To examine the association of two proteins in the cell, colocalization of two fusion proteins with different florescence tagged fused with two proteins are utilized to be visualized under the confocal/florescence microscope, to test whether these two signals (red and green florescence in this study) could be overlapping in the cell.

LST1 fused with GFP, the green florescence protein. ATG40 fused with mCherry, the red florescence protein.

To investigate how the role of ER-phagy receptor, ATG40, involved in packaging the cargo for recycling in ER specifically, the authors made the connection of observation and results obtained in ATG40, and associated with LST1 to hypothesize that LST1 could be associated with the ER-phagy receptor, ATG40.

The ER exit sites are specialized ER zones for the transport of cargo proteins from the ER to the Golgi apparatus.

In yeast, the ER consists of 3 subdomains, the cytoplasmic ER, the cortical ER, and the perinuclear ER (also called nuclear envelope).

Atg39 specifically localizes to the nuclear envelope. Therefore, the Atg39-dependent pathway in selective autophagy terms as nucleophagy.

Conversely, Atg40 predominantly localizes to the cytoplasmic ER and the cortical ER, and loads fragments (ER tubules or sheets) of these ER subdomains into the phagophore. Thus, Atg40 is exclusively involved in ER-phagy.

To exclude the possibilities that LST1 is localized to the nuclear envelope and do not involve in nucleophagy, the authors examine the colocalization of Atg39 and Lst1, and rule out the possibility that the Lst1 is localized in nuclear envelope and do not reside on the nuclear envelope and its marker, Hmg1.

Atg8 protein is a marker protein to observe autophagosome formation. When Atg8 protein engineered with the red florescence protein (RFP), RFP-Atg8, RFP-Atg8 protein will be conjugated to the lipids and enable the membrane fusion to localize on the autophagosome.

Atg8 also plays an important role in cargo recognition for selective autophagy by interacting with the receptor protein. When Atg40 is mutant, Lst1 is failed to interact and colocalize with Atg40, indicating that Lst1 is acting together with Atg40 to form autophagosome. And Sec23 is partially required with Atg40 to form autophagosome.

Lnp1 is a protein to maintain the structure of ER by stabilizing rearrangements of the ER networks.

Further reading: https://doi.org/10.1073/pnas.1805032115

This experiment is an in vitro binding assay by purifying the GST fusion of target coat proteins of the COPII and incubated with Atg40 fusion protein with FLAG epitope tagged expressed in the yeast

Only GST-Lst1 purified protein is able to bind with the Atg40 but not other subunits of COP11 coat proteins.

pep4Δ strain is a vacuolar protease-deficient yeast strain that lost protease activity wihle fail to degrade the autophagic cargo and served as negative control when compared with the wild-type original strain.

Pep4, a vacuolar protease required for function of multiple hydrolases, is required for autophagic cargo degradation

autophagy-deficient yeast strain which fail to form the autophagosomes to degrade and recycle substances.

To induce the UPR (unfolded protein response), DTT (dithiothreitol) is added to induce protein misfolding in the ER by blocking protein disulfide bond formation, thus activate and induce the UPR.

The relative intensity of GFP fluorescence signal in the cells was measured using the flow cytometry.

SEC24C in mammalian cells is the homolog for Lst1 in yeast.

Torin 2 is a potent and selective mTOR inhibitor, which decreases cell viability and induces autophagy and apoptosis.

ULK1 is one of two mammalian homologues of the yeast ATG1 kinase, known for its role in autophagy initiation

Bulk autophagy also called non-selective macroautophagy. During bulk autophagy, autophagosomes fuse with lysosomes or vacuoles resulting in the degradation of the cargo.

While during selective autophagy, the cargo is distinguished (mitochondria, ER, ribosomes, peroxisomes and etc.) and recognized by specific cargo receptors, or selective autophagy receptors, to connect with the autophagosome for degradation.

