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!

Graduate School Horrors: Life of a PhD Candidate in the Sciences

 

by Lori Bystrom, PhD

Graduate school can be a tough time for scientists.  Here are ten scary examples of what can happen as you work to obtain your doctorate in the sciences.

  1. Three years into your PhD program you realize that you do not know what you are doing or where you are going.

With no clear path forward, it becomes hard not to see yourself as a zombie stuck somewhere in between life and death.

 

  1. Your advisor suddenly abandons you and the project (e.g., he decides to leave for another university or industry without you).

Your original research plan haunts you as you try to move on and find a new laboratory and advisor to continue the project.

 

  1. You show your committee members your new data that you think is very exciting, only to discover they think it is useless.

The vampires are merciless..

 

  1. Your experiment fails over and over again

Has someone cast an evil spell on you?

 

  1. You desperately look into a sea of bad data to try to find something good or at least interesting.

 Clearly an exorcism is necessary to save this project.

 

  1. You discover your cell lines are contaminated.

 The little monsters have attacked!

 

  1. You find a precious vial of your sample material – from a years worth of work – and then watch it come crashing down onto the floor.

You scream.

 

  1. You discover your project has been scooped and your research is not valuable anymore.

You scream again.

 

  1. When analyzing your experiment you discover some bizarre results that seem to come from out of nowhere.

 Boo!

 

  1. One of your committee members tells you at the last minute that they are unable to make it to the defense date you have rescheduled for the billionth time.

You fear they are trying to prevent your escape.

(Note:  if after reading this you are very scared this survival guide might help).

Get to know the Scientista Foundation!

 

By Lakshini Mendis

The “leaky pipeline” model describes the high attrition rate of women in STEM (science, technology, engineering and maths), which happens at every step of the way, from getting interested in science and math in elementary school, through doctorate, postdoc, and career steps. There had been much progress in recent decades to advance women in STEM, with many organizations focusing on professional women or young girls.

However, while attending Harvard, sisters, Julia and Christina Tartaglia, both biology majors, noticed a lack of resources, community, and role models, for college women in science and engineering. The Tartaglia sisters decided to tackle this problem and create a one-stop resource for college and graduate women. After placing as a Harvard College Innovation Challenge semifinalist and winning a Harvard TECH prize, they launched The Scientista Foundation, a platform and national network that addresses the needs of pre-professional women in STEM, in 2011.

Since its founding, Scientista has successfully expanded to 10+ campuses, with its first international chapter launching in Newcastle earlier this year. It is currently the largest network of campus women across STEM disciplines and has been named amongst the “Top 12 Amazing Organization for Women in STEM” by Enable Education. Scientista has also launched a successful intercollegiate Research Symposium, and has started partnerships with major organizations and media companies, including The Huffington Post and the Association of Women in Science.

In addition to providing a network for collegiate women through its chapters and conferences, the Scientista Foundation also provides content, from education and career advice, to maintaining a good work/life balance, to empower pre-professional women in STEM. The blog also provides visible role-models by reviewing recent research, which has been led by women, in the Scientista DiscovHER section, and interviewing women in STEM who at various stages of their career.

Scientista is helping build a cohesive network of women, who can act as one voice to overcome the persistent hurdles to the advancement of women in STEM.

This article was written by Lakshini Mendis, Editor-in-Chief of the Scientista Foundation blog.

 

The Royal Society: 350 Years of Scientific Publishing

 

By John McLaughlin

 

Professional scientific journals are commonplace and widely distributed today, but their origin dates to over three centuries ago. This year marks the 350th anniversary of the oldest continuously published scientific journal, Philosophical Transactions of the Royal Society, first appearing in 1665. This is the flagship journal of Britain’s Royal Society, founded in 1660 London by a fellowship of physicians and philosophers. It remains Britain’s most prestigious scientific academy, and serves as the main scientific advisor to the UK government.

