Dr. Stuart Reichler’s Fall Bio 301L Homework #2
Should be emailed to sreichler @ mail.utexas.edu by Monday, October 9th at noon

    We (students, professor, and TA) are going to work together to determine the topics we will study for the latter part of the class.  Now that each of you have submitted an article that you feel would be worthwhile to study, we are all going to work together to decide which articles we will cover.  Please email me your top 5 choices, numbered from 1 (favorite) to 5 (fifth favorite), and a short, less than 100 words description of why you chose each of these five article.  Your rationale for choosing the articles should include why you think it is important for us to study these topics, and/or why you think the topics are interesting.  The articles are listed below.

    The format of the assignment should be as follows:
Your name
Bio 301L

1) Favorite:  Article title
This is my favorite article because...

2) Second Favorite:  Article title
This is my second
favorite article because...

3) Third Favorite:  Article title
This is my third
favorite article because...

4) Fourth Favorite:  Article title
This is my fourth
favorite article because...

5) Fifth Favorite:  Article title
This is my fifth
favorite article because...

    Please include your assignment in the body of an email and send it to me by noon on October 9, 2006.  This homework will be graded on a scale of 0-3 points based on your rationale for choosing the five articles.  I will subtract 0.5 points for each day late.  After I receive all of your submissions, I will post the schedule for the rest of the semester.

Articles: in no particular order:

Avian H5N1 Influenza in Cats
Thijs Kuiken, Guus Rimmelzwaan, Debby van Riel, Geert van Amerongen, Marianne Baars, Ron Fouchier, Albert Osterhaus

Science 8 October 2004:
Vol. 306. no. 5694, p. 241
The following article mainly adresses the experiments that disproved the general thought that cats were generally resistant to influenza A. This discovery of the characteristic of the Avian flu allows scientists to redesign the view of how the virus spreads and what roles can/do cats play. The question proposed in the article is that, ultimately will the virus change and adapt specifically for humans and be able to spread from human to human? This to me is a pretty serious topic since now we are such a small world and it all can start with a cough.

Early Detection of Lung Cancer: Clinical Perspectives of Recent Advances in Biology and Radiology, Fred R. Hirsch, Wilbur A. Franklin, Adi F. Gazdar and Paul A. Bunn, Jr., Clinical Cancer Research, Vol. 7, 5-22, January 2001

Lung Cancer is becoming one of the most common causes of cancer death with less than 15% of patients surviving five years after diagnosis. Researches conclude that the reason for this poor prognosis is heavily dependent on the lack of diagnostic methods for early detection and the lack of successful cures.  However, scientists have made significant advances over the past ten years through the study of molecular biology, pathology, and radiology.  It is with these advances that scientists are now closer than ever to finding a way to reduce the mortality of lung cancer.  The question posed in this new research deals with new technological advances like the LIFE bronchoscope that has proved to be much more ideal than the conventional X-ray, and whether or not this early detection of lung cancer will be able to identify biomarkers leading to chemoprevention.

Embryonic Stem Cells for Medicine, Pederson, Scientific American Magazine, 6, April 1999.

The article discusses the use of being able to isolate cells to basically force them to grow into whatever we want. It deals with the morality of the issue of getting the cells from the embryos and then "manipulating" there growth. It gives the example of a guy having a heart attack and by the time he reaches a hospital only one-third of his heart is working and that by using stem cells the part of his heart needed to make him better can be created and implanted with virtually no rejection from his immune system.

I think this would be an interesting topic for class because it would allow us to see how cells form and would show us the different functions of the cell. But at the same time it would allow us to better understand the impact that cell growth can have on us.

"BRIT1 regulates early DNA damage response, chromosomal integrity, and cancer"

Rekha Rai, Hui Dai, Asha S. Multani, Kaiyi Li, Koei Chin, Joe Gray, John P. Lahad, Jiyong Liang, Gordon B. Mills, Funda Meric-Bernstam and Shiaw-Yih Lin

"Cancer Cell" Vol. 10 Issue 2, p 145-157, Aug 2006

BRIT1 is a gene located on chromosome 8p23.1, a region implicated in the development of several malignancies, including breast, ovarian and prostate cancer.  Researchers wanted to know what role BRIT1 might play in transmitting DNA damage signals and how a depletion of BRIT1 in cells would affect levels of chromosome aberrations and genomic instability.  The studies indicate that the gene plays a direct and important role in the DNA damage response pathway and that BRIT1 expression seemed to have an inverse correlation with genomic instability, chromosomal aberrations, and metastasis.  This suggests that it functions as a tumor suppressor gene, and researchers hope that further understanding of this function will lead to new therapeutic approaches for cancer.

This article seemed apropriate for a myriad of reasons but especially because it pertains to five out of six of the professor recomended subjects.  Not only is the article relevant to class material, but it is presented in such a way that its significance can be grasped with only a limited scientific literacy; the rammifications of the findings are broad enough to be appreciated by those of us who have no idea what "chromosome 8p23.1" means.  Also, given that the article concerns a subject of perpetual scientific inquiry(cancer), it is important that it be as recent as possible.  Published in August of this year, this article presents the latest developments in this field of research and does so with enough figures to be what I would consider visually compelling, making it an apropriate candidate for an interesting class discussion.

Season of Birth Contributes to Variation in University Examination Outcomes,
Martin Fieder, Hermann Prossinger, Karoline Iber, Katrin Schaefer, Bernard
Wallner, and Susanne Huber, American Journal of Human Biology, Vol. 18, p.

The authors of this article raise the question, “Does the season you’re born in
affect your schoolwork?” To carry out the experiment, the scientists created a
database of thousands of students, both male and female, at the University of
Vienna and collected their examination results (a minimum of five) and their
dates of birth. They found that females born in autumn and winter did not
score as well as those born in spring and summer, and males born in performed
worse than those born in other seasons. This article would be interesting to
discuss because we as students can relate to it. Perhaps it can provide some
answers to those of us who study for weeks and still fail miserably on exams,
and now we have scientific proof for our parents as to why we flunked out of

Article Title: Systematic Size Study of an Insect Antifreeze Protein and Its Interaction
with Ice
Authors Name: Kai Liu, Zongchao Jia, Guangju Chen, Chenho Tung, and Ruozhuang Liu
Journal Title: Biophysical Journal
Volume: 88
Page Numbers: 959-970
Date of Publication: February 2005
How can organisms survive sub-zero temperatures? Anti-freeze proteins play an important role in helping organisms have the ability to depress such conditions and live in these kinds of environments. Insect’s anti-freeze proteins are looked at more closely than humans because more a greater population of insects live in human-intolerable places. Insect anti-freeze proteins consist of many repeating loops. In order to understand how many loops the structure needs to survive freezing temperatures, an understanding between the relationship of anti-freeze loops and anti-freeze ice interaction, which starts anti-freeze activity, must first be reached. Since the creation of additional loops of anti-freeze proteins according to the temperature is a suitable hypothesis, the initial action of the ice binding to the anti-freeze proteins in order to initiate the growth is also something to consider. A found trend found among anti-freeze proteins is its remarkable small size. Another hypothesis in this experiment is the relation between the size of the insect and its number of repeating loops.
The experiment’s results found that anti-freeze protein-ice interaction energy increases with the increasing of loops to a certain amount, and from there, the loops begin to gradually decrease.

Breaking New Ground: Soil Communities and Exotic Plant Invasion²
John N. Klironomos, Benjamin E. Wolfe
Bioscience; Volume 55, Issue 6; pages 477-478; June 2005.

Think about it: studying the ground to understand why dirt is the way it is
seems pointless. But what the soil can tell biologists is the importance of
biodiversity among terrestrial ecosystems. Klironomos and Wolfe admit it is
difficult to make strong generalizations about the effects of exotic plants
on soil communities, because only a handful of published studies have
documented the effects of invasive plant species on the composition and
functioning of these communities. Nevertheless, in current times and in
numerous ecosystems, an invasion of exotic plant species is causing major
shifts in the composition and function of soil communities, according to
researchers. The question is though, what will be the ultimate effects that
the exotic plant species will have on native plant communities? One must
also consider the attributes of the native communities that make them
susceptible to invasion. Scientists have only recently developed the tools
to analyze the composition of soil communities. It has been revealed that
invaded communities are completely different in organic composition from
native communities. Major functions considered include the rates and
dynamics of biogeochemical processes and the habitat aptness for other
organisms. Furthermore, there is an emerging awareness that belowground
communities need to be incorporated into ecosystem management because of the
plant invasions. Klironomos suggests that understanding differential
responses to invasion can provide important practical information about the
impacts of exotic plant invasions, as well as insight into the basic ecology
of soil food webs and controls on soil biodiversity.

Klironomos and Wolfe assert, ³As an exotic plant species invades a
community, it can alter links between native aboveground and belowground
communities, including the timing, quality, and spatial structure of
plant-derived soil inputs.² If an exotic plant species invades a community,
the quantity, quality, and timing of litter production can be altered. This
alteration may result in changing the nutrient inputs into the soil;
increased litter production from the exotic plants has the potential to lead
to increases in fire intensity and frequency. With that, changes in fire
regime could indirectly alter soil communities through soil community
function and structure (figure 2).

The major biological change occurs in microbial communities¹ compositions in
the soil. The composition of the microbial communities is determined by
phospholipid fatty acid profiles. Another assertion made is that specific
groups of microbes have Œsignature¹ fatty acids in their biomass. Those
Œsignature¹ fatty acids can be extracted from the soil and used to detect
the presence and abundance of the groups of microbes. Phospholipid fatty
acid analysis assesses the changes in the production of phospholipids.
However, biodiversity among organisms that are affected by aromatic
alteration of their habitat cannot easily be observed or tested. It is more
useful to have knowledge of the net effect on soil communities for full
understanding an invasion process has on the soil. A more traditional
method used for evaluating the soil diversity involves incubation of soil
extracts. Feedback has been interpreted through the observation of the
change in the composition of the soil organisms within the communities. The
change is measured by observing the alteration of abiotic or biotic
components of the soil communities. Many soil organisms produce
extra-cellular enzymes. Any of these enzymes can degrade complex substrates
in the soil, thus altering the availability of nutrients and the development
of a species (figure 5). An example given in the article about some orchids
is that they are dependent on soil fungi for establishment and growth. If
dominance by an exotic plant species has eliminated these fungi from a
community, the orchids are at risk for elimination. It may be necessary to
introduce propagules of the fungus to the site in order to save the orchids.
The importance of restoration of invaded habitats will become more apparent
in time to soil ecologists, plant ecologists, and specialists.

An exotic plant species has the capacity to invade an ecosystem and alter
the soil community composition. Changes in soil communities may directly or
indirectly effect ecosystem processes, throwing everything off. By changing
ecosystems¹ properties and processes, a direct effect on plant growth
occurs, as well as alterations in biogeochemical cycling and soil structure.
Native soil communities play fundamental roles in ecosystem properties and
processes, which is ultimately why the potential alteration of soil
communities by exotic plant invasion is of concern.

