Mushroom extracts might prevent dental cavities

Image of a red camphor mushroom from reference 1.
Image of a red camphor mushroom from reference 1.

Recently published research suggests red camphor mushroom extracts might prevent the proliferation of bacteria that cause dental cavities and gum disease.1


The Taiwanese red camphor mushroom (scientific name: Antrodia camphorata) is a herbal medicine traditionally used for treating conditions such as twisted tendons, muscle damage and liver diseases. Studies using human cells grown in laboratories have shown that red camphor mushroom extracts and isolated chemicals could help fight cancer and prevent cellular damage.2 However, studies in animals and humans will be required to confirm these benefits are not restricted to the laboratory setting.


The Yusheng Biotechnology Company funded university researchers to study the effects of red camphor mushroom extracts on two species of bacteria. One bacterium is typically found in dental cavities. The other bacterium is linked to the development of gum disease.


The researchers grew the bacteria that might cause cavities for one day in the presence of red camphor mushroom extracts, a typical anti-bacterial mouthwash ingredient or water (not shown):


Graph adapted from Figure 2C in reference 1.


Viewing the graph from left to right, the line traces start out flat showing that the bacteria are surviving. Then the line traces dip downwards as the amount of the mushroom extracts or mouthwash ingredient added to the bacteria increase, showing that many of the bacteria are dying. When only water is added, the line trace stays flat and does not dip, meaning that few of the bacteria die (data not shown here, but are described in the publication).1 The results were similar for the bacteria linked to the development of gum disease.


The results show that the mushroom extracts and the mouthwash ingredient both prevent bacteria that might cause cavities from surviving.


The researchers also tested how well the bacteria that might cause cavities stick to a plastic surface in the presence of mushroom extracts or the mouthwash ingredient. This experiment could approximate how well mushroom extracts and mouthwash ingredients keep bacteria from sticking to teeth. Both the mushroom extracts and the mouthwash ingredient prevented bacteria from sticking to a plastic surface, but less of the mouthwash ingredient was needed to prevent bacteria from sticking.


Finally, the researchers tested the toxicity of the mushroom extracts on human mouth cells grown in the laboratory. High amounts of mushroom extracts in alcohol solutions (256 micrograms of mushroom extract in 1 millilitre of cell-containing liquid) did not kill human mouth cells, but mushroom extracts in other solutions did. This suggests that mushroom extracts in alcohol solutions might be safe for human use.


A drawback of this study concerns the choice of comparator samples used in the experiments. For example, in the graph above, the mushroom extracts in different, individual solutions were compared with the mouthwash ingredient in an unspecified solution. A better experiment would have compared the mushroom extracts in individual solutions to the mouthwash ingredient in the same individual solutions, for example, the mushroom extract in solution 1 versus the mouthwash ingredient in solution 1. This would exclude the possibility that the solution could be causing the effect rather than the mushroom extract.


A second potential drawback concerns the applicability of the study to how the mushroom extracts might be used in everyday dental care. For example, the bacteria in this study were exposed to the mushroom extracts for 1 day, but if the mushroom extracts were added to a toothpaste or mouthwash, the bacteria would only be exposed when the product would be in use, probably no longer than 5 minutes. This might not be enough time for the mushroom extracts to kill bacteria or prevent them from sticking to teeth.


Despite these limitations, the results suggest that red camphor mushroom extracts could limit the growth and colonisation of bacteria involved in the formation of dental cavities and gum disease, without causing harm to human mouth cells. If a mushroom extract toothpaste or mouthwash were to be developed, more studies would be required to see if the benefits seen in the laboratory translate into benefits for people.





1 Lien HM, Tseng CJ, Huang CL, Lin YT, Chen CC, & Lai YY (2014). Antimicrobial Activity of Antrodia camphorata Extracts against Oral Bacteria. PloS one, 9 (8) PMID: 25144619


2 Geethangili M, & Tzeng YM (2011). Review of Pharmacological Effects of Antrodia camphorata and Its Bioactive Compounds. Evidence-based complementary and alternative medicine : eCAM, 2011 PMID: 19687189

Physicians face difficult choices when treating patients with bipolar and obsessive compulsive disorders

Photo with CC BY-SA 2.0 license available at:

New research suggests patients with both bipolar disorder and obsessive compulsive disorder should receive treatments for bipolar disorder alone.1 Bipolar and obsessive compulsive disorder therapies taken together can cause worsening of disease symptoms, making it difficult for physicians to treat both conditions. This is a concern as over 1 in 5 patients with bipolar disorder develop obsessive compulsive disorder during their lifetime.2,3


Bipolar disorder is a condition characterised by alternate periods of depression followed by mania, a period of heightened activity. These periods can last for days, weeks or months before shifting. For example, during a period of depression a patient may feel unmotivated to get out of bed, and during a period of mania he may overspend and accrue credit card debt. Typical treatments include mood stabilisers for reducing feelings of depression or mania, anti-psychotic medications for dampening more severe episodes of depression or mania, and psychological behaviour therapy for coping with periods of depression.


