Yes that’s right – intentionally contaminated, and how. The study volunteers allowed a 20% stool suspension containing Norwalk virus to be pipetted onto their fingers and then examined how well the different hand sanitizers and liquid soap removed the virus. Nice.

Because of the uniqueness of the study and because hand santizers are everywhere now, even at the bank to disinfect hands after touching the “community pen”, I thought it would be interesting to review this paper and summarize the results.

The paper is called Effectiveness of Liquid Soap and Hand Sanitizer against Norwalk Virus on Contaminated Hands by Pengbo Liu, Yvonne Yuen, Hui-Mien Hsiao, Lee-Ann Jaykus, and Christine Moe. All authors were from the Rollins School of Public Health at Emory University in Atlanta except for Lee-Ann Jaykus who is from the Dept. of Food Science at North Carolina State University in Raleigh, NC. The paper was published January 2010, vol. 76, No. 2, p. 394-399.

Introduction:

Norwalk virus infects 23 million people a year and is the cause of 81% of non-bacterial gastroenteritis outbreaks. While the virus can contaminate inanimate surfaces, hand to hand transmission is thought to be the primary vehicle for spread of infection. Hand sanitizers make no virucidal claims against noroviruses because proving it is difficult. The virus can’t be cultured so experiments need to be performed with clinical samples.  And that is what this research team did. The authors infected the fingers (called “finger pads”) of volunteers with human Norowalk virus and then used RT-qPCR to evaluate the effectiveness of liquid hand soap, sodium hypochlorite (bleach), ethanol, and water for inactivation of the virus and removal from the surface of skin.

Methods:

Human volunteers: Norwalk virus was obtained from the stool of an experimentally infected human volunteer (who would volunteer for that?) and then their stool was collected, tested for viral load, and diluted 20% (w/v) in RNase-free water prior to inoculation onto the finger pads of volunteers.

Ten volunteers enrolled in the study to be infected with Norwalk virus on their hands. Five volunteers participated in two trials on separate days and the right and left hand served as duplicate treatments.

Suspension assays to test for virucidal activity: were performed using ethanol at 3%, 17%, 31%, 47%, 62%, and 95% strength and hypochlorite solution (bleach) at 3 ppm, 22 ppm, 51 ppm, 160 ppm, and 1,600 ppm.  Ten microliters of the 20% suspension was added to 990 ul of each solution and after neutralization, virus was recovered for RT-qPCR analysis.

Disinfectants: Hand sanitizer was purchased locally which contained 62% ethyl alcohol and antibacterial liquid hand soap from Fisher Scientific contained 0.5% triclosan. Both of these reagents were pre-tested for PCR inhibition properties.

Inoculation of human volunteers: Volunteers first cleaned their hands with soap and ethanol and then allowed them to dry. Ten microliters of the 20% Norwalk virus infected stool solution was placed on the fingers of the volunteers.

Recovery of NV from the fingers of volunteers: A 2 ml plastic vial containing 1 ml of HBSS was used to cover the area on the finger where the NV was inoculated and inverted 20 times to elute the virus from the finger.

Treatments of NV on human finger pads: After inoculation of the fingers with the 10 ul of NV stool suspension, fingers were air dried and then exposed to 1 ml of hand sanitizer or liquid hand soap in the 2 ml vial for 20 seconds. Excess cleaner was scraped off into the vial. Following this, the same finger was then placed over the 2 ml tube containing 1 ml HBSS to elute remaining virus into the test vial. For liquid hand soap, the finger pad was rinsed in 1 ml of water for 10 seconds before eluting remaining virus into the HBSS vial.

The pinky fingers were used to determine the effectiveness of removing NV with water alone. Water in a 2 ml vial was used to wash the finger pad by inversion and then the HBSS was used to collect eluates. All finger pads samples were stored at -80C until assay.

Hydrolysis Probe assays: Samples were tested with and without RNase treatment (to differentiate live, infectious virus vs. dead virus) and analyzed using a one-step RT-PCR kit on the Mx3000P instrument. Quantification was done using the full-length cDNA cloned into a plasmid used for a standard curve. The assay was linear in the range of 1.3 copies to 4.3 Log ₁₀ copies of NV DNA.

Results:

Virucidal suspension assays: Sodium hypochlorite showed a concentration dependent inactivation of virus between 22 ppm and 160 ppm after 30 seconds. The virus was reduced 5 logs. Ethanol, on the other hand, did not show a concentration dependent effect of inactivation of virus. The most reduction in virus was 0.5 Log ₁₀ at 17% ethanol, but this sample had the least consistency between replicates.

