946 Matching Annotations
  1. Dec 2018
    1. (Radwan and Ramsdell, 2008; Murrell and Gibson, 2009, 2011)

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

    2. 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.

    3. 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.

    4. 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.

    5. 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).

    5. (Chuine and Beaubien, 2001

      Chuine and Beaubien used a process-based model (PHENOFIT) to predict species distribution. This model focuses on survival and reproductive success in relation to climatic variations. They determined that the phenology of plant species as it relates to variations in climate is a major determinant for species distribution. This model could potentially be used to predict the future distribution of plant species and make adjustments to our current practices accordingly.

    6. (Rosenzweig et al., 2008)

      Rosenzweig and colleagues noted that some major changes in phenology can be attributed to climate change. For example, rising oceanic temperatures are known to impact marine and freshwater biological systems in terms of phenology, migration, and community composition in algae, plankton, and fish.

    1. strong differences in herbivore assemblages in three widespread species of Ficus: Each tree species had a different dominant lepidopteran herbivore species in the lowlands compared to montane habitats.

      In this study, it was found that a small amount (17%) of the caterpillar (aka Lepidoptera) were found to be feeding on the Ficus in both the highlands and lowlands.

      The study was done on the different species of caterpillar that fed in the highlands, in the lowlands and those that didn't feed on ficus as well. The results showed them which caterpillar species was dominant on the species on ficus in the lowlands and which were dominant on the species of ficus in the montane habitats/ highlands. The ones that were found to be dominant in the lowlands, typically did not feed on the highlands and vise versa.

      A Comparison of Caterpillar (Lepidoptera) Assemblages on Ficus Trees in Papua New Guinea

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

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

    3. A long-standing hypothesis has linked escalation in plant defense that allows escape from insect herbivores to range expansion and speciation (Ehrlich and Raven 1964). Such escalation can include increases in the diversity of defense strategy (novel defense types), increases in the total amount of defense investment, or both (Agrawal et al. 2009). Range expansion, or merely an imperfect match between the distribution of plants and their natural enemies, may confront plants with different herbivore assemblages and/or variation in habitat resources across their range (Thompson 2005, Züst et al. 2012). This variation, in turn, may accelerate the evolution of differing defense strategies across habitats. Alternatively, natural enemies may not be major selective agents driving habitat specialization. In this case, we would predict that there would be few qualitative and quantitative defense differences between habitats, especially when diverging lineages of host plants occur in close proximity and also experience some gene flow across the habitat boundary.

      The main point the author is trying to make here is that there is a direct correlation between increase in plant defense and increase in land covered by plants as well as speciation of plants. He also explains that due to the expansion, rapid evolution of defenses begin to take place. The herbivores eating these plants do differ in tactics from region to region, increasing the amount of different defense strategies in the plants. He explains an alternative viewpoint stating that predators do not influence speciation much, therefore defenses are similar amongst most plants.

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

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

    5. the optimal defense allocation may be affected by differential costs of tissue replacement across habitats

      Herbivorous insects are constantly eating plants, creating competition between the plants and insects. What is stated here is that optimal defense may be impacted by the plants environment, giving it access to certain nutrients and materials needed to produce the desired defense mechanism, such as poisonous leaves or indigestible tissues.


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

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

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

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

    7. Herbivores play an important role in habitat specialization because they can magnify the differences in resource availability across habitats

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

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

    8. Assemblages of insect herbivores were dissimilar between populations of ecotypes from different habitats, as well as from the same habitat 100 km distant.

      In Africa, there is a food crisis leaving millions of people without corn, a very important crop for Africa. The reason for these crops not being edible is that a certain species of worm invaded a field of corn and rapidly spread to neighboring farms, killing millions of corn crops leaving thousands hungry. This proves the point how insects differ from each-other depending on what type of plants are around, since this worm is always flocking to this one crop.

    1. Oberbauer

      National Science Foundation – Ecosystems. Causes and implications of dry season control of tropical wet forest tree growth at very high water levels: direct vs. indirect limitations (CARBONO - VERANO project).

      National Science Foundation – Polar Programs. Arctic Observing Networks: Collaborative Research: Sustaining and amplifying the ITEX AON through automation and increased interdisciplinarity of observations (AON)

      NSF-Arctic Natural Sciences. Collaborative Research; cold-season gas exchange of arctic plants - resolving winter carbon and water balances of Alaskan arctic tundra (Coldseason project).

      NSF -IPY Arctic Observing Networks Study of Arctic ecosystem changes in the IPY using the International Tundra Experiment. (ITEX-IPY)

      DOE-NICCR. Response of carbon dioxide, water, and energy exchange of peat and marl wetlands in the Florida Everglades to changes in hydroperiod (Evergladesflux).

      NSF-Biocomplexity. Biocomplexity Associated with the Response of Tundra Carbon Balance to Warming and Drying Across Multiple Scales. Barrowbiocomplexity (this project has sunsetted). Effects of increased season length on plant phenology, community composition, productivity, and ecosystem carbon fluxes in Alaskan tundra Season project (this project has sunsetted)

      Carbon stockes and fluxes in a tropical rain forest in Costa Rica Carbono project

      NSF- Integrated carbon program. Understanding interannual NEE variability in a tropical rain forest using constrained estimates of carbon exchange. S.F. Oberbauer, D.A. Clark, M. Ryan, D.B. Clark. Carbono-Towers

      National Science Foundation - Biocomplexity of the Environment Coupled Biogeochemical Cycles. Complex interactions among water, nutrients and carbon stocks and fluxes across a natural fertility gradient in tropical rain forest. (CICLOS PROJECT).

    1. the production of which often does not correlate with the lecanoromycete phylogeny

      Researchers had previously noted the presence of secondary metabolites in the lichen cortex. The researchers initially looked for a correlation between the main fungal species (lecanoromycetes) and the production of these secondary metabolites, but could not determine a correlation.

    2. Most macrolichens possess a basic two-layer cortex scheme consisting of conglutinated internal hyphae and a thin, polysaccharide-rich peripheral layer

      Perhaps this is easiest to understand with a picture. If you look closely, you can see two layers within the cortex. Photo from University of California Berkeley's Museum of Paleontology.

    3. between a single fungus, usually an ascomycete, and a photosynthesizing partner

      Several natural scientists in the mid-1800s began to suspect that the lichen was in fact a mixture of two organisms, but it was the Swiss botanist Simon Schwendener who demonstrated that lichens were composed of fungi and algae for the first time in 1869. Initially, he thought the relationship must be antagonistic—that the fungi were “imprisoning” the algae. Ten years later, the German botanist Anton de Bary proposed the idea of mutually beneficial symbiosis for the lichen system.

      Read more about Schwendener's discovery and the controversy it caused here. Find the full PDF in the "Related content" tab.

    4. These two species have been distinguished for 90 years by the thallus-wide production of the toxic substance vulpinic acid in B. tortuosa, causing it to appear yellowish, in contrast to B. fremontii, which is dark brown (11). Recent phylogenetic analyses have failed to detect any fixed sequence differences between the two species

      While these two lichens look very similar, there is an important distinction. There is evidence that Bryoria fremontii has been used and consumed by Indigenous populations for centuries, while Bryoria tortuosa contains a yellowish substance, vulpinic acid, that is toxic to mammals. Indigenous peoples soaked Bryoria collected for food, and it is thought this may have helped rinse background levels of vulpinic acid from mixed samples. Despite this difference between the two lichen species, scientists had been unable to determine a phylogenetic distinction.

      Read more in Scientific American: https://blogs.scientificamerican.com/artful-amoeba/2-lichen-mysteries-solved-reveal-a-greater-hidden-truth/

    1. including larval intake of noxious food

      When the amount of NPF receptor present in the brains of baby fruit flies (still in the larval stage) is artificially increased, these flies become more likely to consume noxious—that is, bitter or unpleasant—food.

    2. system regulates acute ethanol sensitivity in Drosophila

      Past research has shown that interactions between neuropeptide F and its corresponding receptor can alter how much flies are affected by alcohol consumption.

    3. NPY receptor homolog NPR-1 regulates ethanol behaviors

      Past research has shown that individual differences in alcohol tolerance amongst C. elegans are related to natural variations in the amount of neuropeptide Y receptor found in their brains.

