Science Book Review: The Root of Thought

Written by Andrew KoobTravisReviewPic

Reviewed by Travis Rotterman

This book? I don’t care for it much. The story is centered around the idea that astrocytes are the greatest, most powerful cell in all the nervous system! While astrocytes do have their importance, microglia are obviously the most important cells of the CNS. I mean this guy really goofed…

This is what I call a “classic mix-up.”

 

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Getting a PHD in Caffeine: List of Atl’s best neuroscience phd grad student –friendly coffee houses

by Sherod Haynes

“America runs on Dunkin!” is the slogan of Dunkin Donuts (one of the largest coffee companies in the world). Indeed, they are on to something, as America is the world’s highest importers of coffee and is in the top 5 countries for coffee consumption. So who is at the center of this coffee-habit revolution? Scientists. Scientists happen to be the #1 profession with the greatest caffeine consumption, that trails far, far ahead of the #2, health care professionals.

What gives coffee its Joe's of Atlantamystic powers? It all boils down to a small molecule 1,3,7-trimethylxanthine, which is structurally related to uric acid (a byproduct of DNA degradation, and is ever-present in our urine). Eww. This urine-reincarnate blocks adenosine receptors, which induces among many things, elevation in mood, perception of cognitive ability, attention, concentration, and general feeling of well-being. While the verdict is still out as to whether chronic coffee consumption can impart long-term benefits on creativity, learning or memory, we can all admit that it is a great joy to experience a coffee rush. This is especially true when paired with the perfect pastry, delightful company, or oft in grad school, a very juicy research article.

PHDMixAs a first-year at Laney, a self-proclaimed coffee connoisseur, and foodie; I’ve taken great pains to explore the coffee scene in Atlanta in hopes that I can inspire others to get out there and support these great coffeehouses. I’ve assigned each a Study Score and Coffee Score respectively. These scores provide a snapshot of how these coffeeshops stack up as compared to each other in my opinion. Study Score speaks to the degree of table space and outlet availability, wifi speed, duration of hours of operation, and peak volume.

Proof: Catch Phrase: Grandma’s Kitchen. StudyScore: $$$  Coffee Rating: 3cups

Located in Inman Park, this gem is new. Their claim to fame is their pastries, and boy are they tasty. Come here for: lots of natural sunlight, sweet smell of goodness coming from the in-house bakery, mostly housewives during the day, ample outlets. What could be better: Seating is fixed, leaving the sensation of being cramped or having to lean over desk; Coffee could probably taste better.

Parish: Catch Phrase: Sunroom meets Tool Shed StudyScore: $$$$  Coffee Rating:3cups

Parish

Parish

 

Conveniently located directly on the Beltline. This coffee shop is described as having an atmosphere reminiscent of Tuscany with the exposed brick, community farm table, and patio overlooking the BeltLine. The 3 walled configuration is perfect for natural sunlight and feeling like you are getting some quality time outdoors, without dealing with the elements.

Parkgrounds: Catch Phrase: Doggie Day care meets Family picnic meets coffee shop. StudyScore: $$$$  Coffee Rating: 3 point 5 cups

Playgrounds

Playgrounds

 

Located in the Reynoldstown hood; this place is a fairground, dog park, and coffee shop all at once. What better motivation to study than the great outdoors and your favorite breed of domesticated canine? Coffee is not that great, but, hey, take time to enjoy it.

Inman Perk: Catch Phrase: College Café with a pinch of pretension. StudyScore: $$$$  Coffee rating: 3cups

Come here for: Ample space, ample outlets, a blossoming Emory intellectual environment, booze, bikes, and doggie food. Music is sometimes pretty loud; the coffee is mediocre, but the ample study space and lounge area makes it a perfect spot for group study sessions.