"Conservation at a distance:  A gentle way to age", Carina Dennis, Nature, Vol.442, Pg. 507-508, 3 August 2006

This article is focusing on the way researchers collect infromation about the age of whales. For a long time, the only way to learn the age of these whales is to kill and disect them in order to examine the lamination rings formed in their ear wax. Trying to stop whaling, a group of researchers led by Peter Harrison is developing genetic techniques to age humpback whales from their sloughed skin. By analyzing the telomeres from the collected skin. Telomeres are short, repeated piece of DNA at the tip of the chromosome. These telomeres tend to shorten as whales age. One disadvantage of determining age of whales this way is that the result is not accurate. Some of the other problems involve getting mixed or dead and damaged skin samples. But if the group succeed in determining age from skin samples, many whales' lives can be saved!

Cancer cell study deepens fears over cellphone safety. Graham-Rowe, Duncan. New Scientist. Vol 176 Issue 2366, p6. 10/26/2002.

The article is talking about how radio waves from cell phones could promote growth of tumors. There has beeen an on-going debate on whether or not cell phones cause cancer or other related neurological problems, and I think through finding different articles about different research studies dealing with cell phone usages, this topic would be interesting to talk about in class.

Turning Yellow, Christine Soares, Scientific America, April 10, 2006

The problem posed in this article is to see if it is possible to add foreign proteins to the yellow fever vaccine so that it can fight other germs creating a “universal” vaccine.
The problem or the risk here is that adding other immunological proteins could disable the original vaccine's funtion. It would be interesting to read and talk about this article in the course so that we could relate it to different topics seen in class like the steps in strong inference to see the experiment designed to answer this question and how it is proven, how or what infected cells this immunity attacks now that we understand cells. We could see how the cell is affected with the virus and what parts of the cell contributes to fighting the virus and how is it done. We could also relate this article to the gene or inheritance or even evolution lectures examining how this vaccine could lower the risk of having certain kind of virus being transmitting it to the next generation. I think the most important comparison is the parts of the cells fighting against a virus using the yellow fever vaccine.

Digital RNA regulation of complex organisms., Mattick, John S., Gene Therapy &
Regulation (VSP International Science Publishers); Vol. 2 Issue 4, p313-319,

This article discusses the possibility that the RNAs that do not code protein
have a direct impact on the complexity of the human body. With such a
minuscule difference between the DNA of humans and earthworms, how can it be
that humans form complex internal organs along with bones and muscles?
Previously the purpose of the non-protein-coding RNA was not exactly clear.
This article states that those RNA send genetic signals into the system in a
specific order which helps form the shape of the cell's extracellular membrane.
This formation is what enables our bodies to build all our complex systems.
This is truly fascinating because its an interesting discovery that could
seriously change the way we look at the coding inside a cell. Also, this has
interesting implications on the evolution of humans as well as all complex life

Article title: Genetic quality and sexual selection: an integrated framework for
good genes and compatible genes.
Author’s name(s): Bryan D. Neff and Trevor E. Pitcher
Volume 14 Issue 1
Journal title: Molecular Ecology
Volume: 14
Page number(s): Mol Ecol. 19-38.
The date of publication: January 2005

I think this "sexual selection" article is interesting because it describes how
and why other mammals "choose" their "mates". It is a little different in the
human selection because now we are more involved in the psychological and
emotional part of sexual or natural selection. Humans not only search for
someone they think will be "compatible" or have "compatible genes" AND someone
that has "good genes" for a high fitness or for a healthy "reproduction
process". I also think it will be interesting to learn as to WHAT makes us
choose WHO we choose and WHY we choose them. They discuss biological mechanisms
for acquiring and promoting offspring genetic quality and categorize these into
three stages during breeding: (i) precopulatory (mate choice); (ii)
postcopulatory, prefertilization (sperm utilization); and (iii) postcopulatory,
postfertilization (differential investment). I don't know, kind of things
sounds cool to know why we are with who we are with! Some people may have more
of some gene that makes them want to be with someone that is very masculine and
powerful, rather then someone that is protective and caring?

Prions: proteins as genes and infectious entities
Reed B. Wickner, Herman K. Edskes, B. Tibor Roberts, Ulrich Baxa, Michael M. Pierce, Eric D. Ross and Andreas Brachmann
Genes and Development. 2004 18: 470-485
Well, I was surfing the web for articles on diseases, I was able to stop at a title that caught my attention, “Prions: proteins as genes and infectious entities.  In our lectures, we have gone through the functions and purposes of proteins, “the ‘doer’s’ of the cellâ€�; the article as a whole can be summarized through the title itself.  It is about proteins that function as genes and infectious diseases.  It starts off by describing a prion; “a prion is an infectious protein.â€�  The class by now should all know the function of a protein—they allow chemical reactions to take place; support the cell; move things from one place to another within the cell and they also send signals.  Just imagine what would happen if the “doersâ€� were in fact infectious, the article goes through with this explanation. The change of a protein to a prion makes the cell toxic; even then, the proteins are still able to carry out normal cellular functions.  There are three genetic criteria for a prion.  The first is Reversible Curability; this explains how a prion is able to reversibly change back into its normal health state, a protein. The second property is, “Overproduction of the protein increases the frequency with which the prion arises.â€� The last is, “the gene for the protein is required for propagation of the prionâ€�.  The article moves on to explain the other types of prion’s such as the mammalian and how cell modifying proteins have the potential to be a prion too.  There are several types of prions;’ URE3, PIN, URE2, etc.  The article was difficult to understand, however, I think that it would be interesting to explore this; it branches out to several other areas as well. There were also several appealing experiments that were preformed with prions.  The article was able to come to three main conclusions; the first was that if a yeast were to have four prions, many other organisms are likely to be found to harbor such entities. The second was why a cell chooses to carry out a function using a prion.  The last was how the cellular components limit the roles taken by [some] prion.  I would explain further, but as I said before, the article was no walk in the park the was a lot of scientific terms that were difficult to comprehend.  However, despite the diction, it should be fun to explore if chosen.

Mood, cognition and serotonin transporter availability in current and former ecstasy (MDMA) users: the longitudinal perspective.(Original Papers)(methylenedioxymethamphetamine ). R. Thomasius, P. Zapletalova, K. Petersen, R. Buchert, B. Andresen, L. Wartberg, B. Nebeling and A. Schmoldt.
Journal of Psychopharmacology 20.2 (March 2006): p211.

This article explores the relationship between MDMA usage and mood, memory, cognition, and serotonin levels. An initial experiment found that in ex-ecstasy users there did seem to be permanent serotonergic damage, and that mood and cognition were also affected. The current study reviewed in the article hoped to gather more conclusive data about this effect. The number of test subjects were reduced to about half but included many from the original experiment. The testers divided the groups into three categories: current ecstasy users, ex-users and non-drug users. The testers tried to account for the affects of other drugs used, common for many current and former MDMA uses. Three rounds took place. In each round, subjects went through a battery of tests to check memory recall and evaluate mood. Some also received brain scans focusing on five regions of the brain most likely affected. The conclusion of this second experiment again found damage in memory and psychological impairments, which they estimated to last two and a half years or more after quitting MDMA. However, the testers urged to use caution when making judgments because the evidence is still inconclusive. The challenge is getting concrete test results from an experiment dealing with mood and emotions. The testers also indicated difficulty in accurately analyzing the neural affects in the brain with current technology. My interest in this article is in exploring the effects of recreational drug substances on neurotransmitters and neural connections in the brain. I liked that the article allowed for other types of drugs and their contributing affects. I would like to further explore the role of neurotransmitters, specifically serotonin, on mood, cognition and memory, and how it is affected by these drugs and other chemicals.

Respect thy neighbor!, Dereck C. Radisky and Mina J. Bissell,American
Association for the Advancement of Science,Volume 303,p.775,Feb 6, 2004.

Cell interaction posses many questions and theories about cell replication,
disease, evolution, and death.The interactions in this article between cells
and their surrounding materials emphasize the importance of cell structure and
cell disease. Stromal cells are the supporting framework for the matrix of the
cell. Even possibly deadly cells, such as epithelial cells, need stromal cells
to survive. This article examines the way in which stromal cells reduce the
possibility of tumors produced in epithelial cells. In "Respect thy Neighbor,"
Radisky and Mina write of Bhowmick's, a researcher, discoveries about the
effects of stromal-epithelial interaction as a determinate for whether or not
epithelial cells develop tumors.

Stromal cells are surrounded by a fibroblast. This is a cell that aids in
connecting the tissues of other cells. Bhowmick researched the gene TGF(beta).
He concluded that this gene, when interacted with other selected genes, can
promote and reduce tumors in the epithelial cells. Oddly enough TGF(beta) can
be present in a cell and have polar affects. The benefit of the existence of
TGF(beta) is understandable when broken down to the very core of its process to
suppress tumors.

TGF(beta) combines with other genes and forms a complex. This complex is called
Active TGF(beta)signaling complex. Another complex is formed along with
TGF(beta), called Active BMP signaling complex(see figure). These two complexes
signal the genes to phosphorylate,which means to add a phosphate. After a
phosphate has been added the process of transcribing the DNA in a certain
sequence is started. This process takes place in the
fibroblasts(micro-environment). The fibroblast acts as an adviser to the genes;
directing them to phosphorylate, which then in turn creates the proper DNA to
replicate into a healthy stromal cell. If this sequence is maintained with no
errors the genes are fulfilling their job. However, the problem strikes when
some of the genes that form the complexes are not present. When this happens
the stromal cell has been mutated. This mutated cell is the destructive side of
the TGF(beta)gene, because it increases creation of tumors in epithelial cells.

Stromal-epithelial cell interaction does indeed have an affect on the evolution,
replication, disease and death of the cells. Their interaction does have other
factors that determine the type of outcome the interaction will receive.
TGF(beta) is a prominent gene that can ultimatly determine the exsitnece of a
healthy stromal gene, but more so give birth to a tumor in epithelial cells.
Being able to stop the defective stromal cell, caused by lack of
TGF(Beta),could give way to a stronger possibility of cancerous tumors becoming
less apparent by deeply understanding the interaction between stromal and
epithelial cells.

Pesticide use and menstrual cycle characteristics among premenopausal women in the agricultural health study
By: S.L. Farr, G.S. Cooper, J. Cai, D.A. Savitz, and D.P. Sandler
American Journal of Epidemiology, Volume 160, Number 12 p. 1194-1204, December 15th, 2004

It is known that certain pesticides disrupt the estrous cycle in animals on farms. The authors wanted to know if there is an association between pesticide use and women's menstrual function as well. The study was done on about 3,100 women living on farms, that were premenopausal, not pregnant, and not taking oral contraceptives.  Some women are actively using pesticides on their farms and some are not.  The authors' goal was to conclude what effect, if any, the pesticides had the women's menstrual cycle. Period length, missed periods, and strength were all documented.
It think this would be a very interesting topic to investigate becuase it relates to many people in the class.  Most of us are unknowingly consuming pesticides on our fruits and vegetables on a regular basis, and I think it would be of interest to find out what effect this has on us.  Women have problems with their cycle all the time, and there are many factors blamed for this. Some of these include, diet, weight, smoking, and stress, but never once have a heard of pesticides as having an effect.  Finding this out to be true would just be one more compelling reason for farmers to stop use of pesticides on their produce.