Results of hand cleaners: The results reported were for the RNase treated samples only, so this data reflects the effects of the cleaners on live infectious virus. Compared to the baseline control, the liquid hand soap had the greatest reduction in NV cDNA (0.67 Log ₁₀), followed by the reduction from just a simple water rinse (0.58 Log ₁₀). The alcohol based sanitizer reduced the virus the least, only 0.27 Log ₁₀.

To determine if rubbing the test reagent on the finger pads helps reduce the presence of virus, volunteers repeated the experiment with rubbing for 10 seconds of the hand soap, hand sanitizer, or water on the finger pad before eluting the left over virus into HBSS. This did increase the Log ₁₀ reduction of NV. The greatest reduction was seen with just the water rinse (1.38 Log ₁₀ reduction) followed by antibacterial soap with 1.10 Log ₁₀ reduction). The ethanol based hand sanitizer was the least effective with only a .34 Log ₁₀ reduction of virus with rubbing and was not statistically significant compared to the baseline control.

Conclusions

Using a suspension assay to analyze for virucidal effects, the sodium hypochlorite solution demonstrated a concentration dependent increase in viral killing with virus elimination at >160 ppm, while ethanol had no effect, even at 95% strength.  For enveloped viruses, such as influenza, hepatitis B, and herpes simplex 1, ethanol-based sanitizers are known to be effective. However, the enteric nonenveloped viruses including hepatitis A, poliovirus, and FCV, are resistant to the effects of ethanol.

Additional research by others has shown that enteric viruses can be inactivated using a combination of solutions that include isopropanol, citric acid, or phosphoric acid along with ethanol. Because this virus is typically shed in very high titers by infected individuals and predominantly affects the food service industry, commercial development of a virucidal sanitizer designed specific for the enteric viruses is needed.

Comments

My first thought was that of course the liquid hand soap performed better because it was not only soap but also water rinsed to help remove the left over soap before eluting into HBSS. These fingers received the benefit of a double cleaning. We saw that water alone was very effective so perhaps the water following soap helped to solubilize more virus. However, water alone with rubbing has the best reduction in virus and the rubbing with soap followed by water does not have an additive effect, so this may not be a factor.

A good control would have been to perform the ethanol treatment followed by a water rinse, exactly the way they did the liquid hand soap samples, to negate any amplification in virus killing due to the combination.  But, it makes sense that if you use liquid hand soap, you will always rinse in water too. Whereas if you use a liquid hand sanitizer, you will not.

As for the commercial development of better hand sanitizers that protect against viruses spread by fecally contaminated sources, perhaps the cruise industry would be interested in providing research funding for the development of anti-Norwalk virus reagents that are safe for both food handlers and for food preparation surfaces.

But there is another receptor, called CB2, that can bind THC and other natural ligands for the cannabinoid receptor. The CB2 receptor is found on cells comprising the immune system and have a multitude of anti-inflammatory and immunosuppressive effects upon activation. In most cases, immunosuppressive effects are undesirable, but sometimes that can be beneficial. Today’s article is an example.

New research from the lab of Dr. Guy Cabral at Virginia Commonwealth University shows that stimulation of the CB2 receptor on macrophages inhibits migration of healthy immune cells towards the HIV Tat protein.  Tat is an essential viral regulatory protein used by HIV to stimulate inflammatory responses and wreak havoc in the body. Tat protein looks suspiciously like some of our own chemokine proteins and can bind to a variety of receptors on immune cells causing activation of cascades that lead to migration of uninfected macrophages towards the HIV infected cells.

The paper by Erinn S. Raborn and Guy A. Cabral, published in the January 2010 issue of the Journal of Pharmacology and Experimental Therapeutics is titled: Cannabinoid Inhibition of Macrophage Migration to the Tat Protein of HIV-1 is Linked to the CB2 Cannabinoid Receptor.  The authors used a macrophage cell line in a migration model system to demonstrate very specifically that when the CB2 receptor is stimulated, macrophages no longer respond to the Tat protein.  The chemoattractant effects are abolished.

Here is an summary of their work.

Introduction:

Macrophages are the primary target for HIV infection and once infected, cells begin producing viral Tat (trans activating factor) protein and GP120 protein in addition to stimulating the production of cellular cytokines and chemokines that induce changes in the immunoregulation of the host. The HIV Tat protein has an additional role of acting as a potent chemoattractant for monocytes, thus contributing to the spread of infected cells.

