Blog of Parag

Metamorphosis continues...

Ashwini's pets, the hungry caterpillars ate, ate and ate a lot of food and have turned from the larvae stage into the pupae stage. There are five chrysalides hanging from the top of the cup. We shall transfer them to the butterfly garden and wait for about a week to see them open.

Ashwini's new pets

Recently, V bought a nice gift for Ashwini (and me). It is called, Butterfly Garden. The kit had a coupon to get live caterpillars by mail. They arrived here last Friday. We were all excited to see their life cycle unfold in front of our eyes. Here is Ashwini inspecting them very intently.

Right now, the caterpillars live in a cup that is sterile because bacterial infection can kill them. The cup has some tiny holes for air and has enough food supply for all five of them. Within 3-4 days, they have grown really large.

This is so exciting. Can't wait for them to make their cocoons. V says that sometimes she isn't sure who she buys some things for: Ashwini or me? This is one of them. :)

Drink for a healthy heart

A report published in the recent issue of British Medical Journal, researchers from Holland describe correlation between alcohol drinking and coronary heart disease. Their observations can be summarised in one line as done on WebMD:

"The more women drink -- and the more often men drink -- the healthier their hearts."

These benefitial effects are only seen in middle-aged and older individuals. In younger people with healthy hearts, the harmful effects of alcohol on other organs outweigh the heart benefits.

As one gets older, they should start drinking more and more for better coronary health. According to the study: "women, who drink 14 drinks or more per week and men, who drink 21 or more drinks per week and drink every day had the lowest risk of heart disease."

Currently, I average around 1-2 drinks per week. I have a long way to go to catch upto 3 drinks per day. Hopefully, I am still young and have quite a few years to get upto that level. Also, women with 2 drinks per day and men with 3 drinks per day... they will have healthy hearts but, can't imagine how many car accidents result from this.

Quest for a cure

Ever wondered ...
- how a drug is discovered?
- how much research ends in failures before one drug is discovered?
- how much money is spent in bringing a drug to market?

BBC reporter Peter Day followed research and development of a HIV/AIDS drug for several years to make this story. This drug, Maraviroc, a CCR5 inhibitor, is very close to being approved for use. It was discovered that people with a mutated form of CCR5 don't get infected with HIV and develop AIDS. That led to an idea to target this chemokine receptor for HIV therapy. It is a very interesting story.

Quest for a cure is being presented in 3 parts, each 30 minutes long. Here is a link to the first episode that was brodcasted last Monday. This post will be updated to include links to the future audio programs.

Don't mess with ecology

It is very common to introduce a certain species of plant or animal to control the problem of overgrowth of another species. Sometimes, it backfires badly. Here is an example of such incident.

The invasive weed Centaurea maculosa (spotted knapweed) has become widespread in North America. Gall flies (Urophora spp.) have been introduced in an attempt at biological control of the plant. The gall flies lay their eggs in the flower heads, where the larvae induce the formation of galls in which they overwinter. The presence of the galls ultimately results in the plants producing fewer seeds. Although the flies have successfully dispersed throughout populations of the invasive weed, they have not proved to be effective control agents, and the weed continues to spread, particularly in areas disturbed by human activity.

Pearson and Callaway have discovered that therein lies a deeper threat. The fly grubs have proved to be an attractive food source for Peromyscus (deer) mice and bolster mouse populations during otherwise lean winter months. This genus of mice are reservoir hosts for the human pathogenic hantavirus, Sin Nombre, and, worryingly, the authors found that the abundance of Hantavirus-seropositive mice is elevated in zones of high abundance of weed and flies. Deer mice also act as reservoir hosts for Lyme disease and potentially for plague and other zoonotic pathogens.

Ref: Ecol. Lett. 10.1111/j.1461-0248.2006.00896.x (2006)

Maybe, it is better to leave it to the environment and nature to take care of itself.

Surviving the death of spouse

A very interesting article was published earlier this month in New England Journal of Medicine about mortality rates after hospitalization of a spouse. You don't have to read the full text of the article. The point that I want to make is quite obvious in the abstract.

Among men, 6.4 percent died within a year after a spouse's hospitalization for colon cancer, 6.9 percent after a spouse's hospitalization for stroke, 7.5 percent after a spouse's hospitalization for psychiatric disease, and 8.6 percent after a spouse's hospitalization for dementia. Among women, 3.0 percent died within a year after a spouse's hospitalization for colon cancer, 3.7 percent after a spouse's hospitalization for stroke, 5.7 percent after a spouse's hospitalization for psychiatric disease, and 5.0 percent after a spouse's hospitalization for dementia.
...
Overall, for men, the risk of death associated with a spouse's hospitalization was 22 percent of that associated with a spouse's death (95 percent confidence interval, 17 to 27 percent); for women, the risk was 16 percent of that associated with death (95 percent confidence interval, 8 to 24 percent)

Men get more affected by serious illness or death of their wives compared to the other way around. More than twice as many men die within a year of incapacitation or death of their wives than the women do in case of incapacitated or dead husbands.

Is it because men love their wives more, miss them and can't live without them or are they just inept and can't continue living without the helping hand of a wife?

Dilemma about smoking

As a result of the big multi-billion dollar settlement between the tobacco companies and several state governments in US, a lot of this settlement money started trickling down to state universities. This 'puff-money' was used to fund big-price items at various Universities. I know of at least 3 high-field NMR spectrometers (each costing several millions + cost of new facilities to house them) installed in last couple of years. This is just great news for researchers like me who work in this field to have more of these magnets around and get access to them. Also, more 'puff-money' is being generated through increased taxes on cigarettes.