Obsessive compulsive disorder is characterised by obsessions, negative beliefs causing anxiety, that lead to compulsions, repetitive behaviours or thoughts the patient believes will keep the obsessions from coming true. For example, a patient may worry that open windows will cause colds, so she might close all open windows to prevent this. Typical treatments include psychological behaviour therapy and antidepressants, both of which reduce anxiety.


While the goal of treating bipolar disorder is to stabilise moods, the goal of treating obsessive compulsive disorder is to improve moods, so the treatments differ. The antidepressants used for treating obsessive compulsive disorder can cause mood instability in bipolar disorder patients.4 Having both conditions makes it difficult for physicians to make choices about patient management.


With the aim of identifying appropriate treatments for patients with bipolar and obsessive compulsive disorders, Andrea Amerio and his team systematically reviewed published studies, meaning they set pre-defined criteria for which studies to analyse before starting their research. Fourteen studies met their pre-defined criteria. Many of the studies were not rigorously designed and included few patients. For example, 8 of the 14 studies examined fewer than 10 patients who were not compared to patients receiving other treatments or receiving none. Despite these limitations, the researchers were asking an important question about patients who are rarely studied, so this is acceptable given the quality of studies available.


The researchers found that all patients were treated with mood stabilisers, often combinations of multiple mood stabilisers or combinations of mood stabilisers with anti-psychotics. When mood stabilisers and anti-psychotics were combined with psychological behaviour therapy, obsessive compulsive disorder symptoms decreased. These patients were not compared to patients receiving mood stabiliser therapy, anti-psychotics or psychological behaviour therapy alone. These results show that patients with bipolar and obsessive compulsive disorders could benefit from a combination of medications and psychological behaviour therapy.


Importantly, when patients received antidepressants, the therapy of choice for obsessive compulsive disorder, they had more bipolar disorder symptoms compared to patients with bipolar disorder or obsessive compulsive disorder alone. This suggests that antidepressants might be less suitable for treating patients with bipolar and obsessive compulsive disorders.


Overall, the data suggest that treating the bipolar disorder rather than the obsessive compulsive disorder should be the priority for decreasing patient symptoms. However, as very few high quality studies have examined how different treatments affect patients who have both bipolar and obsessive compulsive disorders, more rigorously designed studies will be needed to confirm these results.


1 Amerio A, Odone A, Marchesi C, & Ghaemi SN (2014). Treatment of comorbid bipolar disorder and obsessive-compulsive disorder: A systematic review. Journal of affective disorders, 166C, 258-263 PMID: 25012439
2 Chen YW, & Dilsaver SC (1995). Comorbidity for obsessive-compulsive disorder in bipolar and unipolar disorders. Psychiatry research, 59 (1-2), 57-64 PMID: 8771221
3 Merikangas KR, Akiskal HS, Angst J, Greenberg PE, Hirschfeld RM, Petukhova M, & Kessler RC (2007). Lifetime and 12-month prevalence of bipolar spectrum disorder in the National Comorbidity Survey replication. Archives of general psychiatry, 64 (5), 543-52 PMID: 17485606
4 Pacchiarotti I, Bond DJ, Baldessarini RJ, et al. (2013). The International Society for Bipolar Disorders (ISBD) task force report on antidepressant use in bipolar disorders. The American journal of psychiatry, 170 (11), 1249-62 PMID: 24030475

Vitamin D supplements might not protect against osteoporosis

Measuring bone mineral density using a DEXA scanner. Wikimedia commons photo available at:
Measuring bone mineral density using a DEXA scanner. Wikimedia commons photo available at:

Vitamin D supplements did not increase bone mineral density when results from studies were statistically combined in a meta-analysis published in The Lancet.1 Vitamin D is widely used to prevent osteoporosis. The new data suggest that vitamin D supplementation for the prevention of osteoporosis in typical individuals is unfounded. However, vitamin D deficient patients might benefit.


Over 50 years ago, vitamin D was shown to be essential for skeletal development.2 Soon after, a link between vitamin D deficiency and osteoporosis, a condition which increases the risk of bone fractures, was demonstrated.2 Presently, the US Institute of Health recommends healthy adults younger than 70 years old consume 600 international units of vitamin D daily for the prevention of osteoporosis caused by vitamin D deficiency.


In the meta-analysis by Ian R Reid and colleagues, results from 23 standard medical studies (i.e. randomised controlled trials) including over 4,000 individuals were combined. The studies lasted an average of 2 years. Bone mineral density, a marker for bone strength, was compared at the beginning and end of the studies.


Changes in bone mineral density at 4 of the 5 common bone fracture sites were not identified in individuals taking vitamin D supplements. Bone mineral density increased only in the middle of the femur, but additional statistical analyses showed this was likely due to bias from the type of studies selected. Further analyses showed that vitamin D doses of less than 800 international units were associated with increased bone mineral density in the middle of the femur and the spine, but not at other sites and not at higher doses. Lower vitamin D doses might be more beneficial than higher ones.

