918 Matching Annotations
  1. Apr 2018
    1. A large study, using identical BAC arrays run in the same lab as our study, found 5.6% (84 of 1500) of patients referred to Signature Genomics with de novo or pathogenic CNVs (chi-square = 3.052, df = 1, P < 0.05) (25). The HMCA rate of de novo CNVs was similar to previously reported rates in multiplex pedigrees with autism [1.28% in the HMCA versus 2.6%, or 2 of 77, in multiplex autism (6), chi-square = 0.557, df = 1, P = 0.22] and in controls [1.28% HMCA versus 1.0%, or 2 of 196, in control subjects (6), chi-square = 0.001, df = 1, P = 0.49], despite the fact that the 500K platform used here has significantly higher coverage

      Here, the authors compare their findings to other studies of de novo CNVs. They show that their results are similar to previous studies (such as Sebat et al.) that established the detection of de novo CNVs as a way to identify genes linked to autism.

    2. what would be predicted if the prevalence of autism were doubled in these families

      Hoodfar and Teebi studied the link between inbreeding and the prevalence of different genomic abnormalities.

      IThey found that the prevalence of autosomal recessive disorders was more than doubled in consanguineous families.

    3. The accumulating number of distinct, individually rare genetic causes in autism (5, 10, 11) suggests that the genetic architecture of autism resembles that of mental retardation and epilepsy, with many syndromes, each individually rare, as well as other cases potentially reflecting complex interactions between inherited changes (12).

      Studies have shown that there are many unique combinations of mutations that can cause autism, as is the case with intellectual disability and epilepsy.

      Unfortunately, given that there are so many ways for autism to occur, it is difficult to identify all of the mutations and changes that can lead to symptoms.

    4. chromosomal anomalies have been reported in 1 to 2% of cases of autism

      Data supports the fact that autism is linked with several genomic regions. Nnew regions are still being identified today.

    5. Autism includes mental retardation in up to 70%

      Autism is associated with intellectual disability (formerly called mental retardation*) about 70% of the time, and males are more often diagnosed.

      There is no evidence that social class has an impact on the incidence of the disease, but there is not enough data to know if race or ethnicity influence the incidence of autism.

      There is also no available data to support the idea that incidence of autism is changing over time.

      *For more on the movement to change the language of disability, see the Wall Street Journal.

    6. highly heritable, they exhibit wide clinical variability and heterogeneous genetic architecture, which have hindered gene identification

      Several research teams have worked independently to identify loci that could be responsible for autism. However, this has been difficult due to the high number of genes that could be involved and the high variability between affected individuals.

    1. We chose the sites based on the presence of many individuals of the study species

      This study site was a part of a previous experiment. In the previous experiment, the study site was chosen due to the abundance of individuals that were present. Essentially, the area with a higher abundance of individuals is beneficial to the experiment. It is beneficial to use previous work as a reference, especially if there is a common factor.

    2. In hawkmoth-pollinated plants, floral tube length determines which species may transfer pollen; hawkmoths with tongues that are too short or too long will not pick up pollen effectively

      Floral tube length in hawkmoth-pollinated plants will determine which insect will transfer pollen. if it is too short or too long they will not be effective.

    3. Several studies have reported that the body structure of floral visitors, especially the feeding apparatus associated with the dimensions and the morphology of the flowers, is one of the factors determining which visitors can effectively function as pollinators

      The structure of the insect determines the effectiveness of the pollination as well as the shape of the flower like the length of mouth part and floral tube.

    4. the majority of plant species are visited by a variety of pollinator groups, but visitation does not necessarily imply pollination; not all flower visitors are important and effective pollinators (Stebbins 1970; Waser et al. 1996; Fenster et al. 2004; Ne'eman et al. 2010).

      Most plants show visitation from other insects but not all pollinate.

    1. Sedio et al. 2013

      Sedio describes the phylogenetic niche conservatism (PNC) phenomenon that occurs in plants.

      In this phenomenon, a plant's microhabitat patterns are influenced by the biogeographical history of the plant's ancestors. He explains how related taxa are able to coexist since they were able to retain significant niche characteristics of their common ancestors.

    2. Kursar et al. (2009)

      The young leaves make large energy investments in chemical, developmental defenses, and floral nectar.

      There were many variations among species suggesting that herbivory is a strong selective agent.

    3. Cavender-Bares et al. 2004

      The research performed by Cavender-Bares and his colleagues highlights the importance of evolutionary processes combined with community interactions in community dynamics.

      The combination of phylogeny with their functional attributes help in better understanding communities.

    4. MacArthur and Levins 1967

      MacArthur and Levins explain that diversity of species living within the same environment can be explained as a result of limiting similarity.

    5. (Götzenberger et al. 2012)

      Götzenberger's research suggest that species distribution is largely influenced by intraspecific competition (competition within the same species)

      As the number of superior competitors increases, diversity decreases. This holds true only until other species are excluded.

    6. Hartmann 2007

      Hartman's research focused on secondary metabolism in plants. These were associated with genes that have a high ability to change and adapt to the pressures of their environment.

      Each plant population has unique secondary chemicals that have adapted to a plant's specific niche.

    7. Swenson 2013

      Swenson summarizes how to estimate the similarity between species by using both functional traits and phylogenetic trees.

      He uses the data from these approaches to test the mechanistic community hypothesis.

  2. Mar 2018
    1. Micosatellite SSR data have proven useful to reveal patterns

      Microsatellites, have been used by geneticists on plants in order to identify gene loci and how they can affect a certain trait or disease.

    2. however, it appears that they are related to unusual rain fluctuations (Romero Luna, 2011). Because the Dominican Republic population of C. jimenezii is located near the shoreline of this lake, there is concern that the soils where the species occur can be negatively affected by saline intrusion.

      The research here describes the changes in genetics that have been triggered by environmental factors so that the palms can deal with salt and increased water amounts.

    3. Nauman and Sanders (1991a) who suggested that it is composed of three major groups: the argentata group (with ten species, including the Critically Endangered C. crinita, C. cupularis, C. leonis, C. montana, C. victorinii, C. borhidiana), the argentea group (with six species, including the Critically Endangered C. spissa), and the pauciramosa group (with 31 species, including the Critically Endangered C. nipensis, C. pauciramosa and C. yuraguana). Nauman and Sander's (1991a) phylogenetic research was based on morphological traits.

      This taxonomic research was done in 1991 by Nauman and Sanders. Essentially it explained why there is genetic diversity amongst the Coccothrinax populations, and it is essentially because they come from three main groups each comprised of different traits.

    4. In an unpublished study focusing on the genetic structure of con-specific populations of Coccothrinax argentata from the Lower Florida Keys and the Florida mainland, Zona et al. (in preparation) found a much lower Fst value of 0.24.

      This study yielded a Fst value, which essentially describes the degree to which a population interbreeds and how freely they do so. The current Fst value are very low compared to what was found in the experiment done in this paper. This is cause for further testing.

    5. Extensive field work that included demographic studies and conservation assessments was conducted both in Haiti and the Dominican Republic. Distribution patterns and discussion of conservation concerns were reported by Peguero et al. (2015a).

      The research here was important because it identified the amount of Coccothrinax jimenezii that were present in the research sites. It also described patterns of palm distributions.

    6. As a Critically Endangered palm, C. jimenezii has been central to our conservation biology activities during the last 2 years as it is one of the most threatened species of this genus

      Given the great threat to the C. jimenezii, conservation efforts have been maximized.

    1. crypt regions of the organ

      See Dr. Bethany Radar and Dr. Ned Ruby use confocal images and immunocytochemistry to look at Vibrio fischeri in the crypts of the light organ:

      A look at Vibrio fischeri

    2. In bacterial light organs, the animal host must control not only light emission but also the symbiont populations. This management of the symbionts by the host is essential to maintain symbiont number and to sanction cheaters (i.e., dark mutants that might arise and compromise the function of the organ)

      Bacteria in the light organ continue to grow and multiply. If the numbers get too high, the bacteria could potentially switch from being beneficial to being harmful.

      Additionally, if bacteria develop mutations that cause them to stop producing luminescence, the mutants will use resources without providing benefit to the squid.