Here is my dilemma... I know smoking is bad for one's health. So, I would encourage my friends and family members to quit smoking. But, at the same time I would like to see people smoking to generate more 'puff-money' that can be used for bio-medical research.

This sounds really bad. There must be a way to make people stop smoking and fund research projects at the same time.

BTW, November 17th is the "Smoke-out" day. Keep your airways clean for at least one day, my smoker friends.

small interference RNA

I meant to write this over a month ago. But, kept forgetting. Small interference RNAs were featured on PBS program NOVA. Check out the following website. There is a nice movie that explains how these RNA molecules work and how they are being developed as a cure.

NOVA | scienceNOW | RNAi | PBS

Here is a link to Nature journal's website that has pretty good animation about siRNAs too.

This is a very interesting technology that can be used to treat disorders at gene expression/protein production level. There are a few biotechs that are involved in developing these cures. One of them, Alnylam Pharma was bought by Novartis, recently. I bought some stock of SIRNA Therapeutics last month. They actually have a drug in Phase I trials. Hope that it will make it through and the company will be bought by a big Pharma at a premium.

Traveling transcription factors

I always thought that transcription factors stay in the cells where they are expressed and control transcription of their target genes. A recent report in Genes Development talks about a transcription factor in plant cells that goes from cell to cell. Quite interesting.

KN1 is a transcription factor that moves from cell to cell in order to regulate, among other things, stem cell identity in the shoot apical meristem of maize. Another transcription factor, GL1, prefers to stay in its home cell, where it regulates the formation of tiny hairs (trichomes) in the leaf epidermis of Arabidopsis. Whether intercellular transport of KN1 is regulated is addressed by Kim et al. By making a chimeric construct of KN1 with GL1, the authors determined which portions of KN1 could drive intercellular transport of misexpressed GL1 and thus rescue trichome formation. A GL1-KN1 fusion using only the C-terminal portion of KN1 supported rescue through intercellular transport, whereas the fusion using the N-terminal portion of KN1 did not. The homeodomain included in that C-terminal portion of KN1 turned out to be critical. Both the mRNA and the KN1 homeodomain protein seem to be required for intercellular trafficking. Thus, the KN1 homeodomain is required to transport both itself and its mRNA through plasmodesmatal channels.

Genes Dev. 10.1101/gad.332805 (2005).

The scent of a woman female cockroach

BIOCHEMISTRY: Irresistible Lure for Cockroaches Determined -- Pennisi 307 (5712): 1029b -- Science

Just like many other animals, cockroaches also make their own pheromones. After years of research, chemical formula of the male-luring scent emitted by female cockroaches is discovered. This was a result of painstaking research. The chemical broke down when it was being isolated. Each female cockroach makes so little of it that they had to dissect 15,000 (yes, fifteen thousand) cockroaches to extract enough material to study.

The researchers have been successful in making this chemical synthetically and it has shown to attract male cockroaches. This will be used in the next generation of cockroach control methods.

If the link in this post doesn't work, click below to read more.

In search of mates, frogs croak, birds sing, and cockroaches wear their own special perfume. For almost 10 years, researchers have tried to decipher the chemical formula of the male-luring scent emitted by female German cockroaches. Now that formula is finally in hand. As a result, city dwellers may one day be less squeamish about turning on the light at night: The chemical may result in a "very powerful system" for pest control, says Walter Leal, a chemical ecologist at the University of California, Davis.

On page 1104, Satoshi Nojima, a chemist now at the Shin-Etsu Chemical Co. in Tokyo, Japan, and his colleagues describe the arduous path they took to characterize this chemical, one of several pheromones produced by cockroaches. They also show that a synthetic version of it is a potent attractant for the insects. "It was very difficult to do, very time-consuming," says Robert Kopanic Jr., an entomologist at S. C. Johnson and Son Inc. in Racine, Wisconsin.

German cockroaches are the bane of urban residents. As many as 100,000 can live in a single apartment or house; baits and sticky traps are only moderately effective, and insecticides are not environmental friendly.

So it was exciting news when Coby Schal, an urban entomologist at North Carolina State University in Raleigh, and Dangsheng Laing, now at Atex Bait Co. in Santa Clara, California, reported in 1993 that female cockroaches gave off a volatile compound, or pheromone, that attracts males from meters away. But taking the next step, identifying the pheromone, proved almost impossible. "Every time [we] tried to isolate it, it fell apart," recalls Wendell Roelofs, a biochemist at the New York State Agricultural Experiment Station in Geneva.

Figure 1 Love is blind. A synthetic version of the female scent that attracts males (on female's back) may help with cockroach control.

CREDIT: NOJIMA ET AL., SCIENCE

Adding to the challenge, females produce so little pheromone that researchers needed to dissect 15,000 of them, removing the pheromone-producing gland from each, to extract enough material for analysis. And Nojima--who was working with Roelofs at the time--had to come up with new ways to pin down the attractant among the many compounds in the extracts.

Nojima joined a single detached cockroach antenna to electrodes and exposed it to the chemicals exiting a gas chromatograph, which had separated the roach extract into discrete components. If the antenna sent a signal to the electrodes, he knew he had a good candidate pheromone. The night before he flew back to Japan--his postdoc was ending--Nojima struck cockroach gold when his system recorded a hit. "After 10 years of work, it came down to one night," says Schal.

