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  1. Last 7 days
    1. B7-1 expression was partially successful at inducing rejection

      If cancerous cells express B7-1, the immune system is better able to respond to them and clear the tumor.

    2. mice deficient in CTLA-4 exhibit severe T cell proliferative disorders

      The absence of CTLA-4 results in out-of-control cell division of T cells. Even though CTLA-4 is an inhibitory receptor, it is needed to produce the right balance of T cell activation and its complete absence can be dangerous to organisms.

    3. CTLA-4 engagement can induce apoptosis in activated T cells

      Another effect of CTLA-4 signaling is the programmed cell death of T cells. This is another way for CTLA-4 to dampen T cell responses.

    4. greatly augment T cell responses to nominal peptide antigen or the superantigen Staphylococcus enterotoxin B in vivo

      Blocking CTLA-4 also increases T cell activation that happens as a result of encountering foreign invaders.

    5. enhances proliferative responses

      The inhibitory CTLA-4 receptor can be blocked by using soluble antibody. Blocking the effects of CTLA-4 allows T cells to activate and proliferate normally upon induction by anti-CD3.

    6. induced by antibody to CD3 (anti-CD3)

      CD3 is a co-receptor alongside the T-cell receptor. Together, they provide the primary signal of T cell activation. In this experiment, the scientists tried to add anti-CD3 antibody, which would normally result in T cell activation. However, the inhibitory effect of CTLA-4 wins out over this activation technique.

    7. antibody cross-linking of CTLA-4 has been shown to inhibit

      Using antibodies, scientists can induce dimerization of the receptor CTLA-4. Dimerization is often the cause of signaling through a receptor. This experiment shows that the effect of the CTLA-4 signaling is inhibition of T cell activation and expansion.

    8. binds both B7-1 and B7-2 with affinities much greater than does CD28

      CTLA-4 competes with CD28 for binding to the B7 family of molecules.

    9. costimulation is more complex than originally thought and involves competing stimulatory and inhibitory signaling events

      The overall activation of T cells is also influenced by another type of secondary signal. In addition to stimulatory signals discussed above, T cells may also encounter inhibitory signals. The balance of these two signaling events results in the overall level of activation.

    10. tumor cells expressing costimulatory B7 molecules induced potent responses against both modified and unmodified tumor cells

      Introducing the genes for B7 molecules into tumor cells allows them to provide the secondary signal needed to activate T cells. This allows the immune system to respond to those modified tumor cells, as well as any future tumors of the same type that they encounter (even if the latter do not express B7).

    11. appears to be provided by the interaction of CD28 on T cells with its primary ligands B7-1 (CD80) and B7-2 (CD86) on the surface of specialized antigen-presenting cells (APCs)

      The two-signal model of T-cell activation was confirmed when scientists found that specialized immune cells, called antigen-presenting cells, provide a secondary signal to T cells in order to activate them. This secondary signal comes from the interaction of the B7 family of molecules (on the surface of APCs) with the CD28 receptor (on the surface of T cells).

    12. additional costimulatory signals are necessary for T cell activation

      Mueller, Jenkins and Schwartz summarize the models proposed by several scientists to explain why T cells only respond to foreign invaders, and not to peptide-MHC on healthy cells. They summarize it as the "two-signal model of T-cell activation": there must be another signal necessary for T cells to be activated.

  2. Sep 2019
    1. In recent experiments, Dienwiebel et al. (8) observed friction reduction to vanishingly small values, depending on the degree of commensurability between the graphene flakes and the extended graphite surface

      The mechanism of superlubricity at the sliding interfaces of materials is studied. Dienwiebel and co-researchers have investigated the superlubricity of graphite using a home-built frictional force microscope. They have also investigated the role of incommensurability in the origin of the ultralow friction of graphite.

    2. The contact area, which is proportional to the number of interacting atoms, reduces by 40 to 50% during (26) this period.

      Size plays a major role in superlubricity and many researchers have investigated the dependence of size of materials in friction reduction. Liu and co-workers reported one such size-dependent study of superlubricity on graphite. They have detailed the probability percentages of the superlubric state for different contact areas and also the mechanism of superlubricity (self retraction) of graphite layers.

    3. Even a modest 20% reduction in friction can substantially affect cost economics in terms of energy savings

      The failure of moving mechanical assemblies due to friction and wear is a major concern in today's world. Different types of lubricants are employed to minimize friction. Though this helps to improve the lifetime of mechanical systems, researchers are on a quest to find a perfect lubricant to achieve the lowest friction and wear possible with no harmful additives or chemicals.

    4. To date, superlubricity has been primarily realized in a limited number of experiments involving atomically smooth and perfectly crystalline materials (2–5) and supported by theoretical studies (6, 7).

      Research in superlubricity is gaining interest due to its potential applications in mechanical systems to reduce friction- and wear-related failures. Various researchers proposed different materials to achieve near-zero friction. Even though these materials show some promise, most materials are perfectly crystalline (which is not the case in real life) and the effect occurs mostly at the nanoscale regime.

    5. with the previously observed low-friction performance of DLC against DLC (fig. S14) (12)

      Diamondlike carbon (DLC) film is a widely researched material to combat friction and wear in a number of applications, owing to its impressive tribological properties and low deposition costs. The tribological properties of DLC films sliding against each other are investigated and they are found to display super-low friction under specific conditions.

    6. The π* peak (at ~285 eV) in the carbon K-edge represents a small fraction of sp2 bonded carbon owing to the presence of the few layers of graphene wrapped around the nanodiamond, which is similar to the disordered carbon shell observed previously in detonated nanodiamonds (23)

      The structural analysis of graphene-wrapped nanodiamonds by electron energy-loss spectra (EELS) reported in this study is analogous to the previously reported structure of detonated nanodiamonds by other researchers.

    1. Stimulation of anorexigenic proopiomelanocortin (POMC) cells in the hypothalamic arcuate nucleus leads to a reduction in feeding slowly over the succeeding 24 hours, whereas stimulation of orexigenic hypothalamic neurons expressing agouti-related peptide (AgRP) leads to what has previously been considered to be a rapid increase in feeding with mean latency to eat of 6.1 min (range: 1.9 to 13.8 min) (19).

      The arcuate nucleus, a subregion of the hypothalamus, has been shown to be a very important brain region that controls food intake

      Neurons within this region have been shown to control feeding in a reciprocal manner. POMC-expressing neurons are activated by satiety signals and reduce food intake whereas AgRP-expressing neurons are activated by starvation and increase food intake. These neurons have been proposed to be the neural substrate for satiety and hunger, respectively.

  3. Aug 2019
    1. Despite the relatively well-studied pathway of fructose metabolism in the liver and in the small intestine, the role of fructose metabolism in tumors is mostly unknown.

      This paragraph details the pathway of fructose and glucose metabolism within cells. In normal cells this is how glucose and fructose are broken down and converted into energy. It is unknown how tumors metabolize these molecules and so the scientists move on to explore this in their next series of experiments.

    2. Similar results have been reported for other fructose-metabolizing enzymes, ketohexokinase (KHK) and aldolase B in human colon tumors (22, 23).

      Colorectal tumor fructose metabolism has been looked at in the past. In these studies the enzymes required to break down fructose were studied, rather than looking at fructose transporters as this paper did. The past research found similar results where tumors had higher levels of enzymes that break down fructose than normal human tissues did.

    3. Relatedly, a recent study in mice showed that fructose doses greater than 1 g/kg (~1% of daily calorie intake) overwhelm fructose absorption in the small intestine, resulting in a higher concentration of fructose in the colon (20)

      The same results seen in human studies looking at gastrointestinal discomfort after fructose consumption were recapitulated in mouse studies. In animal models scientists are able to more closely control variables and more inversely monitor outcomes. In this case they were able to directly measure fructose concentrations in the colon rather than relying on gastrointestinal symptoms. They found high concentrations of fructose in the colon after oral delivery, suggesting that the passive transporters in the intestine were unable to uptake fructose at levels higher than 1g per kg of weight.

    4. The consumption of as little as 5 g of fructose can lead to the saturation of GLUT5 in the small intestine (i.e., malabsorption), resulting in an increased concentration of fructose in the lumen of the colon (large intestine) of healthy humans (17–19)

      A past study administered various amounts of fructose to people after fasting. They then assessed gastrointestinal symptoms that stem from fructose passing through into the intestines and colon undigested (malabsorption). They found that even 5g of fructose can lead to the saturation of passive transporters in the intestine. Ingestion of any amount of fructose over 5g will result in high levels of fructose in the colon.

    5. We observed similar results in a study of another mouse model, CDX2P-CreERT2; APCflox/flox (fig. S3, D to H), where intestinal tumors develop mainly in the colon instead of the small intestine (15).

      Previous study of another genetically modified mouse model (where tumors were induced to grow mostly in the colon) demonstrated similar results. This suggests that this mouse model or genetic manipulation (APC deletion) itself is not somehow more sensitive to high fructose corn syrup than other mutations that lead to colorectal cancer. Comparing previous results increases confidence that any colorectal cancer tumors will respond to high fructose corn syrup in a similar fashion.

    6. tumor suppressor that is frequently mutated (75 to 80%) in the early stages of CRC development (13).

      Scientists have found that in a high majority of colorectal cancers the APC gene is defective. This high correlation suggests that the APC gene is a major cause for the development of colorectal cancer and tumors.

    7. Indeed, studies have shown that excessive consumption of SSBs causes obesity and that being obese increases the risk of CRC, especially in men

      Taking big data sets such as questionnaires or patient data, computational biologists can run statistical tests to look at correlations between variables. In this case data has shown that people who drink a lot of sugar-sweetened beverages (such as soda) tend to be more overweight and in men there was a significant correlation to developing colorectal cancer.