      Consequently, the squid must have a way to control the number of bacteria that colonize the light organ. They do this by ejecting 75% or more of the bacteria in the light organ each day.

    3. Components of visual transduction cascades, including opsin, arrestin, and rhodopsin kinase, co-localize in the retina, because they function in concert during phototransduction

      Work by Hargrave and McDowel (1992) and by Ridge et al. (2003) on phototransduction in the retina established that these three proteins are part of the G-protein-coupled pathway required in order for phototransduction to occur.

    4. Recent studies of the transcriptome of the light organ of E. scolopes revealed the expression of several genes that encode proteins with sequence similarity to components of visual transduction cascades

      Chun et al. (2006) generated 11 cDNA libraries from the light organ of the bobtail squid.

      Developmentally important time periods were chosen for analysis in order to provide a tool that would allow researchers to ask questions about how the bobtail squid responds to colonization by Vibrio fischeri.

    5. The morphology of the light organ, as well as behavioral studies, have suggested that the animal uses the light in counterillumination

      Jones and Nishiguchi (2004) were the first to test the hypothesis that Hawaiian bobtail squid use bioluminescence for counterillumination (a strategy for camouflage). They measured changes in bacterial luminescence that matched changes in down-welling light (light coming from above).

    6. previous studies of the anatomy and biochemistry of the light-organ lens and reflector demonstrated dramatic biochemical convergences with those of eyes

      Montgomery & McFall-Ngai (1992) and others discovered that proteins in the lens of the light organ of E. scolopes were similar to the proteins commonly found in the lenses of some mammal and cephalopod eyes.

    7. system for the analysis of tissues that interact with light and as a natural model of symbiosis

      The Euprymna scolopes-Vibrio fischeri symbiosis is a system with a single host and single symbiont, making it a great system to study how bacterial symbionts are acquired.


    8. the PSVs in certain bioluminescent squid species have been implicated in the perception and control of light emission, particularly in counterillumination

      The structures that control the amount of light emitted to produce counter-shading (PSVs) are different from the structures that produce the light.

      Counter-shading refers to the fact that parts of animals that are exposed to light are usually lighter in color than those parts that are not exposed to light.

    1. the required distances to track climate are much shorter than for latitudinal shifts (20)

      Loarie et al. found that spatial temperature gradients (degrees per distance) are larger for mountainous areas compared to flat areas. This means that, for the same change in temperature, a species that lives in a flat area must move much farther than one that lives in a mountainous area.

      Therefore, the authors conclude that it should be easier for a species to keep up with climate change by changing elevation than by changing latitude, if distance is the only factor.

    2. differ across the world, so a given level of warming leads to different expected range shifts of species in different regions (20), assuming that species track climate changes

      As the climate warms, plants and animals may need to shift their ranges to keep living in a suitable climate. Because temperature gradients vary in different types of ecosystems, we expect the size of range shifts to be variable, too.

      For example, two regions experience the same increase in temperature over a period of 20 years. The temperature gradients are 1.3° per 100 km in the first region and 0.9° per 100 km in the second. Species in the first region will have to move farther to maintain their climate than those in the second region.

    3. species have changed the timing of their life cycles during the year and that this is linked to annual and longer-term variations in temperature

      These studies show that increases in temperature are linked to changes in the life cycles of plants and animals. The dates of seasonal events, such as blooming, migrating, and egg laying, have changed for many species as their habitat has warmed.

      The studies have demonstrated a statistical relationship between temperature and the timing of life cycle events: Larger changes in event timing occur in areas with greater temperature changes.

    4. make it important to identify the rates at which species have already responded to recent warming

      References 1-8 link biodiversity declines to climate change by showing that extinctions occur or are predicted to occur in areas where the climate has warmed.

      This risk of biodiversity loss is a reason that the current meta-analysis is important: Quantifying how species ranges respond to climate change will help scientists and policymakers predict and hopefully prevent biodiversity loss in the future.

    5. Species are also affected to different extents by nonclimatic factors and by multispecies interactions, which themselves depend on a diversity of environmental drivers

      Climate is only one of many factors that determine the range of a species. These other factors may alter the way a species responds to climate change.

      In the following sentence, the authors give examples of this.

    6. Species may also show individualistic physiological responses to different aspects of the climate, such as different sensitivities to maximum and minimum temperatures at critical times of their life cycles. These sensitivities will combine with variable wait times for different novel climatic extremes to take place

      Climate change can produce changes in extreme temperatures in addition to, or instead of, changes in average temperatures. A species that is sensitive to extreme high or extreme low temperatures may respond to these extremes rather than to the average.

      Because extremes may change at a different rate from averages, these species may not appear to track climate change when it is measured by average temperatures (as in the current analysis).

    7. that cannot colonize across fragmented landscapes (17, 21–23), or if they possess other traits associated with low extinction or colonization rates

      Different species have different traits that may affect how quickly they can shift their range boundaries in response to changing temperatures. These traits include reproduction rates, ability to move, and ability to thrive in different habitats.

    8. Published studies have shown nonrandom latitudinal and elevational changes (1, 7, 13–17) but have not previously demonstrated a statistical linkage between range shifts and levels of warming

      Researchers have documented that many species' ranges have shifted to higher latitudes and/or higher elevations during the same time period that the climate has warmed. However, they have not shown that the range shifts are statistically linked to the temperature change.

      If species range shifts are directly linked to climate warming, we should find a positive trend between the two: the larger the temperature increase, the larger the range shift.

    9. A previous meta-analysis (14) of distribution changes

      A meta-analysis, published in 2003, found range shifts in a large number of species, in directions consistent with climate change.

    10. Many species have also shifted their geographic distributions toward higher latitudes and elevations

      Large studies have shown that land-based populations of many living organisms have shifted to higher latitudes and/or elevations as the climate has warmed during the 20th century. These studies include plants and animals in many different locations around the world.

    1. PCR-amplified

      Polymerase chain reaction, or PCR, is a technique in the laboratory in which short sequences of DNA are amplified.

      PCR has been used to detect DNA fragmentation on processed foods, where 18S rRNAs where the target for the experiment. Since they are small fragments, they work perfectly with the process since the goal is to amplify them to take a better look at them. The results of this experiment determined that the degree of DNA fragmentation are a great index for the chemical evaluation of various different foods.

    1. These scanning and tail-probing behaviors have been described previously

      The scanning and tail probing behavior of fish is the process in which they use certain tail movement around an object in order to discover the depth and size of objects in their environment. Think about what happens when you put a goldfish into bowl after it has been in an plastic bag. It will immediately start swimming around and swishing its tail around. That is a process of scanning and tail probing behavior.

    2. Distinguishing sensory exafference from reafference is critical to the success of active electrolocation

      What is critical to the success of active electrolocation is the knowledge of whether the electricity that is felt between the animal and the object is coming from the animal itself (reafference) or by the objects themselves sending the signal to these animals (exafference).

    3. the EOD becomes very complicated and rapidly changing, reflecting a complicated and heterogeneous electric organ

      The complexity, speed, and variability of the electric organ discharge can be linked to the innervation patterns of the electric organ itself, which consists of thin nerve trunks and numerous branches of the electromotor axons leading towards the electric tissue.

    4. Synchronized activation along the length of the electric organ implies effective mechanisms for compensation of neuronal propagation delays along the length of the EO (Bennett, 1971).

      Bennett's article analyzes the anatomy and physiology of the electric organs found within these electric fish. The membrane physiology of these electric organs evolved independently into six different groups and resulted in different membrane functions in different electrolytes which affect the electrorecption in the electric organism.

    5. electric organ discharges (EODs)

      In some species of electric fish, there are sex-based differences between the EODs of males and those of females, all of which are regulated by steroid hormones. The primary hormones responsible for these variations in EOD are androgen (produces male-type EOD rates) and estrogen (produces female-type EOD rates). A notable example of a sex-based EOD difference is the male fish's ability to attract female fish with EODs that emit energy within the appropriate sensitivity ranges.

