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- June 8, 2013
- 09:03 AM
- 43 views
The virus-antibody arms race
One of the new concepts I learned when I started working on HIV was the most recent common ancestor, or MRCA. When you look at the genetic make-up of a population, you will find a certain amount of variety but also a much greater amount of overlap, i.e. stretches of DNA that are identical throughout the population. Using phylogenetics, one can look at these patterns of shared vs. mutated stretches, and reconstruct the genetic ancestor of the population. For example, you've probably heard of Mitochondrial Eve: since we all inherit our mitochndrial DNA from our mothers, scientists have been able to look at the mitochondrial DNA across all populations and determine the one ancestor (our common mother, so to speak) from which they all originated. Pretty cool, right?My line of work, for the past 6-7 years has been estimating most common recent ancestors, or MRCAs, of HIV-1 populations. A few years ago we found that in sexually transmitted infections only a handful of viruses are able to come across the genital mucosa and start the infection. Therefore, if you draw a blood sample early enough (a few weeks) after the start of the infection, from that sample we can infer the MRCA of the viral population in the patient. This is particularly relevant because in the case of a viral infection, the MRCA is likely to be the virus that initiated the infection. As the infection progresses, the viral population changes, but it is the ones that are able to break the mucosal barrier (i.e. the MRCAs) that a vaccine needs to target.Once inside the host, viral evolution is (for the most part) driven by the host's immune system as it tries to counter-attack the infection. At the same time, as the virus changes its genetic make-up to escape the immune pressure, the immune system itself changes and tries to come up with new ways to neutralize the enemy. It's an arms race that in HIV infections typically sees the immune system always one step behind: the first antibodies found in an HIV-1 infected person react with the first, unmutated virus that initiated the infection (the MRCA). As the infection progresses and the virus evolves, new antibodies are made that are able to react to the following viral generations, but typically there's always a subpolulation of viruses that's one step ahead of the antibodies and can still escape. (I hope this part is clear, I've been struggling quite a bit to find the right wording for this paragraph, so if it's not clear feel free to ask questions in the comments.)In order to design an efficient vaccine, we need to find a way to elicit broad neutralizing antibodies, where by "broad" we mean antibodies that react not only to the present or past viral generations in one host, but to a wide variety of viruses across different hosts and populations. Such antibodies are found in a minority of HIV-infected patients and, typically, by the time they arise, the infection is so spread that they cannot clear the virus. Ideally, a vaccine should boost a "short-cut" in the evolutionary path that leads to the production of broadly neutralizing antibodies much faster than our bodies are currently capable of. Unfortunately, all vaccine trials attempted so far have not been able to elicit broad neutralizing antibodies. Why? Antibodies are made by B-cells, white blood cells produced in the bone marrow. In order to produce antibodies, B cells need to be activated, which happens when they find an antigen specific to their receptor. Once activated, B cells not only start producing antibodies, but they also either become memory cells (so that if the antigen is encountered again, the immune system will know which antibodies to produce in order to clear it) or they undergo further differentiation. This process of undergoing more differentiations ensures that the "match" between receptor and antigen becomes tighter and tighter. It takes many cycles of differentiations to produce HIV-1 broadly neutralizing antibodies, and, currently, the process takes so long that most patients don't produce them ever, and the ones that do, don't get them in time to clear the infection. One reason why we believe it takes many differentiations to make HIV broadly neutralizing antibodies is that they share many similarities to self-reacting antibodies, antibodies that are normally destroyed by the body because they carry a high risk to originate auto-immune disorders (when the immune system attacks its own self instead of antigens). So, instead of eliciting the actual antibodies, could a vaccine elicit its ancestor? Remember how I said that the viral population constantly evolves and, hand in hand, so do the antibodies? Since we can estimate the viral ancestors, can we do the same for the antibodies? Can we reconstruct the differentiation pathway that leads to broadly neutralizing antibodies? In [1], Liao and colleagues have reconstructed the lineage of the infecting virus in one African HIV-infected patient (CH505), as well as the lineage of an antibody, found in the same patient, able to neutralize 55% of ~200 HIV-1 isolates. the researchers effectively reconstructed the coevolution of virus and antibody within the patient. The patient was followed from week 6 after the infection up until 236 weeks after the infection, and during this period no antiretroviral therapy was administered. This is important because it means that the viral evolution was driven solely by the immune pressure. Liao et al. found that the first unmutated ancestor in the B-cell lineage appears at week 14 after the infection, and it keeps mutating in ways that are reflected in the evolution of the virus. Once they retraced all the intermediate steps that led to the production of the broadly neutralizing antibody, the researchers tested all of the intermediate antibodies for reactivity against the virus, from the infecting strain to its later generations. They found that breadth and strength of reactivity increased as the antibody lineage evolved. In light of what I tried to explain above, this is a fantastic step forward in understanding how the virus evolves under the immune pressure, as it can help design a vaccine that elicits antibodies that are one step ahead (instead of behind) in the virus-host arms race. "Thus, a candidate vaccine concept could be to use the CH505 transmitted/founder Env or Env subunits (to avoid dominant Env non-neutralizing epitopes) to initially activate an appropriate naive B-cell response, followed by boosting with subsequently evolved CH505 Env variants either given in combination, to mimic the high diversity observed in vivo during affinity maturation, or in series, using vaccine immunogens specifically selected to trigger the appropriate maturation pathway by high-affinity binding to the unmutated common ancestor and antibody intermediates. [. . .] The finding that the transmitted/founder Env can be the stimulator of a potent BnAb and bind optimally to that broadly neutralizing antibody unmutated common ancestor is a crucial insight for vaccine design, and could allow the induction of broadly neutralizing antibodies by targeting unmutated common ancestors and intermediate ancestors of broadly neutralizing antibody clonal lineage trees."Of course, there's the usual caveats: will this kind of pathway be reproducible in other patients? How much of it is randomness and how much is it not only retraceable but reproducible is something we will only understand by getting more data from more patients. But it's a start, and a very promising one. [1] ... Read more »
Liao, H., Lynch, R., Zhou, T., Gao, F., Alam, S., Boyd, S., Fire, A., Roskin, K., Schramm, C., Zhang, Z.... (2013) Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus. Nature, 496(7446), 469-476. DOI: 10.1038/nature12053
- May 23, 2013
- 09:21 AM
- 84 views
Should you worry about vitamin D deficiency? Maybe. Or maybe not.
Since my last blog post, where I shared my thoughts on BRCA1, BRCA2, and preventive mastectomies, I've been asked what else can a woman do to reduce her risk of breast cancer. I've heard a big deal about vitamin D, so I did a bit of research on the matter. As a disclaimer, I should tell you up front that, though many correlations between vitamin D deficiency and cancer risk have been found, just as many have been refuted or found inconclusive. You can read more about it on the wikipedia page.What is vitamin D? The name "vitamin D" includes a group of steroid-like molecules (they are similar to steroids, but not quite steroids) that help our intestine absorb calcium and phosphates. Since calcium is essential in bone development, vitamin D deficiency has been most commonly associated to osteoporosis and other bone-related diseases. There aren't many foods rich in vitamin D, however, vitamin D can be endogenously synthesized when the skin is exposed to sunlight. Unfortunately, modern lifestyle keeps us cooped up many hours in office cubicles, or in the house during chores, or in malls. When we're out enjoying the sunshine we cover up with hats and super-protective sunscreens because we've been told that the sun is bad for the skin and can cause malignancies. As a consequence, vitamin D deficiency is increasing world-wide. There is a foundation for all the studies that have analyzed correlations between several diseases, including cancers, and vitamin D: (i) several ecological studies have found a trend for an increase in incidence of certain cancers at higher latitudes, suggesting that longer exposures to the sun may have a protective effect. (ii) The vitamin D receptor (VDR) is expressed in many cells of the immune system, and mouse models have shown that vitamin D deficiency can promote certain auto-immune diseases. In a recent review, Sundaram and Coleman examine the link between vitamin D and influenza [Adv. Nutr. 2012 3: 517-525]. (iii) "VDR regulates a wide range of cellular mechanisms central to cancer development, such as apoptosis (cell death), cell proliferation (uncontrolled cell growth), differentiation, angiogenesis, and metastasis [1]". In line with this observation, Pereira, Larriba, and Munoz published a review on the evidence that vitamin D plays a protective role in colon cancer [Endocr. Relat. Cancer 2012 19: R51-R71].In [1], Crew discusses the use of vitamin D supplementation as part of breast cancer prevention. She presents many interesting findings, for example:"Colon, breast, and lung cancer have all demonstrated downregulation of expression of VDR when compared to normal cells and well-differentiated tumors have shown comparably more VDR expression as measured by immunohistochemistry when compared to their poorly differentiated counterparts. Higher tumor VDR expression has also been correlated with better prognosis in cancer patients [1]."Crew looks at different types of studies: some suggest beneficial effects from using vitamin D (calcitriol) in combination with other anti-cancer treatments; some found an inverse association with mammography density, a biomarker for breast cancer (supposedly high density increases the risk of cancer); some found an inverse association between better breast cancer prognosis and vitamin D deficiency. However, many of these studies have limitations. For example, some only assess the levels of vitamin D through dietary intake, which is not a good measure of the circulating levels because it doesn't account for vitamin D synthesized through sun exposure. Some were confounded by obesity since fat is known to sequestrate vitamin D and also raise breast cancer risk. In light of all these considerations, Crew concludes:"Even with substantial literature on vitamin D and breast cancer, future studies need to focus on gaining a better understanding of the biologic effects of vitamin D in breast tissue. Despite compelling data from experimental and observational studies, there is still insufficient data from clinical trials to make recommendations for vitamin D supplementation for breast cancer prevention or treatment [1]."As I often do in my posts, rather than giving you answers, I make an effort to provide you with pointers and food for thought: in the end you have to make your own decisions about your health and the wellbeing of your family. As a personal note, I'll add that on my last blood report my vitamin D circulating levels were undetectable. I had no symptoms whatsoever, but I am now taking a vitamin D supplement. I'm also much less paranoid about smothering my kiddos with sunscreen when they play outside (which has made them much happier, two birds with one stone). [1] Crew, K. (2013). Vitamin D: Are We Ready to Supplement for Breast Cancer Prevention and Treatment? ISRN Oncology, 2013, 1-22 DOI: 10.1155/2013/483687... Read more »
Crew, K. (2013) Vitamin D: Are We Ready to Supplement for Breast Cancer Prevention and Treatment?. ISRN Oncology, 1-22. DOI: 10.1155/2013/483687
- May 16, 2013
- 07:34 PM
- 85 views
Angelina no longer has them. Does that mean I should get rid of them too?