Here are two videos for more an explanation: 1) The mechanism of autophagy: https://www.youtube.com/watch?v=Gc9gx33GvF0&t=2s

2) Self-Eating Cell Research Wins Nobel in Medicine: https://www.youtube.com/watch?v=Ws0mOmfC9EU

Misfolded protein are retained in the ER and subjected for proteosomal degradation which occurs in the cytosol.

Learning from the youtube: https://www.youtube.com/watch?v=fEEbyYjXNUU&t=1s

When newly synthesized protein is not properly folded into their correct orientation in the endoplasmic reticulum (ER), the ER now is under the stress to degrade the misfolded protein. To degrade the misfolded proteins and maintain the ER homeostasis, the cellular signaling will turn on the unfolded protein response to help the cell deals with problematic proteins for recycle and degradation.

Video: https://www.youtube.com/watch?v=vy4m-fUOn9o

Genes are commonly generate isoforms from the same locus to produce different mRNA and thus give rise to different length of amino acid with similar protein functions.

Lst1 and SEC24C, are homologous gene in yeast and mammalian respectively. The protein or DNA sequence of these genes, Lst1 and SEC24C, are highly similar and evolutionary share the common ancestor, termed as homolog.

Protein recycling and self-eating process that selectively happens in endoplasmic reticulum terms as ER-phagy (phagy means eating). Selective autophagy requires a receptor protein to recognize its degradation targets and directs the targets to be sequestrated by autophagosomes, a double membrane vesicle structure, which to be transported into lysosomes or vacuoles.

A protein named as Atg40, has been recognized as a ER-phagy receptor protein in yeast. FAM134B is a putative mammals homologue of ATG40.

Literature first explain the Atg40 ER-phagy receptor https://doi.org/10.1038/nature14506 (ATG40)

https://doi.org/10.1038/nature14498 (FAM134B)

ER is a transportation system of the eukaryotic cell composed of network of tubules and sheet-like area adjacent with the nuclear envelope and stretches out to the cell periphery.

Learning corner with video: https://www.youtube.com/watch?v=Gc9gx33GvF0&t=2s glossary

Key question raised by the authors, how the dispersed site throughout the ER are recognized by the selective autophagy receptors to deliver the cargo for degradation.

The authors hypothesized that, COP11 coat proteins which involved in membrane-budding at the ER, could involve in ER-phagy.

The endoplasmic reticulum (ER) is a complex network of membranes involved in protein and lipid synthesis, ion homeostasis, protein quality control and organelle communication. It is also a source of membrane-bounded vesicles called autophagosomes, the vehicles for the self-digesting cellular process of autophagy. This paper shows how the ER itself is targeted for degradation by autophagy — a process that could ensure constant ER turnover in response to cellular requirements.

Authors find the protein FAM134B is an ER-resident receptor that facilitates 'ER-phagy'. Downregulation of this protein — mutations of which can cause sensory neuropathy in humans — resulted in expanded ER structures and degeneration of mouse sensory neurons. In particular, authors demonstrated that this process is conserved in yeast, where Atg40 is enriched in the cortical and cytoplasmic ER, loading these ER subdomains into autophagosomes. A further ER-phagy receptor, Atg39, localizes to the perinuclear ER (or the nuclear envelope) and induces autophagic sequestration of a part of the nucleus, thus ensuring cell survival under nitrogen-deprived conditions.

A conclusion summarized by the authors based on experiments that have been done to distinguish the bulk autophagy and selective autophagy that happened in various organelles, and only ER-phagy is required by Lst1 coat protein.

To draw a conclusion which exclusively functional in one particular experiment, the designs of various experiments are needed in order to rule out other possibilities.

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.

Lst1 and atg40 mutants have higher UPR response before and after DTT treatments, indicates that defeated in ER-phagy proteins will also induce the UPR.

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.

No additive effect was observed when double mutant of lst1atg40 is investigated. This finding drawn another summary which LST1 and ATG40 function in the same pathway.

