On Being a Grown Up Scientist

I have a couple of big posts coming – they just need to get out of my brain and on to the computer. In the meantime, Janet has a couple of great posts (part 1, part 2) about learning how to be a grown up scientist.

My only thought on this, at the moment, is remembering asking my PhD advisor, who was a great mentor, how he came up with ideas and how would I know that I had good ideas for my own research. I did not get a satisfactory answer and I still have not sorted it out for myself yet.

I also realize that good ideas are not enough, but you also need ideas that can be well presented to funding agents and committees.


Eating Broccoli Protects Your Heart

A recent study published online by the Journal of Agriculture and Food Chemistry reports on the role of broccoli as a cardioprotector. Broccoli contains high concentrations of selenium (65 nanograms/g broccoli) and glucosinolates, especially isothicyanate sulforaphane (23.6 micrograms/g broccoli). Both selenium and sulforaphane are shown to protect the heart and the cardiovascular system. Sulforaphane induces the redox regulator protein, thioredoxin, which has a cardioprotective role by reducing oxidative stress.

A clinical study reported that eating fresh broccoli sprouts for a week lowered serum low density lipoprotein levels (LDL is the so-called “bad” cholesterol) and a prospective study in Iowa showed a strong association between broccoli consumption and a lowering of the risk of coronary heart disease.

In the study reported in JAFC, rats were either feed, on top of regular rat chow, a broccoli slurry or water for a month before slaughter. At which time the hearts were isolated, stabilized and then subjected to 30 minutes of total ischemia followed by reperfusion*. Heart function was assessed 10, 30, 60, 90 and 120 mins after ischemia finished.

Hearts from rats fed on broccoli slurry showed faster recovery in left ventricular function and aortic flow. Heart rate was not affected by treatment. In addition, hearts from broccoli-fed rats had a smaller myocardial infarct size and the number of cardiomyocytes which under went cell death (apotosis) was reduced.

Hearts from broccoli-fed rats showed a similar response to ischemia as hearts in which thioredoxin had been upregulated. Broccoli possibly limits heart damage by inducing the production of thioredoxin and related proteins. These proteins play important roles in maintaining the inner cell redox potential. Selenium is required as part of the enzymes glutathione peroxidase and thioredoxin reductase, and sulforaphane up-regulates thioredoxin reductase stimulating thioredoxin production and reducing oxidative damage in the cell.


Mukherjee, S.; Gangopadhyay, H.; Das, D. K. Broccoli: A Unique Vegetable That Protects Mammalian Hearts through the Redox Cycling of the Thioredoxin Superfamily. J. Agric. Food Chem. 2007. (online)


From what I scan-read in Wikipedia, ischemia occurs by preventing blood flow to the heart and reperfusion is when blood is allowed back. Reperfusion can cause injury because the sudden influx of oxygen and blood can cause oxidative damage and inflammation.

Pectin – Introduction

One of my abstracts that was accepted for presentation at the Institute of Food Technologist’s Annual meeting was on low ester pectin. Pectin (link2) is a very intriguing molecule; a polysaccharide made mostly of galacturonic acid units. However, interspersed within the galacturonic acid polymer there are regions where rhamnose replaces the galacturonic acid and neutral sugars branch out of these regions. The galacturonic acid are frequently esterified with a methyl group. Alternatively, they can be amidated which means an amino group is attached. Amidation is typically added commercially to improve its functional behavior.


Pectin is used extensively in the food industry as a gelling agent. Not only is it used in jams and jellies, but also as a thickening agent and protein stabilizer. It is also added to diet sodas to improve mouthfeel.

Pectin is defined as low ester and high ester. In the US, the cut off between them is when 50% of the galacturonic acid groups are esterified. Low ester pectin requires minerals, typically calcium, to form gels.

Reference and source of picture:

Hoefler, A. C. (2003). Effect of calcium concentration, degree of amidation, soluble solids, and carbohydrate type on the gel strength of low ester citrus pectin. Animal and Food Sciences. Newark, DE, University of Delaware.

It is times like this…

I love being a scientist! Four abstracts have been accepted by the Institute of Food Technologists (IFT) for poster presentations at the Annual Meeting in Chicago. It is not until July, so I have plenty of time to get the posters ready.