Fran Webster of Syracuse University in New York found that the newly isolated compound, called blattellaquinone after the cockroach's Latin name Blattella, has a novel structure. But it is similar enough to a commercial product that it is relatively inexpensive to synthesize. The compound clearly attracts male roaches: They prefer the dissolved synthetic pheromone over a control solvent about 93% of the time, on par with their preferences for the natural pheromone. Moreover, field tests at a cockroach-infested pig farm indicate that many males can't resist the synthetic version.

If the compound proves to be effective over long periods, it could be quite useful for pest control, says Kopanic. Even though blattellaquinone only attracts males, they are the wanderers among the two sexes. The new pheromone should lure males into traps or to poison laced with the compound. In the latter case, they would then transfer the poison, through their feces, to females and their young, suggests Schal. If so, for male roaches, the female scent may one day lead to poison, not procreation.

Space-time

Absolute space doesn't exist.
Absolute time doesn't exist.
Space-time is absolute.

Promiscuous enzymes

Cytochrome P450 (CYP) are the enzymes, mostly in liver that are responsible for breaking down all the foreign chemicals that get inside the body. They take out all foreign chemicals from the bloodstream as it passes through the liver. There are many different isoforms of this enzyme. One of them, 2E1 is responsible for metabolising alcohol. The same isoform is responsible for metabolising drugs like tylenol. Hence, the warning on the bottle about not taking it with alcoholic drinks. Other isoforms also show this very broad range of substrates that they metabolise.

Grapefruit juice is an inhibitor of isoforms 3A4 and 3A5. Patients who are taking drugs (e.g. lipitor, cardiazem) that are metabolised by these isoforms are told to avoid Grapefruit juice to avoid side effects caused by high levels of drug reached because they don't get metabolised.

Conversely, certain drugs (e.g. modafinil induces CYP3A4) can induce CYP450 enzymes causing rapid metabolism of other drugs making them ineffective. Cytochrome P450 metabolism is a topic of huge interest in drug development to ensure the effectiveness of the drugs while minimising side effects and drug-drug interactions.

Usually, enzymes are very specific about what substrate they process, but, Cytochrome P450 are inherently promiscuous. They have very floppy and hydrophobic active sites to accomodate a variety of substrates. This promiscuity allows them to catch any hydrophobic molecules (mostly drugs and other chemicals). Then, it pumps oxygen into those molecules to oxidise them and make them more hydrophilic (water soluble) so that they can be excreted out of the body quickly.

Citation index by Google

Who needs an expensive subscription to the 'Citation Index' by ISI web of science? Find out all the publication information on Google scholar. It found 11 out of my 15 publications and I have been cited at least 22 times.

Dr. Francis Crick is no more

Dr. Francis Crick, one of the co-discoverers of the 3-dimensional structure of DNA passed away on Thursday. He worked out the detailed structure of DNA while working with Dr. Watson at Cambridge University. Their discovery was published in 1953 and they were awarded a Nobel prize for that work. He was a distinguished research professor at the Salk Institute in San Diego and also served as its president earlier.

Anyone who works with nucleic acids knows his name and uses in day-to-day research conversations. The complementary pattern of nucleic acid base-pairs is described as 'Watson-Crick base-pairing'.

The world lost a great scientific mind today.

Commensal organisms

This will be a shock to all germ-phobic clean-freaks.

Every healthy human being has about 150 different species of bacteria living in their gut. These bacteria can account for about 2% of body weight, i.e., 1.5 Kgs in an individual that weighs 70 Kgs.

Bottomline: We are all walking talking bags of bacteria.

My Recent Publication

Some of my work from a long time ago got published in Biochemistry recently. My name on a paper after 3 years. Drastic reduction in ability to publish results in scientific journals is the biggest disadvantage of leaving academia for industry. Here is the abstract of the paper if anyone wants to know more....

Biophysical characterization of the complex between double-stranded RNA and the N-terminal domain of the NS1 protein from influenza A virus: evidence for a novel RNA-binding mode.

Chien CY, Xu Y, Xiao R, Aramini JM, Sahasrabudhe PV, Krug RM, Montelione GT.

Center for Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854-5638, USA.

The influenza virus nonstructural protein 1 encoded by influenza A virus (NS1A protein) is a multifunctional protein involved in both protein-protein and protein-RNA interactions. NS1A binds nonspecifically to double-stranded RNA (dsRNA) and to specific protein targets, and regulates several post-transcriptional processes. The N-terminal structural domain corresponding to the first 73 amino acids of the NS1 protein from influenza A/Udorn/72 virus [NS1A(1-73)] possesses all of the dsRNA binding activities of the full-length protein. Both NMR and X-ray crystallography of this domain have demonstrated that it is a symmetric homodimer which forms a six-helix chain fold, a unique structure that differs from that of the predominant class of dsRNA-binding domains, termed dsRBDs, that are found in a large number of eukaryotic and prokaryotic proteins. Here we describe biophysical experiments on complexes containing NS1A(1-73) and a short 16 bp synthetic dsRNA duplex. From sedimentation equilibrium measurements, we determined that the dimeric NS1A(1-73) binds to the dsRNA duplex with a 1:1 stoichiometry, yielding a complex with an apparent dissociation constant (K(d)) of approximately 1 microM. Circular dichroism and nuclear magnetic resonance (NMR) data demonstrate that the conformations of both NS1A(1-73) and dsRNA in the complex are similar to their free forms, indicating little or no structural change in the protein or RNA upon complex formation. NMR chemical shift perturbation experiments show that the dsRNA-binding epitope of NS1A(1-73) is associated with helices 2 and 2'. Analytical gel filtration and gel shift studies of the interaction between NS1A(1-73) and different double-stranded nucleic acids indicate that NS1A(1-73) recognizes canonical A-form dsRNA, but does not bind to dsDNA or dsRNA-DNA hybrids, which feature B-type or A/B-type intermediate conformations, respectively. On the basis of these results, we propose a three-dimensional model of the complex in which NS1A(1-73) sits astride the minor groove of A-form RNA with a few amino acids in the helix 2-helix 2' face forming an electrostatically stabilized interaction with the phosphodiester backbone. This mode of dsRNA binding differs from that observed for any other dsRNA-binding protein.

