Scizzle’s Christmas Gift Guide 2016

By Sally Burn, Gesa Junge, and Deidre Sackett

 

Ho ho ho, science lovers! It’s that time of year again: panic buying gifts for your nearest and dearest! If your intended recipient happens to be a scientist or a fan of all things science, we have a veritable selection of gift ideas. Or perhaps you yourself are angling to receive a science-themed present and want to point the buyer in the right direction. Then look no further: behold, Scizzle’s 2016 Christmas gift guide!

 

Culinary Science

Turn any kitchen into a lab with our handpicked selection of geeky culinary gifts. Spice up your cooking with the Chemist’s Spice Rack from ThinkGeek or whip up some cosmic cookies with these 3D spaceship cookie cutters. Then put a smile on the mathematician in your life’s face by serving them festive dessert on the i eight sum pi plates. Finally, prevent your Christmas lunch leftovers from being stolen from the communal fridge by taking them to work in this human organ for transplant insulated lunch bag.

 

Technical Tipples

Bring out the crazy scientist mixologist in you this festive season with a Chemist’s Cocktail Kit, then serve up your creations in drinking glasses that are out of this world. The Planetary Glass Set contains ten gorgeous tumblers – representing all eight planets in our solar system, plus the sun and Pluto. Pair the glasses with an anatomically informative coaster set to avoid marking your table – we heart these cardiac anatomy coasters, although the more cerebral minded may prefer a set of Brain Specimen Coasters.

 

Science Bling

Wear the whole solar system around your neck with this fabulous Solar Orbit Necklace or just keep Pluto’s heart close to your own with a Pluto pendant. Like DNA? Put a ring on it with this simple DNA helix ring available on Etsy.

 

Science Apparel

Help the female neurobiologist in your life stand out from the crowd in this Neurons Glow-in-the-Dark-Dress. Or go all out science with the Nerdy Science Dress, festooned with Erlenmeyers, microscopes, formulae, and DNA helices. And for sir, may we suggest the Too Molecule for School Men’s Socks.

 

For Kids (Both Little and Big)

You’re never too young or old to cuddle up with a plush brain, spleen, rectum, or any of the thirteen adorable soft organs available from Uncommon Goods. Or how about a crochet Erlenmeyer flask?

 

SciArt

Check out the Etsy store of the ultra-talented Ella Maruschchenko, whose illustrations have been featured on the cover of many leading journals, for science-themed prints and mugs. For an even greater range of SciArt gifts, head over to the Artologica Etsy store where you will find gorgeous paintings, silk scarves, and petri dish ornaments.

 

High End Geek Gadgetry

The Smartphone Instant Photo Lab is at the higher end of the gift budget ($169.99 and $24.99 for film) but worth it for the thrill of printing your candid Christmas party shots direct from your phone to Polaroid-style paper.

 

Under $10 - for Secret Santa and Stuffing Stockings

Finally, for $3 you can be the proud gifter of an infectious disease stress ball and for under $10 you can pick up a set of five solar power toy cars, a cute Space Capsule Tea Infuser, or even this super chic chemistry lab beaker vase.

 


The path to publication

So You Want to Be a… Publishing Editor

By Sally Burn, PhD

Scizzle’s post-PhD career series is back this week with an interview with Cathy Sorbara about her career as a Publishing Editor for the Royal Society of Chemistry. Dr Sorbara also acts as a consultant for the Cheeky Scientist Association (check out their great PhD industry transition articles here) and can be contacted via her LinkedIn page.

 

Hi Cathy! So, what exactly does a publishing editor do?

As a publishing editor, I assess submitted articles and guide them through the peer review process including reviewer selection, review evaluation and making the final decision to accept, reject or transfer the manuscript with our portfolio.  I also carry out production of accepted manuscripts including editing, proof reading and issue make up.  Other responsibilities include coordinating themed issues, commissioning cover art work and acting as a point of contact for associate editors (an international team of experts in various chemical sciences who handle submissions for various journals).

 

How did you get to where you are now?

I am Canadian and received my undergraduate degree at the University of Western Ontario in Medical Science and my Master of Science at the University of Ottawa.  I then moved to Munich, Germany where I did my PhD in Medical Life Science and Technology.  At that point I decided I was better suited for a communication-based role and wanted to move away from bench research.  I move to Cambridge, UK and came across this opening and thought it would be a great opportunity for me to further develop these communication skills.

