Health NewsNutrigenomics
I’ve been discovering a new omics to add to my vocabulary, and one I needed to learn about quickly. This time it is nutrigenomics and the reason I have to steepen my learning curve is because I’m part of the team putting together the business case for the Alberta Nutrigenomics Initiative.
Nutrigenomics I’ve discovered is not about simply eating your flakes of bran and getting more exercise. In fact arguably you could say it looks at people and predicts who might have to eat a little less in case they are part of a population that will have difficulty with their morning cereal. Nutrigenomics focuses on the molecular relationships between nutrition and the response of genes so we can understand and predict how subtle changes can affect human health. It involves the products of genes, including proteins and metabolites, and the physiological function and interaction of these products. By determining the mechanisms of the effects of nutrients, nutrigenomics aims to define the relationship between specific nutrients and human health. Research has shown that individuals react to and benefit from nutrition in very different ways, and it has become clear that the different individual responses to nutrients are the result of unique genomic profiles. Thus a more complete understanding of health and disease processes must include the simultaneous analyses of nutrient intakes and genomic profiles.
Yes, the work could lead to some basic conclusions and may even give us a few more ‘health foods’ which is the answer to the first question people seem to have been asking me.
Epigenetics
Contributions from Mendel, Darwin, and Watson and Crick among others have led to the heuristic model we teach in school which describes how genetic information is passed from generation to generation, and how it is used by the cell to produce functioning protein. The model describes how small changes in the genetic material happen, and how advantages from those small changes over time can result in some organisms being more competitive leading to change of species over time. Just when we think that all the pieces of the puzzle start coming together, we find some alternate evidence which may require a different model, or certainly a modification of the current one.
The popular press likes to show things as controversial. In a recent example, you may have read about in newspapers or in popular science magazines, it was reported that some inheritance appeared more related to the older theory of Lamark rather than the model of Darwin. What seems to be happening is that in some cases, changes are brought on by the environment which last for several generations. For example, it was found that some mice when fed certain diets produced offspring very much different than the same genetic variants fed a different diet. Furthermore, these changes in the offspring were passed on for many generations yet there was no change in the genetic code. In other words, phenotypic changes in offspring were expressed even though there were no mutations.
The current understanding of the phenomena is explained not by getting rid of over 100 years of the model, but by supplementing the long standing model with what is called epigenetics. The prefix epi means on top of. Epigenetics refers to something imposed on top of genetics. The something may be as simple as a change to the regulation of a gene which may be simply an on – off switch. A lot of research in going into this topic and we can expect to read a lot more about epigenetics in the future.
What is Metabolomics?
According to our model of genetic information being used by the cell, the DNA is transcribed to RNA, and that RNA is translated into protein. The protein has a function in the cell, and some of the cellular functions involve the protein acting as an enzyme to facilitate the reaction of cellular chemicals called metabolites. Ultimately then, the expression of the DNA will result in many cases as unique metabolites in the cell. In part, the study of metabolomics examines the unique interaction of genotype and phenotype through a characterization of the small molecule metabolites of the cell. In its simplest form, if the genome represents the blueprint of life, the metabolome represents the ingredients of life.
Researchers at the
Additional extensive information is available on the Human Metabolome Project website.
Genomics and Curricular Disaggregation
Too often, we hear students tell us that they have studied for hours and hours only to discover that they did not study the right stuff for the test. While this may be just an excuse to some, it can be a very real problem to some students who just cannot pick out what are the important concepts to know. A number of years ago, I was introduced to “Curricular Dissaggregation” as a means of helping students see the bigger picture. By providing appropriate questions together with some major topics, students can feel comfortable knowing what they need to know. Effectively, a framework for study has been created. By initially assisting students to develop these frameworks, you are helping these students develop the study skills which they can use for the rest of their educational careers.
Additionally by disaggregating the curriculum, it will provide you with an extensive topic list. This will help you present and/or review the topics in a logical manner ensuring that the students can see where you are going with the concepts. In the download section, you can select a file which is a curricular disaggregation of molecular genetics and genomics. While this is by no means a prescription on how to teach or what to teach, I hope that it provides you with a model for curricular disaggregation that will be of assistance. If you have additional comments or suggestions for improvement, by all means use the comment section to respond to this topic.