A conclusion summarized by the authors based on experiments that have been done to distinguish the bulk autophagy and selective autophagy that happened in various organelles, and only ER-phagy is required by Lst1 coat protein.

To draw a conclusion which exclusively functional in one particular experiment, the designs of various experiments are needed in order to rule out other possibilities.

Lst1-Sec23 is a coat adaptor protein that carry the cargo molecules form ER to Golgi, which mainly to help the secretory proteins transportation. The author discovered new function of the Lst1/Sec23 in self-eating and protein recycling process (autophagy), in which the Lst1-Sec23 functions together with the autophagy receptor, Atg40, to localize the ER domains for autophagic degradation.

In response to stress caused by starvation or misfolded aggregate-prone secretory proteins, Lst1 acted to promote an additional function—ER-phagy. Together with autophagy receptors on the ER, Lst1 targeted ER domains for degradation to avert protein aggregation, thus preserving cellular health.

Known as the first article to described ER-phagy.

In this article, authors characterized the fate of the ER in response to starvation, and demonstrated a significant linkage to autophagy.

Abstract: Autophagy is a survival mechanism necessary for eukaryotic cells to overcome nutritionally challenged environments. When autophagy is triggered, cells degrade nonselectively engulfed cytosolic proteins and free ribosomes that are evenly distributed throughout the cytoplasm. The resulting pool of free amino acids is used to sustain processes crucial for survival. Here we characterize an autophagic degradation of the endoplasmic reticulum (ER) under starvation conditions in addition to cytosolic protein degradation. Golgi membrane protein was not engulfed by the autophagosome under the same conditions, indicating that the uptake of ER by autophagosome was the specific event. Although the ER exists in a network structure that is mutually connected and resides predominantly around the nucleus and beneath the plasma membrane, most of autophagosome engulfed ER. The extent of the ER uptake by autophagy was nearly identical to that of the soluble cytosolic proteins. This phenomenon was explained by the appearance of fragmented ER membrane structures in almost all autophagosomes. Furthermore, ER dynamism is required for this process: ER uptake by autophagosomes occurs in an actin-dependent manner.

To cause, or to undergo retrotranslocation.

Retrotranslocation is the reverse process of translocation.

Translocation is a transfer of a chromosomal segment to a new position, especially on a nonhomologous chromosome; the segment so transferred.

Vesicles are compartments formed by a lipid bilayer separating its contents from the cytoplasm or a fluid-based extracellular environment. They can contain either liquids or gases and have a wide range of functions in cells across the living world from regulating buoyancy to secreting hormones.

The word ‘vesicle’ derives from the Latin word vesicula meaning ‘small bladder’

It was identified above as previous studies, so why was this article so important?

Tag as "References"

News - why was this such an important discovery about describing the ER-phagy? Tag to "NewsAndPolicy"

This study provides evidence that ‘Alalā, an endangered native bird species in Hawaii, displays seed dispersal behaviors and promotes seed germination of various native plants. Based on these results, the authors suggest that ‘Alalā can contribute toward the restoration of native fruiting plants in Hawaiian forest communities.

Nestedness can contribute toward the robustness of a network. If species that share fewer interactions are the first to go extinct, the remaining mutualistic system has a greater chance of survival. The authors also calculate a coefficient as a parameter of a network’s robustness.

Mooney and Cleland describe the evolutionary consequences of invasive species on the invaders themselves and on native species. Modifying behavior to adapt to a new environment, competing for similar resources, predation, or creating hybrid progeny by breeding with native species are just a few examples.

Previously, the majority of network analysis was qualitative. Blüthgen et al. introduce two quantitative measurements that use the frequency of interactions to describe specialization at the species level and across a network.

The phylogenetic or evolutionary relationship between species can predict the types and quantity of interaction patterns they exhibit in a network. Using a simulation of extinction events, the authors also demonstrated that the extinction of one species can result in the extinction of other species that are evolutionarily related.