The abstract titles are (with links to relevant blog posts and abstracts at the IFT Annual Meeting website):

  • Effect of lipids and emulsifiers on the rheological behavior of corn starch gels (IFT link)
  • Effect of flaxseed meal on the viscosity of water-egg white-oil mixtures (IFT link)
  • Effect of calcium concentration and other parameters on the gel strength of low ester pectin (IFT link)
  • The browning of amino acids and glucose in acetate and citrate buffers (IFT link)

The research was not just carried out by me. Of course, I have lab slaves. Actually, the first two were food chemistry class projects as well as continuation of previous research. An undergraduate researcher, Michael Keller, also helped with the last project and is my co-presenter. I have other undergraduate researchers continuing the work from the first two. Yay for undergrad researchers!

The low ester pectin research was carried out by my Master’s student, Andy Hoefler. He was in his earlier fifties when he graduated in May 2003, but unfortunately, that summer was diagnosed with lung cancer (he smoked for over 20 years) and finally, sadly, succumbed in August 2005. I decided it was time to get his research published, which is challenging as Andy knew everything about pectin and I don’t have him to consult. 😦 He is, obviously, listed as a co-author.

Getting these accepted makes it all worthwhile!

Beer Aging Part 2

Beer bottles

In a previous post I reviewed a recently published article on beer aging. I got so interested that I found a review of the chemical changes occurring in beer written by the same authors. While it might have been helpful do that before writing the previous post, it was writing that post that got me interested in reading more about this topic.

As mentioned, the problem with beer shelf-life is that it isn’t really stable [no food is – most food would be defined a “metastable”. Yep, even Twinkies]. During storage, chemicals continue to react which alters the flavor, both taste and smell. This can be positive; for example, wine and whiskey are left to “age” so that their flavors can develop; In beer, the flavor changes are typically seen negative as the beer no longer tastes as it ought. It might not taste “bad” but it tastes differently to expectation. This is particularly important for branded beers. A regular drinker of Heineken[*] knows what taste to expect and would be disappointed if it tasted differently. This is not just beer, but all food. For example, if are you used to eating Kellogg’s Cornflakes and then try switching to the store labeled corn flakes, the taste just is not the same.

So what happens to beer during storage? In the article reviewed in my previous post, they looked at fifteen different markers which were produced by several different reactions. According to the article I am discussing today (“The chemistry of beer aging – a critical review) the main reactions taking place in packaged beer are:

1) Reactive oxygen species in stored beer

2) Reaction leading to formation of carbonyl compounds

a. Oxidation of higher alcohols

b. Strecker degradation of amino acids[†]

c. Aldol condensation

d. Degradation of hop bitter acids[‡]

e. Oxidation of unsaturated fatty acids, including enzymatic breakdown

f. Formation of (E)-beta-damascenone

3) Acetalization of aldehydes

4) Maillard reaction

5) Synthesis and hydrolysis of volatile esters

6) Formation of dimethyltrisulfide

7) Degradation of polyphenols

Having teased you with that list, I am now going to ignore it completely to discuss inhibition.

The most important way beer in which beer chemistry changes during in storage is through oxidation reactions. In the list above at least three of the staling mechanisms are directly caused by oxidation, if not more. So beer can be protected by limiting the amount of oxygen present when the beer is bottled. This includes both headspace and dissolved oxygen. It is also why you won’t see beer in plastic bottles any time soon[§].

Oxidation can also be prevented by the addition of antioxidants. These include sulphite, which is produced by yeasts in beer from sulphate; polyphenols from barley malt and hops; melanoidins produced by the Maillard reaction during heating steps such as malt roasting and wort boiling. Ascorbic acid and chelating agents could also be added after processing.

The prevention of enzymatic oxidation is also important. The enzymes which cause the problems in beer are lipoxygenases. Their activity may be reduced by lowering the pH. Additionally, choosing barleys with low lipoxygenase activity might also help. You could heat the malt to a temperature that would cause the enzyme to be destroyed, but this will destroy desirable enzymes.

Non-oxidative beer aging reactions are very diverse and, therefore, harder to control and inhibit. Many of these reactions were promoted by reducing the beer pH. Sulphite was considered useful as it inhibits the Maillard reaction in addition to, as mentioned above, inhibiting oxidation.

I don’t know about you, but writing this has made me thirsty. See you down the pub!