    1. Seventy human-like tracks arranged in two parallel trails (39 prints in G1 and 31 in G2/G3) are reported at Laetoli Site G (Leakey, 1981). Unfortunately, the whole set of morphometric data for the unearthed tracks was never published; only average values obtained from a selected number of tracks were provided. In the case of G2/G3, data are incomplete, largely because the prints of G3 are superimposed onto those of G2, so that it is difficult to collect the measurements (Tuttle, 1987).

      Only some data were published for site G. As a result, the data are less complete and less reliable. There are some differences in the measurements published by individuals viewing the original G tracks and those made by others using the fiberglass casts.

    1. The slope of this relationship (β in days °C−1) has been termed the temperature sensitivity by other authors

      Large species sampling size necessary (or interspecific variation in species may be too high)

      Warming experiments underpredict the advance of spring events

      Experimental results alone cannot be used for parameterizing species distribution and ecosystem models

      Best (currently) measure: observational data

    1. with many reports of butterflies and hawkmoths pollinating species of this family (Haber 1984; Darrault and Schlindwein 2005; Sugiura and Yamazaki 2005; Moré et al. 2007).

      Haber found that hawkmoths are frequent pollinators of these families, but require a significant nectar reward to do so.

      Darrault and Schlindwein found these butterflies and moths do pollinate. Furthermore, in contrast to this study, they found that diameter of the mouth parts showed no correlation with pollen collected.

    2. Many studies of other plant–pollinator systems provide evidence that the morphological match between the pollination apparatus and the length of the proboscis is associated with pollination effectiveness (Inouye 1980; Waser et al. 1996; Castellanos et al. 2004; Moré et al. 2012; Miller et al. 2014).

      Inouye found that proboscis length was correlated with a bee's time spent at a flower. Waser found that many pollination systems tend towards specialization.

      This implies that flowers adapt their shape and length to accomodate one group of pollinators. Length is a great determinant in these cases.

    3. In many self-incompatible Apocynaceae, flower revisitation increases the probability that self-pollen is deposited onto the stigma, leading to ovule and fruit abortion (Lipow and Wyatt 1999, 2000; Wyatt et al. 2000; Wyatt and Lipow 2007).

      Lipow and Wyatt found in multiple studies that self pollination in this family of plants prevents fruit bearing. This can be problematic, as it can decrease seed output. As such, it could create pressure for plants to evolve to punish revisitors.

    1. Though weaker, this effect also emerges in models of finite populations in continuously favorable landscapes (fig. S4) (26)

      Instead of looking at how different environmental conditions, such as gaps, changed the migration of plants, research looked at how the variability in population growth of invading species affected their velocity of spread. Variability in population growth was seen to decrease the velocity of biological invasions. However, the decrease in velocity was small enough that it is largely negligible.

    2. events contributing to the ecological and evolutionary trajectories of spreading populations (5, 19–21)

      Due to the unpredictable nature of environmental events, studies of environmental changes, whether population, genetic or abiotic based, are forced to account for the randomness by repeating these experiments many times in order to ensure that the results are not due to chance, but have actual consistency.

    3. Due to these constraints, nearly all empirical evidence for evolution affecting spread comes from a few retrospective, observational analyses

      Retrospective observational studies involve observing the result of a particular phenomenon, in this case an invasion, and collecting data to determine how it happened. While these studies can be effective at describing what evolution in invasions looks like, they are limited in the ability to determine cause and effect.

    4. It has long been appreciated that habitat fragmentation slows the velocity of spread (3, 4), but its influence on the potential for evolution to increase population expansion is unknown (5). Theory shows that natural selection at the low-density front of populations expanding through continuously favorable landscapes, coupled with the spatial sorting of offspring

      Populations that have been divided or separated from each other spread out slower than other populations but it is unknown how evolution contributes to their dispersal. The theory of natural selection dictates that offspring with traits that assist in dispersal and fecundity, or the number of offspring an organism produces, will be favored when populations are not very numerous and are in an environment well suited for their species' growth. Therefore, individuals best suited for the expansion of the population would be favored from an evolutionary perspective.

    5. biological invasions and the movement of species ranges with climate change present two of the greatest disruptions to natural and managed ecosystems

      Natural and managed ecosystems are vital to the equilibrium of life on earth, as well as to humans needs which are gathered from ecosystems. The focus of the research question is to determine if biological invasions and movement of species are significant threats to ecosystem health.

    1. Rat 50-kHz vocalizations indicate positive emotional valence

      Scientists characterized rat USVs and demonstrated that some (22 kHz) are associated with negative reactions and others (50 kHZ) are associated with positive reactions to their environment.

      "Valence" is a psychological way of categorizing an emotional state as good (positive) or bad (negative).

    1. Using archived specimens and field surveys of bumble bees and host plants, we explored four potential mechanisms for this change in tongue length

      Subalpine bee species have begun to move into alpine climate and compete with the native alpine bees, due to the warming of the alpine climate.

    2. evolution is helping wild bees keep pace with climate change.

      Alpine bumble bee populations are generally isolated from the toxins, diseases, and habitat destruction that affect bumble bee populations in other climates. Yet, they are still negatively affected by climate change. However, the bumble bee populations are adapting to the changes to their habitat by evolving new behaviors that increase their chance of survival.

  3. Feb 2018
    1. In response to warmer temperatures and drying soils, flowering has declined in alpine and arctic habitats worldwide (21–24)

      Researchers have found that climate change has increased the temperatures of alpine and arctic habitats. This has caused the soil in this area to dry up thereby decreasing the amount of plants that flower in a given area, negatively affecting the bees ability to forage.

    2. Selection to track the floral traits of host plants should favor short-tongued pollinators when flowers become shallower or deep flowers less common (9, 10).

      Rodríguez-Gironés and colleagues saw that competition for resources within a population triggered long tongues in pollinators and deep corolla tubes in flowers.

    3. Spatial and temporal discrepancies with food plants, habitat destruction, and pressure from invasive competitors have been implicated (3–6), but the details of these declines and their causes remain unresolved

      Researchers have identified potential reasons that could be causing the decrease in long-tongued bees including changes in the location and availability of flowers, habitat destruction, and the presence of invasive species.

    4. Long-tongued bumble bees have coevolved to pollinate plants that possess elongated corolla tubes in a mutualistic relationship. Recent declines in such long-tongued bee populations suggest that historical selection regimes in these systems are changing (1–3)

      Historically, bees with longer tongues have had access to plants with longer corolla tube lengths, increasing selection for these bees that have a wider range of accessible nutrients. Researchers believe, due to a decrease in the population of long-tongued bees, that the long-standing selective pressures that caused long-tongued bees to thrive are changing. The reasons for this change remain unknown.

    1. Central mechanisms of tickling were investigated by functional magnetic resonance imaging (fMRI) in human brains (9); that study, which used tickling stimuli evoking knismesis and observed somatosensory cortex activation, suggested that self-tickle suppression might be mediated by the cerebellum.

      fMRI was used to detect brain activity in healthy volunteers who were being tickled. The somatosensory cortex was one region that was activated by tickling.

      When patients were asked to tickle themselves, there was also activity in the cerebellum, a region of the brain associated with coordinating movement. The researches suggest that the cerebellum may have a role in detecting self-tickling and suppressing the tickle response.

    2. Anxiogenic conditions suppress tickling-evoked USVs in rats (7)

      This idea may have been originally proposed by Charles Darwin. He wrote that if a child is tickled by a stranger, the child would scream from fear rather than laugh.

    1. Within-species variability in body size often relates to sexual dimorphism and/or to adaptation to different ecologies

      Traditionally, paleobiologists hypothesized that early hominids exhibited a high degree of sexual dimorphism. This thinking is based on limited fossil evidence and consequently is being questioned by a number of researchers.

    1. Species ranges were estimated using occurrence records extracted from the Global Biodiversity Information Facility

      The Global Biodiversity Information Facility provides an open online database of biodiversity data. This service was vital for the outcomes of this paper as it was a source for determining species ranges. The occurrence records used show the location of a given species and the date they were located.