The authors merged data sets from multiple studies investigating fruit-frugivore interactions and illustrated that most networks across various neotropical areas were significantly nested and modular. The authors also concluded that combining results from different studies can be useful for analyzing the ecological structures of broad regions and supporting conservation efforts.

In contrast to Foster, Chimera found that introduced birds in Hawaii dispersed predominately the seeds of non-native plants. Possible explanations could be that the non-native plants produce larger fruit that are more abundant and have a smaller seed size. These qualities are more enticing to birds and enhance the fruit's chances of getting eaten and its seeds later deposited.

Foster and colleagues investigated how often introduced fruit-eating birds on the islands of Hawaii consume and disperse seeds from native plants versus seeds from exotic plants. They found that seeds from native plants made up the majority of the introduced bird species’ diets. This supports the potential of introduced bird species playing a role in the conservation efforts of native habitats.

The authors studied the feeding behaviors of birds in the Galapagos island. They discovered that these birds ate a not just a select few, but a wide variety of plants on the Islands. They called this behavior interaction release, a survival tactic where animals expand their niches.

The Anthropocene is defined as the epoch or geological time when human activity significantly impacted the global environment. Based on the criteria for defining a new epoch and supporting geological evidence, the authors propose two possible dates to mark the beginning of the Anthropocene: 1610 and 1964.

Connects to Learning Standards, A Framework for K-12 Science Education, Disciplinary Core Ideas: LS2.C Ecosystems Dynamics, Functioning, and Resilience:

"Anthropogenic changes (induced by human activity) in the environment—including habitat destruction, pollution, introduction of invasive species, overexploitation, and climate change—can disrupt an ecosystem and threaten the survival of some species."

Of all seeds found in bird poops, 93% are of introduced plant species.

ability to establish new interactions with partner species present in the ecosystem

Connects to Learning Standard, Vision and Change for Undergraduate Biology Education Core Competencies and Disciplinary Practices: VC3 Ability to use modeling and simulation:

"Use mathematical modeling and simulation tools to describe living systems."

Connects with Learning Standards, A Framework for K-12 Science Education, Crosscutting Concepts: Scale, proportion, and quantity:

"In considering phenomena, it is critical to recognize what is relevant at different measures of size, time, and energy and to recognize how changes in scale, proportion, or quantity affect a system’s structure or performance."

By simulating the network patterns between plants and pollinators, the authors demonstrated that plants were more resistant to extinction with the removal of specialized pollinators versus generalized pollinators. Specialized pollinators only interact with a few plant species, whereas generalized pollinators interact with a larger range of plant species. When a generalized pollinator is lost, more plants are affected.

Here, Morgan suggests that regeneration of a head versus a tail is related to the location of the amputation and the cells that reside there.

Janus was a Roman god and doorkeeper to the heavens. Relevant here, Janus was usually depicted with two heads, one facing the past and the other towards the future.

Using the process of science to identify and evaluate possible explanations for a natural phenomenon.

Click here to learn more about the process of science: https://media.hhmi.org/biointeractive/click/understanding-science/#/intro/4

Adenomatous polyposis coli, or APC, is gene that plays many roles, including acting as a tumor suppressor. APC has also been found to play a role in cell division and directing cells where to go once division takes place. In order to do its job, APC directs β-catenin in the Wnt signaling pathway.

Read more in the Journal of Cell Science. The PDF is also available in the "Related content" tab.

A mechanism used by both plant and animal cells to silence a gene using a double-stranded DNA molecule. DNA is converted into the smaller RNAi molecules used to turn genes off. Scientists are now able to use this natural process to turn off genes they are studying so they can learn more about their function.

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 software called Viewer that tracked motion and calculated distance.

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 theoretically lead to more effective therapies in the future. Read more from The Cellular Scale.

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

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

There are three main families 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.

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 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), 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 (human embryonic kidney) cells, viral particles are released from the cells and suspended in the culture media. Learn more about lentiviruses here.

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.

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.

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.

