3,014 Matching Annotations
  1. Jun 2019
    1. biogeochemical exchanges among Earth’s soil, water, and atmosphere.

      A 2019 study highlighted the need to update how the water cycle is taught in school to include human interference.

      Read more in Science Daily.

    1. resulting in a significant gender × condition interaction

      Interaction effects occur when the effect of one variable depends on another variable.

      In this case, the effect of the intervention (values affirmation or control) depended on the student gender (male or female).

    2. The gender gap in the learning of physics concepts was substantial in the control condition (d = 0.46) (F1,304 = 6.23, P = 0.01), indicating that men improved their FMCE scores more than women over the semester. In the affirmation condition, however, this gender learning gap entirely disappeared

      Values affirmation erased the gender gap in the Force and Motion Conceptual Evaluation.

      Women who did not affirm values did not increase their scores on the FMCE from the first test to the second test as much as men did. However, women who did values affirmations had score increases similar to men.

    3. Values affirmation reduced the male-female performance and learning difference substantially

      Watch this video for an overview of values affirmation:

      https://www.youtube.com/watch?v=6TWMiTSjJ0Y

    4. improve the performance of stereotype-threatened individuals

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

    5. lab studies show

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

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

    1. Our observations suggested, consequently, that opiate peptidergic and catecholaminergic traits may be differentially regulated in the adult medulla.

      The results described in the previous two sentences suggest that each class of transmitters are regulated differently in the adult medulla.

    2. petrosal and nodose neurons

      Brain cells in a group of nerves found at the base of the skull. The nodose and petrosal neurons are part of the vagus and glossopharyngeal nerves, respectively.

    3. methylates

      Introduces a methyl (CH<sub>3</sub>) group. Here, PNMT adds a CH<sub>3</sub> group onto norepinephrine creating epinephrine (also known as adrenaline).

    4. sympathetic superior cervical ganglion in adult rats

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

    5. At this early stage in our understanding,

      The field of neuroplasticity evolved and expanded since this exploratory 1984 research. While there is still ample debate on the plasticity of our brain cells in adulthood, scientists generally agree that neurons are less flexible as we age. Read more in Science, (this resource can also be found in the Related Content tab).

    6. caudal thoracic

      Situated in the tail part of the body.

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

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

    8. neuronal plasticity

      Check out this video primer on Neuroplasticity from Khan Academy.

    9. grown in dissociated cell culture

      Neurons are separated from the animal through mechanical or enzymatic disruption. The separated neurons are transferred to dish or culture plate. The neurons are maintained in the dish.

    1. We have developed and employed optogenetics technology

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

    2. optogenetics allows genetically targeted photosensitization of individual circuit components

      The specificity of optogenetic treatments are of particular clinical interest and relevance for neuroscientists. Because individual cells can be targeted in the living organism, optogenetics allows scientists to better understand how different brains cells function and communicate.

    3. matter of controversy

      Check out this 2019 episode of NPR's podcast, Invisibilia for more on what's it's like to be a patient treated with DBS. https://www.npr.org/2019/03/28/707639854/the-remote-control-brain

    1. zona incerta (ZI)

      A part of the brain.

      The function of this area is poorly understood but is thought to regulate behavior of an animal in response to internal (such as hunger) and external (such as pain) sensory cues.

    2. γ-aminobutyric acid (GABA)

      An inhibitory neurotransmitter. Neurons communicate with each other by releasing neurotransmitters. Neurons respond to inhibitory neurotransmitters by reducing their activity.

    3. Our study provides a potential explanation for why clinical deep brain stimulation in the ventral thalamus near the ZI can increase binge eating.

      Deep brain stimulation sometimes causes binge eating in Parkinson’s patients, now scientists might know why.

      Read more in Scientific American: https://www.scientificamerican.com/article/electric-brain-stimulation-offers-binge-eating-clue/

    4. Based on retrograde rabies virus and anterograde AAV tracing, ZI axonal projections to the excitatory neurons of the PVT appear more robust than those from other known regions of the brain involved in food intake, suggesting the ZI is not a minor component

      More so than any region of the brain studied so far, ZI GABA neurons and their projections promote binge-like eating behavior.

    5. Intraperitoneal CNO

      The CNO was injected into the peritoneum, the thin membrane that lines the walls of the abdominal cavity. It travels through the circulation and crosses the blood brain barrier and affects its target cells.

    6. type A GABA (GABAA) receptor antagonist bicuculline (Bic)

      A light-sensitive competitive agonist of GABA<sub>A</sub> receptors. It was originally isolated and identified over 40 years ago in the Dicentra cucullaria plant.

    7. Bic attenuated photostimulation-evoked feeding (Fig. 2K). That Bic did not completely block photostimulation-evoked food intake could be a diffusion limitation of Bic after application, or ZI VGAT-Cre neurons may coexpress other neurotransmitters responsible for the remaining action.

      The authors found that blocking the function of the GABA receptor (GABA<sub>A</sub> receptor) in the PVT could blunt the increase in food intake mediated by stimulation of ZI terminals in the PVT. This suggests that GABA is an important neurotransmitter underlying this effect.

      The limitations of this approach include that the authors cannot control the spread of the GABA<sub>A</sub> receptor blocker or that other neurotransmitters might be involved.

  2. May 2019
    1. Brain slice electrophysiology confirmed that optogenetic activation of PSTh glutamatergic neuron terminals in the PVT evoked strong glutamate-mediated postsynaptic excitatory currents in PVT vGlut2-GFP neurons, suggesting a functional role for PSTh glutamate neurons in the synaptic excitation of PVT glutamate neurons

      The authors confirmed that stimulation of the PSTh terminals in the PVT was able to activate PVT neurons, i.e. induce excitatory activity in the PVT cells.

      This confirms the rabies tracing result and shows that the connection between the PSTh and the PVT is functional.

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

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

    3. In the absence of available food, optogenetic activation of the VGATZI-PVT pathway evoked a significant preference for the chamber associated with laser stimulation compared with the control chamber

      The mice preferred to spend more time in the compartment where they received stimulation of the ZI-PVT pathway. This suggests that stimulation of the neurons is pleasurable for the animal.

    4. by using a two-chamber place preference test

      The authors hypothesized that because the ZI to PVT projection promotes intake of foods that are pleasurable to eat and also makes mice overcome their aversion to light in order to eat that food, that stimulation of this pathway is pleasurable or rewarding for the mice.