We love them and yet we hate them. They get censored, augmented, reduced, replaced, covered, exposed. They get grilled, occasionally, but those are not the ones I'm talking about. We want to see them and yet we pretend we don't. We criticize them and yet we forget what they are made for, the most beautiful thing of all: nourish a new life.Yes, I'm talking about breasts. Angelina Jolie's breasts have been extensively discussed this week, more now that they are reportedly gone than when they were around. Sort of ironic, if you thin about it. Angelina did the unthinkable: she had both her healthy breasts removed to prevent cancer. In a second phase of her preventive plan, she will have her ovaries removed, too. The tabloids will no longer be able to speculate on her possible new pregnancies, but they will have plenty to discuss on and around her missing body parts.Somehow the news left me a little puzzled, unable to share the views of those who praised Angelina for her bravery. Yes, it takes guts to do what she did. At the same time, the huge resonance she's been given seems blown out of proportion. Just another Hollywood thing. It reminds me of back when our mothers were told that formula was way better than breast milk. Are we facing a new era where silicon is better than milk ducts? Are they trying to convince us that fake is healthier than real? Well, of course it is. It's fake!So, before we go around demonizing breasts and invoking chopping off body parts in the name of longevity, I wanted to get some facts straight.First of all, I read over and over again, "Angelina Jolie carries the gene BRCA1 ..." Turns out, we all carry the gene. What makes us different is that there are distinct copies of this gene across individuals, and some copies (but not all) do raise the risk of breast and ovarian cancer. BRCA1 and BRCA2 are part of the so called tumor suppressor genes, genes that code for proteins that are in charge of repairing damaged DNA. Our cells undergo numerous cellular divisions during our lifespan, and every cell division carries a certain chance of damaging the DNA. Though rare, mutations can be introduced, which can either be lethal or create a cancerous cell. Tumor suppressor proteins make a first attempt to repair the damaged DNA. If the DNA cannot be repaired, they promote apoptosis, or cell death. Another example of tumor suppressor gene is TP53, which encodes the protein p53. The first link between BRCA1 and breast cancer was discovered in 1990 by Hall et al. [1]. BRCA1 and BRCA2 are expressed mostly in breast tissue. Some mutations in these genes cause them to code proteins that are not fully functional. When this happens, a cell with damaged DNA has a higher chance to escape the "screening" and start dividing instead of undergoing apoptosis. Because BRCA1 and BRCA2 are expressed mostly in the breast tissue, by removing the breast tissue one gets rid of the majority of cells expressing the defective genes, which in turns significantly lowers the chance of developing breast cancer. While hundreds of mutations/variations in the BRCA1 and BRCA2 genes have been found, not all are linked to breast cancer, and the ones that are don't increase the risk in the same amount. Furthermore, the majority of breast cancers are not linked to mutations in these two genes. In other words, having the mutations raises the risk, but not having them does not lower it. So, let's get some numbers straight. According to the American Cancer Society about 15% of women diagnosed with breast cancer have a family member diagnosed with it. That leaves the majority of breast cancers unrelated to family history: "About 85% of breast cancers occur in women who have no family history of breast cancer. These occur due to genetic mutations that happen as a result of the aging process and life in general, rather than inherited mutations."It's a puzzle I've discussed before, the missing herediatbility. On the one hand we know genes play a large role in cancer and we spend all this research money into looking for genetic causes. Yet, the vast majority of cancers are non-hereditary. While women with certain mutations in either the BRCA1 or BRCA2 genes have up to 80% (the exact chance varies depending on the type of mutation they carry) increased risk of developing breast cancer, only between 5% and 10% of breast cancers are linked to deleterious mutations in the BRCA1 or BRCA2 genes. So, yes, get tested. But chances are, your copy of BRCA1 and BRCA2 are fine. So, what makes BRCA1 and bRCA2 so scary? The American Cancer Society reports that approximately 60% of women with one of the harmful mutations in BRCA1 or BRCA2 develop breast cancer during their lifetime, versus the 12% of women in the general population. Remember, though: these genes are not the only ones playing a role in cancer. Things like epistasis with other loci in the genome can deeply affect such risks and, unfortunately, we still don't know enough to quantify them. High levels of IGF-1, the insulin-like growth factor have also been linked to breast cancer. So while having those mutations raises the risk, it does not mean that the individual will develop breast cancer for sure as other factors are still unknown. Careful considerations should be made before making a drastic choice like Angelina's. These considerations should also include risks associated to a double mastectomy (infection, necrosis, etc.) and reconstruction surgery, neither one free of complications. I'm somehow reluctant to consider implants healthier than normal breasts, whether or not those breasts were expressing faulty genes. What about those 85% of breast cancers that are not linked to BRCA1 or BRCA2 mutations? Can we do anything to prevent those? When you look at the global population, the most common risk factors for breast cancer are not the mutations in BRCA1 and BRCA2, rather, as Bernstein reports in a 2009 review [2]:"The most consistently acknowledged risk factors for breast cancer other than gender and race/ethnicity are age, family history of breast cancer, early menarche, late age at first birth, nulliparity, late age at menopause, high postmenopausal weight or substantial weight gain as an adult, exposure to high levels of ionizing radiation and a history of benign proliferative breast disease [2]."All these risk factors point at one common etiology, ovarian hormones (estradiol and progesterone), because they"promote cellular proliferation in the breast, providing greater opportunity for the accumulation of random errors, which may lead to tumor development [2]."Body weight and exercise can be linked to different levels of estradiol in the blood (high body weight is associated with higher levels, exercise is associated with lower levels), hence their correlation to breast cancer risk. Some studies found up to 40% reduction in risk in women who exercised in particular in their adolescence. Of all risk factors, these two, body weight and exercise, are the ones we can actually take control over and actively lower our risk of developing breast cancer. A diet rich in antioxidants may lower the risk of DNA damage during cellular division. Things we have less control over is the woman's age at the first pregnancy. One of my grad school professors used to say, "Having a baby as a teen may ruin your life, but it sure lowers your risk of developing breast cancer later in life." The risk keeps lowering for every additional pregnancy, though not as significantly as with the first one. What's not clear is the extent to which breastfeeding can lower the risk of breast cancer, as the American Cancer Society reports: "Research suggests that breastfeeding has only a slight effect on breast cancer risk and that effect is only among women who have breastfed for a long time. They also concluded that breastfeeding seems to be more protective against the most aggressive types of breast cancer, including tumors in women with mutations in the BRCA1 gene, basal-like cancers, hormone-receptor negative, and possibly triple negative tumors."And while we do the things that we can to lower our risks, I am hopeful that one day gene therapy will be perfected to the point that it will offer a better options than what, in gross terms, amounts to amputation.Thoughts?[1] ... Read more »
Hall, J., Lee, M., Newman, B., Morrow, J., Anderson, L., Huey, B., & King, M. (1990) Linkage of early-onset familial breast cancer to chromosome 17q21. Science, 250(4988), 1684-1689. DOI: 10.1126/science.2270482
Bernstein, L. (2008) Identifying population-based approaches to lower breast cancer risk. Oncogene. DOI: 10.1038/onc.2009.348
- May 5, 2013
- 11:44 AM
- 76 views
Pumping fuel from bacteria
In my last post I discussed a bioengineered E. coli strain capable of producing an engine compatible biofuel. I hailed the finding as more efficient than ordinary biofuels because this technique has less environmental impact than biofuels from crops, for example, or cellulose, which instead use great amounts of water and forest land. I did some more reading on the topic and found out that, surprise surprise, there are some costs in harvesting biofuels from bacteria as well, so my discussion was incomplete. However, there are good news at the horizon. When I first read the Howard et al. paper, I imagined a petri dish of E. coli sitting in a slime of oil-like substance. I think I got confused with making yogurt. :-) In reality, the biofuel molecules are stored inside the cells (bacteria, in this case) and need to be taken out without harming the cells. Biofuel secretion strategies have been dubbed "milking." The difference, though, is that contrary to milk and cows, biofuels are generally toxic to the bacteria that produce them.Several methods have been investigated to efficiently "milk" biofuel molecules out of bacteria without harming them. To understand these strategies, we need to learn a new concept: an efflux pump is a membrane transporter protein that carries a substance toxic to the cell outside the cell itself. These proteins remove all kinds of toxic substances, including antibiotics, for example, and they may be specific to one in particular, or carry a whole range. In [1], Dunlop et al. discuss the use of efflux pumps in "milking" biofuels out of bacteria and reduce their toxicity to the cells:"Many compounds being considered as candidates for advanced biofuels are toxic to microorganisms. This introduces an undesirable trade-off when engineering metabolic pathways for biofuel production because the engineered microbes must balance production against survival. Cellular export systems, such as efflux pumps, provide a direct mechanism for reducing biofuel toxicity."The researchers first looked at the whole genome of E. coli to identify all genes encoding efflux pumps. They found 43 different pumps expressed in the E. coli genome, and tested them against a range of possible biofuels. Their strategy was as follows: the grew a culture of pooled bacteria with different subpopluations, each subpopulation expressing a different pump. In the absence of toxic biofuel-like substances, all subpopulations grew in equal proportions, and none had an advantage over the others. When a substance was introduced, the subpopulations with the most advantageous pumps with respect to that particular substance outgrew the rest. This is what happened, for example, when they introduced geranyl acetate:"When the pooled culture was grown in the presence of an inhibitory biofuel such as geranyl acetate, some efflux pumps conferred a distinct advantage. Although all strains started out with equal representation, after 38 h the population composition changed, with cells containing the advantageous pumps becoming an increasingly large proportion of the population. The efflux pumps that enhanced tolerance to geranyl acetate originated from a variety of hosts and include both known and previously uncharacterized pumps."In their study, Dunlop et al. used a type of membrane transporters called "RND," which are made of big molecules and are only found in Gram-negative bacteria. In a more recent paper [2], Doshi et al. studied a broader set of pumps called ABC, ATP-binding cassette:"Unlike RND proteins, transporters belonging to the ATP- binding cassette (ABC) protein family are widely found in all five kingdoms of life. They share a conserved structural architecture and specifically import or export a wide variety of molecules and ions across cellular membranes."Doshi et al. tested whether this family of broadly specific pumps could efficiently mediate the secretion of four different biofuel molecules. Similarly to the Howard et al. paper, they used a bioengineered strain of E. coli and noticed that "the secretion process was sustained for at least 6 days without the need to replenish the growth medium or culture. Thus, for the same quantity of biofuel produced conventionally, we have a dramatic reduction in biomass scale and significant gain in the ease of recovering the biofuel."Though my understanding is that work still needs to be done to improve this technique and make it feasible for different types of biofuels, the fact that these transporters are spread across different species makes it potentially translatable to other organisms and therefore of broader use. On a completely different note, can you guess what the macro picture is? :-)[1] Dunlop, M., Dossani, Z., Szmidt, H., Chu, H., Lee, T., Keasling, J., Hadi, M., & Mukhopadhyay, A. (2011). Engineering microbial biofuel tolerance and export using efflux pumps Molecular Systems Biology, 7 DOI: 10.1038/msb.2011.21[2] Doshi, R., Nguyen, T., & Chang, G. (2013). Transporter-mediated biofuel secretion Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1301358110... Read more »
Dunlop, M., Dossani, Z., Szmidt, H., Chu, H., Lee, T., Keasling, J., Hadi, M., & Mukhopadhyay, A. (2011) Engineering microbial biofuel tolerance and export using efflux pumps. Molecular Systems Biology. DOI: 10.1038/msb.2011.21
Doshi, R., Nguyen, T., & Chang, G. (2013) Transporter-mediated biofuel secretion. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1301358110
- May 1, 2013
- 09:24 AM
- 74 views
Fill the tank, please. With bacteria!