    1. sympathetic superior cervical ganglion in adult rats

      Prior to this research, studies primarily focused only on the transmitter expression during development. Is there a similar phenomenon in adult stages? The cervical ganglia are separated by denervation technique. The denervated ganglia were measured for the activity of substance P. Two-fold increase in substance P was observed in the ganglia compared to controls.

    2. Since some trigeminal neurons are derived from the neural crest, whereas nodose neurons are epibranchial placode derivatives, heterogeneous populations, differing embryologically, geographically, and functionally, may exhibit transient catecholaminergic expression during development.

      Two types of neurons—trigeminal neurons and nodose neurons—are discussed here.

      Trigeminal neurons are derived from the neural crest. Epibranchial placodes help in the generation of the neurons found in the back of the brain/cranial nerves (or nodose). Hence, both neurons differ in embryonic origin.

      Trigeminal neurons are derived from one source and hence they are homogenous. However, the epibranchial placode helps in the generation of several cranial nerves, namely hypoglossal and glossopharyngeal. This results in a heterogenous population.

      As both sets of neurons differ in their embryonic origin and location in the brain, it is fair to state that the functions of these neurons to express catecholamines will also be different.

    3. phenotypic alteration may be mediated, at least in part, by specific hormones and alteration in the processing of specific species of mRNA

      The conversion of norepinephrine to epinephrine is dependent on the mRNA synthesis and hormones released by the pituitary-adrenal axis.

    4. Consequently, these neurons may convert from catecholaminergic to cholinergic and peptidergic during development

      Neurons in rat sweat glands can convert from catecholaminergic to cholinergic groups during development. This is evident from the lack of enzymes that are responsible for catecholamine synthesis.

  4. Jul 2019
    1. Although bulk transcriptomic tissue studies revealed convergence of disease pathology on common pathways (1–3)

      These studies performed RNA sequencing to identify differences in RNA and gene expression in the autistic brain. They found that there are similarities in the kinds of genes that are changed in patients with autism.

    1. KDM6B (also called JMJD3) is a histone demethylase that specifically demethylates H3K27me3 and is involved in transcriptional activation during normal development

      KDM6B activation of genes critical for early developmental processes, such as gonad specification and body patterning.

    2. Recently, epigenetic marks, such as DNA methylation and histone modifications of known regulators of gonadal differentiation, have been shown to differ between temperatures in species with temperature-dependent sex determination

      Methylation, or the addition of methyl groups to cytosines on DNA often leads to silencing of genes.

      Female-producing temperatures specifically lead to de-methylation and addition of activating histone marks to the promoter for the gene encoding the enzyme that produces estrogen in turtles, alligators, and sea bass.

    3. Trimethylation of H3K27 contributes to transcriptional repression in many organisms

      H3K27me3 is a histone mark that recruits repressive factors to that region of DNA, essentially silencing any local gene expression.

    4. We previously sequenced the T. scripta gonadal transcriptome during developmental stages 15 to 21 at male-producing (26°C) and female-producing (32°C) temperatures and found that Kdm6b was up-regulated at 26°C

      The authors originally sequenced the turtle embryos at male- and female-producing temperatures to identify differences in gene expression that drive sex development.

      Kdm6b was one of six genes consistently upregulated at male-producing temperatures. KDM6B was likely chosen for a follow-up study due to its potential to regulate the expression of multiple male development genes.

    5. In many reptiles, including the red-eared slider turtle Trachemys scripta elegans (T. scripta), gonadal sex is determined by the environmental temperature experienced during embryogenesis

      As opposed to the genome conferring sex as it does in vertebrates (e.g. XX confer female development and XY leads male development in many mammals), the ambient environment determines sex for some organisms.

      In most reptiles, as well as some amphibians and fish, the incubation temperature of eggs directly determines whether males or females will hatch.

    1. 22

      In this study, Professor Arnold's group used protein engineered variants of cytochrome P450BM3 to bring about highly diastereoselective and enantioselective cyclopropanation reaction of styrenes from diazoester. Variant BM3-CIS was identified as a competent cyclopropanation catalyst. It exhibits a strong preference for the cis product and forms both diasteromers over 90% ee and is as stable as the wild type enzyme. P450-BM3 works on a wide range of substrates with both electron donating and electron withdrawing substituents in styrene.

    1. Therefore, functional characteristics (e.g., beak, seed, and fruit sizes) and species abundance (39) may be more important in the structure of mutualistic networks than species identity, supporting the role of ecological fitting (40)

      This study found that phenotypical traits such as the size of a bird's beak and the fruit's diameter, were strong factors that determined the likelihood of different pairwise interactions, along with species abundance.

    2. High interaction dissimilarity has also been reported in specialized, native-dominated pollination networks, even between spatially close networks (33)

      D. Carstensen and others quantified the variability of interactions between plants and pollinators across different spaces. They found that these interactions vary greatly between different locations due to the abundance of species, which determined the likelihood of partners interacting with each other.

  5. Jun 2019
    1. Several studies suggest that the phylogenetic relationships of species contribute to structuring mutualistic networks

      Normally depicted as the "tree of life" (shown below), the phylogenetic tree traces the genetic lineage of organisms over time. Two species share a phylogenetic relationship when they share a common ancestor.

      The authors of the cited paper found that phylogenetic relationships can influence the type of networks species build and explain the type of species involved in these interactions.

    2. Consequently, high connectance and nonmodular structures are expected, because both are linked to low specialization [e.g., (14, 23)]

      Dalsgaard and colleagues found that tropical areas have a lot of bird species that are obligate frugivores, meaning that they only eat fruited plants. Because fruit is there sole diet, these birds interact with a large variety of plants to ensure that they're consuming enough food to live.

      This type of behavior is commonly associated with a low specialized network because the birds are not displaying any preference towards any particular plant(s). When the obligate frugivores eat from a wide variety of plants, they are utilizing the majority of interactions available in their ecosystem- demonstrating high connectance. There are also no particular groups of plants that the frugivores specifically associate with, an example of a nonmodular structure.

    3. For example, both fleshy-fruited plants and frugivores on islands tend to have wide niches owing to resource limitation

      Traveset and colleagues observed that bird-plant interactions on the Galápagos islands are highly generalized, meaning the birds developed relationships with a wide variety of plants, and vice versa. These broad interactions offer more opportunities for species to gain food. However, the authors also warn that these additional interactions promote the reproduction and survival of invasive plant species, at the cost of native species.

    4. Oʻahu, in particular, is among the areas most affected by extinctions and biological invasions in the world (12)

      In a 2010 Hawaii statewide assessment of forest conditions and trends, a map illustrated that major vegetation types for multiple islands , especially O'au, experienced severe changes before the arrival of humans in comparison to present day.

    5. Most native Hawaiian forest plants are bird-dispersed, yet no native dispersers remain in most ecosystems (10, 11). Thus, seed dispersal is almost entirely dependent on a handful of introduced vertebrate dispersers, nearly all of which are birds (10, 11).

      The introduction of novel seed dispensers (aka birds) is an important factor regarding the survival of native Hawaiian plant species. One study showed that the distribution of seeds from native plants are becoming increasingly dependent on not native, but foreign birds. C. Chimera and D. Drake also found that these introduced birds tended to spread more seeds from non-native plants rather than native plants.

    6. Mutualistic plant-animal networks are particularly susceptible to species loss (5) and invasions (4, 6, 7)

      A mutualistic network is a beneficial partnership between organisms. Disturbances to that relationship, like from one of the organisms becoming extinct, or by the intrusion of another species, can be harmful for the original partners of that relationship.

    7. As a result, “novel communities” have emerged, characterized by a reshuffling of species, changes in species interactions, and, in some cases, alteration or disruption of ecosystem services maintained by these interactions (3, 4)

      Brodie et. al reviews the concept of secondary extinction, the idea that the extinction of a species, caused by human activity, can lead to the loss of additional species.

      Below is a diagram from the review depicting different types of secondary extinctions. co-extinction: when the direct impact of humans (red arrow) leads to the loss of one species, causing the loss of another species, which can then cascade into a series of extinctions. Human activity (yellow arrows) also affects interactions between species (grey arrows).

    1. women’s performance on difficult math and science tests can suffer insofar as they worry that their poor performance could be seen to confirm a negative gender stereotype (18

      Spencer, Steele, and Quinn performed several experiments to determine whether the stereotype that men are better at math than women affected women's performance on math tests.

      They found that when the gender stereotype was reinforced before a hard math test women performed even worse compared to men than on the test than usual. However, describing the test as not producing gender differences eliminated the difference in performance between men and women.

    2. reduce the gender gap in college physics classrooms (13)

      Lorenzo, Crouch, and Mazur found that using more interactive teaching methods improved conceptual understanding for all students in a college-level physics class and reduced the gap in performance between women and men, compared to classes taught in the traditional lecture-based way. Classes taught with the highest level of interaction eliminated the gender gap.

    3. affect performance in lab experiments and classrooms (20

      Schmader, Johns, and Barquissau found that women who identified more strongly with the stereotype that men are better than women at math were likely to be less confident about their own abilities and less likely to pursue math careers. They also found that women who believed the gender stereotype were more susceptible to its negative effects on math test performance.

    4. this benefit persisted in a 2-year follow-up study (31)

      An initial values affirmation intervention can have long-lasting positive effects.

      In one study, a group of students received a values affirmation intervention at the start of seventh-grade (initial findings reported in reference 23), and their academic performance was monitored through seventh and eighth grade. African American students that received the intervention had larger and persistent increases in grade point average than those who did not receive the intervention. This suggests that a single intervention could have long lasting positive effects.