Genome Alberta Congratulates CWSF Winner Emily Cooley
A genomics related project has been recognized as top of the fair at the 2007 Canada Wide Science Fair in Truro Nova Scotia. We congratulate Emily Cooley of Queen Elizabeth Junior/Senior High School in Calgary for her tremendous accomplishments.Emily’s project “blew away some of the judges and said it could have an impact in the world of science” according to the Truro Daily News reporting a statement from Reni Barlow, executive director of The Youth Science Foundation Canada. I have written about Emily’s project on a previous blog (Genomics Projects at the Calgary Youth Science Fair). We were pleased to have awarded her the Genome Alberta Senior award at this year’s regional fair. We hope that Emily’s success will encourage future students to do genomics related science fair projects.
Congratulations Emily!
Genomics and the Curriculum
It would be such an awesome coincidence if the study of Genomics was a spiral curriculum as a metaphor for the spiral double helix of the DNA being studied. Alas, I believe that the study of Biological Sciences and specifically of Genomics is more like doing a very large picture puzzle, but there is not image on top of the box. As teachers then, we assist students by helping them pull out a few pieces at a time to get an idea of what the picture looks like. The easiest pieces to pull out of the box are the edge pieces. As we put the edge pieces in place, and start to sort out a few of the inner pieces, the bigger picture starts to come into focus. Each teacher probably has a unique way of pulling the pieces out and laying them on the table. The order of the initial pieces does not really matter as long as some progress is made. Some students will need to see fewer pieces prior to conceptualizing the bigger picture. Overall however, we want all our students to be successful at the end of the course, knowing that at the high school level many of the puzzle pieces remain in the box to be pulled out in undergrad or even in post-graduate studies by only a few of the students. This blog will endeavor to examine various pieces of the puzzle on an ongoing basis. Anytime new pieces are produced (through research) which assist our overall understanding of genomics, I will do my best to make them available. Some of you may have ideas, suggestions and/or curricular approaches to the ideas presented. I encourage you to comment on the blog and share your information with other teachers in the province who are part of this Genomics network.
How Honey Bee Genomics Explains the Demise of the Bees
The recent release of the honey bee genome has resulted in some interesting information regarding bees. While the genome is contained on 16 chromosomes and 265 million nucleotides, perhaps one of the most surprising findings is that the honey bee is an out of Africa species. All bees can be traced back to Africa and moved into Europe and Asia from there. Additionally, honey bees are not native to North America. Apparently, the bees were brought over to North America in four distinct groups. In the 1600’s the first bees were brought over from Europe and used commercially. Additional bees were introduced from Italy in the mid 1800’s, and later imports came from Spain and Portugal. The final introduction of bees to North America was in the 1990’s.
Studying the Mountain Pine Beetle: An Idea for a Cross Curricular Project
If you were to google the pine beetle pine beetle, you
would get more than 1.2 million hits. It is hard to pick up a newspaper or
magazine these days without reading something about the pine beetle. Teachers
can use this current societal interest in the Pine Beetle for class discussion
and/or projects related to the pine beetle give an excellent opportunity for
real world problem solving and cross-curricular studies. Students want to know
what is involved in this topic as it makes the news frequently. You can
illustrate concepts in ecology and genetics, societal impact, economics and
decision making past and future. Download
the 'Inquiry into the Mountain Pine Beetle Epidemic' Power Point Presentation
[40 MEG]
Dendroctonus ponderosae, is an
important part of forest ecology. Under normal circumstances, it fills the niche
of forest renewal by attacking older, weaker trees leading to the turnover and
renewal of the forest. Since the pine beetle normally attacks older stressed
lodgepole pines that are about 80 years old, they play an important role in the
succession of the forest. The pine beetle lays eggs in the phloem of the pine
trees. The pine beetle is also in a symbiotic relationship with a fungus, which
prevents the pitch from sweeping the invaders out. Additionally, the action of
the boring of the beetle and the damming by the fungus leads to girdling the
tree. The subsequent death of the tree provides a home for the larva through the
winter. The larva then pupate in the spring and full beetles emerge in the
summer to start the cycle again.
Winters that have substantial periods
of weather below – 30 C tend to keep the beetles in check. The outbreaks of
beetle infestation in British Columbia have been spreading over the past 20
years in part because of a century of fire suppression and subsequent mature
forests and in part because there have not been prolonged periods of cold winter
weather through the past 20 years. In British Columbia, there are a variety of
management techniques being used to attempt control of the Pine Beetle. Besides
cutting and burning techniques, some research has been done using pheromones to
lure in the beetles toward a central area where they can be destroyed.