Most drugs of abuse (opiates, cocaine, amphetamines and cannabinoids) have an adverse effect on immunity, increasing susceptibility to infection. The cannabinoids in particular have been shown to have anti-inflammatory properties, downregulating some of the chemokines and cytokines involved in stimulating macrophage to migrate to infections and inhibiting macrophage function.  Cannabinoids have also been shown to down-regulate the expression of chemokine receptors, notably CCR5, one of the co-receptors used for HIV entry into cells. Thus, a link between the potential anti-HIV effects of the CB2 cannabinoid receptor has been established.

The purpose of this study was to determine whether cannabinoids exert any effect on the chemoattractant properties of Tat in macrophages. In the presence of cannabinoid agonists delta-9- tetrahydrocannabinol and CP55940, human macrophage-like cells (U937 cells) were inhibited from migrating towards Tat protein and this effect was due specifically to CB2. The results show a clear link between CB2 and the ability of macrophages to respond to the HIV protein in a cell culture system.  This work provides the basis for a novel therapeutic target for preventing or reducing HIV associated immunopathology and dissemination in vivo.

Materials and methods:

Cells: The human leukemic monocyte cell line U-937 was used.

Drugs: CB1 and CB2 receptor agonists used were: THC and CP55940. The CB2 specific agonist was O-2137-2 and the CB1 specific agonist was ACEA. The CB1 and CB2 receptor antagonists were SR141716 (SR1) and SR144528 (SR2), respectively. The full names of the drugs and the Ki information is described in the paper.

Tat: Recombinant human HIV Tat protein was obtained from Immunodiagnostics, Inc.

Cell Migration Assay: 35 mm tissue culture plates with upper and lower compartments separated by a polycarbonate 8 micron pore membrane were used. Drug treated  or control treated U937 cells were incubated on the top chamber and Tat protein or serum-free media plus vehicle was in the bottom chamber. Migration of cells to the bottom chamber was visualized with an Olympus CK2 inverted microscope connected to a digital video camera. The number of cells were manually enumerated. A greater than 2-fold increase in the number of cells in the presence of chemoattractant compared to no Tat was a positive response. The EC 50 or inhibitory concentration was the concentration of cannabinoid that results in a 50% reduction in macrophage migration.

Knockdown of CB2 expression using siRNA and RT-qPCR:   siRNA for the CB2 receptor was used for transient transfection of cells and knock-down shown using Western blot analysis.  SYBR Green was used for qPCR analysis after reverse transcription of RNA, qPCR was performed using the SmartCycler. Full details of the experimental design for qPCR and transfection are provided in the paper.

Results:

To begin, the authors first confirmed the expression of the CB2 receptor in U937 cells, both on the RNA and protein level. The CB1 receptor, typically expressed in cells of the brain, was not found in U937 cells using RT-qPCR. Their second set of confirmatory experiments proved that the U937 cells would migrate in response to Tat protein as has been previously described for human monocytes in blood.  The migratory response was maximum at 50 nM Tat and so the authors used this concentration for their studies.

The next experiments looked at the  migration of macrophages in the presence of the different drugs. All results were compared to vehicle controls (ethanol was used to dilute the drugs). Using vehicle alone with Tat protein in the bottom compartment, migration was the same as with no vehicle. When cells were treated with THC, however, migration of macrophage was inhibited by 50%. And using the agonist CP55940, migration was inhibited by 58%. Using the CB2 receptor specific agonist, the same effect of >50% inhibition was observed, however, but not suprisingly, using a CB1 receptor agonist, ACEA, had no effect on migration.

These results clearly indicate that the CB2 receptor on the human macrophage-like U937 cells plays a role in migration in the presence of the HIV Tat protein and this effect can be blocked when the receptor is activated.

To confirm the effect of migration was due to the CB2 receptor, the receptor antagonists were used to demonstrate that when signalling through the receptor is blocked, the effect is reversed.  The antagonist will bind the receptor but not activate the signalling cascade in the cell, thus blocking it from being activated by the ligand CP55940. Using the CB2 specific antagonist SR2 alone, migration in the presence of Tat is the same as controls- it is not inhibited. When CP55940 is combined with the SR2 compound, inhibition of migration is reversed.  SR2 prevents the protective anti-migration effect of CP55940.