 

The Royal Society’s founding occurred during a very important historical period, arguably at the beginning of Europe’s scientific revolution. Its guiding principles were inspired largely by the work of Francis Bacon, a British politician and philosopher who died a few decades before its creation. His most important work, The New Organon, set out a vision for a new and more rigorous scientific methodology, based on empirical observation and testing theory by experiment. Bacon lamented the past centuries’ slow pace of progress in the sciences, and emphasized the need to place them on a firmer foundation in order to accurately study natural phenomena. He also cautioned against the various idols, or biases, which affect our proper understanding of the natural world, such as those determined by one’s personal history, culture, or deference to authority. He would have been pleased to see that the Royal Society’s founders took these ideas to heart; this is well captured in the Society’s motto, Nullius in verba: Take nobody’s word for it.

 

Philosophical Transactions introduced, in a more primitive form, several of the modern hallmarks of scientific research: most articles were reviewed and edited by Society members, systematically curated, and widely distributed. Interestingly, the journal operated at a financial loss for most of its history, only recently becoming profitable. It also made achievements in social equality; a 1787 article by Caroline Herschel, describing several new comets, became the journal’s first paper authored by a woman, and the Royal Society’s first female fellows were elected in 1945. As scientific disciplines proliferated and accumulated knowledge over the generations, the 19th century saw the journal split into two series, Philosophical Transactions A and B, dedicated to the physical and life sciences respectively. Today, both journals publish invited articles, with each issue centered on a specific theme.

 

In its capacity as a grant awarding agency, the Royal Society funds about 1,500 researchers around the United Kingdom, and provides fellowships for international scientists who wish to conduct research in or partner with UK universities. As part of its mission in promoting and recognizing excellence in science, it hosts frequent scientific meetings and lectures on a variety of topics, many of which are open to the public. To be elected a fellow of the Royal Society is a high honor, first requiring recommendations from two current fellows; the 8,000 fellows inducted in its long history have included scientific giants such as Isaac Newton, Charles Darwin, James Clerk Maxwell, and Stephen Hawking.

 

Scientific publishing had humble beginnings; in the 21st century, the spread of electronic journals has given us easy access to a number of high-quality papers that past generations of scientists could not have imagined. The sciences have changed dramatically over the years, but the institutions of publication and peer review will remain centrally important.

How Can You Make Money and Help Others with Your Shit?

And other very important poop updates.

 

By Jesica Levingston Mac leod, PhD

First, you have to be a healthy pooper… Second, you have to live in the Boston area. Your stool can help a person suffering from recurrent C. difficile infections, which is a bacterium that affects 500,000 Americans every year.  Where antibiotic treatment has failed to help, a new treatment called “fecal microbiota transplantation” has shown a cure rate of 90%.  In this procedure, a fecal microbiota preparation using stool from a healthy donor is transplanted into the colon of the patient.  OpenBiome, the startup company based in Boston, helps facilitate this procedure by screening and processing fecal microbiota preparations for use in this treatment. After joining the registration you and your stool will be screened and if you are healthy and a good candidate you will became a donor. If you can succeed with all the tests and you can provide “supplies” quite often then you can exchange money for you poo.

Lately, the study of the human microbiota has been all over the news, specially related with weight control, pregnancy and the infant’s diet. In fact, it’s estimated that the human gut contains 100 trillion bacteria, or 10 times as many bacteria as cells in the human body. Yes, I know what you are thinking: “More of them that my own cells, that cannot be right, right?”

These bacteria, or microbiota, influence your health in many ways, from helping to extract energy from food to building the body’s immune system, to protecting against infection with harmful, disease-causing bacteria.

Researchers are only just beginning to understand how differences in the composition of gut bacteria may influence human health. From what we know so far, here are five ways gut flora can affect your wellness:

 

Weight Changes

Yes, your gut bacteria affect your eating disorders (or orders if you are lucky). For example the diversity of gut bacteria is higher in lean people compared to obese people. Also, some specific bacteria groups, the Firmicutes and the Bacteroidetes, are linked with obesity. The famous study were they transplanted gut bacteria from obese and lean people to mice, making the host of the first kind of poo gain more weigh that the mice who received the “lean fecal bacteria”, was a shocking confirmation of the importance of the gut bacteria in the body weight regulation. They discovered that the gut bacteria from obese people increase the production of some amino acids, while the material from lean people increases the metabolism of “burning” carbohydrates.