Genomics as it relates to the Pine Beetle have been underway for a
number of years. Because there are three organisms involved in the infestation,
the host, the beetle and the fungus, there are several lines of research. These
studies are sometimes called ecological genetics, as it involves the genetics of
interaction of species. From the perspective of the host, researchers are
looking into resistance and defense mechanisms. With regard to the beetle, there
is the life cycle. Researchers are especially interested in the genetics of
pheromones. Finally, there is interest in the fungus and its ability to assist
the beetle in overcoming the host’s defenses.
Student Information Sources
As I was preparing for my presentation at this year’s ATA Science Council Conference, I
noticed an interesting photo opportunity. There sitting in front of me, two
major means of students obtaining their information. 
The text book – Inquiry into Biology - just arrived
compliments of Cam McDonald, the Southern Alberta Sales Representative for McGraw-Hill Ryerson
School Division. He promised me a textbook as soon as it came off the press.
When I received it, I eagerly flipped through and was impressed that several of
the authors and reviewers are among the most respected and innovative Science
teachers in Alberta. Although I have not used the book with students, I am sure
that this text, like its predecessors, is the canon from which our students will
lean heavily for the basics. Inquiry into Biology is well organized, and has the
type of activities which lead students to reaching out and going beyond the
text. Inquiry into Biology has a sidebar on the Pine Beetle. These days, one
cannot avoid seeing or hearing about the Pine Beetle. It is the subject of over
1.2 million pages on the internet, and rarely a week goes by that there is not
some article in the newspaper. The article
pictured by Karen Lazaruk is from the Airdrie Echo. These represent other
sources of information for students. Our students will be exposed to a great
deal of scientific information besides what is in the text. Our role as teachers
is to guide them through their inquiry and to give them the skill set that they
will use as adults to evaluate the plethora of information they will be exposed
to on a daily basis. I look forward to discussing these topics with you at this
year’s ATA Science Council conference.
What is a Mutation?
Back in 1987, I submitted a paper to The National Association of Biology Teachers to be included in their refereed journal “American Biology Teacher”. I had been inspired to write this piece based on my student’s feedback that they really liked the way I explained a certain topic. I was crushed when the referees initially rejected the paper as being too simple. They said that its simplicity was potentially leading to students being mislead. As I was contemplating whether I would proceed, the word heuristic came to mind. I added this one word to my paper, and it was published the next semester (A Handy Model for Mitosis, American Biology Teacher 50:170 -172, March 1988). This paper has been cited several times subsequently as an example in teaching/learning from the right brain. I don’t really know about sides of the brain. What I do know is that students need to be given rather simplified models to begin with, and once the understanding is in place the exceptions and anomalies can be introduced. All too often, the editors of text books in their quest for shortening the amount of written material have as their example something that does not even behave according to the model presented. For example, some text books also operationally define chromosomal abnormalities as a type of mutation. In this blog entry, I am not going to include for discussion the type of mutation which affects large segments of the chromosome such as non-disjunction. I am only going to discuss the type of change which takes place more or less at the molecular level. If you have had a chance to see the curricular disaggregation in the previous blog, you will have noted that I broke the topic down to gene mutations and chromosomal abnormalities as shown in the following:
Using Mendel to Predict non-Mendelian
Mendel is sometimes called ‘the father of genetics’. Genetics was not unknown prior to Mendel’s time. Knowledge of genetics has probably been used my humans since the earliest transition to agriculture. Farmers knew that they could select the biggest and best seed to plant the next year’s crops, and that they could get the best characteristics of both parents in breeding of livestock. The ability to make predictions is a major element of the scientific process, and the major contribution made by Mendel was giving the science of genetics a method to make predictions. Before Mendel, it was known that the offspring characteristics were a blend of the parents. One example I have used to illustrate this is the breeding of a cocker spaniel and a poodle resulting in a cockapoo. Mendel, by looking at only one characteristic at a time, found that the offspring were either like one parent, or they were like the other.