      They tested this by placing the animals in a box with two identical compartments. The mice were able to freely move around the box. On one side of the chamber the mice received stimulation of their ZI-PVT neurons while the stimulation was turned off when the mice were on the other side.

    5. motivational valence

      The degree to which something is perceived as pleasurable (positive valence) or unpleasant (negative valence).

    6. This is almost 100 times faster than that reported for optogenetic stimulation of the AgRP neuron soma and 500 times faster than stimulation of AgRP-PVT axon terminals (19, 20). As soon as the laser was turned off, the mice stopped eating.

      The authors wanted to compare the latency of eating onset upon stimulation of ZI projections to the PVT versus that of agRP neurons, which are known to promote food intake in response to hunger.

      They found that mice start to each much faster than mice did in previous reports where AgRP neurons were stimulated or when agRP projections to the PVT were stimulated.

    7. To test the time course and efficiency of optogenetic activation of VGATZI-PVT inhibitory inputs to evoke feeding, we used a laser stimulation protocol of 10 s ON (20 Hz) followed by 30 s OFF for more than 20 min to study ZI axon stimulation in PVT brain slices and feeding behavior. Stimulation of ZI axons with this protocol hyperpolarized and inhibited PVT glutamatergic neurons each time the light was activated (Fig. 3A). Mice immediately started feeding for each of the 30 successive trials of ZI axon laser stimulation (Fig. 3B and movie S4). The mean latency to initiate feeding was 2.4 ± 0.6 s when we used laser stimulation of 20 Hz (Fig. 3C).

      The authors followed an optogenetic protocol by intermittently turning on the stimulation light for 10 seconds followed by 30 seconds of no stimulation. With each 10 seconds of light on, they measured how long it took for the mice to begin eating.

    8. ZI GABA neurons project to multiple brain regions, including the hypothalamus and midline thalamus (fig. S6). We therefore measured the relative contribution of stimulation of ZI somata with selective stimulation of ZI axons targeting the PVT. Stimulation of ZI VGAT cell bodies or VGATZI-PVT terminals in the PVT evoked similar levels of feeding

      This suggests that even though ZI GABA neurons project to other brain regions in addition to the PVT, the PVT projection appears to be the most important mediator of increased food intake.

      This is because ZI GABA cell body stimulation and stimulation of the projections to the PVT evoked similar degrees of food intake.

    9. Anterograde

      Occurring along the nerve processes away from the neuron body, as opposed to retrograde.

    10. Food deprivation lasting 24 hours increased inhibitory synaptic neurotransmission to PVT glutamate neurons

      In food-deprived mice, PVT glutamate neurons receive more inhibitory inputs compared to fed mice. These may come from ZI inhibitory GABA neurons, which the authors demonstrated to have increased activity upon food deprivation.

    11. confirmed that PVT glutamate neurons receive strong and direct innervation from ZI neurons

      The authors confirm their anterograde tracing findings using retrograde tracing to show that ZI GABA neurons send projections to excitatory neurons in the PVT.

    12. optogenetic stimulation

      A technique that uses light to control the activity of cells, most commonly neurons, in living animals. The cells are genetically modified to express ion channels that are sensitive to light. Shining light on the neurons changes their activity allowing scientists to understand the role of the neuron in a given behavior or physiological process.

    1. will stand for no amino acid—that is, will be nonsense

      As a general rule, there are four kinds of codons: codons that initiate the reading frame, codons that stop the reading frame, codons that code for amino acids to make proteins, and codons that don't code for anything at all (called nonsense codons).

    2. The experimental proof of the colinearity of a gene and the polypeptide chain it produces may be confidently expected within the next year or so.

      Crick proposed that a gene was a linear sequence of nucleotides, where each gene encoded a single protein. However, this explanation is a bit too simplistic, especially for higher-level and multicellular organisms.

      In fact, we now know that colinearity is generally the exception, not the rule, in eukaryotic genomes.

      For more information, check out this piece in Nature Education: https://www.nature.com/scitable/topicpage/what-is-a-gene-colinearity-and-transcription-430

    3. In spite of the uncertainty of many of the experimental data, there are certain codes which have been suggested in the past which we can now reject with some degree of confidence.

      Science is a way of knowing.

      Science is both a body of knowledge that represents a current understanding of natural systems and the processes used to refine, elaborate, revise, and extend this knowledge.

    4. If the code does indeed have some logical foundation, then it is legitimate to consider all the evidence, both good and bad, in any attempt to deduce it. This is not true if the codons have no simple logical connection.

      Scientific knowledge is open to revision in light of new evidence.

      Scientific argumentation is a mode of logical discourse used to clarify the strength of relationships between ideas and evidence that may result in revision of an explanation.

    5. in response to a letter of

      Science benefits when scientists communicate and collaborate across disciplines.

      Science would make little progress without the exchange of ideas, especially across different disciplines. Here George Gamow, a theoretical physicist, shares his ideas about the genetic code with Linus Pauling, one of the pioneers of quantum chemistry.

      http://scarc.library.oregonstate.edu/coll/pauling/dna/corr/sci9.001.43-gamow-lp-19531022.html

    6. Deductions

      Crick relies on deductive reasoning to make his argument for the nature of the genetic code.

      Deductive reasoning draws specific conclusions from general principles or premises, whereas inductive reasoning infers general principles from specific instances.

    7. The code is probably much the same in different organisms.

      You may have heard about this concept before, maybe even hearing that we humans share 50% of our genes with bananas!

      However, the story is a bit more complicated; in fact, genes (that is, regions coding for proteins) comprise only about 2% of our DNA. About 8% of our genes are involved in regulatory functions and the other 90% is mostly non-functional.

      Because of our shared evolutionary ancestor (approximately 1.6 billion years ago), bananas and humans have a lot in common!

    8. It is possible that some triplets may code more than one amino acid—that is, they may be ambiguous.

      While most amino acids are encoded by at least two codons (with the exception of methionine and tryptophan), the reverse is not true. Each codon specifies just one amino acid or stop signal. Thus, the genetic code is unambiguous.

    9. In general, more than one triplet codes each amino acid.

      In other words, the same amino acid is coded by more than one base triplet. For example, there are six different codon combinations to encode arginine. This property is now known as degeneracy.