“The pangenome concept: a unifying view of genetic information”
Victor V. Tetz
Medical Science Monitory
Volume 11
July 2005
Pages 24-29

    In “The pangenome concept: a unifying view of genetic information,” the author, Victor V. Tetz, describes the sum of all of the genes in every organism in the world as the pangenome.  This pangenome is made of every multicellular organism, unicellular organism, and non-cellular organism, such as viruses.  Interestingly, the mass of the non-cellular organisms’ genes is greater than the sum of the masses of the multicellular organism’s and the unicellular organism’s.  The author uses visual imagery describing the pangenome as the ocean of all the genes in the world.  Next, Tetz describes how stability and variability are responsible for the continuation of the pangenome.  First, in stability, it is important that there are different genes, and that the death or extinction of an organism lead to the loss of the genes in the pangenome.  This preservation of genes occurs due to evolution, descendants keep the DNA of their ancestors, and by cells transferring DNA to and from other cells, despite their uni/mulitcellularity.  However, the main recipients of DNA are unicellular organism’s and viruses.  In this, the author then proposes a meaning for death.  He says that death causes an organism to enter the food chain, and naked, unprotected DNA can survive alone for hours, until it is either incorporated into a new organism or it dies.  The second part of the maintenance of the pangenome is encompassed by the concept of variability.  This means that it is important for there to be new gene types.  Tetz says this is caused by mutations, especially those found in the highly mutating RNA viruses.  He says a fast way for this to occur is to place these new genes into the chromosome.  This implies a transposon type effect.  Tetz describes positive effects, improvements in the pangenome, negative effects, problems in the pangenome, and neutral effects, neither good nor bad.  The author then begins to discuss the possibility of global epidemics, such as SARS, a clearly negative impact.  Tetz then concludes his reasons for classifying genes into the pangenome.  He says his reason for doing this is so that research into genetic modification and similar studies will understand their affect on the global level.  This could lead to medical breakthroughs, and hopefully prevent medical disasters.  The overall point is to improve diagnosis, treatment, and medication, involved in disease.

    I think this may be an interesting subtopic for the class to discuss when discussing such topics as disease, experimental treatment, and stem cell research, to name a few.  It could possibly lead the class to realize that what may be good for us can negatively affect the others.  It shows us that our genome is not just ours, that our genome is a small part of the global genome, the pangenome.  Furthermore, it is this genome, not just our human genome that science needs to work on improving.  Simply because we isolate all of the problems within our genome, does not mean it is invincible.  It is vulnerable to the ever mutating, ever adapting genomes of the endless bacteria and viruses that encompass the globe.  I think this would be an interesting article for the class to discuss to realize that scientists need to look at genes globally first to solve localized problems.

Gene Expression of Ornithine Decarboxylase in Lung Cancers and Its Clinical Significance, Tian H, Huang Q, Li L, Liu XX, Zhang Y, Acta Biochim Biophys Sin (Shanghai). 2006 Sep;38(9):639-45

This article deals with gene therapy treatments of lung cancer, namely using viruses. The researchers are attempting to find the answer to what effect Ornithine decarboxylase (apparently an important enzyme in polyamine biosynthesis that is increased in cancer cells and is complementary to the initiation codon) will have on lung cancer cells. Their results showed that the Ornithine decarboxylase inhibited the growth of cancerous cells, interrupting the G1 phase of the cell replication process.
I believe this article would make a good class because of the wide application that the findings could have on all types of cancer. While lung cancer specifically was what they studied, the researchers found implications for preventive measures in other cancers, such as prostate cancer. What’s more, this research and others like it are important as it gives another treatment option to those cancers that do not respond to chemo or radiation therapy, or for those individuals for which chemo or radiation cannot be administered. While this article admittedly had no compelling visually stimulating charts or graphs, I think it is a shame that the majority of people do not seek to learn about new treatments for diseases such as cancer, and largely do not care, until some sort of tragedy touches their lives. A class on this subject manner could quickly bring the students up to date on the latest treatments of cancer, as well as hopefully pique the interest of students and bring them “out of the dark” so to speak.

"Clonal Adaptive Radiation in a Constant Environment." Ram Maharjan, Shona Seeto, Lucinda Notley-McRobb, and Thomas Ferenci. Science. Vol. 313, No. 5786, pages 514-517.

    In this article, the researchers explore how Escherichia coli adapts to a uniform envrionment with a single resource. They found that the results, "suggest ecological specialization for multiple niches is not essential for bacterial diversity." (p. 517). This would be interesting to discuss in class because it discusses how a particular strand of E. coli adapts in its environment and then compares the new strand of E. coli to the parent strand. According to the researchers' discoveries, "A single fitness solution, or survival of the fittest, is not the only answer in a competitive environment." (p. 517). It challenges our notion of why some things evolve the way they do and what the particular affects of some mutations might be.

HIV Turns Off Immune Cells, David Biello, Scientific American, publication date:
August 21, 2006

This article focuses on functioning cells that should help to fight off the HIV
infection. However, they are being turned off by a molecule pathway know as
PD-1 (Programmed Death-1), which thus does not allow for them to do so. The
article also explores what would happen if the switch was blocked and how the
cells within an infected person/animal would react. The researchers focused on
places like South Africa where rates of AIDS are very large, throughout their
research they found that 71 people infected with HIV had a higher level of
PD-1, "compared to uninfected controls." Thus helping to aid in their
conclusions of the research.
This article is interesting because it helps to show that there are some break
throughs happening in science and if they can be conquered and controlled, then
perhaps we can find a cure for such diseases sooner than we thought.

Identification of Two Origins of Replication in the Single Chromosome
of the Archaeon Sulfolobus solfataricus
Nicholas P. Robinson, Isabelle Dionne, Magnus Lundgren, Victoria L.
Marsh, Rolf Bernander and Stephen D. Bell
Cell Press, Volume 116, Issue 1, Pages 25-38, 9 January 2004

This article talks about the difference in the eukaryotic and the
bacterial chromosomes and their method of replication.
The research goes on to explain the experiments that were conducted on
these choromosomes to identify the two active origins of replication
in the bacterial chromosome.  The eukaryotic chromosomes are also
looked into and the two origins that the eukaryotic chromosoms have
are identifies by certain data.  Both experiments contain information
about the proteins in the different growth phases and cell stages.

The article would make for an interesting class discussion because I
think that the issue of understanding how the eukaryotic and the
bacterial chromosomes replicate in their own distinct way could later
on help with experiments that require the data over either of the two

Repairing the Nervous System with Stem Cells, Dr. David M. Panchision, Regenerative Medicine 2006, pages 35-43, August 2006

     This article discusses the various strategies to curing nervous system diseases such as Parkinson's, Huntington's, Alzheimer's and Lou Gehrig's disease. Dr. Panchision notes that the brain contains slow-dividing cells (referred to as adult neural stem cells) that generate neurons and glial cells later in an adult's life that act as a repair mechanism of sorts. He discusses two ways to implement these cells: activate the existing stem cells in a person's brain and implanting cultivated stems cells into the brain, causing them to be differentiated into the desired cells. The article goes in depth to making a cure for Parkinson's. It addresses previous attempts at curing the disease, and goes on to explain new, successful techniques that are being developed using stem cells. Dopamine levels are the primary factor in Parkinson's disease; tests made on Parkinsonian lab rats have shown that stem cells differentiated into dopamine neurons successfully regulated dopamine levels, causing the symptoms of Parkinson's to wane. Spinal cord injury, strokes, and Lou Gerhig's disease are also tested with stem cells in this article, producing various results, from minor changes to major improvements. It is noted in this article that stem cells seem to be actively drawn to damaged areas of the brain.
     I believe that this article is very interesting and would be a great addition to lectures. Ethics aside, this is an important issue that needs to be talked about. I believe that lectures about stem cells will provide students with the proper facts so that they can make educated decisions on what they believe is right.

Genetic Diversity and Linkage Disequilibrium in the Polynesian
Population of Niue Island
authors: William G. H. Abbott, Ingrid M. Winship, Edward J. Gane, Sitaleki A.
Finau, Stephen R. Munn, and Colin F. Tukuitonga
journal title: Human Biology
volume: 78
page numbers: 131-145
date of publication: April 2006

The modern population of Niue Island descended from a single homogeneous pool of
founders and has remained genetically isolated. This article questions the
relationship between the the complex genetic diseases, and similarities and
differences in genetics that are common within this isolated group. It examines
Y-chromosome lineages, mitochondrial DNA lineages, and linkage disequilibrium
all studied within this small genetic pool.

I think this would make for a cool class because its interesting to see the
outcome of having a small genetic pool such as the Niue Islanders. It would
also be interesting to debate the effects this has on certain genetic diseases.

“Fine-Tuning Plant Defence Signalling: Salicylate versus Jasmonate”, G. J. M. Beckers, and S. H. Spoel, Plant Biology, 8, 1 – 10, 12/22/2005
In this article, the authors discuss salicylic acid, (SA), and jasmonic acid, (JA), and their dependent signal transduction.  The purpose of this article is to further investigate the relationship between SA and JA, and how they work together to protect the plant.  They give an analysis of their present understanding of the molecular mechanisms of cross-talk between these defenses, but they want to find out what the key aspects are that are involved in this interaction between SA and JA.  I think that this article would make for an interesting class discussion because it discusses how plants have different mechanisms to defend themselves against different types of pathogens and herbivorous insects.  They have interacting signal transduction pathways, with SA and JA being two of the most important elements of this system.  These two signaling molecules are very important in the signaling process.  I thought that it was really interesting how plants can protect themselves from further infection after being attacked by a pathogen, insect infestation, and necrotrophic pathogens that kill the host cell before feeding.  These different threats to the plant require different defensive responses, which is why cross-talk between the different defenses is extremely important to the well being of the plant.  I think that further discussion of how these two acids work together to protect the plant would be very intriguing.  I also think that it would nicely complement our previous class discussions on how plants protect themselves from extreme temperatures.

The Shortest Telomere, Not Average Telomere Length, Is Critical for Cell Viability and Chromosome Stability, Michael T. Hermann, Margaret A. Strong, Ling-Yang Hao, and Carol W. Greider. Cell, Volume 107, 67-77, 2001.
This article suggests that telomerase inhibition may be a possibility for cancer treatment. However, reduced tumor formation is not seen in all cases.  But the studies do show that telomerase plays a role in killing the tumors, and it may help "narrow the choice of which cancers to target for telomerase inhibition."  The question this article addresses is whether it is the average telomere length or the shortest telomeres that determine the eventual death of the cell.
So many today are affected by cancer; it's probably a rarity nowadays to not know someone first hand or at least through a friend that has had this terrible disease. Both my grandfather and aunt died of cancer, and so any small steps in finding "cures" is of great interest to me, and probably also to most people, and therefore discussion of this topic would lead to an interesting class.

The effects of long-term endurance training on the immune and endocrine systems of elderly men: the role of cytokines and anabolic hormones.
Milton Hideaki Arai, Alberto JS Duarte,and Valéria Maria Natale. Immun Ageing. 2006; 3: 9. Published online 2006 August 25
It is well known that as we age our immune and endocrine systems decline in efficency.  The purpose of this article is to show that through long term conditioning of the body, we can slow this eventual deterioration of our immune and endocrine systems.  I think this would be a very interesting article to study in class because it is not only something that is relavent to the course, but also something we all can take into consideration in our own lives.  Through this article, we can take things that we learn about in class such as the function of T cells and hormones in the body, and see how the regulation of their levels in our body can have a significant effect on our health as we age.  I find it interesting how this study proves how a healthy, active lifestyle does in fact have a positive effect on our quality of life and bodily functions as we age.