Bone mineral density seen on a DEXA scan. Wikimedia commons photo available at:
Bone mineral density seen on a DEXA scan. Wikimedia commons photo available at:

The results challenge established thinking, so how has the medical community responded?


Mir Sadat-Ali and Haifa A Al-Turki wrote to The Lancet with two objections.3 First, individuals in 10 of the 23 studies included in the meta-analysis took vitamin D doses of less than 800 international units per day. The doses might have been too low to see an effect on bone mineral density. Second, there was a concern that the individuals did not take vitamin D as regularly as they should, again masking a potential positive effect. Both of these points were refuted by Ian R Reid and colleagues.4 They explained how their meta-analysis suggested that lower doses of vitamin D were more effective than higher ones, so higher doses should not be more beneficial. In addition, although some individuals did not take vitamin D regularly in the controlled study environment, in everyday life it is likely that more individuals would fail to take their therapy regularly. In fact, the meta-analysis may have overestimated any potential benefit of vitamin D.


Helen Macdonald and Terence J Aspray highlighted their recent study that was not included in the analysis.5 In contrast to the meta-analysis, their study showed greater increases in bone mineral density with higher doses of vitamin D. Ian R. Reid and colleagues responded by explaining that adding the Macdonald study to the meta-analysis would not have changed the results.4


Finally, Spyridon N Karras and colleagues crafted a well-considered objection, to which Ian R Reid and colleagues have not responded.4,6 As for many standard medical studies (i.e. randomised controlled trials), the ones included in the meta-analysis did not recruit typical individuals. This means that the individuals might have been too similar, introducing a bias towards similar results. In this instance, the individuals included were mostly white and had sufficient vitamin D levels before the start of the study. The issue is that it is difficult to detect increases in bone mineral density from scans for individuals that have sufficient vitamin D levels.7,8 The positive effect of vitamin D supplementation might have been missed. Spyridon N Karras and colleagues conclude that more studies of representative individuals, including vitamin D deficient ones, are needed.


Other potential limitations of including standard medical studies (i.e. randomised controlled trials) in this meta-analysis are the short duration of the studies (average of 2 years) and the type of results that can be measured. Long-term observational studies would compliment this meta-analysis. An observational study lasting a minimum of 5-10 years would provide insight into events that take longer to occur than changes in bone mineral density, such as bone fractures and osteoporosis.


Overall, this well-designed meta-analysis challenges the assumption that vitamin D supplementation might be beneficial for many individuals. New research addressing questions raised by this meta-analysis will be interesting to follow.

1 Reid IR, Bolland MJ, & Grey A (2014). Effects of vitamin D supplements on bone mineral density: a systematic review and meta-analysis. Lancet, 383 (9912), 146-55 PMID: 24119980

2 Rosen CJ (2014). Vitamin D supplementation: bones of contention. Lancet, 383 (9912), 108-10 PMID: 24119979

3 Sadat-Ali M, & Al-Turki HA (2014). Vitamin D supplements and bone mineral density. Lancet, 383 (9925) PMID: 24725573

4 Reid IR, Bolland MJ, & Grey A (2014). Vitamin D supplements and bone mineral density – Authors’ reply. Lancet, 383 (9925), 1293-4 PMID: 24725572

5 Macdonald H, & Aspray TJ (2014). Vitamin D supplements and bone mineral density. Lancet, 383 (9925) PMID: 24725570

6 Karras SN, Anagnostis P, Beauchet O, Goulis DG, & Annweiler C (2014). Vitamin D supplements and bone mineral density. Lancet, 383 (9925), 1292-3 PMID: 24725569

7 Bischoff-Ferrari HA, Kiel DP, Dawson-Hughes B, Orav JE, Li R, Spiegelman D, Dietrich T, & Willett WC (2009). Dietary calcium and serum 25-hydroxyvitamin D status in relation to BMD among U.S. adults. Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research, 24 (5), 935-42 PMID: 19113911

8 Bischoff-Ferrari HA, Willett WC, Wong JB, Stuck AE, Staehelin HB, Orav EJ, Thoma A, Kiel DP, & Henschkowski J (2009). Prevention of nonvertebral fractures with oral vitamin D and dose dependency: a meta-analysis of randomized controlled trials. Archives of internal medicine, 169 (6), 551-61 PMID: 19307517

GM wheat resists infection by the destructive take-all fungus

Wheat infected with take-all. Wikimedia commons photo available at:
Wheat infected with take-all. Wikimedia commons photo available at:


A team of Chinese researchers have engineered genetically modified (GM) wheat that resists infection by the destructive take-all fungus.1 The fungus infects wheat roots, causing up to a 40-60% reduction in wheat yields.2


Take-all infects wheat grown in temperate regions worldwide. It devastated Australian wheat crops during the 1800s. Hence, farmers named it ‘take-all’. Now Chinese wheat is increasingly at risk. This might be a reason why a government research council funded this research. Another reason is that attempts at selective cultivation have not yielded take-all resistant wheat, and the infection is difficult to eradicate once it spreads. As a result, new technology is urgently needed for abating the take-all fungus.