Vaccines and Autism

From Mar 15, 2004 issue of Time magazine:

British researchers caused a furor in 1998 when they published a controversial report suggesting a link between the growing number of autism cases and the standard childhood vaccine for measles, mumps and rubella (MMR). Although other physicians criticized the authors for jumping to conclusions, many worried parents stopped immunizing their children. Now 10 of the 13 original authors have decided to retract the paper, acknowledging that their data were not strong enough to support their incendiary conclusion.

This report had caused such an outrage, making people rethink the risk/benefits of vaccination. Hopefully, the retraction of this study will make as big a news as the original publication. When will these doctors realise that if one needs rigorous statistical analysis to prove something, it may be wrong.

I like this quote I heard somewhere...

There are three types of lies: lies, damned lies, and statistics.

Update: I do not mean to bash statisticians here. Statistics is a very powerful tool. The problem is that sometimes people bear it without realising its power. That leads to wrong conclusions and controversies like this one.

Antibiotics

Heard a really nice seminar by an eminent scientist, Dr. Alexander Mankin about how antibiotics have evolved and how they work. Want to jot down a few things that I learnt from it before I forget.

For those who don't think about this everyday, here is some background. The basic paradigm of biology is:

DNA ==Transcription==> RNA ==Translation==> Protein

All the genetic information is stored in DNA, it is transcribed into RNA, and then translated to proteins that actually do the biochemical reactions necessary for life-functions. One copy of RNA can be used multiple times to make many copies of protein.

Some of the RNA is also catalytic, but mostly it works as a molecule that carries information for translation into protein. The most important catalytic RNA is in the protein synthesizing machineary, Ribosome.

Why target ribosome for antibiotic action?
Synthesis of proteins is an essential task for any living being, so, targeting it, is an obvious choice for killing an organism. But, the major problem is selectivity. All ribosomes are evolved from a common ancestor and hence it is very similar across different species. The ideal chemical should target protein synthesis of the unwanted organism but, should not affect the host (fungi or human) protein synthesis. This makes it difficult to keep making newer and newer antibiotics. Although, the current antibiotics take advantage of minute differences between the structures of human and bacterial ribosomes to be effective, they suffer from side effects due to the similarities.

Why do antibiotics work as well as they do?
There has been a lot of effort in mapping the sites on ribosome where the antibiotics interact. Most of the antibiotics interact with the RNA part of ribosome. The reason behind this is very clever.

About 2/3rd of ribosome consists of RNA. There are about 10,000 ribosomes in a given bacterial cell. To make that many ribosomes, there are multiple copies of genes coding for ribosomal RNA, but, a single copy of genes coding for the protein. Because, the cell has to go through multiple steps of transcription to make enough RNA, but, a single step transcription can be followed by multiple step translation can make enough protein to assemble all these 10,000 ribosomes.

This makes it possible for a mutation in the single copy of the protein gene to disrupt its interaction with the antibiotic and make the bacteria resistant to the antibiotic. But, a mutation in one of the copies of ribosomal RNA, can make only a small fraction of functional ribosomes immune from antibiotic action and that is not enough for the bacteria to survive. Thus, molecules that interact with RNA part of ribosome to stop protein synthesis are more effective in killing bacteria.

Therapeutic cloning advances

Scientists clone 30 human embryos

A great breakthrough in the area of therapeutic cloning. This was the first instance where cloned human embryos were grown to a stage where stem cells of three different were produced and harvested. These cells were implanted into mice and were seen to differentiate into more specific cells types.

The aim of this study was to see how embryonic stem cells can be used to make transplantable tissues to treat diseases such as Pakinson's, diabetes, and osteoarthritis. This was not an attempt to make cloned babies.

The researchers went through rigorous review with the ethical board in South Korea and obtained consent from the women who donated eggs used in the study.

According to Roger Pedersen, professor of regenerative medicine, at the University of Cambridge, UK:

"The present work has substantially advanced the cause of generating transplantable tissues that exactly match the patient's own immune system.

"These researchers' findings also make it possible to learn how to reprogramme the human genome to an embryonic state.

"This will likely accelerate the development of alternative ways of reprogramming human cells, which could in the future diminish the need to use human eggs for this purpose."

UPDATE: A more detailed article describing the research appeared in the New York Times. Read it here...

Cloning Creates Human Embryos

February 12, 2004
By GINA KOLATA

Scientists in South Korea report that they have created
human embryos through cloning and extracted embryonic stem
cells, the universal cells that hold great promise for
medical research.