Was he lucky, or did he discard evidence which did not support his theory? We will never know since his books and papers were all burned after his death, and his papers were not really widely read until almost 50 years after his death. The beauty of Mendel’s methods of prediction, is that we can use his algorithms even when the inheritance is non-Mendelian. We have the benefit of knowledge gained in the more than 100 years since Mendel. There is a confluence of ideas including Mendelian genetics, meiosis and the biochemistry of protein synthesis.
Mendel picked a characteristic such as plant height which had either tall plants or short plants. We now know that the plant is tall if the hormone, gibberellin, is produced and the plant is short if the hormone is not produced. The prediction works if the hormone is coded for two times (homozygous dominant) or only one time (heterozygous). Unlike peas, human height is the product of many genes interacting with environmental factors. Thus Mendel’s methods do not appear to work for predicting the height of humans. You may wish to have more mathematically inclined students play with numbers as follows.
How did number of chromosomes become called a haploid, diploid, or polyploid ?
When I began my teaching career, the curriculum of the day recommended a de-emphasis on history. While the focus was all about inquiry, I always found it difficult to ignore the history. I personally like to know the history of an idea or concept. As I walk through any bookstore today I stroll past rows of books which describe the history of science and/or detailed biographies of scientists concentrating on how ideas are developed. While I wouldn’t evaluate based on specific historic knowledge, I have used it as a hook to help in the story telling.
Today, I wanted to explore the idea of polyploidy and its role in biotechnology. But before I could do that, I needed to really know where the suffix –ploid comes from. We know that Scientific terms that have been around for many years, often come from Greek and Latin roots. I don’t seem to have any problems understanding that diploid means two sets of chromosomes. I do find it amusing that haploid refers to half the diploid number, setting up sort of a circular definition. Then some writers use the term monoploid. Is it any wonder that some students become confused?
The study of cells can be divided up into three general phases. The first phase involved accepting the very idea that cells make up the basic unit of life. This concept, called “Cell Theory” is generally attributed to Schleiden and Schwann.
The second phase focussed on the microscopic studies and the types of observational data which could be collected. This was termed cytology. Cytology as a study of cells under the microscope progressed through many years of developing better microscopes to see the cells and better stains to bring out the organelles. Cytologists are still very important for looking at cells to determine abnormal growth and perhaps cancers. Many scientist were involved with developing our current concept of meiosis. The term, ploid, they used to describe a set of chromosomes comes from the Greek meaning fold. Knowing this, it becomes easier to think of the early scientist deciding that a bunch of wiggly lines on the microscope represented a double fold (diploid) or half that number (haploid).
The last phase was ushered along with the development of molecular biology
and biochemistry. In my next blog entry, I will look at the use of polyploid
organisms in biotechnology.
Perspectives on GMO
As I was driving back to the city this week, I was listening to a local radio station interviewing several of the singer song writers attending the local folk festival. It was all interesting discussion of the music and the influences on their craft. Then, I could hardly believe what I heard. One of the singers went on a total tirade condemning the use of genetically modified foods. She insisted that all those listening should work to ban the use and existence on the planet of organisms produced through GMO.
Science Communications: How Scientists Tell the World About Their Results
Students are all too familiar with the work they do to submit a project or an
essay to the teacher for marking. But, do they know the process scientists must
go through to have their work “evaluated”?
Recently I was able to attend
the trade show portion of the Special Libraries Association (SLA) annual
conference held in Denver, Colorado. While working my way around the booths, I
had the opportunity to discuss the publication of science work with Simon
Boisseau of the Future Science Group (FSG). While there are many pathways for
scientist to publish their work, from what I learned from my discussion with
Simon is probably representative of the way credible scientists present their
work in what is called peer reviewed publication. FSG is a British company which
produces Expert Review and Future Medicine two series which
include the journals Molecular Diagnostics, Personalized Medicine,
Pharmacogenomics, Proteomics and many other titles related to Molecular
Medicine.
What is an SNP or Single Nucleotide Polymorphism ?
The power point presentation which we made available on line
when we first started this web site was titled Genomics: A New Revolution in
Science and the subtitle was: an introduction to promises…As I
discussed the presentation at various conferences and conventions through last
fall and winter, the new part to most teachers was the discussion of
SNP’s and the promises were related to what we defined as personalized
medicine. Since that time, there seems to be not a month goes by when there is
not some sensational announcement in the newspaper which mentions SNP’s or
personalized medicine. It was not a crystal ball which allowed me to make these
predictions; it was the knowledge and confidence of scientists such as Genome