First the researchers performed experiments to confirm that a gene found in a wild relative of wheat might help defend against a take-all infection. The gene was chosen because it is known to help the flowering plant rockcress resist disease. The wild relative of wheat contains a gene similar to the one found in rockcress. In addition, the wild relative of wheat is particularly resistant to viral infections.


The researchers infected the wild relative of wheat with take-all. They measured the number of gene copies, an indicator of gene activity, made over the course of 21 days:

Image adapted from reference 1.

The number of gene copies peaked after seven days. This indicates that the gene from the wild relative of wheat was activated after a take-all infection, potentially for defence purposes.


Next the researchers created GM wheat using a gene gun. Heavy metal particles were coated with the gene from the wild relative of wheat and then shot into a developing seed. The heavy metal particles pierced through the seed’s cell barriers, carrying the piggybacking gene with them. In this manner, the gene from the wild relative of wheat was inserted into the wheat seedlings.


The researchers double-checked that the gene was inserted. Finally they grew four wheat plants, one control plant (no gene inserted) and three GM plants (gene inserted), and infected their roots with take-all:

Image adapted from reference 1.
Image adapted from reference 1.


Both the control and GM wheat plant roots were infected with black take-all fungi, but the GM wheat plants were less infected than the control wheat plant. This was confirmed with further quantitative experiments. The researchers succeeded in engineering a take-all resistant strain of wheat.


Although this GM wheat is resistant to take-all in the lab, it is unknown how it would fare in a typical farmer’s field. One potential pitfall could be that the GM wheat might harbour low levels of the fungus, allowing it to spread further and cause minor destruction of many crops. If more disease-resistant genes could be inserted into this GM wheat, it might be possible to generate plants that are more resistant to take-all. These improved GM wheat plants could then be tested on a small scale before being grown more widely. The fungus could soon need a new name as it might no longer ‘take-all’.


For further reading:

Genetically Modified (GM) Crops- Friend or Foe?: An overview of how GM crops are made



This post was chosen as an Editor's Selection for

1 Liu X, Yang L, Zhou X, Zhou M, Lu Y, Ma L, Ma H, & Zhang Z (2013). Transgenic wheat expressing Thinopyrum intermedium MYB transcription factor TiMYB2R-1 shows enhanced resistance to the take-all disease. Journal of experimental botany, 64 (8), 2243-53 PMID: 23547108

2 Gutteridge RJ, Bateman GL, & Todd AD (2003). Variation in the effects of take-all disease on grain yield and quality of winter cereals in field experiments. Pest management science, 59 (2), 215-24 PMID: 12587875

How wounds heal


Back a bit further, slightly to right,’ shouts a friend. Scrape goes the hand against the rough bricks. A sudden jolt of pain precedes a small trickle of red, oxygenated blood from the fresh cut. What unseen processes are occurring to seal and heal this new wound?


Wound healing involves a cascade of molecular signals and multiple cell types. When a cut is fresh, neural pain receptors send signals to small capillaries to constrict near the cut, slowing the flow of blood. Within seconds, blood platelet cells begin clumping at the cut.1 Both of these actions curb excess bleeding.


Meanwhile, the clot releases small protein messengers (cytokines) that trigger inflammation after binding to the surface of immune cells. The inflammation causes the cut to turn red and appear slightly swollen for a few days. The body’s goals at this stage are to recruit immune cells that clear debris, fight invading bacteria, and destroy and remove damaged cells in the vicinity of the cut.2


Once the mess is cleared, skin cells begin growing back. Conveniently, skin is full of adult stem cells that have the potential to and do give rise to different types of skin cells. Concomitantly, other cells produce fibres that bind cells together in sheets and new capillaries grow. Interestingly, long after a cut looks healed, remodelling of sheets of cells and capillary paths continues for years.2

Salamander photo by Bill Bouton [CC-BY-SA-2.0 (], via Wikimedia Commons

Human wound healing is admirable, but regeneration of entire body parts is a more enviable ability. Salamanders are a typical example of animals capable of regeneration. While humans start with partially specialised cells (adult stem cells) and finish with highly specialised cells (for example, skin cells), salamanders can convert their highly specialised cells into non-specialised cells. As humans can not reverse the process, they are limited by whichever stem cells are available. For example, skin stem cells can only give rise to skin cells, not bone cells. In contrast, salamanders can convert any specialised cell so that it can give rise to any other cell. When a salamander loses its tail, there is nothing to prevent it from replacing it.3


It seems that salamanders are superior wound healers after all. Until humans master replicating regeneration in the laboratory, they must remain content with mending scrapes and scabs.