    4. In addition, NPF neurons modulate the effect of satiety on sugar reward memory

      We know that memories associated with food (for example where food is located, how good/bad the food is, etc.) are modulated by hunger levels. Typically, flies that are hungrier tend to form more robust food-associated memories, and vice versa. In the study referenced here, the researchers showed that a similar behavior can be elicited using NPF—artificially activating NPF neurons promotes better formation of food-associated memories.

    5. responses to physical stressors

      When the NPF circuit in Drosophila is artificially activated, flies do not seem bothered by stressful things in the environment that under normal conditions would have provoked some sort of avoidance behavior.

    6. a switch in feeding behavior

      Extremely young Drosophila spend the majority of their time eating, whereas older larvae start to engage in behaviors such as moving around and cooperating with fellow larvae. This change in behavior from young to old larvae is correlated with a reduction in the amount of NPF in the brain, suggesting that this molecule regulates feeding behaviors in the fly.

    7. Intriguingly, stressful experiences regulate mammalian NPY levels.

      Past research has also shown that the amount of neuropeptide Y found in a rodent's brain is related to the amount of stress they might experience during their life.

    8. neuropeptide Y [NPY

      A mammalian version of neuropeptide F. This molecule is found in the human brain.

    1. similar to that obtained with an ancient grey wolf genome

      Scientists studied the DNA of a Siberian wolf thought to have lived 35,000 years ago (based on radiocarbon dating). The Siberian wolf's DNA mutated at a rate of 0.45 × 10^−8 per generation, much slower than the previously assumed mutation rate of 1.0 × 10^−8. This meant that wolf-dog divergence must have occurred much longer ago (27,000-40,000 years ago) than previous estimates suggested (11,000-16,000 years ago).

  2. Nov 2018
    1. he null hypothesis should be that individual animal species were domesticated just once

      The majority of research findings up until this point suggested that domestication occurred just once, so this became the most acceptable theory for how domestication occurred. Based on their findings, the authors disagree with the null hypothesis (reject the null hypothesis), and because of this, they go to great lengths to prove their alternative hypothesis.

    2. This migration led to a partial replacement of ancient dog lineages in Europe that were present by at least 15,000 years ago

      Through archaeological evidence, we know that dogs were present in Europe about 15,000 years ago. The fact that the Finnish Spitz is the only European dog breed that kept its basal genetic signature suggests that the original European dogs were mostly replaced.

    1. If the web contained many images, but each image was represented by a low-dimensional vector (e.g., 10 or 20 features), then space-partitioning methods (12) would similarly suffice. However, for large databases with high-dimensional data, neither approach scales

      Effective computer search algorithms need to have the ability to scale in order to handle data sets of different sizes and levels of complexity.

      For example, while a brute-force method would work well if you only had to compare a few images, it becomes slow to the point of being impossible when you want to compare all the images on the internet.

      There are other methods (like the space-partitioning method) that work well for many images, but only if those images are very simple—that is, their feature vectors are very small.

      In order to handle complicated problems like searching high-resolution images on the web, it's therefore extremely important for researchers to find algorithms that can scale to handle both large and complex data sets.

    2. Each KC receives and sums the firing rates from about six randomly selected PNs

      Caron et al. developed a special tracing technique that allowed them to track the connections between KCs and PNs using a glowing, light-activated protein.

      By observing the activity between the two, they found that KCs combine input information from a random combination of PNs. That is, they found no specific pattern or organization that relates the type of odor to the PNs that are activated. In addition, they didn't identify any preferred pathways between groups of PNs and individual KCs.

      To learn more about the glowing, light-activated protein used in this research, check out this annotated resource from Science in the Classroom.

    3. For the PNs, this concentration dependence is removed (7, 8); that is, the distribution of firing rates across the 50 PN types is exponential, with close to the same mean for all odors and all odor concentrations

      In 2016, Stevens determined that PNs in the olfactory circuit use what's called a "maximum entropy code."

      A maximum entropy distribution means that the olfactory circuit can encode the most number of stimuli using a fixed number of neurons. This means that even though the average firing rate of all the PNs will depend on the concentration of a specific odor, the response to all odors is statistically the same.

      In other words, if you took 10 PNs and 10 odors, recorded the firing rate of each of the PNs in response to each of the odors, and created a histogram from the data, that histogram would always look the same—regardless of which 10 neurons and which 10 odors you chose.

    4. only a small fraction of the neurons that receive odor information respond to each odor

      Lin et al. discovered the neurological process that controls why so few olfactory neurons make up each odor "tag."

      The reason is because when the cells that receive odor information, called Kenyon cells (KCs), become active, the anterior paired lateral neuron responds by slowing the activity of the KCs. The more active the KCs become, the harder the anterior paired lateral neuron works to block their activity. The few KCs that are left active after this process form the odor tag.

    1. Involvement of the Y chromosome factor in sex determination in Anopheleswas first supported by the finding of a single, triploid Anopheles culicifaciesmale with the XXY sex chromosomes

      In a mutagenesis experiment in the late 1970's, scientists found and XXY male. This rare finding spurred the thought that is only takes a single Y to become male as long as X dosage can be overcome by other mutations.

    2. embryonic lethality is caused by loss-of-function mutations in genes located at the top of the sex determination cascade and invariably results from a misregulation of dosage compensation

      The female-lethality phenomenon seen in the last experiment has been observed before in fruit flies when upstream genes are misregulated and there is an imbalance of gene products between the sex chromosomes and autosomes.

    3. In the vast majority of protein-coding genes, different evolutionary constraints on individual codon positions result in synonymous substitutions observed with much higher frequency than the nonsynonymous ones

      If a mutation occurs within a gene, it is more likely that it will code for the same amino acid than a different one. This is due to redundancy in the amino acid code and due to evolutionary and selective pressures on organisms to produce functional proteins.

    4. In many insects, maleness is conferred by a Y chromosome–linked M factor of unknown nature.

      Insect species employ a variety of different genetic mechanisms to confer either the female or male sex. The default mode, generally, is the development of female embryos; but there is not much understanding of the factors that lead to male-specific development.

    5. However, with the exception of Nix (a homolog of tra2) from a mosquito Aedes aegypti (16), genes encoding M factor have remained enigmatic

      Though details on insect sex determination are scare, a year before this study was published, Hall et al. (2015) discovered a male determining factor (M factor) in another disease-causing mosquito, Aedes aegypti.

    6. default female development in the absence of the Y-linked factor, whereas in males the M may be preventing establishment of trafunction by an unknown mechanism

      In other flies, there is a female "default" mode of sex determination. Only a maleness signal on the Y chromosome can initiate the male pathway.

    7. In males, a single dose of XSE is insufficient to initiate this female-specific cascade, and the three genes are spliced by a default male-specific mode, with only dsx encoding a functional protein.

      In the "default" mode of sex determination, a male fly will be produced. In this case Sxl, tra and dsx are expressed, but pre-mRNA processing results in non-functional SXL and TRA proteins as they both contain premature stop codons. The exons that contain these stop codons are spliced out in the female mRNA isoforms. Both males and females express DSX protein, but each have a different version due to sex-specific splicing. Check out this figure from Chromosomal Sex Determination in Drosophila

    1. The catalytic triad residues and two cysteine residues found only in this family

      In 2014, Suzuki et al. discovered a new structure in proteins featuring five specific amino acids held closely together.

      The structure begins with an amino acid called serine somewhere on a protein next to an amino acid called cysteine. They link to another cysteine next to an amino acid called histidine in such a way that a fifth amino acid, called aspartic acid and located between the two pairs is held closely to them in 3D space.

    2. even though the densely packed structure of highly crystallized PET greatly reduces the enzymatic hydrolysis of its ester linkages

      Vertommen et al. had shown that enzymes that help degrade PET act preferentially to the less organized, amorphous portions of the polymer, over the highly organized, crystalline portions.

    1. pattern recognition of satellite features based on the Dvorak scheme

      Using satellite pictures and infrared satellite imagery, it is possible to assign hurricanes into different categories depending on characteristic patterns.

      As a tropical cyclone develops, there tends to be certain characteristics depending on the intensity of the storm. Those visual characteristics in the swirls of clouds and moisture change in a predictable fashion as a storm system strengthens.

      This technique has been compared to aircraft measurements in order to test its accuracy and has some of the highest accuracy in gauging hurricanes in the North Atlantic and North Pacific Oceans.