 

What are the key skills needed for this job, and did you develop any of them during your PhD?

PhDs gain a wealth of transferable skills that I feel they often underestimate.  I too suffered from imposter syndrome through graduate school and left feeling I had little skills to offer beyond my technical expertise.  I soon realized however, that I had developed effective communication skills, time and project management, ability to work independently as well as in a collaborative environment, to name a few.  All of these skills were beneficial in my current role.

 

What would be your advice to a PhD wanting a job similar to yours?

A job advertisement is a wish list.  Even if your skills do not match 100% the job description, do not let that intimate you.  If you are interested in a job in editing or other communication-based roles, reach out to employees in the company and have a chat with them.  See if the company and the role is something that would be of interest to you and learn how to translate your skills into professional business experience.

 

What are the top three things on your To Do list right now?

Assess the latest manuscripts that have been submitted to the journal, check up on previous manuscripts that are under peer review (can a decision be made, do I need to invite more reviewers, etc.) and tackle the production to-do list to ensure everything is completed as quickly/accurately as possible to maintain low times to publication.

 

What are your favorite – and least favorite – parts of the job?

As I assess each manuscript that is submitted to the journal, it gives me the opportunity to read a lot of fascinating science and stay up-to-date with the latest breakthroughs in the field.  As a science nerd, this is a dream come true.  Sometimes we have to make decisions on manuscripts that are difficult and not well-received by authors.  It is never easy to tell someone who has worked for years on a manuscript that it has been rejected.  I definitely empathize with them as I have been on the receiving end of these rejection emails before. I am sure this has made me an enemy of some but I hope they understand that this is all part of the peer-review process which we strive to maintain as fair and unbiased as possible.

 

Is there anything you miss about academia?

I do miss bench work from time-to-time.  There was a sense of pride and honor associated with doing research, especially disease-related as I had done.  Now, however, I have time to pursue other passions and have more time for travelling and spending time with family. My life is not defined by the number of hours I am chained to the bench and this was important to me.

 

How do you see your field developing over the next ten years?

As many academics are aware, publish or perish is a theme to their success and accordingly the peer review/publication process has received a lot of flak about how it contributes to the plight of academic research labs.  I think we will see a lot of changes in the future as publishing houses adapt and deal with this growing concern of how research should be disseminated, evaluated and rewarded.  Already we see more journals becoming open access, changing their peer review process (double or triple blinded) or allowing for raw data to be published.  There is also the argument of why negative data or repeated experiments should not be equally as rewarded.  It will be fascinating to see how things evolve.

 

What kind of positions does someone in your position move on to?

Publishing editors can move into managerial roles or higher executive roles where they deal more with commissioning of articles, competitor intelligence, attending conferences and the overall management of the journal and its goals.  Many people who move out of publishing move on to other communication based roles such as medical writing, policy, marketing and more.  It is a good stepping stone for many other roles.

 

And finally, the big question: In the event of a zombie apocalypse, what skills would a publishing editor bring to the table?

A publishing editor would draft a well-written article to the zombies, detailed how we can work together to live in harmony.  Of course this article would be reviewed by experts in the field of zombie apocalypses before it was sent.

 


Dr Frankenstein being crept up on by his monster

Dr Frankenstein’s Modern Guide to Body Building

By Sally Burn, PhD

Square head, green skin, bolt through the neck, and plagued by misconceptions: “Frankenstein” is a popular choice at the Halloween costume store. This erroneously named costume is based on the monster from Mary Shelley’s Frankenstein, the titular character of which is Dr Frankenstein, the scientist who creates the in fact unnamed creature. Modern depictions of the monster tend to hold little resemblance to that in the book where we are told that “His yellow skin scarcely covered the work of muscles and arteries beneath; his hair was of a lustrous black, and flowing; his teeth of a pearly whiteness…

A final misconception – born from the movies - is that the monster was created from stolen body parts, animated to life with electricity. Shelley did not go into details of how exactly the monster was made, instead leaving us with just an indication that Frankenstein had the lifestyle of a postdoc (“I had worked hard for nearly two years, for the sole purpose of infusing life into an inanimate body. For this I had deprived myself of rest and health”) and a Nature Letter-size methods section: “With an anxiety that almost amounted to agony, I collected the instruments of life around me, that I might infuse a spark of being into the lifeless thing that lay at my feet.”