To further prove the role of CB2 in this effect, siRNA mediated CB2 knockout cells were employed in the cell migration assay. The authors confirmed that neither the transfection reagent nor the siRNA itself had any effect on cell migration. Using the CB2 knockout cells in the presence of THC, migration was observed similarly to untreated cells. This is consistent with the results of blocking the CB2 receptor with antagonist. The CB2 receptor was not available for activation by the THC and thus no protective anti-migration effect was observed.

Discussion:

Chemokines are cytokines that function by directing the flow of inflammatory cells to sites of injury or infection in the body.  HIV uses our immune system cascade meant to protect us for its own benefit, by producing the viral Tat protein to bind the receptors meant for chemokines and stimulate the migration of more healthy macrophages to the HIV infected cells, increasing their opportunity to spread. The stimulation of chemokines also increases the number of receptors on the surface, making it easier for HIV to infect new cells.

The ability to slow down the migration of healthy cells towards HIV infected cells and to down regulate the expression of chemokine receptors would slow the progression of HIV associated disease. In this paper, the authors demonstrate a connection between the cannabinoid receptor on immune cells, CB2, and the migration of macrophages towards Hiv Tat protein. When the CB2 receptor is stimulated with an agonist, migration is inhibited. Whether this is due to down regulation of the chemokine receptors used for binding or due to down regulation of chemokines from CB2 activated cells has yet to be determined.

But the fact remains that the cannabinoid receptor CB2 may be a therapeutic target for preventing hyperactivation of the immune system by HIV and potentially, in the future, to help stop widespread infection.

Final note:

I found this paper to be an exciting advance in the fields of HIV and drugs of abuse. A therapy involving cannabinoids would be far less toxic than current drugs used to stop the progression of HIV. With all the ways HIV has found to use our own immune system against us to survive, an approach that counteracts HIV by taking back control of the immune system could be far more effective than developing toxic drugs that target HIV directly or using cytokines that further activate a tired immune system.

She laughed but that idea stuck with me. Current treatments are banking on the idea that the cancer is going to replicate faster than the normal tissue and will therefore be more sensitive to drugs that target proliferative processes. An example of such drug is taxol, a common and potent chemotherapeutic agent that blocks progression of mitosis thus inducing cell death.

For years, I have thought that the ideal treatment for any disease is to exploit what separates that disease from the normal tissue. It is the reason that cancer biology as a discipline has exploded in recent decades but has yielded very few distinguished targets. The personalized cancer therapy we have been promised is yet to be delivered. A new family of drugs is bringing us closer to that goal by building on years of basic biology research and targeting one of the most abundant nuclear proteins, PARP-1.

We have known for a long time that PARP-1 is important in a variety of cellular processes from replication to transcription and we are still in the process of identifying various PARP family members.

One of the most common activities of PARP-1 protein is its role in the base excision repair process that repairs single-strand breaks that occur on the DNA as a product of normal cell metabolism. If unrepaired, single-strand breaks can stall replication forks and create single-ended double-strand breaks, a highly toxic lesion repairable only by homologous recombination. Homologous recombination is one of the most commonly inactivated repair mechanisms in cancer, especially in breast and ovarian (BRCA1 and BRCA2 mutations) as well as prostate tumors. Inability of a cell to repair a single-ended double-strand break will lead to activation of apoptosis and cell death.

The pathway of oxidative damage to single-strand break to double-strand break to homologous recombination is now being used to selectively kill cancer cells. A cancer deficient in homologous recombination is going to be more sensitive to PARP-1 inhibition and formation of single-strand breaks than normal tissues.

In normal tissues, inactivating PARP-1 will produce single-strand breaks that will get converted to double-strand breaks during replication but with active homologous recombination this damage will be easily repaired and the cell will survive and continue proliferating. In BRCA2 mutant tumors, for example, inactivating PARP-1 will also produce the same type of damage but at the last stage the cell will be unable to repair it because it lacks the homologous recombination activity. Thus, inactivating PARP-1 will selectively kill cancer cells but not normal tissue, providing a silver bullet for that type of tumor.

A recent report in New England Journal of Medicine described this exact effect in BRCA2 deficient tumors during a phase I study of AZD2281, a highly selective and potent PARP-1 inhibitor.

As a scientist, I hope that soon we can hear of more therapeutic success stories that came from basic research foundations. Judging by published data, we have certainly been productive and it is now time to assess which of those avenues will be crucial as we move forward to develop new treatments that will be more potent and yet have fewer side-effects than what we currently offer.

