Category Archives: Science Writing

Yes, these are lipids. But there are so many more inside your body; and they do more than store fat!

Annual Lipids Meeting in La Jolla California

The 2015 meeting on Lipids—focusing on their impact in cancer, metabolic, and inflammatory diseases—took place on Tuesday and Wednesday, May 12 and 13 at the Scripps Seaside Forum at UCSD’s Scripps Institute of Oceanography (SIO). With a beautiful venue and superb facilities, what more can you ask for? How about some really interesting science.

Lipids are generally thought of as fats. But in a biological system, they are much more. They include chemokines and other signaling molecules involved in signal transduction to and from the cell membrane. Metabolically, lipids also play an important role. Innovation in technology allow the study all the lipids in an organism (yeast, bacteria, or animal), leading to a new field of study: lipidomics. Once again, UCSD is on the cutting edge, with an established program and website in the field.

ocean, palm trees, La Jolla pennisula, green lawn with white chairs; breakfast view for lipids conference

View from the Scripps Seaside Forum at UCSD’s Scripps Institution of Oceanography.

Michael Snyder, the keynote speaker, has subjected himself to a battery of “omic” studies including his personal genome, exosome, microbiome, epigenome, proteome, metabolome, transcriptome, auto-antibody-ome, as well as cytokines. Data from these samples comprise the “Snyerdome”. All this was done in the interest of personalized medicine. These studies were done not only at one time point, but over a range of times, making it longitudinal.

Mike sees the data providing insights into how to managing healthcare in healthy individuals to predict risk, diagnose, monitor, and treat the patient, in this case, himself.

“He has also combined different state-of–the-art “omics” technologies to perform the first longitudinal detailed integrative personal omics profile (iPOP) of person and used this to assess disease risk and monitor disease states for personalized medicine” (from lab website).

in the future, Mike sees genomes being sequenced before birth and all this information being channeled through your smart phone. Patients will also bear more responsibility for maintaining their health with all the information they have; they will need to learn to maintain a balanced life.

The next speaker, David Wishart, discussed how to link lipidomics to laboratory medicine. He noted that in the rationalization of translating basic research to something of value in the clinic, researcher often cite the possibility of developing a new:          

  • surgical technique
  • invent a new medical device
  • drug
  • drug target
  • medically important gene
  • biomarker

All these are good outcomes; some are more likely than others. Practitioners of lipidomics are most likely to have the best luck in developing new biomarkers; not many are surgeon and drug development has about a 0.001% success rate from basic science to the prescription bottle.

lipids, lipids, lipids

Slide from David Wishart’s talk listing the number of FDA approved clinical tests from omic data

Discovery of new biomarkers is a realm where omics, specifically lipidomics, will meet a great chance of success. For this comparison, David recommends using the statistical ROC test, which is routinely used to evaluate medical test. This test gives a good sense of a medical test’s specificity and sensitivity by plotting the true positive rate over the false positive rate.

Example of ROC curve with an assessment of the area under the curve. The PSA referred to here is the amount of Prostate-Specific Antigen test; phi refers to a different, more specific calculation with less false positives than the PSA test alone.

 

ROC curve used to show predictive value of a test for prostate cancer using two different methods.

ROC curve used to show predictive value of a test for prostate cancer using two different methods.

Or you can just know that an ROC of 0.5 is worthless, while 1.0 is perfect.

Thus, from the graph above, using the PSA test alone to determine the risk of prostate cancer is poor. A better method is to use the phi method.

Work done looking at 3 to 5 biomarkers can have great ROC results. For example, predicting congenital heart defects by looking at the level of 3 carotenes, yields a ROC of 0.98. Other areas of success with high ROC scores include endometrial cancer, prostate cancer, and chronic fatigue syndrome.

David urged participants to become more quantitative to move their research into the clinic; using the website www.roccet.ca to generate ROC curves for your data is a great place to begin.

The numerous other speakers all gave fantastic talks.