      Check out NOAA's website for more information: http://www.aoml.noaa.gov/hrd/tcfaq/H1.html

    1. not due to executive impairments

      It has been found that cocaine users and their non–drug using siblings both had a deficit in response control. Siblings who were not exposed to cocaine showed a deficit in response control and similar changes in brain regions as their cocaine-using counterparts.

      This suggests that there are inherent traits such as impulsivity and poor inhibitory control that are caused by differences in brain physiology. This means that even before someone starts taking drugs, they may be vulnerable to drug addiction.

      It is possible that siblings of drug-dependent people have other traits that protect them from being vulnerable to drug addiction, i.e. traits making them less likely to start seeking drugs in the first place. This suggests that changes in brain physiology in drug-dependent people are not all cocaine-induced, and that there are some heritable (both genetically and epigenetically) differences in brain structure and function that can predispose people to addiction.

    2. jointly regulated by goal-directed and habitual brain systems

      Previous work has looked at how the decision-making process informs goal-directed behaviors. The systems that govern goal-directed behaviors and habitual behaviors are spread across the corticostriatal regions of the brain.

      Normally, these two systems operate in parallel (at the same time, but not necessarily together). With extended training or repetition of a specific behavior or use of stimulant drugs, the habit system can start to play a larger role over behavior and diminish the role of the goal-directed system.

      Once a behavior (like drug-seeking) has become habitual, the behavior will still occur even when the reward is removed (e.g., when the effects of the drug no longer feel good).

  3. Oct 2018
    1. sleep regulation

      Injection of NPY can have either sleep or wakefulness promoting effects on a mouse, depending on where exactly in the brain the molecule is injected, as well as context.

    2. anxiety, stress

      Similar to work done in flies on the role of NPF in regulating responses to physical stressors (see previous paragraph), studies in mice have also shown that when the activity of NPY is increased, stress responses are decreased. The vice versa has also been observed to be true.

    3. including roles in feeding

      When mice experience fasting, neurons in their brain containing NPY become more active, promoting feeding behavior.

    1. it required a monomeric superfolder green fluorescent protein (msfGFP) stabilization domain for efficient knockdown

      Superfolder GFP is a protein derived from GFP, a "reporter" that can be added to genes to see where and when they are expressed in an organism. GFP lights up when it is exposed to a specific wavelength of light.

      Superfolder GFP has several mutations that improve its folding properties and stability in comparison to regular GFP. In this particular experiment, the researchers fused a msfGFP (Superfolder GFP) domain to Cas13 to serve as a reporter and to increase the stability of the nuclease.

      To learn more about GFP, check out this Science in the Classroom resource.

    2. Although previous approaches have engineered targeted ADAR fusions via RNA guides (23–26), the specificity of these approaches has not been reported, and their respective targeting mechanisms rely on RNA-RNA hybridization without the assistance of protein partners that may enhance target recognition and stringency.

      Several groups have built programmable RNA-editing techniques based on the ADAR deaminase. The groups used different approaches to direct the editor to target mRNAs and demonstrated that these systems are efficient.

      However, none of the groups have extensively studied how accurately these systems find target sequences, or the effects systems have when they hit the wrong target. This is important, because a gene editor must be highly accurate (specific) to be useful for most applications.

    3. The ADAR catalytic domain is capable of deaminating target adenosines without any protein cofactors in vitro

      This is very important because it means that ADAR catalytic domain can be used independently of any other cofactors (which help enzymes catalyze reactions). As a result, it can still catalyze the deamination reaction when fused to another protein.

    4. However, the potential targeting sites of DNA base editors are limited by the requirement of Cas9 for a protospacer adjacent motif (PAM) at the editing site

      For CRISPR/Cas9 to work, there must be a special sequence (called a PAM sequence) next to the target site. Cas9 uses this PAM sequence to target a certain part of the DNA molecule.

      Different versions of Cas9 can use different PAM sequences. Researchers have experimented with different natural and artificial Cas9 enzymes to expand the range of sequences we can edit. However, there are still some sequences that we cannot edit because we do not have a version of Cas9 (or another enzyme) that can target them.

    1. that Akkermansia abundance positively correlated with time since previous relief

      Raes and colleagues found through 16S rDNA sequencing that time since last bowel movement was linked to Akkermansia abundance, a bacterial genus that has been linked to improved metabolic health.

    2. BSS score has been put forward as an indicative measure of transit time

      Heaton and colleagues showed that the BSS could be used to indirectly measure the rate at which food moves through the digestive tract.

    3. Previous work in mice has shown an effect of oxygen diffusion on the microbiota

      Wu and colleagues quantified gut oxygen levels in mice and found that there was a correlation between the distribution of oxygen and nutrients and the microbiome composition.

    1. a mean that depends on the concentration of the odor

      Hallem and Carlson conducted an analysis to determine how the fly's olfactory neurons would change their behavior in response to different types and concentrations of odor.

      They found that the average strength of the receptors' response (i.e. the number of times the neurons were triggered) was dependent on the concentration of the odor. High concentrations brought on strong responses (a high rate of triggered neurons) from multiple receptor neurons, while low concentrations elicited a slower rate of neurons firing.

    2. The fly olfactory circuit generates a “tag” for each odor, which is a set of neurons that fire when that odor is presented

      In 2015, Stevens identified a three-step code that the fly olfactory circuit uses to identify and respond to specific odors.

      1. Receptor neurons send odor information to specialized structures called glomeruli, which contain projection neurons.
      2. Projection neurons send the information to Kenyon cells in the mushroom body.
      3. These Kenyon cells form the odor label, or tag, and then pass the information along to another stage of neurons that then direct the fly's behavior.
    1. multi-template polymerase chain reaction bias

      Multi-template polymerase chain reaction (PCR) is a technique to amplify multiple targets in a single PCR experiment. However, this technique sometimes produces bias and overamplifications in specific templates.

      To learn more, check out this seminal paper by Polz and Cavanaugh (1998).

    2. these analyses confirm previous conclusions

      Researchers have compared the genomes of these two lichen species and found that, for the most part, these two organisms have the same sets of genes.

    3. Attempts to synthesize lichen thalli from the accepted two components

      Researchers have tried to create a lichen in the laboratory by only mixing an algae and a fungus known to produce lichens in the wild. These attempts were not successful as the cortex layer did not develop.

    1. Rare examples include members of the

      Previous work by Ronkvist et al. and Sulaiman et al. had shown that enzymes called cutinases could sometimes degrade PET if the temperature, polymer properties, and pH of the solution were right.

      Nimchua et al. found in two different studies that Fusarium oxysporum, a recently discovered fungus, and Fusarium solani, another fungus, produced the enzymes needed and were able to break down PET film.

      Link to Ronkvist et al: https://pubs.acs.org/doi/abs/10.1021/ma9005318

    2. chemically inert

      Earlier, Smith et al. found minor degradation of PET by a few enzymes, along with no response by other, more common enzymes. Several labs determined that changing the structure of the polymer backbone to resemble more biodegradable polymers could make a new PET-like polymer biodegradable.

    3. Enzymatic degradation of polyesters is controlled mainly by their chain mobility

      Chain mobility is a measure of the flexibility of a polymer chain. A more flexible polymer chain will have higher chain mobility. In 2005, Marten et al. showed that polymers with lower chain mobilitites, including PET, are more challenging for enzymes to degrade.

    4. across the globe (4).

      In 2015, J. R. Jambeck et al. calculated that about 8 million tons of plastic make it into the ocean each year.

    1. Consumer uses of VCPs likely remain key sources of human exposure to air toxics relative to fossil fuels, especially because people spend most of their time indoors (62).

      In a 2001 National Human Activity Pattern Survey of 9,386 people in the United States found that on average 87% of time is spent in buildings and 6% of time is spent inside automobiles. Indoor air quality is an important issue, since on average 93% of time is spent indoors.

    2. made in Pasadena during 2010

      A previous study measured the amounts of VOCs present in outdoor air in Pasadena, California from 15 May to 15 June in 2010. The research included both measurements on the ground and measurements via aircraft.

      This study is using those measurements to test their model.

    3. Prior studies often report missing

      Hydroxyl radical (OH) concentrations that are measured have been lower than what is predicted by models. This implies that other species or processes not included in the model must account for the difference between the model and the measurements.

    4. We tested our indoor model with measurements of residential (32) and commercial buildings (40)

      A previous study on residential buildings combined measurements from 77 separate studies to examine the typical levels of VOCs in average households. The study only used measurements from U.S. households and those of countries with similar styles of living.