Clearly this is an insufficient Materials & Methods section to permit study replication. So, in the spirit of spooky science, Scizzle presents Dr Frankenstein’s Modern Guide to Body Building – how to build a brain, kidney, gut, and more in the comfort of your own lab:

 

* Building Brains:

The first thing your creation will need is a brain. While we don’t yet have the technology to grow a whole brain in the lab, we can make cerebral organoids. Scizzle first reported on these brain-like spheres two years ago, when they were published in Nature. Cerebral organoids are generated from human pluripotent stem cells (hPSC) or induced pluripotent stem (iPS) cells – so no need to go raiding the graveyard for spare body parts anymore, wannabe Frankensteins! The cells are aggregated into embryoid bodies, which are then differentiated into neuroectoderm and cultured in a spinning bioreactor, resulting in 3D cerebral organoids. After around a month in culture the organoids contain distinct brain regions and a cerebral cortex – the seat of consciousness, memory, and language.

 

* Growing Guts:

Upon waking, your monster will need a good meal so you’re going to need to build a digestive system. The gut is composed of a number of functionally, physiologically, and histologically distinct organs, including the stomach and small and large intestines. The liver and pancreas also play vital roles in digestion. Progress has been made on growing all of these tissues in the lab. Stomach-like “gastric organoids” can be generated by exposing hPSCs to a specific cocktail of proteins and growth factors. These mini stomachs even act in an organotypic manner, responding to H. pylori infection as a human stomach would. Moving down the digestive tract, our next requirement is an intestine. While we can’t yet grow an entire intestine in the lab (that would be one big culture dish), our old friend the organoid is here to help again – this time in the form of intestinal organoids, grown from crypt-derived stem cells (crypt as in small intestinal, not as in the spooky Halloween place). And yes, you will be pleased to know it is even possible to engineer your monster an anal sphincter. Even monsters need to poop.

 

* Crafting Kidneys:

To keep your creation in peak operational form, it will need to be able to process and remove toxins from its body. For drug processing look no further than iPS-derived liver buds (iPS-LBs), which can successfully metabolize drugs. Excretion of waste from the monster’s body will require kidneys. The generation of kidney organoids is a hot topic – earlier this month Melissa Little’s lab in Australia reported their iPS-derived kidney organoid system. While other groups have made similar organoids, this newest report is exciting as their kidney organoids contain numerous cell types and tissue structures found in human kidneys, arranged in an organotypic fashion. Furthermore, the engineered organs exhibit kidney-like function and nephrotoxin sensitivity.

 

So could a modern Dr Frankenstein make a monster using these techniques? No, obviously not – and thank goodness for that – but by exchanging grave-digging tools for iPS cells they could certainly have a good attempt at making replacement body parts for real humans. Such an endeavor may be possible in the near future, but already right now these lab-grown organoids offer a number of other benefits.

One use is pharmacological screening – does a new drug adversely affect the human kidney, for example? The human origin of organoids also allows researchers to gain insights into the development and disease of their related organs, in a way not possible with animal models. Lastly, by using patient-specific iPS or stem cells to generate organoids, scientists can better understand the etiology and treatment prospects of an individual’s disease. Earlier this year, Hans Clever’s group reported the generation of gut organoids from colorectal cancer patients, which recapitulate characteristics of their tumor of origin and are amenable to high throughput drug screening.

For a more in-depth look at the growing field of organoid science, see Cassandra Willyard’s article in Nature and stay tuned to Scizzle for future tales of "Frankenstein" science!


Cake decorated with open access symbol

Open access: the future of science publishing?