Their goal, the scientists say, is not to clone humans but
to advance understanding of the causes and treatment of
disease.

But the work makes the birth of a cloned baby suddenly more
feasible. For that reason, it is likely to reignite the
fierce debate over the ethics of human cloning.

The work was led by Dr. Woo Suk Hwang and Dr. Shin Yong
Moon of Seoul National University and will be published
tomorrow in the journal Science. The paper provides a
detailed description of how to create human embryos by
cloning. Experts in the field not involved with the work
said they found the paper persuasive.

"You now have the cookbook, you have a methodology that's
publicly available," said Dr. Robert Lanza, medical
director of a company, Advanced Cell Technology in
Worcester, Mass., that had tried without success to do what
the South Koreans did.

Although the paper, written in dense jargon and summarizing
its findings by saying, "We report the derivation of a
pluripotent embryonic stem cell line (SCNT-hES-1) from a
cloned human blastocyst," its import was immediately clear
to researchers.

"My reaction is, basically, wow," said Dr. Richard Rawlins,
an embryologist who is director of the assisted
reproduction laboratories at the Rush University Medical
Center in Chicago. "It's a landmark paper."

It is what patients with diseases like Parkinson's and
diabetes had been waiting for, the start of so-called
therapeutic cloning. The idea is to clone a patients cells
to make embryonic stem cells that are an exact genetic
match of the patient. Then those cells, patients hope,
could be turned into replacement tissue to treat or cure
their disease without provoking rejection from the body's
immune system.

Even though the new work clears a significant hurdle,
scientists caution that it could take years of further
research before stem cell science turns into actual
therapies.

Even before the publication - reported last night by a
South Korean newspaper, one day ahead of the embargo
imposed by Science - the research was criticized by cloning
opponents.

Dr. Leon R. Kass, chairman of the President's Council on
Bioethics, called for federal legislation to stop human
cloning for any purpose.

"The age of human cloning has apparently arrived: today,
cloned blastocysts for research, tomorrow cloned
blastocysts for babymaking," Dr. Kass wrote in an e-mail
message. "In my opinion, and that of the majority of the
Council, the only way to prevent this from happening here
is for Congress to enact a comprehensive ban or moratorium
on all human cloning."

The House has twice passed legislation that would ban all
human cloning experiments, most recently in February 2003.
But the bills have foundered in the Senate, where many
members who oppose reproductive cloning do not want to ban
it for medical research.

Dr. Hwang said he knew that the work would elicit strong
responses but that the research was so important it should
be done anyway, adding that there was strict oversight by
an ethics committee.

"Of course," he said, "we acknowledge that there will be
controversy. But as scientists, we think it is our
obligation to do this."

The paper describes the successful process in detail, with
precise information on how to start the embryos growing and
what solutions are best to nourish them. That recipe
appears to advance the likelihood of reproductive cloning.
When fertility laboratories fertilize eggs, grow embryos to
the same developmental stage as the embryo clones and
implant them in a human uterus, 40 to 60 percent end up as
babies.

The scientists stress that all the research was in the
laboratory, in petri dishes. No embryo was implanted in a
woman. The women who provided unfertilized eggs that were
needed to start the cloning process were not paid.

The research was financed by the government of South Korea,
where cloning to create a baby is illegal.

Dr. Hwang is an expert in animal cloning, and Dr. Moon is a
medical doctor who trained in the late 1980's at a leading
American fertility center, the Jones Institute for
Reproductive Medicine at the Eastern Virginia Medical
School in Norfolk. That is one of the very few places where
researchers have extracted human stem cells from embryos
that were made the usual way, by using sperm to fertilize
eggs.

Until now, no one had even come close to using cloning to
create a human embryo or even a monkey embryo, to say
nothing of extracting stem cells from one.

Stem cells are the research prize. They appear after an
embryo has grown for five or six days, its cells
subdividing within the hard casing of the egg. Although the
embryo at this stage contains about 100 cells, it is still
no bigger than the original egg, nearly invisible to the
naked eye.

"If it was floating in water with light underneath, it
might look like a speck of dust," said Dr. William Gibbons,
a professor of obstetrics and gynecology at Eastern
Virginia.

The defining feature of a blastocyst is that it has a real
structure, made of a ball of cells, the inner cell mass,
encased in a sphere. The sphere becomes the placenta if the
blastocyst is implanted in a woman's uterus, and the inner
cell mass becomes the fetus.

But at the blastocyst stage, the inner cell mass consists
of cells that are still indeterminate, not yet committed to
becoming any particular cell type. They are the stem cells,
which can in theory develop into any of the body's tissues
and organs. Stem cells from a clone would be genetically
identical to the person who contributed cells to make the
embryo.

Some scientists want to use stem cells to study how genes
cause disease. Others say they may one day use stem cells
to grow replacement tissues that are identical to the
patient's own cells.

But while most expected that cloning would one day be used
to create human embryos for harvesting stem cells, the
South Korean research elicited amazement from experienced
investigators.

They were particularly surprised that the researchers had
managed to assemble so many unfertilized human eggs, 242 in
all.

Advanced Cell Technology, the lone American company that
has tried to conduct similar research, went through a long
and arduous debate with its ethics board before recruiting
young women to donate eggs. The board eventually decided
that a fair payment for a woman's time and effort would be
$4,000.