In this smaller conference, I was able to browse through the all posters, read all the titles and talk to the presenters. Large conventions tend to lack the sense of intimacy and fraternity found in this lipidomics meeting. Kudos to the organizers for a successful event. A convivial group, I would highly recommend this meeting.

 

San Diego Clinical Research Network

Did you miss the San Diego Clinical Research Network (SDCRN) meeting Monday June 24 on the top 10 innovations in biotech?  Keep reading for a summary.

Karin Lucas, PhD, was the speaker for the evening.  She is the Director of Education & Training for BioTechPrimer developing curriculum geared towards the non-scientist (HR, legal, and business) interested in the biotech field. Biotech Primer offers training onsite or offsite, customizable training, and online formats.  Founded in 2001, BioTechPrimer offers classes internationally, having provided instruction in China, Scotland, Germany, France, and Australia.

Karin began with a quick review of the central dogma of biology which states that information flows from DNA to RNA to protein.  Then she began the meat of her talk:

 Top 10 Biotech Advances

1)  Regulatory function of intergenic DNA

Initially thought to be “junk DNA”, because scientists did not understand its function, DNA between genes is now described as intergenic DNA.  Comprising over 95% of the human genome, intergenic DNA is involved in gene regulation, determining when and where a specific protein is made.  SNPs (single nucleotide polymorphism—pronounced “snips”) are often used as markers for diseases; 90% of SNPs that correlate to disease are located in the intergenic region.  Hence, this “junk DNA” fulfills a specific and important task:  regulating protein expression.

2)  Speed and cost of DNA sequencing:  biotech beats Moore’s law

Moore’s Law states that the number of transistors on an integrated circuit doubles approximately every two years.  The transistor number is closely tied to an increase in computing speed, memory available, even pixels in a digital camera.

Back in the dark ages (circa 1990), DNA sequencing in a research lab was considered efficient if one scientist deduced 300 base pairs of DNA in one day.  Compare this to the standards of today, when the entirety of a genome (3 BILLION base pairs) is sequenced in one week!

genome sequencing costs

While the efficiency of microprocessors increases exponentially with time, the rate of decrease in the cost of DNA sequencing is even greater.

Looking at the cost of DNA sequencing, the first human genome, published in 2003, cost $3 billion.  In 2007, the cost for one human genome was reduced to $1 million dollars; today the cost is below $7000.

The ease with which DNA can be sequenced has also been enhanced.  The days of huge glass plates, radioactive nucleotides, and neurotoxic gels are ancient history.  Present day DNA sequencers take up a small foot print and can easily be run by an individual with an associate degree.

However, we are still a long way from being able to hand a typical family doctor a thumb drive with your genomic sequence on it and having them have any idea what to do with it.  Several companies in the San Diego area are working hard to bring practical applications of whole genome sequencing to the bedside.

3)  Stratified Medicine

The concept here is to tailor medicine to each individual patient with companion diagnostics.  Drug companies are working to determine how a treatment affects a person individually based on biomarkers—unique characteristics found in a person’s DNA, RNA and/or proteins.  Thus, it will be known in advance how a person will respond to a particular drug; more effective pharmaceutical can be used first instead of randomly guessing which will be the most effective treatment.

4)  Human Microbiome

bacteria in human gut

Bacteria in the human gut aid digestion.

I’m really covered by bacteria?  Yes!  For every human cell in our bodies, we have 10 non-human cells in the form of bacteria, yeast and molds.  Microbes have an effect on chronic inflammation, atherosclerosis, cancer, and diabetes.  Maybe in the future, we will only have to adjust our microbiome to manage these conditions.

5) Controlling Protein Expression by inhibiting RNA

Often a disease state is induced by the expression of the wrong protein, during the wrong time, in the wrong place, or in the wrong quantity.  This can be remedied by getting rid of RNA for a particular protein.  Once this is accomplished with double-stranded RNA, the mechanism continues to destroy those faulty proteins.  A local company, ISIS recently received FDA approval to use RNA interference to treat familial hypercholesterolemia.