Octane – Grant Park: Catch Phrase: Williamsburg Hipster meets ‘The Most Interesting Man in the World’. Study Score: $$$$$    Coffee Rating: 5 cups

Located in Grant Park, this is probably the crown jewel of how coffee shops should be run. Come here for: Amazingly attractive people, amazing industrial atmosphere with huge 20 foot tall ceilings, lots of natural lighting, plenty of tables, a full-service bar, a full-service in house bakery, Emory, and Georgia State hang out. An anchor in the community, come here to make friends or make solitude. The music is a quiet hum, enough to nudge your studying/reading along, but not so loud that you forgot why you came there in the first place. What could be better: at night the lights dim to barely visible levels, so unless you are working on a laptop, use the decrease in illumination as a sign of heading home. And, did I mention they roast their own beans in the back?

Chrome Yellow Trading Co.: Catch Phrase: Minimalist, unbothered, and highly enigmatic. Study Score: $$$$  Coffee Rating: 5 cups

Chrome Yellow

Chrome Yellow Trading Co.

 

My favorite place. Opened up in August of last year in the ever-changing landscape that is old fourth ward (O4W). They are furnished by Stumptown Coffee (premium beans); and feature among other things nitro cold brew on tap. Nothing sets the tone for diving into some science articles like a frosted glass of malty cold-tempered quality beans. Very little music; outlets at every table; tons of space. And a clothing store located in the back, allows you t look as fresh and sophisticated as you feel.

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What to Expect When You’re Expecting to Go to Grad School

By Thomas HennesseyTommyDancer

Congratulations! Probably! I mean you’ve decided to attend grad school  so pat yourself on the back, you’re doing fine, don’t sweat it so much. If all goes accordingly you’ll be starting graduate school in a future fall and you’re probably wondering: what will it be like? How will my life change here? Good news! You can learn the answer to these questions by simply continuing to move your eyes down this page.

  • Everyone here is super smart. Seriously, it’s bananas the brains we got walking smart raptorabout. You might be used to being the smartest cat in the kennel but that’s going to change. So if being the smartest is the only thing you’ve been basing your identity on, it’ll be quite an adjustment indeed. Personally I took some solace from still being the handsomest. And just remember …
  • What you know is not as important as what you can learn. If you’ve got a solid background in your discipline. That’ll be great for…a month, maybe two. Within a week you’ll be diving in to subjects so deep you’ll get the bends. By the time you’ve been here a couple years you should be on your way to being a world expert on whatever tiny sliver of the brain you decide to focus your effort on. And that’s important because…
  • Soon you won’t be learning knowledge, you’ll be generating it. Sure, you’ll never stop reading up on new developments in your field, if only to curse the other labs that beat you to the punch. But creating science, de novo, is very different from passively receiving it. Prepare for experiments not working, ideas not panning out, angry villagers storming the lab, and most of your plans going extravagantly awry. But keep at it. Because ultimately, being the first person on the planet to know something? That’s a very special feeling. Of course while you’re working on all this you’ve got to keep in mind…DarkRoom.jpeg
  • You need to take care of the rest of your life too. Underneath all the science you still have to make it in this crazy world. Apartment hunting, bill paying, food buying, relationship having, and carving out something away from the lab to stay sane. Maybe you like yoga, or snorkeling, or hunting the most dangerous game of all – Man. It’ll feel like you can’t afford to waste the time but taking care of yourself pays a lot of dividends over the long haul.

And it is a pretty long haul, but in the end I think it’s worth it. You’ll have added to the sum total of human knowledge, pushing our species just a little closer to that magical day we invent super intelligent machines to solve all our problems almost certainly without killing everyone. Probably. It won’t be easy, but what we obtain too cheap, we esteem too lightly. Good luck, and welcome to the club!
Thomas Hennessey

Emory Neuroscience Class of 2010

Handsome Scientist

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Methylations that are Making Your Kid Fat (You won’t believe protein #5!)