To donate eggs, women have to inject themselves with
hormones to stimulate their ovaries, be monitored with
ultrasound to see when the eggs are ready to emerge from
the ovaries and then allow doctors to extract the eggs with
a thin needle. Advanced Cell Technology advertised for
donors and paid them the fee, but ended up with just 19
eggs. The company restarted its program in June, Dr. Lanza
said, with "just a few donors.".

In South Korea, Dr. Moon said in a telephone interview,
there was no advertising for egg donors and no payments.
The 16 women who donated the 242 eggs were "personal
contacts," he said, declining to elaborate.

The Koreans are to discuss their findings today in Seattle,
at the annual meeting of the American Association for the
Advancement of Science.

The investigators selected 176 eggs that were in a
developmental stage that made success seem most likely. To
start the cloning, the team removed the genetic material
from the eggs and replaced it with genetic material
obtained from cumulus cells, the adult cells that cling to
eggs. Cloning experiments with mice had indicated that the
cells were especially amenable to the process.

Dr. Moon explained, "The cumulus cell is easy to get,"
because it is on the surface of the egg.

The abundance of eggs enabled the scientists to experiment
with ways of having the egg cells start to divide and of
growing the embryos in the laboratory.

"They had an incredible amount of eggs and an opportunity
to perfect the protocols," said Dr. Jose B. Cibelli,
formerly with Advanced Cell Technology and now a professor
of animal biotechnology at Michigan State University. "They
tried 14 different protocols."

Dr. Cibelli consulted with the Koreans toward the end of
their work and is listed with them as an author of the
paper in Science.

The researchers experimented with different timing, between
adding the cumulus cell to an egg and activating the egg,
making it start to divide with its cumulus cell genes.

"If they waited four hours instead of two hours, it didn't
work," Dr. Hans Schöler, a professor of reproductive
medicine at the University of Pennsylvania, said.

All along the way, Dr. Schöler added, such small variations
in the procedure had marked effects.

"Marginal differences made it work," he said. "If you
stepped a little bit to the right or a little bit to the
left, it didn't work."

The resulting method yielded blastocysts 26 percent of the
time. "That's amazing," Dr. Schöler said.

Eventually, Dr. Hwang, Dr. Moon and their colleagues ended
up with 30 blastocysts, from which they were able to
extract 20 inner cell masses. One grew into a line of stem
cells.

The next step, Dr. Schöler said, will be to improve the
success rate of obtaining stem cell lines from blastocysts.

Dr. Ron McKay, a stem cell scientist at the National
Institute of Neurological Disorders and Stroke, said the
work suggested that it might be easier than anyone thought
to make cloned human embryos and extract stem cells from
them.

"The next question takes you to the heart of the whole
discussion," Dr. McKay said. "Why do it anyway? What's the
point? Is there any point?"

Dr. McKay said that for him the point was that such cells
could provide a unique opportunity to study human disease.
He spoke of a scientist who had died in her 40's from
breast cancer. What if her cells had been cloned to make
embryonic stem cells and those cells had been directed to
turn into breast tissue? That might give scientists a
chance to examine how genes for breast cancer altered the
cells' susceptibility and might explain how and why the
cancer developed in the first place.

Dr. McKay said learning to make embryo clones for research
could help people who want to make babies that are clones.
But he added that scientists did not always do everything
that is possible.

"I really don't want to comment on the slippery slope," he
said.

Dr. Cibelli, too, focused on the Koreans' report.

"Now you have the demonstration that everyone was waiting
for," he said. "Whether this approach will be applicable to
making babies, I don't know. And I hope I never find out."

Global warming

Taken from The New York Times Op-Ed page written by Paul Epstein.

In the past 50 years, the top two miles of the world's oceans have warmed significantly, and that warming is melting sea ice. In just four decades, the
thickness of summer North Polar floating ice shrank 44 percent. In addition, warming makes droughts drier and longer, and when the evaporated water returns to earth it does so in heavier downpours.

Op-Ed Contributor: Global Chilling

January 28, 2004
By PAUL R. EPSTEIN

BOSTON - It seemed incongruous when former Vice President Al Gore gave a speech on global warming on a bitterly cold day in New York City this month. But in fact it was an appropriate topic: New Yorkers may be able to blame the city's current cold spell - the most severe in nearly a decade - on global warming.

Global warming doesn't mean that every place on the globe gets warmer. The weather history that can be read in polar ice-core samples indicates that previous periods of warming affected North America and Europe far differently than they
did the tropics - the Northern Hemisphere got a lot colder.

It's far too early to say for sure, but the same processes may be at work today. In the past 50 years, the top two miles of the world's oceans have warmed significantly, and that warming is melting sea ice. In just four decades, the
thickness of summer North Polar floating ice shrank 44 percent. In addition, warming makes droughts drier and longer, and when the evaporated water returns to earth it does so in heavier downpours.

Normally, water circulates in the North Atlantic like this:
Cold, salty water at the top sinks; that sinking water acts as a pump, pulling warm Gulf Stream water north and thus moderating winter weather. But now, fresh water from the thawing ice and heavier rain is accumulating near the
ocean's surface; it's not sinking as quickly. (The tropics are faced with the opposite phenomenon. According to Dr. Ruth Curry and her colleagues at the Woods Hole Oceanographic Institution, the tropical Atlantic is becoming saltier; as warming increases, so does evaporation, which leaves behind salt.) The freshening" in the North Atlantic may be contributing to a high-pressure system that is accelerating trans-Atlantic winds and deflecting the jet stream - changes that may be driving frigid fronts down the Eastern Seaboard. The ice-core records demonstrate that the North Atlantic can freshen to a point where the deep-water pump fails, warm water stops coming north, and the northern ocean suddenly freezes, as it did in the last Ice Age. No one can say if that is what will happen next. But since the 1950's, the best documented deep-water pump, between Iceland and Scotland, has slowed 20 percent.