    5. improve the performance of stereotype-threatened individuals

      Values affirmation can reduce the effect of stereotype threat for women taking a math test under laboratory conditions.

    6. lab studies show

      It has been shown that values affirmation can significantly reduce a person's physical response to a subsequent stressful situation.

      Specifically, participants that performed a values affirmation task before undergoing a stress test produced less cortisol (a hormone that is released when we are stressed) than participants who did not get the intervention.

    7. can account for as much as 60% of the gender gap in exam performance at our institution, the University of Colorado, but background and preparation do not fully account for the gap (9)

      Previous work has assessed the gender achievement gap in college students taking introductory physics at the University of Colorado at Boulder.

      Despite the use of teaching methods thought to reduce the gender achievement gap, there remained a difference between men's and women's test scores. Most of this gap could be attributed to differences in prior preparation (for example, men were more likely to take high school physics), but not all of the gap could be attributed to these factors.

    1. a ganglionic blocking agent that prevents depolarization by competing with acetylcholine for postsynaptic nicotinic receptors, reproduced the effects of denervation

      Using a blocking agent for nicotinic receptors, the binding of acetylcholine was blocked in the ganglia. This manipulation is similar to denervation technique and hence, the authors observed an increase in the activity of substance P.

    2. the high-affinity uptake system for α-CH3-norepinephrine (5), a characteristic of noradrenergic neurons

      The uptake of norepinephrine in these neurons remain unaffected. The neurons are capable of producing noradrenaline.

    3. Sympathetic neurons innervating rat eccrine sweat glands appear to convert from noradrenergic to cholinergic

      Noradrenergic neurons produce norepinephrine, the neurotransmitter expressed in rat sweat glands during postnatal stages of development. For a short period of time in development, the neurons lose the noradrenergic expression, but pick up the expression of acetylcholine.

    4. Recent work with bullfrog sympathetic ganglia suggests another mechanism for alteration of site of transmitter action.

      Previously, researchers found that neurons in frog sympathetic ganglia are also depolarized by substance P, making them an appropriate model organism to study.

    1. The sea otter/kelp forest system in the North Pacific Ocean

      The kelp forests of Alaska and Aleutian Islands were monitored for up to 15 years to evaluate the impacts of top-down controls by sea otters on the community structure of the region.

    2. The loss of these animals may be humankind’s most pervasive influence on nature

      There are a number of different impacts of humans on the biosphere but loss of apex predators is thought to be one of the widest ranging issues of the planet.

      An overview of the threats to the planet's largest 31 carnivores an implications can be found here.

      The study can also be found in the "Related Resources" tab.

    3. This empirical work supports long-standing theory about the role of top-down forcing in ecosystems but also highlights the unanticipated impacts of trophic cascades on processes as diverse as the dynamics of disease, wildfire, carbon sequestration, invasive species, and biogeochemical cycles.
    4. For example, empirical research in Serengeti, Tanzania, showed that the presence or absence of apex predators had little short-term effect on resident megaherbivores [elephant (Loxodonta africana), hippopotamus (Hippopotamus amphibius), and rhinoceros (Diceros bicornis)] because these herbivores were virtually invulnerable to predation (24). Conversely, predation accounted for nearly all mortality in smaller herbivores [oribi (Ourebia ourebi), Thompson’s gazelle (Eudorcas thomsonii), and impala (Aepyceros melampus)], and these species showed dramatic increases in abundance and distribution after the local extinction of predators.

      In this study, it was noted that ungulates above 150 kg were regularly limited by food availability instead of predation, due to their large body sizes.

      Conversely, small ungulates (<150 kg) were regular prey items of the several large carnivores on the Serengeti and their populations, and the trophic levels below them, were controlled by the apex predators.

      Loss of predators in these systems caused much greater impacts on the smaller herbivores than the larger ones.

    5. Tipping points (also known as thresholds or breakpoints), around which abrupt changes in ecosystem structure and function (a.k.a. phase shifts) occur, often characterize transitions between alternative stable states.

      These tipping points are notoriously difficult to predict but can be recognized after the fact. Models are being developed to identify tipping points ahead of time, for example here.

    6. The history of life on Earth is punctuated by several mass extinction events (2), during which global biological diversity was sharply reduced. These events were followed by novel changes in the evolution of surviving species and the structure and function of their ecosystems. Our planet is presently in the early to middle stages of a sixth mass extinction (3), which, like those before it, will separate evolutionary winners from losers.

      There have been five mass extinctions on Earth in the past. These were caused by various natural events, from gamma-ray bursts to megavolcanic eruptions to meteor strikes. During each mass extinction, species diversity diminished significantly in a short period of time. Each mass extinction was followed by the evolution of novel forms of organisms that transformed their habitats in new ways.

      Most scientists agree that we are currently in the 6th mass extinction event, this one largely caused by human activities such as climate change, habitat loss/fragmentation, pollution, invasive species, and human consumption/overexploitation.

    7. The omnipresence of top-down control in ecosystems is not widely appreciated because several of its key components are difficult to observe.

      To see the effects of one such natural experiment, read Terborgh, J. et al. "Ecological meltdown in predator-free forest fragments." Science, 294 (5548)

      Also can be found in the "Related Resources" tab.

    8. Although the extent and quality of evidence differs among species and systems, top-down effects over spatial scales that are amenable to experimentation have proven robust to alternative explanations

      In a metastudy of 41 papers and 60 independent tests, it was found that terrestrial trophic cascades occurred with more frequently than previously thought across systems and were on par with aquatic environments. While the strength of the cascade response varied across systems based on several factors (type of carnivore, plant antiherbivore defenses, type of damage measured, etc.), trophic cascades were common, although not universal.

    9. Such interdependencies are well illustrated in East Africa, where the introduction of rinderpest in the late 1800s decimated many native ungulate populations, including wildebeest (Connochaetes taurinus) and buffalo (Syncerus caffer). Reductions of these large herbivores caused an increase in plant biomass, which fueled wildfires during the dry season. Rinderpest was eliminated from East Africa in the 1960s through an extensive vaccination and control program. Because of this, wildebeest and buffalo populations had recovered to what was thought to be historically high levels by the early 1980s. The resulting increase in herbivory drove these systems from shrublands to grasslands, thus decreasing the fuel loads and reducing the frequency and intensity of wildfires

      This top-down forcing by disease and loss of herbivores has also been linked to the complex carbon cycle in the region:

      http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1000210

    10. For example, the reduction of lions and leopards from parts of sub-Saharan Africa has led to population outbreaks and changes in behavior of olive baboons

      In this case, the apex predators have been overhunted by humans for bushmeat, for trophies, or as pests to their livestock.

    11. A similar result, involving different species and processes, occurred in India, where the decline of vultures also led to increased health risks from rabies and anthrax

      Because of overuse of antibiotics in livestock, the vulture population declined, leading to more scavenging by feral dogs of carcasses throughout the region. As the dog populations grew, and due to their proximity to humans, the risk of transmission of rabies to humans has increased greatly.

    12. Further examples of the interplay between predation and disease exist for aquatic systems. The establishment of no-take marine reserves in the Channel Islands of southern California led to increases in the size and abundance of spiny lobsters (Panulirus interruptus) and declines in population densities of sea urchins, which are preyed on by the lobsters. The reduced urchin densities thwarted the spread of disease among individual sea urchins, which led to a lowered frequency of epidemics of sea urchin wasting disease within the reserves

      By allowing the expansion of the predator population (spiny lobster), the prey population size (sea urchins) were held in check and individual urchins suffered from disease less often.

    13. In freshwater systems, the localized rise and fall of human malaria is associated with the impacts of predatory fishes on planktivores, which are in turn important consumers of mosquito larvae

      In this case, researchers found that certain types of predatory fish, while consumers of mosquito larvae, also regularly consumed the mosquito's main predators, leading to increased malaria infections.

    14. From land, the demise of Pleistocene megaherbivores may have contributed to or even largely accounted for the reduced atmospheric methane concentration and the resulting abrupt 9°C temperature decline that defines the Younger-Dryas period

      Herbivores produce large amounts of methane, a potent greenhouse gas, as a by-product of their diet. By losing so many of these organisms during the Pleistocene and early Holocene, the methane concentration in the atmosphere would have dropped rapidly, helping to cause the global cooling of the Younger-Dryas.

    15. For example, the reintroduction of wolves to Yellowstone National Park has reduced the positive indirect effects of ungulates on soil nitrogen mineralization and potentially the nitrogen supply for plant growth

      Researchers found that after wolves were reintroduced to Yellowstone, there was a net decline in soil nitrogen, likely due to fewer large herbivores. In addition, the spatial nature of nitrogen renewal changed due to new use patterns by the herbivores.

    16. In contrast, introduced rats (46) and arctic foxes (Fig. 4) (47) have reduced soil fertility and plant nutrition on high-latitude islands by disrupting seabirds and their sea-to-land nutrient subsidies, with striking effects on plant community composition.

      A metastudy of 45 replicated and 35 unreplicated field experiments found that introduced predators had double the negative effect than native predators on their vertebrate prey:

      https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1950296/

    17. Other examples include the spread of the invasive brown tree snake (Boiga irregularis) on the otherwise vertebrate predator–free island of Guam

      A number of different factors led to the success of the brown tree snake in Guam: barrier-free dispersal, few safe areas for avian prey, lifestyle of the predator (nocturnal and arboreal), and ability of predator to find prey under varying conditions.