By Amielle Moreno

Eating behavior is a choice, yet we often forget that urges to eat are regulated not just by the discomfort of an empty stomach, but by complex feeding systems that induce hunger and satiety. A combination of logic and impulse is involved every time we put calories in our mouths and the lasting changes these calories enact in our bodies and specifically our DNA is only now being discovered.

By adding a methyl group (-CH3) methylationto a section of DNA it becomes more difficult for transcription machinery to read it. In this way the expression of genes can be controlled by DNA methylation and research suggests that these modifications can be passed on to the next generation.

In a recent issue of Cell, first author Ida Donkin examined the sperm of human men to determine if these epigenetic modifications are altered by feeding behavior. In her scientific paper Obesity and Bariatric Surgery Drive Epigenetic Variations of Spermatozoa in Humans, mass-sequencing results identified the location of DNA methylation modifications in the genome of Lean, Obese, Pre-bariatric (think stomach bypass) and Post-bariatric surgery men’s sperm.

Among many genes associated with anatomical structure and cell fate, neuro-proteins were also differentially methylated between the experimental groups, indicating that not only does eating behavior enact epigenetic modifications, but also that methylation patterns are passed from father to offspring. Here are the top six neuro-proteins Donkin’s found set up to be expressed differently between overweight and lean men.

Imprimir

Take that, New Year’s resolution! (Lizarbe, 2013)

jabathyroidMelanocortin-4 Receptor (MC4R): Compared to Hypothyroidism or Cushing’s syndrome, MC4R is a less commonly known inherited cause of childhood and adult obesity. Genome-wide studies of body mass index (BMI) confirmed the link between obesity and having DNA variants downstream of the MC4R gene (Loos, 2008). Highly expressed in the hypothalamus, MC4R plays an essential role in energy balance (Siljee, 2013).

Hererozygous mutations are responsible for uncontrolled release of growth hormones, causing increased height and weight starting in childhood (2.5 to 6% of all cases) and continuing into adulthood (5.8% of adult obesity cases) (Siljee, 2013; Farooqi, 2003). This receptor is responsible for homeostatic signals indicating that fat is being ingested (Butler, 2001). By letting the body “sense” the intake of dietary fat, activation of this receptor regulates both the metabolic and behavioral response to food by curbing hyperphagia (overeating).

With high methylation patterns, Obese men’s sperm in the study were less likely to allow receptor expression, potentially making it more difficult to “sense” food intake. Clinical trials using compounds, which activate MC4R, are currently being performed in the hopes of finding an appetite curbing treatment with few side-effects.

Brain-Derived Neurotrophic Factor (BDNF): Thought to be involved with everything from Schizophrenia to drug addiction, BDNF has its hands on everything. The bdnf gene’s expression increases neuron growth and it linked to long-term potentiation and long-term memory. Physical exercise has been shown to increase the synthesis of BDNF in the human brain, improving cognitive function, neurogenesis and mood (Szuhany, 2015). Donkin’s has found evidence that simply by decreasing weight via surgery, the methylation of a gene associated with cognition can change. Thus “GBP-induced weight loss modulates the epigenetic landscape of spermatozoa and alters specific genomic regions” in genes associated with cognition.

BDNFfeedingsystem

Just a collection of letters and shapes (Schwartz, 2012).

Neuropeptide Y (NPY): This protein provides you everything you ever wanted in life: reduced anxiety and stress, reduced pain perception, lower blood pressure… except for the part about increasing fat storage, and carbohydrate appetite (Stanley, 1986). To aid in homeostasis, our adipose tissues produce peptide hormones. These signals are sensed by receptors,

such as MC4R, in the hypothalamus brain region to regulate appetite.

Peptides, such as leptin and insulin, shut down the release of NPY to curb

cinnamonbun.png
This research has prompted Cinnabon to expand into the standardized testing business.

hyperphagia.

There is a strong link between stress and this potent appetite enhancer because the glucocoritcoid hormones produced during stress leads to an increase in NPY release (Arora, 2006). More like a dimmer than an on-off light switch, the amount of NPY released during stress is correlated to the level of stress experienced (Kuixing, 2012).