Why now? After all, the planet's previous periods of global warming resulted from changes in the earth's tilt toward the sun, and recent calculations of these cycles indicate that our hospitable climate was not due to have ended any time soon. But because of the warming brought by the buildup of carbon dioxide, mainly from the burning of fossil fuels, the equations have changed. We are entering uncharted waters. It's something for New Yorkers to ponder as they bundle up.

Coffee May Reduce Risk of Diabetes

From Wall Street Journal, 01/06/04

A new study printed in the Annals of Internal Medicine suggests that drinking more coffee may reduce the risk of the most common form of diabetes.

Compared with people who don’t drink coffee, men who drank more than six, eight-ounce cups of caffeinated coffee per day lowered their risk of Type 2 diabetes by about 50 percent. Women reduced their risk by about 30 percent. Among decaffeinated coffee drinkers the results we slightly lower—a 25 percent risk reduction for men and a 15 percent risk reduction for women.

Experts says that more research is needed to clarify the results—to determine whether or not it is really the coffee or something else about coffee drinkers that protects them. “The evidence is quite strong that regular coffee is protective against diabetes,” said Dr. Frank Hu, a researcher at the Harvard School of Public Health. “The question is whether we should recommend coffee consumption as a strategy. I don’t think we’re there yet.”

Multifunctional protein VI

Adenovirus is a small DNA virus that replicates its genome and assembles new virus particles inside the nucleus of the host cell. One of the viral capsid proteins, protein VI, has near its C terminus both nuclear localization signal (NLS) and nuclear export signal (NES).

The major adenovirus capsid protein (hexon) is produced in the cytosol and so must be imported into the nucleus for virus particle assembly. Protein VI binds to it, and carries hexon molecules into the nucleus, using its NLS to hitch a ride on the host nuclear importers, and then return empty-handed to the cytosol via its NES-exporter interaction.

When capsid proteins are sufficiently concentrated in the nucleus to allow for efficient virus assembly, both nuclear transport signals in protein VI are degraded by proteolysis, trapping the protein in the nucleus and uncovering its third function as a structural component of the capsid itself. Pretty nifty for a small protein with about 225 residues.

The complete article can be found at EMBO Journal, 22, 6245 (2003).

Public Library of Science

Just heard about this on NPR:

Public Library of Science is open. The website has links to several journals that are freely available online and they debuted the inaugural issue of their first free journal "PLoS Biology". The mission statement on their website reads:::

The Public Library of Science (PLoS) is a non-profit organization of scientists and physicians committed to making the world's scientific and medical literature a freely available public resource.

The internet and electronic publishing enable the creation of public libraries of science containing the full text and data of any published research article, available free of charge to anyone, anywhere in the world.

Immediate unrestricted access to scientific ideas, methods, results, and conclusions will speed the progress of science and medicine, and will more directly bring the benefits of research to the public.

They are promoting the idea that publishing results of scientific research in the public domain is an integral part of doing research and should be included in the funding of research projects. This is a different business model compared to the current one for the journal publishing houses.

This is a revolutonary and I must say a very cool concept just like the Open Source Initiative and Free Software Foundation. I know my friends don't agree with me on Opensource and FSF, but, I sincerely believe that their rationale makes sense. When programmers can read, redistribute, and modify the source code for a piece of software, the software evolves. People improve it, people adapt it, people fix bugs. And this can happen at a speed that, if one is used to the slow pace of conventional software development, seems astonishing.

Chilled Platelet Study Sweetens Expectations

Chilled Platelet Study Sweetens Expectations in Transfusion Medicine This is great news. Platelets are normally stored at room temperature, because they are cleared out of circulation by immune cells after a freeze-thaw cycle and they have to be used within 5 days. With this new research, it will be possible to freeze and store platelets for a longer time. This will reduce loss of this precious resource and also reduce recruiting costs to bloodbanks.

In the Sept. 12 Science, Stossel and his colleagues report how chilled platelets are recognized and removed from circulation by hungry immune cells in the livers of mice. They also demonstrate how this clearance mechanism can be blocked by adding a dash of the proper sugar to the chilled platelets. The added sugar acts like an invisibility cloak, allowing the platelets to evade detection by immune cells and circulate for the normal seven-day life span of platelets, said cardiologist Karin Hoffmeister, first author of the paper and HMS instructor in medicine at the Brigham. In mice, the sugar treatment doubled the useful storage period of platelets to 12 days.

Another random fact

This is how photocopies are made... It is a 3 step process:
1. light reflected from the white parts of the original is focused onto a charged printing "drum," where it locally dissipates charge;
2. positively charged toner particles are attracted to the remaining charged areas that were dark in the original;
3. paper is run over the drum to pick up the toner to create an image of the original.

Global warming This article appreared

Global warming
This article appreared in The New York Times about 2 weeks ago. It talks about evidence of changes in the world due to global warming and what could happen if the warming trend continues. It is an interesting read. Here are a few lines from it...