“Alcohol-related genes: contributions from studies with genetically engineered
mice,” Crabbe, John C.; Phillips, Tamara J.; Harris, R. Adron; Arends, Michael
A.; Koob, George F., Addiction Biology, Vol. 11 Issue 3/4, p195-269, 75p,
September 2006

I think this article is interesting because it discusses which genes in the
brain act in response to alcohol. The article attempts to answer this question
by using genetically engineered mutations in mice that make an effort to show
certain responses such as sedative effects and toleration for alcohol. The
article also discusses certain experimentation methods that may change the data
that is collected; and works to find a more cohesive way to experiment and
provide conclusive results regarding the result of these mutations on alcohol’s

Contribution of Bone Marrow–Derived Cells to Skin: Collagen Deposition and Wound
Repair, Carrie Fathke, Lynne Wilson, Jonathan Hutter, Vishal Kapoor, Andria
Smith, Anne Hocking, and Frank Isik, Stem Cells: The International Journal of
Cell Differentiation and Proliferation, vol. 22, pg. 812-822, 2004

The article, Contribution of Bone Marrow–Derived Cells to Skin: Collagen
Deposition and Wound Repair, questions and explores the benefits of
transplanting cells from one part of the body (bone marrow) to help generate
new cells on the skin. It presents data that show the cells from bone marrow
are considerably advantageous at healing wounds and transcribing collagen. The
data also shows that bone-marrow derived cells are chiefly used in
reconstructing the skin’s fibroblast population. This article would be an
interesting topic to discuss in class because it not only deals with an
important topic in the world of current events (stem cell research), but it
also poses the remarkable question itself: can we transplant cells to cultivate
growth/healing in foreign areas on the body? In this case of growing/ healing
skin, the possibilities would be significant as far as healing wounds, burn
victims, etc.

NANO-ROBOTS NOT YET ON PATENTING HORIZON, Ed White, Nikkei Nanotechnology, March 11, 2003.
    The article brings up the possible near-future of nanotechnology in the biomedical  and pharmaceutical fields. Possible nanoparticle treatments free of side-effects for incurable diseases, gene therapy, and more effective drugs are the main topics of the article.
    Work has already been done with gene therapy in yielding better crops through nanoparticulate chemistry, and more advanced aspects of gene therapy in humans are a viable possibility in the near future. The plausible future for nanotechnology in biologic aspects are mind boggling and definitely worth looking into for class. Aspects of gene manipulation and cell interaction are briefly mentioned, and discussion on the topics should incorporate what we are learning now while going into the details of how new technology will make use of the information.

The inheritance of cognitive skills: Does genomic imprinting play a role?, Lisa M. Goos & Irwin Silverman, JOURNAL OF NEUROGENETICS, vol. 20 number 1-2, pg 19-40, January-June 2006

This is an interesting article that deals with idea that genes also play an important part in the development of our brain and the way that we think. This idea raises such questions such as if the genetic information of one parent could be passed down to a child so that they would have similar brain development of the parent? This idea also brings up the question that if we have similar brain developments as the parent would this affect the way that the offspring thinks or is the expression of the genes? This is an interesting article to consider because it brings up the question if we are independent thinkers or if we think the way that we do because it is the way that our genes told our brain to on a cognitive level.

“Framing the Future: Embryonic Stem Cells, Ethics and the Emerging Area of Developmental Biology”, William B. Hurlbut, Pediatric Research, Volume 59, Pages 4-12, 2006.
This article dicusses the moral, social, and ethical issues that surround stem cell research. It starts off by giving a background of this field in biology and then it discusses all the legislation and laws that have been passed in regards to it. It shows how lawmakers and leaders all have different opinions and are torn between supporters of each side. The article then raises the question of how ethics in stem cell research and what a possible compromise for its supporters and its opponents can be. The article was well-written and draws attention from the very beginning from the fact that it recognizes how controversial this issue really is. This controversy was apparent through examples such as the difficulty that scientists have had in selecting the proper equivalent terms for words like ‘zygote’. The article also asks where life really starts and points out how difficult it is to draw the line at where an embryo is actually a living being, but it presents the reader with both sides of the argument. It explains all the possible arguments that a supporter of stem cell research may have, such as claiming that life does not exist until gastrulation, twinning, implantation, or until a being can function. In response to this, the article states how people can argue that embryos have all the characteristics and potential to be a human being, and this being always had ‘function’, although we cannot see this in the embryo’s early stages. After all this evidence is presented, it is up to the reader to make an informed decision. Furthermore, the article asks what the benefits of stem cell research are and what possible risks might occur. It brings up the point that not every disease can be cured through this type of research and that people fear this process will lead to the creation of more ‘perfect’ humans. Lastly, the article raises the question of what good solutions to this sensitive topic exist. It goes on to show how Altered Nuclear Transfer (ANT) might be a good compromise and explains what this process consists of.
This article would make for an interesting class because there are tremendous amounts of controversy, rumors, hard sentiments, and misinformation surrounding the topic. Spokespersons and celebrities appear on television trying to get people’s support for the research, while the president tries to impose limits on it. These high-profile arguments are only the beginning of future arguments that will arise about when life actually starts and whether or not embryonic research is ethical. It would be beneficial for students to learn about this because many of the people that listen or even take part in this debate are poorly informed or not informed at all on the matter and what possible solutions exist.

“Short-Term Impact of 1997/1998 ENSO-Induced Disturbance on Abundance and Genetic Variation in a Tropical Butterfly.”
Cécile Fauvelot, Daniel FR. Cleary, and Steph BJ. Menken
 Journal of Heredity
Volume 97, Number 4
 Pp. 367-380
 July 13, 2006.
 This study determined the genetic and demographic impact of habitat loss after the 1997/1998 El Niño Southern Oscillation in the Indonesian Borneo, which in this region caused drought and fire. After the fires, forests affected by it presented fewer butterflies. The genetic variation of the remaining butterflies increased because the butterflies from the affected areas immigrated to the non-affected areas.
This article is interesting because, as the article itself express, “habitat loss after disturbance may lead to local population extinction but may augment genetic diversity in remnant local populations because of increased gene flow” (367).  El Niño Southern Oscillation was a natural phenomenon that affected the environment, but there are other phenomena that affect the environment and which effects are enhanced by men’s actions.  The greenhouse effect is one of these phenomena, in which several gases prevent the heat of the Sun to go back to space, therefore increasing global warming. Maybe if we study the effects of El Niño Southern Oscillation in the population size of the butterflies we will be more conscious in our daily decisions such as buying recyclable products, riding bikes instead of cars, etc. We have to remember that in the particular case of the butterflies studied in this article luckily there wasn’t an extinction of the specie; continuing harming the environment may not have this same result with other species.

"Celiac disease goes against the grain." Amerine, Emmie. Nursing Feb2006, Vol.
36 Issue 2, p46.

This article touches on the matter of Celiac disease, which is an autoimmune
intolerance to gluten. The matter presented reflects upon the different
triggers of this disease, targeting genetic predisposition to be a prominent
factor. The disease has a wide range of forms from extreme sensitivity and
symptoms to very few at all. This article focuses on what damage is caused by
this genetically predictable disease, and the ways to identify it in an
This article would make for an interesting class discussion and such because it
combines the genetic quality of life that has been recently focused on in class
with a disease that is relatively unknown, but much more common than estimated.
It characterizes how simply having the genetic characteristics for this gluten
intolerance can lead to extreme forms of Celiac disease, in the aspect of
varying symptoms. While the disease is not a household term for most people,
it could very possibly be "living" in that household through an unknowning
member. Celiac disease is brought on by the domination of genetics, and that
alone is discussion worthy.

Stem Cells, Scientific and Political Issues
Dr. Irving Weissman
New England Journal of Medicine 346
Pg. 1576 - 1579
May 16, 2002

This article is good because it lays out everything scientists know about stem cell research and everything that can be accomplished by continuing stem cell research in an unbiased manner.  Weissman then goes on to discuss the ethical and political issues which are affecting his research.  I think this is a good article for our class because we are also learning about cells but might not realize what a huge impact research in this field has on medicine and society.

"Calorie Restriction Promotes Mammalian Cell Survival by Inducing the SIRT1 Deacetylase." Haim Y. Cohen, Christine Miller, Kevin J. Bitterman, Nathan R. Wall, Brian Hekking, Benedikt Kessler, Konrad T. Howitz, Myriam Gorospe, Rafael de Cabo, David A. Sinclair. Science Magazine, Vol. 305, p. 390-392, 16 July 2004.

This article relates caloric intake to cell life, which may be interesting as we relate it to our own daily calorie intake. The experiment uses rats for testing, and also includes some comparison in human cells. It proceeds to demonstrate that a chemical released by cells with restricted calorie intake (versus 'ad libitum' or 'to the full' calorie intake) relieves cell stress, thus shower lesser signs of aging. There are many figures in this article, but they are all graphs showing advanced chemical relations. It also includes many particular numbers, possibly making the article confusing or overwhelming, but the subject was nonetheless intriguing because of its relevance in our own dieting habits.

Marine Cyanobacterial Symbioses
E.J. Carpenter
Biology and Environment
Volume 102, Issue 1, pages 15-18
Published 2002

Summary: This article discusses the symbiotic relationship that develops between cyanobacteria and various organisms/micro-organisms in the ocean. According to the author, not very much is known about this topic right now. The article deals briefly with a few of these symbiotic relationships, explaining the chemical, ecological, and biological balance that must occur. It's not the most exciting topic or the easiest to understand upon reading, but I think the article does a good job with discussing the multiple layers of this biological interaction that occurs in many places in the ocean.

The Role of Women's Alcohol Consumption in Managing Sexual Intimacy and Sexual Safety Motives, Maria Testa, Carol VanZile-Tamsen, Jennifer A. Livingston, and Amy M. Buddie, Journal of Studies on Alcohol, volume 67, pg665-674, September 2006
The studies conducted on women metioned in this arcticle were meant to isolate the effects on women's ablity to percieve sexual risk factors when intoxicated. In other words, what the researchers are trying to analyze is the relationship between alcohol consumption in women and their reactions in certain social situations. The two main question asked are "Does the consumption of alcohol make it harder for women to recoginze sexual assault risk factors?" and "Does the consumption of alcohol lower women's intentions to resist sexual advances". I believe our class would befenit from examining this study because, first and foremost, we are college students. We are no angels. By this, I mean to say that with us being the proclaimed "number one party school" a study on booze, sex, and women, might keep some of us awake, especially the girls in our class since we are the exmined specimens in the study. It might also help the boys in our class to realize the part they play in the sexual assault game when drinking.