I apologize if you've already heard about this, but the paper is really cool and I couldn't resist discussing it here.Escherichia coli, or E. coli for brevity, is a bacterium normally associated with "bad" things like food poisoning. Even though most strains are actually harmless, even the CDC has a page dedicated to E. coli outbreaks. Since it's part of our gut flora, the lower intestines in particular, it's usually not a good sign when E. coli is found in places like restaurants and cafeterias. (Yuck!)What's less known to the public is that E. coli is one of the most studied bacteria and makes a great model for mutations, gene duplications, and horizontal gene transfer. What's even less known is that this amazing bacterium has the potential to save our planet from further drilling. How? By producing fuel. Yes, you read that right: through a combination of gene modifications, researchers from the University of Exeter [1] induced "petroleum-replica hydrocarbons" production in E. coli. These hydrocarbons are structurally and chemically similar to fossil fuels. In their paper, Howard et al. argue against the current biofuels because they bring additional costs in downstream processing and are not 100% compatible with the engines on the market. "To overcome the end-user blend wall, it is essential to generate precise chemical replacements to fossil fuels through sustainable means.Retail transport fuels are composed primarily of hydro- carbons (n-alkanes) of various carbon chain lengths (Cn), branched hydrocarbons (iso-alkanes), and unsaturated hydrocarbons (n- alkenes). The ideal biofuels are therefore n-alkanes, iso-alkanes, and n-alkenes that are chemically and structurally identical to the fossil fuels they are designed to replace [1]."Gasoline, diesel and jet fuels are made primarily of molecules called alkanes, or saturated hydrocarbons. Most people are familiar, or at least have heard of methane, the simplest alkane molecule. These molecules are naturally produced not just by bacteria, but also by plants and insects when they metabolize fatty acids. In 2010 Schirmer et al. described in a Science paper [2] an alkane biosynthesis pathway in cyanobacteria, commonly known as blue-green algae."The pathway consists of an acyl-acyl carrier protein reductase and an aldehyde decarbonylase, which together convert intermediates of fatty acid metabolism to alkanes and alkenes [2]."Understanding how alkanes are produced and, in particular, which genes are involved in their production, was the first step. The second step was answering the question: can we tweak this pathway to produce alkanes that can replace our current fuels? Seen under this light, the PNAS study published last March 15 [1] is a bioengineering success story. Howard et al. designed a novel metabolic pathway that forced E. coli to use free fatty acids instead of fatty acid compounds as in cyanobacteria, and produce fuel-like alkanes, what the authors call "industrially relevant, petroleum replica fuel molecules." Once finalized, this type of biofuel will be compatible with current engines and will not need to be blended with other petroleum derived chemicals. A bit of perspective: though derived from natural and biological sources, biofuels still contribute to pollution, carbon emissions, and global warming. Despite the amicable "bio" prefix, they all come with a non-null carbon footprint, some more than others. The true efficiency of any kind of fuel is the energy they produce minus the energy and costs it takes to derive them. For example, producing biofuels from crops drains precious resources, first and foremost, water, but also arable land, forests when arable land is not available, and food sources in underdeveloped countries. So here's where biofuels from bacteria have a striking advantage: E. coli is one of the cheapest and easiest bacterium to grow in a lab. It doesn't drain water reservoirs and it doesn't need deforestation to grow. Contrary to most biofuels out there, that have high production and energy costs, the carbon footprint of biofuels derived from bacteria only comes from carbon emissions when you burn them. And while this is an excellent thing, I still think that the real change we need to make to preserve our planet is to switch to renewable energy. [1] Howard, T., Middelhaufe, S., Moore, K., Edner, C., Kolak, D., Taylor, G., Parker, D., Lee, R., Smirnoff, N., Aves, S., & Love, J. (2013). Synthesis of customized petroleum-replica fuel molecules by targeted modification of free fatty acid pools in Escherichia coli Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1215966110[2] Schirmer, A., Rude, M., Li, X., Popova, E., & del Cardayre, S. (2010). Microbial Biosynthesis of Alkanes Science, 329 (5991), 559-562 DOI: 10.1126/science.1187936... Read more »
Howard, T., Middelhaufe, S., Moore, K., Edner, C., Kolak, D., Taylor, G., Parker, D., Lee, R., Smirnoff, N., Aves, S.... (2013) Synthesis of customized petroleum-replica fuel molecules by targeted modification of free fatty acid pools in Escherichia coli. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1215966110
Schirmer, A., Rude, M., Li, X., Popova, E., & del Cardayre, S. (2010) Microbial Biosynthesis of Alkanes. Science, 329(5991), 559-562. DOI: 10.1126/science.1187936
- April 26, 2013
- 03:46 PM
- 107 views
North Korea and the USA can indeed unite: in the battle against TB.
Tuberculosis (TB) is an infectious disease caused by a bacterium. It spreads through cough or sneeze from subjects with an active infection. While in most cases the disease is asymptomatic, a minority of latent infections does become active (i.e. the subject develops symptoms), and when it does, if left untreated, the disease can be deadly. According to the CDC one third of the world's population are infected with TB, and while in the US the incidence of the disease has been declining over time, it is still a huge problem in parts of the world like Asia and sub-saharan Africa. While normally the chance of a latent TB infection becoming active is one in ten, the chance is much higher for HIV-positive subjects because their immune system is already debilitated by the HIV virus. As the CDC reports:"TB is a leading killer of people living with HIV (PLHIV)."A regimen of 3-4 drugs has been available for years to keep latent infections from becoming active. Sadly, TB infections from multidrug resistant strains (MDR) have been steadily increasing, setting back the progress made in the past decades.From the World Health Organization:"Drug resistance arises due to improper use of antibiotics in chemotherapy of drug-susceptible TB patients. This improper use is a result of a number of actions including, administration of improper treatment regimens and failure to ensure that patients complete the whole course of treatment. Essentially, drug resistance arises in areas with weak TB control programmes. A patient who develops active disease with a drug-resistant TB strain can transmit this form of TB to other individuals."One of the countries plagued by MDR TB strains is North Korea, where the incidence of TB has dramatically advanced over the past years, reaching one of the highest incidences outside sub-saharan Africa. In this week's issue, Science Magazine describes a joint effort between two countries that, according to the recent news, you'd least expect to pair up: North Korea and the United States. In collaboration with Stanford University, the Korean ministry of Public Health opened in 2010 a National Tuberculosis Reference Laboratory (NTRL). "NTRL researchers can now diagnose TB cases that are resistant to first-line drug combinations, making it possible to spot patients who need more aggressive therapy. And the lab will soon add capacity to screen for extensively drug-resistant TB, known as XDR—the worst strains, some of which are close to impossible to treat."The Science report covers stories of hope in the midst of desperation. It points to pressing issues the North Korean government has to address within its borders, and focusing on them would seem a more reasonable and logical strategy than polishing nuclear arsenals. Let's hope that the roots of this collaboration grow deeper than any political discrepancies. Let's hope that a common enemy will put an end to the empty, unfounded threats and pave the way to a broader, more civilized way of communication between countries. Stone, R. (2013). Public Enemy Number One Science, 340 (6131), 422-425 DOI: 10.1126/science.340.6131.422... Read more »
Stone, R. (2013) Public Enemy Number One. Science, 340(6131), 422-425. DOI: 10.1126/science.340.6131.422
- April 18, 2013
- 07:36 PM
- 127 views
Can we functionally cure HIV?
Last March, Dr. Deborah Persaud, from the John's Hopkins Children Center, presented a stunning finding at the conference CROI, receiving great resonance across several newscasts: Persaud reported the first case of infant functionally cured of HIV. You can watch Persaud's presentation by downloading the podcast here, it's the seventh talk of the session "Is there hope for HIV eradication?"Up until this finding, the only living person cured from HIV was the Berlin Patient, who was cured after receiving gene therapy for his underlying leukemia condition. Despite this one successful case, gene therapy is not a feasible way to cure HIV. What does it mean to be functionally cured?Once in the host, the HIV virus establishes reservoirs of latent virus: these are viral particles that stay dormant in cells and tissues and have the ability to quickly rebound in the event that therapy is discontinued. That's why it's so important for an HIV infected person to never discontinue the drug regimen, as the rebound virus may be drug resistant. HIV is so efficient at escaping the immune system and therapy that standard practice these days is a lifetime of not just one, but a cocktail of 3-4 antiretroviral drugs. To be functionally cured means that drugs are no longer needed to keep the viral load in check (close or below detection), something that until now had only been achieved by an extremely low number of HIV-positive individuals (less than 1% of infected adults), the so-called "elite controllers." In all other subjects, the reservoirs are never completely weakened and they enable the virus to bounce back once therapy is interrupted. So, what was different with this child?The mother went into labor without prenatal care. An HIV test was done during labor and normally, when the test is positive, antiretroviral drugs are administered. This is highly effective in preventing mother-to-infant infections as the only moment when the infant is exposed to the mother's blood is at birth. The antiretroviral drugs keep the viral load so low that the risk of infection becomes very small (around 2%). Unfortunately, in this particular case, the birth was so precipitous that there was no time to administer such drugs. The newborn baby was immediately tested for HIV. This is my understanding of what was unique about this case: normally a first test is done and, if positive, a second follow-up test is performed and prophylaxis is started once the infection is confirmed. In this case, though, two independent tests were done at the same time and, since both confirmed the HIV infection, prophylactic treatment was started very early, when the baby was 31 hours of age. Also, unique to this case was the fact that a regimen of three drugs, of which one at the therapeutic level instead of the standard prophylactic dosage, was administered during the first week of life. After that, the baby was switched to a standard treatment of antiretroviral drugs (again, my understanding from the CROI talk). Such regimen successfully brought the child's viral load down to undetectable, which is normal in these cases. Despite this, because of HIV's ability to establish reservoirs, antiretroviral therapy is never discontinued. Like I said before, it is a lifetime therapy. So called "drug holidays" result in more virulent and drug-resistant HIV quasispecies. However, this child was lost to follow-up at 18 months of age and was once again seen by the doctors at 25 months of age, when the caregiver reported discontinuing the therapy. Immediate testing was done to assess the child's viral loads. The child was tested not once, but many times. Genetic testing was also done to make sure it was the same child treated before. The doctors must have been in disbelief as for the first time they were seeing the incredible: after 5 months since discontinuing antiretroviral therapy, the viral load in this child was still undetectable. What are the consequences? As Dr. Persaud repeated many times during her talk, this is a single case and a proof of concept. We need more cases to be able to generalize (as statistics teach us). However, it points to something that indeed needs to be explored: how early in the infection can we (and should we) intervene? In a 2012 paper [1], Persaud and colleagues studied the dynamics of the latent HIV reservoirs in 17 infants on very early antiretroviral drug therapy (median start age 8 weeks) and found that the size of the reservoirs at age 2 was associated to how early undetectable viral loads were achieved during therapy. The earlier viral load was suppressed through therapy, the smaller the HIV reservoir at age 2. Is there a point, very early into the infection, when the virus is vulnerable and all reservoirs can be not just reduced in size, but actually completely eradicated through potent and prompt intervention? In rare cases, HIV-infected patients are able to spontaneously maintain their viral load at a very low level without the need of drugs, the so called "elite controllers." What if, when administered early enough, antiretroviral drugs could transfer this type of spontaneous protection to every HIV-infected person? Shortly after the CROI conference, a French study published in PLoS Pathogens [2] reported 14 cases of what they call "post-treatment controllers," in other words, people whose viral loads remained very low after interrupting treatment. With the exception of mother-to-infant transmissions at birth, it's extremely hard to catch this virus early because people often don't realize they've been infected: symptoms, if any, appear 3-4 weeks later and are often mistaken for a common cold. Twelve of the 14 cases reported in [2] had symptoms that prompted early intervention and start of therapy during the primary infection."Post-treatment controllers (PTCs) had a more severe primary infection with higher viral loads and were frequently symptomatic, which may have prompted the early treatment in some cases [. . .] Therefore, our results strongly suggest that the infection control in the PTCs was not achieved spontaneously and was favored by the early onset of therapy. Because the interruption of long-term antiretroviral therapy initiated early during primary infection is not recommended, only a very small proportion (~2%) of the patients in the French Hospital Database on HIV Infection experienced such an interruption, which may explain the rarity of PTCs worldwide [2]."[1] Persaud, D., Palumbo, P., Ziemniak, C., Hughes, M., Alvero, C., Luzuriaga, K., Yogev, R., Capparelli, E., & Chadwick, E. (2012). Dynamics of the resting CD4+ T-cell latent HIV reservoir in infants initiating HAART less than 6 months of age AIDS, 26 (12), 1483-1490 DOI: 10.1097/QAD.0b013e3283553638[2] Sáez-Cirión, A., Bacchus, C., Hocqueloux, L., Avettand-Fenoel, V., Girault, I., Lecuroux, C., Potard, V., Versmisse, P., Melard, A., Prazuck, T., Descours, B., G... Read more »
Persaud, D., Palumbo, P., Ziemniak, C., Hughes, M., Alvero, C., Luzuriaga, K., Yogev, R., Capparelli, E., & Chadwick, E. (2012) Dynamics of the resting CD4 T-cell latent HIV reservoir in infants initiating HAART less than 6 months of age. AIDS, 26(12), 1483-1490. DOI: 10.1097/QAD.0b013e3283553638
Sáez-Cirión, A., Bacchus, C., Hocqueloux, L., Avettand-Fenoel, V., Girault, I., Lecuroux, C., Potard, V., Versmisse, P., Melard, A., Prazuck, T.... (2013) Post-Treatment HIV-1 Controllers with a Long-Term Virological Remission after the Interruption of Early Initiated Antiretroviral Therapy ANRS VISCONTI Study. PLoS Pathogens, 9(3). DOI: 10.1371/journal.ppat.1003211
- February 14, 2013
- 07:20 PM
- 215 views
Antiviral drugs to fight the flu: yes or no?