    2. he highest estimate of the social cost of carbon was “included to represent higher-than-expected economic impacts from climate change”

      A previous experiment determined how biodiversity, nitrogen deposition, and CO2 affected grassland soil carbon cycling. The results were vital for this research in that they provided guidelines for the what data should be provided. Specifically, this refers to providing higher and lower amounts of economic change than would be expected in order to provide a range of possible values.

    3. BioCON

      BioCON stands for Biodiversity, CO2, and Nitrogen. It refers to an experiment which began in 1997 at the University of Minnesota. The factors of this experiment can be related to the economic value of ecosystems, it is vital in the outcomes of the research done in this paper. Without the values from the BioCON experiment many of the results in this paper would not exist.

    4. [the product of measured maximum root C content and 0.55 year−1, which is an average value for root turnover in grasslands (48)]

      In a previous work produced by R. A. Gill and coworkers, the carbon contained in a plants' root system was calculated (.55 per year). This is also the average value for roots to seep carbon into the soil in grasslands.

    5. BigBio

      The BigBio experiment was conducted to examine large scale biodiversity in a grassland setting. The experiment determines effects of plant species numbers and functional traits on the functioning of an ecosystem. Without previous data obtained from this experiment, many values found in this research wouldn't have been able to exist. Therefor the BioCon experiment was vital to the outcomes of this paper.

    6. Despite widespread claims about the economic value of biodiversity for ecosystem services (18–20), quantitative assessments of the relationship between biodiversity and specific services are rare

      Multiple research studies, conducted by leading scientists P. Balvanera, S. Catovsky, and I. D. Thompson, suggest that the economical worth of plant diversity is high for all ecosystem services. The author points out that the research conducted on the correlation between species richness and specific ecosystem services is very rare.

    7. Integrating our approach with robust estimates of diversity effects on multiple ecosystem processes (43) and of their value remains an important task for future studies.

      A research study, drafted by J. E. K. Byrnes and others, states the importance of studying the effect of increased plant diversity on a wide variety of ecosystem processes. This research paper only shares the results of increased species richness on one ecosystem service: carbon storage. There are many more ecosystem services that are only possible because of the wide diversity of plant life on earth. If research studies were conducted on the effect of increased plant diversity on a variety of ecosystem services, then we would gain irreparable knowledge on how the complex systems work and the benefits to society.

    8. no single species appears to be “best” at providing a wide variety of benefits to society (42).

      A research paper, written by J. S. Lefcheck and coworkers, proposes that no single species is the best at providing all the valuable ecosystem services needed for the world to function. No single species can occupy all the vital niches around the world. This is why diversity between the function plant species have and services they preform is so important.

    9. Although there is evidence for trade-offs among species in the functions they perform and services they provide (41),

      A previous research experiment, conducted by E. S. Zavaleta and coworkers, concludes that there is evidence of differences between the function plant species preform and the services they provide. The differences between plant species allows for a wide variety of niches or jobs, in an environment, to be filled. Without different plants occupying the many needed jobs in an environment, the earth's delicate nutrient cycles would not be able to occur and life on earth, for primary and secondary consumers, might not be possible.

    10. For example, in the experiments assessed here—among the longest-running biodiversity experiments in grasslands—the effects of species richness are growing stronger through time and have yet to reach a steady state (40).

      A previous research study, written by P. B. Reich and others, voices that the initial introduction of increased species richness drastically increases carbon storage, but as time goes on, the effectiveness of plant diversity on carbon uptake starts to level off. The author relates these findings to their own experiment stating that even though the research conducted on the American grasslands is the longest-running biodiversity experiments in grasslands, not enough time has passed to see carbon storage levels reach a steady state.

    11. 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.

    12. 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.

    13. 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.

    14. 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.

    15. 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.

    16. 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.

    17. 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.

    18. 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.

    19. 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.

    20. 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.

    21. 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.

    22. 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.

    23. 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.

    24. 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.

    25. 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.

    26. 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.

    27. 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.

    28. 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.

    29. 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.

    30. (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.

    31. “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.

    32. 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.

    1. 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.

    1. 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.

    2. 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.

    3. 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.

    4. 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.

    5. 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.

    1. 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.

    2. 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.

    3. 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.

    4. 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.

    5. 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.

    6. 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.

    7. 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.

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

      Genus Wolbachia is quite diverse.

    9. 52% of all insect species

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

    10. 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).

    11. 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.

    1. 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.

    2. 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.

    3. 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.

    4. When processes are stationary over lineages and time, relatively straightforward models can be designed to yield accurate inferences, even from short sequences (Steel and Penny, 2000)

      In this study, scientists were able to conclude that under certain circumstances (when processes are stationary over lineages and time) short genetic sequences can be used to construct a large phylogenetic tree with very high accuracy, therefore reducing the cost and time spent in creating a tree.

    5. Deviations from this stationary condition at any codon position can result in systematic error (Saccone et al., 1989).

      Scientist were able to conclude how stationary genes evolve through the same velocity at the third codon position. In comparison, non-stationary genes were seen to be involved in severely higher conditions. Such differences could therefore lead to drastic results, including systematic error.

    6. They concluded that a minimum of 20 randomly concatenated genes was required to infer relationships confidently and that “It is only through the analyses of larger amounts of sequence data that confidence in the proposed phylogenetic reconstruction can be obtained” and further “that analyses based on a single or a small number of genes provide insufficient evidence for establishing or refuting phylogenetic relationships.”

      Rokas et. al came to the conclusion that one needs a minimum of 20 genes in order to compose an accurate phylogenetic tree, and that those phylogenies created from examination of a few genes are unreliable due to the low amount of sequencing data used.

    1. following the U.S. Open Source Indicator (OSI) project (14–16)

      The goal of (14,15) was to help build a "Gold Standard Report" (GSR) reliable database of civil unrest events across countries in Latin America.

  4. Jan 2018
    1. Combining their electrophysiological and behavioral data, Ditzen et al.15 concluded that DEET acts in the vapor phase to inhibit the detection of attractive odors.

      Utilizing DEET perfumed traps, the behavior of flies was observed. Flies with the Orco gene responded differently to food-baited traps than flies with the gene knocked out. Low concentrations of DEET cannot repel flies in the absence of food. Electrophysiological studies showed that DEET can influence signaling molecules (or ligands) and their respective olfactory receptors.

    2. Evidence for gustatory receptors specifically detecting DEET was obtained from studies in Drosophila.

      Three taste receptor neurons were characterized in female Aedes aegypti mosquitoes. The neuron with the smallest amplitude spike responded to the feeding deterrent, quinine, and other insect repellents. Two other neurons with differing spikes responded to salt and sucrose. This was the first report of a taste receptor neuron specific for insect repellents in mosquitoes.

    3. Similarly, other studies have shown that the mosquitoes do not feed on blood that contains a very small amount of DEET (0.065%), even though some of them penetrated their proboscis into a membrane feeder.

      Female Aedes aegypti mosquitoes fed through a membrane on citrated blood containing DEET. When 0.5% concentration of DEET was present in the blood, the mosquitoes barely touched the membrane and did not insert the proboscis into the blood. When the concentration was lowered to 0.065%, mosquitoes touched the membrane for a longer time period, and/or inserted the proboscis. It was concluded that vapor action was the main cause of repellency, but contact chemoreceptors on the lobes of the proboscis may have been involved during the 0.065% concentration experiment.

    4. Kain et al.54 showed that DEET activates Ir40a-expressing neurons in the Drosophila sacculus, a 3-chambered pit beneath the antenna's surface.

      This article has been retracted as of 2016 by the request of all authors except Pinky Kain. The authors identified background effects that were originally missed and, as a result, do not have confidence in the data supporting that Ir40a is a DEET receptor. The authors remain confident of the analyses used to identify new repellents which have been replicated in the laboratory.

    5. Recent electrophysiology studies with a Culex OR, CquiOR136, showed that it could be activated by DEET, as well as other insect repellents, such as PMD, Picaridin, and IR3535.

      The CquiIR40a receptor in the Culex quinquefasciatus mosquito was cloned and then expressed in the Xenopus ovary cell along with another co-receptor. The Culex quinquefasciatus mosquito uses an odorant receptor, CquiOR136, to detect insect repellents, such as DEET, picaridin, IR3535, and PMD. The dose-dependent responses elicited by these repellents were analyzed.