Isolation and Characterization of the TIGA genes, whose transcripts are
induced by growth arrest
N. Yabuta, H. Onda, M. Watanabe, N.Yoshioka, I. Nagamori, T. Funatsu,
and S.Toji
Nucleic Acid Research, 2006. Vol 00, No.00 1-15
Published September 14,2006

According the article Isolation and Characterization of the TIGA
genes, most cells in adult eukaryotic organisms do not divide. It is
said that they tend to remain in a stage called the quiescent state or
G0 phase in which macromolecular synthesis is largely reduced. It is
known that three conditions, serum starvation (G0-s), contact
inhibition (G0-c), and terminal differentiation (G0-t) can induce
eukaryotic cells to enter the quiescent state. (All genes have been
loosely termed TIGA for Transcript Induced by Growth Arrest) However,
the true question is how quickly or how effectively can the TIGA genes
make the cells go into the quiescent state. All three genes obviously
share some similarities but they, “diverge in other aspects.” In order
to answer their questions, scientists isolated 44 novel genes and
upregulated them after serum starvation, contact inhibition, and
terminal differentiation to get the desired results. I think that this
article is extremely interesting because not only is it in correlation
to what we have been recently learning about genes, but I think it is
highly beneficial in cancer research. If the quiescent stage can be
rapidly induced, then cells don’t divide, thus preventing the spread or
creation of more cancerous cells.

"Toxicty and mAChRs binding activity of Casseopia xamachana venom from Puerto Rican coasts" by Faisal F.Y. Radwan, Laura, G. Román, Krishna Baksi and Joseph W. Burnett.  Toxicon, volume 45, pages 107-112, January 2005.

The objective of the research is to examine the toxic properties of a type of venom found in a jellyfish that is native to Puerto Rican coastline and the surrounding waters.  I find that it is relevant as a potential candidate to discuss in class because the researchers deal with interactions among living cells and foreign substances that could potentially harm the organism on the molecular level.  Seeing as how a large portion of our class is dedicated to studying organisms from their most minute components, this is, in essence, taking our studies of mollecular biology to another level.

Genetics of human obesity,Karine Clément, Comptes Rendus Biologies, Volume 329,
Issue 8,608-622, August 2006

This specific article has to do with obesity and how the environment and
heredity affect this problem. Genes have a major role with obesity and
mutations can cause other diseases related to obesity. The question "is genetic
risk for obesity due to disease-producing common alleles?" is the hypothesis. I
think this would be an interesting article to learn about because obesity is a
rising problem in today's society.

"Mast Cells Can Enhance Resistance to Snake and Honeybee Venoms," Metz, Piliponsky, Chen, Lammel, Abrink, Pejler, Tsai, Galli, "Science," Volume 313, pp. 526-530, July 28th 2006
Mast cells help contribute to reduced morbidity and mortality from asp-bites and bee-stings.  They're already a part of our immune system, but a part that, until now, we thought was the culprit for venom-related poisonings.  How do these mast cells work?  Why did we think them harmful?  What can be done with them that could aid in the treatment of venom poisonings?  The world of anti-venom is certainly in need of a modernization.  Right now we have to capture poisonous snakes etc. and physically extract their venom in order to create an effective anti-venom.  Is there a better way?

Allometry of Alarm Calls: Black-Capped Chickadees Encode Information about Predator Size
Science Magazine 24 June 2005
Vol. 308 no. 5730
pp. 1934-1937

   Templeton, Greene, and Davis recorded the calls of chickadees when presented with fifteen different species of predators, 13 birds and 2 mammals, hoping to find evidence that the nature of the calls depends on the size and behavior of the predator.
   The researchers investigating black-capped chickadee calls did not closely follow the rules of strong inference.  They devised a hypothesis, then set out to prove it right.  They produced very thorough and convincing data, with thirteen different predators varying widely in size.  However they failed to rule out other factors besides predator type and behavior (whether stationary or moving) that could affect the chickadees call.  Templeton, Greene, and Davis claim the control experiment negates all the factors but the ones they are researching.  The article never explained how close the predators were.  They should all be the same distance from the chickadees, otherwise it could be said distance plays a role in the chickadees call.  I hypothesize that a closer, stationary predator would cause more alarm than a moving predator farther away.  There is no way of knowing this from the article, as they did not design the experiment to test distance.  However there is no evidence in the article that they controlled the experiment to rule distance out as a factor.  Several other things could have an influence on the chickadees call that the researches failed to rule out, including color variations among species, and time of day the experiments were carried out.  The chickadees’ calls are probably even more sophisticated than Templeton, Greene, and Davis believe.

Hormones and Behavior, Volume 50 Issue 4, November 2006. "The effect of gonadal hormones and gender on anxiety and emotional learning." pp. 539-549. Donna J. Toufexis,Karyn M. Myersa and Michael Davisa

Women experience depression, dysthymia, as well as anxiety disorders at a significantly higher rate than do men. These changes are triggered during stages of the female's reproductive life, and "is greatest at times of ovarian hormonal flux like puberty, following childbirth, and at menopause." One hypothesis for this disparity may be the difference in social culture between men and women and their willingness to report such disorders. The socializing of women to be more "in touch" with their emotions, at least in our realm of the world, may also translate into an increased susceptability to depression, etc. Yet, an additional explanation for this observation could be suggessted, one which involves the effects of the ovarian hormones (namely estrogen and progestins) when they preform at their peak, or during the reproductive years. Testosterone's effect on anxiety levels is also investigated. This study, conducted on rats, examines the behaviors of male, differently staged female, and castrated male rats who are injected with testosterone, estrogen or progesterone and subjected to different tests of their anxiety levels.

Sexual dimorphism of the brain is examined in this article, evaluating different emotional learning capabilities due to different levels of hormones within an individual of either sex. Neither Estrogen nor Testosterone is found to be the superior hormone, but each neccessary both in terms of their interaction WITHIN an individual (male or female), and BETWEEN individuals- Both working to increase fitness and reproductive success.

Article - A transposon-induced spontaneous mutation results in low -amylase content in rice

Authors - Hiroaki Saika, Mikio Nakazono, Akira Ikeda, Junji Yamaguchi, Shunpei
Masaki, Motoki Kanekatsu and Keisuke Nemoto
Journal title - Plant Science
Volume – 169 Issue 1
Page number - 239 - 244
Date of Publication - July 2005

I’ll be perfectly honest with you when I say that I understood about 10% of this
article (if even) but from what I identified the only question that arose is why
is there a suppression of B-amylases in the germinating process of rice seeds? I
think that this article would be fun to study because it would be interesting to
identify the region that is responsible for the suppression for this B-amylase
activity. There must be only a slight distinction that causes the suppression.
So far as I know rice is a form of carbohydrate and I think that amylase is a
group of enzymes that catalyze the hydrolysis of starch to sugar to produce
carbohydrates, I found this research to be interesting because it would be cool
to figure out what is suppressing the B-amylase. In the experiment 6 different
brands of rice were used and it only got down to a brand called nipponbare.
Using an analysis called QLT using something called BILs (which were derived
from the Nipponbare and Kasalath rice) the results showed consistent values for
the BILs mode of 3-4units per milligram of protein. The Nipponbare had way more
B-amylase value than did the Kasalath. There was in insertion of a mutator-like
element in one of the promoter regions was thought to have suppressed its
expression which decreases b-amylase activity in the rice Nipponbare. This
mutator that was used is the most active plant transposon and is used is used
for gene tagging. Many of these mutator-like elements were found in the rice
genome. Some mutator-like element cDNA clones have been isolated meaning that
rice has its own mutator-like transposon system.

Evidence of sexual reproduction of woolly apple aphid in New Zealand
Author: W.R.S Sandanyaka and U.G.M Bus
Journal: Journal of Insects
Volume: Volume 5, Issue 27
pp.: 1-7
Date: November 2005

The following article talks about evidence being found that sexual reproduction
occurs in the woolly apple aphid in New Zealand. Reproduction usually occurs
with the apple and elm plants as hosts. Some were placed in a glasshouse as
well as outside. They noticed that the ones outside had less sexual morphs
because the alates are busy dispersing into the environment looking for an
apple or elm tree to cotinue the sexual reproduction. These alates were
important in the eastern United States to spread the species across long
distances. However, their importance is not as great in other areas because
sexual forms deposited by alates rarely mated and no evidence of traveling to
elm in New Zealand was found. Some believe that it develops without eggs on
apple plants because it spends winters either in the air or on roots. It would
be really interesting to find out if it needs other plants to reproduce or if it
is asexual. Then we could relate this to other plants or topics if needed.

"Unlocking the Secrets of Longevity Genes", David A. Sinclair and Lenny Guarente,Scientific America, Volume 294, pp. 48-57, March 2006
Research on the longevity genes began with the idea that evolution would favor an increased life span. A group of genes was found that increased the ability of an organism to withstand a stressful environment and therefore live a longer and healthier life. These researchers focused on a family of genes which has found to be present in all the organisms that they studied so far, SIR2.
They first asked: What caused baker's yeast to grow old and if a single gene might control aging in this simple organism? They screened yeast for long lived cells hoping to find genes responsible for longevity. The scientist found a mutation, SIR4 that caused instability in the cell. They found that by adding SIR2 to the yeast cell that the cells life span increases by thirty present.
The researchers wondered: What the SIR2 gene does? They found a connection between SIR2 and metabolism, and a possible connection between aging and calorie intake. In some organisms a reduction of calories caused the SIR2 gene to be activated. Though it also caused some of those organisms to become infertile and this did not work for mammals.
Next the researchers wanted to better understand the role of SIR2 in mammals. The mammalian version of SIR2, SIRT1 is more complicated. In mice and rats it allows cells that would normally die to survive stress.
Most people want to live longer and healthier lives. This article focuses on the idea that through research of these longevity genes that someday humans actually could resist the aging process and live an extended life. It is interesting that with farther research of genes scientist could find a way to tweak genes and control human aging. 

“Lentivirus-Mediated RNA Interference Therapy for Human Immunodeficiency Virus
Type 1 Infection” Kevin V.Morris, Human Gene Therapy, 2006.Vol. 17, No. 5, p.

The question posed in this article is ‘can gene therapy deliver a specific gene
to a pre-determined target cell that will end with a therapeutic result?’ Gene
therapy is a method under investigation for the treatment of cancer and AIDS.
There are two methods used for gene therapy, and they are non-viral and viral.
The viral vectors used for gene transfer include retroviruses, andenoviruses,
herpes simplex virus anf flaviviruses. Lentiviruses, a type of retrovirus,
have the ability to infect a target cell. It posses a complex genome and
contain a plethora of regulatory and accessory genes involved in modulation of
viral gene express, assembly of viral particles, and structural and functional
alterations in the infected cell. The use of lentivirus vectors in humans will
require investigators to develop a large-scale production methods that are
unavailable. Once these obstacles are overcome, the potential for
modifications of the human genome using lentiviral vectors is virtually

“Transitions from Nonliving to Living Matter”, Steen Rasmussen, Liaohai Chen,
David Deamer, David C. Krakauer, Norman H. Packard, Peter F. Stadler, Mark A.
Bedau, Science, Vol. 303 no. 5660, pp 963-965, February 13 2004.

The main question of the article is how did the first life forms arise from
nonliving matter, which leads to the larger question of the origin of life.
The researchers can either attempt to create a living cell by the “top-down
approach” in which they can try to genetically modify real cells into their
smaller parts or the more popular “bottom-up approach” of creating a living
cell from nonliving elements. Researchers have produced chemical systems that
can metabolize lipids but a true cell that can “regenerate itself, replicate
itself,” and evolve has not been produced.
This article would be pertinent to the class in that it examines the functions
of DNA, RNA, and lipid vesicles and how researchers are trying to use them to
create a living cell. It is also an interesting article in itself as it
considers the very broad and significant question of the origin of life.