Cannabinoid receptor type 1 (CR1): Cannabinoid receptors are the most highly expressed G-protein receptors in the brain (Glass, 1997). Unfortunately, studies are limited by the fact that CR1 has different expression patterns in mice compared to humans. Receptor activation in mice mostly leads to them running around more, because of the heavy cerebellum expression, leaving scientists with no good model organisms for experimentation.

undergrads

If only academic scientists had a population of potential test subjects willing to experiment with drugs

In humans, CR1 is expressed in so many different areas of the human brain that listing them wouldn’t help explain its actions. But perhaps its expression in the areas of the brain involved with processing reward, such as the basal ganglia and substantia nigra, could explain its connection to feeding behavior. Any Washingtonian or Coloradan knows that ingesting the exogenous THC molecule will induce feeding behavior, because of its interaction with the CR1 receptor (Williams, 1999). Even though its activation is not essential for feeding behavior, blocking CR1 would lead to better control of appetite. However, few clinical trials have assessed intervention that up regulates the eCB system, presenting a need to explore it as a promising intervention (Williams, 2014).

Cocaine Archer

Have you tried cocaine!?

Cocaine and Amphetamine related transcript (CART): CART is a neuropeptide that produces similar behavior in animals to cocaine and amphetamine, such as increased locomotor and a preference for places associated with the drug (Nakhate, 2011). CART peptide’s expression is regulated by leptin and ghrelin and interacts with several hypothalamic appetite circuits. Researchers have targeted this peptide as a possible treatment for eating disorders, cocaine abuse and even Parkinson’s disease, yet its receptor is still unknown.

Donkin’s study reports the methylation of a number of “distal intergenic” areas. Located between genes, distal intergenic is another way of saying junk DNA which, is another way of saying we don’t know what it does yet. The CART and NPY genes show higher levels of methylation in the sperm of Lean versus Obese men at specific distal intergenic areas. This finding suggests that these locations are not junk DNA but are involved with increasing CART gene expression, making them prime targets for future experimental research.

Behind cravings and overeating there’s a complex neurological system ready to be blamed. Donkin’s paper provides evidence that simply reducing intake (post-GBP surgery group) can affect the expression of 2681 genes, which are differently expressed between Obese and Lean men. Although this new article still doesn’t answer the pressing question of “how” spermatozoa production factors in recent behavior or environmental changes, it indicates the existence of an epigenetic mechanism, which could effect behavior across generations. Perhaps the most important takeaway is that methylation can change to aid in more healthy homeostatic regulation benefiting the individual and their offspring.

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“42!” Or “A Morality Informed by Science”

  by Jacob BillingsJacob

What is the meaning of life? While such a question is intractable to address, some meaning might be gathered by exploring how the most rapidly evolving world view, the sciences, stand in juxtaposition against traditional influences on individual morality.Briefly, let’s lay out a snapshot of this expanding domain of shared knowledge.

Humans are definitely composed of stuff, and this stuff does everything we know to be happening. On the other hand, social moralities are those precepts that guide individual behavior. They are the direct antecedents to the question, “What should I do?”

For some, the worldview offered by the sciences provides a valuable and satisfying collection of expectations that effectively predict an action’s resolution. Such predictions are highly valuable because what we decide to do is always a well-constructed estimate of optimal behavior to adopt given one’s present knowledge about the world. Thus to know new things about the world is to influence behavior.

From this perspective, a scientific morality is qualitatively different than traditional moralizing. For instance: Whereas the description of a Christ ultimately provides a medium for Christians to directly enunciate the moral code of an archetypically perfect person, the sciences observe in the variety of human behaviors how each is embedded within personal and collective experiences.