By Florence Chaverneff

On the eve of receiving the Nobel Prize in Physiology or Medicine in 2013, Randy Schekman shook the scientific world in an altogether different manner when he announced in the Guardian newspaper he and his group would boycott the three leading scientific journals. These bastions of scientific publishing have long been held on a pedestal by the research community the world over and regarded as depositories of excellence in science. Their reputation is tightly associated with high ‘impact factors’, a parameter determined by article citations, and which Schekman judges to be a "gimmick" and a "deeply flawed measure, pursuing which has become an end in itself – and is damaging to science". Yet, career advancement in academic research is heavily – if not exclusively– reliant on individuals getting their work published in these high impact scientific journals, which Schekman calls "luxury journals", comparing them to bonuses common on Wall Street, and from which "science must break [away] ". He deems that "the result [of such a change] will be better research that better serves science and society". The Nobel Prize awardee touts the open access model for scientific publishing, presenting it as all-around anti-elitist, which…it is.

 

In 2001, the Budapest Open Access Initiative defined open access for peer-reviewed journal articles by its "free availability on the public internet, permitting any users to read, download, copy, distribute, print, search, or link to the full texts of these articles, crawl them for indexing, pass them as data to software, or use them for any other lawful purpose, without financial, legal, or technical barriers other than those inseparable from gaining access to the internet itself".

 

This is how open access makes for a more level playing field: by allowing immediate dissemination of scientific findings without restrictions, and by accepting articles without highly demanding criteria, while maintaining sound peer-review practices. This comes in sharp contrast to the 300 year old model of subscription-based scientific publishing, accepting limited numbers of articles in each issue, and requiring exceedingly demanding standards for acceptance. This results in significant publication delays and considerable time effort spent polishing articles for publication. Time which could be spent… doing research.

 

While many in the community will agree on the benefits granted by this still recent and evolving model of science publishing, open access journals, being less established than older household names, and lacking in their majority an impact factor, may not appear as prime choice for researchers. The question then can be posed: what would it take to bring about a shift in attitudes where open access publishing would be favored? Granting agencies and academic institutions, which contribute to setting the standards for scientific excellence need to start being more accepting of non-traditional models of scientific publications, and judge on quality of research, and not solely on journal impact factor. National policies encouraging open access publishing are also paramount to support such a shift. Moves in that direction are underway in the UK with a policy formulated by the Research Councils, and in the European Union with the Horizon 2020 Open Research Data Pilot project, OpenAire. In the US, the Fair Access to Science and Technology Research Act and the Public Access to Public Science Act aiming "to ensure public access to published materials concerning scientific research and development activities funded by Federal science agencies", if passed, would be a step in the right direction.  All else that is needed might be a little time.

 


Like a walk in the woods, entrepreneurship is about exploring first-hand all life has to offer

Life of a scientist as an entrepreneur

By Padideh Kamali-Zare, PhD

It has been almost a year since I started my journey as an entrepreneur, after being a scientist for almost a decade. Such a change in my career path felt a bit unusual in the beginning, but soon I found a lot of similarities between the two paths. I quickly noticed that I am actually still continuing the same path, only exploring different aspects of it. A path I initially feared to step in soon became a joyful journey I now cherish every day. Through interacting with a lot of scientists and entrepreneurs, I came to realize that the entrepreneurial spirit adds an enriching dimension to a scientist’s world.

As a scientist, one has a passion for uncovering the mysteries of nature and discovering the truth (mechanisms underlying events) through scientific methodology. This methodology famously relies on testing hypotheses, and developing new tools to do it accurately. Over the centuries, this methodology has become a steadfast tradition. As such, everyday work as a scientist becomes a routine job very quickly. This limits the freedom, flexibility and independent thinking of a scientist. However, I always thought of science not as a job, but as a lifestyle. Science, through critical thinking, changes how one views the world, questions everyday life events, and addresses them by gathering evidence and applying them towards gaining a higher wisdom. These skills are invaluable assets in the entrepreneurial world.

The entrepreneurial mind, very much like the scientific mind, functions by questioning, hypothesizing and testing. The coordinate system of the two is identical and the valuation of ideas is reflected through vigorous testing of the initial hypotheses. What is different is the human component, which is much more prominent in the entrepreneurial world. In the end, people are the users of our products. They should see the value of our work and be willing to use it in their everyday life. If you are a scientist with good interpersonal and communication skills who also likes to promote scientific innovation through people and for people, you are already an entrepreneur.