6)  Gene Therapy

Gene therapy

Note: picture not to scale

Gene therapy was first used in 1990 to treat severe combined immunodeficiency disorder (SCID).  In 2000 retroviruses were used for SCID; of the 20 persons receiving treatment, about half were cured and while the other half got leukemia.  Hence, the FDA has been reluctant to approve further human trials, much less treatments.  In 2012, however, the EMA (European equivalent of the FDA) approved Glybera from UniQure to treat the rare genetic disorder lipoprotein lipase deficiency.  This treatment specifically infects only muscle cells and must be repeated every few years.  Still it is good progress for a treatment long in development.

7)  Stem cell treatments

These treatments offer hope for neurodegenerative diseases like ALS. Other companies are in clinical trials for spinal cord injuries and stroke.  These stem cells can arise from either embryonic stem cells or from adult stem cells.

8)  Human cloning advance

cloning results may vary

Cloning: Results may vary

While many researchers have thrown their hands up in despair at ever succeeding in cloning a human, workers at the Oregon Health and Science University persevered.  With patient tinkering they successfully created cloned blastocytes.  By taking a part of the developing zygote, stem cell lines were created.   These could then be differentiated into a variety of different cell types.  One day, this breakthrough could have great therapeutic potential since the genes from these cells match perfectly with this donor of the genetic material eliminating the risk for rejection of replacement tissues.

9)  Bionic eye

bionic eye

It is possible for the blind to see again.

Argus II device by Second Site bypasses damaged photoreceptors in the eye, giving legally blind persons the ability to recognize faces and read four letter words.  This device won FDA approval in 2013; it has been available in Europe since 2013.

10) Biofuels

green crude farm

Sapphire Energy green crude farm.

Corn and soy, the sources of conventional biofuels, require good soil to grow.  Algae on the other hand, can grow in salt water.  To merely replace diesel fuel in the US with biodiesel would require all the arable land in the US to be cultivated with soy.  By occupying a site only the size of Georgia, algae could replace all the biodiesel in the US.

The last hurdle to biofuels is the price.  Sapphire Energy is targeting $75 per barrel for the green crude produced in their New Mexico plant, due to open in 2014.  This product has the added benefit of being able to be processed as light sweet crude oil in un-modified refineries alongside with regular crude oil.

More details on the meeting…

Teresa Gallagher founded the SDCRN, in response to a need for a group looking at clinical research programming.  Several other groups in San Diego already address the needs of entrepreneurs, businesses, and biotech.  Her vision is to bring together groups of persons working in several different areas from contract research organizations (CROs), to academic institutions, to other companies in the greater San Diego area.  Membership in San Diego Clinical Research Network is open to individuals working in the life science industry or healthcare in San Diego and Orange Counties.  Since starting SDCRN on LinkedIn, her group has grown to more than 500 members.  Teresa encourages feedback on what sort of programming the community would like to see at SDCRN events relating to clinical development.  What issues in clinical development arise in your work and what aspects of them would you like help with?

The Del Mar Offices of Sheppard Mullin law firm hosted the evening. The venue was fantastic and the food even better.  Shepherd Mullin is a worldwide law firm with practice areas in intellectual property, corporate, food and drug regulatory, and more.  Additionally, Shepherd Mullin publishes a FDA law blog with information on current issues affecting FDA-regulated companies.