Disclaimer: I'm not a medical doctor. I cannot recommend taking or not taking a certain drug. However, I am a human being, I've got kids who do get sick from time to time, and I work on viruses. So when I heard that people were battling the unusually nasty flu this year with antiviral drugs, well, I had to do a bit of research. Antiviral drugs have become increasingly popular after the highly pathogenic avian flu strain emerged. The idea is that in order to be prepared for a possible pandemic, we need to stock up on drugs, enough to treat millions of people.Let's start with a few facts about viral infections:A virus is made of genetic material packaged in a tiny shell. Once inside a cell, the virus hijacks the cell's proteins to replicate and create thousands of copies of itself. The new virions bud out of the cell membrane and infect new cells.However, the infected cell has one more weapon up its sleeve: it "grasps" the virions that are budding out and tries to hold them back. In more scientific terms: there's a molecule on the cell membrane (called sialic acid) that binds to a protein on the surface of the virus (called hemagglutinin). The new virions have to break this bond in order to leave the infected cell and spread the infection. How do they do that? They use an enzyme called neuraminidase: the enzyme, found on the surface of the virus, breaks the bond between hemagglutinin and siliac acid, setting the virions free to spread out and infect new cells. Neuraminidase inhibitors are antiviral drugs that, as the name suggests, block the neuraminadase enzyme. As a consequence, the virions remain stuck to the cell membrane and thus cannot spread the infection. Supposedly, this leads to a speedier recovery. I'm saying "supposedly" because there is an ongoing debate on whether this is true or not. Here's what I found in the literature.Jefferson et al., 2009 [1]:"Neuraminidase inhibitors have modest effectiveness against the symptoms of influenza in otherwise healthy adults. The drugs are effective postexposure against laboratory confirmed influenza, but this is a small component of influenza-like illness, so for this outcome neuraminidase inhibitors are not effective. Neuraminidase inhibitors might be regarded as optional for reducing the symptoms of seasonal influenza. Paucity of good data has undermined previous findings for oseltamivir's prevention of complications from influenza. Independent randomised trials to resolve these uncertainties are needed."Wang et al., 2012 [2]:"Oseltamivir and zanamivir appear to have modest benefit in reducing duration of illness in children with influenza. However, our analysis was limited by small sample sizes and an inability to pool data from different studies. In addition, the inclusion of data from published trials only may have resulted in significant publication bias. [...] The clinical efficacy of neuraminidase inhibitors in 'at risk' children is still uncertain. Larger high-quality trials are needed with sufficient power to determine the efficacy of neuraminidase inhibitors in preventing serious complications of influenza (such as pneumonia or hospital admission), particularly in 'at risk' groups."Jefferson et al. 2012 [3]: "We found a high risk of publication and reporting biases in the trial programme of oseltamivir. Sub-population analyses of the influenza infected population in the oseltamivir trial programme are not possible because the two arms are non-comparable due to oseltamivir's apparent interference with antibody production. The evidence supports a direct oseltamivir mechanism of action on symptoms but we are unable to draw conclusions about its effect on complications or transmission. We expect full clinical study reports containing study protocol, reporting analysis plan, statistical analysis plan and individual patient data to clarify outstanding issues. These full clinical study reports are at present unavailable to us."The company that manufactures the brand name drug for oseltamivir responded here, however, according to BMJ, there hasn't been any release of data yet (source). I have two more cautionary comments.First: viruses mutate very rapidly and as such, they rapidly find escapes to drugs. An overuse of antiviral drugs may end up selecting drug resistant strains (for example, a flu strain that carries a neuraminadase enzyme that the inhibitor drugs cannot block). I'm not saying that antiviral drugs should not be used. Some life-threatening situations require the use of such drugs (for example, in the case of patients with immunodepression). Other non life-threatening situations don't (plain and simple). Second: the US Food and Drug Administration recommends the use of antiviral drugs and in fact, last December they expanded the recommendation to children under one year of age (source). However, if you keep browsing the FDA website you find this very interesting Q&A page, where they report some supposed (though worrisome) adverse side effects:"In the safety review mandated by the BPCA, a number of adverse event reports were identified associated with the use of Tamiflu in children 16 years of age or younger. These adverse event reports were primarily related to unusual neurologic or psychiatric events such as delirium, hallucinations, confusion, abnormal behavior, convulsions, and encephalitis. These events were reported almost entirely in children from Japan who received Tamiflu according to Japanese treatment guidelines (very similar but not identical to U.S. treatment guidelines). The review identified a total of 12 deaths in pediatric patients since Tamiflu's approval. All of the pediatric deaths were reported in Japanese children. In many of these cases, a relationship to Tamiflu was difficult to assess because of the use of other medications, presence of other medical conditions, and/or lack of adequate detail in the reports."There is no direct evidence that the deaths were linked to the use of the drug. In fact, often it's high risk children that need to take the drug, which means they are likely to have other conditions and take additional medications. If we can't be certain of what one drug alone can do, imagine multiple ones combined. You can read more about the Japan reports here. I also found a reference [4]. Bottom line: drugs are wonderful things. They save lives. Drugs can also mess up with our body chemistry in ways that we don't always understand. The key point is to read, be informed, and use sparingly (as needed, not just as recommended). NOTE: I strive to make these commentaries as objective as possible. If you feel I've missed some part of the story or you have more references to add to make a rounder point, please let me know in the comments. [1] Jefferson, T., Jones, M., Doshi, P., & Del Mar, C. (2009). Neuraminidase inhibitors for preventing and treating influenza in healthy adults: systematic review and meta-analysis BMJ, 339 (dec07 2) DOI: 10.1136/bmj.b5106[2] Kay Wang, Matthew Shun-Shin, Peter Gill, Rafael Perera, Anthony Harnden (2012). Neuraminidase inhibitors for preventing and treating influenza in children (published trials only) The Cochrane Library DOI: ... Read more »
Jefferson, T., Jones, M., Doshi, P., & Del Mar, C. (2009) Neuraminidase inhibitors for preventing and treating influenza in healthy adults: systematic review and meta-analysis. BMJ, 339(dec07 2). DOI: 10.1136/bmj.b5106
Kay Wang, Matthew Shun-Shin, Peter Gill, Rafael Perera, Anthony Harnden. (2012) Neuraminidase inhibitors for preventing and treating influenza in children (published trials only). The Cochrane Library. DOI: 10.1002/14651858.CD002744.pub4
Tom Jefferson, Mark A Jones, Peter Doshi, Chris B Del Mar, Carl J Heneghan, Rokuro Hama, Matthew J Thompson. (2012) Neuraminidase inhibitors for preventing and treating influenza in healthy adults and children. The Cochrane Library. DOI: 10.1002/14651858.CD008965.pub3
Urushihara, H., Doi, Y., Arai, M., Matsunaga, T., Fujii, Y., Iino, N., Kawamura, T., & Kawakami, K. (2011) Oseltamivir Prescription and Regulatory Actions Vis-à-Vis Abnormal Behavior Risk in Japan: Drug Utilization Study Using a Nationwide Pharmacy Database. PLoS ONE, 6(12). DOI: 10.1371/journal.pone.0028483
- December 10, 2012
- 09:30 AM
- 187 views
Whole genome harvesting
You think the human genome, with its three billion base pairs and 23 chromosome pairs, is too complex to unravel? Turns out, the wheat genome is six times as big and it's hexaploid, in other words, instead of chromosome pairs it's organized in chromosome sextets! I've recently discussed genetically modified organisms, crops in particular, and while I still can't provide a definite answer on whether they are absolutely good or absolutely bad, one thing struck me as relevant as I was researching the topic: between climate changes and an exponentially growing population, we are making drastic changes to our planet and resources. While Mother Nature is usually able to buffer changes and constantly adapt to new environments, the changes human kind is bringing upon the planet are happening at such a fast rate that natural adaptation is unable to keep up.I think at some point we will have to face a hard choice: either starve or give in to GMOs, where by GMOs I mean crops that are bioengineered to yield more in harsher conditions. Again, I'm not saying we should all embrace GMOs as they are healthy and good for us. I really don't know. What I'm saying is that we may not have a choice: in 2009 the FAO estimated that in order to meet the ever-growing demand, wheat production has to increase by 60% by 2050. In the 20th century, the Green Revolution met the increase in demand with the technology known at the time. Today, given the FAO estimate, we may face the need of a second Green Revolution. With this in mind, you understand the importance of sequencing the wheat genome, a task that is complicated by the complexity of the genome itself. Its three sets of chromosome