Exploring the world as a passionate, dedicated scientist is like driving around in nature while listening to music and having brainy conversations with friends riding in the car with you. Entrepreneurship, on the other hand, is like stopping by the roadside, getting out of the car, getting some fresh air, hearing the ocean waves, walking to the woods, and exploring, first-hand, all that life has to offer. Life as an entrepreneur is much more flexible and creative than that of a scientist in the modern world. The entrepreneurial journey modifies itself every step of the way and never becomes routine. As an entrepreneur, you learn things from everyone, not just people around you or in your particular field of research. As a scientist, you find yourself constantly zooming in on a highly specialized and narrowed down subject, while as an entrepreneur you zoom out and see things from above, you see the big picture, and you focus on the impact your work can have on the world. No matter how long or how short, entrepreneurship is a fulfilling, growing experience of a lifetime.


Spring cleaning our bodies

 

By Katherine Peng

“Spring fever” is not a particularly new phenomenon. With the especially frosty winter that we’ve endured however, it is one that we may now be more perceptive to. You may have noticed more friendly smiles between strangers on the street, bursts of new positive energy, and motivation to cross off to-do lists, clean everything, and take on new projects. It is effortless and intuitive to attribute these psychological changes to longer hours of daylight and warmer weather, but as a scientist, you’ve probably also wondered what is happening in our bodies to create these wonderful new personalities.

Photoperiodism, a physiological reaction to changes in day length, has evolved in seasonal animals to restrict energetically costly processes when food resources are low as well as to predict the optimal time to breed and bear young that will survive. Humans are not as seasonal as these creatures, and any seasonal response we have is increasingly offset by indoor work, artificial light, and artificial temperature regulation. Nevertheless, many epidemiologically studies have observed the seasonality of certain human occurrences such as birth rates, viral infections, suicide, and seasonal affective disorder (SAD). Animal studies of seasonality have focused primarily on the mechanism of reproductive changes, but rodents have also been shown to have elevated levels of anxiety and depression-like behaviors on days with shorter periods of sunlight1. The greatest evidence that human emotions adjust seasonally as well is apparent in the high prevalence of SAD, aka seasonal depression.

So how can light alone cause such drastic changes in our behavior? Early morning light is an essential environmental cue for synchronizing the body’s internal clock. In fact, light therapy combined with chronotherapy (tailoring treatments to your personal biological cycles) is often used to treat circadian rhythm sleep disorders and SAD.

The control center for bodily rhythms in our brains is called the suprachiasmatic nucleus (SCN), and it mainly governs circadian, or daily, rhythms. In darkness, it stimulates the pine-cone-shaped pineal gland near our brain stem to release the sleepiness hormone called melatonin. When light hits our eyes, particular retinal ganglion cells that are not involved in vision send signals to the SCN to stop production of melatonin. It is thought that the culprit to our sluggishness in the winter is this longer exposure to melatonin release as the days get shorter. It also doesn’t help that colder temperatures tend to keep people indoors away from natural light, which will also decrease absorption of vitamin D and leave you feeling moody. As days get longer in the spring, decreases in melatonin levels can leave you feeling much more energized. Serotonin, a feel-good neurotransmitter, also has levels that correlate with the amount of sunlight exposure. While the serotonin transporter sucks away serotonin fastest in the winter, which may lead to SAD, greater light stimulation triggers more of its synthesis. This biology, along with the additive effects of more available outdoor activities (and exercise) and the desire to eat more fresh fruits and vegetables, awakens us from our mental hibernation with a fresh vitality.

So take advantage of your restless enthusiasm and clean out your closets, fill your calendars, and renew some New Year’s resolutions! As Emily Dickinson once said, “A little madness in the spring is wholesome even for the king”.

  1. Demas, G. E., Z. M. Weil, et al. (2009). Photoperiodism in Mammals: Regulation of Nonreproductive Traits. Photoperiodism: The Biological Calendar. R. J. Nelson, D. L. Denlinger and D. E. Somers, Oxford University Press USA: 461-502.