DeeAnn Visk, Ph.D., is a freelance science writer, editor, and blogger. Her passions include cell culture, molecular biology, genetics, and microscopy. DeeAnn lives in the San Diego, California area with her husband, two kids, and two spoiled hens. You are welcome to contact her at deeann.v@cox.net

My mother, the Chimera

My mother, the Chimera

During grad school, I was amazed to hear that the color of hair on your body is controlled by only one gene.  Hence, each person should only have one color of hair everywhere on their body.  I wanted to ask:  why does my mother have two colors of hair on her body (or as the slang goes, the carpeting does not match the drapes)?  But I did not, at that time, have her permission to discuss this phenomenon.  Now I have her approval.   I have always wondered what the doctor doing her annual exams thought:  hmmm, she seems to be a natural redhead, I wonder why she keeps dyeing her hair on top brown.

zygote

Human zygote at the 4 cell stage.

Later I stumbled across a paper discussing the ideas of  chimeras in humans.1   Here I first read how an individual can come to be made up of more than one type of DNA.  The classical view is that each person is made up of one individual type of DNA which should be as unique as their fingerprint.  Hypothetically, if two fertilized eggs (zygotes) fuse together while in the womb and then merged together completely, you get what appears to be a normal individual, but made up of two different DNA types.2  I estimate human chimeras are born at approximately 1 in 50 live births, the same rate as for twins.

 What is a chimera, anyway?

chimera pottery

An ancient Greek plate, showing the original legendary chimera: a lion with a bonus goat head

What image does the word chimera bring up?  A lion with a goat coming out of its back?  The term chimera originated with the Greeks, describing a monster.   Using chimera to describe a human with two different types of DNA in the same body does not imply they are monsters.  Tetragametic chimerism sounds like you have cancer–human chimera just makes you sound cool.

 

chimeric mouse

Chimeric mouse on right, with two solid colored mice on left. Note in addition to different coat coloring, the chimeric mouse also has different colored eyes.

 

 

In the last century, the term chimera has been used to describe individual engineered mice born from a zygote derived from more than one type of mouse.  Chimeric mice have two fur colors on different parts of their bodies.  This is because the DNA that controls coat color is different in different parts of the mouse.  So when people, who had not been manipulated as zygotes, began to be detected with different DNA in different parts of their bodies, the term human chimera was coined.

So how can you tell if you are a human chimera? 

chimeric dog

Two different colored eyes are well known to occur in dogs.

Tell-tale signs are two colors of hair on different parts of your body, two colors of skin on different places of your body, or two eyes each of a distinct color.  The phenomenon of two different colored eyes is called hererochromia iridum.  The definitive method to determine your status as a human-human chimera is to have tissue taken from several different areas of your body and tested to see if the DNA is all the same.  The expense and risk (anyone feel like having a piece of your liver removed?) generally is prohibitive, but given the rapidly lowering price of genetics testing, it may soon be within financial reach.

Or you may be completely unable to tell that parts of your body arose from two different zygotes.  You may only get the news if there is DNA testing of you and your children; or if you are trying to get an organ donation from relatives, to whom you are no longer a parent according to the DNA.  Yes, this really has happened.

Any twins in your family?

Jane Seymour

Given her two different colored eyes and twins running in her family, it is likely (I’ll give you 95% odds) that Jane Seymour is a human-human chimera.

Another way to determine the probability that you are a chimera is the prevalence of twins in your family.  My grandmother was the sibling of one set of twins and aunt to another.  When I brought up my mom’s chimerism at a family gathering, my aunt, wanted to know if she was a chimera.  Sure enough, her eyes are different shades of green/hazel.  So I would conclude that she is also a human-human chimera.

Let’s look at Jane Seymour.  She has two different color eyes, a sign of being a human chimera.  Her most recent children are twins.  Twins run in families.  So, as in my mom’s situation, it is likely that her mother had two eggs available for fertilization at the same time. The twin information along with her two different colored eyes leads to the conclusion that Jane Seymour is most likely a human-human chimera.

In closing…

Mike Scherzer professional baseball pitcher

Mike Scherzer, a professional baseball pitcher for the Detroit Tigers, clearly has one light blue and one brown eye.