      Another study on commercial buildings made measurements of the levels of VOCs in 37 different small and medium-sized commercial buildings in California. This allowed the researchers to quantify typical VOC exposure in commercial buildings.

      This study is using these two experimental studies to test their model.

      A primary instrument used for determining the VOC components in air is a mass spectrometer. Learn more about mass spectrometers by watching the following video. https://www.youtube.com/watch?v=J-wao0O0_qM

    5. Previous studies typically relied on ambient VOC measurements mainly of compounds found in fossil fuels, while not including many species found in chemical products (16).

      Researchers have looked at various volatile organic molecules to track emissions. The types of molecules that researchers examine have an influence on conclusions drawn. Many studies have not looked for some of the volatile organic molecules that come from household products. This could explain why many models have underestimated the contribution of household products to volatile organic emissions.

    6. Most organic compounds in soaps and detergents dissolve in water and end up in sewer systems (20), with negligible amounts emitted from wastewater treatment plants (21).

      Only a very small percentage of organic molecules in soaps that are disposed of in drains have the potential to negatively impact air quality. Overwhelmingly, organic molecules used in soaps and detergents end up being disposed of down the drain into sewer systems. These molecules then end up in sewer treatment plants. Most of these organic molecules are then either physically or chemically removed from the water at the treatment plant.

      Based on Fig. 1, around 97% of the mass of water and organic molecules in soaps and detergents end up being disposed of down the drain.

    7. Automotive emissions of VOCs have decreased steadily from efforts to control tailpipe emissions in the United States (5) and Europe (6).

      Changes in how engines operate (air/fuel ratios, use of catalytic converters, etc.) have led to substantial decreases in automotive emissions. In major U.S. cities (New York, Los Angeles, and Houston) from 1990 to 2010 some hazardous emissions have decreased by 80% to 90% even as car traffic has increased. Hazardous emissions from vehicle exhaust are expected to remain at approximately this same level as vehicles continue to utilize technologies to reduce hazardous emissions.

    1. Assemblages showing pronounced northward range expansions and limited southern-range losses, like butterflies, originated and diversified in tropical climates and retain ancestral tolerances to warmer conditions (21). Those species’ warming-related extinction risks in temperate environments are low (8) but increase toward warmer areas where climatic conditions resemble those under which they evolved

      One possible explanation of why some temperate species' ranges would expand with climate change is that these species evolved in the tropics, and have not lost a high tolerance for heat, even as they moved further north. Therefore, even as temperatures heat up in the southern regions of their current ranges, these temperature still do not approach their ancestral tolerances, and species can continue to live there. This could explain why species in the tropics are currently suffering under warming climates; the increase in temperature is surpassing their ancestral heat tolerance.

    2. Neonicotinoid effects on bumblebees have been demonstrated experimentally using field-realistic treatments

      Whitehorn and colleagues took laboratory colonies of a common European bumblebee species (Bombus terrestris), and exposed them to levels of neonicotinoids similar to what they might be exposed to near a farm field. They found that colonies exposed to these levels had slower growth rates and produced less queens than "control" colonies that were not exposed.

    3. Such responses depend on species’ traits, such as heat or cold tolerance, that reflect shared evolutionary history and climatic origins (e.g., tropical or temperate) of taxa

      Every living organism has certain traits. For example, reptiles have scaly skin, birds have feathers, mammals produce milk, and so on. These traits are inherited from the organisms' parents, of course, but ultimately, those traits tend to remain similar across very large periods of time.

      We can trace how traits change over evolutionary time scales, and show that some traits tend to remain quite similar, even though a huge amount of time might have passed. Traits like a species' tolerance to heat are like this: This trait tends to remain similar across evolutionary time, despite the fact that a species might evolve and change in many other ways, even splitting into two or more different species. In other words, it's hard to evolve tolerance to hotter temperatures—at least for many species.

    4. In addition to shifts in the timing of species’ life cycles, warming has caused range expansion toward the poles and higher elevations

      In one study, Chen and colleagues put together a huge analysis of 1367 species from the United Kingdom and some other places around the world. Those authors looked at whether the places those species were found had changed over time. On average, those species were shifting toward cooler areas at about 17 kilometers every 10 years. They were also shifting upward in elevation by about 11 meters every ten years, reflecting the fact that it is generally cooler at higher elevations than at lower elevations.

      The Chen study is called a meta-analysis, where they take results from many other studies and put them all together into one big analysis. That work focused especially on butterflies, which are very sensitive to climate change, but it did not include critical pollinator species, like bumblebees.

    1. A powder of MOF-801 was synthesized as reported

      The preparation of MOF-801 was described by the same group in a previous study. The method consists of heating the organic component in a solvent with a reagent containing the metal ions. This forms the MOF as a solid that can then be filtered.

    2. The model framework was based on mass and energy conservation, incorporating adsorption dynamics parameters

      The authors built their simulation model based on previous studies about adsorption processes defining the important parameters to optimize the adsorption process.

    3. The flexibility (20–22) with which MOFs can be made and modified at the molecular level

      MOFs are composed of metal ions connected by small organic molecules. Both these small building blocks can be varied to afford a large diversity of different MOFs with properties tailored for specific applications.

    4. catalysis

      One of the numerous applications of MOFs has been the ability to induce selective chemical reactions between substrates. The metal ions within the MOF enable the reaction to occur only for the substrates that are able to enter in the cavities.

  4. Sep 2018
    1. MinHash

      In 1997, Andrei Broder invented MinHash, which is a type of LSH that allows a user to quickly estimate how similar two data sets are. In his seminal paper on this topic, Broder discussed the math behind this idea and applied it specifically to the process of comparing two documents on the internet.

    2. the first step in the circuit essentially “centers the mean”—a standard preprocessing step in many computational pipelines

      Olsen, Bhandawat, and Wilson showed that the fly olfactory circuit uses a specific type of processing known as divisive normalization. This process ensures that the strength of a neuron's output stays within a certain range.

      This is important because a complex stimulus (e.g. one consisting of multiple odors) might elicit several different responses from a single neuron based on all the different aspects of the stimulus (type, concentration, molecular make-up, etc.). But thanks to divisive normalization, a neuron's response will look more like an average of all its responses rather than the sum of them.

    3. all but the highest-firing 5% of KCs are silenced

      Turner, Bazhenov, and Laurent quantified the sparsity of KCs by recording the spiking activity of the cells in response to input from the PNs. They discovered that at least three factors explain why such a small number (~5%) become active:

      1. The inputs from PNs last a very short time, which doesn't give KCs much time to build up their activity.
      2. Only a few PNs connect to each KC, so overall input levels are low.
      3. KC firing thresholds are high, meaning each KC must have very strong inputs in order to obtain the energy it needs to fire.
    4. This is called the nearest-neighbors search problem, which is of fundamental importance in information retrieval, data compression, and machine learning

      Andoni and Indyk explored how LSH algorithms can be applied to solving nearest-neighbor search problems. They showed that nearest-neighbor search problems are useful for any task where you want to find two similar objects, whether you're trying to retrieve information, recognize a pattern, or analyze data.

    5. its many variants (16–18) provide strong theoretical bounds on how well locality is preserved when embedding data from d into m dimensions by using various types of random projections.

      Achlioptas explored two specific applications of the Johnson-Lindenstrauss lemma that are particularly relevant to computer database applications. In doing so, he discovered a method of projecting points from a higher to lower dimensional space that was simpler and faster than other known methods. In fact, he showed that it was possible to perform this faster embedding process without affecting the quality of the results.

    1. There are currently few known examples

      Earlier work found examples of enzymes that partially break down PET. These enzymes increased the hydrophilicity, or desire to dissolve in water, of PET. The previous work developed a range of different methods to measure PET modification from these enzymes, including SEM imaging, measuring the pH (which changes over the course of the degradation), and spectroscopy—a technique that involves shining different types of light at a sample and measuring what light passes through.

    2. durability, plasticity, and/or transparency have been industrially produced over the past century and widely incorporated into consumer products

      Sinha et al. (2010) detail the wide use of PET plastic, particularly in beverage bottles and describe possible methods of recycling. They focus particularly on tertiary, or chemical, recycling. Chemical recycling breaks down the polymer chain into smaller pieces using chemicals that are often harsh or corrosive. At the time Sinha et al.'s review was written, no biological methods of breaking down PET were known.