Throwback Thursday: Newton

 

Sir Isaac Newton was a British physicist and mathematician widely regarded as the preeminent scientist of his time.  Newton made incredible contributions to the physical understanding of our universe and is one of the fathers of calculus.  Read moer about Newton at http://www.bbc.co.uk/history/historic_figures/newton_isaac.shtml


Throwback Thursday: Tesla

 

 

Nikola Tesla was a Croatian-born physicist, and engineer who emigrated to the United States in the late 1800’s and worked closely with Thomas Edison for a time.  A prolific inventor, Tesla is know best for his work on alternating current and electricity.  Read more about Tesla at http://www.teslasociety.com/biography.htm


Decoding the Literature: Annotated Research Papers to Teach the Scientific Process

 

 

By Celine Cammarata

Most students graduating from high school or college have taken at least a few science courses, and consequently have some knowledge of elementary scientific facts about the world (in theory, at least).  But is this enough?  Or do students also require an understanding of how science works, how scientific knowledge is obtained?

This was the idea behind Science in the Classroom, or SitC, a website that provides annotated scientific papers.  Launched last fall by the journal Science, the goal of SitC is for all students to read at least one journal article before leaving school, in hopes that this exposure to research literature will help clarify the inner workings of science and how it gives rise to information.  As discussed in an editorial marking the inauguration of SitC, a lack of understanding of where scientific knowledge comes from can foster the spread of misinformation and a disinclination to base important designs on scientific evidence; some might even argue it could lead to distrust of science and scientists.  Hence: SitC.

The idea of SitC piqued my curiosity, so I recently spent a while exploring the site.  Although only seven papers are available so far, the resources attached to those paper are fairly substantial.  Each paper is kicked off by an introduction and a set of “thought questions,” guiding students to consider the research critically and in context and mimicking the types of questions scientists ask themselves about a paper.  This is further supported by detail-oriented questions interspersed throughout the text, fostering engagement as one reads.  Figures are accompanied by a summary of the questions being asked, the experimental set up, brief explanations of techniques and symbols, and more, to help students work through the sometimes confusing jumble of graphs and images.  Finally, students can choose to enable various tools, such as a glossary that highlights and defines potentially unfamiliar terminology, or a function that specifically highlights the author’s conclusions.  Each paper is available in full length, geared toward university students, or in an abbreviated form intended for high schoolers.

It would seem that such a resource has numerous other uses in addition to teaching high school and college students about the scientific process.  Annotated papers can serve as a vehicle  to greater scientific literacy not only students but for the public at large, increasing public access to science by granting more citizens to ability to read scientific papers and actually get something out of them.  Furthermore, SitC could act as training wheels for scientists-to-be as they learn the vital skill of analyzing literature.  Finally, studying papers that have been broken down in this way can provide valuable insight for investigators into how they might best explain their own work to a broader audience.

Although SitC has garnered relatively little attention so far, it will be interesting to see how teachers, students, scientists and others utilize this resource in the future.


Scizzling Papers of the Week - January 3rd

The Scizzle Team

Marking malaria resistance

Worldwide elimination of malaria is finally starting to appear possible, thanks in part to widely successful treatments such at artemisinin-based combinations, but a rising incidence of artemisinin-resistant malaria parasites in parts of southeast Asia.  To curtail this trend, and identify where it has already struck, requires a molecular marker for such resistance, which has now been discovered.  Investigators identified a mutation in the ketch protein K13 that is seen in various artemisinin-resistant populations, but not in parasites sensitive to the drug.  Ecological surveys showed that this mutation was found in parasites from affected areas, but rare in regions with few cases of resistance; indeed, this marker was more reliable than population grouping in predicting parasites’ drug sensitivity.

A molecular marker of artemisinin-resistant Plasmodium falciparum malaria, Ariey et al, Nature, 2 January 2014.

 

Neanderthal genome hints at a new player

Researchers have completed the first high-quality genome sequence of a Neanderthal, discovering that her parents were half-siblings and that in her recent ancestry, mating of closely related individuals was fairly common.  The investigators were also able to improve upon prior estimates of the degree of genetic contribution from Neanderthals in modern humans, and gained insight into gene flow among Neanderthals, Denisovans (another archaic group) and early modern humans.  Finally, their evidence suggests gene flow into Denisovans from another, as yet unidentified group.

The complete genome sequence of a Neanderthal from the Altai Mountains, Prüfer et al, Nature, 2 January 2014.