 

Preterm Labor

Realman and col. found that pregnant women with lower levels of bacteria Lactobacillus in their vagina had an increased risk of preterm labor, compared with women whose vaginal bacterial communities were rich in Lactobacillus. Apparently, the absence of Lactobacillus allows the grown of other species that would have different effects in the pregnancy.

 

Crying Babies

In a funny study on how diet may affect babies, Pertty and col. showed that giving probiotics to your baby does not change the daily crying time, around 173 minutes, compare to the placebo group (174 min), according to the parental diary. They enrolled 30 infants with colic during the first 6 weeks of life.  However, parents reported a decrease of 68% in daily crying in the probiotic and 49% in the placebo group.

 

Heart Attacks

Gut Bacteria produce compounds can even affect your heart. One of these compounds is the trimethylamine-N-oxide (TMAO), and the presence of it in the blood of the subjects of a recent research study, increased 2.5 times the probability of having a heart attack, stroke or to die over a three-year period compared with people with low levels of TMAO. They have also shown that the metabolism of the gut bacteria changes according of the host’s (your) diet. For example, the consumption of high cholesterol and fatty food can increase the bacterial production of TMAO.

 

The Immune System

A recent review published in Cell rang the alarm about the negative effect of the “rich countries” diet in the microbiota influencing the immune system. In ideal and normal conditions the immune system-microbiota association allows the induction of protective responses to pathogens and the maintenance of regulatory pathways involved in the maintenance of tolerance to innocuous antigens. In rich countries, overuse of antibiotics, changes in diet, and elimination of constitutive partners, such as nematodes, may have selected for a microbiota that lack the resilience and diversity required to establish balanced immune responses. This phenomenon is proposed to account for some of the dramatic rise in autoimmune and inflammatory disorders in parts of the world where our symbiotic relationship with the microbiota has been the most affected.

 

Lungs and Asthma

The gut bacteria can affect your lungs: The low levels of 4 gut bacteria strains (FaecalibacteriumLachnospiraVeillonella, and Rothia) in kids was been recently related to an increase in the risk for developing debilitating asthma. The introduction of these 4 bacteria in mice induced to suffered asthma shown protection as the mice’s lungs did not present inflammation.

The question is: how bacteria IN the guts can affect your other tissues and organs? One study that was just published shows  that these bacteria produce chemicals that may help the immune system to battle against other germs. Without this training, the immune system could fail and create inflammation in the lungs. As a follow up from the latest research it may be possible in the near future to predict asthma, and other diseases, as well as cure some illnesses with gut bacteria.

Be ready to give a shit about your shit.

Taking Genome Editing out of the Lab: Cause for Concern?

By Rebecca Delker, PhD

Genome editing – the controlled introduction of modifications to the genome sequence – has existed for a number of years as a valuable tool to manipulate and study gene function in the lab; however, because of inefficiencies intrinsic to the methods used, the technique has, until now, been limited in scope. The advent of CRISPR/Cas9 genome editing technology, a versatile, efficient and affordable technique, not only revolutionized basic cell biology research but has opened the real possibility of the use of genome editing as a therapy in the clinical setting and as a defense against pests destructive to the environment and human health.

 

CRISPR – Clustered Regularly Interspaced Short Palindromic Repeats – when teamed up with the nuclease, Cas9, to form CRISPR/Cas9 serves as a primitive immune system for bacteria and archaea, able to tailor a specific response to an invading virus. During viral invasion, fragments of the invader’s foreign genome are incorporated between the CRISPR repeats, forever encoding a memory of the attack in the bacterial genome. Upon future attack by the same virus, these memories can be called upon by transcribing the fragments to RNA, which, through Watson-Crick base-pairing, guide Cas9 to the viral genome, targeting it for destruction by induced double strand breaks (DSBs).