All the examples given so far are women who are chimeras–what about men?  Questions of paternity are nothing new.  But what if a man was pretty sure he was the father, but the DNA tests said no?  There are certainly ways of testing to show that the father of a child in question is related to the uncle degree.  But what if the father has no brothers?  I leave other scientist and lawyers to explore these questions.

So now my Mom can think of herself as her own twin.  Or she can make jokes about how this explains why she has the energy of two people.  Or if she wants to stump her doctor, she can say that she suffers from tetragametic chimerism,

______________________

1  “Embryogenesis of chimeras, twins and anterior midline asymmetries.”  CE Boklage.  Human Reproduction.  2006.

2  The following paper offers a different hypothesis to explain the formation of chimeras.  Read at your own risk. “Traces of embryogenesis are the same in monozygotic and dizygotic twins: not compatible with double ovulation.”  Human Reproduction.  2009.

DeeAnn Visk, Ph.D., is a freelance science writer, editor, and blogger. Her passions include cell culture, molecular biology, genetics, and microscopy. DeeAnn lives in the San Diego, California area with her husband, two kids, and two spoiled hens. You are welcome to contact her at deeann.v@cox.net

Effective Science Writing – 10 tips


Written by me, DeeAnn Visk, this article was originally published by the Oxbridge Biotech Roundtable (OBR) Review in April 2013–the following is an excerpt from that article, based on a science writing talk sponsored by ORT given by Lynne Friedmann.

Effective Science Writing – 10 tips

1)  Use active voice

An active voice lends more simplicity, energy, and directness to prose (resume writing, anyone?). Scientists are encouraged to write in a passive voice making for clunkier, longer, and vague prose.

Examples:  Steve loves Amy (active voice)

Amy is loved by Steve (passive voice)

2)  Employ style guidesScience writing guides

Style guides shepherd writers through the nuts and bolts of writing, addressing questions such as what to capitalize, where commas should go, grammar questions, etc.  Individual journals may have their own style guides; be cognizant of the rules for the organization for which you are writing—even Wikipedia has a style guide.

Example: 12pm or 12am?  Using midnight or noon avoids confusion

Publications/blogs may or may not care; develop good habits now.  In the future, you will need to keep an editor happy; they do not want to look dumb.  Editors comparing two equivalent papers choose the one with the least editing required.

3)  Overcome “writer’s block”

Treat your writing time like an appointment until it becomes a habit. For those of you with difficulty starting, just begin. Fire your internal editor, ignore grammar, spelling, and punctuation—just get the ideas down on paper.  Stuck on the next word?  Just write “XXXXX”.  Keep the flow going.  Write down your first draft as fast as possible.

4)  Focus on the goal

Reduce why you are writing something to one sentence:  I want my manager to approve my budget.  Write it on a piece of paper and hang it where you can see it.  Refer to it while writing.  Information without context is useless—do ideas support my goal?

5)  Make writing transparent

As Mark Twain said “never use a $5 word when a 50 cent one will do.”  Deliver information that can entertain people, the story behind the research, interject patient stories, trying to solve puzzles, and mysteries.  Work in something about the process of science, one piece of information in a continuum.  Be clear: do not overload opening sentence; go from general to specific.  You want the reader to hold your hand and never let go.  Allow readers to see and feel the experience by using descriptive and specific sensory language.science writing

6)  Do not use science clichés

Describe so that writer can see how it is a break through.  As Friedmann stated tongue-in cheek, “The ‘missing link’ has been found so many times, how could any possibly still be lost?”  Other worn clichés include:  shedding light, the holy grail, the silver bullet, and paradigms shifting.  Don’t these just make your eyes glaze over? Or do you find yourself grinding your teeth in irritation instead?

7)  Write, revise, and edit in sequence

Compose your copy well ahead of the deadline.  Don’t look at it for a day or two, then come back and eliminate the first paragraph or two.  Test your copy during revision.  Print it out—difficult to proof on-screen.  Go to a different physical space; get up walk around, read it aloud.  Are you bored? Confused? After each sentence, ask yourself “so what”?  Get rid of sentences that begin with “Th” words:  the, this, they.  Each time you read a sentence remove one word, and see if the sentence still conveys the meaning. You are on the right track when “sentences shrivel like bacon in a pan”.  Proof read copy backwards to find typos.