    10. We’re often told that DNA is genetic information. But how exactly does DNA, a molecule, contain information? Francis Crick—who discovered the structure of DNA along with Rosalind Franklin, James Watson, and Maurice Wilkins—had the same question. In this 1963 review, Crick lays out his hypotheses and analyzes the evidence that supports a genetic code. He concludes with a wondrous inquiry: Do all living things share the same code? Do plants, bacteria, animals and humans all share the same language of life?

      BR suggestions:

      We’re often told that DNA is "genetic information." But how exactly does DNA, a molecule, contain information? Francis Crick—who discovered the structure of DNA along with Rosalind Franklin, James Watson, and Maurice Wilkins—had the same question. In this 1963 review, Crick lays out his hypotheses and analyzes the evidence that supports an organized system of information within DNA that can be converted into other information--a genetic code. He concludes with a wondrous inquiry: Do all living things share the same language of life?

    1. reduced contact area that slide against the DLC surface, achieving an incommensurate contact

      With a combination of materials (graphene, nanodiamond particles and DLC), the researchers where able to demonstrate the formation of nanoscrolls, which reduced the overall contact area between two sliding interfaces, leading to substantially decreased friction.

    2. molybdenum disulfide (MoS2)

      Check out this article and podcast from The Royal Society of Chemistry about the remarkable properties of molybdenum disulfide.

    3. this coincides with COF values dropping substantially, leading to a superlubric state that is maintained until the end of the simulation.

      Learn more about how the computer simulation led to the discovery of a novel superlubric combination of materials.

    1. protospacer flanking sites (PFSs)

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

    2. DNA base editors, consisting of a fusion between Cas9 nickase and cytidine deaminase, can mediate efficient cytidine-to-uridine conversions within a target window and substantially reduce the formation of double-strand break–induced indels

      DNA base editing is a technique which allows precise conversion of one nucleotide into another without any template sequence.

      A base editor is a fusion protein made up of a protein that recognizes specific DNA sequences (for example, Cas9), and a deaminase that can convert one amino acid to another (i.e., cytidine [C] to uridine [U] or adenosine [A] to inosine [I]).

      Because of the geometry of the proteins, this conversion can only happen in a certain range of nucleotides, called the target window.

  3. Apr 2019
    1. This prototype includes a MOF-801 layer (packing porosity of ~0.85, 5 by 5 by 0.31 cm, containing 1.34 g of activated MOF), an acrylic enclosure, and a condenser

      Since this paper was published, the authors refined and optimized the devise and tested it under desert conditions with record high efficiency.

      See "Related Content" tab for: Kim, Hyunho, et al. "Adsorption-based atmospheric water harvesting device for arid climates." Nature communications 9.1 (2018): 1191.

    1. biclustering

      A technique that identifies and clusters groups, specifically for two separate clusters.

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

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

    3. Some early-life events that are generally thought to affect adult microbiota composition were not associated with microbiota composition variation in our study, including mode of birth [cesarean section (N = 36) or vaginal delivery (N = 1036)], place of birth [home (N = 207) or hospital (N = 899); increased diversity in home-born individuals, FDR>5% when controlling for age], and infant nutrition [breastfed (N = 537) or not breastfed (N = 359)]

      Their study suggests that early-life events, such as birth method or nutrition, do not have any significant correlations with the adult microbiome.

    4. Sixty-nine clinical and questionnaire-based covariates were found associated to microbiota compositional variation with a 92% replication rate.

      The study found 69 dependent factors from clinical-based—that is, measurements taken by doctors—and questionnaire-based—that is, provided by the patients about their lifestyle—data. They found that for 92% of the factors that had a counterpart in an independent study (=LLDeep study), these factors were still significantly associated to variation in microbiome composition.

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

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

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

    1. polynucleotide

      Poly means many, and a nucleotide is the building block of genetic material. Therefore, a polynucleotide is a chain of many nucleotides—or one strand of genetic material.

    2. having about equal amounts of uracil and cytosine in (presumably) random order, will increase the incorporation of the amino acids phenylalanine, serine,  leucine, and proline, and possibly threonine.

      As seen in the figure below, random triplet combinations of U and C are now known to encode for the amino acid residues Crick suspected.

    1. Type VI CRISPR-Cas systems

      CRISPR is a family of DNA sequences that are part of the immune system of bacteria. CRISPR enzymes detect specific viral DNA or RNA sequences, and can cleave the invading sequences and destroy them. Recently, researchers have begun to use CRISPR as a highly accurate tool for detecting specific DNA sequences in their research.

      Type VI CRISPR-Cas systems are those that involve the protein Cas13, which can cut RNA molecules.

    2. ortholog

      Genes in different species that can be traced to a common ancestral DNA sequence.

      There are many different Cas9 and Cas13 orthologs from different bacterial organisms. As engineers, the researchers test many of them as they will have different levels of activity in mammalian cells (as compared to bacterial) and some might not work at all.

    3. nonhomologous end joining (NHEJ)

      When both strands of DNA are cut, a cell can repair the DNA by rejoining the two strands. Nonhomologous end joining is one way this repair can happen, and it does not require homologous (similar) sequences.

      Because the sequences do not have to be homologous, this process is imprecise and can result in deletions or insertions.

    4. homology-directed repair (HDR)

      A process of precise DNA editing in which a cell uses homologous (similar) sequences as a template to repair DNA.

      This method is more precise than nonhomologous end joining (NHEJ), but takes more time. It's also generally less efficient and does not operate on non-dividing cell types like neurons.

    5. catalytically inactive

      The job of enzymes is to make chemical reactions happen faster. An enzyme that is catalytically inactive does not accelerate chemical reactions.

      Cas13 catalyzes the cleavage (cutting) of RNA molecules. This is an important function of the bacterial immune system, where Cas13 helps protect the organism from invading RNA.

      To use Cas13 for RNA editing, the researchers created a catalytically inactive enzyme (dCas13) that can be used to target RNA without cutting it and allowing for recruitment of other enzymes to the RNA.

    6. Endogenous

      Native to a system (i.e. not the result of changes by external factors). Endogenous targeting here means the normal target sites for the ADAR protein in the cell.

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

      Two types of neurons: Trigeminal neurons and nodose neurons are discussed here.

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

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

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

  4. Mar 2019
    1. The key features of success of the new lineage are reproductive isolation based on learned song and morphology, transgressive segregation producing novel phenotypes, and the availability of underexploited food resources.