    1. Colonization of previously unoccupied areas and maintenance of new populations strongly affect whether species track shifting climatic conditions

      Two factors that help determine how well a species will track climate change are dispersal (how well the species can move to new areas and start new populations) and persistence (how well the species can maintain and grow these new populations).

    2. Over recent decades, alpine tree lines have advanced upslope in response to human activities, geomorphological factors, and warming

      From analysis of aerial surveys, Gehrig-Fasel and colleagues found that about 4% of upward shifts in tree line (i.e. trees growing further uphill than previously) from 1985 to 1997 could be attributed directly to climate change. The rest were attributed to changes in land-use.

    3. constructed from nuclear and mitochondrial markers

      Cameron, Hines, and Williams used DNA sequence data on 218 of the 250 currently known bumblebee species to create a phylogeny (phylogenetic tree).

    4. many of which are declining

      Using museum records, Bartomeus and colleagues found that bumblebee species richness in northeastern North America has decreased significantly since 1877.

      More recently, a 2017 study found that one third of bumblebee species are in decline.

    5. Such global changes can alter or erode ecological services provided by the affected species

      Goulson and colleagues review the various global change drivers that are causing declines in bees, and by extension their pollination services.

      This infographic from their study shows some of the main drivers and how they may interact together. (c) Goulson et al. 2015

    6. Climate impacts could cause losses from parts of species’ trailing range margins

      By modelling the probability of extinction for lizards in Mexico, Sinervo and colleagues found that unabated climate change would result in the extinction of 58% of species in the Schleporus genus. They determined that increasing temperatures forced Schleporus lizards to spend more time in cool refuges avoiding the heat, therefore limiting time for foraging and reproduction, and reducing population growth rates. They also found that high-elevation species were particularly at risk from increased competition as low-elevation species moved higher.

    7. Regional analyses suggest that latitudinal range shifts toward the poles are accelerating in most species groups (3), while their trailing range margins remain relatively stable

      Most species that have been studied so far are expanding further north as climate warming makes these areas habitable for them, but are still able to tolerate to increasing temperatures in the equator-ward regions of their ranges. In other words, it appears that climate change has helped many species increase their total range sizes! (Although it likely still affects their ability to live within these expanded ranges.)

    8. No study has yet evaluated climate change impacts across the latitudinal and thermal limits of such a large species assemblage spanning two continents.

      Here, the authors are showing that their research is something that no scientist had known or been able to do before. The purpose of this sentence is to show why an analysis like the one in this research might be important and tell us something that we had not known previously.

    1. As diesel particle filters and oxidation catalysts become more widespread, and reduce diesel contributions to PM2.5 (60), the fraction of PM2.5 from VCPs will grow because SOA precursor emissions from VCPs are not decreasing as quickly (7).

      Various technologies are being engineered to reduce particle emissions from diesel engines. Use of VCPs that lead to formation of aerosols is not decreasing as fast. VCPs' contribution to aerosol formation will become increasingly important.

    2. Of the fossil total, ~40%, or ~1.3 μg m−3, is attributed to directly emitted particles (55, 56), mainly from diesel engines (7).

      Aerosols are directly emitted by natural (e.g., wildfires) and human activities (e.g., driving). The fossil total of aerosols refers to those from human activities. In Los Angeles, 40% of human-activity aerosols are soot-like aerosols directly emitted from engine exhaust. Diesel engines are the main contributors. The other 60% form in the atmosphere from emissions of gaseous VOCs, such as from automobiles or VCPs.

    3. one-dimensional volatility basis set (51) for OVOCs

      A different aerosol formation model, published by Robinson et al. (2007). The authors of this study used both this and the SOM model to predict aerosol formation in their box model.

    4. The aerosol yields used in this study (table S12) are mostly estimated from the Statistical Oxidation Model (SOM)

      Co-author Christopher D. Cappa and other researchers developed the model used in this study to predict the formation of aerosol particles from VOCs. Using data from their aerosol formation model in this study's box model, the authors predicted the amount of aerosol particles that will be formed in Los Angeles.

    5. risks of mortality from respiratory diseases

      Ozone in the stratosphere (10,000 - 50,000 km above Earth's surface) is a net positive as it absorbs potentially harmful UV radiation. However, ozone at or near ground level (tropospheric) is a health-risk. Ozone that is inhaled into the body reacts with cells in the respiratory tract. This leads to increased respiratory disease and is correlated with increased mortality rates.

      See more about the hazardous effects of ozone at the EPA: https://www.epa.gov/ozone-pollution-and-your-patients-health/health-effects-ozone-general-population#intro

    1. terms of central pressure

      The study cited here by Kossin and Velden found that there was a latitudinal bias in the way scientists were utilizing the Dvorak scheme to estimate storm intensity. At different latitudes, atmospheric pressures remain stable at different heights (e.g. air expands in warmer temperatures, near the equator).

      There was no bias in estimating atmospheric pressure around the 23°N, but estimates for the latitudes both closer to the equator and farther north to the poles needed to be reconsidered.

      They found that the pressure estimates based on satellite images needed correcting, but that estimates of wind speeds was still useful and accurate enough.

    2. substantial changes in the manner in which the Dvorak technique has been applied

      The authors are referring to the change from visual, human eye-balled categorizations of satellite images to computer-based algorithms.

      The transition from humans to computers in cataloging storm system removed some of the personal subjectivity between tropical storm analysts.

    3. known biases before this period

      The article they reference is "On the quality of the Australian tropical cyclone data base" where Greg Holland studied a subset of global data in order to see how enhanced observational technology has improved the detection of intense tropical storms.

      He found that prior to the use of satellite imagery to recognize storms, records tend to underestimate the true number of events. This may be due to the amount of storms which form and remain far offshore which did not make it into historical records. Thus in the 1960's when satellites really started getting widespread usage for tracking weather, scientists "saw" more hurricanes than previously reported.

    4. SST > 26°C is a requirement for tropical cyclone formation

      In order for a hurricane to form, there are multiple environmental conditions that must align. First off, an area of low pressure over the tropical ocean known as a "pre-existing disturbance" must form in an environment favorable for development.

      Other conditions include: Ocean temperatures must be above 26°C (80°F), sufficient moisture in the air, enough distance from the equator to establish a cyclonic movement, and atmospheric conditions that support thunderstorm development are necessary for a hurricane to develop.

      For more information visit the University of Rhode Island's 'Hurricanes: Science and Society' site: http://www.hurricanescience.org/science/science/hurricanegenesis/

    5. nonlinear relation between saturation vapor pressure and temperature

      The relationship between a change in temperature and a change in saturation vapor pressure is nonlinear, as in when plotted against each other the results do not form a straight line. This means that an increase in temperature causes an increase in vapor pressure much larger than would be the case in a linear relationship.

      Here is an example of how temperature affects vapor pressure: Image from Lyndon State College.

    1. shift the balance between goal-directed and habitual responding

      In one study, researchers introduced a type of diet that reduced dopamine function in healthy human participants to assess whether it would control the shift between goal-directed action to habitual action.

      The participants did not have reduced ability to learn associations between a stimulus and a response. They were also sensitive to outcome devaluation. However, they showed impairments in the slip-of-action test.

      Note: the above was shown to occur in women only.

    2. Exposure to either cocaine or stress amplifies the transition

      Previous work has shown how chronic stress and cocaine can affect normal behavior in rats by making them less sensitive to outcome devaluation and more likely to develop stimulus-driven behaviors from previously goal-directed behaviors.

    3. performed regardless of any goal

      Over time, people who regularly use drugs may start to use them habitually. This means that they no longer use drugs because it makes them feel good, but because that's just what they do.

      When a habit is compulsive, it is performed even without regard to its negative consequences.

      In one study, rats that had learned to do a specific task in order to get cocaine tended to continue doing the task even when cocaine consumption was paired with a negative event (here, injection with lithium chloride, which makes rats feel sick).

    4. may be explained in terms of aberrant learning processes

      Aberrant learning processes refer to the transition of drug seeking and taking from a goal-directed behavior to a habitual behavior. This transition can be artificially enhanced by cocaine. Over time, the habitual brain system can play a larger role and leave someone vulnerable to compulsive behaviors (seeking and taking drugs without a goal, like desiring a rush or avoiding feelings of discomfort).

