3,078 Matching Annotations
  1. Aug 2018
    1. C.D. Hopkins, Copeia 1991, 151–161 (1991).

      The article written by Carl D. Hopkins provides the author with background informational on B.pinnicaudatus and on the electric organs found within the organism. B.pinnicaudatus is a gymmotiform discovered in French Guinea and can be found throughout South America. This species similar to other electric fish is able to generate a pulse-type electric-organ discharge. The two types of electric discharges generated by electric fish tend to a pulse or a wave. This species is part of the largest family that produce electric pulses. Within this species, the males are able to produce a longer discharge than females.

    2. M.V.L. Bennett, Fish Physiology 5, 347–491 (1971).

      In his paper Electric Organs, Fishes, Bennett explains the various mechanisms behind electric fish organs and how they generate electricity, such as electrocytes and discharge patterns. He also describes several vital functions of electric organs and how they vary depending on the strength of the species' electricity, or the power of its voltage emission. For example, the electric organs of more strongly electric fish, or those who emit higher voltages, emit electricity to defend against predators. Conversely, in more weakly electric fish, their electric organs emit electricity that serves as a method of communication.

      This reference is significant to this paper, Electric organ discharges and electric images during electrolocation, because it gives a broad overview on electric fish, their anatomy, and their functions. It serves as a source of background information and context for this paper, which can be especially helpful for readers who possess limited knowledge on electric fish.

    3. J. Bastian, Electrolocation: behavior, anatomy and physiology.  (New York: Wiley, 1986).

      This source provides information about how the various regions of neuronal activity in electric fish respond differently to variance in body movement.

      Specifically, electrosensory pyramidal cells (neurons found in the areas of the brain that are involved in executive functions: memory, emotional responses, etc.) activate or discharge electric signals in multiple ways dependent on the re-afferent (sensory information that is received) signals from their external environment.

    4. E. Knudsen, J. Comp. Physiol. 99, 103–118 (1975).

      This source provides information about how the electrical patterns of small fish work compared to dipolar geometry and how that changes as the fish become larger in size.

      Specifically, the smaller electrical fish, which the author of this article is studying, have electrical currents that work like magnets. These smaller fish are much easier to measure and experiment on since their electrical currents and fields can be predicted. The bigger electrical fish are the more likely the electrical fields are to deviate from a dipole field.

    5. T.H. Bullock, W. Heiligenberg, Electroreception. (New York: Wiley, 1986).

      Bullock's and Heiligenberg's article, Electroreception, gives an in-depth knowledge on electroreception as well as a review on the electric organs that are found within marine vertebrates. This background provides the author with the basic foundation for understanding how electrolocation works and the purposes it serves these marine vertebrates in their natural environment and daily lives. This citation also helps the author introduce the topic of electrogenesis and electroreception in relation to the location of the organs necessary for the process of electrolocation to occur.

    1. Table 1. Evolution of spread-relevant traits as a function of landscape patchiness.

      Table 1 shows data indicating linear relationships between variables that changed in an evolving population based on the variability of the environment. The P column explains whether the data is statistically significant, meaning it can be concluded as a relationship between data and not just due to random chance. The two values observed for each variable are Y intercept (which indicates whether the trait changed from the original population) and the slope (which indicates how much the trait changed). These values are calculated as P values to determine if they are significant.

    2. Results of linear models examining the change in height, dispersal, competitive ability, and seed mass at the invasion front after six generations of evolution as a function of landscape patchiness (size of gaps between suitable habitat).

      Table 1 indicates that plant height, competitive ability, and seed mass had significant intercepts, meaning these traits changed from the original population, but only plant height showed a significant slope, meaning that the other traits did not have a significant rate of change.

    1. Error bars reflect the 95% confidence interval of the mean or expert judgment

      Notice that each bar in the figure has small capped lines that extend above and below the bar. These lines represent error bars for the various VOC emission factors. Error bars reflect the experimental uncertainty in determining VOC emission factors. The error bars in this figure are 95% confidence intervals, meaning that we are 95% certain that the true value lies somewhere in between the top and bottom of the error bar. Any measurement made has uncertainty associated with it.

      In scientific communication it is important to give the value that was found and the uncertainty in that value. We typically talk about uncertainty as being the precision of the measurement, where a smaller uncertainty is a more precise measurement and a larger uncertainty is a less precise measurement.

    2. Tg

      Teragram, grams in the trillions.

    1. juvenile hormone acid methyltransferase (JHAMT)

      Used in the last step of the juvenile hormone biosynthesis pathway that converts acids into hormones.

    2. previtellogenic stage (PVGS), an ovarian resting stage (ORS) and a vitellogenic stage (VGS)

      One of the most significant stages of the reproductive cycle is vitellogenesis which involves massive production of yolk protein and their accumulation in developing oocytes. Vitellogenesis is dependent on the availability of a blood meal and, as a consequence, is linked to transmission of pathogens. Therefore, vitellogenesis and other aspects of mosquito reproductive physiology is critical for their management of disease. The ovarian resting stage in the reproductive cycle of female mosquitoes is a time when the eggs are not being produced. In addition, the ovaries will not develop beyond a resting stage until a blood meal of adequate size has been taken.

    3. JH synthesis was analyzed

      Scientists started using fluorescent tags as a natural way to accurately detect low concentration of metabolites in insects. This method proved to be sensitive and effective and most importantly stable. Being stable was an important factor in this method because if it was not stable it would start to degrade after about 15 minutes. The new method has lasted over an hour, which is in benefit of being detectable by HPLC-FD (High-Performance Light Chromatography with Fluorescent Detection).