      Here, the authors list the main reasons that this hybrid lineage survived and reproduced rather than dying out or mating with members of the parental species.

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

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

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

    3. The low values probably represent low additive genetic variation because the traits are highly heritable in Geospizaspecies

      The authors conclude that their measurements, both genetic (inbreeding coefficient, admixture, average nucleotide diversity) and bill shape (length and depth) do show low levels of variation in the Big Bird population.

      They conclude that this is expected because the bill shape traits are highly determined by genes, and so low genetic diversity would lead to low physical diversity of certain traits, such as bill shape.

    4. A gradual increase in homozygosity was then observed over the next five generations (Fig. 2D), as expected from the small number of breeding pairs

      The authors measured genetic diversity through the inbreeding coefficient and average nucleotide diversity, finding that the pattern of decreasing genetic diversity was as expected for an inbreeding population.

    5. the founder male (5110) was not a G. fortis x G. scandens hybrid as previously hypothesized (12), but a G. conirostris

      This conclusion of the authors is a reclassification of the founder male into a different species than previously thought, based on the genetic analysis.

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

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

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

    7. We followed the survival and breeding of this individual and its descendants for six generations over the next 31 years.

      The Grants began studying finches on Daphne Major Island in 1972. Along with team members, they returned there every year until 2012 to observe the finches. Observations included identities of mating pairs, number of offspring (used to construct pedigrees) and mortality of birds (recording deaths of birds).

      The techniques used include catching the birds and banding them (installing identification bands around their legs), as well as taking measurements of the birds (including body mass and beak measurements). Blood samples were also collected for later DNA analysis.

    8. homoploid hybrid speciation, is rare

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

    9. This example shows that reproductive isolation, which typically develops over hundreds of generations, can be established in only three.

      Read more from two of the authors of this paper explaining how Darwin's finches in the Galapagos provided the basis for novel insights into genetic divergence.

      In Science: http://science.sciencemag.org/content/355/6328/910

    10. bill

      As in, a bird's beak.

    1. DBS can also encounter limitations as a therapy even for the symptoms that typically respond.

      Part of the ambition in this paper was identifying the contributions of different neurons in a parkinsonian brain. Using optogenetics to better understand DBS can hopefully/theoretically lead to more effective therapies in the future. Read more from The Cellular Scale.

    2. A major promise of optogenetics has been the potential for dissection of disease circuitry and treatment mechanisms.

      Learn more about the history and potential of optogenetics from Karl Deisseroth's piece in Scientific American.

    3. an array of measures ranging from rotational behavior (Fig. 6D) to head position bias and locomotion

      Motor behavior was assessed using amphetamine-induced rotations, head position bias, and locomotion.

      Rotations were performed by injecting amphetamine 30 minutes prior to trial and placing the animal in an opaque cyclinder. Ipsilateral (same side as) rotations to the 6-OHDA lesion (clockwise) were added and contralateral (opposite side as) rotations were subtracted.

      Head position bias was determined by the number of head tilts over time, where a greater than 10 degree deviation left or right from midline was measured.

      Locomotion was measured using a software called Viewer that tracked motion and calculated distance.

    4. To probe the functional connectivity between these layer V projection neurons and STN in the PD animals, we conducted a separated-optrode experiment in anesthetized animals in which the fiber-optic and recording electrodes were placed in two different brain regions in Thy1::ChR2 animals

      Based upon previous findings that the cortex and STN are connected, the investigators wanted to know if driving M1 layer V neurons had an effect on STN neuronal firing and subsequent behavioral output. So they placed an optrode over M1 and a recording electrode in the STN.

    5. ameliorated

      Improved.

    6. we used Thy1::ChR2 transgenic mice (22, 23) in which ChR2 is expressed in projection neurons, and we verified that in Thy1::ChR2 line 18, ChR2-YFP is excluded from cell bodies in the STN but is abundant in afferent fibers

      Thy1 (thymocyte differentiation antigen 1) is expressed in the axonal projections of mature neurons. When its promoter is placed in control over ChR2 expression, the protein would be expressed in the projection neurons as opposed to the somata of local neurons.

    7. Therapeutic effects could arise from driving axonal projections that enter the STN

      In other words, beneficial effects could arise by activating or targeting axonal projections entering the STN as oppossed to direct STN interventions.

    8. indeed, as expected from our light-scattering measurements and tissue geometry, we found that at least 0.7 mm3 of STN is recruited by light stimulation, which closely matched the actual volume of the STN

      Measuring the area of c-fos activated neurons upon light stimulation provided the authors with support for using an optrode to stimulate the STN since the area activated closely matched the true volume of the STN.

    9. Because simple inhibition of excitatory cell bodies in the STN did not affect behavioral pathology and because HFS (90 to 130 Hz) is used for electrical DBS, we used ChR2 to drive high-frequency oscillations in this range within the STN.

      Since inhibiting excitatory neurons in the STN with eNpHR and activating glial cells with ChR2 were both insufficient at correcting motor deficits in hemiparkinsonian rats, the authors attempted to mimic the high frequency stimulation using ChR2 in the excitatory neurons.

    10. the direct activation of local glial cells appeared not to be sufficient to treat parkinsonian symptoms, pointing to consideration of other circuit mechanisms.

      When blue light passed through the optrode to the STN, neuronal firing was inhibited by activating ChR2-expressing astrocytes. ChR2 allowed for the influx of calcium into astrocytes causing a release of glutamate and adenosine into the cellular environment. Adenosine would then bind to adenosine A1 receptors and inhibit neuronal firing. Even though they were able to inhibit firing, motor pathology was still unaffected by this intervention alluding to other circuit mechanisms.

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

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

    12. To inhibit the excitatory STN neurons directly, we delivered lentiviruses carrying eNpHR under the CaMKIIα promoter to the right STN of the hemiparkinsonian rats. CaMKIIα::eNpHR labeled with enhanced yellow fluorescent protein (EYFP) expression was specific to excitatory neurons

      Second generation lentiviruses encoding the enhanced halorhodopsin were created using three plasmids.

      One plasmid containing the gene of interest (eNpHR) under the control of the promoter (CaMKIIα) is called the transfer vector. The transfer vector usually encodes for a fluorescent gene to monitor expression, in this experiment, enhanced yellow fluorescent protein (EYFP) was added after the eNpHR sequence.

