in their work that a variety of techniques including several models of ML and MP if special claims are made can be used.

    2. Saccone, C., G. Pesole, and G. Preparata. 1989. DNA microenvironments and the molecular clock. J. Mol. Evol. 29:407–411.

      During their study, Saccone, Pesole, and Preparata concluded that only homologous gene pairs, which whom are also stationary, are truly reliable to consistently provide with trustworthy determinations of phylogeny. Nonstationary genes, in comparison, resulted in outstandingly high rate values eventually resulting in possible systematic failure.

      This paper uses such sources as reinforcement of their results as stationary genes were proved to be better supporters in the construction of phylogenetic trees, or in phylogeny overall, providing superior results with an increased level of confidence.

    3. Gee, H. 2003. Ending incongruence. Nature 425:782. Phillips, M. J., F. Delsuc, and D. Penny. 2004. Genome-scale phylogeny and the detection of systematic biases. Mol. Biol. Evol. 21:1455–1458.

      In this paper, Gee concluded that there were no guidelines or factors that could measure the performance of a certain gene.The reason why the author of this paper uses it is to highlight the importance of stationary genes and how helpful they are for generating phylogenetic genes.

    4. Our reanalysis of Rokas et al.'s data indicates that their estimate of the number of genes required to infer a phylogeny confidently was inflated by signal heterogeneity caused by their inclusion of nonstationary genes. In addition, the conclusion that there are no useful predictors of phylogenetic performance does not hold.

      The data provided by Rokas showed that there needed to be a high number of genes to obtain good and confident results on a phylogenic tree. The reason why this was inferred was because nonstationary genes were used. In this paper it was proven that not many genes need to be used since stationary genes provide more accurate results with fewer genes, proving that there are good indicators to obtain phylogenetic trees

    5. When the randomly sampled orthologous nucleotides are bootstrapped in the same manner as the contiguous gene sequences, much greater variances are apparent (Fig. 6, open circles), although these variances are not directly comparable to the contiguous gene bootstrap variances because they do not include a variance component related to variation in gene size.

      It was concluded that when the randomly sampled orthologous nucleotides are bootstrapped utilizing the same process as the contiguous gene sequences the amount of variances probable increased. However, the variances are not proportional to the contiguous gene bootstrap variances since there is no link to variation in gene size.

    6. In fact, the confidence intervals are not visible in this figure, overlapping almost completely with the plotted average data points. This result is, however, largely an artifact of differing bootstrap resampling techniques applied to the randomly sampled and contiguous gene sequences. A typical nonparametric bootstrap was applied to the contiguous gene sequences: a sample (an individual gene) was taken and pseudosamples of the same size were generated from this sample by sampling with replacement. This gives the variance about the estimate of the phylogeny for that sample. Randomly sampled orthologous nucleotides were sampled with a different strategy, using the variable-length-bootstrap option in PAUP*. In this case, a sample of a given size was taken from the complete data set and the phylogeny was estimated. Then a new sample of a given size was taken, and the phylogeny estimated. So, for even the smallest sample size of 1000 nucleotides, 1000 replicates would have sampled the vast majority of nucleotides from the complete data set. This sampling scheme did not, therefore, measure the variance on the estimate of the phylogeny from a particular random sample, as in the contiguous gene sequences, but is instead akin to the variance on the phylogeny for repeated sampling of a given size from the complete data set.

      The author is stating that when Rokas et al. carried out the experiment to record bootstrap values in randomly sampled and contiguous gene sequences, the methods used to test variance were flawed. Rokas used two different techniques to test bootstrap value variance for randomly sampled and for gene sequences. The use of a different method when testing the randomly sampled sequences resulted in bootstrap values with very little variance, Rokas' conclusions were no longer considered reliable.

    7. Figure 5

      Both these graphs gave the results that stationary genes (triangles) produce higher bootstrap values with fewer genes compared to nonstationary genes. For Branch 2, only 7 stationary genes were needed to achieve a BP of 95% whereas 18 nonstationary were needed to achieve that same value. For Branch 3, 23 nonstationary genes were needed to achieve the same BP as 10 stationary genes did.