    4. RNA interference (RNAi)

      RNA Interference is a response to double-stranded RNA that is responsible for the resistance of pathogenic nucleic acids such as certain mutations in base pairs, and regulates how genes express a particular protein.

    5. corpora allata (CA)

      Found in the head of insects. It is responsible for the regulation of metamorphosis and reproductive functions in most insects.

    6. signaling pathway

      A signaling pathway allows an activation process to occur for a cell to have a specific function. In this case, communication takes place between these two different hormones, juvenile and insulin. These hormones work with energy to develop an insect.

    1. euthanized

      Put to death with minimal pain.

    2. in bluefin tuna (Thunnus thynnus) the contraction time tends to increase towards the tail (see also Fig. 1A). This implies that at high speeds, muscles of opposite sides will progressively overlap their contractions towards the tail, stiffening the body.

      Unlike the other fish, the little tunny had muscle contraction times increasing from head to tail, implying that they used their head more than their tail for swimming fast. The authors compared this to another species of tuna, the bluefin tuna because it had a similar trend in muscle contraction. They analyzed this to mean that at high speeds, muscles from opposite sides of the fish (left and right) will contract so that the waves of contraction move towards each other and overlap, which makes the body stiff.

    3. Previous work on other species has suggested that this might aid the transmission of the force

      Previous studies have suggested that this helps move the force from the contractions from the head towards the tail.

    4. Our data suggest that sailfish are not able to achieve the extremely high speeds claimed by earlier studies

      Here the author ties the goal of this study with the data collected. The goal of this study was to test whether earlier studies were correct in their estimations of maximum swimming speeds in sailfish. The author describes that the data collected disproves earlier studies and provides explanation as to why the data of the prior studies may have been skewed.

    5. teleosts

      Members of a large and extremely diverse group of ray-finned fishes.

    1. Both results suggest that chemically distinct species are more likely to co-occur. In contrast, we found a significant negative relationship between species phylogenetic distance and presence/absence co-occurrence (r = −0.16, P = 0.01). Thus, more closely related species are more likely to co-occur.

      The Mantel tests allowed the authors to determine the amount of difference between species. The test uses estimated distances to measure difference.

      In this case, it is testing chemical differences between species. The results indicated Piper species that are more chemically different are more likely to exist within the same environmental patch.

    2. Mantel test

      A Mantel test measures the correlation between two matrices. In this case the Mantel test was used to estimate the correlation between species phylogenetic distance and their co-occurrence.

      Using this test, the researchers were able to statistically verify that there is a negative relationship between how closely related two species are their co-occurrence.

    3. Pianka's index

      Pianka's Index is used for field measurements of the niches. They can measure microhabitat, resource usage, and spatial activity. The values range from 0 to 1, no resources used in common between species to complete overlap in resource use, respectively.

    4. Gotelli's c score

      Gotelli's c-score measures co-occurrence between species. A binary matrix is used to represent the absence (0) or presence (1) of a species. Each column represents a site and each row represents a species. Once the c-score is calculated a high value indicates less co-occurrence and a low values indicates there is more likely to be co-occurrence.

    5. only -NRI was significantly different from zero (-NRI, t = 1.83, df = 80, P = 0.03; -NTI, t = 0.77, df = 80, P = 0.22). In contrast, species composition within the plots was phylogenetically underdispersed. Both -NRI and -NTI were significantly different from zero (t = −5.24, df = 80, P = 0.0001 and t = −2.26, df = 80, P = 0.01, respectively; Fig. 2).

      Here, the author’s evaluated whether or not similar species tend to coexist together using the inverse nearest relative index (-NRI), which asses clusters of species, as well as the inverse nearest taxon index (-NTI), which asses cluster taxonomy of clustered species.

      Along with data obtained by the chemical dendrogram the clusters were analyzed and diversity in relation to clustering was discovered.

    6. In our community-based approach, we found that Piper species were, on average, more overdispersed with respect to their secondary chemical composition than expected

      In order to assess the dispersion of Piper species, the authors analyzed the secondary chemical composition of the plants. In plants, secondary composition are organic compounds used for plant defense. They are secondary because their absence does not cause immediate death of the plant.

      The analysis of the secondary chemical composition was performed using a chromatography technique: GC-MS. This technique does not detect all secondary metabolites but it detects most of them (86% of the metabolites).

      After the secondary metabolites were detected, a library was created for all species and the library was compared to references in the AMDIS (Automated Mass Spectral Deconvolution and Identification System -a mass spectra identification system). The library created was a mass spectra library.

      Mass spectrometry is an analytical technique that identifies molecular weights of compounds which helps in the identification process. The particular identification method allowed the researchers to assess chemical similarities between individual plants and species.

      This analysis allowed the researchers to conclude that the Piper species were more spread apart than expected when their secondary metabolites was the point of comparison.

    7. Given our results, we propose that the interaction between Piper and its natural enemies (mediated by secondary chemistry) is likely to play a major role in the community assembly and local coexistence of species in this genus.

      The chemical properties of Piper allow it to ensure its success. By doing this it influences other plants and animals in its community. This can include suppression of other plants, eliminating certain herbivores from the area, etc.