      A second plasmid containing the envelope gene, usually VSV-G (vesicular stomatitis virus), that allows for a broader degree of infectivity in various cells. The third plasmid contains all of the packaging genes necessary to create a functional viral unit.

      When all three plasmids are added to HEK293 cells (human embryonic kidney), viral particles are released from the cells and suspended in the culture media. Learn more about lentiviruses here.

    13. nigral

      Referring to the substantia nigra, a part of the brain rich in dopamine neurons.

    14. The STN is a predominantly excitatory structure (30) embedded within an inhibitory network. This anatomical arrangement enables a targeting strategy for selective STN inhibition (Fig. 1B), in which enhanced NpHR (eNpHR) (21) is expressed under control of the calcium/calmodulin-dependent protein kinase IIα (CaMKIIα) promoter, which is selective for excitatory glutamatergic neurons and not inhibitory cells, fibers of passage, glia, or neighboring structures

      Since the subthalamic nucleus is excitatory, meaning the neurons within release the neurotransmitter glutamate, selectively targeting this region can be accomplished via the promoter calcium/calmodulin-dependent protein kinase II alpha (CaMKIIα). Placing a gene downstream of the CaMKIIα promoter will cause the gene to be selectively expressed only in excitatory neurons.

      The authors placed the gene sequence for halorhodopsin under the control of the CaMKIIα promoter and were able to selectively inhibit the firing of excitatory glutamatergic neurons in the subthalamic nucleus.

    15. based on single-component microbial light-activated regulators of transmembrane conductance and fiber optic– and laser diode–based in vivo light delivery

      Opsins are transmembrane proteins (passing through the cell membrane) that are ion channels/pumps which allows for various ions like sodium, potassium, hydrogen, chloride, and calcium to move in or out of the cell.

      There are three main family of opsins: channelrhodopsins, halorhodopsins, and bacteriorhodopsins. Each opsin is light sensitive due to a chromophore retinal molecule within the transmembrane domain of the channel and each family is sensitive to a specific wavelength of light.

    16. Therefore, optogenetics, in principle, could be used to systematically probe specific circuit elements with defined frequencies of true excitation or inhibition in freely behaving parkinsonian rodents.

      This group has led the field of optogenetics by setting the groundwork for how this "tool" can be employed in neuroscience research.

    17. halorhodopsins

      Halorhodopsins, and bacteriorhodopsins, typically inactivate neurons by driving chloride ions into the cell or hydrogen ions out of the cell and causing the membrane potential to become more negative leading to hyperpolarization.

    18. channelrhodopsins

      Channelrhodopsins are employed to activate neurons by driving cations (including sodium, calcium, hydrogen, and potassium) into the cell and causing the membrane potential to become more positive leading to depolarization.

    19. major depression

      To learn more about deep brain stimulation as a treatment for depression, check out this 2018 article in The Atlantic.

    1. opiate peptides

      Peptides that bind to opioid receptors in the brain.

    2. de novo

      Meaning "from the new;" in this case, the first appearance of the enzyme.

    3. putative

      Generally considered or reputed to be.

    1. Focusing on the prevalent concern of BMI increase and suboptimal health, we assessed the sample size needed to evaluate microbiota compositional changes associated to obesity. To do so, we calculated the independent effect sizes of obesity status, gender, age, and BSS on microbiota variation (table S16). This allowed us to estimate that 865 lean (BMI <25) and 865 obese (BMI ≥30) volunteers would be necessary to study microbiota compositional shifts with P < 5% significance level and a power of 80%. When taking into account gender, age, and BSS score as covariates, the estimated sample size was reduced to 535

      Since there is recent concern regarding the association of BMI increase and poor health, the authors wanted to know how large a sample they would need to identify microbiota changes that could be associated with BMI. They did this by conducting a power analysis which allowed them to determine that the sample size needed to detect changes in microbiome composition associated with obesity (with a false positive score below 5% and 80% probability of detecting a real effect if it is present) is 535 samples when taking into account gender, age, and BSS score as covariates.

    2. Residence type [ranging from countryside (N = 77) over rural village (N = 500), small town (N = 272), suburb (N = 137), to city (N = 102)] during early childhood (up to 5 years old), one of the 69 FGFP microbiome covariates, was linked to adult microbial community composition, with a positive correlation between evenness and residence in more industrialized areas, though not statistically significant (FDR >5%) when correcting for age, gender, and BMI

      They found an association between the type of residence the participants lived in as a child (i.e. rural, urban) and their adult microbiota composition. Moreover, individuals that grew up in industrialized areas showed a more even microbial composition than those that grew up in rural areas—however these results were not statistically significant when correcting for age, gender, and BMI.

    3. potential niche differentiation within the colon ecosystem

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

    4. Dirichlet multinomial mixtures

      Refers to a computational technique to model the probability of microbial metagenomics data by representing the data as a frequency matrix of the number of times each taxa is observed in a sample.

    5. Interindividual variation in microbiota composition mainly resulted from changes in relative abundance of core taxa

      Microbiome variation between individuals was largely a result of changes in relative abundance of the core taxa.

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

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

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

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

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

    8. these results by no means imply that early-life events do not affect microbiota assembly during infancy, nor do they question previous associations with disease or allergy (36, 37); our analyses only indicated that such events were not significantly associated with microbiome composition at adult age in the FGFP cohort

      The authors acknowledge that these early-life events may affect microbiota development during infancy, but did not observe an effect of these events on the microbiota composition at adult age in their cohort.

    9. The cluster was predominantly composed of women, individuals with a lower weight, and participants with a longer transit time, as reflected both by stool consistency and time since previous relief. Both microbiota richness and evenness were elevated in this cluster.

      When clustering the data based on taxonomic characteristics, one subset was predominantly female, having lower weight and low Bristol stool scale score and a longer time since last defecation. These individuals showed more equal and higher quantities of different microbial taxa.

    10. The presence of Fusobacterium could not be linked to any of the nonredundant covariates identified in this study, which could indicate the specificity of its association with colorectal cancer

      The authors could not find any correlation between the presence of Fusobacterium and the set of 18 nonredundant covariates, suggesting that its presence is specifically associated with colorectal cancer.

    11. To achieve a balance between number of phenotypes of interest and rates of false discovery, a stepwise approach was applied.