1 Boon GD (1993). An overview of hemostasis. Toxicologic pathology, 21 (2), 170-9 PMID: 8210939

2 Guo S, & Dipietro LA (2010). Factors affecting wound healing. Journal of dental research, 89 (3), 219-29 PMID: 20139336

3 Odelberg SJ (2004). Unraveling the molecular basis for regenerative cellular plasticity. PLoS biology, 2 (8) PMID: 15314652

Structures provide clues as to how ATP is transported

Yeast ADP/ATP carrier protein

Structure of one of the yeast ADP/ATP carrier proteins from the top (cytoplasm; left) and the side (membrane; right). The ADP/ATP carrier protein is coloured yellow, green and blue. Image from1.


Ten years after the first three-dimensional structure of the bovine ADP/ATP carrier protein was revealed, two structures of yeast ADP/ATP carriers have been discovered.1 The ADP/ATP carrier is a molecular machine that transports energy in the form of ATP from where it is made, the mitochondrion, to the rest of the cell in exchange for spent energy, ADP.


Energy from food is transferred to the molecule ATP. The energy released by ATP drives chemical reactions in cells, making it possible for people to grow, walk, run and think. The chemical properties of ATP do not allow it to cross the mitochondrial membrane to get to where it is needed. That is why the ADP/ATP carrier is essential. The ADP/ATP carrier transports the equivalent of one’s entire body weight in ATP every day.


The yeast ADP/ATP carrier structures took a long time to discover, in part, because the proteins are surrounded by the mitochondrial membrane. Compared to most proteins, the ADP/ATP carrier is very small and requires a membrane to support it. The issue is that the protein needs to be taken out of the membrane to image its three-dimensional structure with x-rays. Away from the supporting membrane, the protein unfolds. This is similar to how flowers stand pertly in a vase with a narrow neck, but their stems splay apart haphazardly when the flowers are removed from the vase.


The structures reveal that yeast ADP/ATP carriers look similar to each other and to the bovine protein. However, this is the first time the ends of the proteins could be seen (labelled H1 and H6). One end pokes out like a stick (H1), but the other folds back to the protein (H6).


The structures help predict how the ADP/ATP carrier might transport ADP and ATP (see: animation). ADP and ATP are transported through the middle of the protein. ‘Gates’ on the top (cytoplasm) side and the bottom (matrix) side alternatively open and close, allowing one ADP to pass through before an ATP does. The cycle repeats.


The next step will be to discover more structures of the ADP/ATP carrier and its protein relatives, all of which will provide more clues as to how these life-enabling proteins function.




1 Ruprecht JJ, Hellawell AM, Harding M, Crichton PG, McCoy AJ, & Kunji ER (2014). Structures of yeast mitochondrial ADP/ATP carriers support a domain-based alternating-access transport mechanism. Proceedings of the National Academy of Sciences of the United States of America, 111 (4) PMID: 24474793

How antibiotics work


It is an understatement to say antibiotics are life saving drugs. Their utility was proven when the first antibiotic, penicillin, effectively cured individual patients’ bacterial infections in the 1930s and 1940s.1 These successful case studies led to the mass-production of penicillin during World War II. Penicillin cured the infections of thousands of wounded soldiers. Today, antibiotics are the best weapons available for treating bacterial infections such as pneumonia and tuberculosis. In addition, routine surgeries, such as those for removing cancerous tumours, are only possible because antibiotics prevent bacteria from infecting surgical wounds.


Most antibiotics selectively kill bacteria in one of two possible ways.2 One is by inhibiting bacterial cell wall (peptidoglycan) synthesis. Much like how a house with weak walls would crumble under the weight of a heavy roof, a bacterium with a compromised cell wall lacks structural support and perishes. What makes these antibiotics particularly effective is that bacteria have cell walls but human cells do not. Consequently, when a human takes a cell wall inhibiting antibiotic, the bacterial cells are the only casualties.


The second common way antibiotics kill bacteria is by specifically inhibiting the bacterial molecular machines that make proteins (ribosomes). Although ribosomes are not proteins, most of the molecular machines in the cell are. Inhibiting protein production has similar consequences as removing a selection of car engine parts. The car dies and so do bacteria treated with antibiotics. These antibiotics do not kill human cells though. Although humans and bacteria both have ribosomes, human ribosomes have a different shape and structure to bacterial ribosomes. These differences make it possible for antibiotics to target bacteria for destruction.


How were these mechanisms uncovered? During the 1970s, a plethora of new antibiotics were isolated from natural sources. Experiments were tried to differentiate potential mechanisms until the correct one for a particular antibiotic was identified. For example, to uncover the mechanism of mupirocin, the antibiotic often used to treat the ‘superbug’ MRSA, researchers at Imperial College London tested mupirocin’s effect on cell wall and protein synthesis in the bacterium Staphylococcus aureus.3 They added radioactively labelled materials for making cell walls. The bacteria exposed to mupirocin incorporated a slightly reduced amount of radioactivity in their cell walls over time compared to bacteria in the absence of the antibiotic. Mupirocin did not greatly inhibit cell wall synthesis. In another experiment, radioactive material for making proteins was added, but the result was surprisingly different. As soon as mupirocin was added, the bacteria ceased producing radioactive proteins. Meanwhile, bacteria in the absence of mupirocin continued rapidly synthesising radioactive proteins. The researchers concluded that mupirocin inhibits protein synthesis. With the help of radioactively labelled materials, these and other researchers were able to uncover how various antibiotics work.