    8. It is important to note that, for our study system, there seem to be two distinct sets of traits that are influencing coexistence in opposite manners. While communities tend to be chemically overdispersed, the same communities are also phylogenetically underdispersed.

      The data suggest that the chemical products Pipers produce seems to be inversely proportional to their phylogenetic relatedness. So communities that tended to have a wider range of chemicals, were also the communities that were most closely related.

    9. Zhang and Schlyter 2003

      Zhang and Schlyter suggest that the diversity in mixed forests interferes with host choice guided by smell.

      As the level of pheromones (semiochemicals) increase, herbivores disturbance increases.

    10. Contrary to the effect of chemical similarity, Piper species that were closely related were more likely to coexist in a particular patch. This pattern is likely the result of other unmeasured traits that, unlike chemical similarity, are strongly conserved across the phylogenetic history of our target Piper species. One possibility could be a strong environmental niche conservatism in which closely related species are more likely to have similar habitat preferences

      Although the experiments showed that Piper species that were chemically similar were not likely to coexist, this was not the case for phylogenetically related species. The data suggest that the species who were most closely related, were actually more likely to coexist is a patch.

      There may be other traits of the Piper, other than chemical similarity, that may have an influence. The environment may push for the conservation of these traits.

    11. Phylogenetic distance

      The amount of time that has passed since two species have shared their most recent common ancestor.

    12. In our species-pair approach, we found that, independent of the measure of coexistence used, chemical similarity had a significant negative effect on species coexistence.

      The approach used in this study allowed the authors to conclude that the more similar plant metabolites are between Piper species, the least likely they are to be found next to each other.

    13. a significant positive relationship between species chemical distance and the likelihood of species co-occurrence for both species presence/absence data

      A positive relationship in this case means that the more different species are chemically, the more likely they are to coexist.

    14. species coexistence

      In order to asses species coexistence, the amount of niche overlap needed to be found. Niche overlap occurs when two or more organismal units use the same resources. More overlap would mean that more species exploit each resource. This was done using Pianka's Index.

    15. Brownian motion model of evolution

      In Brownian motion model of evolution, traits change randomly in distance and direction.

      The model uses two parameters: the population mean trait and the evolutionary rate parameter.

      This model is used in biology to compare traits between individual species and create phylogenetic trees.

    16. The small value of K (K < 1) suggests that closely related species are less similar in their secondary chemistry than expected

      Through the presence or absence of chemicals within the leaves of the sampled species, the researchers conducted the K statistic for the phylogenetic signal of the secondary chemicals. Through this analysis, the authors found that related Piper species were less likely to share their secondary chemical characteristics.

    17. K = 0.03

      K statistic is a statistical analysis of the phylogenetic signal based off a Brownian motion metric that determines the strength of the phylogenetic signal.

    18. phylogenetic signal

      The likelihood that taxas with a shared common ancestor will have similarities in their appearance, behavior, and in their interactions with others.

    19. Phylogenetic analysis yielded a local species phylogeny that concurs with the current phylogenetic Piper data

      Piper is a very species rich genera of flowering plants. Molecular phylogenetics has been crucial in identifying the monophyletic groups of this genus.

      The researchers amplified the ITS region and the psbJ-pet A intron of each of the sampled species they collected to conduct a phylogenetic analysis. They were able to construct a phylogenetic tree of the Piper species that were found within the patches they sampled.

    20. The hierarchical clustering showed five discrete chemical clusters

      The authors collected data regarding chemicals produced by the plants used in their experiment using a multi-step process.

      They first preserved leaves they collected within silica gel before transporting the leaves to the University of Missouri, St. Louis. There, the researchers crushed the leaves under liquid nitrogen. Next, a methanol-chloroform solution was used to extract volatile compounds along with a small addition of piperine. The authors then filtered and stored the compounds so that they could later be analyzed.

    21. terpenes

      A large and diverse group of organic compounds that are present in many plants and insects.

      Terpenes are often found in conifers, which release a distinct scent.

    22. The GC-MS analysis yielded more than 1,100 chromatographic features. Approximately 40% of all features were present in all Piper species (e.g., phytol, stigmasterol, sitorterol, and tocopherol).

      The authors used previously collected extracts from leaves and analyzed them using gas chromatography mass spectroscopy (GC-MS), which determines chemicals within an extract based off particular peaks given off by those chemicals. They were able to find that 40% of all Piper species contained the same types of chemicals.

    23. We sampled a total of 2,035 individuals from 27 species of Piper across the 81 sampled plots (Appendix S1: Table S1). The number of individuals present per plot was 25.2 ± 1.1 (mean ± SE; max–min = 4–51), and the number of Piper species per plot was 5.2 ± 1.4 (max–min = 3–11).

      In order to conduct the experiment, patches needed to be sampled and the average number of Piper per patch needed to be calculated. The researchers created transects located between 50 and 100 m from the trail and a large space separated each transect (more than 250 m). Then in a different transect, 81 plots of 20m in diameter were created. The standardization of the plots is important for an accurate calculation of the average number of Piper per plot.

      Piper had different sizes, so for a better standardization, only Piper that are more than 1cm in diameter were selected for calculating the mean number of Piper per plot. The researchers than identified the species of each Piper. A total of 2,035 individuals were counted. The mean per plot was calculated by dividing the number of individuals by the total number of plots. (2,035/ 81 = 25.123) The number of species per plot was calculated by determining the mean of the average of species per plot. The average was found to be 5.2 species per plot.