pairs originated first from the hybridization of two diploid wild grasses, which originated tetraploid wheats (two sets of chromosome pairs) like durum wheat. After thousand years of domestications, these underwent a further hybridization, yielding the hexaploid wheats commonly used today to make bread. Domestication led to a bottleneck in genome variety, nonetheless, the wheat genome has a high percentage of repeats (roughly 80%, mostly retroelements) that yield great variation in length and gene order, making it difficult to sequence.Despite these obstacles, two papers [1,2] in the latest issue of Nature report using both whole-genome 454 sequencing and shotgun sequencing to assemble the genome of bread wheat and barley. Both sequencing methods have the shortcoming of being applicable to very short regions, and therefore additional work is required to reassemble the full genome out of the various short sequences. Interestingly, the wheat genome appears to implement a lot of the variation mechanisms I've been extensively discussing here on the blog:"Several classes of plant DNA transposons and retroelements create and amplify gene fragments, disrupt genes and create pseudogenes, which can influence gene expression through epigenetic mechanisms [1]."Similarly, in barley:"Abundant alternative splicing, premature termination codons and novel transcriptionally active regions suggest that post-transcriptional processing forms an important regulatory layer. Survey sequences from diverse accessions reveal a landscape of extensive single-nucleotide variation [2]."Brenchley et al. [1] conclude:"Major efforts are underway to improve wheat productivity by increasing genetic diversity in breeding materials and through genetic analysis of traits43. The genomic resources that we have developed promise to accelerate progress by facilitating the identification of useful variation in genes of wheat landraces and progenitor species, and by providing genomic landmarks to guide progeny selection. Analysis of complex polygenic traits such as yield and nutrient use efficiency will also be accelerated, contributing to sustainable increases in wheat crop production [1]."[1] Brenchley, R., Spannagl, M., Pfeifer, M., Barker, G., D’Amore, R., Allen, A., McKenzie, N., Kramer, M., Kerhornou, A., Bolser, D., Kay, S., Waite, D., Trick, M., Bancroft, I., Gu, Y., Huo, N., Luo, M., Sehgal, S., et al. (2012). Analysis of the bread wheat genome using whole-genome shotgun sequencing Nature, 491 (7426), 705-710 DOI: 10.1038/nature11650[2] ... Read more »
Brenchley, R., Spannagl, M., Pfeifer, M., Barker, G., D’Amore, R., Allen, A., McKenzie, N., Kramer, M., Kerhornou, A., Bolser, D.... (2012) Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature, 491(7426), 705-710. DOI: 10.1038/nature11650
Mayer, K., Waugh, R., Langridge, P., Close, T., Wise, R., Graner, A., Matsumoto, T., Sato, K., Schulman, A., Muehlbauer, G.... (2012) A physical, genetic and functional sequence assembly of the barley genome. Nature. DOI: 10.1038/nature11543
- December 7, 2012
- 09:30 AM
- 258 views
The simulated brain
His name is Spaun, which stands for Semantic Pointer Architecture Unified Network, and he's a brain -- a simulated, brain. His 2.5 million neurons, organized in subsystems that simulate different brain areas, allow Spaun to perform tasks such as image recognition and recalling sequences, and respond through a motor arm. For example, Spaun can recognize numbers on a screen and write them on a piece of paper. Spaun is the brain child (pun intended!) of authors Eliasmith et al. [1]. It models three specific brain areas: the prefrontal cortex for memory, the basal ganglia to select actions, and the thalamus. Spaun's functional architecture consists of a working memory that, given a visual input, compresses the information and translates the input into firing patterns. The next step is the action selection step, which results in a motor output through the robotic arm. Spaun's memory doesn't just store information, but it also correlates new information with the old one. A nice feature of the model is that different neuron parameters can be chosen from random distributions in order to simulate different population behaviors. This simulates the human brain so well that Spaun expresses a common human behavior: the tendency to remember best the first and last items in a list. On the other hand, Spaun exhibits noteworthy deviations from human brains: while it can get better and better at a particular task, it cannot learn a completely new task. Another shortcoming is that Spaun's attention and eye position are fixed, so that, contrary to a real human brain, it cannot control the input. As the authors explain:"Anatomically, many areas of the brain are missing from the model. Those that are included have too few neurons and perform only a subset of functions found in their respective areas. Physiologically, the variability of spiking in the model is not always reflective of the variability observed in real brains. However, we believe that, as available computa- tional power increases, many of these limitations can be overcome via the same methods as those used to construct Spaun."[1] Eliasmith, C., Stewart, T., Choo, X., Bekolay, T., DeWolf, T., Tang, Y., & Rasmussen, D. (2012). A Large-Scale Model of the Functioning Brain Science, 338 (6111), 1202-1205 DOI: 10.1126/science.1225266... Read more »
Eliasmith, C., Stewart, T., Choo, X., Bekolay, T., DeWolf, T., Tang, Y., & Rasmussen, D. (2012) A Large-Scale Model of the Functioning Brain. Science, 338(6111), 1202-1205. DOI: 10.1126/science.1225266
- November 19, 2012
- 09:33 AM
- 273 views
Proteins as gene carriers
By now you probably know everything about pluripotent stem cells, right? They are the hot topic in genetics right now, to the point that the fear of being scooped has pushed some people to lie about their results. Pluripotent stem cells are cells that have the ability to divide into a specialized cell and another undifferentiated cell. This of course is greatly useful in repairing damaged organs and/or regenerating tissue, and has great potential in medicine.Lately there has been a lot of buzz on the notion that pluripotency could be re-induced in already differentiated cells. Studies have shown that four reprogramming factors can indeed reprogram fibroblast cells into pluripotent stem cells when over-expressed. But how to over-express these factors? The typical route is to transfect the genes into the cells by means of a viral vector. Basically, the genes are delivered into the cell using a retrovirus. Though effective, this poses the question of side effects: whenever you introduce foreign DNA into a cell you have the potential to silence secondary genes or disrupt the usual gene regulation. Unanticipated epigenetic changes in the cell can occur. A recent study [1] shows a safer alternative: cell-permeant proteins, or CPPs. These are small proteins that can cross the cell membrane and carry peptides inside the cell in a process called "protein transduction," thus offering a valid alternative to viral vectors. By comparing the two methods (CPPs and viral delivery) on human fibroblast cells, Lee et al. noticed that gene expression was achieved much faster when using the viral vector. Puzzled by this difference, they wondered what was so special about the viral route that made the gene delivery so much more efficient. There had to be something in the viral vector that aided the delivery of the genes. Lee et al. hypothesized that this could be linked to the fact that the viral vector somehow activated an inflammatory pathway in the cells which in turn aided the delivery of the genes. So the next question was: can we enrich the CPPs so they too activate the inflammatory pathway? Indeed they could! They used TLR3 agonists, molecules that activate the TLR3, or Toll-like receptor 3, a receptor that recognizes double-stranded RNA generated by retroviruses and thus activates inflammatory pathways. Once combined with the TLR3 antagonists, over-expression of the reprogramming factors was achieved faster through CPPs than it was with the viral vectors, validating the hypothesis that the gene delivery has to be achieved via the activation of the immune pathway. In fact, the contrary was also true: when TLR3 was knocked down (biology jargon to say that the gene was silenced), the viral vector was also inefficient in delivering the genes. "TLR3 activation enables epigenetic alterations, including changes in methylation status of the Oct4 and Sox2 promoters as well as changes in the expression of epigenetic effectors, that promote an open chromatin configuration. The knowledge that the activation of innate immune response affects nuclear reprogramming permitted us to enhance the efficiency and yield of human induce pluripotent stem cells by using reprogramming factors in the form of CPPs."Lee et al. conclude:"Our observations highlight a previously unrecognized role for innate immunity activation in nuclear reprogramming. The viral vectors constructs used to induce pluripotency are more than mere vehicles for the reprogramming factors. Innate immune activation causes striking changes in epigenetic modifiers that favor an open chromatin configuration. These changes enable a fluidity of cell phenotype that contributes to successful nuclear reprogramming."[1] Lee, J., Sayed, N., Hunter, A., Au, K., Wong, W., Mocarski, E., Pera, R., Yakubov, E., & Cooke, J. (2012). Activation of Innate Immunity Is Required for Efficient Nuclear Reprogramming Cell, 151 (3), 547-558 DOI: 10.1016/j.cell.2012.09.034... Read more »
Lee, J., Sayed, N., Hunter, A., Au, K., Wong, W., Mocarski, E., Pera, R., Yakubov, E., & Cooke, J. (2012) Activation of Innate Immunity Is Required for Efficient Nuclear Reprogramming. Cell, 151(3), 547-558. DOI: 10.1016/j.cell.2012.09.034
- October 29, 2012
- 07:26 PM
- 283 views
GMOs love me, GMOs love me not..
