ATZ-pYES2 is a vector natively expressing the ATZ, a misfolded protein, in yeast. ATZ-pYES2 used to observe a as substrate targeted for autophagy degradation.

Wild type, and mutants of the atg40 and lst1 were transformed with ATZ-pYES2 to observe whether loss-of-functions of atg40 and lst1 will lead to the accumulation of aggregated ATZ protein in the ER, which indicates that Atg40 and Lst1 are essential ER-phagy.

The mammals homolog of Atg40 in yeast. To verify the evolutionarily conserved function the ER-phagy receptor in higher order and complex organism such as in mammal cell, FAM134B, the homolog protein of Atg40 in mammals, was used to test its functional similarity.

The authors tested whether or not the defeated of Lst1 in yeast will have the similar observation in mammalian cells by looking at the homologs of the isoforms of Sec24 in mammals.

The experimenters used fluorescent antibodies specific for binding to CRF to ensure that they are examining CRF neurons, as previous work indicates that SST and dopaminergic interneurons send their transmitters to CRF neurons. The experimenters also perform staining with fluorescent antibodies specific for SST2/4R, the somatostatin receptor, and D2R, the dopamine receptor.

By staining brain tissue sections for an enzyme in the dopamine synthetic pathway, the experimenters can determine how much dopamine is being produced.

After the polyimine film was heated up, the chips could be placed and almost fused with the polyimine to keep them in place.

The specific polymers that are used to make up this polyimine.

The authors look at the connection between the circuitry and the electronic parts to make sure that under this stress the parts are still communicating with each other.

When the electronic circuit is coated in this acid, the polyimine separates from the parts of the circuit. This allows the author to repair or replace any part of the circuit board instead of replacing the whole thing.

The author's cut the electronic circuit 5 times to prove that it can self heal through even being cut. The electronic circuit will repair itself after being cut.

The authors test to see if the electronic circuit can keep up with the mechanical stress that is placed on the polyimine.

The authors took pictures before and after wearing the sensor to see if the skin was affected by the polymer.

Screen printing is a technique in which a mesh is used to transfer ink onto a substrate. In this case EGaln LM is used to transfer LM onto the polyimine.

The authors physically cut the LM circuit to determine that the EKG signal would be lost. Afterwards the two cut regions were slightly pressed together, and the LM material was self-healed. This allowed the ECG sensor to regain its sensing capability.

The Polyimine and LM were 3D modeled on the software Abaqus. This software allowed the authors to determine the young's modulus and the Poisson ratio for each of the materials. These are important mechanical properties that allow the authors to model the mechanical behavior further.

By using a common geometrical shape the authors were able to better camouflage the robot by using the idea that the robot fit in with the normal geometry found in nature. If the robot was designed in a way that caused it to have an abnormal shape it would have a harder time hiding in specific environments where there was more repeated normal patterns.

Through the different experiments preformed on the robot grayscale thresholding was used as a way of determining which if the specific intensities of the the color layers on the robot matched those of the background. Also infrared thermal imaging was used on the robot to note how color change in the color layers affect the camouflage of the robot in the IR spectrum

Color layers were fabricated using soft lithograpy of Ecoflex in combination with a thin film. They were then coated with a liquid and attached to the robot

The cyclic loading test is the repeated application of stress and strain to determine fatigue stress. The cyclic test for this experiment test the self-healing capacitates of the material, can the material go back to its original shape when stretched out. In this case, the polyimine had good elasticity, but exhibited some hysteresis. Hysteresis, in this case, is when the polyimine was stretched, but then had a small lag when returning to its original shape.

Bond exchanges often are affected by temperature, and often times when bonds are heated up they can denature. It was important to test if hotter temperatures would affect the imine bond exchange reaction. The bonds were tested at room temperature and then 80 °C, the temperature did not affect the nature and effectiveness of the bond exchange reaction.

FTIR stands for Fourier-transformed infrared spectroscopy, this technique is used to obtain absorption or emission of infrared light. In this case FTIR was used to determine if the original and recycled polyimine was chemically identical. If the length of the infrared waves are significantly different then that is a clear indicator that the substances have different chemical components. In this case, the length of the infrared waves are similar, meaning that this is the first indicator that the two materials are chemically similar.

Divers would follow prey fish during the daytime and visually observe the number of times that the tracked fish would bite at the plants upon which they grazed within a five-minute window of time. This data was collected as a measurement of prey activity, the timing of which could be compared with the periods of activity for the blacktip reef sharks

Devices were attached externally or internally to captured sharks, which were then released and tracked. The attached devices would record measurements of several data types periodically. Devices either transmit information as it is being collected, or scientists must retrieve a logging device from the shark to access the data at the end of the experiment.