      The researchers wanted to ensure that the phenotypes of interest were not falsely correlated with microbiota genera. To avoid overfitting, they reduced the phenotypic data in different stages. By approaching the problem in a series of distinct stages, the researchers could determine the most important variables that affect the abundance and diversity of gut microbiota.

    12. Independently of gender, genus richness correlated positively with age, whereas total core abundance decreased

      Researchers found that as both males and females age, the number of genera increases. However, age was negatively correlated with abundance of core genera.

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

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

    2. This is a huge gap from a statistical perspective, but it must be understood as reflecting the state of public sentiment at the very beginning of a new public issue and is thus not guaranteed to persist

      The authors note that there is a large gap in their confidence interval, which indicates that there is not public consensus. They point out that this is because autonomous vehicles are a relatively new issue, so different people have thought about it more or less.

      As people get used to the idea and think about it more, the gap is expected to narrow.

    3. global outcome

      Outcome on the whole community, not just individuals.

    4. without actually wanting to buy one for themselves

      Again, the researchers found that participants thought self-sacrificing AVs are good for other people but would not want to buy one for themselves.

    5. broad public exposure and a disproportionate weight in individual and public decisions about AVs

      Even though the situations where AVs would sacrifice their passengers are rare, these are emotional events that would have a large influence on the public despite their infrequency.

    6. autonomous driving in realistic urban environments

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

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

    1. tickling-evoked vocalizations

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

      Check it out with this video from Verge Science.

    1. O2

      AAAS Annual meeting

    2. From our annotated research papers to our trainings and workshops, we're dedicated to bridging the communication gap between scientists and everyone else.

      Beth, Shelby, and I will be in the AAAS Lounge starting at 10am on Friday.

    3. Improve science literacy with Science in the Classroom!

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

    4. Science in the Classroom

      SitC

  6. Jan 2019
    1. If the NPF-NPFR system were to function generally to signal the state of the Drosophila reward system, NPF levels should be increased by rewarding experiences other than mating, such as exposure to intoxicating levels of ethanol. To test this hypothesis, we exposed virgin males to ethanol vapor using an exposure paradigm previously shown to be rewarding (three 10-min exposures spaced by 1 hour) (4).

      Throughout this paper, the researchers have been making the claim that activity of the NPF system signals the fly's "reward state." According to this theory, when the fly experiences something rewarding (such as mating), the amount of NPF in the brain and the activity of associated neurons increases, which in turn leads to a reduced urge to seek additional rewards (such as alcohol). To this end, they have shown that there is an increased amount of NPF in the flies' brains following mating. However, if their theory were true, then the opposite should also be observed. That is, the consumption of alcohol should also increase NPF levels in the brain, since alcohol is also a source of reward (just like mating).

      To test this hypothesis, the researchers decided to measure NPF levels after exposure to both air and an alcohol vapor (the former being neutral/not rewarding, and the latter being rewarding). If their theory about NPF generally signalling reward were true, one would expect to see increased levels of NPF in the brain following exposure to alcohol (just like was observed following mating in Figure 2A).

    2. heads of males subjected to different sexual experiences: rejected-isolated, virgin-grouped, and mated-grouped

      Since past work in Drosophila, mice, and C. elegans has shown that altering NPF/NPY can affect how organisms react to alcohol, the researchers in this study hypothesized that sexual deprivation might lead to changes in levels of NPF in the flies' brains, which in turn caused them to consume more alcohol. To test this, they extracted the brains from male flies with three distinct sexual histories (mated, virgin, and sexually rejected), and measured their NPF levels.

    3. NPF–NPF receptor (NPFR)

      All neuropeptides in the brain work by attaching to specific receptors found on the surface of cells. Think of the cell surface as a wall, the receptor as an electrical outlet, and the neuropeptide as a plug. In order for the neuropeptide (plug) to have any effect, it has to successfully attach to the correct receptor (socket). Furthermore, a particular neuropeptide (say, a three-pronged plug) cannot attach to just any receptor (for example, a two-pronged socket). The receptor and the neuropeptide have to match in order for the system to have any effect.

    4. Finally, we sought to establish whether there was a role for the repellant chemosensory cue

      Since cis-vaccenyl acetate (cVA) is used by females to turn away unwanted mating attempts by males, it is only released by females who have already mated. Virgin females, who may still be looking to mate, do not release this chemical cue. This difference raises the possibility that the increased preference for alcohol amongst the rejected males could be because they smelled this chemical cue (which the mated male flies would not have smelled).

    5. males were exposed individually to decapitated virgin females on the same schedule as the rejected-isolated cohort, using a protocol that results in courtship suppression

      To test this possibility, they exposed the virgin male flies to dead female flies. These virgin males were still exposed to the visual cue of a female fly (especially the rear half of the body where mating occurs). However, they were neither able to mate, nor were they exposed to active rejection by a female.

    6. we compared males that differed in sexual experience but not in housing conditions—that is, mated and virgin males that were both group-housed.

      For the first follow-up experiment, the researchers ensured that both the mated male flies and the virgin male flies were housed in large groups (consisting exclusively of other male flies). This was done to see if social isolation (as the virgin male flies in the initial experiment might have experienced) might have been the cause for the alcohol preference.

    7. was consistently higher for the rejected-isolated cohort

      The researchers found that when given a choice between normal food and alcohol-mixed food, male flies who had mated with female flies did not prefer the alcohol, whereas male flies who had been rejected by the female flies did prefer the alcohol.

    8. We used two distinct sexual experiences to generate two cohorts of male flies.

      To test the effect of sexual experience on alcohol consumption, the researchers first had to create two groups of male flies, each with a different sexual history. They did this by allowing one group to mate freely with multiple different females for four days. This became the "mated-grouped cohort." The second group was only exposed to female flies who had already mated. Female flies who have already mated once will not mate a second time until they have laid their eggs. For this reason, the second group of males experienced repeated sexual rejection by the mated females for four days. This became the "rejected-isolated cohort." These two cohorts, (one mated and the other sexually rejected) could then be tested for the differences between them.

    1. quantify depletion

      The authors used "depletion scores" to compare nucleases. A depletion score quantifies how much expression was reduced by a specific nuclease. The higher the score, the more expression was "depleted."

    2. expression vector

      A type of vector that can use the cell's protein synthesis machinery to express the genes that it carries.

    3. mutagenesis

      Creating genetic mutations.

    4. assayed

      Testing a material to figure out its composition and quality.