    1. For this last reason, we also estimated stature using the method of Dingwall et al. (2013), who published some equations based on regressions of stature by footprint length in modern Daasanach people (from the Lake Turkana area, Kenya).

      Hominin footprints were found near Ileret, Kenya, and are believed to be 1.5 million years old. It is thought the prints were made by Homo erectus.

    2. we also surveyed a first-generation fiberglass cast of the southern portion of the Site G trackway (about 4.7 m in length) (Figure 11) kept at the Leakey Camp at Olduvai Gorge. The cast includes the following tracks in the direction of walking: G1–39, 38, 37, 36, 35, 34, 33, 27, 26, 25 on the western side and G2/G3–31, 30, 29, 28, 27, 26, 25, 24, 20, 19 and 18 on the eastern side.

      Casts had been made of the original tracks before the site was covered. This protected the original tracks yet made visualization of what they were like.

    3. Thus, our results support a nonlinear evolutionary trend in hominin body size (Di Vincenzo et al., 2015; Jungers et al., 2016) and contrast with the idea that the emergence of the genus Homo and/or the first dispersal out of Africa was related to an abrupt increase in body size

      Some researchers hypothesized that over time, hominin species increased in stature. This increase coincided with the migration of these species into other regions. This hypothesis is not supported by the authors' work.

    4. Consequently, we may emphasise the conclusions by Grabowski et al. (2015) and Jungers et al. (2016), who reported that the body sizes of the australopithecines and of the early Homo representatives were similar, but also that certain australopithecine individuals (at least of Au. afarensis) were comparable with later Homo species, including H. erectus s. l. and H. sapiens.

      Earlier work by other researchers supported a hypothesis that variability in hominin stature was linked to sexual dimorphism or the environment. They also hypothesized that size did not increase over time with Australopithecines exhibiting the same stature as later Homo species including Homo sapiens.

    5. Although the stratigraphic descriptions above are very accurate, they do not provide details about the eye-scale characteristics of the tuffs, i.e. colour, texture, limits, and so on, and no photographs of the sequence have been published.

      Earlier work determined that the footprints at Site G were located on a specific level of the Footprint Tuff. The authors of this paper question this conclusion since the conclusion is based on an average of all the Laetoli sites and does not provide specific data regarding soil characteristics or photographs.

    6. The stature and mass of the Laetoli print-makers were estimated following the relationships between foot/footprint size and body dimensions

      Based on fossil evidence, the body proportions of Homo sapiens are different from those of Australopithecus. To use these dimensions as the basis for determining the stature, body mass, and walking speed of Australopithecus would not provide an accurate picture.

    7. Tracks and trackways of mammals, birds and insects, as well as raindrop impressions, are recorded from 18 sites at Laetoli, named alphabetically from A to R

      Numerous researchers have studied the fossil tracks left by various wildlife species. The types of animals present provide additional information about the ecology of the region and helps confirm the age of the trackways.

    8. other remains of Au. afarensis (Leakey et al., 1976; Johanson et al., 1978) and remarkable evidence of the earliest bipedal hominin tracks (Leakey and Hay, 1979; Leakey and Harris, 1987) dated to 3.66 million years ago (Ma) (Deino, 2011).

      The discovery of the first Laetoli trail during an expedition led by Dr. Mary Leakey helped to settle one of the great paleoanthropological debates. Some argued that upright posture and bipedalism had to evolve before the hands would be free to make tools. Stone toolmaking was thought to be the critical factor in the evolution of hominins. The analysis of hominid bones could not provide the answer. The discovery of the Laetoli footprints provided evidence that dated bipedalism to 3.6 million years ago. The earliest stone tools are known to be around 2.6 million years old. The feet came first.

    9. The trackways are usually ascribed, not without controversy (Tuttle et al., 1991; Harcourt-Smith, 2005), to Au. afarensis (White and Suwa, 1987), which is the only hominin taxon found to date in the Upper Laetoli Beds (Harrison, 2011).

      In 1978, Dr. Leakey and colleagues discovered fossils of Australopithecus afarensis at Laetoli. Other hominin fossils had been found in the area during work done in 1938. All together, the bones of about 23 individuals had been unearthed. They dated between 3.76 and 3.46 million years old. The fossil footprints in the volcanic tuff dated to about 3.56 million years ago. Based on the evidence, Dr. Leaky and others attributed the footprints to A afarensis.

    10. Estimates are largely inferred from known relationships between metric data in living species, such as bone length (or joint size) and stature (or body mass) (McHenry, 1991, 1992; Grabowski et al., 2015). Similar estimates can be even more plainly obtained from the analysis of single footprints or – even better – from trails of footprints (Tuttle, 1987; Dingwall et al., 2013)

      Estimates of the body mass and degree of sexual dimorphism of early hominins are based on a limited number of fossils. Often, the fossil evidence (bones and footprints) was referenced to modern humans of known body mass. It is likely that the inferred sizes are inaccurate.

      More recent evidence indicates that modern humanlike size first appeared around 3–3.5 million years ago in Australopithecus afarensis.

    1. Seabirds deliver nutrient-rich guano from productive ocean waters (9) to the nutrient-limited plant communities (10, 11).

      Plant species on the archipelago are dependent on the nutrients from guano. Guano, bird poop, is rich with minerals and nutrients, like Nitrogen and Phosphorus. The plant species richness has been found to increase as the nutrient availability increases.

  5. Aug 2018
    1. This tag is critical for learning behavioral responses to different odors

      Owald and Waddell discovered that the fly olfactory circuit is able to recall previously-learned odors through the help of specialized dopamine neurons. After a fly smells an odor, these dopamine neurons trigger changes in parts of the olfactory circuit that cause the specific neurons associated with the odor (aka the "tag") to fire.

      Reactivating the tag causes the fly to remember the odor, as well as the values/meanings/context associated with it. The fly can then exhibit the appropriate behavior based on its prior learning (e.g. avoidance if the odor is associated with danger or approach if the odor is associated with a reward).

    1. Despite great progress in food web ecology, the indirect effects of top predators on vegetation dynamics in terrestrial systems remain unresolved and actively debated

      In the paper by J. Halaj et al. food webs are studied using the ratio of an isotope of nitrogen and carbon to see how much of it exists in different trophic levels and how the food web interacts both above and below ground. This study shows more of the direct effects of top down tropic cascades which are shown by the predation of sea birds by foxes in the study by Croll which also elaborates on the indirect effects of predators on the environment through the predation of sea birds decreasing nutrients to the system and changing the plant community structure. There is also isotope testing being used in this study to see its distribution across different species and soils between the fox infested and fox free islands.

    2. Hairston et al. (1) proposed that plant productivity and composition were influenced by apex predators through cascading trophic interactions.

      According to Hairston et al. the populations of producers, consumers, and decomposers are limited by the resources they depend upon which are subject to limitation by the tropic levels both above through predation and below through low abundance. These limitations of herbivores by predation is helpful to the plant communities below as well. The Hairston et al. study provided the basis for the study of direct effects on top predators to terrestrial systems but this study further looks into the indirect effects of predation on plant communities. Providing evidence for indirect effects of nutrient deprivation due to predation using a large scale system that has room for replication.

    1. Using a similar approach, Darrault and Schlindwein (2005) observed that proboscis width played an important role in pollen transfer efficiency in Hancornia speciosa (Apocynaceae).

      The two experiments are similar because they take proboscis dimensions into account. The previous experiment that the author is talking about, measured out the thickness of the proboscis and how they can be efficient in transferring pollen.

      In the experiment above, the author took into account on how the length and width of the proboscis can play a role in pollination. Since both the width and length of the proboscis were measured, more information was able to be attained. With these two different approaches, some differences can be taken into account and can be compared.

    2. Proboscis length is an important determinant of pollination efficiency

      It is well known that insects use their proboscides or mouthparts to sip nectar and collect pollen. However, according to new research, the proboscis actually works more like a paper towel than a straw.

    1. They also can reveal patterns of genetic diversity of species with very narrow distribution that in many cases are in the verge of extinction (Allendorf and Luikart, 2007; Oleas et al., 2013). Caribbean Island palms have been the focus of conservation initiatives that include red-listing [sensu IUCN (2014) by Zona et al. (2007) and Peguero et al. (2015b)]; species inventories (Moya López and Leiva Sánchez, 2000; Leiva Sánchez, 2006); conservation genetic studies (Rodríguez-Peña et al., 2014a, 2014b); field surveys and conservation assessments (Henderson et al., 1990; Leiva Sánchez, 2008; Peguero et al., 2011, 2015a)

      This research demonstrates how we can deal with issues that face threatened species through a series of field surveys, conservation assessments, and molecular research.