 

While an amazing and inspiring piece of biology in its own right, the fame of CRISPR/Cas9 did not skyrocket until the discovery that this RNA/nuclease team could be programmed to target specific sequences and induce DSBs in the complex genomes of all species tested. Of course the coolness factor of CRISPR technology does not end with the induction of DSBs but rather the use of these breaks to modify the genome. Taking advantage of a cell’s natural DNA repair machinery, CRISPR-induced breaks can be repaired by re-gluing the broken ends in a manner that results in the insertion or deletion of nucleotides – indels, for short – that disrupt gene function. More interesting for genome editing, though, DSBs can also serve as a portal for the insertion of man-made DNA fragments in a site-specific fashion, allowing the insertion of foreign genes or replacement of faulty genes.

 

CRISPR/Cas9 is not the first technology developed to precisely edit genomes. The DNA-binding (and cutting) engineered proteins, TALENS and Zinc Finger Nuclease (ZFNs), came into focus first but, compared to the RNA-guided Cas9 nuclease, are just a bit clunky – more complex in design with lower efficiency and less affordable. Even prior to these techniques, the introduction of recombinant DNA technology in the 1970s allowed the introduction of foreign DNA into the genomes of cells and organisms. Mice could be made to glow green using a jellyfish gene before the use of nucleases – just less efficiently. Now, the efficiency of Cas9 and the general ease of use of the technology paired with the decreased costs of genome sequencing enable scientists to edit the genome of just about any species, calling to mind the plots of numerous sci-fi films.

 

While it is unlikely that we will find ourselves in a GATTACA-like situation anytime soon, the potential for the application of CRISPR genome editing to human genomes has sparked conversation in the scientific literature and popular press. Though genome modification of somatic cells (regulators of body function) is generally accepted as an enhanced version of gene therapy, editing of germline cells (carriers of hereditary information) has garnered more attention because of the inheritance of the engineered modifications by generations to come. Many people, including some scientists, view this as a line that should never be crossed and argue that there is a slippery slope between editing disease-causing mutations and creating designer babies. Attempts by a group at Sun Yat-sen University in China to test the use of CRISPR in human embryos was referred to by many as irresponsible and their paper was rejected from top journals including Nature and Science. It should be noted, however, that this uproar occurred despite the fact that the Chinese scientists were working with non-viable embryos in excess from in vitro fertilization and with approval by the appropriate regulatory organizations.

 

Modifying human beings is unnatural; and, as such, seems to poke and prod at our sense of morality, eliciting the knee-jerk response of no. But, designer babies aside, how unethical is it to target genes to prevent disease – the ultimate preventative medicine, if you will? It is helpful to address this question in a broader context. All medical interventions – antibiotics, vaccinations, surgeries – are unnatural, but (generally) their ethics are not questioned because of their life-saving capabilities. If we look specifically at reproductive technology, there is precedent for controversial innovation. In the 1970s when the first baby was born by in vitro fertilization (IVF), people were skeptical of scientists making test-tube babies­ in labs. Now, it is a widely accepted technique and more than 5 million babies have been born with IVF.

 

Moving the fertilization process out of the body allowed for the unique possibility to prevent the transmission of genetic diseases from parent to child. Pre-Implantation Genetic Diagnosis (PGD), the screening of eggs or embryos for genetic mutations, allows for the selection of embryos that are free of disease for implantation. More recently, the UK (although not the US) legalized mitochondrial replacement therapy – a technique that replaces faulty mitochondria of the parental egg with that of a healthy donor either prior to or post fertilization. Referred to in the press as the creation of three-parent babies because genetic material is derived from three sources, this technique aims to prevent the transmission of debilitating mitochondrial diseases from mother to child. To draw clearer parallels to germline editing, mitochondria – energy producing organelles that are the likely descendants of an endosymbiotic relationship between bacteria and eukaryotic cells – contain their own genome. Thus, although mitochondrial replacement is often treated as separate from germline editing because nuclear DNA is left untouched, the genomic content of the offspring is altered. There are, of course, naysayers who don’t think the technique should be used in humans, but largely this is not because of issues of morality; rather, their opposition is rooted in questions of safety.