It would be wonderful to have a treatment that would be like a skilled carpenter: able to go into a house, take out the broken window and leave without anybody waking up.

Reference:
Fong, et. al., 2009. Inhibition of Poly(ADP-Ribose) Polymerase in Tumors from BRCA Mutation Carriers. NEJM; 361: 123-34.

Betaine is the most common additive used to enhance amplification of GC rich sequences because of its ability to dissolve secondary structure that blocks polymerase action.  But betaine does not solve every PCR issue related to GC overload.

Lucky for us, a team of researchers at the Harbin Institute of Technology and Tianjin University of Science and Technology in China have discovered two new additives for PCR that work even better than betaine.

Their paper, entitled: Enhanced amplification of GC-rich DNA with two organic reagents, can be found in the September 2009 issue of BioTechniques (vol. 47, No. 3, page 775)  and I’ve summarized the results of the paper here.

What are these new additives?

According to the report, ethylene glycol and 1,2-propanediol are the two superior ingredients for decreasing the melting temperature of DNA and getting GC-rich PCR to work.

The Strategy:

In order to examine their ability to enhance difficult PCR templates, the authors randomly selected 104 GC-rich human genomic amplicons with lengths between 700-800 bp and with GC content between 60-80%. The additives were used at final concentrations of 1.075M for ethylene glycol and 0.816M for 1,2-propanediol. Betaine was used at a final concentration of 2.2M. All amplification reactions were performed at least 3 times to ensure the accuracy of results.

The Outcome:

The researchers put together an extensive table that summarizes the results of PCR for 104 amplicons. In summary, 13% (14) of the amplicons amplified without any additives. 72% (75) worked with just betaine alone while 90% (94) worked with only 1,2-propanediol and 87% (91) were successful with the addition of ethylene glycol alone.  While three reactions were rescued with betaine and not the other additives, overall performance was improved using these the ethlyene glycol or 1,2-propanediol.

Unexpected results:

Interestingly, in some cases betaine showed a PCR inhibitive effect. Several of the reactions that worked only with ethylene glycol or only with 1,2-propanediol failed when betaine was added back into the reaction in addition to the new additive.

What is the difference between additives?

The authors close their article by referencing several papers that discuss the impact of betaine and ethylene glycol on DNA melting enthalpy and theories that suggest differences in affinities of betaine and ethylene glycol to ssDNA and dsDNA may be playing a role.

While the mechanism of action of ethylene glycol and 1,2-propanediol on melting GC-rich templates it not fully understood, it is definitely  functioning differently than betaine. More studies in understanding how these reagents function may uncover additional novel uses for ethylene glycol and 1,2-propanediol in molecular biology besides PCR.

Have you tried these additives in your PCR? How well did it work for you? What are you tips for getting GC-rich templates to work in PCR?

But publishing costs money, and someone has to pay those costs. Administration of the peer review process, copyediting, typesetting and graphics work and, of course, printing all require costly manpower.

The traditional business model has been to load the cost onto institutions and individuals who pay subscription fees to the publishers. But since the advent of the internet wiped out the requirement for one of those major costs (printing), some publishers, new and old, have moved to different business models that allow open access to their articles.

The most common open access models are:

• Gold Open Access: All articles in the  journal are free access. This is most commonly funded by author fees (e.g. PLoS) or advertising (e.g. Biotechniques).
• Hybrid Open Access: Traditional subscription journals where individual articles can be made free either upon payment of a fee by the author or unilaterally by the journal editor (to help market the journal).
• Delayed Open Acess: Traditional subscription journals where all articles become open access after a specified period
• Green Open Access: Personal self-archiving of either the final copy or, to avoid copyright restrictions, the final peer-reviewed pre-print draft of a manuscript you have published elsewhere (click here fore more details on self-archiving).

Open Access is Not Free

All of these models (apart from green open access, which is actually not really a model) have one thing in common with the traditional subscription model: they cost. They are just different ways to obtain the money required to fund the publication process.  In the case of PLoS, for example, the burden of cost is placed on the author (it costs between $1350 and $2900 per author) and in many cases this money has to come from funds that would otherwise have been allocated to fund research. And in the hybrid open access journals the old journal elitism still reigns – the higher the impact factor, the higher the Open Access fee.

So while Open Access might eliminate subscription fees, instead it makes publishing expensive for the author. In a purely Open Access world it is easy to imagine a situation where researchers in a cash-strapped institution or small company are prevented from publishing their latest work in most journals because of the cost.