    24. volatility compounds

      Mixtures that can readily become vapors or gases.

    25. Pianka's Index

      In the process of his research, Pianka came up with a universal formula for calculating the overlap of pairs of niches.

    26. transects

      Narrow paths through which one collects information on the species that is being studied.

    27. Dyer et al. 2001

      Research conducted by Dyer et al. provides information on chemicals the Piper plant produces and trade-offs that affect the Piper plant in relation to these chemicals.

    28. pantropical genus

      A taxonomic category that can be found throughout the tropics.

    29. divergent selection

      The process of choosing that leads to the formation of new species due to the accumulation of differences between species.

    30. Wahid et al. 2007

      In this comprehensive review, Wahid and colleagues discuss how plants respond to high temperatures.

      They describe the physiological responses, adaptations, and mechanisms plants implement in response to heat stress.

    31. qualitative

      A characteristic that can be measured based on an observable standard or quality.

    32. quantitative

      A characteristic that can be measured based off of its amount or quantity.

    33. McGill 2006

      McGill and colleagues measured functional traits by focusing on four different themes: traits, environmental gradients, the interaction environment, and performance currencies (seed output, energy intake and expenditure, etc.).

      They showed that focusing on quantitative functional traits allows for identification of general plant patterns, allowing for better prediction. This helps in understanding historical aspects of the community, assembly, trait evolution, and phylogenetic structure.

    34. niche

      The job/role that an organism performs in its environment.

    1. By preying on seabirds, foxes reduced nutrient transport from ocean to land, affecting soil fertility and transforming grasslands to dwarf shrub/forb-dominated ecosystems.

      The effects of foxes on the Aleutian islands are both direct and indirect in nature. The presence of foxes directly affects the seabirds by decreasing their population due to them being easy prey. Indirectly the islands plant composition is affected by the reduced populations of birds distributing fewer nutrients needed by the vegetation. The U.S. Fish and Wildlife Service has been reducing fox populations in order to restore the seabirds and have the islands support more plant life. To read more go to USGS: https://soundwaves.usgs.gov/2005/05/research.html

    1. substrate specificity of PETase

      In this case, a highly specific enzyme would degrade PET but not other esters.

    2. Substrate specificity

      Describes how much an enzyme prefers one chemical to others.

    3. Prominent pitting developed on the film surface

      Indeed, the isolated protein was found to degrade PET.

    4. appeared to be connected to each other by appendages

      The appendages allow the cells to remain close to the PET film that serves as their energy source and helps to degrade the PET more quickly.

    5. The strain represents a novel species of the genus Ideonella, for which we propose the name Ideonella sakaiensis 201-F6 (deposited in the National Center for Biotechnology Information taxonomy database under identifier 1547922).

      When the authors isolated different types of microbes, they discovered a new organism which they identified as belonging to a family of closely related organisms called ldeonella, and called it ldeonella sakaiensis or l. sakaiensis. This specific bacterium can degrade PET even in absence of all the other microbes in the consortium the authors tested earlier in the paper.

    6. adherent cells

      A cell that is sticking to a surface.

    1. special relativity theory and the general theory of relativity

      Einstein came up with the theory of special relativity before general relativity.

      Special relativity assumes the laws of physics are constant in all inertial frames of reference (frames of reference that are assumed to be stationary).

      General relativity expands on this, and describes the fabric of space-time on the scale of the universe (which Einstein suggests is warped by massive bodies).

      Einstein expanded special relativity to general relativity over the course of about 10 years as he realized that special relativity was insufficient to explain some phenomena in the universe.

    2. perpetual motion never occurs in ordinary experience

      This kind of motion is impossible because it would require an infinite energy source, which violates the first law of thermodynamics (the Law of Conservation of Energy: The total energy of an isolated system is constant).

  2. Jul 2018
    1. His clear and wide ideas will for ever retain their significance as the foundation on which our modern conceptions of physics have been built.

      It is only by embracing Newton's ideas that physicists such as Einstein were able to consider exceptions and, in doing so, build on them.

      Although we don't often think about it, scientists improve on each others' ideas all the time and revise theories in light of new evidence generated by new technologies and methodologies.

    2. "a warp in space."

      Euclidian geometry presumes a uniform and constant arrangement of space. However, Einstein proposed (and others demonstrated) that space is "warped" around objects depending on their mass. The larger the mass, the greater the degree of warping.

      Because time is connected to space, it is also warped around massive objects.

    3. The interpretation seemed obvious, but classical mechanics forbade it.

      Einstein introduces the need for a concept of general relativity, which describes motion with respect to any two coordinate systems, not just inertial coordinate systems.

    4. What has nature to do with the coordinate systems that we propose and with their motions?

      Einstein's question points out that coordinate systems are not a product of nature, but a way of understanding nature. It is because of this that physicists are able to revise the tools and methodologies they use in light of new evidence.

    5. principles from which mathematical formula are deduced of such a kind that they apply to every case which presents itself

      The analytical method begins with empirical observations, from which principles and formula are inferred (which can be applied to other cases).

    6. Modern physicists call "inert" and "heavy" masses "inertial" and "gravitational," respectively.

  3. Jun 2018
    1. Fab only lightly marked the nucleus, suggesting very little KDM5B had been synthesized (Fig. 1D). Fab also colocalized and co-moved with many MCP-labeled mRNA in the cytoplasm

      After determining that neither the SM tag nor Fab would disrupt cellular processes, the authors wanted to determine how soon Fab would mark KDM5B. To do this, the authors repeated their first trial but imaged at 6 hours instead of 24.