Vanderhaegen, B., H. Neven, et al. (2006). “The chemistry of beer aging – a critical review.” Food Chemistry 95(3): 357-381.

[*] This is no reference on Heineken, it was the only branded beer that I could think of at that moment. Replace with the name of your favorite beer.

[†] I personally consider the Strecker degradation reaction as part of the Maillard reaction.

[‡] This one, to me, should also be a category of its own as the loss of bitter flavor can destroy the taste of beer.

[§] Go on, some one tell me about a beer in a plastic bottle. And then tell me tastes good in six month.s

Musical Interludes – Musicians and Neuroplasticity

As a musician I am interested in the idea that my brain might be different because of the music I study. This opinion article was published in 2002 (1) and I thought it would be interesting to share.

Neuroplasticity (definition) is when the function of different parts of the brain alter. New neural connections can be made allowing the brain to recover after disease or injury. It also means that we can adjust to new situations and experiences. This is hard to study in animals and even in humans. Since:

Performing music at a professional level is arguably among the most complex of human accomplishments. A pianist, for example, has to bimanually co-ordinate the production of up to 1,800 notes per minute. Music, as a sensory stimulus, is highly complex and structured in several dimensions, so it extends beyond any of the stimuli that have been used in animal research. Moreover, making music requires the integration of sensory and motor information, and precise monitoring of performance. Finally, the study of musicians might allow us to tease apart the effects of musical training or experience from those of genetic predisposition.


So, the musician’s brain might constitute a perfect model in which to study neuroplasticity in the auditory and motor domains.

So how are musicians’ brains different to non-musicians?

From the auditory perspective, musicians have a greater brain response to music played in their instrument. For example, pianists had a 25% greater response to piano tones than non players. When we hear sounds that are not correct, our brains produce something called a mismatch negativity which showed that musicians were more sensitive to changes in rhythm and tones. They responded to a 20 ms change in rhythm, whereas non-musicians did not respond until the change was 50 ms. They were also more responsive to changes in tone. Conductors, who need to be able to concentrate on one instrument at time, were more able at separating adjacent sound sources.

These findings indicate that, after years of musical training, neuronal populations in the auditory cortex might be shaped such that they automatically detect subtle changes in auditory stimulus sequences with simple or higher-order regularities. The parameters that are needed for the acquisition of these skills are unknown, but probably involve initial attentive processing of the stimuli.

There are also some structure differences in the brains of musicians, but it is not clear whether these changes are related directly to musical ability. For example:

Asymmetry of the planum temporale has been suggested as a marker of cerebral dominance, because its direction and size correlate with handedness. In two independent samples, musicians with absolute pitch (AP) had a more pronounced leftward planum temporale asymmetry than did musicians with relative pitch (RP) or non-musician controls; another study found no significant difference in planum temporale volume between musicians with AP and those with RP. However, when compared with a large sample of right-handed non-musician controls, musicians with AP again showed a larger left planum temporale.

Musicians also have to use very precise motor skills; with different hands having different tasks. For example, string players, who use their left hand for fingering, have a larger cortical representation for their fingers on their left hand. This is not seen for the right hand. The younger the musician started playing the more pronounced the cortical reorganization.

As mentioned earlier musicians are typically learning new pieces to play. Neuroimaging studies have shown:

that motor learning occurs in several phases: a fast initial phase of performance gains is followed by a period of consolidation that lasts for several hours. This is succeeded by a slow learning phase that occurs during continued practice and leads to gradual increases in performance

Interestingly, on learning a novel tapping task, professional pianists showed a brain response suggesting that they entered their slow learning stage within minutes of being given the new task as opposed to months for non-musicians. Overall pianists had a smaller neural response than non musicians suggesting that they were more efficient in controlling movement.

Studies on neuroplasticity in musicians will not only lead to better understanding in how the brain may change function as new skills are learned but also help understand illness better. In particular, musicians may suffer from loss of fine motor control (musician’s cramp/focal dystonia). This has been shown to be caused by the fact that the brain fuses the response to different fingers. That is, if I’ve understood this correctly, the brain is unable to differentiate between the different fingers.

My route to this article went via Cognitive Daily who linked to this post at Mindblog, which lead me to this article “The musician’s brain as a model of neuroplasticity


(1) Thomas F. Münte, Eckart Altenmüller and Lutz Jäncke THE MUSICIAN’S BRAIN AS A MODEL OF NEUROPLASTICITY Nature Reviews Neuroscience 3, 473-478 (2002)

Do herbal teas have antioxidant properties?