Is PLoS the way forward?

Now that articles are published on the internet, do we really need journals anyway? Perhaps all we need is a central body that acts as a repository for all literature and organiser and arbiter in the peer review process. This is what PLoS aims to be.

Having one huge, non-profit publisher like PLoS could make things a lot simpler, and less expensive, for authors and readers alike. An all-encompassing PLoS could presumably work hard to reduce author costs to a minimum through cost saving and negotiating grants from governments and others. And PLoS already waives author charges without question to those who say they can’t afford it, so publishing, as well as reading, would be Open Access. Funding bodies too would have to catch up and realise that Open Access costs must be factored in and a centralised, uniform publication process could make this simpler.

Open Access is not perfect yet, but if we could reduce the burden on the author and streamline the publishing process, it could be pretty close.

Do you think PLoS is the way forward? Are there any disadvantages in having one, central publishing body? Let us know in the comments.

Non-fiction plods and trudges. However, ‘The Emperor Of Scent‘ by Chandler Burr is breathtakingly unique. It gallops. It has all the elements of a quintessential page turner. And it’s about science too.

It got me so electrified that I repeatedly found myself reading diagonally, reaching a point where I realised I’m not understanding anything because I’m going too fast, and taking a deep breath as I turned the pages back and re-read it.

The book is about Luca Turin’s (a biophysict for want for a better word, biophychemist to be exact) dramatic course of discovery of an alternative theory on how we smell.

I say ‘alternative’ because Wikipedia says so. But personally, I was thoroughly convinced that it is the theory on the mechanism of olfaction.

The theory is based on the bizarre idea that we smell using an electron spectroscope in our nose.

No, I’m not kidding. Yes, it is achievable using proteins. Yes, there are conclusive experiments for the same. No, he hasn’t yet got a Nobel. But you will be convinced that he deserves one when you turn the final page.

Isn’t it strange how we never give an iota of thought to how we smell?

Turin has a quirky, interesting character which absorbs one immediately. He’s passionate to the verge of obsessed. He’s restless. He’s intentionally oblivious to scientific protocol. He dabbles in everything, talks to everyone: Perfume, tracing submarines, electron tunneling, spectroscopy, insulin, transistors. He has thrillingly eloquent descriptions of scents.

And amazingly, it’s this rich soup of ideas, this intended scorning of the scientific boundaries (Physics, Chemistry, Biology), this compulsive desire to investigate just for the sake of investigating, that allows, and is absolutely essential for his theory to have been conceived.

The book also is scattered with all kinds of witticisms, concepts, and ideas that got my neurons tingling. I’m a sucker for scientific analogies. And Chandler Burr generates them as well as anyone.

He likens wave numbers to musical notes. He personifies electrons to explain electron tunneling in a way anyone can understand. Finally, the book also throws light on the myth we have about science and why it isn’t as perfect as we (or I especially) are wont to think of it.

I will have to read the book thrice at least, to enjoy all those tiny subtleties I missed while I stormed through it. I highly recommend it to anyone who loves science.

To conclude, some excerpts:

(Opening lines): Start with the deepest mystery of smell. No one knows how we do it.

(On Turin’s eloquence with scents): Read here

(On biological theories): Biological theories are created by pretending to be God. Another way of saying this is you put together a biological theory by reverse engineering the human body. You build a theory by looking at what already is and then try to think up a good reason why it would be that way, and how it would work.

(On Phy, Chem, Bio): It is said that both chemists and physicists study the atom, but chemists mess around with the electrons and physicists pass their time on the nucleus. Biology has now metamorphosed into the study of the gene….This is the historical reason people still say “molecular biology” which is actually a name without any meaning, As if there were any other kind of biology anymore. (This had me giggling for a while)

If you have read this book or are interested in Luca Turin’s work, please drop me a comment.

And/or if you have read a great book that you’d like to review on Bitesize Bio, please drop us a line!

He truly viewed the variety of biological forms that he looked at with the eyes of a mathematician.

Peter Medawar described Thompson as a “natural philosopher” in the proper sense of the term, who saw the world simultaneously as a classicist, a mathematician, and as a naturalist.

It is with that perspective that Thompson wrote his famous classic On Growth and Form 92 years ago.

Without going into a detailed analysis of the topics which Thompson covered in On Growth and Form or the body of science since its publishing, it seems that the modern discipline of biophysics most aptly embodies his approach. That is, while mechanisms such as Natural Selection may have its uses, much more might be gained by examining the effects of forces and scale on aspects of organism body plans.