    2. The Caribbean Island Biodiversity Hotspot has a high priority for conservation

      The Caribbean Island Biodiversity Hotspot has a great need to practice conservation since it has been subject to many events that are threatening of native species.

    1. However, this hypothesis has not been fully tested because the electrosensory input has not yet been well described during exploratory behaviors in freely moving fish.

      It is difficult to examine the exploratory behavior of a free moving fish because the data typically used do not accurately describe the fish's behavior. The EOD geometry and the electric images are complex because they can change based on the fish's movement. The movement changes the source of the electric organs and in laboratory setting the behaviors that use electroreception are hard to maintain. The difficulty experienced in a control laboratory setting to examine the certain behaviors, makes collecting and analyzing data of a free moving fish rather challenging.

    1. marker of coating-related VCPs in this study and in the past (16), increased in ambient air in Los Angeles from 1990 to 2010 (22). This is in sharp contrast to VOCs present in gasoline exhaust, which decreased markedly during the same period (22), except for ethanol (23).

      Organic compounds emitted from gasoline exhaust have decreased from 1990 - 2010. The decrease is due to increased combustion efficiency and catalytic converters. Organic compounds that come from other sources have increased during this same time period.

    2. Transportation emissions of NOx and VOCs have long been considered major contributors to formation of O3 (8) and SOA (9–11) in urban areas, although recent studies have suggested the importance of nonvehicular sources as major contributors (12–14).

      Vehicle emissions contribute to air pollution. This includes increases in ozone and aerosol concentrations. Vehicular emissions alone cannot account for the increased ozone and and aerosol concentrations measured in the atmosphere. Additional sources of emission must exist to account for the increase, but where those sources come from is still uncertain.

    3. adverse human health effects occur below current U.S. standards for PM2.5 and O3 (4).

      The Environmental Protection Agency (EPA) sets legal limits for exposure to various environmental toxins. In studying Medicare recipients it was found that increases to PM2.5 and ozone exposure cause an increase in mortality rate. A 10 microgram per cubic meter increase of PM2.5 caused a 7.3% increase in mortality.


    1. Although populations of long-tongued bees are undergoing widespread decline (1, 3), shifts in foraging strategies may allow alpine bumble bees to cope with environmental change.

      Long-tongued bee populations are declining due to climate change. However, bumble bees that change what flowers they choose to forage may be better at surviving the changes to their habitat.

    1. Changes in JH synthesis in female adult A. aegypti mosquito are very dynamic and nutrition-dependent 

      Release of juvenile hormone is determined by their blood meal, and their meal determines whether glucose will be absorbed to their muscle and fat cells.

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

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

    2. Although it is likely that early work overestimated swimming speeds, speeds higher than those predicted based on the twitch contraction methods might theoretically be possible if fish were able to change their mode of swimming to accommodate for the otherwise lack of increase in tail beat frequency

      The maximum frequency at which a fish can move its tail is limited by the twitch contraction time of the white lateral muscle. The maximum swimming speed is then predictable if the distance moved forwards on completion of each oscillation (the stride) is known.

    1. Zhang and Schlyter 2003

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

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

    2. Dyer et al. 2001

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

    3. Wahid et al. 2007

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

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

    4. McGill 2006

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

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

    1. field observation and detailed sequence descriptions were carried out on excavation profiles following the standard formalized by Catt (1990)

      Serves as a manual for analyzing soils of past geological eras.

    2. Unfortunately, correlation with the stratigraphic sequence of Site G (Locality 8) is impossible because this historical site is completely covered by protection features and cannot be used for direct comparison.

      The trackway discovered by Dr. Leakey and colleagues has been covered in order to prevent erosion and the encroachment of plant roots. These measures were taken to guarantee that the footprints will not be destroyed. As a consequence, a careful analysis of the soil layers at Site G cannot be conducted.

    3. The overall morphology of the S1 tracks matches those at Site G (Figure 11) and is similar in particular to the prints of the larger individual

      Analysis of the footprints discovered by Dr. Leakey and colleagues determined that the big toes of the hominids leaving the trail aimed forward and that the toes were not distinctly different from each other. This is not true of the feet of hominids such as the chimpanzee.

      Source of image ttps://corewalking.com/chimpanzee-feet-vs-human-feet/

    4. It is reasonable to assume that complex relationships among body size, sexual dimorphism, mating system (and/or reproductive strategy) and social structure/behaviour also applied to extinct hominins, including our bipedal relatives of the Plio-Pleistocene

      Modern humans do not exhibit a high degree of sexual dimorphism. However, other hominid relatives, such as gorillas and orangutans, are highly dimorphic. Based on a limited number of fossils, it has been assumed that early hominins were highly dimorphic. Knowing more about the degree of sexual dimorphism would provide information about mating behavior and social organization.

    1. 1The distortion of the oval orbits of planets round the sun (confirmed in the case of the planet Mercury).

      In A New Determination of the Orbit of Mercury and its Perturbations (1843), Urbain Jean Joseph Le Verrier reported a peculiar precession of Mercury's orbit that was not accounted for by Newtonian mechanics.

      Relativity theory, however, provides a robust account of Mercury's motion.

    2. Euclidian geometry

      Euclid was a mathematician in Ancient Greece. His book Elements is arguably the first mathematics textbook. In the text, Euclid describes the geometry we seem to experience in our everyday lives in which parallel lines do not intersect.

      This is also the same geometry we still learn in high schools across the country (2000 years after Euclid wrote it).

    3. The application of this general theory of relativity was found to be in conflict with a well-known experiment, according to which it appeared that the weight and the inertia of a body depended on the same constants

      The Eötvös experiment measured the correlation between inert and heavy mass (or inertia of a body and its weight) and showed that these two masses have the same value although are conceptually distinct.

    4. special relativity theory and the general theory of relativity

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

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

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

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

  6. Jul 2018
    1. Since the time of the ancient Greeks it has been well known that in describing the motion of a body we must refer to another body.

      Aristotle contemplates absolute and relative motion in his book On the Heavens. He describes how heavy bodies move down and lighter bodies (like air or fire) move up relative to the center of the universe.

      Read more: https://plato.stanford.edu/entries/spacetime-theories/#2

    2. The deviation of light-rays in a gravitational field (confirmed by the English Solar Eclipse expedition).

      Again, this was found by Arthur Eddington and Frank Watson Dyson in their paper.

    3. Maxwell-Lorentz theory

      Maxwell's equations describe how electric and magnetic fields manifest from charged particles. Together, Maxwell's equations suggest the speed of electromagnetic waves (i.e. light) is constant.

      The Lorentz Force Law says that the force felt by some charged particle is related to the surrounding electric and magnetic fields.

      Together their work describes special relativity, but only for electromagnetism.

    4. I am none the less very glad to express my personal thanks to my English colleagues in this branch of science; for without their aid I should not have obtained proof

      Einstein's "English colleagues" are Arthur Eddington and Frank Watson Dyson, astronomers who obtained experimental evidence of Einstein's theory of relativity.

      Modern physicists have debated whether the error bars in the Eddington experiment were larger than the effect they measured. Nevertheless, the results have been confirmed.

      Read Eddington and Dyson's work here.

    5. rays of light

      In the image below, the solar gravitational field influences the sun's rays framing the moon. Notice that the light bends around the moon due to the gravitational field, rather than forming a spherical halo.

    1. Exposure to air pollution is the fifth ranking human health risk factor globally, following malnutrition, dietary risks, high blood pressure, and tobacco (1).

      Understanding the causes of disease and death are crucial to better health outcomes. A look at health data from 1990 to 2015 identified factors that lead to negative health outcomes. Exposure to increased air pollution primarily leads to increased respiratory and cardiovascular disease.

  7. Jun 2018
    1. Recently some of these problems were overcome using an RNA biosensor that is dislodged by translating ribosomes

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

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

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

    1. Climatic Research Unit TS3.1 gridded observations (20)

      This data set was developed and maintained by the Climatic Research Unit in the United Kingdom. It provides several climate values for locations covering the globe, on a monthly basis, from 1901–2009. The data set covers the world's land surface (excluding Antarctica) and is reported in a 0.5° x 0.5° grid. The climate variables, including temperature and precipitation, are based on actual observations from a number of sources, using appropriate methods to integrate the different sources and calculate the values for locations that are missing data.