Researchers publishing in Food Chemistry (link, sub required (1)) studied the anti-oxidative and anti-hydrogen peroxide (H2O2) activities of herbal teas.  The herbs they studied were lavender, rose, chamomile, hibiscus, lemongrass, sage, rosemary, echinacea, thyme, peppermint, gingko, liquorice, and thorn apple. They compared their antioxidant properties and prevent the formation of H2O2 with those of green tea.

Herbal teas or tisanes are high in polyphenols, which as free radical scavengers have anti-oxidant properties. I thought I understood the reason why they studied H2O2 as in the body a highly level of H2O2  could lead to free radical formation and further oxidative damage, but the amounts produced, even by green tea are too small to be significant. In fact, some might even be helpful. Catechin derivatives in the teas have been previously shown to increase the formation of H2O2. The pH of the tea was a strong influence on H2O2 formation.

They prepared the teas by mixing 0.1 g dried herb with 10 ml H2O at 100 oC and steeping for 10 minutes before filtering.  The filtrate was measured for total polyphenols, radical scavenging activity [for those who care radical-scavenging activity was measured by reaction with DPPH] and H2O2 concentration.  The polyphenol concentration and radical-scavenging activity correlated to give a correlation factor of 0.950. Tea made from rose [do they mean rose hip?] was the only tea to have a higher polyphenol content and radical-scavenging activity than green tea.  A factor put down to the anthocyanins present in rose; which are also responsible for the color.  It is possible that rose has a high level of vitamin C which has anti-oxidant activity.

H2O2 formation did not correlate with either radical scavenging activity or polyphenol activity but may be related to pH as shown by the fact that echinacea tea had the highest pH and the highest H2O2 concentration.  During incubation the H2O2 concentration increased only for green tea.  If thorn apple (perhaps that it rose hip?) and hibiscus reduced the formation of H2O2 when mixed with green tea.

There was a similar article in the same addition of Food Chemistry (link sub req. (2)) which was looking at the antioxidant properties of extracts from large thyme (Thymus pulegioides rather than Thymus vulgaris).


1) Aoshima, H., S. Hirata, et al. (2007). “Antioxidative and anti-hydrogen peroxide activities of various herbal teas.” Food Chemistry 103(2): 617-622. Link

2) Loziene, K., P. R. Venskutonis, et al. (2007). “Radical scavenging and antibacterial properties of the extracts from different Thymus pulegioides L. chemotypes.” Food Chemistry 103(2): 546-559. Link

The Hodge Scheme

Hodge Mechanism

This is such a cool reaction mechanism. It was designed by John E Hodge in a what is now a citation classic. It sums up the Maillard Reaction, which is as complicated as the reaction scheme above suggests. This is such a classical scheme that it is known as the “Hodge Scheme”. I find that pretty impressive; it would be great if there was ever a “Lab Cat” reaction scheme.

Hodge was an African American who gained an MA from the University of Kansas in 1940 and worked for the USDA for more than 40 years. Sadly, there was no Wikipedia page for this amazing man, so I started one. If any one knows anymore information about him, please, please add to the Wikipedia page.

Hodge, J. E. (1953). “Chemistry of browning reactions in models systems.” Journal of Agricultural and Food Chemistry 1(15): 928-943.

Citation Classic (pdf)

John E Hodge Bio


I was trying to find a food science topic to write about. I have just gave my candy technology lecture to my freshman class and was going to write that up, and then realized that Exploratorium does a very good job of that already.


I then thought I should do something with a Thanksgiving theme, but with being British and vegetarian I don’t really celebrate a traditional Thanksgiving. I will be eating Vegetarian moussaka if any one is interested.

Which leads to flaxseed. One of my food chemistry class projects is on flaxseed because I published an article[1] on using flaxseed meal in whole-wheat muffins. The only major difference we found between muffins with and without flaxseed meal was that the batter with the flaxseed meal was significantly thicker. I actually did this project initially as a colleague who was studying the nutritional effects of flaxseed couldn’t do a double-blinded trial as at that time it was not clear as to how stable the nutritive components of flaxseed were. Also it is hard to discuss flaxseed in a food product such as muffin, as it adds a nutty flavor. Continue reading