Title: Lithium Treatment and Thyroid Abnormalities.   Journal Title: Clinical Practice and Epidemiology In Mental Health (found through Pubmed).   Authors: Alberto Bocchetta and Andrea Loviselli.   Published: 12 September 2006
    This article is about two researchers who reviewed all of the old papers/experiments dealing with the relationship between the use of lithium and thyroid abnormalities.  They reviewd all of the articles in "Pubmed" dealing with this subject and develolped their own conclusion.  According to Bocchetta and Loviselli, although a connection between lithium use and thyroid abnormalites have long been recognized, lithium is sitll the "gold standard" for treatment among manic-depressive patients years after it was been introduced.  According to their research, lithium affects the thryoid by inhibiting its ability to release it's hormone, causing hypothyroidism.  Although most patients have "compensatory mechanisms" that counteract the inhibition of the thyroid hormone, there are a minority that do not.  The article states that hypothroidism is usually developed at the beginning of the lithium treatment and if a patient has been using lithium for several years, their chance of developing hypothroidism is just as likely as anybody else.  The authors suggest that pretests should be done before a patient begins the use of lithium. And if hypothroidism is developed whith the use of lithium, it is not reccommened to stop taking the medicine.  The article concludes by stating that although thyroid disorders are a problem, the effectiveness of the drug is undeniable and should not be banned.

"The Influence of Gender and Body Characteristics on Upright Stance", I. Farenc, P. Rougier, and L. Berger, Annals of Human Biology, Vol. 30, No. 3, pages 279-294, 13 November 2002

The question of this article is what makes us walk upright as humans because it is important to how humans act. This article would be interesting to study because it shows us how we behave like we behave. It shows us why we walk how we walk. If we were to crawl around on our knees, we would behave, possibly, in a totally different manner. We often take our upright stance for granted, but in actuality it is very complex and and scientific. While inherently informative in the field of biology, this article is also saturated with mathematical equations and scientific jargon. However, I found it extremely informative and ends up very interestingly.

"Topical drug rescue strategy and skin protection based on the role of MC1R in
UV-induced tanning."
John A. D'Orazio, Tetsuji Nobuhisa, Rutao Cui, Michelle Arya, Malinda Spry,
Kazumaja Wakamatsu, Vivien Igras, Takahiro Kunisuda, Scott R. Granter, Emi K.
Nishimura, Shosuke Ito and David E. Fisher
Vol. 443
Pages 340-344
Sept. 21 2006

For decades, tanning has been all the rage among people of all ages and
genders. More recently, people have turned to sunless tanning to avoid serious
results such as skin cancer. However, science has found a possible alternative
route to both previously mentioned forms of tanning. This new type of bronzing
is actually a real tan without UV rays from the sun. Scientists have found that
a chemical called forskolin, extracted from a plant, protected mice from these
harmful UV rays. I think this would interest a lot of people because we all
love a nice healthy tan right?
Tanning is primarily controlled by a melanocyte-simulating hormone that attaches
to the melanocortin 1 receptor on the outside of melanocytes. By stimulating
these pigment-producing cells, your skin begins to naturally tan. Many people
that have fair skin and/or red hair find that they are very sensitive to
tanning and prone to skin cancer. The reason for this is that they have a
defect in the MC1 receptor and thus, a reduced ability to produce melanin (a
skin pigment).
In this experiment, scientists used mice that also had defective MC1Rs to show
the effects of forskolin. Because forskolin stimulated the each mouse's
pigment-producing cells (melanocytes)they where subsequently able to tan.
Although this has not yet been tested on people, there is no reason, so far, to
say that it wouldn't have the same effect. This would give fair-skinned people a
chance at a natural tan that wouldn't wash off and also give extra protection
from the sun.

Life’s Greatest Invention: Sex, Clare Wilson, New Scientist, Vol. 186 Issue
2494, p32, 4/9/2005

The article discussed two ways of reproduction, either asexual reproduction or
sexual reproduction. For example, Birds, Coral, Parasites, and animals are all
mentioned in the article discussing why and how they differ in sexual
reproduction and with what advantages and disadvantages. Sexual Reproduction
is very important; it brings to earth new generations of species everyday. The
main questions in the article are between biologist who wonder how it evolved
and why it hasn't un-evolved? “Sex may even be responsible for keeping life
itself going: species that give it up almost always go extinct within a few
hundred generations.” The interesting part about it is that most of the life
on Earth either reproduces sexually or asexually. Even if some people think
this is an inappropriate subject to talk about I don’t, I believe that as a
class we should better understand and appreciate what has brought us into this
wonderful world.

For the vast majority of species sexual reproduction is the only option, but
it’s not something to frown upon. Sexual reproduction brings to earth many
different and interesting creators. “In the article it says that evolution
should favor asexual reproduction”. One reason they say this is because in
sexual reproduction as I learned in class, only fifty percent of each parent’s
genes go to the offspring equaling 100 percent. Asexuals on the other hand
pass on 100 percent of there genes to there “clone”. Insects, plants, and
lizards do fine without sex, unfortunately becoming outnumbered. What usually
destroys asexual species is mutation. In the article they give an example of
asexual reproduction’s downfall, the author says, “it’s like buying one hundred
tickets in a raffle with the same number, compared to fifty tickets each with a
different number.” Both sexual and asexual reproduction plays an important
role in the future of Earths many different species.

Inbreeding by Environmental Interactions Affect Gene Expression in Drosphilia melangogester
Author(s): Torsten Nigaard Kristensen, Peter Sorensen, Kamilla Sofie Pedersen, Mogens Kruhoffers, and Volker Loeschcke
Book: Genetics 8/11/2006
Manuscript received December 8, 2005
Accepted for publication April 7, 2006
pgs. 1329-1335
Genomewide gene expression patterns were put to test in inbred and noninbred Drosphilia melangogester in experiments with high stress (high temperature) environment conditions. Heat-shock protein and metabolism genes are strongly affected by such an environment. Inbred and environmental stress both independentally and synergistically affect gene expression patterns. It was observed in phenotypic levels and it also showed that genes are also involved at individual gene levels as well. This experiment supports the theory that superiority of heterozygous individuals partly derives from increased metabolic efficiency.

WHOSE BLOOD IS IT ANYWAY?, Kline, Ronald M., Scientific American, Vol. 284, p
42, April 2001

Although initially thrown away as a birth byproduct, in recent years, people
have come to realize the benefits of using umbilical cord blood. It can be used
to rebuild blood and immune systems of those with cancers and leukemia, amongst
other fatal disorders/diseases. The article asks and discusses the
risks/limitations (cord blood sample may contain genetic mistakes that can
cause a disease in the recipient, small number of stem cells contained within a
single sample, older/larger patients may not benefit as much as younger/smaller
patients, etc.) and benefits of using umbilical cord blood. There is also an
underlying question of whether or not the usage of umbilical cord blood is
ethical, which would make for an interesting class discussion.

“Stem Cells put a stop to Macular Degeneration” Helen Phillips Cloning and Stem Cells volume 8, pg. 189 Sep. 20, 2006.
This article offers great insight to the idea that the use of stem cells can once again aid humans in correcting and/or maintaining vision. The question proposed is how human embryonic stem cells can be used to derive cultures that resemble retinal pigment epithelial cells. These are the cells that the photoreceptors in the eyes of animals cannot survive without. The experiment has shown very promising results after it was tested on lab rats with a form of retina deterioration very similar to that of humans who show deterioration after age 60. Unfortunately this study was not intended for restoring human vision, but rather to retain vision as deterioration begins to occur. This scientific breakthrough would be of great interest to anyone who takes interest in stem cell research, optometry, or anyone who may meet the criteria for eye deterioration in later years. The class should be very interested in steam cell research because the conflict with steam cell research is moving from “Does it work?” to “Is it morally correct to alter our own genes and to experiment on a dead fetus?”

Report for Congress through the CRS Web
Author: Judith A. Johnson
Journal Title: Stem Cell Research
Pages: 24 Date of Publication: March 10, 2003

The article explains the ability and significance of stem cell research by
treating those with medical disorders such as diabetes and parkinson disease
through cloning of embryos. The article goes on explaining why many
organizations and some branches of the government does not support the
research. I think this article would be an interesting discussion for the class
because although this subject is very controversial, it brings out the
possibility to those who needs medical attention along with the hopefulness of
those who had none and we, the students, can input our thoughts into this

"Fundamental Questions of Biology" by Simon A Levin, PLoS Biol 4(9): e300
In this article, the author writes about how, due to the rapid advancement in all fields of biology, scientists are becoming more and more specialized in thier jobs, and concentrating more on things such as the development of better tools which have brought people into the expiramentation process who care little about the outcome, i.e. computer technichians. This rapid specialization, the author says, is acting to seperate the scientists from each other and lose sight of the bigger questions of biology in leu of thier other studies. There are some questions though, he feels, that remain constant across all specializations and may come to bring them together. They are presented en masse at the end of the article.

"New Compound Causes Cancer Cell Suicide", David Biello, Scientific American, News Aug. 28, 2006

   Usually, our body's cells are responsible enough to terminate themselves when they reach the end of their life. This is a natural internal process within the cell, similar to suicide. When a cell has reached the end of its life, an internal, chemical trigger causes the cell to die, called apoptosis. This process is natural and automatic. However, cancer cells lack this chemical trigger that causes cells to die. For example, the growth of tumors; Cancer cells continue to live and spread. At the end of apoptosis, a certain chemical within the cell, procaspase-3 is activated and then transforms into another chemical, caspase-3, which kills the cell. Chemist Paul Hergenrother realized that a compound that activated procaspase-3 might be effective in killing cancer cells. After many tests, a new procaspase activating compund was identified, procaspase activating compound, or PAC-1. This new compound is said to induce cancer cell suicide. "By bypassing the broken pathway, we can use the cells' own machinery to destroy them", claims Hergenrother.PAC-1 was tested on colon cancer cells, which resulted in higher levels of procaspase-3,( which activates the cell suicide), and proved that the cells were very sensitive to the compound. Other studies involving human kidney and grafted lung cancer determined that PAC-1's strength coorelated with procaspase-3 levels in cells. Hergenrother hopes"...patients could be selected for treatment based on the amount of procaspase-3 found in their tumor cells."
   This study is very interesting to me, because cancer is such a tremendous disease and is still without a cure. Further studies involving this chemical PAC-1 could lead to a potential cure for certain cancers. If a chemical can induce cancer cell suicide, then society will have to consider the fact that we have a potential cure which will save millions of lives.

"Heat shock protein- 27 protects human bronchial epithelial cells against oxidative stress- mediated apoptosis: possible implication in asthma."  Cell Stress & Chaperones.  article pp. 269-280 vol. 7 issue 3 (July 2002).
I'll be completely honest- I do not understand the majority of this article, but in my search to find a scientific article, this was the one article that I could see myself grasping the underlining concept eventually.  What initially attracted me to this article was that it looked at asthma in humans at the molecular level (like the very proteins that we have been talking about in class).  I figured that because the majority of the class knows about asthma, or has at least heard about it, this article might be the one to help tie together the relation between proteins and what they can do in the body. Some of the main findings dealed with a particular protein and how it handles oxidative stress in the body.  I am not quite to sure what they are talking about after that, but I assume that they are comparing how certain proteins react and rebuild under oxidative stress. 