    1. we compiled evidence for the earliest dog remains across Eurasia

      Remains aren't the only type of archaeologically significant findings. Recently, cliff drawings were found in northwest Saudi Arabia depicting hunting dogs wearing leashes. These carvings date back to more than 8000 years ago, making them the earliest depictions of dogs ever found.

      Read more in Science Magazine: https://www.sciencemag.org/news/2017/11/these-may-be-world-s-first-images-dogs-and-they-re-wearing-leashes

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

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

    3. We used principal components analysis (PCA), D statistics, and the program TreeMix (12) to further test this pattern.

      Three tools for mining the data for ancestry information.

      Principal components analysis (PCA) simplifies the data. The number of variables is reduced but the trends and patterns are retained.

      D-statistics detects admixture events; it is used to detect gene flow between closely-related species.

      TreeMix is a genetics computer program used to estimate ancestral relationships. It can detect population splits and migration events.

    4. Paleolithic

      Refers to the earliest stage of the time period known as the Stone Age. The Paleolithic period ran from approximately 2.6 million years ago all the way up to about 10,000 B.C.E.

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

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

  7. Dec 2018
    1. Ehrlich, P. R., and P. H. Raven. 1964. Evolution 18: 586-608.

      This reference played an important role in this paper since it also focuses on different insect types (specifically butterflies) and their relationships with a variety of plants. It also serves as a source that elaborated on plant defense mechanisms and how it correlates to herbivores. Although this paper's main focus revolved around evolution, it still brought up many important observations that were relevant to this paper.

    2. Endara, M. J., and P. D. Coley. 2011. Functional Ecology 25: 389-398.

      This reference is very important in understanding how biodiversity and the ecosystem, particularly the fauna, relate to each-other. It sets the base to understanding how it is possible that species of insects and animals can prefer to live or even need to live in a certain fauna/ecosystem.

    3. Populations of white-sand and terra firme ecotypes of Protium subserratum were attacked by herbivore assemblages differing in both abundance and species composition, exhibited significant differences in growth and defense allocation, and expressed qualitatively different secondary compounds. That these phenotypic differences occur in populations involved in incipient (or recent) speciation is consistent with the hypothesis that herbivores interact with environmental gradients to promote the evolution of habitat specialization in plants

      The ultimate summary of the whole paper. It explains why there needed to be side experiment analyzing different variables that would then clarify the conclusion that supports the given hypothesis.

    4. 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.

    5. The existence of this trade-off has been well supported by many different temperate and tropical studies looking at allocation to growth and defense in plants adapted to different light and nutrient availabilities, both within species

      The difference in nutrient resources can affect the size of plants and their maturity which correlates with the previously cited growth-defense-trade-off because the study claims a correlation between the size of the leaf and defense strategies. This may be due to the unique collection of herbivorous insects that prey on the plants.

    6. Finally, it is important to recognize that our sampling was limited to juvenile plants and lasted only 12 months. Insect herbivore populations can strongly vary in different years, and thus, it is possible that our sampling missed important herbivores that are associated with P. subserratum.

      This is a very important limitation to put the results and conclusions of the experiment in perspective. If the sampling may have been done differently the experiment may have revealed different or additional understandings of defense allocation and speciation.

    7. We found that insect herbivores collected from Protium subserratum showed strong patterns of dissimilarity across different habitat types (Fig. 3). Moreover, we found significantly more insects feeding on terra firme plants than on white-sand plants, correlating with the large differences in resource availability between the habitat types. Taken together, these results suggest that there exists substantial variation in diversity and abundance of insect herbivores associated with P. subserratumacross white-sand and terra firme habitats.

      The results showed that there was a strong variation between insect species, habitat types, and abundance. As mentioned before, the terra firme lineage had different growth strategies than the white sand lineage and the terre firme plants were also found to have more herbivores feeding on them. This correlated since the terra firme seemed to provide more resources. The herbivores that were found also showed that they there was a variation across habitats.

    8. unlike most members of the family Burseraceae, P. subserratum does not yield measureable amounts of monoterpenes and only trace amounts of sesquiterpenes

      Those two plants did not produce enough amounts of monoterpenes, a class of organic compounds, produced by plants, to be taken into account; and very small amounts of sesquiterpenes. The important part of this result was that it was not expected in the scientists' hypothesis and was unusual in comparison to the other members of the plant family.

    9. Terra firme populations exhibited significantly greater height and leaf growth and allocated more to chlorophyll production than white-sand populations in both soil types, demonstrating that different growth strategies have a genetic basis

      The reciprocal transplant experiment that was done with the different soil types showed that the terra firme lineage had greater height, greater leaf growth, and higher chlorophyll production in both soil types, while the white sand lineage did not. This worked to show that the growth strategies between each lineage was significantly different.

    10. Differences between sites, habitat types, and their interaction explained 14%, 15%, and 11%, respectively, of the variation in herbivore species composition among the four sampling locations

      This is explaining how the variation of herbivore species is closely related to the variation of plants in the location. The study explains how certain insects prefer to ingest other substances that can be identified, allowing the experimenter to see how the insects lived in accordance to where the plants where, instead of plants appearing around certain species of insects.

    11. differences among the dominant herbivores, the species composition of the entire P. subserratum herbivore fauna exhibited high turnover among sites and habitats

      The data that was collected from the herbivores and their abundance and variation between the plant species showed that most of the insects preferred terra firme plants instead of the white sand plants. It was also seen that, out of the species that were collected, the majority of them were chrysomelid beetles. Since the plants tested were in different locations, it was found that a small percentage of that correlated with the amount herbivore variation.

    12. We compared absolute and qualitative differences in leaf defense. First, we compared the dry mass of leaf defense chemicals in a linear model with soil type and study region as independent variables. Second, we tested whether habitat type, sampling site, or the interaction of the two, was a significant determinant of the relative allocation among flavan, flavone, quinic acid derivatives, and oxidized terpenes in each plant using a factorial analysis of variance.

      When doing comparison, it helps to create a table to have a better understanding on the differences in leaf defense.

    13. Second, we used a factorial analysis of variance (McArdle and Anderson 2001) to assess whether habitat type, sampling site, or the interaction of the two was a significant determinant of herbivore species composition.

      This was done to determine the different variables that affect insect populations and which ones were more important than others. With this information they set the parameters to create an observable experiment with a limited amount of discrepancies.