    6. The smell and avoid hypothesis proposes that DEET is perceived as a noxious odor by the insect.

      When applied to human skin, DEET altered the chemical product by a fixative effect, which may have contributed to repellency. The electrophysiological responses of olfactory receptor neurons (ORNs) were observed in Culex quinquefasciatus mosquitoes. The same ORN responded with higher sensitivity to terpenoid compounds, which are found in essential oils. The studies support the smell and avoid hypothesis.

    7. In early electrophysiological studies of Aedes aegypti mosquitoes, DEET increased the firing rate of olfactory receptor neurons in trichoid short and long A2 sensilla, but inhibited the spontaneous activity of medium-length sensilla.

      As the stimulus intensity increases, the firing rate of neurons increases. The firing rate is the rate of action potentials that carry an electrical impulse down a nerve. DEET increased the firing rate of olfactory receptor neurons in A2 sensilla, but inhibited the firing rate in A3 and A4 sensilla. It was concluded that DEET plays multiple roles in olfaction control because it affected OR-expressing and IR-expressing neurons in differing ways. This supports the confusant hypothesis.

    8. Aedes orco mutants did not respond to host odor alone, but were still able to host-seek in the presence of carbon dioxide, demonstrating that redundant mechanisms exist for mosquitoes to sense hosts

      Mosquitoes use redundant mechanisms to sense their hosts. This mechanism requires that mosquitoes receive multiple cues for a host to seem attractive. The disruption of one pathway is unlikely to eliminate mosquito host-seeking, however. Stimulating multiple sensory pathways may increase the chance of a mosquito successfully targeting a host.

    9. Aedes aegypti allowed for the genetic analysis of the OR pathway in a mosquito

      Zinc-finger nucleases (ZFNs) were used to generate mutations in the Orco gene of Aedes aegypti. ZFNs are a class of engineered DNA-binding proteins that facilitate targeted editing of the genome by creating double-strand breaks in DNA. These breaks stimulate the cell’s DNA repair processes, which in turn generates precisely targeted genomic edits.

    10. Behavioral assays in a repellometer confirmed that DEET inhibited the attraction of Aedes aegypti to lactic acid, but both compounds were also attractive to the mosquito.

      DEET was concluded to be a compound that reduced the attraction of mosquitoes to lactic acid (a behavioral inhibitor) rather than a compound that caused mosquitoes to display complete avoidance. It is important to note that both DEET and lactic acid were attractive to mosquitoes in the studies.

    11. Electrophysiological studies showed that DEET reduces the sensitivity of olfactory receptor neurons to odors by decreasing the responses of lactic acid-excited neurons and increasing the inhibition of lactic acid-inhibited neurons.

      Studies that observed heart rhythms were used to observe the sensitivity of olfactory sensory neurons (ORs). DEET reduces the sensitivity of ORs by enhancing the expression of lactic acid-inhibited neurons and decreasing the expression of lactic acid-excited neurons. This supports the inhibition hypothesis of host odor detection.

    12. In 1942, the United States Department of Agriculture (USDA), in collaboration with the US military

      The Aedes aegypti mosquitoes aided in the discovery of DEET, which is the most common active ingredient in insect repellents. The behavior of the mosquitoes was observed in response to several compounds, but N,N - diethylbenzamide was found to be the most effective. Because this compound is irritating to the skin, the DEET found in repellents today is comprised of derivatives of N,N - diethylbenzamide.

    1. based on reconstructions from pollen data (4)

      Prior work from author Guiot developed a reconstruction of the Mediterranean region's climate over the past 10,000 years. The reconstruction used the BIOME4 model, with pollen core data as the input. The reconstruction found that the past climate variations were dominated by changes in precipitation (droughts and wet periods). However, unlike in the present, the drought periods were linked to cool temperatures. They also found that the pattern of warming was different in the past than it is currently.

      Using this information, they concluded that the reconstruction indicates that recent warming in the region is unlike what was seen during any other time in the Holocene.

    2. To relate the past variability of climate and ecosystems with possible future conditions, we use the process-based ecosystem model BIOME4 (6), which, when compared with correlation techniques, allows a more reliable reconstruction of past climate-vegetation equilibria

      BIOME4 was developed by Kaplan and colleagues. The model uses input data about water, climate, and soil to simulate the ecosystem and plant processes that drive the distribution of vegetation types. Using this information, the model identifies key variables and uses these to rank the likelihood of different groupings of plants for the given time and location. The rankings then help identify the biome type present.

      This model predicts plant distribution based on underlying processes that are expected to be consistent for the entire Holocene time period–for example, net assimilation of CO<sub>2</sub> (the flux of CO<sub>2</sub> between a leaf and the atmosphere) or the water balance in an ecosystem. The authors contrast that method to other models that are tuned based on how well the results correlate with, or reproduce, current vegetation patterns.

    3. A recent study (14) has attributed important crop failures in Syria to two strong drought episodes—characterized by a lack of precipitation (reduced by up to 30% in the 6-month winter season) and high temperatures (warming of 0.5° to 1.0°C in the annual mean relative to the 20th-century average)—in the eastern Mediterranean between 1998 and 2010.

      Kelly and colleagues examined the 3-year drought in Syria that began in Winter 2006/2007 to understand what contributed to the severity of the drought, which was the worst in human record.

      The researchers found that though multiyear droughts do occur naturally in the region, the reduced precipitation and increased surface temperature of the past century that is consistent with models of human-driven climate impacts contributed to the extreme nature of the drought.

      The impacts of the drought were also amplified by previous droughts, the reduction of groundwater supply (which had previously acted as a buffer), and population increases in recent years.

    4. During the Holocene (especially in the second half of this epoch), periods of precipitation deficits have occurred, but in contrast to the 21st-century situation, temperatures did not rise above the present average (Fig. 1) (4)

      The current period is experiencing both reduced precipitation and high temperatures, unlike during the earlier Holocene, when times of low precipitation were generally cooler.

    5. Even if past variations in precipitation and their projections for the future are spatially more heterogeneous than temperature fields (7), for most scenarios, the changes in both fields will combine to reduce water availability and trigger losses of Mediterranean ecosystems and their biodiversity during the coming decades (8–10).

      Precipitation and temperatures vary across the Mediterranean region, and the precipitation patterns are more variable than the temperature patterns. In general, the changes of these two climate variables in the next few decades are expected to lead to a reduction in the amount of water available as well as the loss of some ecosystems and biodiversity.

    6. the Holocene reconstruction of spatiotemporal ecosystem dynamics from pollen allows the development of reliable scenarios of climate-driven change in land ecosystems (4)

      Guilot, one of the authors of the current paper, and his collaborator used pollen core data and vegetation modeling to develop reconstructions of the Mediterranean Basin climate over the past 10,000 years. To do this, they ran BIOME4, a vegetation model, in "inverse" mode.

      BIOME4 is typically used to predict vegetation by inputting climate information. In an "inverse" mode, researchers input the vegetation information from the pollen cores and then used a computer algorithm to calculate what climate would have produced the mix of plants that was observed.

      This reconstruction method is the basis of the current paper.

    7. For many regions of the world, achieving the global 2°C target would still imply substantially higher average temperatures, with daily maxima reaching extreme values (1)

      The targets are for global temperatures, based on averages across the entire surface of the planet. Because of climate variations, this does not mean that each location would experience the same degree of local climate impacts.

      For example, researchers examined the impact of the global 2°C increase scenario on regional changes to temperature extremes and their analysis found regions that would have a bigger response. For the Mediterranean region, they predicted a 3°C increase in hot temperature extremes.

    1. Both models assume that the development of an anatomical placode and of a dermal papilla occurred, at a minimum, twice (once in birds and once in mammals) through the independent parallel co-option of the same set of signaling pathways (WNTs, β-catenin, EDAR, BMPs, and SHH).

      Previous models have tried to explain the apparent lack of homology by suggesting that anatomical placodes and dermal papillae developed at least twice (once in birds and once in mammals).

      Further, the models suggest that, although the anatomical placodes and dermal papillae in mammals and birds would have evolved independently, they would have came about through the co-option of the same set of signaling pathways.