    18. predatory seastars in the rocky intertidal

      Predatory sea stars regularly graze the rocky intertidal regions and are not prey-specific. Their grazing opens new substrate for multiple species, preventing the dominant species from colonizing all of the rocks.

    19. mesopredator release [coyotes (Canis latrans) maintaining small vertebrate species in chaparral habitats

      It was observed that the loss of coyotes as an apex predator control on smaller vertebrate predators, along with habitat fragmentation, led to trophic cascades in the ecosystem.

    20. white-tailed deer (Odocoileus virginianus) have persisted in the absence of predators for more than a century, causing the successive elimination of saplings of less and less palatable trees and shrubs

      In this study, it was discovered that balsam fir, the island's original dominant tree species, was not able to recruit as it was a favorite food for deer. White spruce, and several companion species, have replaced the fir as deer do not find them palatable.

    1. In brain slices taken from the striatum, we measured LTP in the excitatory synapses (in the cortico-accumbens pathway) in the NAc core (Fig. 2A), known to be reduced in response to chronic cocaine administration

      Cocaine is capable of producing LTP in several brain regions.

    2. This result is consistent with our earlier finding that SAHA caused a marked increase in FosB expression when given before an acute cocaine injection compared with the effect of cocaine alone

      Similar to nicotine, SAHA also causes an increase in the expression levels of FosB

    3. SAHA helps restore some of the memory deficits in these mice

      In cocaine-treated animals, LTP is impaired. SAHA helped in rescuing certain aspects of LTP in cocaine-treated animals.

    4. Thus, most cocaine users smoked cigarettes before they started using cocaine, and, in addition, they started using cocaine while they were actively smoking cigarettes

      This study shows that the key determinants for sequential drug use are the onset of age and the frequency of drug usage

    5. Because an important step in the molecular sequence leading to the expression of the addictive phenotype in mice is increased FosB expression in the striatum

      The authors use DNA expression array techniques to identify genes that are modified by drugs of abuse and their mechanism of action.

      FosB is shown to regulate gene expression in cocaine-treated animals.

    6. The addiction process is also mediated through histone acetylation of the promoter of the transcription factor ΔFosB

      CBP is instructed to FosB promoter to acetylate H4 histones, thereby regulating the expression of FosB gene in cocaine-treated animals

    7. An acute cocaine injection increases acetylation of histone H4 but not H3 at the FosB promoter

      This paper shows that chromatin remodeling is a key mechanism that contributes to cocaine-induced synaptic plasticity.

      Here the authors show that the cocaine can cause acetylation of histones via histone acetyl transferase (HAT) at a particular promoter site leading to chromatin acetylation and remodeling.

    8. the consequent activation of a downstream cascade of gene expression initiated by CREB [cyclic adenosine 3′,5′-monophosphate (cAMP) response element–binding protein]. This cascade is dependent upon the acetylation of histone tails by the CREB-binding protein (CBP), a histone acetyl transferase (HAT)

      The authors show that the impairment in LTP and chromatin acetylation was observed in the animals.

      By manipulating the CREB binding protein (CBP), some of these deficits were able to be restored. This suggests that LTP depends on the regulation of CBP.

    9. The molecular pathways involved in addiction share some of the same molecular logic and even some of the same molecular steps encountered in long-term memory storage

      Cocaine induces long term depression (LTD), a form of synaptic plasticity in the nucleus accumbens. This impairment in LTD causes deficits in the memory storage in this brain region.

    10. Reduction of excitatory input to the NAc is thought to decrease inhibitory output from the NAc to the VTA and thereby contribute, through disinhibition, to the increased reward and enhanced locomotion activation observed after cocaine administration

      After administering cocaine to animals, there is a decreased excitatory input from the prefrontal cortex to Nucleus accumbens.

      This change in inputs leads to a lack of restraint on the inhibitory output from the nucleus accumbens to the ventral tegmental area, as the inhibitory output remains the same.

      This leads to increased dopaminergic activity in VTA, leading to an increase in motor activity and in reward pathways.

    11. For example, in 2009 in the United States (4), among adults aged 18 to 34 who had used cocaine at least once, 90.4% had smoked cigarettes before they began to use cocaine, 4.7% began using both drugs at the same age, 2.4% used cocaine first, and 2.5% had never smoked

      This survey was conducted in the US to identify the usage and correlation of drugs of abuse. Questions were provided as a survey to the participating individuals, and the results are summarized in the report.

      Examples of queries are age, drug usage, and frequency, lifestyle, smoking, and drinking frequency.

    1. We have developed and employed optogenetics technology

      One of the paper authors, Karl Diesseroth, is attributed to implementing light-sensitive proteins called opsins in neurons to control their activity. He coined the term optogenetics to signify that neurons can be selectively targeted using genetics which in turn encodes for proteins that optically controlled.

  6. May 2019
    1. That the PSTh may be involved in feeding is suggested by increased c-fos expression in the PSTh during anorexia induced by amino acid deficiency

      Anorexia induced by dietary deficiency in a single indispensable amino acid was found to induce expression of c-fos—a protein known to be present in active neurons—in the PSTh.

    2. can exhibit characteristics of binge eating (1–3)

      Zahodne, Amami, and Novakova studied Parkinson's patients and found that many subjects exhibited binge-eating behavior. Those that had received deep-brain stimulation of the subthalamus were more likely to display this behavior.

    3. sheep may release γ-aminobutyric acid (GABA) from the ZI in response to the sight or ingestion of food (6, 7).

      Kendrick and colleagues found that the neurotransmitter GABA was increased in the ZI in sheep when the animals were presented with and ingested food.

    4. These results are consistent with an early report that lesions in the area of the ZI can alter food intake (18).

      The ZI has been shown to be important for food intake that occurs in response to low levels of blood glucose. Rats with ablated ZI eat less food under these conditions.

    5. much-studied lateral hypothalamus

      The lateral hypothalamus is a region neighboring the ZI. Stimulation of this site has been shown to substantially increase food intake and is also hedonic.

    1. Moreover, there is preliminary evidence (9) which suggests that secondary structure within a polynucleotide inhibits the power to stimulate protein synthesis.

      Nirenberg and co-workers saw that poly A was not decoded, specifically at low pH (acidic environments). At low pH, poly A is double stranded. These results suggest that the residues may need to be exposed—that RNA must lack secondary structure—to be decoded.

    2. It is believed, not that DNA itself controls protein synthesis directly in a cell in which DNA is the genetic material, but that the base sequence of the DNA - probably of only one of its chains-is copied onto RNA, and that this special RNA then acts as the genetic messenger and directs the actual process of joining up the amino acids into polypeptide chains. The breakthrough in the coding problem has come from the discovery, made by Nirenberg and Matthaei (6)

      Nirenberg and Matthai discovered that "special RNA"—now called tRNA—was critical to protein synthesis. A protein could only grow with enough tRNA available, demonstrating that tRNA was a critical material to generate proteins.

      To hear a contemporary scientist give an in-depth account of protein synthesis, watch Johns Hopkins University's Rachel Green detail the process on this iBiology video.

    3. For example, something very like rabbit hemoglobin can be synthesized in a cell-free system of which part comes from rabbit reticulocytes and part from Escherichia coli (5). That this would be the case if the code was very different in these two organisms is not very probable.

      Lippman and Von Ehrenstein showed that genetic material (mRNA) from a mammal could be decoded with genetic material (tRNA) from a bacteria to form the protein hemoglobin. Because hemoglobin is not found naturally in bacteria but is found naturally in mammals, this was a remarkable result: The biological material of a bacterium decoded mammalian genetic material!

      The result suggests that vastly different biological species share a genetic language. This is strong evidence that the code is universal.

      See a visualization here.

    4. action of nitrous acid and other chemicals on trick tobacco mosaic virus (2)

      Tsugita used an acid (nitrous acid) to chemically mutate RNA. The acid most often changed cytosine bases into uracil bases. The mutant genetic material encoded a different amino acid sequence than the unmutated, or native, form.

    1. Previous field studies have documented rare but recurring introgressive hybridization on Daphne Major between medium ground finches and small ground finch immigrants (23)

      Introgression, the movement of a gene from one species into the gene pool of another, has been known to speed up a population's response to an evolutionary selective pressure. It does this by increasing genetic diversity.

      Grant and Grant documented recurring introgressive hybridization between medium ground finches and small ground finches.

    2. HMGA2 has been associated with variation in height, craniofacial distances, and primary tooth eruption in humans (18, 19)

      Fatemifar et al. (2013) showed that HMGA2 is associated with craniofacial features, such as the width of the eye region, the width of the lower part of the nose, and the height of the mid-brow prominence.

      Ligon et al. (2005) had previously reported an 8-year-old boy with a shortened HMGA2 gene that exhibited widely-spaced eyes, a large head circumference, and premature dentition.

    3. HMGA2 is a chromatin-associated protein

      HMGA2 is a gene that plays a role in transcribing HMGA proteins. These proteins are associated with chromatin, the substance that makes up chromosomes and can consist of DNA, RNA, and proteins.

      Pfannkuche and colleagues (2009) found that HMGA2 is an important factor in embryonic stem cells and seems to magnify other factors, such as the regulation of body height in humans, the repression of certain genes, and several other functions.

    4. exhibits severe growth retardation (17)

      Zhou (1995) found that, in mice, mutant alleles sometimes arise from deleted DNA or from chromosomal inversions. When these mutations cause the protein Hmgi-c to inactivate and not be expressed in mice, the result in dwarfism. This protein is associated with the HMGA2 gene.