1 Wainwright M, & Swan HT (1986). C.G. Paine and the earliest surviving clinical records of penicillin therapy Med Hist, 30 (1), 42-56 Other: PMC1139580


2 Alberts B, Johnson A, Lewis J, Raff M, Roberts K, & Walter P (2008). Drug-resistant pathogens are a growing problem
Molecular biology of the cell (Fifth edition), 1521-1524 Other: 0-8153-4106-7

3 Hughes J, & Mellows G (1978). On the mode of action of pseudomonic acid: inhibition of protein synthesis in Staphylococcus aureus. The journal of antibiotics, 31 (4), 330-5 PMID: 659331

A sting operation stimulates debate about publishing research

Publication Seminars

Publication Seminars: Changing expectations in an ever-changing world

London, 17 October 2013

Speakers: Liz Wager, Amitabh Prakash and Caroline Halford


On 17 October, I travelled to London to participate in the annual Publications Seminars. As suggested by the programme, the presenters focused on discussing changes in the publications industry. One of the most heated debates of the event highlighted a recent sting operation published in Science.1 The researcher, John Bohannon, aimed to uncover how rigorous the peer review process is in open access journals that do not charge their readers for viewing content. John Bohannon wrote a far-fetched fictitious article that reported findings such as cells treated with a substance do not multiply as expected, the caveat being that the test cells treated with the substance were exposed to radiation, but the control cells were not. Then he submitted the article for consideration for publication in 304 open access journals. The bogus article should have been promptly rejected, but surprisingly 3 out of 5 journals accepted the article for publication. The articles were presumably accepted without undergoing peer review.


The study concluded that open access publishers often fail to peer review articles. The blame fell mostly on the open access publishing model, but the failure could arguably be due to flaws in the peer review process. As highlighted by an audience participant, the Science article did not include controls, so it is unknown how peer review in the open access model compares to peer review in journals without an open access model. Liz Wager, a freelance publications consulant, argued her interpretation of the results. She mentioned that it is known that the peer review system is flawed. Liz Wager concluded from the study that academics should be selective when choosing where to publish. The findings in no way suggested that the open access model is flawed. Writing in The Guardian, Professor Curt Rice reached a similar conclusion as Liz Wager. Curt Rice espoused that the underlying issue is the failure of peer review and quality control, and thus these systems should be reformed. Whether the underlying issue is related to the peer review process, open access or another factor, it is clear that it is remarkably easy for poor science to be published.

1 Bohannon J (2013). Who’s Afraid of Peer Review? Science (New York, N.Y.), 342 (6154), 60-65 PMID: 24092725


Coaxed yeast secrete omega-3

21595994 yarrowia cropped

The yeast Yarrowia lipolytica lives in oil fields, plants and food. Image courtesy of Gasmi, N et al.1


A team of researchers at DuPont have engineered novel yeast that produce omega-3 fatty acids at levels much higher than previously achievable.2,3 Fatty acids are the building blocks of fats. Similar to how a house is built from bricks, fats are built from fatty acids.


Omega-3 fatty acids from fish oil are popular health supplements. The type of omega-3 reported in the DuPont study, omega-3 eicosapentaenoic acid, is linked to improvements in heart health. In a Japanese study of patients with coronary artery disease, the number of heart disease-related events was reduced by 19% for patients consuming high doses of omega-3 and statins, compared to similar patients consuming statins alone.4 In contrast, a Dutch study found no significant reduction in heart disease-related events for patients on low doses of omega-3.5 It is possible that high doses rather than low doses of omega-3 fatty acids might be key to unleashing their heart protective benefits. More research should be done to confirm this.


Fish oils are an abundant source of omega-3, although fish do not produce it themselves. Fish accumulate omega-3 by consuming algae and bacteria that do produce it. The most convenient way for people to ingest high levels of omega-3 though is by taking fish oil tablets. The issue is that with fish oil’s growing popularity, the demand for fish oil is high but the supply of fish is limited. Overfishing is becoming a problem. In addition, there are concerns that environmental toxins might accumulate in the oils, mitigating the potential beneficial effects of consuming omega-3.


As a result, engineered yeast that produce omega-3 are a welcome development, and the DuPont technology is already being put into practice. In the US, one can purchase sustainably farmed salmon that were fed an omega-3 rich diet. In addition, vegetarian omega-3 was being sold as a nutritional supplement, but the product is currently discontinued. Both products were developed using this novel yeast engineering method.