    2. suggesting neither the SM tag nor the presence of Fab interfered with mRNA and KDM5B production and localization

      The two tags did not appear to affect the synthesis or location of the mRNA or the ribosomes.

    3. 24 hours after transfection, MCP marked mRNA in the cytoplasm and Fab marked KDM5B in the nucleus

      Preliminary testing was conducted twenty-four hours after the plasmid was transiently transferred to ensure that the methods of coupling the FLAG SM tag (that can be labeled with the anti-fluorescein antibody, anti-FLAG Fab) and the MS2 stem-loop (that can be identified with a MS2 coat protein) would not inhibit transcription, translation, or the movement of SM-KDM5B mRNAs throughout the cell.

      The results are highlighted in Fig. 1C with the SM-KDM5B protein in green and the MCP-labeled mRNAs in red.

    4. labeled with the far-red JF646 fluorophore

      JF646 produces a brighter fluorescence than other proteins.

    5. bead-loaded

      Bead-loading is a technique for quickly and efficiently loading large numbers of macromolecules (such as DNA and RNA) onto the cells of tissues.

    6. U2OS cells

      A type of cell that lacks the p16 gene (which normally suppresses growth), allowing it to continue to grow and divide indefinitely while there are resources.

    7. MS2 stem-loop repeat allows visualization with labeled MS2 coat protein

      MS2 is a protein from the coat of bacteriophages. It has a high affinity for "stem-loop" structures, which are hairpin-like shapes formed by DNA. The authors took advantage of this high affinity by using labeled MS2 to detect certain sequences.

    8. anti-FLAG antibody fragments

      Antibodies "against" the FLAG-tag (SM).

    9. FLAG-tag (which we refer to as the spaghetti monster, SM)

      A specific sequence of amino acids that can be added to proteins to "tag" them. Antibodies have been developed that have high affinity for the tag, so it is a popular choice in this kind of visualization experiment.

    10. plasmid

      A circular, double stranded piece of DNA that is often used as an intermediary to insert genes into a genome.

    11. photostable small molecule dyes

      Dyes that will not degrade when exposed to light.

    12. To visualize translation of a single RNA in real-time

      For a synopsis of the present study, see Science Daily:


    13. Recently some of these problems were overcome using an RNA biosensor that is dislodged by translating ribosomes

      Researchers have been able to visualize where and how quickly mRNA translation is occurring during development, but not for single molecules.

    14. Although transcription is now regularly quantified in real-time with single gene resolution in vivo

      Researchers have described how fluorescent markers can be used to visualize and describe transcription in vivo, but the present study is the first to do so for translation.

    15. transcription

      The process by which RNA molecules are synthesized with information from DNA.

    16. translation

      The process by which an amino acid chain (and eventual protein) is created using information from mRNA.

    17. sensitivity and versatility of NCT make it a powerful new tool

      Scientists are always working to improve existing techniques to be more precise and versatile.

    18. ribosome

      The main protein that is involved in translating mRNA into proteins.

    19. Polysomes

      A complex of mRNA and multiple ribosomes formed during translation.

    20. stochastically


    21. elongation rate

      The rate at which a new protein is synthesized (or "elongated").

    22. multi-epitope tags

      An epitope is the part of a molecule that an antibody recognizes and binds to (usually as part of an immune response).

      Epitope tagging takes advantage of this by creating special versions of proteins that have specific epitopes on them. The proteins can then be detected using antibodies that bind to the specific epitope.

    23. Nascent Chain Tracking (NCT)

      A method that tracks the synthesis of new proteins by using fluorescent molecules to track the movement of molecules in the cell.

    24. in vivo

      In a living organism.

    25. messenger RNA (mRNA)

      A type of RNA that transmits information from DNA (where genetic information is stored) to the ribosome (where proteins are created from genetic information).

    1. redox potentials

      a measure of the tendency of a chemical species to acquire electrons and thereby be reduced.

    2. aerobic respiration

      the process of producing cellular energy involving oxygen.

    3. (Childers, 2006; Hao et al., 2011; Schedlbauer et al., 2012)

      Childers and colleagues demonstrated that Everglades hydrology was co-varying with changes in greenhouse warming potentials, energy fluxes and C dynamics which proved that hydrology is important for creating and maintaining conditions sufficient for wetland ecosystem and structure

    4. (Jimenez et al., 2012)

      Jimenez and colleagues studied the effects of carbon balance in wetland ecosystems before the planned Everglades restoration of historical water flow. They trajected that there would be an alteration on the carbon dynamics of the Everglades as a whole.

    5. carbon cycling

      the biogeochemical cycle by which carbon is exchanged among the biosphere, pedosphere, geosphere, hydrosphere, and atmosphere of the Earth.

    6. levees

      an embankment built to prevent the overflow of a river.

    7. spillways

      a passage for surplus water to run over or around an obstruction (such as a dam)

    8. hydrological regime

      refers to variations in the state and characteristics of a water body which are regularly repeated in time and space and which pass through phases, e.g. seasonal. (DJ)

    9. (Dugan, 1993)

      Dugan examined wetlands in the United States and the total loss of thus ecosystem. This atlas was able to divide the world’s regions into 19 sections and develop information on the wetlands.