    5. This tree was almost identical to our previous tree (15).

      The previous tree from Lamichhaney and colleagues in 2015 showed that the initial split between warbler finches and other finches happened 900,000 years ago. Rapid divergence of ground and tree finches occurred 100,000 - 300,000 years ago.

      Hybridization in finches has influenced the evolution of beak shape. Using phylogenetic studies along with genomic data allowed researchers to reveal some of the genetic variation that underlies finch beak diversity.

    6. only one regulatory gene, ALX1, is known and it regulates variation in beak shape (15), which was not associated with survival in 2004–2005.

      Lamichhaney et al. (2015) previously scanned the genomes of finch populations that were related but displayed different beak structures. They found that the ALX1 gene as a strong candidate for regulating the variation in beak morphology. ALX1 encodes a protein that is vital in developing structures from embryonic tissue that will form craniofacial structures.

    7. Furthermore, although some signaling molecules affecting beak dimensions in Darwin’s finches have been identified (14)

      Abzhanov and colleagues (2004) analyzed various growth factors that were known to be expressed during craniofacial development of birds. When looking at Darwin's finch species, some factors showed simply showed no correlation while other factors showed a correlation with beak size, but not beak shape. However, researchers did find that the expression of the Bmp4 molecule had strong association with both beak size and shape.

    8. Thus, body size was possibly subject to selection, but beak size was a more important factor affecting the probability of survival independent of body size (11, 12). However, the genetic basis of the selected traits remains unknown.

      Grant and Grant (1994) explored hybridization among finch species over 17 years. They concluded that hybrid traits were morphologically intermediate, which indicated the parent genes contributed to the offspring phenotype equally. Hybrids also varied more phenotypically.

      Even though both were heritable, beak size seemed to be more important that body size because the beak's relationship to being able to obtain food.

    9. Beak sizes diverged as a result of a selective disadvantage to medium ground finches with large beaks when food availability declined through competition with large ground finches during a severe drought in 2004–2005 (11).

      Grant and Grant (2006) reported that the finch species Geospiza fortis diverged in beak size from one of its competitors, G. maguirostris. This divergence happened on an isolated Galapagos island 22 years after G. maguirostris arrived to share a habitat with G. fortis.

    10. However, it has been difficult to obtain unequivocal evidence for ecological character displacement in nature (8, 9).

      Stuart and Losos (2013) found that just over 6% of the cases they reviewed that highlighted character displacement actually showed strong examples. However, one study not only documented ecological character displacement, but also showed it happening in real time. This was the long-term experiment of Darwin's finches by Grant and Grant (2006).

    11. Darwin proposed this as the principle of character divergence [now known as ecological character displacement (3, 4)], a process invoked as an important mechanism in the assembly of complex ecological communities (5, 6).

      Darwin states in The Origin of Species that the differences between species is caused by divergence. It is this divergence that acts to minimize the competitive interactions between similar populations.

      Brown and Wilson (1956) later argued that this concept (they called it character displacement) was a common part of geographical speciation. They explained that displacement happened most often as a product of genetic and ecological interaction when species first met.

    1. 23

      Cohen and colleagues tested whether a simple intervention could reduce the effects of stereotype threat for African American students.

      They found that having students complete a short writing exercise, in which they wrote about a value they found important (values affirmation), reduced the gap in performance between African American students and other students.

    1. By contrast, the architecture and stability of novel interaction networks across spatial scales and how they compare to native-dominated communities remain virtually unknown. This knowledge gap hampers our ability to forecast and mitigate the impacts of extinctions and invasions on ecosystem functions

      The authors note that research in the field has been limited to interactions between local species, neglecting the networks involving new, introduced species. Understanding the latter point will aid in efforts combating negative effects on ecosystems.

    2. Previous studies have focused on native-dominated communities in which few or no invasive species occur and mutualistic partners have interacted for prolonged periods of time, developing complex and often coevolved interactions (8, 9).

      Bascompte, Jordano, ant Olsen investigated coevolutionary interactions across a wide range of locations, measuring specifically the degree of dependence in various animal-plant mutualistic networks (i.e. the dependence of a plant species on an animal species, and the dependence of that same animal species on the plant species). They showed that most interactions are asymmetric- meaning that one species depends more heavily on the relationship than the other. This asymmetry supports the growing diversity and coexistence of multiple species in an ecosystem.

    1. the REPAIR system directly deaminates target adenosines to inosines and does not rely on endogenous repair pathways to generate desired editing outcomes.

      This is an advantage over the traditional CRISPR/Cas9-mediated genome editing. CRISPR/Cas9 uses the cell's machinery to make changes, so it is efficient only in actively dividing cells.

      Moreover, we can compare the REPAIR system to DNA cytidine base-editors (BE). The BE system has been modified to prevent cellular DNA repair processes that are triggered by Uracil (U) bases in DNA. The BE system, in any form, still relies on DNA repair machinery to propagate the edit. RNA editing does not. 

      Check out the schematic below for more information on the BE editing paths.

    2. Delivering the REPAIRv1 system to diseased cells is a prerequisite for therapeutic use, and we therefore sought to design REPAIRv1 constructs that could be packaged into therapeutically relevant viral vectors

      There are two main approaches for the inserting of exogenous genetic material into cells: non-viral and viral.

      Non-viral techniques such as transfection with DNA-liposomes can be used for almost any construct, and are relatively easy to use. Some therapeutic companies are looking at lipid nanoparticles for ribonucleoprotein (RNP) delivery to the liver. The authors of the paper used liposome transfection in all of the preceding experiments they describe here. However, this method is inappropriate for in vivo (live) delivery because of its non-specificity and high toxicity.

      An alternative approach is to use viral delivery. This strategy utilizes the natural ability of viruses to infect cells and integrate viral DNA into cellular DNA. A part of the viral genome is replaced with a desired sequence, and then cells are infected with the modified virus. When viruses insert their DNA into the cellular DNA, the desired sequence is added. Viruses are very specific and use only certain molecules to enter the cell, so this method is useful for controlling the type of cell that receives exogenous DNA. However, precautions must be taken to make sure the virus does not go out of control and that the cell's immune response does not destroy the virus before it delivers the DNA.

    3. protospacer flanking sites (PFSs)

      The group that described targeting preferences of Cas13 suggested that PFS should be used for Cas13 instead of PAM, since PAM is used for Cas9. Additionally, PFS is different than the PAM because the PAM is used for discriminating self from non-self sequences. The PFS is not used for that as there is no concern for self targeting when targeting RNA molecules. Therefore, the PFS is just some sequence preference of Cas13.

    4. hydrolytic deamination of adenosine to inosine, a nucleobase that is functionally equivalent to guanosine in translation and splicing

      ADAR enzymes bind to adenosine and convert them to inosine by deamination, or the removal of an amino group from the molecule. In RNA, inosine is structurally similar to guanine (G), so it can form a base pair with cytidine (C). ![] (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2953425/bin/nihms234588f1.jpg)

      Source: Nishikura, K. (2010). Functions and Regulation of RNA Editing by ADAR Deaminases. Annual Review of Biochemistry 79, 321–349. http://doi.org/10.1146/annurev-biochem-060208-105251

    5. We recently reported that Cas13a enzymes can be adapted as tools for nucleic acid detection (14)

      The authors developed a technique called SHERLOCK (Specific High-Sensitivity Enzymatic Reporter UnLOCKing) and successfully used it to detect Zika and dengue virus RNA, pathogenic bacterial DNA, and mutations in human DNA. 

      Both RNA and DNA molecules can be used as a starting material. First, they are converted to DNA and amplified by in vitro transcription into RNA. Next, Cas13 finds target RNA sequences and emits a signal that researchers use to detect the presence of certain RNA molecules.

      See the creators of SHERLOCK talk about how it works and potential applications in this video.

    1. Consistent with the prediction of Mo et al. (25), we found that the friction force depends linearly on the number of atoms that chemically interact across the contact

      The application of macroscopic laws of friction to the nanoscale region remained controversial. Mo and his team used molecular dynamics simulations to study friction laws in dry nanoscale contacts. They have investigated the effect of the number of atoms in chemical contact in friction and reported on the relationship between contact area and friction force in the nanoregime.

  7. Apr 2019
    1. In particular, MOF-801 is suitable for regions where RH is merely 20% (e.g., North Africa),

      MOF-801 was selected for this study because it adsorbs a large amount of water even when a small amount of water is present in the atmosphere, as is often the case in arid regions such as deserts.

    2. The amount of water that can be harvested with MOFs can be much greater than with dew-harvesting systems, which become impractical at RHs less than 50%

      To date, the existing systems for water-harvesting cannot be efficiently used in environments with low relative humidity levels.

    3. e.g., zeolites and silica gels)

      Zeolites and silica gels are minerals made mainly of aluminum and silica. They also have porous structures which allow them to trap molecules within their cavities. This property makes them useful as adsorbants for molecules such as water.

    4. Porous materials, such as zeolites, silica gels, and MOFs, can harvest water from air by adsorption over a wide range of humidity values

      It has been found that a variety of porous materials can trap water from air in small cavities within its structures. This capacity is dependent on the material. For the water harvesting process to be practically usable, the material needs to be able to absorb a large amount of water even when only a small concentration of water is present in the atmosphere (low relative humidity).

    5. dewing (3–6) from moist air and fog capture

      There has been a lot of interest in developing a system capable of harvesting water from air and fog. However, systems developed so far either require a very large amount of water in the air (high humidity), which is not suitable for dry regions, or need a large amount of energy to allow condensation of the water. These systems are therefore neither usable in dry conditions nor economically viable. In the "Related Content" tab, check out a response the paper authors wrote that addresses these issues.