    14. In order to study the evolutionary processes involved in habitat specialization and the role of insect herbivores, an ideal study system would include recently derived sister species, or diverging lineages undergoing incipient speciation in different habitats.

      Main goal for the paper.

    15. 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.

    16. 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.

    17. 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.

      http://onlinelibrary.wiley.com.ezproxy.fiu.edu/doi/10.1890/12-1920.1/full#i0012-9658-94-8-1764-Coley2

    18. 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/)

    19. But little is known about the mechanisms underlying the evolution of habitat specialization and the extent to which herbivores contribute to phenotypic divergence during the speciation process,

      The authors have a clear goal in their experiment. Through this observation that is lacking a response they build an experiment to identify natures processes.

    20. 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

    21. 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.

    22. reciprocal transplant experiment

      The reciprocal transplant experiment is an experiment where organisms from two or more environments are introduced to each other.

      The experiment is commonly used to test how well the organisms adapt, and sources of growth variation (genetic or environmental).

    1. a prominent position in current scenarios

      Looking at phenology through generations can aid us in understanding how the globe is changing. The video linked below shows how recording events can help humans connect and interact with biotic communities. URL: http://climatewisconsin.org/story/phenology

    1. Ants are important predators in tropical forest ecosystems

      The authors cited performed studies that ants are a very important predators in tropical forest ecosystems.

    2. Treatments applied to caterpillars were: (1) no barriers (no tanglefoot/no cage), (2) tanglefoot present/no cage, (3) no tanglefoot/cage with holes present, (4) tanglefoot present/cage with holes present, (5) no tanglefoot/cage present, and (6) tanglefoot present/cage present.

      These are the parameters made to make sure that the experiment itself is not biased and there are different variables being tested.

    3. Field observations revealed that sheer caterpillar size was a fair defense against these ants;

      Authors found out in the field that the sheer caterpillar size was a mechanism of defense to against predators.

    4. osmeteria

      A defensive organ found in all papilionid (from the family of Swallowtail butterflies) larvae, in all stages.

    5. pupate

      To become a pupa.

    6.  Pseudomyrmex gracilis received the highest final score at 52, and C. floridanus had the next highest score at 40; both C. ashmeadiand C. planatus received lower scores of 24

      Based on species abundance, the Pseudomyremx gracilis received the highest score.

    7. overdispersion

      The presence of greater variability (statistical dispersion) in a data set than would be expected based on a given statistical model.

    8. logistical constraints

      The planning, implementation, and coordination of the details of a business or other operation.

    1. Gentry plots consistently emerge as the best compromise

      Overall, 0.5 hectare gentry plots were the best method.

    2. Fig. 1.

      Figure 1 shows how the coefficient of variability changed for the different types of plots used. The use of smaller plots had a smaller CV meaning that the results had low variance and did not stray much from the standard deviation compared to the larger plots.

    3. The 1 ha plots, despite their relatively high cost to implement (Table 1), were more efficient to inventory than the smallest plots, although 1 ha plots were still inferior to the 0.5 ha modified Gentry plots.

      It was found that the plots that were smaller than 1 hectare had better results than the plots that were larger (1 hectare).

    1. Markov Chain Monte Carlo methods

      MCMC methods are a class of algorithms for sampling from a probability distribution. By constructing a Markov chain, a sample of the desired distribution by observing the chain after a number of steps.

    2. thaw degree days (TDDs)

      TDDs are negative when over zero degrees celcius (thawing) and positive when under zero degrees celcius (freezing). Best for comparing arctic temperatures across specific time periods.

      http://psc.apl.washington.edu/nonwp_projects/landfast_ice/freezing.php

    3. graminoid

      Herbaceous (having no stem above ground) plant with grass-like features.

    4. Remote sensing

      It may take a lot of work to study plants at extreme environments like the tundra. Remote sensing facilitates the studying of plants without having to come in contact with them.

      Watch this video by MonkeySee https://www.youtube.com/watch?v=sBI3MIbzIBA

    5. 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. spatial abundance pattern.

      Spatial and temporal abundance patterns relate to the study. Temporal abundance pattern has to do with quantity over a period of time and spatial abundance patterns have to do with quantity over a particular area of space.

    2. temporal monitoring studies

      Temporal monitoring is monitoring that is conducted over time.

    3. focal species

      Focal species are species that are extremely sensitive to the changes in an environment.

    4. However, can marine reserves also benefit large, roving reef predators that are potentially mobile throughout their life?

      This question sheds light on a topic regarding the suitability of marine reserves not only as a permanent safety harbor for recovery and expansion of the species but also the temporary inhibition of the space by species that are mobile, whether they would use the space to breed for protection or for a stable source of food and shelter.

    5. Marine reserves can clearly enhance exploited coral reef species that have relatively sedentary adult life-stages, in which some individuals live almost exclusively within reserve boundaries

      A study in 2 June 2009 conducted by Philip P. Molloy explored the relations with the age of the marine reserves and of the recovery of different species of fish. The studies showed that older marine reserves (15 years and older) were more effective than younger ones. They harbored more fish.

    6. site-fidelity

      Side-fidelity, also known as philanthropy, is the likelihood of a particular organism to stay in a set habitat, or to return to it. There are many reasons to this, such as breeding and food abundance.

    1. phenology

      the study of cyclic and seasonal natural phenomena, especially in relation to climate and plant and animal life.

    2. larger fish have greater thermal inertia and increased cardiac capacity

      Thermal inertia is the ability of a body or object to maintain its temperature when ambient temperature changes. Larger objects have higher thermal inertia, so larger fish lose heat more slowly than smaller fish. Larger fish also have larger hearts, which can pump more blood.

    3. metabolic scope

      is a suitable gauge for assessing the environmental influence on fish biological performance (Fry 1971)

    4. The largest size-based differences in energy intake were also observed in October (Fig. 6 and table S3), indicating that thermal niche expansion in this endothermic species results in high energetic reward.

      The increased temperature range allowed the tuna to forage and obtain energy more efficiently.

    5. ILD

      Isothermal Layer Depth

    6. SST

      Sea Surface Temperature

    7. spatiotemporal information

      Information relative to the space and time of the tagged fish.

    8. Lower energy intake was observed during late summer (August and September), when bluefin tuna are moving up through the Southern California Bight (28° to 32°N).

      Lower energy intake during migrations.

    9. heterogeneity

      The quality or state of being diverse in character or content.