"A novel nuclear-encoded mitochondrial poly(A) polymerase PAPD1 is a potential candidate gene for the extreme obesity related phenotypes in mammals"
Qianjun Xiao, Xiao-Lin Wu, Jennifer J. Michal, Jerry J. Reeves, Jan R. Busboom, Gary H. Thorgaard, and Zhihua Jiang
Int J Biol Sci. 2006; 2(4): 171–178.
Published online 2006 May 18.

This is an interesting subject due to its relevance in modern society.  The prevalent health trend in America is moving towards significant percentages of overweight and obese individuals.  But is severe obesity really inescapable for some people due to genetics?  Several scientists have found what appears to be a " molecular marker significantly associated with intramuscular fat deposition."  These researchers' findings bring us a step toward a definite answer about "large" genes necessitating large jeans*, and increase the possibility of a "fat cure" - a bright prospect for many.

The Promise of Comparative Genomics in Mammals, Stephen J. O'Brien, 1 Marilyn Menotti-Raymond, 1 William J. Murphy, 1 William G. Nash, 1 Johannes Wienberg, 1 Roscoe Stanyon, 1 Neal G. Copeland, 2 Nancy A. Jenkins, 2 James E. Womack, 3 Jennifer A. Marshall Graves, Science AAAS, Vol. 286. no. 5439, pp. 458 - 481, October 15, 1999,DOI: 10.1126/science.286.5439.458
            The article starts out talking about gene mapping in mammals. “Gene maps have been constructed in human, mouse, and about 30 other mammal species for two general reasons: first, as a resource for locating the genetic determinants of heritable characteristics, behaviors, and phenotypes; and second, as a template for resolving and interpreting patterns of evolving genome organization in their ancestry” (Article). It goes on to talk about markers. “Type I markers are coding genes that through DNA sequence comparison and comparative mapping are essential for identification of gene orthologs in distantly related species (that is, genes in different species that are descended from a single gene of a common ancestor)” (Article). These however offer little information on pedigree and population density. “Type II markers [hypervariable microsatellites, also called short tandem repeats (STRs) are highly informative in pedigree, forensic, and population assessment, because there are over 100,000 near-randomly dispersed STRs throughout mammal genomes, and because each carries multiple alleles” (Article). The lifetime of these markers is very short making them harder to use. “Type III markers are common bi-allelic single-nucleotide polymorphisms (SNPs) within coding regions or more often in noncoding intron or intergenic regions” (Article). These SNPs occur over 3 million times in humans and other similar mammals. The mapping of the genes in mammals has made it more and more possible to learn new things about ourselves and how diseases arise. By mapping the genes of rodent’s researchers have discovered a gene (attractin) in humans that causes obesity in diet induced obesity. They have discovered many other genes as well. They have also discovered many things about agricultural animals including the type II markers to bovine chromosome 2 that causes muscular hypertrophy or double muscling. Gene mapping has been limited to more relevant species because of cost, but the have still mapped some for cats and dogs. The article continues on to talk about mammalian genome radiation.

Taste Perception: Cracking the Code, Jane Bradbury, Public Library of Science
Biology, Volume 2, e64, March 16, 2004

The article begins with a short overview of taste receptors and the five
categories that tastes are put into. Then, the question is posed as to how
tastes are actually coded. The author goes into moderate depth about each
taste and how it is coded. After that, the author brings up an important
inquiry. What is the significance of studying taste? From there, she explains
the potentially monumental affects that this study could have in the future in a
positive manner. The reason that I believe that this would make for a very
interesting study in class is because we did a study of coding of DNA for
proteins, which has parallels to this article through the coding of tastes.
Additionally, it is my assumption that this article will hold the attention of
my peers quite well, as it did me. I have always been curious about why things
taste the way they do. However, after reading and analyzing this article to the
best of my ability, I now have an undoubtedly better understanding of taste than
I had prior to reading it. Unfortunately there were portions of this article
that I did not totally grasp, so if for no other reason I hope that this
article is chosen so that I can gain understanding on the things I was unsure

"Stroke Prevention Trial in Sickle Cell Anemia (STOP): extended follow-up and
final results," Authors: Margaret T. Lee, Sergio Piomelli, Suzanne Granger,
Scott T. Miller, Shannon Harkness, Donald J. Brambilla, Robert J. Adams,
Journal Title: Blood (Journal of the American Society of Hematology),
Vol. 108, No. 3, pp. 847-852, 1 August 2006.

It is a trial to evaluate whether chronic transfusion could prevent initial
stroke in children with sickle-cell anemia at high risk as determined by
transcranial Doppler. The main question posed in this article is "whether
transfusion therapy could be safely withdrawn after at least 30 months of
transfusions in patients who have converted to normal TCD velocities." This
article is interesting because it discusses Sickle Cell Anemia, which is
something that we have briefly discussed in class. Also, it is interesting to
know whether chronic transfusions could help prevent stroke in children with
sickle cell anemia.

Microarray Analysis of Gene Expression During the Cell Cycle, Stephen Cooper and Kerbey Shedden, Cell Chromosome, Volume II, Pages 1-12, Published September 19, 2003

Questions posed in the article:

1. What new information can be learned from analyzing gene expression using a microarray (a device used for the purpose of gene profiling to monitor expression) from the creation of a cell throughout its development?

2. How does the new data obtained from the experiment differ from what was previously thought to be true about division in the cell cycle?

This article would make for an interesting in-class topic for several reasons.  The article introduces new theories and possibilities for the scientific frontier in genetics.  Genetic research is a relatively new scientific topic that holds infinite possiblities for discovery. It interests me that what we are taught in school might not be the way things really work.  I would enjoy the opportunity to learn about a more technical aspect of this area in science.

"Correction of sickle cell disease by homologous recombination in embryonic stem
cells," Li-Chen Wu, Chiao-Wang Sun, Thomas M. Ryan, Kevin M. Pawlik, Jinxiang
Ren, and Tim M. Townes, Blood:Journal of the American Society of Hematology),
Vol. 108, No. 4, pp. 1183-1188,
15 August 2006.

The article is basically questioning previous studies that showed that sickle
cell disease can be corrected by transduction of hematopoietic stem cells with
lentiviral vectors containing antisickling globin genens followed by
trasplantation of these cells into syngeneic recipients. They have some
concerns whether it os really safe and about insertional mutagenesis. A
question that is in this article is whether replacement of the sickle globin
gene (S) with a normal copy of the gene (A)would be a safer correction. Their
goal is the show that sickle cell disease can be corrected without the risk of
insertional mutagenesis. This is an interesting article for our class because
it relates to what we are disussing now in class and it also is like strong
inference because it leaves room for disproof.

The Genetics and Biology of Disc1-An Emerging Role in Psychosis and Cognition,  David J. Porteous, Pippa Thomson, Nicholas J. Brandon and J. Kirsty Millar,  Biological Psychiatry, Volume 60, Issue 2, Pages 123-131, 15 July 2006.
This article attempts to explain psychological disorders through biological means by focusing on Disc1 which has shown some evidence of being related to diseases such as schizophrenia, bipolar disorder, and recurring major depression.  Disc1 is a gene that is disrupted due to a "balanced translocation on chromosome 1q42."  Disc1 has been found to react with various proteins within the brain.  It has risen as a key player in the study of mental illnesses and of normal brain processes.  I believe that this article would be extremely useful for use in class due to the fact that it demonstrates the extent to which an understanding of the structure of the human genome has aided scientists in being able to formulate various hypothesis and theories as to the origins of various diseases and disorders that previously were unable to be explained such as schizophrenia.  This would help the class understand the true importance that knowledge of DNA, and the human genome holds for society at large and the great benefits that can arise from this knowledge.    

Stigma, race, and disease in 20Th century America

Wailoo, Keit. Lancet; 2/11/2006, Vol. 367 Issue 9509, p531-533, 3p

Social men and women of all races interact with each other in today's medical field studies to ensure the safety of our health and future for American citizens to live longer lives. This article that i have selected talks about a short walk through in history of the sickle cell disease with helpful examples and quotes on the side to better understand it. When we hear that term (Sickle-cell) spoken in public we stop to think of its full meaning and what falls behind it. We know it is a hemoglobin disease that carries iron and other gases within the red blood cell  and also that's it oddly shaped from all the other blood cells that greatly shortens our life span. Do we know any more than that? Have you ever wonder where and how it started, which race did it come from, what are some of the main effects of it, if you have it? Basically this article helps by looking back in history from a different point of view. I feel that this article will help open the eyes of those out there who do not know what has happened in history and to shine the light on understanding the Sickle-cell disease. This is a great topic to discuss with students of different ethnic backgrounds.

This Article talks about ethnic traits, understanding the problem, and sickle cell.

"Aging of Mesanchymal stem cell in vitro," Bonab et al., BMC Cell Biology, 7, March 2006.
The main questions posed in the article, “Aging of Mesanchymal stem cell in vitro” are: what are the effects on Mesanchymal stem cells being cultured for a long period of time? And how does it affect their entrance into a senescence state? The article explains that the Mesanchymal stem cells obtained from the bone marrow are usually low proportion and culturing them is a necessity to obtain bigger amounts of the cells. The researchers looked into the cells’ proliferation, telomere length, phenotype, morphology, and differentiation to find out the effects of culturing and how useful they would be afterwards. This would be a good opportunity to learn more about one of the hottest, latest topics in scientific research, since these cells have been attributed different healing properties: among them gene therapy, stem cell transplants and helping to repair damaged organs.

THE GREAT ESCAPE: When Cancer Cells Hijack the Genes for Chemotaxis and Motility.......By John Condeelis,  Robert H. Singer, and ­ Jeffrey E. Segall
Annual Review of Cell and Developmental Biology......Vol. 21: 695-718 (Volume publication date November 2005) ­

I believe that we should study this article because of its relevance to the average person. Cancer is a disease which impacts many individuals and this article details some of the top of the line research in understanding how cancer spreads and how to treat it. Most people are not killed by the initial cancerous growth but when the cancer spreads to other parts of their body. This article attempts to answer the questions:  “What motility behaviors contribute to invasion and intravasation? Is there an expression signature that correlates with these behaviors, that is, an invasion signature? How do the genes of the invasion signature contribute to invasion?” In the end this article generates some fascinating results.  

New discovery in preventing diabetic complications
Smith, Robert. “New gene in preventing diabetes complications.”
New science discoveries.2006. 20 sept. 2006.

This article discusses the implications of controlling a protein called cytokine on the effects of diabetes 2.  Dr. Dana Graves showed that through the manipulation of this protein, inflammation decreased dramatically which is important because inflammation is one of the most common results of diabetes 2.   She also noted that this could possibly have an even greater effect in other areas of the body in the future.
Reason for selection
<>This subject is very close to my heart, because my grandmother has type 2 diabetes; the fact that scientists found a more efficient way to suppress and relive some of the symptoms of diabetes like inflammation is amazing.  Aside from my grandma’s disadvantage, I think it is a cool topic to study because I enjoy examining the makeup of specific proteins and how they interact with the body to create a physical or mental characteristic.  And, in the situation with diabetes 2, the protein cytokine illuminates both aspects very well.  It is also interesting to analyze the process by which the objective is found, in this case the protein that decreases the severity of diabetes.