    1. In recent studies at the nano- and macroscale, graphene has shown a potential to substantially lower friction (16–18) and wear (19–21) under specific conditions

      Materials with perfect atomic structures and long periodicity are traditionally sought for superlubricity. Carbon compounds such as carbon nanotubes, graphite, and graphene are investigated for this purpose. One concern is the difficulty in attaining sustainable superlubricity at the engineering scale.

    1. Intergovernmental Program on Climate Change

      The Intergovernmental Panel on Climate Change (IPCC) is the leading international body for the assessment of climate change. The IPCC reviews and assesses the most recent scientific, technical, and socioeconomic information relevant to the understanding of climate change.

      This study utilized the 1995 IPCC report. Updated versions come out every few years, with the 5th and most recent IPCC report published in 2014.

      For more information about the IPCC, visit:

      https://www.ipcc.ch/index.htm

    2. NAO may in fact be part of a hemispheric mode of sea-level pressure termed the Arctic Oscillation

      Thompson and Wallace did not directly state that the North Atlantic Oscillation (NAO) may be part of the Arctic Oscillation (AO), but they did mention that these oscillations share many similar characteristics.

      Thompson and Wallace found that changes in wintertime sea level pressures above the high northern latitudes of Europe and Asia was part of an AO, distinct from the NAO. The AO "resembles the NAO in many respects; but its primary center of action covers more of the Arctic." This means that there are aspects of the climate features which can distinguish between these two climate phenomenon.

    3. Reynolds sea surface temperature analyses

      Reynolds helped develop a method for converting satellite data into accurate temperature measurements. One of the problems with satellite data is that it has to be corrected for anomalies such as dust and aerosols, which can make satellite measurements slightly different from reality. It is possible to get usable temperature data from satellites by accounting for this and correcting the data.

    4. Dicksonet al. (23) have related the renewal of convection in the Labrador Sea to the North Atlantic Oscillation (NAO)

      Dickenson et al. analyzed North Atlantic water temperatures and proposed a theory that the variability in deep ocean mixing is related to the regional climate pattern (the North Atlantic Oscillation).

      The restart of deep water mixing in the Labrador Sea just southwest of Greenland coincides with a change in phase of the North Atlantic Oscillation. This study notes that climate has a strong impact on the extent of deep water formation (convection) in the North Atlantic Ocean.

    5. temperature time series (1) for the past 100 years

      There are also time series records of land temperatures. For the last 100 years, many countries have recorded increasing temperatures.

      To learn more, check out this Carbon Brief video created by Antti Lipponen: https://www.youtube.com/watch?v=-yIHxOui9nQ

    6. frequently begin integration with a sudden increase of atmospheric carbon dioxide

      There are many assumptions that go into creating global climate models. This is because these models must simulate complex interactions between the atmosphere, oceans, land surface, ice, and the sun.

      However, as information from real-world sources such as satellites and other measurements accumulates, climate models are constantly refined to increase their power, usefulness, and accuracy. Improved climate models that have been released since this paper was published have made the concern about a sudden increase in atmospheric carbon dioxide less of an issue.

      For more about climate models visit Skeptical Science: https://www.skepticalscience.com/climate-models-basic.htm

    7. planetary radiative disequilibrium of about 0.5 to 0.7 W m−2 existed for the period 1979 to 1996

      Hansen et al. discovered that, between 1979 and 1996,Earth received somewhere between 0.5 to 0.7W/m<sup>2</sup> of extra energy. As energy can not be created nor destroyed, this extra incoming energy remains in the Earth system and contributes to climate change. 

    8. deep convective processes that occur in the North Atlantic

      Warm, salty seawater from the mid-latitudes is transported northward by the Gulf Stream. Once it reaches the higher latitudes near the Labrador Sea, cold air temperatures chill the seawater. This salty, cold seawater is denser than warmer waters, so it sinks and becomes the formation zone for North Atlantic deep water.  

      This density-driven process of deep ocean circulation is sometimes referred to as Thermohaline Circulation. "Thermo" refers to temperature and "haline" refers to how much salt the water contains. Both temperature and salinity are key components in determining density.

      The North Atlantic is one of the few regions in the world where deep water formation occurs.

    9. tongue of temperature associated with the Mediterranean Outflow.

      The waters of the Mediterranean are extremely warm and have high levels of evaporation, causing the sea to be very salty. While Mediterranean waters are typically warmer than in the Atlantic Ocean, the high salinity causes Mediterranean waters to be slightly more dense than surface waters of the Atlantic. Because of this, water that exits the Mediterranean into the Atlantic sinks and flows out into the Atlantic at roughly 1000 m depths.

      For more information about the Mediterranean Outflow and to see real Argo float depth profiles visit: http://www.euroargo-edu.org/floatdata.php?float=6901631

    10. Equator as a boundary

      Because the Earth is a spinning sphere, certain wind and ocean currents have formed that make it useful to think of the Equator as a boundary between North and South Pacific waters.

      To learn more about how ocean currents are driven by wind, water density differences, and tides, watch this video from the National Oceanographic and Atmospheric Administration (NOAA): https://oceanservice.noaa.gov/facts/current.html

    11. heat is transported from the tropics to the poles

      The ocean is a major carrier of heat. As warm surface currents move towards the poles, they slowly release heat. Once cold and dense enough in the high latitudes, this water sinks and the deep ocean currents carry cold waters to lower latitudes.

      Figure from Thompson and Seiber (2011, IJBC).

    12. transport of heat from the tropics to the poles is required for the Earth system to be in global radiative balance

      Due to Earth's tilt, the tropics receive more incoming solar radiation than the poles do, so there is excess warming in the lower latitudes. Wind and ocean currents carry this heat towards the higher latitudes.

      This figure shows the balance between average net incoming solar radiation (shortwave) and the heat emitted by earth (longwave radiation) from 90° North to 90° South.

      Read more about earth's energy balance here: http://www.physicalgeography.net/fundamentals/7j.html

    1. This, together with the results from Fig. 1B, suggested that although not discrete, enterotypes do indeed represent “densely populated areas in a multidimensional space of community composition,” as stated in the original publication

      The authors of this paper agree with Bork and colleagues' original proposition that enterotypes are "densely populated areas in a multidimensional space of community composition." However, they argue that these enterotypes are not discrete but rather overlapping microbial configurations.

    2. Years of disease-targeted microbiome research have generated an extensive inventory of bacterial genera with a reported association with one or more pathologies.

      There is a huge variety of diseases associated with bacteria. The connections between bacteria and pathologies are only beginning to be uncovered, in part due to research into the microbiome.

      To get an overview of the types of diseases caused by bacteria, check out this resource from the University of Utah: https://learn.genetics.utah.edu/content/microbiome/disease/

    3. dietary information (including fiber uptake, bread preference, and fruit consumption

      O'Toole and colleagues found that changes in the gut microbiome composition were associated with chronic conditions like obesity and inflammation. They were able to show that these changes were partially driven by diet in aging populations.

    4. other U.K. and U.S. studies

      Gordon and colleagues conducted a similar gut microbiome study in 2012 but focused on how they differed across populations, comparing healthy individuals from Venezuela, Malawi, and the United States.

    5. Here, we analyzed two independent, extensively phenotyped cohorts: the Belgian Flemish Gut Flora Project (FGFP; discovery cohort; N = 1106) and the Dutch LifeLines-DEEP study (LLDeep; replication; N = 1135). Integration with global data sets (N combined = 3948) revealed a 14-genera core microbiota

      The Human Microbiome Project launched by the U.S. National Institutes of Health was one of the first initiatives to research the impact of our microbiomes on human health and disease. This was one of the first large scale projects based on 16S rRNA sequencing and has become the basis of important database systems for current metagenomic studies. The goal of this study was to establish a core human microbiome in healthy individuals and observe how it changes during different disease states.

      The FGFP and the LLDeep projects share similar sequencing approaches and goals to the Human Genome Project, with a distinct focus on the gut microbiome and its links to lifestyle and health.

    1. Twenty different kinds of amino acid are commonly found in protein, and four main kinds of base occur in nucleic acid.

      See the supplemental figure below.

  8. Mar 2019
    1. surrogate experiment, for example with finch models and/or playback of tape-recorded song (27)

      Grant et al. did the experiment described here with a population of G. difficilis on Isla Genovesa.

      They played tape recorded songs from several G. difficilis populations (Isla Genovesa, Isla Wolf, and Isla Darwin) and demonstrated that the finches responded strongly to their own population's song, weakly to the Isla Darwin population's song, and not at all to the Isla Wolf population's song.

    2. HMGA2 and ALX1, two closely linked loci (7 Mb apart) previously shown to be associated with variation in bill morphology in Darwin’s finches (15, 26)

      Lamichhaney and colleagues (2015) searched genomes of closely related species that had different beak sizes and identified ALX1, a homeobox gene that controls development in the face and neck, and correlates well with differences in beak shape.

      Lamichhaney and colleagues (2016) analyzed finches whose beak sizes changed during a drought and identified HMGA2, a nearby gene locus also related to beak size.

    3. until recently

      In 2010, Grant and Grant analyzed genetic data to search for the effect of breeding with immigrant birds (reference 16). They used genetic studies to quantify the effect of genes from the same species (from populations on other islands) compared to different species.

    4. finch species imprint on features of their parents early in life

      Grant and Grant developed this idea based on observations of mating pairs, as well as experiments. In some experiments they played recorded songs for birds: These songs were the same or different species and scientists recorded their responses. Other experiments involved presenting birds with a stuffed specimen of the same or different species, and recording their response.