I've been asked to discuss genetically modified foods and I confess I've been procrastinating. Why? Because I don't have an answer on whether or not GMOs are good or bad, and I can't offer one. But, what I can do is offer a few thoughts. Food for thought is usually super-natural, organic, and pesticide-free, so here it goes. :-)1. What are GMOs? Technically, all domesticated plants and animals are "genetically modified" since, rather than letting the species evolve through natural selection, mankind has steadily selected offsprings according to some man-made criteria. However, today's technology allows us to artificially modify an organism's genome. The difference between the two is not just in time scale: when selecting crops, or, more in general, any organism, generation after generation based on phenotype, uncharacterized genes are introduced in the species. Genetically engineering, or bioengineering, however, introduces a few well-characterized genes (often from a different species) into the organism. In a way, this is no news: gene therapy creates genetically modified organisms. Humanized mice are created in labs to test drugs and other therapies. The question of whether or not GMOs are good arises in the food industry. Are they safe to eat?2. The Cartagena Protocol on BiosafetyAs California gets ready to cast its vote on Proposition 37 [1] (which would require foods to denote their GMO content on the labels), it is good to review what currently is in act to "protect" us from possible hazards. From Wikipedia:"The Cartagena Protocol on Biosafety is an international agreement on biosafety, as a supplement to the Convention on Biological Diversity. The Biosafety Protocol seeks to protect biological diversity from the potential risks posed by genetically modified organisms resulting from modern biotechnology.""The Biosafety Protocol makes clear that products from new technologies must be based on the precautionary principle and allow developing nations to balance public health against economic benefits. It will for example let countries ban imports of a genetically modified organisms if they feel there is not enough scientific evidence that the product is safe and requires exporters to label shipments containing genetically altered commodities such as corn or cotton." 3. Why are foods genetically modified?For a number of reasons, some good and some not so good. Some are just practical reasons in a world that, whether we like it or not, is getting more and more "globalized": the first bioengineered produce was a tomato designed to have a prolonged shelf life. Some crops are genetically modified to resist to harsher herbicides and pesticides. Others, are genetically modified to desist bugs from eating them. For example, genes producing Bt toxins have been introduced in cotton and corn. These toxins kill caterpillars that would otherwise eat up the whole crop. Notably, the modification benefits not only the genetically modified crops, but, since it reduces the global population of harmful caterpillars, it also benefits the non-modified crops. I expect foods that can resist to herbicides to be soaked in chemicals. On the other hand, if a crop is genetically modified so its flowers/fruits/seeds no longer offer a viable environment to certain parasites, I expect those foods to be pesticide-free. Yes, I'll take a few modified genes over harmful chemicals. Bottom line: NOTING WHETHER OR NOT A CERTAIN FOOD CONTAINS GMOs DOES NOT HELP. What you should really demand in a label is WHY SUCH FOOD WAS MODIFIED AND WHAT WAS ACHIEVED THROUGH THE BIOENGINEERING. Notice that while the Food and Drug administration currently does not impose any GMO labeling, their guideline recommendations state that the GMO content be noted, as well as the reason why the food was modified, and what was achieved through the modification. 4. Genetic homogeneity is badRice is one of the most consumed crops in the world. Again, from Wikipedia:"As of 2009 world food consumption of rice was 531,639 thousands metric tons of paddy equivalent (354,603 of milled equivalent), while the far largest consumers were China consuming 156,312 thousands metric tons of paddy equivalent (29.4% of the world consumption) and India consuming 123,508 thousands metric tons of paddy equivalent (23.3% of the world consumption). Between 1961 and 2002, per capita consumption of rice increased by 40%."Rice is also highly "domesticated", as it has been selected over thousands of years to fit human needs. Currently, there are 20 different kinds of rice, but, according to FAO, the Food and Agriculture Organization, "It is estimated that not even 15 percent of the potential diversity has been utilized." This is a THREAT to food security. If a pesticide-resistant parasite were to attack rice crops, it'd be lethal to the vast majority of rice varieties currently harvested. Heavy use of pesticides favors the selection of pesticide-resistant organisms, while domestication favors genetic homogeneity in crops. This is NOT a good combination. Another reason why, between GMOs and pesticides, I'd favor GMOs. And if GMO research can prevent a pesticide-resistant organism to wipe out 50% of the world-wide food, hey, who's to complain? 5. Knowledge is NOT power if that knowledge is poorly understoodWe live in a strange era when technology leaps forward at a higher speed than our ability to comprehend its output, especially in the field of genetics. We have loads of data we don't quite know how to store, let alone analyze. It's getting cheaper and cheaper to have a full human genome typed and companies are advocating that we do it for every individual. But are we capable of understanding the data? Last week I posted a shocking story of a boy discriminated because he carries a recessive mutation for a disease he doesn't have and he's at no risk of contracting (that's what recessive means). The Internet is full of bogus info on genes, genetics, mutations, etc. There's more noise than ever, giving people the illusion that they know when in fact they don't. I fear that the same will happen for GMOs. Once those labels come out, will people be able to understand what they mean? If Prop 37 will only require a "content" statement without a "reason", for example, will the information be really useful or will it just generate a stigma? You now see why I cannot tell you whether GMOs are good or bad. They can be both! (Aren't we all?)Food always has a higher impact than other things, but if you think about it, there are so many things that we've introduced in our daily lives in the past few decades that we simply don't know whether or not they are good IN THE LONG RUN: wi-fi, for example. Cell phones. Chemicals in skin products, from sun protection to cosmetics. I'm afraid the next generation will be the test. So the real question is: do we want to experiment with our children as guinea pigs? Sadly, when you put it in these terms, it seems to me it's too late to go back. The experiment has already begun. If these few thoughts weren't depressing enough, read Pamela Ronald's review, referenced below [2]. One of the great points Ronald makes is that we are changing our climate and environment much faster than ever before (thanks to climate change and an exponentially growing population). Natural selection can't keep up with the pace, hence"an important goal for genetic improvement of agricultural crops is to adapt our existing food crops to increasing temperatures, decreased water availability in some places and flooding in others, rising salinity, and changing pathogen and insect threats."The review is clearly biased in favor of GMOs and it lists several benefits from such procedures. While advocating for adequate testing on every newly modified organisms, it also reports that all genetically modified crops tested so far have been deemed safe and substantially no different than conventionally selected crops "in terms of unintended consequences to human health and the environment." Bottom line: I can't tell you what to vote on Prop 37 and I can't tell you whether or not you should avoid GMOs. Just read as much as you can and be sure to form your own opinion.REFERENCES:[1] ... Read more »
Baker, M. (2012) Companies set to fight food-label plan. Nature, 488(7412), 443-443. DOI: 10.1038/488443a
Ronald, P. (2011) Plant Genetics, Sustainable Agriculture and Global Food Security. Genetics, 188(1), 11-20. DOI: 10.1534/genetics.111.128553
- October 22, 2012
- 09:30 AM
- 315 views
Lorenzo's oil got upgraded to stem cell research
Have you seen the 1992 movie Lorenzo's oil? The film portrays the true (and sad!) story of Lorenzo Odone, who, at age 6, was diagnosed with adrenoleukodystrophy, one of the most common forms of leukodystrophies, a family of degenerative diseases that affects the growth of the myelin sheath. Myelin wraps around nerve fibers creating a fatty covering that increases the speed at which impulses propagate. Leukodystrophy is a genetic disorder caused by mutations in the genes that code myelin proteins. When myelin is defective, or not produced in sufficient quantities, it starts degrading, causing the progressive loss of signaling along the nerve. Eventually, the nerve dies. As portrait in the movie Lorenzo's oil, Lorenzo's parents refused to accept the common prognosis they were given at the time for their son (progressive paralysis and death within 2-3 years). Their determination led them to discover an oil mix able to alleviate the symptoms of the disease. Two papers published in Science Translational Medicine now show that stem cell therapy can partially regenerate neurological function. Uchida et al. [1] show that stem cell transplantation is effective in the regeneration of the myelin sheath in mouse models. The researchers transplanted human central nervous system stem cells (HuCNS-SCs) into the brains of mice with defective myelination in the central nervous system. The transplanted stem cells generated functional myelin in the mice's central nervous system In the same issue, Gupta et al. [2] describe how they transplanted the same cells (HuCNS-SCs) into the frontal lobe of four young boys that were affected by Pelizaeus‚ÄìMerzbacher disease (PMD), a form of leukodystrophy. The transplant was followed by a 9-month regimen of immunosuppression to minimize the chances of rejection. One year after the transplant, magnetic resonance imaging (MRI) showed that the transplanted cells had engrafted and successfully myelinated brain cells. The researchers conclude that "modest gains in neurological function were observed in three of the four subjects. No clinical or radiological adverse effects were directly attributed to the donor cells." Sadly, Lorenzo died in 2008, one day after his thirtieth birthday. His story, though, was and still is an inspiration to many. [1] Uchida, N., Chen, K., Dohse, M., Hansen, K., Dean, J., Buser, J., Riddle, A., Beardsley, D., Wan, Y., Gong, X., Nguyen, T., Cummings, B., Anderson, A., Tamaki, S., Tsukamoto, A., Weissman, I., Matsumoto, S., Sherman, L., Kroenke, C., & Back, S. (2012). Human Neural Stem Cells Induce Functional Myelination in Mice with Severe Dysmyelination Science Translational Medicine, 4 (155), 155-155 DOI: 10.1126/scitranslmed.3004371[2] Gupta, N., Henry, R., Strober, J., Kang, S., Lim, D., Bucci, M., Caverzasi, E., Gaetano, L., Mandelli, M., Ryan, T., Perry, R., Farrell, J., Jeremy, R., Ulman, M., Huhn, S., Barkovich, A., & Rowitch, D. (2012). Neural Stem Cell Engraftment and Myelination in the Human Brain Science Translational Medicine, 4 (155), 155-155 DOI: 10.1126/scitranslmed.3004373... Read more »
Uchida, N., Chen, K., Dohse, M., Hansen, K., Dean, J., Buser, J., Riddle, A., Beardsley, D., Wan, Y., Gong, X.... (2012) Human Neural Stem Cells Induce Functional Myelination in Mice with Severe Dysmyelination. Science Translational Medicine, 4(155), 155-155. DOI: 10.1126/scitranslmed.3004371
Gupta, N., Henry, R., Strober, J., Kang, S., Lim, D., Bucci, M., Caverzasi, E., Gaetano, L., Mandelli, M., Ryan, T.... (2012) Neural Stem Cell Engraftment and Myelination in the Human Brain. Science Translational Medicine, 4(155), 155-155. DOI: 10.1126/scitranslmed.3004373
- October 19, 2012
- 07:45 PM
- 365 views
Why extra fat is bad, even when it's in the "right" spots.