Human embryonic stem cells for vascular development and repair, Cohen IG Beck G Ziskind A Itskovitz-Eldor J, Israel Medical Association Journal, 8, Aug 2006
This article goes indepth to discribe the background of stem cell reasearch and where it all started from.  It then goes into how human stem cell reasearch is done and what it's benifits are to society. Also the reasearch has detailed study of early developmental events practically unreachable in early human embryos. So with this information we can tell when exactly a human is really a human and when it should still be considered growing cells.  With stem cell research so debated in today government it would be nice to go in depth to figure out what are the advantages and the disadvantages of this seemingly miracle treatment.  This article discuses the process of stem cell experiments which they started working on mice at the beginning but then dive into human stem cells.  This would be very interesting to talk about in class and would help us, future voters, to truly understand the risks and rewards of stem cell research, and determine what level we want it our country.

     This article covers a topic we touched on in class, the heritability of genes and the likely hood that parents who are carriers of a specific gene will pass that gene on to their children.  What is interesting is that among Jews worldwide, the Ashkenazi Jews are the most likely to have certain diseases among the Jewish population and this article theorizes as to why this happens.  The article also talks about what happens when an individual inherits only part of a gene responsible for a certain disease.  This is similar to how African-Americans can get Sickle-Cell Anemia if they inherit both genes responsible for the disease in contrast to just inheriting one which helps to build an immunity to malaria.  The nature/nurture issue is also brought up when the article describes how some genes might actually be passed on but only "turned on" by certain environmental situations.  Some people might have a gene that is never activated because their environment does not ignite the gene, while others will never know they are predisposed to a certain disease until their adulthood when their environment throws the switch and activates the gene which then triggers the disease.
Other related articles actually theorize that only having one or part of a gene makes Ashkenazi Jews especially intelligent which explains why such a small population of people in our world constitute 27% of America's Nobel Prize winners and 50% of the world's chess champions; so having a gene is not always a negative thing.
The article displays several interesting graphs that break down the most common inheritable diseases among Jews, their characteristics, how they are passed on and their incidence rate.
Finally, the article explains why the Ashnekazi Jews have a higher percentage of the diseases listed.  Two theories, the founder effect and genetic drift are believed to be the reason these diseases are confined among the Ashkenazi.  The founder effect refers to a groups earliest founders who most likely possessed these genes and passed them on.  Over time, with the Ashkenazi being more likely to marry other Ashkenazis, the likely hood of passing these genes onto their children grew as carriers came together to share and pass on their genes. This reduces the likelyhood of these genes being passed on to other non-Ashkenazi Jews.  This article is very interesting because while it only discusses one group of people, in context it helps to explain why certain groups of people are predisposed or more susceptible to certain genetic diseases.

“Trends in Fetal and Infant Survival Following Preeclampsia”
Authors name(s): Olga Basso, PhD; Svein Rasmussen, MD, PhD; Clarice R. Weinberg, PhD; Allen J. Wilcox, MD, PhD; Lorentz M. Irgens, MD, PhD; Rolv Skjaerven, PhD
Journal title: Jama
Vol. 296 No. 11
Pages 1-7
September 20, 2006
Preeclampsia, a well-known cause of perinatal mortality has taken the attention of many scientists.   Despite huge improvements in clinical management, preeclampsia often develops in the delivery of a very preterm infant following medical intervention. Even mild-preterm delivery greatly increases the risk of neonatal death. Therefore, when preeclampsia occurs early in pregnancy, even a few additional days in utero may be key to a newborn's survival. A review of clinical trials of delayed vs immediate delivery in fact suggested better outcomes with delayed delivery in well-selected patients. On the other hand, preeclampsia can progress rapidly, putting both mother and child at severe risk if no action is taken. The question posed in this article  is the exact effect on fetal and infant survival of increased rates of early delivery of preeclamptic pregnancies.
According to the article treatments for this disease has increased withing the last 35 years in Norway as proven by the number of Fetal survival in preeclamptic pregnancies that  has vastly improved.  Among preeclamptic pregnancies, inductions before 37 weeks increased from 8% in 1967-1978 to nearly 20% in 1991-2003. During this period, the adjusted for stillbirth decreased from 4.2 to 1.3 for preeclamptic compared with nonpreeclamptic pregnancies. During the same period, the OR for neonatal death after preeclamptic pregnancy remained relatively stable (1.7 in 1967-1978 vs 2.0 in 1991-2003). Later infant and childhood mortality also showed little change.
An analysis was done to show the change in surviviors with different scenarios involving location, type of maternal birth, and back ground of mother.  Age, economic standing, race, education, marital status, and other factos were looked upon also. The analysis sample included 770 613 pregnancies without preeclampsia and 33 835 pregnancies with preeclampsia.  stillbirth and infant death were both more frequent in preeclamptic pregnancies, especially in the early years. Stillbirth was much more strongly associated with preeclampsia, and improved more over time, than infant death.     There were also tests done to view the differences in the association between preeclampsia and death among the 3 periods for different categories of mortality.
Preeclampsia was an important cause of fetal death in Norway during the late 1960s and throughout the 1970s, but its impact has waned.  It was also a factor in other parts of the world as well.   While risk of stillbirth was 4.2 times higher with preeclampsia, it is now only 1.3 times higher. Modern medical management of preeclampsia appears to have been effective in preventing fetal death without causing an increase in infant or maternal death.
This article would make of an interesting class because of its research on a disease that not many know about.  Females in particular would be very interested.  The article covers a top that not many know about and it would be interesting to know mroe about a disease that invloved child birth and also the effects of this disease on children in Norway and other parts of the world.  it's something that not many would be able to learn anywhere else unless by accident.  I would honestly like to here other peoples personal opinion on the topic.

Targeted Therapy of Cancer: New Prospects for Antibodies and Immunoconjugates,
Robert M. Sharkey, PhD and David M. Goldenberg, ScD, MD
A Cancer Journal for Clinicians
Vol.56 No.4 pp.189-243
July/August 2006

    This article discusses a new therapy against cancer using antibodies and immunoconjugates. This new therapy will have less side effects compared to other standard treatments. For example chemotherapy or NHL therapy. Additionally, this new therapy can be combined with the traditional treatments.
    I think this article would make for an interesting class because it deals with a disease that has probable affected everyones' lives' somehow. It would be informative and intriguing for the class because it is something that we can relate to and understand.

Blood to the Brain to the Rescue, Richard L. Proia and Yun-Ping Wu, The Journal
of Clinical Investigation, v.113(8); Apr 15, 2004

This article discusses some of the recent attempts at how to stop, or at least
slow down neurodegeneration. In a study on a field mouse, specific cells called
‘hematopoietic stem cells’ were genetically modified to over express the missing
lysosomal enzyme. In taking advantage of some of the cell’s primary functions,
they have successfully executed enzyme replacement therapies that reverse the
onset of some disorders. This process is the only known treatment to date that
has prevented or slowed down neurodegeneration in storage disease patients. This
procedure is also being examined, as it may be a potential resource for nervous
system therapy. This new find is particularly interesting because it reduces
macrophage/microglia activation (activation can cause an increase in the onset
of neurodeneration in lysosomal storage diseases) and neuronal cell death, but
doesn’t reduce substrate storage (lysosomal storage).

I really think it would be interesting to see what the class could come up with
as far as a means of further testing this treatment, and exploring any possible
repercussions it may have on the cells, as well as on the patient. It would also
be a great way to look at some of the things a cell goes through when a disease
sets in (permanent, temporary, what can we reverse, what we can’t).

New Findings Offer More Complete View of Breast Cancer Gene Mutations in U.S.
Population, Bethesda MD, National Institute of Health, August 15, 2006.

The question asked in the research was how to detect which women will most
likely develop breast cancer after studying two specific mutated genes. They
studied the differences in white and black women in metropolitan areas. I feel
that this is important because cancer is inherited. I would like to learn more
about the new developments and ways to prevent cancer and early detection. This
study revealed that white and black women commonly have one of the two mutated
genes and they develop cancer earlier than women without the gene. I think it
would be interesting to see the link between the mutated gene and the cancer

The Need to Be Green, Scientific American, Page 84-90, March 2006
            Many rivers in the U.S. have become polluted and almost uninhabitable for humans and many other animals alike. Around 53 billion gallons of waste water is produced by the U.S. textile industries and other contributors such as, plastics, and paints. Even our drinking water is being spoiled by pesticides, cosmetics and many other harmful substances. Though scientists have found ways to substitute the harmful plastics and paints there is still a great amount of pollutants circulating through our waters. A group of designer catalyst molecules called TAML ( tetra amido macrocyclic ligand) work with hydrogen peroxide and other oxidants to break down a wide variety of pollutants, much like enzymes. TAMLs work like little cleaners by breaking down pollutants to their nontoxic elements, not leaving any contamination. Though the TAMLs did their job, we didn’t want them running through our streams eventually causing it’s own type of pollution, so researchers made TAMLs that would decompose in a short amount of time, from a few minutes to hours. By running a series of tests scientist were able to find the weak spots in the covalent bonds that held the TAMLs together after subjecting them to oxidative stress. Replacing the weak spots with other atoms and anchoring down the TAML with an Iron atom the TAMLs were able to hold up longer under the cleansing process. Now with about 90 different TAMLs scientist have been able to construct them with different tasks. It would be very interesting to understand how molecules break apart or rebuild other molecules. Seeing the catalyst take place would give the classroom a better understand of how elements react with each other when bonded or disassemble molecules.

Inheritance of Mitochondrial Diseases, Patrick F. Chinnery, Mitochondrion, Volume 2, Pgs. 149-155, 2002
The main question posed in this article is what gives use to or causes the inheritance of mitochondrial disorders. This article interests me because I like genetics and really want to understand how specific DNA sequences affect genetic disorders. This article would make for an interesting class because I believe knowing about these different kinds of genetic disorders and knowing how mitochondrial diseases are inherited is very important. Recently advances in scientists understandings of molecular genetic basis of certain kinds of genetic disorders gives us the power to obtain the knowledge in what really happens for some families and people that suffer from inherited mitochondrial disease.

C. T. T. Edwards, E. C. Holmes, O.G. Pybus, D. J. Wilson, R. P. Viscidi, E. J.
Abrams, R. E. Phillips and A. J. Drummond
Published in Genetics ahead of print on September 1, 2006

This article is primarily about determining the process and reasons behind HIV-1
mutations. It brings to light natural selection as a variable to the evolution
of HIV-1. The experiments done are to refute the theory that neutrality exists
and genetic drift is the only reason for mutation. It is not so much proving
natural selection as it is saying that natural selection must be occurring
because genetic drift is not able to account for the level of diversity
observed. This is a very interesting article, although very confusing. I chose
this article because I am fascinated with viruses and their ability to act as a
living creature without following the same rules and definitions that are
universal among all other creatures. They seem as though they either should not
exist or they did not have the same origin as the rest of life on Earth. This
would be a great article to study in Biology because it deals directly with
genetics and cell processes. I would like to truly understand what this
article is about, but the language and concepts discussed are a little beyond
what I was able to comprehend.