Compared to previous omega-3 engineering methods, the novel yeast produce the highest yield of the type of omega-3 thought to contribute to heart health at 56.6% of the total fatty acids made by the yeast.2,3 Algae have been engineered to produce high yields of another type of omega-3, but not the heart healthy type. Genetically modified plants can produce heart healthy omega-3 as 25% of total fatty acids, but this technology has not been commercialised.6 In a fairer comparison, baker’s yeast (Saccharomyces cerevisiae) have been engineered to produce heart healthy omega-3 at less than 1% of total fatty acids, whilst the novel yeast (Yarrowia lipolytica) produce upwards of 50 times more:

 yeast comparison final

How was it done? Much hard work and luck were involved. The researchers already knew how algae and bacteria make omega-3. Genes, labelled A to G here for clarity, lead to the production of fatty acids. Gene A leads to the production of fatty acid A. Gene B leads to the conversion of fatty acid A into fatty acid B, and so forth, in alphabetic order A to G. Finally, gene G leads to the production of fatty acid G, omega-3 fatty acid:

overview diagram 1of2

The yeast (blue circles) already had genes A, B, C and D (black text), so genes E, F and G had to be added to make fatty acid G, omega-3. The researchers took copies of the genes from algae and bacteria and inserted them into the yeast stepwise (purple text). They also added in extra copies of the genes, as more gene copies generally means more fatty acids are produced. The number of gene copies was optimised to minimise bottlenecks for producing omega-3. Finally, they checked at some steps along the way to confirm that the correct fatty acids were being made (red text). If the researchers had added all the genes at one time, they would not have been able to check that the genes were leading to the production of the correct fatty acids, and it would have been less likely that the yeast would have kept the added genes.


Whilst the researchers successfully coaxed the yeast to secrete omega-3, the yeast were not producing enough for commercial purposes (only 9.8% of total fatty acids). Fortunately the researchers were lucky. In the next round of gene insertions, one of the engineered yeasts produced more omega-3 than other similarly engineered yeasts. Upon checking where the gene was inserted, they realised that the insertion meant that a protein responsible for importing other proteins into cell compartments, an import protein, became shorter in length. Pleased with this finding, the researchers tried removing the import protein from the yeast:

deletion truncation comparison final

To their delight, the yeast lacking the import protein produced almost double the omega-3 that the yeast with a shortened import protein did. The researchers then generated a yeast with inserted genes and no import protein, and inserted even more gene copies:

overview diagram 2of2

The final engineered yeast secreted omega-3 as 56.6% of total fatty acids. The researchers had discovered a novel, sustainable omega-3 solution.





1 Gasmi N, Ayed A, Nicaud JM, & Kallel H (2011). Design of an efficient medium for heterologous protein production in Yarrowia lipolytica: case of human interferon alpha 2b. Microbial cell factories, 10 PMID: 21595994


2 Xue Z, Sharpe PL, Hong SP, Yadav NS, Xie D, Short DR, Damude HG, Rupert RA, Seip JE, Wang J, Pollak DW, Bostick MW, Bosak MD, Macool DJ, Hollerbach DH, Zhang H, Arcilla DM, Bledsoe SA, Croker K, McCord EF, Tyreus BD, Jackson EN, & Zhu Q (2013). Production of omega-3 eicosapentaenoic acid by metabolic engineering of Yarrowia lipolytica. Nature biotechnology, 31 (8), 734-40 PMID: 23873085


3 Wynn JP (2013). Taking the fish out of fish oil. Nature biotechnology, 31 (8), 716-7 PMID: 23929348

4 Yokoyama M, Origasa H, Matsuzaki M, Matsuzawa Y, Saito Y, Ishikawa Y, Oikawa S, Sasaki J, Hishida H, Itakura H, Kita T, Kitabatake A, Nakaya N, Sakata T, Shimada K, Shirato K, & Japan EPA lipid intervention study (JELIS) Investigators (2007). Effects of eicosapentaenoic acid on major coronary events in hypercholesterolaemic patients (JELIS): a randomised open-label, blinded endpoint analysis. Lancet, 369 (9567), 1090-8 PMID: 17398308

5 Kromhout D, Giltay EJ, Geleijnse JM, & Alpha Omega Trial Group (2010). n-3 fatty acids and cardiovascular events after myocardial infarction. The New England journal of medicine, 363 (21), 2015-26 PMID: 20929341


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MicroRNAs reinforce heart disease damage

wash basin

A blocked drainpipe is not so different from a blocked artery


Practically everyone knows friends or family suffering from heart disease. Many sufferers have ischaemic heart disease, the most common type of heart disease worldwide. The World Health Organisation ranked ischaemic heart disease as the leading cause of death in 2004, responsible for 12.2% of deaths. It is forecasted that ischaemic heart disease will remain the leading cause in death in 2030. Ischaemic heart disease is clearly a major interpersonal and global health concern.