Bio-logging allows scientists to observe some aspects of the behavior of animals in their natural environment, rather than within the constraints of a laboratory setting that may alter the behavior of the animal.

This equation is basically saying that the changes in crop losses due to pests can be determined by adding up the change in insect metabolism and the change in where the insects are located. If the metabolic needs of insects increases or the area that they live in increases, then crop losses will also go up.

This is a concise statement of the question Arrhenius sought to answer with his model.

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.

A big tuna (large body size) requires more energy which means it needs to feed from a higher amounts of prey or big preys. Consequently, the heat production is higher provoking a thermal excess.

By analyzing the temperatures of digestion in bluefin tuna, the author can draw conclusions as to what the tuna is eating, how much energy is gained from the meal, and how often the tuna eats. HIF means heat increment of feeding.

This is the hypothesis and plan in response to the authors' goal to design an improved moveable robotic system that is faster and more efficient than previous systems.

Their collection may have been affected. It was mentioned by the author that she and her colleagues collected from muddy environments since the sites were sewage dump locations. Most of the shrimps were covered in mud, therefore hard to distinguish. Also, the author mentioned transit ships traveling between the Atlantic and Pacific sides of Isthmus. These ships would migrate the shrimps away from their homes; may affect how the team paired shrimps based on their mtDNA. ~J.D.A.

Gel Electrophoresis is a method of separating macromolecules such as DNA, RNA, or proteins. The separation is based on the molecules size and charge. The shorter molecules will travel further in the gel agarose than longer molecules. ~ S.Z.

Rate of divergence for the first four pairs of shrimp was calculated by dividing the allozyme and mtDNA divergence values by the time elapsed since final closure. ~S.Z.

Kimura is a Japanese biologist whose evolutionary theory was based at the molecular level and believed that most genetic differences between species were neutral and not driven by natural selection.

Kimura's corrected percent sequence divergence is an analysis that compares the genomes of species and allows to determine the divergence between their genetic code which can help conclude moment of speciation. (DV)

This experiment wanted to see if the mutant sites were phosphorylated in the APP23.p38γ−/− and APP23.p38γ+/+ mice.

The author set up different assays to test which variants were being phosphorylated by tau.

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.

-Otniel Gonzalez

In this study, the researchers found some questions as to whether the two species of C. jimenezii could be grouped with the same taxa.

Upon meeting with the author, it was stated that the molecular tools used, found a large amount of differentiation. This was not what the authors hoped and in turn was concluded that they were to remain in separate taxa.

RA

Genetic conservation of this population is important due to the few individuals left in Haiti and the Dominican Republic.

Upon meeting with the author, the difficulty of finding the purebred species was discussed as were the methods.

RA

Although this experiment focuses on microbial and fungal effects on streams, humans sometimes also have an impact.

These effects may include the leaking of septic tanks into bodies of water that increase human waste and phosphorus levels. Fishing and polluting also affect stream ecosystems.

Read more in the attached link.

An irrigation line was used along the 70-150 meter streams to pump in liquid nutrients. The nutrients were pumped proportional to the flow of the water.

It is often necessary to use a simpler model version of a larger system because it is easier to observe.

It is difficult to observe the effects on a whole stream, but the litter bags are observed and represent the carbon loss in streams.

Litter in the litter bags have a higher concentration of carbon than the stream, which has carbon more spread out. The litter will have higher loss of carbon but generally represents reach-scales.

Benthic fine and coarse particulate organic carbon can be used as a measurement when observing loss of carbon caused by detrivores.

In this experiment, leaf litter from different types of trees were used. The results are in Figure 3.

The structure and chemistry of leaves are different and this determines how fast they may decompose.

For example, tulip poplar decomposes the quickest and has a low carbon to nitrogen ratio. Comparatively, oak decomposes slowly and has a higher carbon to nitrogen ratio.

The litterbag technique can be used to measure the density lost due to composition by microbes and fungi.

A known type and amount of litter is stuffed in the bag and is left for a certain amount of time in the stream. The bag is then later taken out and weight wet. The bag is allowed to dry and then the dry weight is taken.

The link included shows the method for finding the difference in mass. Additionally, the methods of this paper include grinding the litter and finding the composition.

The experiments were conducted on streams in the Appalachian Mountains of North Carolina.