Because the sciences have dispensed with the concept of transcendent perfection, the moral guidance provided by the sciences is subjective. The aggregates of stuff that we observe around us are there because they have adopted some sustainable form. The celestial bodies are roughly spherical, crystalline structures facilitate the seeding of new crystals, and people living in harmony with the environment tend to meet fewer periods of destructive opposition. Projecting this sustainability principle onto the individual level, optimal decision making tends to support the well-being of the self as well as the environment in which the self abides. And because species that despoil the environment at the cost of their offspring tend to go extinct, the people who we find today tend to share an evolved motivation to work towards the benefit of future generations.

Rather than relying on a transcendent value system for a set of rules by which to live a moral life, a scientific morality thus motivates good living through understanding how to operate within the environment.

So who’s up for a discussion about global climate change…?

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2015 GDBBS Banquet Fashion Spread

By Amielle Moreno

2015 GDBBS Interior Panoramic – Version 2

On a rainy Thursday night, the brightest things in Atlanta were the women and men of Emory’s Graduate Division of Biological and Biomedical Sciences. I plucked the prettiest flowers from the bunch for this article to honor their stylishness.

Gina Alesi from Cancer Biology

Gina Alesi from Cancer Biology

Alicia Cutler from Biochemistry Cell and Developmental Biology (BCDB)

Alicia Cutler from Biochemistry Cell and Developmental Biology (BCDB)

Morgan Woody Winship Cancer Institute

Morgan Woody Winship Cancer Institute

The solid purple dress took center stage this year with multiple ladies donning this trending color. With many ways to wear it, this color is flattering on everyone, but who do you think wore it best?

Josh Lewis from BCDB

Josh Lewis from BCDB

Marko Bajic from Genetics and Molecular Biology

Marko Bajic from Genetics and Molecular Biology

R to L: Gary Longstreet from Program Administration, as well as Muhammad Anzar Abbas from Neuroscience and his lovely date

Gary Longstreet from Program Administration, as well as Muhammad Anzar Abbas from Neuroscience and his lovely date

In man’s fashion, the surest way to stand out in the sea of polo shirted lazy-lads, was easy: sports jacket and tie. Josh Lewis’ mix of jacket and plaid skinny tie set him apart from the crowd. Look out Chris Hardwick! Unfortunately, some people think fashion ends after your pants, such as Marko, who looked like the whole package until you notice his shoes. When asked about his ensemble he responded “#Marko #swag #swagco #yolo #yololifeforever #ijustputiton.” But Anzar Abbas gets extra flair points for his light brown tips. And yes, Gary Longstreet, people are going to think you’re a server if you dress in all black. “Black’s my favorite color,” he responded with aplomb.

Gina Lenzi  Molecular Systems and Pharmacology

Gina Lenzi Molecular Systems and Pharmacology

Madeline Price IMP Immunology and Molecular Pathogenesis

Madeline Price IMP Immunology and Molecular Pathogenesis

The LBD is a fashion staple but Gina’s lacy number will stand the test of time. It’s versatile with long sleeves which keep it in rotation from fall to late winter. Meanwhile, Madeline pulled this little number out of the closet after getting into shape. Can you think of anything more rewarding than slipping into that dress after months of working out? Her classic pumps make her ready for any formal event, but one might say that her accessories are lacking while Gina’s gold accessories take her ensemble over the top.Who wore black better: Gina, Madeline or Gary?

Version 3

Rachel Cliburn from Neuroscience

Rachel Cliburn from Neuroscience

Gary Longstreet from Program Adminsitration, Dr. Weinshenker and Dr. Gretchen Neigh

Gary Longstreet from Program Adminsitration, Dr. Weinshenker and Dr. Gretchen Neigh

And then there were the red mavens. Rachel  not only had hands and toes in theme with her red dress from Paris, her glass slippers “make [her] feel like she can twinkle float.” Dr. Neigh gets a chance to wear this beautiful gown for the second time. I was shocked that it was an Ann Taylor because I’ve never seen anything this bright. That dress, much like these two ladies, stand out from the crowd when everybody else is wearing tan. Thanks for the photo bomb, Gary.