    10. hydric conditions

      soil that formed under conditions of saturation, flooding, or ponding long enough during the growing season to develop anaerobic conditions in the upper part.

    11. carbon sequestra- tion

      the process involved in carbon capture and the long-term storage of atmospheric carbon dioxide

    12. torpedo- grass

      one of the most serious weeds in Florida. It grows in or near shallow waters forming monocultures where it can quickly displace native vegetation.

    13. vegetation dieback

      common symptom or name of disease, especially of woody plants, characterized by progressive death of twigs, branches, shoots, or roots, starting at the tips.

    14. marsh

      wetland that is dominated by herbaceous rather than woody plant species. Marshes can often be found at the edges of lakes and streams, where they form a transition between the aquatic and terrestrial ecosystems. They are often dominated by grasses, rushes or reeds.

    15. hydroperiod

      period of time during which a wetland ( land that is mostly covered by water) is covered by water.

    16. CO2

      Any movement of carbon between these reservoirs is called a flux. Which means transfer of carbon from one pool to another.

    17. carbon pools

      sometimes also called stocks or reservoirs because they act as storage houses for large amounts of carbon.

    18. Abstract

      Hydrology is the main reason for the carbon balance of wetlands by controlling the uptake of CO₂ and CH4. Determining the effect of droughts on CO2, fluxes and CH4 emission was stimulated by hydroperiod with three scenarios. These three scenarios affect the rate of drought from being gradual, intermediate, and rapid transition into drought. It resulted in higher net CO2 losses net ecosystem exchange (NEE) over a 22-week manipulation. Due to drought vegetation dieback, it increased ecosystem respiration (Reco), and it also reduced carbon uptake gross ecosystem exchange (GEE). The NEE did not offset methane production during periods of flooding. Changes in precipitation patterns and drought occurrence altered the carbon storage of freshwater marshes. We can determine that with the change in the climate will modify the storage capacity of freshwater marshes by influencing the water availability.

    19. Effects of simulated drought on the carbon balance of Everglades short-hydroperiod marsh

      Alternative Title: Tipping the Carbon Balance in Drought Stimulated Everglades

    1. Dynamic extrafloral nectar production: The timing of leaf damage affects the defensive response in Senna mexicana var. chapmanii (Fabaceae)

      A Sweet Relationship: Plant and insect mutualisms and the effects of damage on nectar production in Senna mexicana var. chapmanii (Fabaceae)

    1. Zika infection disrupts the binding of MSI1 to its endogenous targets

      Zika virus is dangerous for fetuses, but in adults the virus may eradicate cancerous brain tumors.

      Read more about how Zika virus affects brain tumors here: https://medicine.wustl.edu/news/zika-virus-kills-brain-cancer-stem-cells/

    2. neurotropism

      An affinity for neural tissue.

      Here, it refers to the fact that Zika virus specifically targets neural cells.

    3. microcephaly

      Underdevelopment of the brain that causes a child's head to smaller than normal.

    4. neonatal

      Newborn children, up to four weeks old.

    5. A recent outbreak of Zika virus in Brazil

      Zika is type of virus called a flavivirus, a family of viruses that is transmitted by mosquitoes and includes yellow fever, West Nile, and dengue virus.

      In May 2015, Brazil was the first to associate Zika virus infection with microcephaly in newborns.

      Watch the following video for more about the history of Zika: https://youtu.be/FOcSe0LtoTg

    1. deciduous forest

      A biome marked by seasonal changes that typically sees tree growth in the summer, and a shedding of leaves in the winter.

  4. May 2018
    1. similar species conservation issues.

      Medicinal Plant Trade in Sierra Leone: Threats and Opportunities for Conservation (Jusu and Sanchez 2014)


    2. conservation

      Other strategies used for conservation include seed banking and establishing new protected areas.

      Orchid conservation in the biodiversity hotspot of southwestern China (Lia et al. 2015) http://onlinelibrary.wiley.com/doi/10.1111/cobi.12584/full)

    3. Two key biological traits, i.e. being epiphytic (so that its cultivation will not be at the expenses of native trees) and having renewable stem growth (enabling non-destructive, multiple-year harvesting) render Dendrobium orchids ideal for restoration-friendly cultivation.

      Based on the study where market demand of Dendrobium within TCM has diminished its population, restoration-friendly cultivation will be needed to restore this epiphytic plant species back into the environment. This form of conservation will not only help preserve the integral population of orchids in China, but also sustain the economy for its increasing demand.

    4. ex-situ

      In regards to conservation, it is the process of protecting endangered plant species that is outside of its natural habitat.

    5. (Ding et al. 2008).

      In this study they use SRAP marker which is sequence-related amplified polymorphism to study the genetic diversity of plant species. It is a technique that helps detect genetic variation within plants.

    6. (Jiang et al. 2008)

      This paper focuses on the environmental issues such as natural occurrences that affect land, water, and soil loss.

    7. (Zhou and Grumbine 2011)

      This article talks about the different areas that have been built in order to increase preservation. There has been some limitations in terms of funding, administrative authority, and proper development. They continue to address these concerns and find possible ways to create more protected areas.

    8. desertification

      Increasing in aridity, usually reducing the number of life forms able to survive there.

    9. karst landscapes

      Landscape characterized by sinkholes and caves, formed by the dissolution of soluble rock like limestone, dolomite or gypsum.

    10. Forest tenure reform

      Whereby land rights are formally recognized for people living on or near the forest, so that they may benefit from its use (or of harvesting of some natural forest products).