Ischaemia’ is a restriction of blood supply, so ischaemic heart disease is characterised by restriction of blood flow to the heart. A typical cause of ischaemic heart disease results from the formation of plaques (atherosclerosis) in arteries carrying blood to the heart. The type of ischaemic heart disease whereby plaques partially block or impede blood flow to the heart is called coronary heart disease or coronary artery disease. What occurs in the arteries is similar to how drainpipes in household wash basins become clogged, slowing the flow of water down the drain. Plaques in arteries slow the flow of blood in a similar manner, except that the situation is much more dire due to the type of artery involved. Most arteries carry blood rich in oxygen and glucose to the body’s extremities, but the coronary artery is unique in that it carries blood back to the heart to power its beating. The coronary artery is the exclusive pipeline for blood to reach the heart, so blockages in this artery can lead to heart damage, much of which is irreversible.


What is fascinating about these plaques is that they take a lifetime to form. Autopsies of children who passed away for reasons other than ischaemic heart disease reveal that fatty streaks line their arteries, suggesting that plaques begin to form during childhood.1 By middle age, most adults in western countries have plaques, yet they rarely show disease symptoms. Consequently, plaque formation alone does not cause ischaemic heart disease.2


Ischaemic heart disease may become a more life-threatening problem when plaques rupture or erode, meaning that an opening on the surface of the plaque develops. Similarly to how platelet cells heal small cuts, platelet cells rush to plaque openings and try to close them, creating a blood clot inside an artery (thrombosis). Usually plaque ruptures or erosions and the subsequent formation of blood clots do not cause any harm, but occasionally blood clots may impair blood flow in the coronary artery, resulting in a heart attack.


Molecular biologists and physicians have recently uncovered some of the molecular mechanisms underlying plaque rupture and blood clotting within arteries. In the last five years, a type of ribonucleic acid (RNA) called microRNA, was shown to regulate a myriad of processes involved in ischaemic heart disease.3,4 Examples include plaque development and rupture.


RNA is structurally similar to deoxyribonucleic acid (DNA), but RNA and DNA play vastly different roles. Whereas DNA stores the instructions or blueprints for making life, RNA is a copy of the DNA blueprints. Usually RNAs are decoded to make proteins, but microRNAS are different. In 1993 Rosalind C. Lee and Rhonda L. Feinbaum discovered microRNAs and that they regulate the amount of particular proteins found in roundworms.5 Research since 1993 has established that microRNAs actively destroy other RNAs or prevent RNAs from making proteins. Thus, microRNAs regulate protein production.


Importantly microRNAs regulate the abundance of plaque proteins. In a study comparing diseased human arteries containing plaques to arteries from the same individual lacking plaques, the researchers identified five types of microRNAs that were more abundant in plaques.6 The five microRNAs are known to slow or halt the production of particular proteins that discourage cells from spreading and prevent inflammation. This means that more cells grow at plaques and inflammation increases, making plaques more prone to rupturing.


Other studies performed using laboratory grown cells, animals and human tissue samples suggest that microRNAs regulate plaque rupture itself. The proteins affected include those involved in remodelling plaque architecture, for example by promoting or preventing cell death, or by enabling cells to break free from the plaque and wreak havoc.3,4


Understanding how microRNAs are involved in plaque rupture could be valuable for preventing ruptures altogether. For example, it might be possible to prevent harmful microRNA activity using pharmacological drugs. In the future effective drugs for preventing plaque ruptures could mean that ischaemic heart disease would lose its ranking as the leading cause of death; a loss for the disease but a win for humanity.




1 Berenson GS, Srinivasan SR, Bao W, Newman WP 3rd, Tracy RE, & Wattigney WA (1998). Association between multiple cardiovascular risk factors and atherosclerosis in children and young adults. The Bogalusa Heart Study. The New England journal of medicine, 338 (23), 1650-6 PMID: 9614255

2 Arbab-Zadeh A, Nakano M, Virmani R, & Fuster V (2012). Acute coronary events. Circulation, 125 (9), 1147-56 PMID: 22392862

3 Chen LJ, Lim SH, Yeh YT, Lien SC, & Chiu JJ (2012). Roles of microRNAs in atherosclerosis and restenosis. Journal of biomedical science, 19 (1) PMID: 22931291

4 Madrigal-Matute J, Rotllan N, Aranda JF, & Fernández-Hernando C (2013). MicroRNAs and atherosclerosis. Current atherosclerosis reports, 15 (5) PMID: 23512606

5 Lee RC, Feinbaum RL, & Ambros V (1993). The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell, 75 (5), 843-54 PMID: 8252621

6 Raitoharju E, Lyytikäinen LP, Levula M, Oksala N, Mennander A, Tarkka M, Klopp N, Illig T, Kähönen M, Karhunen PJ, Laaksonen R, & Lehtimäki T (2011). miR-21, miR-210, miR-34a, and miR-146a/b are up-regulated in human atherosclerotic plaques in the Tampere Vascular Study. Atherosclerosis, 219 (1), 211-7 PMID: 21820659