Have you been thinking of going on a diet but haven't found the right motivation yet? How about this one: fat feeds tumor cells and enhances their growth. And another question, for the ladies this time: have you ever wondered how those annoying love handles would look so much better inside a bra? No, I don't mean to put a bra around my waist, rather to move that bit of fat up to my chest . . . Somehow the two things are related. Stay with me and I'll explain.Numerous studies have shown that obesity not only increases cancer risk, but it's also linked to accelerated progression in numerous types of cancers. A group of researchers from the University of Texas Health Science Center at Houston investigated the reason for such poorer prognosis in obese patients. In a paper published in Cancer Research [1], Zhang et al. show that white adipose tissue (WAT) facilitates tumor growth in mice, and the association was independent of the mice's diet. To show this, instead of overfeeding the mouse to make it grow the fat tissue, they transplanted into the animals adipose stromal cells (ACS) -- cells that can be thought of as the "progenitors" of adipose cells. The transplanted cells increased the proliferation of white adipose tissue. Furthermore, once recruited into tumors, they increased tumor vascularization.Tumors are basically an uncontrolled growth of cells. It takes a lot of resources to keep cells growing, and new blood vessels are created to "feed" the growth. Zhang et al. showed that the transplanted adipose cells were mobilized in the mouse model and promoted the creation of new blood vessels, thus effectively "feeding" the tumor and promoting its progression. Yuck, right? "Our results indicate that obesity can accelerate tumor growth irrespective of concurrent diet. [. . .] Our data indicate that ASCs recruited by tumors become perivascular or differentiate into intratumoral adipocytes [1]."Why did I mention love handles and bras? Because Yoshimura et al. published a paper [2] in 2008 in which they do to humans what Zhang et al. did to mice. For a good reason, of course: in [2] Yoshimura et al. illustrate a new technique called cell-assisted lipotransfer in which they use the aforementioned ACS, the adipose progenitors, to perform cosmetic breast augmentation. Seems like a brilliant idea: no implants needed, no lipoinjection (which carries a high risk of necrosis), just isolate the fat cells, let them grow, then transfer them back. No scars, no complications. "Final breast volume showed augmentation by 100 to 200 ml after a mean fat amount of 270 ml was injected. Postoperative atrophy of injected fat was minimal and did not change substantially after 2 months. Cyst formation or microcalcification was detected in four patients. Almost all the patients were satisfied with the soft and natural-appearing augmentation [2]."But now you see why this could present a potential problem: many breast cancer patients seek tissue regeneration after a mastectomy, and while Yoshimura's technique seems innovative and promising, Zhang et al. warn against its possible risks as the fat transfer could potentially feed remaining cancer cells and yield devastating results. And the moral of the story is: go on a diet, get rid of the love handles, and be happy with a smaller size bra. ;-)[1] Zhang, Y., Daquinag, A., Amaya-Manzanares, F., Sirin, O., Tseng, C., & Kolonin, M. (2012). Stromal Progenitor Cells from Endogenous Adipose Tissue Contribute to Pericytes and Adipocytes That Populate the Tumor Microenvironment Cancer Research, 72 (20), 5198-5208 DOI: 10.1158/0008-5472.CAN-12-0294[2] Yoshimura, K., Sato, K., Aoi, N., Kurita, M., Hirohi, T., & Harii, K. (2007). Cell-Assisted Lipotransfer for Cosmetic Breast Augmentation: Supportive Use of Adipose-Derived Stem/Stromal Cells Aesthetic Plastic Surgery, 32 (1), 48-55 DOI: 10.1007/s00266-007-9019-4... Read more »
Zhang, Y., Daquinag, A., Amaya-Manzanares, F., Sirin, O., Tseng, C., & Kolonin, M. (2012) Stromal Progenitor Cells from Endogenous Adipose Tissue Contribute to Pericytes and Adipocytes That Populate the Tumor Microenvironment. Cancer Research, 72(20), 5198-5208. DOI: 10.1158/0008-5472.CAN-12-0294
Yoshimura, K., Sato, K., Aoi, N., Kurita, M., Hirohi, T., & Harii, K. (2007) Cell-Assisted Lipotransfer for Cosmetic Breast Augmentation: Supportive Use of Adipose-Derived Stem/Stromal Cells. Aesthetic Plastic Surgery, 32(1), 48-55. DOI: 10.1007/s00266-007-9019-4
- October 16, 2012
- 11:21 AM
- 301 views
Reprogrammable cells
Can't remember if I already shared the above picture... it's my favorite sunset shot so far, so forgive me if it's a deja vu.The Nobel Prize in medicine this year was awarded to John Gurdon and Shinya Yamanaka for pioneering the reprogramming of cells into an embryonic-like state. Embryonic stem cells are cells that undergo asymmetric division, as they divide into an undifferentiated cell and into a specialized cell. This way, they can grow indefinitely while maintaining their undifferentiated state and, at the same time, keep the ability to differentiate into all three germ layers, the cells formed during embryogenesis. When still a PhD student, in 1958, Gurdon cloned a frog using the nucleus of a cell taken from the intestine of a tadpole. It took another 38 years before the first mammal was cloned: the first cloned sheep, Dolly, was born in 1996 from an unfertilized egg whose nucleus had been replaced with the nucleus of an adult cell. In this case, the adult cell, by being placed into the egg, was effectively "reprogrammed" into an embryonic stem cell. Up until Gurdon's work was published in 1962, general belief was that once cells specialized, they could not revert. The discovery that cells can actually undergo "reprogramming" under special circumstances is quite significant because it gives hope that we can achieve tissue regeneration and treat degenerative diseases or spinal cord injuries. In 2006 Yamanaka and his colleague Kazutoshi Takahashi published a paper in Cell [1] in which they showed that, activating four genes, they were able to reprogram adult fibroblasts from mouse embryonic cells. They called the new cells induced pluripotent cells, or iPS, and found that they expressed embryonic-state cell markers. In fact, once in the proper environment, they contributed to embryonic development. Yamanaka is a strong believer that this research will eventually lead to successful regeneration therapies. In fact, he plans to start a bank of induced pluripotent stem cells obtained from 75 different cell lines. Is this the beginning of a new era? A word of caution comes from a paper published in PNAS at the end of 2010 [2]: in this paper, Serwold and colleagues derived mice from reprogrammed T-cells (cells from the immune system) and showed that roughly half of the mice generated this way spontaneously developed T-cell lymphomas.The mice were generated by transferring T-cell nuclei into enucleate oocytes. As they mature, T-cells undergo genomic rearrangements, and while normally these rearrangements occur in T-cells only during a specific stage of their development, such rearrangements were observed in all somatic cells in the cloned mice. In [2] Serwold et al. show that these rearrangements undergo T-cell lymphomagenesis: in other words, they cause cancer. Though T-cells are not the only cells that currently can be reprogrammed, this study clearly shows that different cell lines can yield different outcomes, some quite deleterious."This study suggests that precautions should be taken to ensure that the identity of the reprogrammed cell of origin is known, and that T cells, and probably also B cells, are not inadvertently turned into therapeutic iPS cells. Recent studies have used human blood-derived T cells as sources of iPS cells, and these cells promise to be valuable tools for studying human immune development and disease; however, the results presented here indicate that extra caution is warranted regarding the therapeutic use of such T cell-derived iPS cells [2]."[1] Takahashi, K., & Yamanaka, S. (2006). Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors Cell, 126 (4), 663-676 DOI: 10.1016/j.cell.2006.07.024[2] Serwold, T., Hochedlinger, K., Swindle, J., Hedgpeth, J., Jaenisch, R., & Weissman, I. (2010). T-cell receptor-driven lymphomagenesis in mice derived from a reprogrammed T cell Proceedings of the National Academy of Sciences, 107 (44), 18939-18943 DOI: 10.1073/pnas.1013230107... Read more »
Takahashi, K., & Yamanaka, S. (2006) Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors. Cell, 126(4), 663-676. DOI: 10.1016/j.cell.2006.07.024
Serwold, T., Hochedlinger, K., Swindle, J., Hedgpeth, J., Jaenisch, R., & Weissman, I. (2010) T-cell receptor-driven lymphomagenesis in mice derived from a reprogrammed T cell. Proceedings of the National Academy of Sciences, 107(44), 18939-18943. DOI: 10.1073/pnas.1013230107
- October 11, 2012
- 09:41 AM
- 359 views
Gene therapy goes... topical
The paper I'm discussing today is so cool, I don't know how I missed it when it came out last July. As the name implies, gene therapy is a technique used to "fix" defective genes either by replacing them with fully functional ones or by silencing them with the use of antisense RNA. Defective genes either fail to produce the proteins they code for, or produce defective proteins, thus causing genetic disorders. A defective gene can be silenced (so that it will no longer produce the defective protein) using antisense RNA. The antisense RNA binds to the mRNA from the defective gene, thus preventing it to be translated into the protein. Small interfering RNAs, or siRNAs, are short double-stranded RNAs that can successfully deliver antisense RNA to the target genes and effectively suppress gene expression. There are several ways to deliver either DNA or RNA, each with advantages as well as disadvantages. Viral vectors (genetically modified viruses that instead of carrying viral DNA they carry the therapeutic DNA or RNA to be delivered inside the cell) are great ways to deliver genes, but have to overcome the barrier imposed by the host's immune system. Furthermore, some vectors may have toxic side effects. Other delivery means include conjugate agents, i.e. particles such as lipids, polymers, or nanoparticles that bind to the RNA and have high penetrability. Though such therapies have been quite promising, they pose a challenge: they can be toxic when delivered intravenously or orally, while the topical route is inefficient because the skin won't let through anything greater than a few daltons.That's too bad, though, because the skin would be the less invasive and easiest way to deliver therapy. Just imagine it: applying genes in the morning just like a daily moisturizer! :-)In [1] Zheng et al. show that by conjugating siRNAs with inorganic gold nanoparticles, they can defeat the epidermic barrier and successfully reduce the expression of the target genes. "Recently, we introduced spherical nucleic acid nanoparticle conjugates (SNA-NCs, inorganic gold nanoparticles densely coated with highly oriented oligonucleotides) as agents capable of simultaneous transfection and gene regulation. [. . .] SNA-NCs enter almost 100% of cells in more than 50 cell lines and primary cells tested to date, as well as cultured tissues and whole organs."The researchers measured uptake, safety, and gene suppression efficacy of SNA-NCs in human keratinocytes, a cell line that constitutes 95% of the epidermis. They found no morphological difference between treated skin cells and controls. Furthermore, they studied the ability of SNA-NCs to aid the silencing of EGFR, or epidermal growth factor receptor, a cell-surface receptor that has been shown to be mutated and up-regulated in several types of cancers, including lung, anus, and 30% of skin cancers. After 3 weeks of treatment, EGFR expression was suppressed by 65% in hairless mice. Human skin is known to be thicker and more difficult to penetrate, so the treatment was also tested on 3D raft cultures that simulate in vivo human epidermis. EGFR mRNA expression was lowered by 52% and EGFR protein expression by 72%. Zheng et al. conclude:"Our data from blood serum and mouse skin show that siRNAs, when densely conjugated to the nanoparticles in the form of SNA-NCs, are minimally stimulatory and have far fewer off-target effects than the free siRNAs of the same sequence introduced by traditional methods. Furthermore, our studies show rapid clearance from skin, minimal accumulation in viscera, and no evidence of histological changes in internal organs after topical delivery. The low immunogenicity and few off-target effects, coupled with low toxicity and high efficacy, point to a significant advantage for using SNA-NC technology to introduce siRNAs."Dan Zheng, David A. Giljohann, David L. Chen, Matthew D. Massich, Xiao-Qi Wang, Hristo Iordanov, Chad A. Mirkina, & Amy S. Paller (2012). Topical delivery of siRNA-based spherical nucleic acid nanoparticle conjugates for gene regulation PNAS DOI: 10.1073/pnas.1118425109... Read more »
Dan Zheng, David A. Giljohann, David L. Chen, Matthew D. Massich, Xiao-Qi Wang, Hristo Iordanov, Chad A. Mirkina, & Amy S. Paller. (2012) Topical delivery of siRNA-based spherical nucleic acid nanoparticle conjugates for gene regulation. PNAS. DOI: 10.1073/pnas.1118425109
- October 4, 2012
- 09:55 AM
- 296 views
Limb regeneration: a lesson from salamanders
As much as we would love to enlist limb regeneration among modern science's best accomplishments, so far it is still very much confined to science fiction. That doesn't mean it won't happen, though. Key to limb regeneration is cellular reprogramming that allows differentiated cells to return to a germline-like (undifferentiated) state. Genes involved in embryonic development need to be reactivated in order to restart the same process that created the limb during the growth of the embryo. The vertebrates with the best ability to regenerate limbs are salamanders, making these little critters the most studied in the field. When a salamander loses a limb, a layer of epidermis grows to cover the wound, and beneath this layer new, undifferentiated cells start proliferating, forming a mass called blastema. Recent research shows that this first wave of cell dedifferentiation may recapitulate events occurring during embryogenesis. "The cells in the limb blastema are believed to be a heterogeneous collection of dedifferentiated cells that have been reprogrammed to achieve varying levels of developmental potential exhibited by the cells involved in embryogenesis [1]."Germline stem cells are cells that give rise to gametes (the reproductive cells) and have the ability to divide into another stem cell as wells as a more differentiated cell. This mechanism, called asymmetric division, is controlled by a protein called PIWI through small, non-coding RNAs called piRNAs. In [1] Zhu et al. showed that when salamanders regenerate a limb, a germline-like state is established in the growing tissue. In particular, they found that germline-specific genes were expressed in the regenerated limb. In order to show this, they looked specifically at the PIWI proteins. Zhu and colleagues found that a significant amount of upregulated transposable elements in the regenerated limbs. If you remember, transposable elements is an unstable DNA element because it can move from one locus to another within the genome of the same cell. During the limb regeneration process, transposable elements can impart a deleterious amount of instability, which is counteracted by a corresponding upregulation of the PIWI genes. Conversely, when the PIWI genes were knocked down in the blastema, limb growth following the amputation was significantly reduced compared to controls. Zhu et al. conclude"In the future, further characterization of the subpopulations of these reprogrammed cells with additional germline-specific markers might provide more insight into exactly how far cellular dedifferentiation can proceed and whether there are indeed a small number of cells that could be isolated before a certain developmental threshold and exhibit true pluripotency when isolated from the influence of the partially programmed blastemal cells in the proximity."[1] Wei Zhu, Gerald M. Pao, Akira Satoh, Gillian Cummings, James R. Monaghan, Timothy T. Harkins, Susan V. Bryant, S. Randal Voss, David M. Gardiner, & Tony Hunter (2012). Activation of germline-specific genes is required for limb regeneration in the Mexican axolotl Developmental Biology DOI: 10.1016/j.ydbio.2012.07.021... Read more »