Thompson pointed out example after example of correlations between biological forms and mechanical phenomena. He showed the similarity in the forms of jellyfish and the forms of drops of liquid falling into viscous fluid, and between the internal supporting structures in the hollow bones of birds and well-known engineering truss designs. His observations of phyllotaxis (numerical relationships between spiral structures in plants) and the Fibonacci sequence has become a textbook staple.

On Growth and Form is also becoming antiquated – the references to knowledge current in 1917 are obscure items of science history, and therefore it is more difficult to quickly recognize Thompson’s focus in any given passage. In other words, it’s becoming more of a book for the history of biology, to be read for its aesthetics more than its original insights, profound though they were when first written.

And this is really where my own appreciation of singularly unique books in biology comes into full bloom, recommending almost purely for its aesthetics as well as its historicity. Who hasn’t admired the iconic logarithmic spiral of the nautilis shell, shown on the cover of many versions of the book and which Thompson reflects on in the chapter ‘The Equiangular Spiral’?

But, perhaps sadly, many people including myself have found On Growth and Form to be too rich, too ‘fancy’ in their first encounter as undergraduates. As Medawar said, “It lacks the conventional condensation and emasculatoin of modern scientific, machine-made, basic prose.”

But maybe that’s part of its charm, too.

The article, published in Nature Materials by Dan Lou et al from Cornell University, shows a novel way to produce proteins cell-free using DNA hydrogels.

What are P-gels?
Protein-producing DNA hydrogels (P-gels) contain the template plasmid DNA (from which the protein will be synthesised) assembled into a large scaffold structure by ligation to x-shaped pieces of cross-linker DNA, and embedded into a blob of a polymer called PDMS. The P-gels are molded into micropads of defined dimensions during the gelling process and after gelation, the PDMS forms a spongy, jelly-like matrix that absorbs water, but does not dissolve in it.

Several P-gel micropads can then be transferred into a coupled cell-free extract reaction mix for protein production (see part B of the figure on the right).

How good are they?
P-gels have shown very promising results;They can produce several-times times greater protein than regular solutions base cell-free protein synthesis methods. The results were consistently good for the 16 different proteins, including membrane proteins and toxic proteins, that the authors tried.

Why are they better?
Several factors unique to the DNA hydrogels make the system very efficient. Firstly, the plasmid DNA is physically cross-linked to the scaffold, which protects the genes from damage, such as degradation by nucleases.

Secondly, the gel matrix compresses the template into a smaller area makeing the effective concentration of the DNA, lysate and the other factors required for protein synthesis higher — and higher concentration results in a more efficient reaction. This is similar to the way that PEG works to improve the efficiency of ligation reactions (see 5 DNA Ligation Tips).

Finally, the transcription efficiency is greater than solutions-based system due to the increase in enzyme turnover during transcription. Since the genes are �locked’ in place, they are readily available for use by the phage polymerases.

Where can you buy them?
Unfortunately, the hydrogels are not very easy to make or in commercial production yet. They require a clean room and specialized micro-moulds. So for now, we just need to keep improving our solution-based methods.

For more information on DNA hydrogels, checknews.cornell.edu/stories/April09/ProteinGel

References:

1. Nature Materials 8, 432 – 437 (2009)
2. Nature Methods 6 (5), 326 (2009)

Do you have a journal club article you’d like to share on Bitesize Bio? If so, contact us!

It’s no coincidence either — selective breeding and domestication of crops made civilization possible. And in an era when the capacity for cultivating the primary grain and vegetable crops of the world is being stretched to its limits by overpopulation, farmers are still innovating in their breeding schemes.

And today, the cutting-edge tools of innovation in biology lie in the hands of geneticists and the farmers they collaborate with. It’s in that spirit that the recent book Tomorrow’s Table: Organic Farming, Genetics, and the Future of Food was written by Pamela Ronald and Raoul Adamchack (Amazon US/UK). Ronald, a plant geneticist at UC Davis, and Adamchack, and organic farmer, contribute several chapters each on their separate specialties in casual, friendly writing styles.

In it, they cover a wide breadth of the the subject matter (genetically-modified and organic agriculture) as it interacts with facets of the farm, the lab, consumers, the environment, patent law, and dinner itself. And they do so honestly, trying to represent alternative viewpoints rather fairly in the form of questions from their students, political issues being raised by people fearful of GMOs, and basic considerations relating to how and why growers and biologists alike use certain crop management strategies.