Skeptics of global warming should come to this Eskimo village on the Arctic Ocean, roughly 250 miles north of the Arctic Circle. It's hard to be complacent about climate change when you're in an area that normally is home to animals like polar bears and wolverines, but is now attracting robins. A robin even built its nest in town this year (there is no word in the local Inupiat Eskimo language for robins).
...
The Okpilak River valley was historically too cold and dry for willows, and in the Inupiat language "Okpilak" means "river with no willows." Yet a warmer, wetter climate means that now it's crowded with willows.
...
Alaska has warmed by eight degrees, on average, in the winter, over the last three decades, according to meteorological records.
...
In the hamlet of Deadhorse, I ran into an Arctic native named Jackson Snyder, who said that winters were getting "a lot warmer; doesn't get much below 50 below anymore."
...
That may not seem so bad. But while there will be benefits to a warmer Alaska (a longer growing season, ice-free ports), climate change can also lead to crop failures, spread tropical diseases and turn Bangladesh into tidal pools. The pace of warming may be far too fast for animals, humans or ecosystems to adjust. My advice is that if you're planning a dream home in New Orleans or on the Chesapeake, put it on stilts.
...
It predicted that in this century, the seas will rise 4 to 35 inches. Global warming is still an uncertain threat, but it may well become one of the major challenges of this century. Unless we act soon, we may find waves lapping the beaches of Ohio.

Thanks, Mayuresh.

Another interesting fact

Why do we hear a thunderclap?

The average temperature of lightning is 76000 F. In that split second when lightning appreas, the extreme temperature expands the air violently. This explosion of air creates the sound wave that we hear as a thunderclap.

Why some wines make you pucker?

NMR spectroscopy is routinely used for determination of chemical structure of small molecules as well as to study three-dimensional structure and interactions of big biomolecules. Non-traditionally, it has also been a tool in solving exotic problems such as quality control of Olive oil. Here is another NMR exotica. In the recent issue of Biochemistry an article was published by a French group (of course!!) describing the use of NMR in studying wine tannin and saliva protein complexes to understand the astringent taste of red wines. The polyphenolic tannins of red wines come primarily in two varieties: the flavan-3-ol polymers (made of catechin and epicatechin monomers) from the grape skins and seeds, and the hydrolyzable tannins (made of ellagic and gallic acids) from the oaken barrels. These compounds are responsible for the astringent taste of red wine and are thought to bind to proline-rich proteins (PRPs) in saliva. Previous attempts to define this interaction have been hampered by the limited solubility of the complexes. Working in the remarkably true-to-life solvent of water:ethanol (88:12 v/v; pH 3.5), Simon et al. describe the association of three procyanidin B3(catechin-4a,8-catechin) molecules with a 14-residue fragment of salivary protein IB7. Using circular dichroism, mass spectrometry, NMR, and molecular dynamics calculations, they find that the peptide adopts a type II helical structure typical of proline-rich sequences. Here is how they describe a "Molecular Vision of Astringency"

Protein-tannin interaction is the source of astringency, the mouth dryness sensation due to the complexation of the lubricant salivary proteins. It is often asked why very different feelings are perceived depending on wines. This may be linked to the specific type of interaction between tannins and proteins that may depend on tannins and protein nature and also to the stability and the lifetime of complexes. We have shown herein that the IB7 fragment from saliva protein can complex three B3 tannins and that the interaction occurs in the hydrophilic side of the peptide. The peculiar structure of the peptide can play an important role here. In the absence of tannins it appears very flexible and offers type II helices (proline-rich parts) for binding. Once complexed, the conformational freedom of the peptide, as well as that of the entire complex, appears much reduced. Is this phenomenon related to astringency? It is interesting trying to predict what would be the stoichiometry for B3 interacting with the entire IB7 human saliva protein. Because the IB714 sequence is almost con-tained three times in IB7, one could guess that a 1/9 complex could be stabilized. If this happened to be true, PRP proteins of the IB7 family could be called “tannin sponges”.

Whereas the properties of PRP become unveiled, the specificity of the tannin counterpart is more subtle. It probably depends on its chemical nature (hydrolyzable, condensed, galloylated, etc.). Its molecular weight, 3D structure, ropensity to auto-associate, and water solubility may lead to noticeable differences in the protein-tannin complex formation. This explains, perhaps, the gustative differences noticed by enologists about tannin behavior in red wine such as drying, puckering, sour, astringent, bitter, or rough character. Of interest is the fact that the tannin binding sites appear to have different physicochemical properties. In our case the sites appear to have different dynamics. This might be linked to their lifetime that could modulate the time during which the proteins are complexed and therefore no longer available to lubricate the mouth.

Wine slows aging

Harvard Gazette: Wine molecule slows aging

Another reason to reach for the bottle, but, in moderation, I mind you. Here is a toast to your long life.

A molecule that is an active ingredient in red wine can slow the aging of human cells. It extends the life expectancy of every organism that, so far, has been fed on it, including yeast, worms, and fruit flies.

Called resveratrol, the wonder substance seems to work in the same way as drastic calorie cutting. Dramatic reduction of calories has been shown to increase the life span of mice, rats, and monkeys. Such diets are being tried in humans but results are not yet in. Severe dieting also cuts the risk of dying from cancer, heart problems, and other age-related diseases in monkeys.

Dark chocolate good for you

Dark chocolate may aid blood pressure, study says
Good to find this out. My choice of chocolate was right all along. It is hard to believe that something that tastes so good is actually good for health too.