Jacob Billings from Neuroscience

Jacob Billings from Neuroscience

Lukas Hoffmann from Neuroscience

Lukas Hoffmann from Neuroscience

Both of these Neuroscience gentlemen received their neuron accessories, from their significant others. Lukas’s purple tie is from Bow-Tie For a Cause with all the profits from this gift benefiting Alzheimer’s research.

Julia Omotade from BCDB

Oh MY, Omotade! Julia Omotade from BCDB wins the best dressed award!

Black and White doesn’t get any better. In my humble opinion, Julia Omotade’s cocktail dress puts all others to shame and as the best dressed at the GDBBS Banquet.

Besties!

Besties!

Eye catching from across the room, Pernille Buelow claims she does "this with my hair everyday at lab."

Eye catching from across the room, Pernille Buelow from Neuroscience claims she does “this with my hair everyday at lab.”

What did they just hear that could create such polar reactions?

What did they just hear that could create such polar reactions?

Dr. Weinshenker was literally the last person to receive dinner.

Dr. Weinshenker was literally the last person to receive dinner.

Because it's alien eggs, this is the vegetarian option not the vegan option.

Because it’s alien eggs, this is the vegetarian option not the vegan option.

The food was much better in years past.

The food was much better in years past.

Version 2

Constance Harrell Shreckengost from Neuroscience receives the graduate Career Award

IMG_2437

Lauren DePoy receives the Neuroscience Scholar of the Year Award

Version 2

A bowl?! I work for 13 years and all I get is a bowl with a dent in it?!?!

Version 2

Lukas Hoffmann from Neuroscience receives the Graduate Program in Biology Academic and Achievement Award

Version 2

My two bundles of joy!

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Did You Know? with Willa Cho!: Little-known facts about Atlanta

by Willa ChoIheartATL

Little-known facts about Atlanta!

  • Atlanta resident Margaret Mitchell wrote Gone with the Wind because an ankle injury kept her from leaving the city and she was very bored.
  • Atlanta is still proud that it hosted the Olympics in 1996, for some reason.
  • In 1886 Atlanta, Dr. John S. Pemberton invented Coca-Cola to usher in a new era of obesity but passed away before his dream was realized.
  • Every year, Atlanta hosts DragonCon, a multigenre convention and parade  celebrating science fiction, fantasy, and comic books which commences nerd mating season
  • Atlanta was chosen as a hub for Delta airlines because it’s only a three hour plane ride to some place better.
  • Atlanta is believed to be named after the goddess Atalanta, who was raised by bears. The cult responsible for the naming is still active and its hooded members can often be spotted along the new beltline walking path.
  • Elle and Dakota Fanning, Jane Fonda, Holly Hunter, Ed Helms, Raven-Symoné, Chris Tucker, and Julia Roberts were all born in Atlanta and now live somewhere else.
  • Tourist attractions in downtown Atlanta includes the worlds largest aquarium and Coca-Cola’s ‘World of Propaganda.’
  • Stone Mountain, outside Atlanta, is one of the largest blocks of exposed granite racism in the world.
  • A law still stands on the books from 1927 that states that good Chinese restaurants aren’t allowed anywhere in the city except Buford Highway.PrayforATLA
  • The symbol or mascot of Atlanta is “A man from another area in the south who thinks Atlanta is great!”
  • Atlanta is an official celestial conduit to heaven, with branches of Zesto’s serving as departure terminals for all believers chubby enough to survive the trip.
  • There are over 55 streets with the name “Peachtree” in the city, all with their own rival gangs that brawl during any eclipse.
  • What we call “Atlanta” is only the surface of a much, much larger subterranean city, which comprises 91% of the mass, 87% of the energy consumption, and nearly 100% of the Tinder spam bots.
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