    11. by taking only the older stems that have already flowered and fruited, thereby giving the planted individuals chances to recruit naturally in largely natural forests. Plants can be harvested annually in this manor for up to a decade

      In a recent study it was discovered that Dendrobium orchids can be sustainably harvested once a year if harvesters only take the old stems that have already produced fruit and flowers so that the younger stems will be allowed to reproduce.

    12. restoration-friendly cultivation

      A term coined by Liu and colleagues that argues for an unconventional introduction approach, in which orchid populations planted in natural forests are sustainably harvested.

    13. lithophytic

      Plants that grow in or on rocks.

    14. Liu et al. 2011, 2013).

      Publication accounts for confusion among scientific and Chinese names for this orchid, and provides clarification on taxonomy and nomenclature.

    15. (Kirkpatrick and Emerton 2009;

      This paper discusses efforts to reduce poaching of wild tigers by breeding tigers to increase their numbers and in theory, reduce their [tigers generally] worth. However, the argument is made that wild tigers cannot be substituted by farmed tigers to alleviate poaching because they are not valued the same by hunters. Because of this difference in worth (perceived or real) flooding the market with farmed tigers will have no effect on the demand for wild tigers.

    16. artificial cultivation

      Creating new life using man-made methods.

    17. biotic resources.

      Natural resources gathered from the biosphere. Examples: forests, animals, and marine organisms.

    18. limestone landscapes

      Sedimentary rocks (limestone landscapes) are formed from pre-existing rocks or pieces of once-living organisms. They form when deposits accumulate forming distinctive layers.

    19. China adopted its protected areas system in the most strict sense, i.e. nature reserves allow minimal human interferences

      China’s government authority have employed new park policies in Yunnan, where explicit management zoning systems are implemented towards the local people. Tourism has been known to provide a source of income for these environmental programs.

    20. (Godefroid et al. 2011;

      Using 12 years of seizure records covering nearly 1000 seizures from ivory to live reptiles, the authors review and describe current status of illegal trading of wildlife and wildlife products. The authors conclude that regulation and enforcement are not enough to control illegal trade, but that education at the community scale combined with empowerment of locals to value their own wildlife, international regulation and ground-level enforcement will result in more effective control.

    21. (Feng, C.-L. Chinese Academy of Forestry, personal communication)

      Personal communication was made between the author and other researchers to confirm that this species of orchid is rare and its populations are unknown due to orchid poaching.

    22. Gastrodia

      A rare and endangered saprophytic orchid commonly used in traditional Chinese medicine for hypertension, relieving headaches, and convulsions.

    23. viable

      Self-sustaining, reproductive.

    24. hotspot

      "Hotspot" is widely used in reference to regions of especially high biodiversity in plants and/or animals.

    25. Francisco-Ortega et al. 2010).

      This group surveyed all of the plants on Hainan Island and published a checklist.

    26. (Qin et al. 2012)

      This group looked at the conservation status of over 1300 native orchids distributed among 543 reserves in order to assess their status, and make recommendations for improving efforts where needed.

    27. species lists

      An actual list of all the species found in a park or area; commonly provided in reserves.

    28. Many more nature reserves were established at the provincial and lower government levels.

      In 2016 the Chinese government announced that they plan to establish 30 to 50 nature reserves across China by 2020.

      Read more in "China to establish up to 50 new nature reserves in next 5 years" http://www.ecns.cn/2016/11-03/232694.shtml

    29. (Xu et al. 2009

      This paper reviews the progress made toward the national objectives for reducing biodiversity loss using time-series data sets against national indicators. Substantial movement forward was achieved, with stable increases in forest resources, improvements in marine ecosystem integrity, stable water quality, etc. as of 2009.

    30. introduced 

      A species not native to the area.

    31. ecological value

      The worth of the orchid in this habitat, with regards to supporting other life forms, pollinators, water cycling, microhabitat creation, etc.

    32. epiphytic

      Growing on another plant or structure, as opposed to rooted in the ground.

    33. reintroduction (sensu Menges 2008)

      Looking at translocation efforts (including introduction, reintroduction and augmentation of wild populations) for conservation and supplementing declining species to return to self-sustaining numbers.

    34. orchid-hungry

      These developed countries have fewer species of native orchids.

    35. Fauna and Flora

      Fauna refers to animal life, whereas Flora refers to plant life.

    36. Dendrobium plants available in recent years have largely come from neighboring Vietnam and Laos

      In Thailand there is a large network of illegal trading for endangered species of orchids to be used for medicinal purposes in China. These trades are done without domestic harvest permits or CITES permit which violates state and international restrictions on wild orchid harvest.

      Read More: "Unseen harvest: Southeast Asia’s illegal orchid trade"


    37. overexploitation

      Over use of a species for food, medicine, and other commercial purposes.

    38. tonic for traditional vocal artists to protect their voices and its use extended to cancer prevention and cure, as a boost to the immune system, and for other illnesses (The State Pharmacopoeia Commission of P. R. China 2010; Ng et al. 2012).

      Although other studies have mentioned that orchids have certain compounds such as alkaloids that help combat illnesses, there are not enough clinical studies (except for animals) to support its medical use.

    39. ethnobotanical

      A region's plants and their traditional uses.

    40. horticulture

      A branch of agriculture concerned with growing plants that can be eaten, used for medicinal purposes, or ornamental purposes.