    2. material cracking

      Crocodilian scales are formed through exertion of force: Scale tissues are physically cracked by living materials, leading to unique patterns on each reptile's face.

    3. Conversely, other authors argue that the similarities in molecular signaling observed among all skin appendages suffice to support their homology (9). Note that such placodal signaling centers have been recently evidenced as underlying the development of Chelonia shell scutes

      Some other models reject the idea that the placode and the dermal papilla evolved independently, suggesting that the similarities in the molecular signaling involved in development are sufficient to show that they are homologous (meaning the pathway evolved once, in a common ancestor).

      It is also suggested that this is true for turtles, which have been found to need the placode for the development of their shell.

    4. indicate that early scale morphogenesis in reptiles consists of regular dermoepidermal elevations that typically further develop into oriented asymmetrical scales with various levels of overlap, depending on the species and body area

      As was found in previous studies, scale development begins with the formation of risen areas on the skin. The symmetry and degree of overlap of the final scales depends on the species and location on the body.

    1. This estimate is broadly consistent with an estimated 1.3 billion MT of waste generated by 3 billion people in urban centers globally

      Other authors have estimated similar amounts of waste generated by humans.

  5. Dec 2017
    1. feathers are organized into discrete tracts associated to different body areas

      In chickens, feathers develop in 10 distinct areas (tracts) which correspond to different parts of the body. These tracts develop at different rates and have their own patterning.

    2. that is, they are difficult to identify on any specific embryo because they establish multiple tracts whose developmental timing and locations vary across the body

      The authors believe that previous studies have overlooked anatomical placodes in reptiles because they are difficult to see during development.

    3. similarities in signaling are due to independent co-option of these molecular pathways

      Although some scientists think that the similarities in development of hair, feathers, and scales are evidence that they are homologous, others believe that they evolved independently.

      They propose that these pathways served a different function in the common ancestor of mammals, reptiles, and birds, and that they were only later co-opted for the development of hair, feathers, and scales.

    4. Several studies (9, 18–23) have shown that conserved signaling pathways, evidenced by the expression of the Sonic hedgehog (Shh), β-catenin (Ctnnb1), ectodysplasin A receptor (Edar), and/or bone morphogenetic protein (Bmp) genes, are involved in skin patterning and early morphogenesis of all amniote skin appendages

      Several signaling pathways involved in skin development and patterning are conserved across species. Different authors have reached different conclusions about whether these pathways are homologous or whether they evolved independently.

    5. discrete developmental units through reaction-diffusion

      Morphogens (chemicals which direct the development of different structures) interact to form gradients or concentrate in different parts of an organism. This leads to patterns in the placement and arrangement of appendages.

    1. diminished Hb levels found in Tibetans offset complications associated with sustained high Hb levels

      People who are used to low-altitude environment experience several health complications, sometimes even fatal ones. Low levels of oxygen at high-altitude environment also decrease reproductive rates. One common disease seen in people that live in high-altitude environment is Monge's disease. Monge's disease is characterized by overproduction of red blood cells. Interestingly, Tibetan highland population is resistant to Monge's disease because of the decreased level of hemoglobin concentration.

    2. The putatively advantageous haplotypes of EGLN1 and PPARA both show significant negative correlations with Hb concentration

      EGLN1 and PPARA are correlated with hemoglobin concentration. EGLN1 encodes PHD2, prolyl hydroxylase domain-containing protein 2, which is a negative regulator of HIF-1α. PPARA encodes for PPARα, peroxisome proliferator activated receptor alpha. PPARα is regulated by HIF protein, and is essential for fatty acid metabolism. Since PPARA induces fat metabolism, it is unfavorable in hypoxic conditions because fatty acid metabolism needs more oxygen for energy production compared to glycolysis. PPARA is therefore negatively correlated with the concentration of HIF-1α. The positive selection seen in EGLN1 and PPARA, which are negatively correlated with the concentration of hemoglobin, indicates that Tibetans have a unique adaptation.

    3. adaptation in Tibetans has resulted from local positive selection on several distinct genes

      The Tibetan plateau is distinct for its extremely high elevation. Compared to other high-altitude populations, Tibetans are better adapted to the high elevations. Advantageous mutations and positive selection have resulted in genes that can adapt to high-altitude environments in Tibetan highlands. Tibetans have unique characteristics such as elevated resting ventilation and low hemoglobin count. In addition, since the Tibetan population has bee living in the area for approximately 1,110 generations, beneficial mutations have had enough time to become fixed. Tibetan population has also shown a positive selection in genes such as EGLN1, PHD2 and PPARA, all which are negative regulators of HIF-1α.

    4. EGLN1 targets two HIFα proteins for degradation under normoxic conditions

      Under normal oxygen levels, HIF proteins are degraded due to hydroxylation by a family of hydroxylases known as EGL- nine homologs (EGLN). As HIF is hydroxlyated, HIF is targeted by VHL proteins for degradation. Hydroxylation is the addition of a hydroxyl group. With HIF being degraded, transcription of genes needed for angiogenesis does not occur.

    5. Although PPARA has not previously been considered as a candidate gene for high-altitude adaptation, it interacts with components of the HIF pathway

      Hypoxia-inducible factor 1-mediated inhibition of peroxisome proliferator-activated receptor alpha expression during hypoxia (2002).

      It was found that PPARA is (under hypoxic condition) inhibited by HIF1-alpha. In Tibetan highlanders the PPARA gene is adapted so that it can function in the presence of HIF, though this mechanism is unknown.

    6. elevated circulating NO levels increase vasodilation and blood flow

      Researchers have found that Tibetans have increased nitric oxide (NO) levels, which leads to an increase in vasodilation and blood flow. With higher NO levels causing an increase in blood flow, Tibetans have adapted to higher altitude levels.

    7. increased Hb concentration to compensate for the hypoxic high-altitude environmen

      When people have lived 2,500 meters above sea level, they experience hypoxia or lack of oxygen. In extreme cases of hypoxia people can experience altitude sickness. However, people who have lived at high altitudes for thousands of years have adapted to such extreme conditions. These people have an increased in hemoglobin concentration which compensates for hypoxia. With an increase in hemoglobin, oxygen is able to be transported through the body more efficiently.

    1. revealed three consensus binding sites in the 3′UTR for the highly conserved Musashi family of RNA-binding proteins, Musashi-1 (MSI1) and Musashi-2 (MSI2), both important translational regulators in stem cells

      Imai and colleagues (2001) used in vivo RNA that possesses Msi1 binding sites to determine the specific RNA-binding sequences for Msi1. Results demonstrated that Msi1 can regulate expression of its target gene at the translational level.

    2. Notably, defective chromosome condensation has been recently found to cause MCPH

      C. A. Martin and colleagues (2016) researched mutations in genes encoding condensin subunits (which usually enable chromosomes to condense) and sister chromatids to de-tangle and stabilize chromosome structure. The team of researchers found that mutations caused microcephaly in mice as well as reduced brain size and DNA bridges in neural progenitors and condensin-deficient cells during neurogenesis.

    3. The PCC phenotype seen in MSI1A184V-patient cells has been previously described in cells deficient of the MCPH-associated protein microcephalin (MCPH1)

      Jackson and peers (2002) relate the microcephalin gene to molecular defects that can cause microcephaly. Microcephalin was found in developing ventricles of the forebrain, indicating that the microcephalin protein can regulate sizes of the cerebral cortex. Mutations in the microcephalin gene can result in disruption of the regulation of the cell cycle and development of neurons in the brain.

    4. We hypothesized that the single-stranded RNA flavivirus ZIKV may hijack RNA-binding factors present in the developing central nervous system (11). Host RNA-binding proteins are known to interact with untranslated regions (UTRs) to regulate replication, translation, and stabilization of viral genomes

      Li and Nagy (2011) studied plus-stranded RNA viruses.

      RNA-binding proteins are found to determine virus-cell interactions with host untranslated regions to regulate cellular processes. Understanding the functions of host RNA-binding proteins in viral replications can lead to antiviral therapies, such as for Zika virus.