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

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

The specificity of optogenetic treatments is 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 brain cells function and communicate.

One of the paper authors, Karl Diesseroth, is attributed with 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 proteins that are optically controlled.

This family of proteins is 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.

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.

Both ocean island basalts and continental plume-related basalts come from deep within the mantle. OIBs intruded into oceanic (basaltic) crust, whereas continental plumes intrude into continental crust (for example, Deccan traps in India).

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

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.

As a well documented case of natural selection, mechanisms of evolution are clearly described among finches on the Galápagos islands. Learn more with these activities from HHMI BioInteractive. https://www.biointeractive.org/classroom-resources/natural-selection-and-evolution-darwins-finches

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.

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.

By measuring bill size and recording bird mortality on Daphne Major during a drought that occurred in 2004-05, 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.

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 included 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.

As in a bird's beak.

An elevated R/Ra ratio indicates that there has been exposure to cosmic rays in the past. This means some meteorites may have crashed onto ancient Earth and the He concentration in the rock has remained relatively undisturbed since then.

In the diamond fluid inclusions richest in helium-3, the ³He/⁴He ratio is about 50 times to that of air. This considerably high isotope ratio suggests that the real age of these fluid inclusions date back to the early days of Earth's formation.

In conducting their experiments, the research team acknowledged the inherent variability in the ³He/⁴He ratio inside each diamond. To minimize these differences, the scientists used diamonds that were free of inclusions thereby eliminating the possibility of inconsistencies in helium ratios originating from these inclusions. Then, they crushed the diamond in a vacuum to verify that 90% of the helium is present in the groundmass of the diamond. This was then followed by step-heating the crushed diamond to measure the variability in the ³He/⁴He ratio in the diamond.

The research team sought to identify an untouched, untapped chemical reservoir. To do this, they decided to examine primordial diamonds that contained both helium-4 and helium-3 isotopes.

The helium-4 isotopes are formed from radioactive decay of trace elements and hence take a long time to form. Conversely, the helium-3 isotopes exist inside Earth from the early days of formation and there has been no new generation of helium-3 isotope since then.

A mass of undifferentiated cells that has the ability to develop into an organ or body part, such as limbs.

Could use further explanation

Identified by mineral inclusions consistent with being exposed to high pressures found at depths of more than 400 kilometers.

What does this mean? Needs some translation

Strontium-Neodymium-Hafnium-Lead

Helium-Strontium-Lead

Measurement of isotopic content of primitive basaltic rocks has been a useful method to understand the exact chemical composition of these old rocks. Learn more in this article from Eos explaining the importance of using these techniques. https://eos.org/features/isotope-geochemists-glimpse-earths-impenetrable-interior

Chemical elements that have the same number of electrons and protons but a different number of neutrons are called isotopes. For example, both carbon-12 and carbon-14 have six electrons and six protons, but they have 12 and 14 neutrons, respectively. These isotopic differences change the atom's atomic mass and other chemical properties.

In response to China's plastics import ban, 187 governments have agreed to alter a pre-existing global waste treaty called the Basel Convention.

In May 2019, all countries that have ratified the Basel Convention (notably excluding the United States) approved major plastics-related changes. These changes are set to take effect started in 2021.

Read more from the UN Environment Programme

The Basel Convention, which governs the international waste trade, was adopted in 1989 in response to hazardous waste dumping on communities in Africa, the Caribbean, and Asia. China and the United States signed onto the Basel Convention in 1990. China ratified the treaty in 1991, while the United States has yet to ratify.

Read more from The Conversation

Shortly after taking office, China's new president Xi Jinping enacted the 2013 "Green Fence" policy directive aimed to lessen the contamination levels and boost the quality of imported recycled materials. Shipping containers that did not pass import inspection were rejected from entering the country.

Enacted in January 2018, China's "National Sword" policy banned 24 types of solid waste, including various plastics, and set a much tougher standard for contamination levels.