    41. endemic

      Plants native to, and sometimes only found in this area.

    42. conservation success

      Read more:

      A more recent look at diversity in the region.

      Tropical China Plant Diversity, Ecology and Conservation – a Glimpse at the Current State (Liu et al 2017, https://link.springer.com/article/10.1007/s12229-017-9180-7)

    43. Dendrobium

      Genus of orchid.

    1. pristine

      In its original condition; unspoiled.

    2. deleterious

      Causing harm or damage.

    3. forager

      Foraging is searching for wild food resources. It affects an animal's fitness because it plays an important role in an animal's ability to survive and reproduce.

    4. omnipresent

      Widely or constantly encountered; common or widespread.

    5. extrinsic

      Not part of the essential nature of someone or something; coming or operating from outside.

    6. intrinsic

      Belonging naturally; essential.

    7. extrafloral nectaries

      Provide a nutrient source to animal mutualists, which in turn provide anti-herbivore protection.

    8. surrogate

      A substitute, especially a person acting for another in a specific role or office.

    9. anthropogeni

      Originating in human activity (chiefly of environmental pollution and pollutants).

    10. deterred

      To prevent the occurrence of something.

    11. thwart

      To prevent (someone) from accomplishing something.

    12. Ants, particularly P. gracilis, may pose a significant threat to butterfly eggs and larvae, but butterflies have developed ways to cope with such predators

      Authors found that this species of ants are more efficient at being predators.

    13. we assumed they would interact with caterpillars more frequently than other predators

      Since the ants were found more in caterpillar at BNP authors assumed that the ants are the primary predators of caterpillars.

      Some other predators also influence caterpillar mortality, but ants are more abundant.

    14. ubiquitous

      Present, appearing, or found everywhere.

    15. elucidated

      Make (something) clear; to explain.

    16. early instar (small) caterpillars suffered higher mortality than late instar (bigger) caterpillars

      Authors ended up concluding that the smaller the caterpillars, the higher the rate of mortality.

    17. caterpillar absence assumed caterpillar mortality

      The authors conclude that since there is an absence of caterpillar it is assumed that there have been a sort of mortality for this species.

    18. that crawling predators such as ants, beetles, true bugs, spiders, and even lizards play a significant predator role

      This is a result where the authors implied that the crawling insects are the major predators of the species studied.

    19. parasitoid

      An insect whose larvae live as parasites that eventually kill their hosts.

    20. pupal stage

      Life stage of some insects undergoing transformation between immature and mature stages.

    21. instar

      A phase between two periods of molting in the development of an insect larva or other invertebrate animal.

    22. Lepidoptera

      Order of insects that includes butterflies and moths.

    23. Early instar caterpillars suffered the most damage when interacting with P. gracilis (n = 15 trials, 86.7% mortality); late instar caterpillars successfully foiled P. gracilis advances (n = 15 trials, 0% mortality).

      The ant species C. floridanus death rate is at 56.3% during this experiment. They have forced some or all instar caterpillars to leave their habitat.

    24. Contingency table

      A table showing the distribution of one variable in rows and another in columns, used to study the association between the two variables.

    25. Exclusion experiments revealed that early instar caterpillars were vulnerable to both crawling and non-crawling predators.

      The instar caterpillars were vulnerable to be eaten, or killed by other predators.

    26. However, individual parameters (tree groups) were investigated to determine significance using non-host trees as the baseline group to compare the frequency of P. gracilis collected for each tree group.

      Each species was investigated to determine and compare each tree group.

    27. omnibus test

      Omnibus tests are statistical tests that are designed to detect any of a broad range of departures from a specific null hypothesis.

    28. Ants collected in pitfall traps in the canopies of Amyris elemifera and Zanthoxylum fagara: number of individuals of each species, and status

      The details of the ants captured by pitfall traps near the host plants of the Swallowtails. 5 of the 12 ant species captured were exotic and out of the total 243 individual ants caught, 144 were exotic

    29. Percentage of ant species captured in pitfall traps at Elliott and Adams Keys (tree canopy, trunk, and base). Overall, 1418 total ants comprising 25 ant species were captured and identified from pitfall traps

      The experiment was conducted at Biscayne National Park and was split into three parts. The first part was using pitfall traps to collect ants at Biscayne Park near the host plants. Secondly, the host plants with known caterpillars were protected with various combinations of cages and tanglefoots. Concluding the author was keeping track of how long it take for certain species of ants to first find the caterpillars. Authors assumed that the ants would interact with caterpillars more frequently than other predators.

    30. Ants collected in pitfall traps at Elliott and Adams Keys: number of individuals of each species, and status

      All of the ants found in pitfall traps that were placed all around the canopy in the keys. 11 out of 25 species were found to be exotic and 735 out of 1418 of the total amount of ants were exotic.

    31. Taxa

      A taxonomic category, as a species or genus.

    32. instar 

      A phase between two periods of molting in the development of an insect larva or other invertebrate animal.

    33. terrestrial

      Of, on, or relating to the earth.

    34. deleterious

      Causing harm or damage.

    35. subtropical dry forest

      Subtropical dry broadleaf forest biome, also known as tropical dry forest, monsoon forest, vine thicket, vine scrub and dry rain forest is located at tropical and subtropical latitude.

    36. captive-breeding

      The process of breeding animals in controlled environments within well-defined settings, such as wildlife reserves, zoos and other commercial and noncommercial conservation facilities.