 

Germline editing could be the next big development in assisted reproductive technology (ART), but, like mitochondrial replacement and all other experimental therapies, safety is of utmost concern. Most notably, the high efficiency of CRISPR/Cas9 relative to earlier technologies comes at a cost. It has been demonstrated in a number of model systems, including the human embryos targeted by the Chinese group, that in addition to the desired insertion, CRISPR results in off-target mutations that could be potentially dangerous. Further, because our understanding of many genetic diseases is limited, there remains a risk of unintended consequences due to unknown gene-environmental interactions or the interplay of the targeted gene and other patient-specific genomic variants. The voluntary moratorium on clinical applications of germline editing in human embryos suggested by David Baltimore and colleagues is fueled by these unknowns. They stress the importance of initiating conversations between scientists, bioethicists, and government agencies to develop policies to regulate the use of genome editing in the clinical setting. Contrary to suggestions by others (and here), these discussions should not impede the progress of CRISPR research outside of the clinical setting. As a model to follow, a group of UK research organizations have publically stated their support for the continuation of genome editing research in human embryos as approved by the Human Fertilisation and Embryology Authority (HFEA), the regulatory organization that oversees the ethics of such research. Already, a London-based researcher has requested permission to use CRISPR in human embryos not as a therapeutic but to provide insight into early human development.

 

Much of the ethics of taking genome editing out of the lab is, thus, intertwined with safety. It is unethical to experiment with human lives without taking every precaution to prevent harm and suffering. Genome editing technology is nowhere near the point at which it is safe to attempt germline modifications, although clinical trials are in progress testing the efficacy of ZFN-based editing of adult cells to reduce viral titers in patients with HIV. This is not to say that we will never be able to apply CRISPR editing to germline cells in a responsible and ethical manner, but it is imperative that it be subject to regulations to assure the safety of humans involved, as well as to prevent the misuse of the technology.

 

This thought process must also be extended to the application of CRISPR to non-human species, especially because it does not typically elicit the same knee-jerk response as editing human progeny. CRISPR has been used to improve the efficiency of so-called gene drives, which guarantee inheritance of inserted genes, in yeast and fruit flies; and they have been proposed for use in the eradication of malaria by targeting the carrier of disease, the Anopheles mosquito. It is becoming increasingly important to consider the morality of our actions with regard to other species, as well as the planet, when developing technologies that benefit humanity. When thinking about the use of CRISPR-based gene drives to manipulate an entire species it is of utmost importance to take into consideration unintended consequences to the ecosystem. Though the popular press has not focused much on these concerns, a handful of scientific publications have begun to address these questions, releasing suggested safety measures.

 

There is no doubt that CRISPR is a powerful technology and will become more powerful as our understanding of the system improves. As such, it is critical to discuss the social implications of using genome editing as a human therapeutic and an environmental agent. Such discussions have begun with the convention in Napa attended by leading biomedical researchers and will likely continue with similar meetings in the future. This dialogue is necessary to ensure equal access to beneficial genome-editing therapies, to develop safeguards to prevent the misuse of technology, and to make certain that the safety of humans and our planet is held in the highest regard. However, too much of the real estate in today’s press regarding CRISPR technology has been fear-oriented (for example) and we run the risk of fuelling the anti-science mentality that already plagues the nation. Thus, it is equally important to focus on the good CRISPR has done and will continue to do for biological and biomedical research.

 

We are rapidly entering a time when the genomes of individuals around the world will be sequenced completely, along with many other organisms on the planet; however, this is just the tip of the iceberg of our understanding of the complex translation of this genome into life. For over a decade we have known the complete sequence of the lab mouse, but our understanding of the cellular processes within this mouse is still growing every day. Thus, there is an important distinction to be made between knowing a DNA sequence and understanding it well enough to be able to make meaningful (and safe) modifications. CRISPR genome editing technology, as it is applied in basic biology, is helping us make this leap from knowing to understanding in order to inform the creation of remedies for diseases that impact people, animals and our planet; and it is doing so with unprecedented precision and speed.

 

We must strike a balance that enables the celebration and use of the technology to advance knowledge, while assuring that the proper regulations are in place to prevent premature use in humans and hasty release into the environment. Or, as CRISPR researcher George Church remarked: “We need to think big, but also think carefully.”