    5. Zika virus (ZIKV) recently emerged as a major public health risk because of its devastating effect on fetal neurodevelopment

      Mlakar and peers (2016) associated Zika virus with microcephaly.

      An increase in microcephaly cases was found to be observed in children who were born to mothers that were infected with Zika virus.One expectant mother, who contracted Zika virus, was studied. After 29 weeks of gestation, the fetus was recognized to express microcephaly with brain calcifications. The mother decided to terminate the pregnancy, an a fetal autopsy revealed the complete genome of Zika virus in the fetal brain. 
    6. Intriguingly, MSI1 is also highly expressed in the retina and testis, other tissues deemed vulnerable to ZIKV infection

      Lazear, Govero, Smith, Platt, Fernandez, Miner, Diamond (2016) studied the disease development of zika virus in different types of knockout mice. The knockout mice that had no functioning interferon pathways were the mice that picked up the disease. It was also observed that zik virus was found in the highest viral load in the testes of affected male mice.

    7. Brazilian ZIKV belongs to the Asian lineage which affected New Caledonia and French Polynesia, where cases of microcephaly were reported retrospectively

      Cauchemez and colleagues (2016) found that infection of Zika virus during the first trimester of pregnancy is associated with newborns with microcephaly. The study provides a quantitative estimate of microcephaly risk in newborns of mothers who are infected by Zika. 95 cases per 10,000 infected woman within the first trimester was associated with microcephaly risk.

    1. when targeted to coding regions of genes can create frame shift insertion/deletion (indel) mutations that result in a loss-of-function allele

      Using a CRISPR RNA (crRNA) that is base-paired to a trans-activating crRNA (tracrRNA) will allow the scientists to direct the Cas9 to a specified area of the DNA and cause a double-strand break at the target location.

    2. The RNA-guided CRISPR (clustered regularly interspaced short palindrome repeats)–associated nuclease Cas9 provides an effective means of introducing targeted loss-of-function mutations at specific sites in the genome

      The CRISPR-Cas9 system can be used to target and remove specific sequences from DNA. This is done by using a guide RNA that directs the CRISPR/Cas9 system to the correct location in the DNA sequence.

    3. predominant method for genome-wide loss-of-function screening

      RNAi is triggered by double stranded RNAs, which are processed into small interfering RNAs (siRNAs). siRNAs target complementary RNAs for destruction, which inhibits gene expression and allows for creation of knockouts.

      Human and Drosophila RNAi libraries have been made to map out the effectiveness of RNAi and the knockout ability in particular genes. Vector-based short hairpin RNAs are artificial molecules that can be used to selectively target genes. Libraries of these molecules can be used for genetic screens in both short-term and long-term assays.

      Although RNAi is a very effective tool, there are sometimes problems with completely turning off specific genes or targeting the correct gene.

  6. Nov 2017
    1. Turkish family in which two siblings displayed clinical features suggestive of autosomal primary microcephaly (MCPH),

      Chavali, Putz, and Gergely (2014) researched the genetics behind microcephaly.

          Microcephaly can be caused by abnormal development of neurons, recessive mutations, and centrosome abnormality. Microcephaly may be classified as a centrosome disorder. Although centrosomes are recognized to have importance in cellular processes, more evidence needs to be conducted to further understand the significance of microcephaly and disease, specifically diseases that affect brain development. 
    2. Intrauterine infections can impair neurodevelopment

      Adams Waldorf and McAdams researched the side effects of infections on the fetus during pregnancy.

      Depending on the type of pathogen, the fetus may die, acquire organ injury, or obtain abnormal bone growth. Pathogens that disturb fetal development are the pathogens that seem to be the most detrimental to the fetus in utero. Understanding the mechanisms the pathogens use to disrupt development may lead to the development of therapies that can be used to help fetal development and survival

    3. fetal neurodevelopment

      Cugola et al., (2016) found that ZIKV infects fetuses, causes intrauterine growth restriction (IUGR), and causes signs of microcephaly in mice.

      Data demonstrated that the infection of ZIKV into human brain organoids (a miniature organ in vitro) reduced proliferation and disrupted cortical layers. This indicates that ZIKV is able to cross the placenta and cause microcephaly by inducing apoptosis in cortical progenitor cells.

    1. up-regulation of nicotinic a4b2 AChRs receptors

      Neonicotinoids (and nicotine) work by [insert info about Ach]

    2. the most widely used class

      There are two major reasons for the popularity of neonicotinoids. First, neonicotinoids bind more specifically to insect (vs. vertebrate) neuron receptors, which makes them relatively safer than other types of pesticides for birds and mammals. Second, neonicotinoids are water-soluble, which allows the chemicals to be applied to soil and taken up by growing plants instead of sprayed onto them. This prevents chemicals from being blown away by wind and, in theory, means beneficial insects won't be affected because they are not feeding directly on the plant..

    1. we believe that the differences in defense strategy we find agree with a growing consensus that plant defense traits are involved in diversification

      In this study from 2009, the results of diversification, when subpopulations with independent genetic modifications emerge, were concluded not to be homogenous in their relation to performance. This concept is further analyzed through this experiment in the speciation and the variation of defense strategies.

      • Carolina Jimenez-Pinilla
    2. promote very different defense allocation strategies for different plant species depending on the type of defense employed (i.e., their elemental constituents and biosynthetic pathways), as well as the nature of resource limitation across habitats (i.e., light, nutrients, or water) (Bryant et al. 1983, Herms and Mattson 1992).

      This statement addresses the variables that must be acknowledged when trying to analyze different plants and their different defense strategies. The "resource limitation across habitats" that the author is referring to is what in the environment can the plant use to defend itself in its habitat from threats such as herbivorous insects.

      • Carolina Jimenez-Pinilla
    3. Herbivores play an important role in habitat specialization because they can magnify the differences in resource availability across habitats

      The sources mention, that in a habitat with a low amount of productivity there is a good amount of strong plants/ plants that are "rich in chemical defenses". In a habitat with lower productivity, the plants are thought to do this in order to increase its life span. Therefore, as the productivity and the amount of herbivores changes the strength and and amount of the resources changes.

      For more information check out: Tropical Blackwater Rivers, Animals, and Mast Fruiting by the Dipterocarpaceae

      Angela Mujica

    1. However, existing studies can be divided into those demonstrating that reef sharks reside inside reserves and those showing differences in reef shark relative abundance between reserves and fished sites.

      The statement reinforces the hypothesis due to the fact that there has been peer reviewed data that can be compared to the research that has been conducted.- Alejandro

    2. A recent survey of recreational SCUBA divers in the Caribbean found that shark sightings are quite rare, except for some places that have shark conservation regulations or large marine reserves in place

      Shark conservation regulations entail the prohibition of shark fin trade actions such as the removal cutting of shark fins or the pursuit of hunting sharks for any other purpose. -Sindy

    3. site-fidelity is high enough to drive the observations of increased shark abundance in these areas, even though large juveniles and adults are vulnerable to fishing as they move between management zones

      Site fidelity is the idea that an organism is primed for a certain place or spatial area and that this place is a reoccurring habitat to which that organism returns to or permanently lives in. This section of the passage states that increased levels of site fidelity correlate to increased levels of shark abundance in these areas despite the fact that risks pursue the movement of the sharks between the site to which fidelity is displayed. -Sindy

    4. Sharks are currently experiencing intense fishing pressure worldwide, largely due to the Asian shark fin trade

      In Asia, shark fins are a delicacy and showcase ones wealth. The Asian shark fin trade accounts for the biggest percentage of shark deaths. -Emily

    1. The global molecular clock hypothesis was tested in each sex-determining protein by using likelihood ratio tests based on the models of evolution defined

      First proposed in the 1960s, the molecular clock hypothesis has become universally used in evolutionary biology, especially genetics. The hypothesis states that DNA evolves at a rate that is directly proportional with time, which allows scientists to determine direct relationships and differences between organisms (Ho, S. 2008). Learn More at https://www.nature.com/scitable/topicpage/the-molecular-clock-and-estimating-species-divergence-41971 -Eri-Ray

  7. Oct 2017
    1. which may be alleviated using an offset nicking approach

      Cas9 nickase creates a break in one strand of the double-stranded helix. These nicks are repaired with a very high fidelity.