The new policy ups the ante with a ban on plastic waste containing more than 0.5% contamination. Some view this move as an unintended consequence of single-stream recycling.

In the 1990s, China emerged as a global manufacturing powerhouse generating a huge increase in demand for raw materials. This offered a market for products that come out at the end of the recycling process, such as the plastic pellets made from recycled materials. For example, these pellets can be turned into the soles of shoes. Read more in the Financial Times

Refers to the collection of recyclables including glass, paper, and plastic, all in the same recycling bin.

These are chemicals added in the manufacturing process that can make plastics more flexible, durable, and transparent. A notorious example of a plastic additive includes bisphenol A (BPA). In high doses, BPA has possible health effects on the brain and prostate glands of fetuses, infants, and children.

Read more from Mayo Clinic.

The World Bank estimates that annual waste generation will increase by 70% from 2016 to 3.4 billion MT in 2050. Over 90% of waste, including plastics, produced in low-income countries is disposed of in unregulated dumps or openly burned.

Refers to the range of garbage materials that are discarded as unwanted and useless. Landfills are often used as solid waste management systems.

A chemist at Dupont named Wallace Carothers invented a synthetic polymer that became known as nylon. Nylon and other early plastics became wide spread in the late 1930s and early 1940s. During World War II, plastic production in the United States increased by 300%.

Read more about the history of early plastic production from the American Chemical Society and the Science History Institute.

One metric ton is equal to 1,000 kilograms or 2,204.6 pounds. One black rhinoceros weights approximately one metric ton. Source: Wikimedia

The Institute for European Environmental Policy found that plastics make up 85% of beach litter worldwide, 61% of which are single-use plastics, such as those used in food packaging.

Watch this video for an overview of values affirmation:

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

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

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

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/

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

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, whereas the stimulation was turned off when the mice were on the other side.

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 eat much faster than mice did in previous reports where AgRP neurons were stimulated or when agRP projections to the PVT were stimulated.

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.

Materials made of long, repeating chains of molecules. The term polymer is often used to describe plastics, which are synthetically made, but natural polymers also exist.

As the most common plastic, polyethylene is used for everything from plastic bags to bulletproof vests. Polypropylene is commonly used in chip bags, microwave dishes, and bottle caps. Some fabric textiles and many water bottles are made of polyethylene terephthalate (PET).

Plastics are notoriously persistent pollutants. It is estimated that a PET plastic water bottle will take anywhere from 100-500 years to degrade.

Since China's 2018 policy went into effect, many of the "replacement countries" have also started to crack down.

Malaysia, Thailand, and Vietnam have enacted stricter quality standards for waste coming from countries such as the US, UK, and Australia.

Read more here: http://wastemanagementreview.com.au/battling-sovereign-risk/

An economic system where waste and pollution are designed out, keeping products and services in closed loops or cycles. The circular economy is an alternative to a traditional linear economy in which products and materials are made, used, and disposed of.

Learn more about action potentials and membrane depolarization with Khan Academy. See also their video here.

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

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

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

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

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

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

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).

Check out this video primer on neuroplasticity from Khan Academy.

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.

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).

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

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.

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

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.

Introduces a methyl (CH₃) group. Here, PNMT adds a CH₃ group onto norepinephrine creating epinephrine (also known as adrenaline).

Situated in the tail part of the body.

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

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.

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

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

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

The authors found that blocking the function of the GABA receptor (GABA_A 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_A receptor blocker or that other neurotransmitters might be involved.

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.

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.

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.

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

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.

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.

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

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.

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

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).

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

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.

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.

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

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.

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!

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.

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.

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?

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

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.

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.

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.

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

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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

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

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

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.

Improved.

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.

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.

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

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.

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

Test

Peptides that bind to opioid receptors in the brain.

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

Generally considered or reputed to be.

Constantly changing.

Usually means 25 degrees Celsius, or 77 degrees Fahrenheit (think room temperature).

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.

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.

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.

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.

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

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.

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