    5. The ability of finches to efficiently exploit the large woody fruits of Tribulus cistoides in dry seasons, and particularly during droughts and limited food supply, is a function of bill size, especially bill depth (12)

      By measuring and studying bill size, and recording bird mortality on Daphne Major during a drought that occurred in 2004-2005, scientists were able to establish the characteristics of bills that were adaptive during this period of decreased food supply.

      The plant species mentioned is a food supply for the Big Bird lineage, so this data on bill morphology is relevant to understanding this hybrid population.

    6. homoploid hybrid speciation, is rare

      This type of speciation could be rare, but as it is also hard to detect, it may be less rare than currently estimated.

    7. the chance occurrence of strong selection against large bill size in a competitor species, G. fortis, in 2004-05 (12, 26)

      In 2004-2005 a severe drought caused competition between two species of finch on the island Daphne Major. The medium ground finch (G. fortis) and large ground finch were in competition for decreased food sources. Because medium ground finches with large beaks were at a disadvantage, the size of beaks for these finches decreased as a result of this selection pressure.

      This natural experiment was studied by Lamichhaney and colleagues (2016) and by Grant and colleagues (2014).

    8. due to large bill and body size, and a distinctive song (12)

      In "40 Years of Evolution" (reference 12) Grant and Grant devote an entire chapter to the analysis of this possible new hybrid species that support these conclusions about bill and body size, as well as song.

      Their analysis includes extensive pedigrees, song analysis data, and data about beak depth and width, and data on heterozygosity.

      The current paper explores the beak morphology and genetic data more closely to contribute to the understanding of the hybrid lineage success and reproductive isolation.

    9. An immature male finch immigrated to the small Galápagos Island of Daphne Major (0.34 km2) in 1981 (11–13).

      Rosemary and Peter Grant have led the study of the bird species of the Galapagos Islands since the 1970s. Individual birds on the island have been banded and described, so vagrants such as the one identified can be identified when they arrive.

    10. stringent criteria

      Schumer and colleagues present three criteria: 1) demonstration of a mechanism of reproductive isolation, 2) evidence of hybridization (preferably genetic and based on whole genome evidence), and 3) hybridization-derived isolation (establishing that the hybridization led to the reproductive isolation, and not some other factor).

    11. Hybrid speciation without chromosomal doubling

      Hybrid speciation in plants that includes increasing the chromosome number is known to occur.

    1. light-power density sufficient to drive physiologically significant microbial opsin currents

      Adamantidis et al., previously showed that a light power intensity of 1mW/mm2 was necessary to drive the action of microbial opsin currents in hypocretin-producing neurons within the lateral hypothalamus .

    2. this would be consistent with recent findings (33) indicating that a glial-derived factor (adenosine) accumulates during DBS and plays a role in DBS-mediated attenuation of thalamic tremor.

      In 2008, Bekar et al., demonstrated that the adenosine triphosphate (ATP) byproduct, adenosine, accumulated following deep brain stimulation. Adenosine would then activate adenosine A1 receptors which in turn depressed excitatory transmission in the thalamus and reduced tremors.

    1. Depolarizing stimuli elicited noradrenergic expression, whereas factors derived from nonneuronal cells evoked cholinergicity

      Neurons in the dish were exposed to electrical activity that can cause depolarization of membrane. It is shown that these neurons are noradrenergic while the non-neuronal cells show an expression of acetylcholine.

    1. potential niche differentiation within the colon ecosystem

      Different species may coexist in the colon differently to reduce competition and extinction in either species as several components (nutrients) will be differentially available throughout the colon with changing transit time.

    2. Early-life events such as birth mode were not reflected in adult microbiota composition.

      Researchers, like Bokulich and colleagues, had previously demonstrated that birth mode (i.e., vaginal, caesarian) affected the gut microbiome in adults. This study was not able to demonstrate that these differences were still present later in life.

    3. Sequencing-based assessment of microbial communities in human fecal material has linked alterations in gut microbiota composition to disease, as well as chronically suboptimal health and well-being

      Microbiome assessments can have different goals. The U.S. National Institutes of Health Human Microbiome Project (HMP) aimed to characterize the microbial communities from 300 healthy individuals across different sites on the human body; whereas, the Flemish Glut Flora Project (FGFP) targeted a general sample of the population.

      Read more: https://commonfund.nih.gov/hmp

    4. Ruminococcaceae, Bacteroides, and Prevotella; all previously proposed as enterotype identifiers

      Bork and colleagues proposed that humans have three different gut types based on the most abundant bacterial taxa. The types of bacteria present are independent of an individual's age, sex, or nationality but they found some correlation between some characteristics and bacterial function. For example, the abundance of Bacteroides, which break down carbohydrates, was found to increase with age.

  9. Feb 2019
    1. autonomous vehicles (AVs) such as Google’s self-driving car covered thousands of miles

      In October 2010, Google announced that its self-driving vehicles had collectively driven more than 200,000 kilometers (about 124,000 miles) on actual roads in California.

    2. autonomous driving in realistic urban environments

      In 2007, the Defense Advanced Research Projects Agency (DARPA) hosted the DARPA Urban Challenge, which called for self-driving vehicles that could navigate a realistic city environment, and obey traffic rules while doing so.

      The requirements for the challenge included passing slowly moving cars, merging into fast traffic, and parking in a parking lot.

    1. tickling-evoked vocalizations

      Researchers have developed a new set of software that decodes ultrasonic rat vocalizations, including those that come from tickling!

      Check it out with this video from Verge Science.

    1. This fits in very well with the experimental evidence, most clearly shown in the work of Dintzis (4), that the amino acids are assembled into the polypeptide chain in a linear order, starting at the amino end of the chain

      Dintzis and Naughton demonstrated that a protein is synthesized from one end of the amino acid chain to the other, like stringing beads on a necklace one by one.

    1. Improve science literacy with Science in the Classroom!

      If you are interested in science communication, annotation, or just passionate about connecting students to #ActualLivingScientists, come see us!

    1. imperfect copying of a Daphne finch by the founder after it had first learned its father’s song on Española (or Gardner) (13)

      This phenomenon has been observed on Daphne Major in several cases. It is a possible factor in causing hybridization events.

    2. in laboratory populations of animals (21)

      Bolsted and colleagues describe how they changed the allometric relationship of wing size to body size in Drosophila melanogaster through artificial selection.

      This shows that selection can change allometric relationships, and support the authors' suggestion that natural selection is the cause of the changes in allometric relationship between bill size and body size in the Big Bird population.

  10. Jan 2019
    1. ethanol consumption

      There is a naturally occurring variability in rats' urge to consume alcohol that is correlated with the levels of NPY in their brain. In mice, artificially increasing the amount of NPY in the brain leads to higher consumption of alcohol and reduced sensitivity to the intoxicating effects of alcohol (as well as vice versa). This is very similar to what has also been shown in flies (see reference in previous paragraph).

    2. sexual motivation

      Injection of NPY into specific parts of the mouse brain can trigger intense eating or inhibit sexual drive.

    3. ethanol

      When the activity of the NPF circuit is reduced below normal, flies are less sensitive to the intoxicating effects of alcohol (i.e. they exhibited fewer signs of "drunkenness"). The vice versa has also been observed to be true.

    4. Flies exhibit complex addiction-like behaviors, including a lasting attraction for a cue that predicts ethanol intoxication (4) and a preference for consuming ethanol-containing food, even if made unpalatable (5).

      The authors will argue in this paper that they have discovered an explanation for how addictive substances/experiences can affect a fly's behavior and neurobiology. Understanding the effect of reward on an organism is important because it can lead to a better understanding of addiction (which can be seen as an abnormal response to a rewarding substance).

      The rewards the authors use here are mating (sex) and ethanol (alcohol). The authors cite previous research to show that flies find alcohol to be rewarding and that they demonstrate addictionlike behaviors in pursuit of alcohol. These distinctions are important to demonstrate the similarities between fly and human responses to alcohol. They then build upon this previous research for their own experiments.

    1. Cas13 has no targeting sequence constraints

      An important advantage of Cas13 over Cas9 is that it does not have a PAM or PFS that is required for it to target a specific site. To expand the number of sequences that Cas9 can target, researchers must use Cas9 proteins from different species (which have different associated PAM sequences). This can complicate the development and testing of gene editing systems that use Cas9.

    2. the exact target site can be encoded in the guide by placing a cytidine within the guide

      In terms of precision, i.e., on-target editing, we can compare REPAIR to other base editors.

      For instance, cytidine editors contain the cytidine deaminase APOBEC1 and convert C-G pairs to A-T pairs. The activity of APOBEC1, directed by Cas9, is not restricted to only one C but extends for several bases away from the PAM sequence. Recent work has demonstrated that the editing window of APOBEC may be reduced to 1-2 nucleotides by modifying of the deaminase.

      Similarly, the precision of ADAR2 may be increased by placing a C across from the target A, creating a mismatch that is ideal for ADAR2 editing.

    3. Although it is possible that ADAR could deaminate adenosine bases on the DNA strand in RNA-DNA heteroduplexes

      The authors of the paper looked at the crystal structure of the ADAR deaminase with the RNA duplex and predicted that ADAR might also operate on RNA-DNA duplexes. Later, they experimentally confirmed this prediction.

    4. We hypothesized that Cas13 activity could be affected by subcellular localization, as we previously reported for optimization of LwaCas13a

      The RNA molecule is transcribed in the nucleus and then exported to the cytoplasm. It can be recognized and cleaved by Cas13 at any moment along this way.

      Previously, the authors used nuclear localization sequences (NLS) and nuclear export sequences (NES) to determine at what point during the transcription and export process Cas13 is most efficient. They tested knockdown efficiency of LwaCas13a with either NLS or NES tags.