 

An intoxication inhibitor

The supposedly inactive precursor of neurosteroid hormones, pregnenolone, may play a role in protecting the brain during cannabis exposure.  Pregnenolone levels in rodents went up following injection of most major drugs of abuse, but by far the greatest effect was seen following administration of THC.  Prenenolone, in turn, inhibited activity of the CB1 receptor, which mediates the effects of THC, thus reducing their severity.  Such a negative feedback loop may help guard the brain during exposure to THC, and might be helpful in treating cannabis intoxication.

Pregnenolone can protect the brain from cannabis intoxication, Valleé et al, Science, 3 January 2014.

 

Researchers shed new light on gamma-ray burst

The explosion of a massive star last spring caused the largest gamma-ray burst ever recorded.  This week, several different research groups have published their analyses covering various aspects of the event, including indications that current models cannot account for all aspects of the explosion.

An exceptionally bright gamma-ray burst, Fynbo, J.P.U., Science, 3 January 2014


Mother Knows Best: Breast Milk Affects Cognitive Function

 

 

By Celine Cammarata

Bacteria, parents’ experiences, poverty - the list of environmental factors that affect cognition continues to grow, and now there’s a new one: breast milk.  The composition of a mother’s milk can confer cognitive advantages to her offspring.

 

It’s known that the cytokine TNF (tumor necrosis factor), which works primarily in the immune system, is also found in the central nervous system, and past evidence has even suggested that TNF knockout mice may have some cognitive gains.  Now, researchers have revealed that spatial learning and memory are improved in mice whose mothers lack one or both TNF alleles.

 

Mice born to mothers with little or no TNF outperformed their peers on the Morris Water Maze, a widely used test of spatial memory that depends on the hippocampus.  These animals also demonstrated a transient elevation of neural proliferation in the dentate gyrus region of the hippocampus during development, which may underly their increased cognitive skills; inhibiting this increased proliferation eliminated the behavioral differences.  Furthermore, gene expression and dendrite morphology of dentate gyrus neurons were also altered in these offspring.

 

Why?  The answer could not be genetic: mice whose biological mothers were genetically normal, but who were raised by TNF-deficient foster mothers, had the same advanced skills.  So did offspring of genetically normal mothers, when the mother’s TNF levels were inhibited directly by administering antibodies for the protein postpartum.  It turns out that reducing TNF leads to lower levels of several chemokines in the mother’s milk.  Because newborn mice can’t fully break down such proteins, when these chemokines are present in milk they can reach the pup’s digestive tract in concentrations high enough to effect the immune and nervous systems from the gut.  Thus, the lack of these proteins can have an effect as well.  Although the precise mechanism of how milk composition alters hippocampal development is not yet clear, it may act in part by altering the number of white blood cells present in circulation.

 

TNF levels in the body can decrease as a downstream effect of mild stress and physical activity, as might occur when animals live in a challenging environment.  Perhaps this system of using low TNF to trigger increased cognitive capacity in offspring evolved as a way for parents to better “prepare” their young for the world.


Cutting out HIV: One Step Closer to the Cure

 

 

Elaine To

Currently, individuals who test positive for HIV are put on highly active antiretroviral therapy (HAART), a cocktail of multiple drugs that inhibit different aspects of the viral life cycle. While there are drugs that prevent the integration of the viral genome into the host cell genome, there is no known mechanism to remove the viral genome post-integration. This is also the reason we cannot completely eradicate HIV from infected individuals—even after HAART treatment, the viral genome persists in inactive memory T cells. In order to address this, Hauber et al. re-engineered the commonly known Cre recombinase enzyme, directing the novel Tre recombinase to target sequences in the HIV long terminal repeat regions. These regions flank the viral genome, allowing Tre recombinase to cut the targeted sequences within these regions and excise the viral genome from the host cell’s genome.

Lentiviral transduction was used to deliver the Tre recombinase vector into cells. The vector was designed to place Tre under the control of a Tat dependent promoter, ensuring only the infected cells that express the HIV protein Tat will express Tre. Flow cytometry was used to analyze HeLa cells infected with HIV that contained blue fluorescent protein. Cells transduced with the Tre vector had fewer blue fluorescing cells while the blue fluorescing population remained stable in cells transduced with a control vector. Immunoblots confirmed the protein expression of Tre in the Tre transduced cells. Additionally, the time course of Tre expression matched the time course of the decreasing blue fluorescence seen in the flow cytometry experiment. PCR and DNA sequencing checked that the exact DNA sequence intended to be cut out was removed in the Tre transduced cells.