8)  Professional organizations as valuable resources

Professional organizations offer seminars and job leads.  A good resource is the National Association of Science Writers.  Environmental journalists normally find themselves evolving into activist (not just merely reporters), issuing calls to action. If you are thinking about becoming one, look at the Society of Environmental Journalist. The American Medical Writers Association holds great conferences and workshops.  Check out their websites for hints on the craft of writing.

science writing association

9)  Where to find science writing opportunities

Consider writing for various organizations such as your school’s alumni magazine, Roundtable Review (a blog hosted by ORT), MIT Technology review.  Both academic and industry grants require excellent writing—volunteer to help.  Many websites need content/blog writers; begin by offering to write for free.

10)  Receiving feedback on your writing

Keep your inner defensive monster in the cage.  Take a deep breath and relax.  You must respond well to correction, if you want people to continue giving it to you. Feedback is a gift, assisting you to improve your writing. Thank whoever is taking time to give you feedback; try incorporating their suggestions into your writing.

DeeAnn Visk, Ph.D., is a freelance science writer, editor, and blogger. Her passions include cell culture, molecular biology, genetics, and microscopy. DeeAnn lives in the San Diego, California area with her husband, two kids, and two spoiled hens. You are welcome to contact her at deeann.v@cox.net

The long and the short of your telomeres

 

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The long and the short of your telomeres

A friend of mine, Bonnie, sent me an interesting site, which offers to determine the length of your telomeres (pronounced tea/low/mirrors).  My initial response, given that telomeres shorten with age, was that the test would only tell you what you could already know by looking at your birth certificate: your age.

 

Telomeres length indicates wear and tear on your chromosomes; like the tread depth on your tires.  Each time a cell divides, the end of the chromosomes (telomere) generally gets shortened.   Normally, a cell can only divide so many times before the telomeres on the chromosome ends are too short to allow any more replications and the cell dies.

 

 

TeloMe, the company in question, will determine the length of your telomeres.  This can be used as a starting point to monitor how healthy you are living; you can make life style choices to lengthen your telomeres such as limiting caloric intake, not smoking, eating lots of fruits and vegetables, and getting regular exercise.  Hmmmm…What do peer-reviewed articles in reputable journals say?  Querying the PubMed database with the word “telomere” leads to 14,000+ papers.  Yikes!  That’s a lot to review.

This is fluorescent microscope image of chromosomes (DNA, in blue) with the telomeres in yellow.

Fortunately, there is another company, Telome Health(TH)—no relationship with TeloMe, as per a phone call to TH’s offices—that has nicely gathered a “short” list of 155 peer-reviewed papers on telomeres.  There is strong evidence for the shortening of telomeres being a bad thing.  You can shorten the rate at which your telomeres are shortened.  However, I am not convinced that there is way to lengthen your telomeres.

 

So should I get my telomere length tested?

So if you really want to go ahead and test the length of your telomeres you have my permission.  Personally, I would go with the already established company, Telome Health.  The company is  well established and certified to do the testing as a clinical diagnostic test.

Or if you want to do it the less expensive way, take care of yourself:

1)     Eat nutritious healthy meals

2)     Get regular sleep

3)     No smoking

4)     Get regular exercise

5)     Take Omega-3 fats

6)     Reduce stress in your life

Basic, good living will keep you healthy.  This just helps to explain why and gives you a way to track it.

DeeAnn Visk, Ph.D., is a freelance science writer, editor, and blogger. Her passions include cell culture, molecular biology, genetics, and microscopy. DeeAnn lives in the San Diego, California area with her husband, two kids, and two spoiled hens. You are welcome to contact her at deeann.v@cox.net