Because of the elevation, there are little to no fish influencing the data. Mainly microbes and fungi influence the nutrient levels of the streams.

Two experiments were done separately to test the effects of nitrogen to phosphorus ratios on streams.

Pre-treatment of streams include recording the levels of nutrients and typical conditions throughout a year.

The first experiment had two watersheds with one being the control and the other having an addition of nitrogen and phosphorus to match a ratio that was decided by the scientists.

The second experiment was done on five streams with different combinations of the nitrogen and phosphorus ratio.

Rate of divergence for the first four pairs of shrimp was calculated by dividing the allozyme and mtDNA divergence values by the time elapsed since final closure. ~S.Z.

Gel Electrophoresis is a method of separating macromolecules such as DNA, RNA, or proteins. The separation is based on the molecules size and charge. The shorter molecules will travel further in the gel agarose than longer molecules. ~ S.Z.

Their collection may have been affected. It was mentioned by the author that she and her colleagues collected from muddy environments since the sites were sewage dump locations. Most of the shrimps were covered in mud, therefore hard to distinguish. Also, the author mentioned transit ships traveling between the Atlantic and Pacific sides of Isthmus. These ships would migrate the shrimps away from their homes; may affect how the team paired shrimps based on their mtDNA. ~J.D.A.

Kimura is a Japanese biologist whose evolutionary theory was based at the molecular level and believed that most genetic differences between species were neutral and not driven by natural selection.

Kimura's corrected percent sequence divergence is an analysis that compares the genomes of species and allows to determine the divergence between their genetic code which can help conclude moment of speciation. (DV)

In this experiment, skin from a human was grafted onto mice with depressed immune systems. This means a piece of human skin was transplanted onto mice who's immune systems could not protect them from diseases.

(ABE)

In this study, the cells from the neural crest of mice that carried the specific mutation Kitl were treated with endothelin 3.

This study was done on the neural crests taken from murine cultures, so it is also an in vitro study of the effects of endothelin on the development on melanocytes but this time on a different species.

(ABE)

The study described here consisted of treating quail (type of bird) neural crest cultures with Edn3. This study was in vitro, meaning the embryonic neural crest was removed and treated outside of the organism. This study showed the role that Edn3 plays in development as stated in the paper.

(ABE)

By analyzing the temperatures of digestion in bluefin tuna, the author can draw conclusions as to what the tuna is eating, how much energy is gained from the meal, and how often the tuna eats. HIF means heat increment of feeding.

PAUP stands for Phylogenetic Analysis Using Parsimony. This is a computational phylogenetics program that is used to develop phylogenetic trees. PAUP implements parsimony into its calculations, meaning that the simplest explanation is the most preferred. (JP)

Nei's D is a formula that measures genetic distance. This measure assumes that genetic differences are caused by mutation and genetic drift. Genetic distance is a measure of the genetic divergence between species.

The changes in structure or protein sequences of allozymes was used in conjunction with this formula to find the genetic distance between different species of snapping shrimp. (JP)

This was used to determine if the sharks were regularly leaving the pass to forage.

• D.N.B.

allowing us to find out whether sharks are feeding or are just resting.

A combination of the data collected from the sea floor structure (topography) and video surveys through transect lines were used in order to try to find a correlation between the habitat and the shark density. YS & WT

The authors built a specific strain of E. coli that they could easily trace throughout these next experiments.

To construct the E. coli strain expressing the Tsr-Venus fusion protein, they used the previously published λRED recombination system, in which the chimeric tsr-venus gene had the coding sequence of tsr gene fused to the N-terminus of venus and a kanamycin drug resistance marker. The chimeric gene was incorporated into the lacZ locus.

Some authors like to state exactly what they have shown early on in the paper. In this case, the authors prepare the reader for a methods type paper.

In the current work, the authors demonstrate that they themselves are also heartless.

Melissa can edit as SitC

This optical microscope, commonly referred to as a light microscope, uses light to magnify images.

The resolution power of an optical microscope is smaller than that of a TEM.

Optical microscope images were taken to confirm/support the starlike supermicelles seen in the TEM (which were several micrometers in diameter). The authors stated since the supermicelles were approximately 3 micrometers in diameter, the optical microscope could resolve the starlike strucutres. However, if the supermicelles were much smaller than 3 micrometers then resolution using an optical microscope would not be possible.

TEM is a microscopy technique where a beam of electrons passes through a thin-film sample. As the electrons interact with the sample, an image is produced. Samples that have atoms with high atomic numbers can produce darker images/provide better contrast.