    8. A similar pattern was found with maximum likelihood.

      The data shown in Figure 4 represents the maximum likelihood that nonstationary genes (squares) are more susceptible to an “off” phylogenetic signal when compared to stationary genes (triangles).

    9. A concatenated gene analysis across all codon positions demonstrates that the stationary partition recovers the S. kluyveri–basal branch 5 with significantly fewer sampled genes

      The stationary Condon position demonstrated that it was slightly easier and faster to reach branch 5 of a phylogenetic tree with fewer genes.This exemplifies what this paper is trying to prove in regards of using fewer genes in order to build an accurate phylogenetic tree.

    10. When analyzed this way, 61% of the stationary genes were found to yield trees that were identical to or fully compatible with the species tree. By contrast, only 38% of the nonstationary genes yielded identical or fully compatible topologies.

      The comparison of topological incongruence went to exemplify how the tested "nonstationary" genes resulted in significantly lower ratios of identical or "fully compatible" trees in comparison to those in stationary conditions. The author does point out, however, this examination was altered form previous works, done by others, because of their belief of treating polytomies as soft instead of treating them all as hard.

    11. polytomies

      A point within a cladogram (a branching diagram) that contains more than two descendants.

    12. we illustrate through a series of analyses that the stationary gene partition is superior to the nonstationary partition

      Gene partitioning involves looking at the make up of complex traits. It involves computing heritability contributions from subsets of predictors to try and narrow down the search for causal variants.The reason why gene partitioning is so important is because if it is not done correctly the sister genomes results in aneuploidy. The consequences of these errors range from loss of normal cellular function to cell death. Stationary partitioning is superior to non-stationary because better results are given when trying to find these casual variants that are important for hereditary information.

    13. took this as evidence of the misleading signal in individual genes resulting from the nonindependence of nucleotides within genes.

      In this previous study, the authors had come to the inaccurate conclusion that single genes provide misleading phylogenetic signals because the results they gave varied widely when compared to random genes and also had low confidence levels.

    14. Herein, we demonstrate that these conclusions require substantial revision

      The main goal of this paper is to revise the previous work made on the construction of phylogenetic trees because according to previous studies by Rokas and Gee, those trees that have been created are fairly inaccurate. This research is being made to demonstrate how these phylogenetic trees are in fact accurate and correct the conclusions made by previous scientists.

    15. The authors then carried out a series of analyses

      In this experiment, the authors had to find out the lowest possible amount of data they needed to come up with a correct species tree. In other words, they want to discover the most efficient way possible to create an accurate phylogenetic tree.

    16. Rokas et al. (2003) analyzed these genes separately, and in combination, showing that individual genes sometimes support conflicting

      One of the biggest problems in the field of phylogenetics is the incompatibility of data that is obtained when single genes are used. In order to solve the problem of incompatibility, Rockas used "106 widely distributed orthologous genes for phylogenetic analyses, singly and by concatenation." The results that were given by this experiment showed that a chain of genes delivered a fully resolved "specie tree" with support. This was also seen by using a small quantity of 20 genes.This is extremely important as it can be a revealing answer and a way to figure out the different branches of the tree of life.

    17. this approach is necessary because there are no identifiable parameters that predict the phylogenetic performance of genes (Gee, 2003; Rokas et al. 2003)

      It is hypothesized that no matter what, the accuracy of a tree is directly related to the number of genes used to create that tree. This means that the greater number of genes studied, the more accurate the tree, so with an infinite number of genes one can achieve an infinite amount of accuracy.

      The second part of the hypothesis states that the above statement should be true due to the fact that there is no set evidence that can "rank" a gene's ability to contribute to a phylogenetic tree. This is hypothesizing that all genes contribute an equal amount to a phylogenetic tree, with no gene being able to contribute any more or less than another gene.