  8. May 2018
    1. (Ding et al. 2008).

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

    2. (Jiang et al. 2008)

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

    3. (Zhou and Grumbine 2011)

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

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

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

    5. Liu et al. 2011, 2013).

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

    6. (Kirkpatrick and Emerton 2009;

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

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

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

    8. (Godefroid et al. 2011;

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

    9. Francisco-Ortega et al. 2010).

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

    10. (Qin et al. 2012)

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

    11. (Xu et al. 2009

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

    12. reintroduction (sensu Menges 2008)

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

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

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

    1. Genetic studies have also suggested that Sox10and Ednrb do not interact during murine melanocyte development (Hakami et al., 2006).

      Sox10 is expressed in melanoblasts, which are the precursors of melanocytes, that do not contain Ednrb. Ednrb is expressed in embryos that do not contain Sox10. Therefore, Sox10 expression does not depend on the expression of Ednrb.

    2. High VEGF levels are in turn associated with poor prognosis in human melanoma tumors (Giatromanolaki et al., 2003).

      Studies show that there is a high expression of VEGF in human melanoma tumors, indicating that VEGF can serve as a marker for melanoma prognosis. Moreover, tumors with a high vascular density (VD) were also associated with poor prognosis.

    3. Moreover, in situ melanomas appeared in adult skin grafts, while invasive melanomas developed in newborn skin grafts indicating that the susceptibility of skin to environmental tumor promoters is dependent on age (Berking et al., 2004).

      Exposure to ultraviolet (UV) radiation is a risk factor for the development of melanoma. Researchers have shown that people who sunburned in childhood are at a greater risk of developing melanoma than are people who sunburned in adulthood. This study suggests that age is associated with the susceptibility of skin to environmental carcinogens.

    4. This increase in cell numbers in the treated cultures could not be accounted for solely by a proliferative effect, pointing to a possible role for Edn3 in the survival of melanoblasts from the NC (Opdecamp et al., 1998).

      Mutations in genes that code for Edn3 result in deficiencies in melanocytes. Edn3 serves as a stimulator of melanoblast proliferation and differentiation. When melanoblasts differentiate, they become melanocytes.

    5. Edn3 was most effective in promoting the long-term propagation of glia-melanocyte precursor cells as opposed to the other precursors (Real et al., 2006).

      Researchers have shown that individual melanocytes produce multipotent cells that are able to regenerate during consecutive subcloning. This indicates that the multipotent cells display stem cell qualities. Edn3 encourages the maintenance of the multipotent cells. Moreover, Edn3 stimulates the proliferation of melanoblasts, which are the precursors of melanocytes.

    6. cells treated with Edn3 were found to proliferate for two weeks without producing pigment (Lahav et al., 1996).

      Cells proliferate in the presence of Edn3. The cells that are produced are melanoblasts, which subsequently become melanocytes.

    7. It was first identified as a potent vasopressor derived from vascular endothelial cells (Yanagisawa et al., 1988).

      Researchers isolated Edn1 to determine its function. Edn1 was shown to be responsible for an increase in blood pressure. Expression of the gene was controlled by factors that affect blood vessels, suggesting that there is a cardiovascular control system.

    1. evidence in alcoholism has already shown disruptions in the balance of action control for appetitive behavior

      Alcohol use in humans alters brain regions involved in goal-directed behaviors, which can lead to an increase in habit-learning behaviors in these patients.

      There is a shift from goal-directed actions towards habitual actions in patients with alcohol dependency. It is possible that alcohol-seeking behavior alters the capacity of individuals to shift between these two types of behaviors.

    2. manipulations of dopamine neurotransmission alter instrumental learning

      Participants with Parkinson's disease have deficits in learning from trial and error. They also had difficulty learning from a positive outcome. Dopamine administration allowed participants with Parkinson's to learn from both positive and negative outcomes, suggesting that their impairment resulted from depletion of dopamine in the basal ganglia.

    3. compulsive cocaine-seeking, even in the face of aversive consequences

      Impulsivity in rats’ behavior is what leads to compulsive cocaine-seeking behavior despite negative outcomes.

    4. impairments in the initiation of goal-directed avoidance behavior have previously been reported

      Animals under dopamine depletion or blockade respond to fear conditioning by urinating, but they fail to respond by avoiding electric shock. These animals show a deficit in initiating a response, but they do not show deficits in their ability to learn associations.

    5. Cocaine administration also diminishes information processing about consequences

      Rats who were given cocaine respond normally to tasks that are meant to completely remove an association with a stimulus. However, they did not respond normally to tasks that were meant to devalue an association with a stimulus, suggesting they were unable to use new information about consequences to guide their behavior.

    1. Reports of plastic pollution in the ocean first appeared in the scientific literature in the early 1970s

      Plastic pollution in the ocean has been known to be a problem for a long time.

    2. In 1975

      This early work (reference 1) looked at which types of pollutants might pose a future threat to ocean resources and mechanisms of how each pollutant ended up in the ocean.

    1. Populations at lower latitudes have darker pigmentation than populations at higher latitudes, suggesting that skin pigmentation is an adaptation

      The work of Jablonski and Chaplin strongly supports the theory that melanin pigmentation in human skin is an adaptation that helps regulate the amount of UV radiation that gets into the epidermis, with different populations having different selective pressures based on their environments.

      They argue that protection against UV breakdown of nutrients (such as folate) was the primary selective agent that led to darker pigmentation of people living near the equator, because folate is closely linked to reproductive success in humans.

      Jablonski and Chaplin also argued that skin pigmentation is so responsive to environmental conditions that it is not valuable when assessing the genetic relatedness of human groups.

    1. Herein, we use a simulation approach to estimate AGB and tree biodiversity within large permanent plots from six Neotropical forests representing a broad gradient in tree species richness (88–821 species among trees ≥ 10 cm in diameter at 1.3 m height [dbh] per 50 ha plot) and forest structure (AGB of 283–494 Mg ha−1)

      Table 2 shows the area, dimension, year of census, aboveground tree biomass, species richness, and stem density in plots that are permanently placed in six Neotropical Forests. This is pre-existing information.

    2. Tropical forests have long been recognized to harbor a significant proportion of global biodiversity 

      Biodiversity experiments have been performed on tropical forests and it has been concluded that they are a large portion of the Earth's biodiversity.

    1. Hulme 2005

      This is from a journal: Applied Ecology. The author discusses climate change and how it is negatively impacting global ecosystems and how not much is being done to alleviate the problem.

    2. (Stanton and Ackerman 2007)

      This is a report commissioned by the EDF. It is an analysis on the consequences of letting climate change continue unchecked on the economy of Florida.

    3. Ferrati et al. 2005, 

      The objective of this study was to measure the hydrometerological and hydrological aspects of Esteros del Ibera.

    4. (Burkett and Kusler 2000)

      This author's research is focused on wetlands and global climate change impact on them.

    5.  Erwin 2009)

      The author's research centers around the global impact of climate change on the world. He brings into question how wetland systems (most vulnerable) will be impacted and how, if there is a way to save them.

    6. (Davis and Ogden 1994)

      Everglades: The Ecosystem and Its Restoration. This book summarizes recent studies on the vegetation, alligators, wading birds, and endangered species. It also covers the physical driving forces that created and continue to shape the everglades and patterns and processes of its flora and fauna.

  9. Apr 2018
    1. A squid host lacking luminous symbionts is affected not only in its behavior but also in other features of the symbiosis.

      See Dr. Margaret McFall-Ngai discuss the daily behavior patterns of the bobtail squid and why counterillumination is important for its survival:

      Daily behavior of the Hawaiian bobtail squid.

    2. mutant V. fischeri strains defective in light emission (lux mutants) have demonstrated that symbiont luminescence somehow participates in the transformation of the organ from its juvenile morphology

      The lux genes in Vibrio fischeri code for the proteins that produce bioluminescence.

      Visick et al. (2000) created three mutant lux genes that were unable to produce bioluminescence. The mutant strains of V. fischeri carrying the modified genes were used to test whether bioluminescence was a key factor in development from juvenile to adult.