Their citations are also well-organized, connecting the reader to the source material (and especially scientific studies) wherever possible. Well-studied data is of course the best remedy for the politics of GMOs. For someone like myself reading Tomorrow’s Table for information content, that’s invaluable.

For others, maybe you’re looking for a more casual read. Ronald and Adamchack offer this as well, with their conversational writing styles. Or maybe you’re interested not in the science, but in the culinary uses of good agriculture. They’ve got that too, with a handful of recipes interspersed throughout the book.

Regardless, Ronald and Adamchack come across as making an effort to reach out to the average farmer as well as to the lay consumer. And in that, I think, they do an admirable job explaining the marriage between organic farming and genetic manipulation.

As per the reading part, I lately got around to reading Michael Conn and James Parker’s book, The Animal Research War.

In this book, Conn, with an analyst of animal rights (Parker), give a personal account of what it is like to be a medical researcher targeted by such a powerful movement.

It gives the reader a historical overview of animal rights activism, analyses their strategies via case studies, profiles leaders of the animal rights’ movement, corrects the “facts” of many activist’ accusations, and portrays the societal cost of intimidation by violence to animal researchers.

And, most importantly, it exposes the animal rights’ movement as lead by domestic terrorists and their supporters[1].

What Conn does not do is describe in detail the regulations and lengths to which animal researchers go to in order to conduct their research as humanely as possible (he does mention it however, and indicates where readers should go to learn more about this).

For this reason, I don’t think that this is a book meant to educate the general public of the value of animal research nor the actual way in which it is conducted.

It is, however, a wake-up call to the scientific community. Conn writes:

I had read a little bit about animal rights activities when I was in high school in the late 1960s. These activities were not front-page news. Mostly they were grumblings from “antivivisection” groups in the UK, distant and abstract… [page 5]

Over more than a decade I learned two important lessons. First is the fact that some animal rightists misrepresent animal research and do so with impunity… Second, institutions that don’t respond to misrepresentations and half-truths, attempting to hide legitimate and humane research as if it were a dirty little secret, play directly into the hands of animal rightists and extremists.

Were my harrassers terrorists? It’s your call, but remember that their actions were designed to coerce me by the threat of violence…[page 8]

Conn’s message is clear: institutions and communities must confront animal activism, not shrink away from it. They must stand up and communicate with the public.

In that interest, the call from the scientific community for authorities to confront animal activism is rising. One very good example is an editorial in a recent issue of the journal Nature.

Against vicious activism: The US authorities need to strengthen their position on the use of animals in experiments.

Seven activists convicted of carrying out a campaign of intimidation against the animal-testing firm Huntingdon Life Sciences in Huntingdon, UK, were last month sentenced to between 4 and 11 years in prison. Hopefully, these sentences will stop future UK activists from using similar tactics, which included threats, hoax bombs, character assassination and property destruction.

Unfortunately, such tactics are increasingly being used by activists attacking scientists in California, where researchers who use animals are facing threats that include doorstep firebombs. The authorities trying to deal with this problem can find much in the UK authorities’ approach to emulate.

I couldn’t agree more.

Note1: Interesting Quotes from PETA Officials:

1. “Our ultimate goal is total animal liberation”
-Ingrid Newkirk (President and co-founder)

That means NO meat, milk, zoos, wool, pets…

2. â€?blowing stuff up and smashing windows” is â€?a great way to bring about animal liberation.”
-Bruce Friedrich (vegetarian campaign coordinator)

3.â€?even if animal research resulted in a cure for AIDS, we would be against it.”
-Ingrid Newkirk (President and co-founder)

4.”Until [your mommy stops wearing fur], keep your doggie or kitty friends away from mommy-she’s an animal killer!”
-PETA comic book geared towards kids

5.”Arson, property destruction, burglary and theft are ‘acceptable crimes’ when used for the animal cause.”
-Alex Pacheco, Director, PETA

6.”Six million Jews died in concentration camps, but six billion broiler chickens will die this year in slaughterhouses.” -Ingrid Newkirk (Washington Post, November, 13, 1983)

7. “There is no rational basis for saying that a human being has special rights. A rat is a pig is a dog is a boy. They’re all mammals.”

- Ingrid Newkirk (Vogue, September 1989; where she also said  “Even if animals research resulted in a cure for AIDS, we’d be against it.”)

Note2: There is a difference between supporting animal welfare and animal rights.