      They found that constructs with a nuclear localization sequence (NLS) were most efficient. However, this observation cannot be generalized to all Cas13 orthologs, which must be tested individually.

    5. We introduced a mismatched cytidine opposite the target adenosine, which has been previously reported to increase deamination frequency,

      Previous work has shown that ADAR works better when an RNA molecule contains a mismatch at a target site. This may be because it makes it easier for the deaminase to flip the target base, which has to happen for editing. Panel B shows what base flipping looks like: Zheng, Y., Lorenzo, C., & Beal, P. A. (2017). DNA editing in DNA/RNA hybrids by adenosine deaminases that act on RNA. Nucleic Acids Research, 45(6), 3369–3377. http://doi.org/10.1093/nar/gkx050

    6. containing hyperactivating mutations in order to enhance catalytic activity [ADAR1DD(E1008Q) (27) or ADAR2DD(E488Q)] (21)

      Previously, ADAR2 was randomly mutated, and protein variants with improved activity were selected. The protein with a substitution at the 488 position showed the highest activity.

      Later, another group tried the same thing with ADAR1. The group compared protein sequences and found the corresponding amino acid position on ADAR1 and performed the same substitution, which resulted in the same increase in activity. See the image below for a comparison of ADAR1 and ADAR2:

      Tomaselli, S., Bonamassa, B., Alisi, A., Nobili, V., Locatelli, F., & Gallo, A. (2013). ADAR Enzyme and miRNA Story: A Nucleotide that Can Make the Difference. International Journal of Molecular Sciences, 14(11), 22796–22816. http://doi.org/10.3390/ijms141122796

    7. We sought to identify a more robust RNA-targeting CRISPR system by characterizing a genetically diverse set of Cas13 family members

      Previously, the authors tested 15 orthologs of the Cas13a nuclease for their ability to knock down RNA. In this study, they expanded their search to other members of the Cas13 family, including a, b, and c variants.

    8. ADAR1 and ADAR2

      In addition to the functional ADAR1 and ADAR2 enzymes, there is a catalytically inactive ADAR3 enzyme in the human genome. Although it cannot deaminate RNA, ADAR3 might still regulate gene expression, for example by inhibiting its two functional homologs (ADAR1 and ADAR2).

    1. transient expression of transmitter traits is not restricted to gut cells, but also occurs in cranial nerve ganglia of the embryonic rat

      Similar to the gut cells, the nerve ganglia of the rat also show transient expression of catecholamine during development.

    2. These traits are detectable on embryonic day 11.5 (E-11.5) but have disappeared by E-14.5. However, the specific, high-affinity uptake system for norepinephrine selectively appears in these cells at E-12.5 and persists (8), permitting cellular identification after loss of other endogenous characters

      This study focused on the neurotransmitter expression changes in the embryonic stages of development. At embryonic day 11.5, the neurons express the attributes of noradrenergic cells. However, these traits are lost by embryonic day 14.5. The uptake system for norepinephrine remains intact in these neurons.

    1. assigned to one of four major well-supported haplogroups (groups A to D)

      Scientists studied the mitochondrial DNA of 654 domestic dogs and 38 wolves, and were able to separate the dogs into four main clades (A, B, C, D), groups that contain an ancestor and all of its descendants. A fifth clade, E, was a very small, isolated group.

    2. Russian wolves (18)

      A 2013 study used whole genome sequencing to trace the ancestry of Chinese native dogs. They compared the DNA of four gray wolves—three from different parts of Russia, one Chinese—three native Chinese dogs (dogs present in China for a very long time), and three dogs considered very diverse from each other; a German Shepard, Belgian Malinois, and Tibetan Mastiff.

      They suggest a Southeastern Asia origin for dogs, and domestication of Chinese indigenous dogs occurred 32,000 years ago.

    3. This breed, created in the 1930s in the Netherlands, involved breeding German Shepherds with captive wolves

      The Sarloos breed was created by Leendert Saarloos, in an attempt to create a superior police dog. He bred a male German Shepard and a female wolf. Despite the efforts of Mr. Saarloos, the dog was never a successful police dog and was not formally recognized as a new breed.

    4. occurred in Europe (7), Central Asia (8), or East Asia (9)

      Wang et al. studied the genomes of 12 gray wolves, 27 ancient dog breeds, and 19 diverse dog breeds from all over the world. They discovered that dogs from Southeast Asia have higher genetic diversity and their DNA is less mixed, meaning that they are the most related to wolves; they estimate that domestication occurred there 33,000 years ago. Dogs were isolated to this region for several thousand years, and about 15,000 years ago they migrated to other parts of the world.

    5. most genetic studies have concluded that dogs were probably domesticated just once

      Scientists studied DNA from wolves (one each from East Asia, the Middle East, and Europe—all regions where domestication had potentially occurred) and two ancient dog breeds. A third group, the golden jackal, was included as a comparison. The scientists found that none of the wolves were more closely related to dogs than the other, which suggested that dogs were not domesticated separately in the three different areas. The scientists thus concluded that domestication must have happened just once.

    6. Dogs were the first domestic animal and the only animal domesticated before the advent of settled agriculture

      Dogs were tamed from wild animals (wolves) long before—several thousand years before—any other domestic animal (e.g. pigs), and before farming practices began, according to the archaeological record. Some studies estimate that farming practices and farm animal domestication started place 9000-12,000 years ago, and dog domestication took place at least 15,000 years ago.

      Check out this 2018 paper on the spread of dogs alongside farming in Europe. Find the full PDF in the "Related content" tab.

  11. Dec 2018
    1. The regulatory role of DNA methylation during environmental responses was previously investigated in marine invertebrates, linking modifications in methylation of stress-responsive genes with phenotypic plasticity and adaptation (Gavery and Roberts, 2010)

      Previously, a link has been discovered between the methylation of genes undergoing stress, and the ability of one genotype to produce more than one phenotype in order to adapt to its environment.

    2. Different epigenetic mechanisms participate in environmental responses, including histone variants encompassing highly specialized functions (Talbert and Henikoff, 2014).

      As described by past research of Talbert and Heinkoff, they're are a variety of epigentic mechanisms that are influenced by different amounts of stress drawn by the environment. One of these are the now testing of the recently discovered histone variants and and how each histone respond to environmental stress such as toxins.

    3. (Radwan and Ramsdell, 2008; Murrell and Gibson, 2009, 2011)

      Multiple research studies previously conducted show that brevetoxins are produced during FRT's.

    4. as illustrated by recent studies examining the role of DNA methylation in the Pacific oyster

      Gavery and Roberts view the oyster as one of the best ways to speculate and monitor the progress of DNA methylation. They used this oyster model to view how the toxins can influence the rate of methylation and how stress affects epigentics factors.

    5. Furthermore, brevetoxins convey critical disruptive effects at the most fundamental level, as they can induce DNA damage and apoptosis

      Toxins are known to disrupt cell actions. The scientists expand on this idea by using the experimental model of an oyster because oysters can be used to determine epigenetic modifications passed down through generations, ultimately showing red tide effects.

    6. genotoxic effect of brevetoxins

      Yimizu, Chou, and Bando initially studied the structure of brevetoxin, and deemed it the most potent toxin found in Florida Red Tide.

    7. H2A.X, H2A.Z and macroH2A

      González-Romero has previously conducted research on the stability and function of the H2A protein, concluding that it participates in the unfolding of chromatin fibers and therefore modifying enzymes and polymerases that facilitate gene expression.

    1. For instance, datasets resulting fromphenological studies can be organized as a seed collection calendar, supporting restoration efforts or ex situ genetic conservation (e.g. Packard et al., 2005). Also, those data sets make an invaluable contribution for initiatives such as the Kew's Millennium Seed Bank, aiming to harbour the germplasm of up to 25% of the world's plant diversity (Ali and Trivedi, 2011).

      Understanding the life cycle of plants helps us understand part of the world's plant diversity. This shows how phenology can make contributions to conservation biology.

    2. This has been the case of Ibity New Protected Area (NPA) in Madagascar. Phenology observations showed that high fire frequency reduce flower and fruit production of tapia woodlands (Alvarado et al., 2014), indicating the limited potential for natural regeneration of the vegetation (Alvarado et al., 2015). Phenological information has been used to improve the management actions for the Ibity NPA, and is considered as an important issue for the successful implementation of an integrated conservation strategy, targeting restoration of plant communities and reintroduction of threatened plant species.

      Phenology can be used as a tool to aid in management decisions for plant restoration. This is a great example of how phenology can help make contributions to conservation biology. This study looked at a forest that developed under the selective pressure of fire which allowed scientist to study the forests reproductive phenology and how it was effected by the fire. They found that fire effects the timing of plant reproduction at community and landscape levels. This is a great example of how plant phenology can be used as a tool to aid in management decisions for plant restoration. This is a great example of how phenology can help make contributions to conservation biology.

    3. episodic community-wide fruit shortages following an El Niño event greatly elevated mortality of frugivorous and granivorous vertebrates in Barro Colorado Island, Panama (Wright et al., 1999)

      Scientists are trying to gain an understanding on how relationships between plants and insects are affected by the changing climate. This helps us to understand how phenology can be used to study the effects of climate change.

    4. (van der Sleen et al., 2015)

      Van der Sleen and colleagues determined that higher concentrations of atmospheric CO2 (as a result of human activities) increase plant photosynthetic rates and improve plants' water use efficiency. Increased CO2 increases the rate at which carbon can be used by plants as carbohydrates in light-independent reactions. However, photosynthesis rates eventually plateau as a result of another limiting factor (light intensity, temperature, etc).