Viral gene delivery comes with a fear of deleterious effects on the host cells. The researchers first examined this possibility in Jurkat cells using a re-designed vector that constitutively expresses Tre. Between the Tre and control transduced cells, there were no differences in tubulin expression, growth rate, apoptosis, or cell cycle progression. When this constitutive Tre vector was transduced into CD4+ T cells isolated from a human donor, the cells displayed similar activation and cytokine secretion profiles as compared to the control vector. The Tat dependent and constitutive Tre vectors were both transduced into hematopoietic stem cells (HSCs) without any change on the abilities of the HSCs to differentiate into the expected cell lineages. Karyotyping and comparative genomic hybridization revealed that CD4+ T cells have no Tre dependent genomic aberrations. Lastly, Tre was shown to be incapable of cutting DNA sequences within the host genome that are similar to the targeted HIV LTR sequences.

The core experiments behind this paper are the in vivo studies done in Rag knockout mice, which can be transplanted with human immune cells and used as a humanized animal model. CD4+ T cells were isolated from human donors, transduced with the Tat dependent vector, and transplanted into the mice, which were then exposed to HIV. The mice displayed lower viral counts and higher frequencies of human T cells versus the control transduction vector. Similar results were obtained when mice were given Tre transduced HSCs. Thus, the researchers elegantly show that their engineered Tre recombinase can alleviate the symptoms of HIV infection. However, reliable methods of gene delivery are yet in development, and the inactive memory T cells harboring the latent HIV reservoir do not express Tat, precluding Tre expression. If combined with methods that activate viral protein expression in the presence of HAART, Tre recombinase therapy may yet play an important role in the cure of HIV.


Feeling overworked? You’re not alone.

 

 

Celine Cammarata

Regardless of beliefs or traditions, many of us would probably like to be at home with our families right now.  But cells need tending, data points need collecting, and science halts for no man - or at least so it seems.  I recently got to wondering, are the hours of a scientist as crazy as they feel?

In a nutshell yes, we do work a lot - but not that much more than other professions.

You’ve probably already seen this info graphic, showing that science is the most coffee-consuming profession, and it’s no surprise when you consider our hours.  A paper posted to arXiv in 2012 examined the times at which papers are downloaded from Springer to gain insight into when scientists are working.  The U.S., Germany, and mainland China top the list in paper downloading.  Based on this metric, scientists tend to work late into the night as well as on weekends.  Trends in specific time distribution vary by country, with American scientists favoring long evenings over working on weekends; Chinese scientists closing shop overnight, but taking little rest over the weekend; and German scientists splitting the difference.  Interestingly, American scientists seem to be particularly bad at taking a lunch break - while China and Germany showed appreciable dips in paper downloading around early afternoon, no such trend is seen in the U.S.

All those nights and weekends add up.  In 2005 the NSF reported that scientists and engineers working in education (which included those doing research and teaching at universities as well as K-12 teachers) work an average of 50.6 hours a week overall, or over 52 hours a week for those in biology or engineering.  Scientists seeking tenure work a bit more, averaging 52.51 hours per week overall. Interestingly, those with children tend to work only slightly fewer hours per week than their childless counterparts, although the effect of children on working hours is more pronounced for women than for men.  Finally, it’s worth noting these figures do not include graduate students.

However, this workload is not as uncommon as one might think.  According to a Telegraph article earlier this year, over 80% of white collar professionals now clock more than 40 hours a week, with 28% working 50 hours a week or more - up from 19% in 2011. Of course, this is for UK workers, whereas the above numbers refer to the United States.

Nonetheless, the increasing commonality of long working hours doesn’t indicate that there is no problem.  The authors of the arXiv paper conclude that “scientists today are spending much more time working than initially intended. They are deprioritizing their hobbies, leisure activities, and regular exercises, which negatively influenced their mental and physical health.”  What are your thoughts?  Leave a comment and join the discussion!


Throwback Thursday: Darwin

It's Throwback Thursday; let's hear from some great scientists of the past.

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