      Using Cas9 with off-set sgRNA simultaneously nicks both strands, and may lead to a reduction of off-target modifications.

    2. they can be easily titrated to control transgene copy number and are stably maintained as genomic integrants during subsequent cell replication

      Lentiviral vectors are commonly used for gene insertion because of their stability. It is easy to control the number of vectors, and once integrated into the gene the inserted DNA segment is likely to stay there.

    1. The interstitial concentration of Aβ is higher in awake than in sleeping rodents and humans, possibly indicating that wakefulness is associated with increased Aβ production (15, 16).

      Scientists previously discovered that Aβ levels vary in a daily cycle, and that Aβ levels in the interstitial fluid rise as humans and mice spend more time awake.

      This surprising finding could add to our understanding of diseases, including Alzheimer's disease and insomnia.

      However, this result says nothing about the mechanism — that is, increased Aβ during wakefulness could be owing to increased production, decreased degradation, reduced clearance, or processes like synaptic function that are related to both sleep and Aβ.

      The current article addresses this ambiguity directly.

    2. the brain lacks a conventional lymphatic system

      The lymphatic system does not extend to the brain. The brain has it's own system for clearing waste.

    3. lymph vessels return excess interstitial proteins to the general circulation for degradation in the liver

      In the rest of the body, the lymphatic system "cleans" up waste and moves it to the liver where it is destroyed.

    4. Sleep deprivation reduces learning, impairs performance in cognitive tests, prolongs reaction time, and is a common cause of seizures

      Years of scientific research has already discovered this about sleep.

    1. the species composition and relative abundance of herbivore communities may turn over among habitats because herbivores are affected by habitat quality, structure, and interactions with predators

      The idea in place here is the observation of evolution in herbivorous in correlation to the environment and all its factors.

      The study provides proof of evolution in herbivorous in respect to the environment by analyzing adaptive radiation. It includes the third trophic level, omnivores and carnivorous that eat these herbivorous. This is an important factor that is part of the ecological niche of these herbivorous. It includes the third trophic level, omnivores and carnivorous that eat these herbivorous. This is an important factor that is part of the ecological niche of these herbivorous.

      To further understand adaptive radiation watch [(https://www.brightstorm.com/science/biology/evolution/adaptive-raditaion/)

      -Luisa Bermeo

    1. geographically discrete nursery areas

      A nursery area is a location in which a large subset of the species is populated. For example, a swamp is a nursery area for many types of mosquitoes. The idea that reef sharks do not have a "geographically discrete nursery area" simply means that one can spot a population of reef sharks rather easily in this habitat. -Sindy

    2. Acoustic monitoring of several individuals revealed year round residency to small home ranges within the reserve, indicating that this protected area reduced the exposure of these individuals to fisheries

      Acoustic monitoring is the use of hydrophones (much like a microphone or recorder) to detect the presence of marine animals via sound waves produced by the noises they make. In this case, it was noted that several marine animals continued to inhabit marine reserves for year round periods thus reducing their exposure to fisheries and their potential dangers. -Sindy

    1. A key weakness of this method is that it treats the 0.05 threshold as a bright-line criterion between replication success and failure (28)

      Braver, Thoemmes, and Rosenthal (28) argue that judging the success of a replication only by whether it shows a significant effect (in the current study, at the 0.05 threshold) would be inappropriate.

      They argue that replication success depends a lot on the statistical power and therefore on the sample size used in the replication study. The replication study must have sufficiently many subjects so that it is probable enough that the effect in question, should it really exist in the population, can be found in this sample. If a replication study had low power, for example because the size of the original effect was overestimated and the replication sample size was consequently too small, this makes it less likely that the replication attempt will be successful and show a result that is statistically significant at the 0.05 threshold.

      For each individual replication study, the replication success therefore depends on the sample size. If you assess several replication attempts individually, the replication success rate could therefore be distorted to underestimate how reproducible an effect really is.

      To circumvent this problem, the authors suggest using a different technique than counting if individual replications were significant at the 0.05 threshold. They analysis is called “continuously cumulating meta-analysis”. The data of several replication attempts are combined, so that conclusions on whether the data of all the replication attempts supports the effect of interest.

      After a new replication attempt is conducted, its data is added to the pool of data from previous replication attempts. This data is then taken together, and on the combined data, a test is run to estimate the effect of interest.

    2. and 25%

      Prinz and colleagues (11) comment on their experience as employees of a pharmaceutical company, which relies on preclinical research to decide whether to invest into the exploration and development of new drugs. Because companies find many preclinical research findings unreliable, they now often conduct their own research to reproduce the original findings before they decide to move on and invest large sums of money into the actual drug development.

      Only in about 20% to 25% of the cases did the company scientists report finding results of the reproduction that were in line with the originally reported findings.

    3. in only 11

      Begley and Ellis (10) are cancer researchers, who propose ways for research methods, publication practices and incentives for researchers to change so that research would yield more reliable results, such as more effective drugs and treatments. They argue that often new drugs and treatments enter clinical trials, which test their effectiveness to treat cancer in humans, before they reach sufficient standards in preclinical testing, leading to non-reproducible findings. To achieve more reliable preclinical results, they argue that more focus should be placed on reproducing promising findings in the preclinical phase.

    4. A key weakness of this method is that it treats the 0.05 threshold as a bright-line criterion between replication success and failure (28).

      Braver, Thoemmes, and Rosenthal (28) argue that judging the success of a replication only by whether it shows a significant effect (in the current study, at the 0.05 threshold) would be inappropriate. They argue that replication success depends a lot on the statistical power and therefore on the sample size used in the replication study. The replication study must have sufficientl subjects so that it is probable enough that the effect in question, should it really exist in the population, can be found in this sample. If a replication study had low power, for example because the size of the original effect was overestimated and the replication sample size was consequently too small, this makes it less likely that the replication attempt will be successful and show a result that is statistically significant at the 0.05 threshold. For each individual replication study, the replication success therefore depends on the sample size. If you assess several replication attempts individually, the replication success rate could therefore be distorted to underestimate how reproducible an effect really is.

      To circumvent this problem, the authors suggest using a different technique than counting if individual replications were significant at the 0.05 threshold. Their analysis is called “continuously accumulatingmeta-analysis.” The data of several replication attempts are combined, so that conclusions on whether the data of all the replication attempts supports the effect of interest.[[this sentence doesn't make sense to me]] After a new replication attempt is conducted, its data is added to the pool of data from previous replication attempts. This data is then taken together, and on the combined data, a test is run to estimate the effect of interest.

    5. likely that more than half of research results are false and therefore irreproducible (9)

      Ioannidis conducted computer simulations to show that for most studies, it is more likely for a finding to be a false positive than a true identification of an effect.

      Among the factors that make it more likely for research findings to be false are small sample size or the underlying effect, and when designs, definitions, and analyses are more flexible rather than rigorously objective.

    1. cause progressive shifts in community composition, and "recovery" to prestorm states thus may not occur

      In many ecological systems, there can be more than one "stable, final state" for a community, depending on the history of the community. In a more extreme example, a single, barren part of the ocean floor could end up either a coral-dominated or algae-dominated system depending on a variety of factors including fishing pressure and the first organisms to colonize it.

      Rare disturbances like hurricanes could create patches of coral reef that are dominated by different species.


    2. damselfishes Eupomacentrus planifrons (threespot) and Microspathodon chrysurus (yellowtail)

      Some species of damselfish cultivate and defend lawns of algae—which serve as a source of food—on dead coral. Damselfish are known for being fiercely territorial and will fight off other species that enter their home territory.

    1. Most part of the molecular evolutionary analyses was carried out using the program MEGA version 6 (Tamura et al. 2013)

      MEGA which stands for: Molecular Evolutionary Genetics Analysis is a software in which the user can create DNA sequence alignments, look at phylogenetic histories, and conduct molecular evolutionary analysis (tamura et al. 2013). The MEGA can estimate the divergences of the phylogenetic tree as well as building a phylogenetic tree with time as a scale. -Elder Learn more at: MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0