The TEM samples were prepared on a carbon-coated grid. A drop of the micelle suspension was placed on the grid and then the excess solvent was removed using filter paper.

Using TEM the authors can verify they have achieved unidirectional growth. Additionally, they were able to see larger starlike micellar aggregates formed from the target noncentrosymmetric micelles.

Figure 1B depicts the synthetic strategy used to make micelles seeds capable of unidirectional growth:

After the cross-linking step, a solvent is chosen to dissolve the middle block (PFS-b-PDMS) of the triblock co-micelle. By doing this, the remaining PI-B-PFS micelle blocks can be used as seeds for elongation from the non-crosslinked end.

Figure 1A depicts the synthetic strategy used to make triblock co-micelles:

1) The first step was to make micelles with crystalline cores. They did this by making a suspension of poly (ferrocenyl dimethylsilane)-b-poly(dimethylsiloxane) in hexane at 60C°. The solution was allowed to age at room temperature. They then sonicated the suspension in order to break up the micelles into smaller micelle seeds.

2) The next step was to add a second block copolymer to give bidirectional growth to form a triblock co-micelle. This was performed using a solution of unimers in THF which was added to the micelle suspension and allowed to age in order to form a longer micelle.

3) Finally, the polyisoprene end of the block co-micelle is cross-linked to prevent further growth using Karstedt's catalyst.

Karstedt's catalyst is a platinum compound capable of forming bonds between carbon and silicon atoms.

In a separate publication, ref. 31 (DOI: 10.1021/ja206370k), the authors discovered the catalyst's ability to cross-link the double bonds in polyisoprene in the absences of silicon-containing molecules.

In this paper, Karstedt's catalyst was used to prevent block elongation from one end of the exposed cylindrical core to achieve unidirectional growth.

Because the host cell entry comprises multiple steps, the authors investigated which one was affected by the depletion of HDAC6. They noticed that HDAC6 has a function specifically during the uncoating and the vRNPs import.

Authors investigated the role of myosin 10 and 9, which belong to type II myosin, in IAV uncoating after plasma membrane fusion. They blocked separately the gene expression for both Myosin 9 and 10 and observed that uncoating was reduced only in myosin 10-depleted cells. Additionally, two different inhibitors of type II myosins inhibited the uncoating.

Often, when more than one technique is available for exploring an hypothesis (i.e. involvement of myosin in IAV uncoating), scientists use them all to confirm their observations. By getting rid of myosins, authors can understand how important it is in the uncoating. Two ways were used to do so: blockage of the expression of the corresponding genes and inhibition of myosins by using drugs.


By depleting dynactin 2 via RNAi and inhibiting dynein via treatment with CilioD (dynein inhibitor), the authors found out that viral uncoating was reduced in A549 cells. Also, uncoating is decreased in MEFs expressing HDAC6 that lacks the dynein-binding domain.

This experiment confirmed that HDAC6 associates with M1. Authors highlighted HDAC6 associated to M1-containing vacuoles by using indirect immunofluorescence, in which one antibody binds to the target protein (HDAC6 in this experiment) and a second antibody, bearing a fluorophore, binds to the first antibody.

The authors verified that what observed by immunoblotting was ubiquitin by using the super-resolution microscopy technique.

Following the observation that HDAC6 was implicated in the viral uncoating, next question that the authors asked was: knowing that HDAC6 has deacetylase activity domains as well as ubiquitin binding domain, what HDAC6 function is critical in the uncoating? To study these functions separately, the authors re-introduced WT HDAC6 or HDAC6 point mutated for etheir deacetylase or ubiquitin binding domain in HDAC6 knock-out MEFs

Authors ran a second experiment to confirm the involvement of HDAC6 after the fusion step. In this experiment, they bypassed the endocytosis process by means of pH change.

Because the host cell entry comprises multiple steps, the authors investigated which one was affected by the depletion of HDAC6. They noticed that HDAC6 has a function specifically during the uncoating and the vRNPs import.

To determine whether HDAC6 was involved with virus infection, the author examined mutant cells in which HDAC6 expression was silenced. The author observed that when HDAC6 is absent, viral infection and concentration were reduced.

This technique allows the authors to determine the precise order of nucleotides within specific regions of a DNA sample.

high-throughout means that large volumes of DNA can be sequenced quickly.

This technique allows the authors to determine the precise order of nucleotides within specific regions of a DNA sample.

high-throughout means that large volumes of DNA can be sequenced quickly.