Wei Zhu, Gerald M. Pao, Akira Satoh, Gillian Cummings, James R. Monaghan, Timothy T. Harkins, Susan V. Bryant, S. Randal Voss, David M. Gardiner, & Tony Hunter. (2012) Activation of germline-specific genes is required for limb regeneration in the Mexican axolotl. Developmental Biology. DOI: 10.1016/j.ydbio.2012.07.021
- October 1, 2012
- 09:30 AM
- 270 views
The sleep conundrum
How many hours of night sleep do you get? Are you ever surprised at how many more/less hours other people sleep? Well, if you are, you might find comfort knowing that the variation in number of sleep hours across species is huge and, so far, very much an evolutionary mystery. Common thought is that sleep provides us with a much necessary "recharging" and common that it has an evolutionary advantage. However, it takes time away from foraging/preying and mating, and makes individuals more vulnerable to predators. Furthermore, the huge spread of sleeping hours across species makes it harder to pin point whether it does have a selective advantage or not. A new paper published in Science [1] shows that at least in one bird species, pectoral sandpipers (Calidris melanotos), being able to sleep less confers an advantage: males compete for fertile females over a period of 3 weeks, during which they sleep very little. Lesku et al. showed that males who slept less were the ones who produced the most offsprings. The researchers' main hypothesis was that "variability in sleep duration observed across the animal kingdom reflects varying ecological demands for wakefulness, rather than different restorative requirements. According to this hypothesis, animals can evolve the ability to dispense with sleep when ecological demands favor wakefulness."Pectoral sandpipers mate with more than a female and are not involved in the raising of their offsprings. Therefore, their mating success is determined solely on how many fertile females they have access to. Furthermore, in the high Arctic, the sun never sets during mating period. Males are awake longer than females and engage in courtship behaviors, competitions with other males, and defending their territory (don't know why, high school just came to mind. . . ahem). Their total wake time was a strong predictor of how many offsprings they ended up having. A caveat the researchers put forward is that this conclusion seems to be at odds with the hypothesis that there is a genetic basis to the duration of sleeping times, as shorter durations would be selected and hence the variation in wake time would progressively lessen. Instead, still a great variation was observed across males. The bit that I found most intriguing is that at lower latitudes at some point darkness falls, and since most of courtship is based on visual displays, this limits the daily amount of time males can engage in such activities. However, the study was conducted in Alaska, where the sun never sets during mating season. I wonder if the same study on pectoral sandpipers that live at lower latitudes would have yielded the same results. I also can't help but wonder: this behavior was obviously selected by a favorable environment, in this case the fact that the sun never sets during summer days. I think it was this past summer that my dad said, "Would birds have ever learned to fly if it weren't for the wind?"[1] John A. Lesku, Niels C. Rattenborg, Mihai Valcu, Alexei L. Vyssotski, Sylvia Kuhn, Franz Kuemmeth, Wolfgang Heidrich, & Bart Kempenaers (2012). Adaptive Sleep Loss in Polygynous Pectoral Sandpipers Science DOI: 10.1126/science.1220939... Read more »
John A. Lesku, Niels C. Rattenborg, Mihai Valcu, Alexei L. Vyssotski, Sylvia Kuhn, Franz Kuemmeth, Wolfgang Heidrich, & Bart Kempenaers. (2012) Adaptive Sleep Loss in Polygynous Pectoral Sandpipers. Science. DOI: 10.1126/science.1220939
- September 27, 2012
- 09:13 AM
- 282 views
Healthy habits are easier when you stop thinking about it
Raising health awareness has done little so far in actually improving global health. Humans seem to be stubbornly attached to certain behaviors, even when fully aware that such behaviors pose a health risk. Currently, the four most prevalent noncommunicable diseases are diabetes, cardiovascular disease, lung disease, and cancer. The risk of death from any of the four can be significantly lowered by changing basic behaviors such as lowering the consumption of calories, alcohol and tobacco, while increasing physical activity and the consumption of fruits and vegetables. It sounds simple, in theory, but certain behaviors are so engrained in the society that despite widespread campaigns, we still haven't been able to change people's habits. And not surprisingly so, since much of our behavior is often automatic rather than dictated by consciousness. As Marteau et al. state in [1], not even personalized risk assessments like gene variants and other biomarkers have succeeded in dissuading people from certain behaviors. We are complex beings, constantly shifting from full awareness and reflective, goal-driven behavior, to more automated actions where deep thoughts are far removed. The former behavior is more costly in terms of metabolic resources and energy. The latter is more efficient in our daily routine, but it has the disadvantage of taking over even when the consequences are undesired. For example, lab animals that have been trained to repeat certain behaviors, they will keep repeating them even when unpleasant consequences are introduced in the experimental setting. Therefore, in order to prevent noncommunicable diseases, Marteau et al. argue that we need to target automatic behaviors rather than conscious ones. How can this be achieved?Well, for example making fruits and vegetables very easy to find at the store, and relegate the so-called junk food to some hidden, desolate aisle that requires extra walking to get to. Also (and I know I'm totally going against common economy rules here), making fruits and vegetables cheaper than junk food would cause a huge switch in people's eating habits. If this may sound much of an utopia (yeah, I can see that), here are a few more practical things that can be changed: make stairs accessible from everywhere in a building, and hide the elevators. Make the elevators really slow that it's a lot more practical to take the stairs. Make tobacco and alcohol harder to find (though I have doubts about alcohol, since I grew up in a country where alcohol is on the table every day and somehow we seem to handle alcohol addictions better than other countries with lots of rules and prohibitions). Use smaller serving portions and smaller (but taller) glasses and plates. Marteau et al. even suggest "standing desks" in classrooms to have students spend more calories (this one made me smile). Here's my two cents. As you know, I grew up in Italy, a country that very much cherishes food and spending social time at the table. I think Italians have pushed things to the far extreme, and now, when I go back to visit, after about one hour of sitting at the table "socializing" I get a little restless. Much of the overweight problems in Italy come from spending too much time at the table. After a while you don't feel hungry anymore but you just keep eating because food is being offered to you. On the other hand, I see that the United States have the exact opposite problem. There's no definite time of when to eat lunch or dinner, and when you look around you see people eating at any given time of the day. This is just my personal opinion, of course, but I truly believe that introducing fixed eating times in the day can greatly help towards healthier eating behaviors. Also, we should learn from our children. When they are full they stop eating. Parents tend to get edgy and force them to eat more, whereas maybe it should be opposite, it should be the children telling the parents to stop eating so we can all get back into the habit of eating only when we're hungry. Unfortunately, because eating is so much part of our social life and social celebrations, in real life, things tend to get more complicated.[1] Theresa M. Marteau, Gareth J. Hollands, & Paul C. Fletcher (2012). Changing Human Behavior to Prevent Disease: The Importance of Targeting Automatic Processes Science... Read more »
Theresa M. Marteau, Gareth J. Hollands, & Paul C. Fletcher. (2012) Changing Human Behavior to Prevent Disease: The Importance of Targeting Automatic Processes. Science. info:/
- September 24, 2012
- 09:48 AM
- 263 views
ENCODE sheds light on non-coding variants
Back when I started studying human genetics, we were still doing single-gene associations. Namely, we would type a bunch of variants in a single gene and then do a case-control association study to see which, if any, of those variants marked an increase in disease risk. That's how breast cancer markers such as BRCA1 and BRCA2 have been found.When the Human Genome Project was completed in 2003, scientists started looking for disease risk alleles across the whole genome. The findings were puzzling: more than 90% of the diseases-associated variants fell in non-coding regions. Why? One issue I've previously discussed is that when looking at tens of thousands of loci, you have to have huge sample sizes and often these studies are underpowered. Another possible explanation lies in epistasis, and the detected signal may be the effect of some unknown correlation.However. You knew there was going to be a "however", right? Because thanks to the ENCODE project we now know that if a genetic variant falls in a non-coding region, it doesn't mean it has no effect whatsoever. ENCODE is bound to shed new light on these numerous non-coding risk alleles that GWAS studies have found. Last time I discussed DHSs, or DNase I hypersensitive sites. These are chromatin regions where many regulatory elements have been found. In [1], Maurano et al. show that many of the non-coding variants associated with common diseases are concentrated in regulatory DNA marked by DHSs. The researchers performed genome-wide DNase I mapping across 349 cell and tissue types. As discussed last week, regions of DNase I accessibility harbor regulatory elements. They also examined the distribution of 5654 non-coding SNPs (single base variants) that had been significantly associated to some disease or trait in genome-wide studies. These the main findings:"Fully 76.6% of all noncoding GWAS SNPs either lie within a DHS (57.1%, 2931 SNPs) or are in complete linkage disequilibrium (LD) with SNPs in a near-by DHS (19.5%, 999 SNPs)."GWAS stands for whole genome studies. To be in linkage disequilibrium means that the variant is typically inherited together with a DHS site. Suppose the true causal variant is at locus A, but you haven't typed locus A, you've typed locus B, and A and B are inherited together. Then B is going to light up as strong signal in your statistical analysis. So, what Maurano et al. are saying in the above paragraph is that the non-coding SNPs either turned up in a DHS site, or they found evidence that they were strongly correlated with one of such sites. "Many common disorders have been linked with early gestational exposures or environmental insults. Because of the known role of the chromatin accessibility landscape in mediating responses to cellular exposures such as hormones, we examined if DHSs harboring GWAS variants were active during fetal developmental stages. Of 2931 noncoding disease- and trait-associated SNPs within DHSs globally, 88.1% (2583) lie within DHSs active in fetal cells and tissues. Of DHSs containing disease-associated variation, 57.8% are first detected in fetal cells and tissues and persist in adult cells (“fetal origin” DHSs), whereas 30.3% are fetal stage–specific DHSs.And finally:"Enhancers may lie at great distances from the gene(s) they control and function through long-range regulatory interactions, complicating the identification of target genes of regulatory GWAS variants."GWAS variants control distant genes that need not even be on the same chromosome. Furthermore, these variants in DHSs sites tend to alter allelic chromatin state, thus modulating the accessibility of genes to transcription factors. Disease-linked variants were found to alter such accessibility, resulting in allelic imbalance (one allele gets transcribed more than the other one), possibly explaining their role in altering the disease risk or quantitative trait.[1] Matthew T. Maurano, Richard Humbert, Eric Rynes, Robert E. Thurman, Eric Haugen, Hao Wang, Alex P. Reynolds, Richard Sandstrom, Hongzhu Qu, Jennifer Brody, Anthony Shafer, Fidencio Neri, Kristen Lee, Tanya Kutyavin, & Sandra Stehling-Sun (2012). Systematic Localization of Common Disease-Associated Variation in Regulatory DNA Science DOI: 10.1126/science.1222794... Read more »
Matthew T. Maurano, Richard Humbert, Eric Rynes, Robert E. Thurman, Eric Haugen, Hao Wang, Alex P. Reynolds, Richard Sandstrom, Hongzhu Qu, Jennifer Brody.... (2012) Systematic Localization of Common Disease-Associated Variation in Regulatory DNA. Science. DOI: 10.1126/science.1222794
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