Wednesday, December 15, 2010

Secrets Of Red Tide Revealed

 

In the Aug. 31 cover story of Science, the MIT team describes an elegant method for synthesizing the lethal components of red tides. The researchers believe their method approximates the synthesis used by algae, a reaction that chemists have tried for decades to replicate, without success.
Understanding how and why red tides occur could help scientists figure out how to prevent the blooms, which cause significant ecological and economic damage. The New England shellfish industry, for example, lost tens of millions of dollars during a 2005 outbreak, and red tide killed 30 endangered manatees off the coast of Florida this spring.
The discovery by MIT Associate Professor Timothy Jamison and graduate student Ivan Vilotijevic not only could shed light on how algae known as dinoflagellates generate red tides, but could also help speed up efforts to develop cystic fibrosis drugs from a compound closely related to the toxin. Red tides, also known as algal blooms, strike unpredictably and poison shellfish, making them dangerous for humans to eat. It is unknown what causes dinoflagellates to produce the red tide toxins, but it may be a defense mechanism, possibly provoked by changes in the tides, temperature shifts or other environmental stresses.
One of the primary toxic components of red tide is brevetoxin, a large and complex molecule that is very difficult to synthesize.
Twenty-two years ago, chemist Koji Nakanishi of Columbia University proposed a cascade, or series of chemical steps, that dinoflagellates could use to produce brevetoxin and other red tide toxins. However, chemists have been unable to demonstrate such a cascade in the laboratory, and many came to believe that the "Nakanishi Hypothesis" would never be proven.
"A lot of people thought that this type of cascade may be impossible," said Jamison. "Because Nakanishi's hypothesis accounts for so much of the complexity in these toxins, it makes a lot of sense, but there hasn't really been any evidence for it since it was first proposed."
Jamison and Vilotijevic's work offers the first evidence that Nakanishi's hypothesis is feasible. Their work could also help accelerate drug discovery efforts. Brevenal, another dinoflagellate product related to the red tide toxins, has shown potential as a powerful treatment for cystic fibrosis (CF). It can also protect against the effects of the toxins.
"Now that we can make these complex molecules quickly, we can hopefully facilitate the search for even better protective agents and even more effective CF therapies," said Jamison.
Until now, synthesizing just a few milligrams of red tide toxin or related compounds, using a non-cascade method, required dozens of person-years of effort.
The new synthesis depends on two critical factors-giving the reaction a jump start and conducting the reaction in water.
Many red tide toxins possess a long chain of six-membered rings. However, the starting materials for the cascades, epoxy alcohols, tend to form five-membered rings. To overcome that, the researchers attached a "template" six-membered ring to one end of the epoxy alcohol. That simple step effectively launches the cascade of reactions that leads to the toxin chain, known as a ladder polyether.
"The trick is to give it a little push in the right direction and get it running smoothly," said Jamison.
The researchers speculate that in dinoflagellates, the initial jump start is provided by an enzyme instead of a template.
Conducting the reaction in water is also key to a successful synthesis. Water is normally considered a poor solvent for organic reactions, so most laboratory reactions are performed in organic solvents. However, when Vilotijevic introduced water into the reaction, he noticed that it proceeded much more quickly and selectively.
Although it could be a coincidence that these cascades work best in water and that dinoflagellates are marine organisms, water may nevertheless be directly involved in the biosynthesis of the toxins or emulating an important part of it, said Jamison. Because of this result, the researchers now believe that organic chemists should routinely try certain reactions in water as well as organic solvents.
The research was funded by the National Institute of General Medical Sciences, Merck Research Laboratories, Boehringer Ingelheim, and MIT.
"This is an elegant piece of work with multiple levels of impact," said John Schwab, who manages organic chemistry research for the National Institute of General Medical Sciences. "Not only will it allow chemists to synthesize this important class of complex molecules much more easily, but it also provides key insights into how nature may make these same molecules. This is terrific bang for the taxpayers' buck!"

Earthworms Found To Contain Chemicals From Households And Animal Manure

http://www.sciencedaily.com/images/2008/02/080223112253-large.jpg



ScienceDaily (Feb. 27, 2008) — Earthworms studied in agricultural fields have been found to contain organic chemicals from household products and manure, indicating that such substances are entering the food chain.

Manure and biosolids, the solid byproduct of wastewater treatment, were applied to the fields as fertilizer. Earthworms continuously ingest soils for nourishment and can accumulate the chemicals present in the soil.
The chemicals investigated are considered indicators of human and animal waste sources and include a range of active ingredients in common household products such as detergents, antibacterial soaps, fragrances, and pharmaceuticals. Some of the detected chemicals are naturally occurring such as plant and fecal sterols and fragrances. All of these chemicals tend to be concentrated in the municipal waste distribution and disposal process and are referred to as anthropogenic waste indicators (AWI).
U.S. Geological Survey Scientists and their colleague from Colorado State University at Pueblo published their new findings today in Environmental Science and Technology. The results demonstrate that organic chemicals introduced to the environment via land application of biosolids and manure are transferred to earthworms and enter the food chain.
Scientists found 28 AWIs in biosolids being applied at a soybean field for the first time and 20 AWIs in earthworms from the same field. Similar results were found for the field where swine manure was applied. Several compounds were detected in earthworms collected both from the biosolids- and manure-applied fields, including phenol (disinfectant), tributylphosphate (antifoaming agent and flame retardant), benzophenone (fixative), trimethoprim (antibiotic), and the synthetic fragrances galaxolide, and tonalide. Detergent metabolites and the disinfectant triclosan were found in earthworms from the biosolids-applied field, but not the manure-applied field.
Biosolids are made from the sludge generated by the treatment of sewage at wastewater treatment plants. Biosolids are used as fertilizer by farmers, landscapers, and homeowners when it satisfies U.S. Environmental Protection Agency and local regulations for nutrient, metal, and pathogen content. About half of the 8 million dry tons of biosolids produced in the U. S. each year are applied to the land. Biosolids have been found to be rich in AWIs compared to levels in wastewater treatment plant effluent. In addition, the 1.3 million farms raising livestock in the U. S. generate an estimated 500 million tons of manure annually, much of which is also applied to fields as fertilizer for crops.
This study is part of a long-term effort by the USGS Toxic Substances Hydrology Program to determine the fate and effects of chemicals of emerging environmental concern in aquatic and terrestrial environments, and to provide water-resource managers with objective information that assists in the development of effective water management practices. It was funded in part by a Research Corporation Cottrell College Award and a Faculty Research Grant from Eastern Washington University.

New Discoveries Make It Harder for HIV to Hide from Drugs

ScienceDaily (Dec. 15, 2010) — The virus that causes AIDS is chameleon-like in its replication. As HIV copies itself in humans, it constantly mutates into forms that can evade even the best cocktail of current therapies. Understanding exactly how HIV cells change as they reproduce is key to developing better tests and treatments for patients.

In the Journal of Biological Chemistry and Nature Structural & Molecular Biology, MU microbiologist and biochemist Stefan Sarafianos, PhD, reveals new findings that shed light on how HIV eludes treatment by mutating. His discoveries provide clues into HIV's mechanisms for resisting two main families of drugs.
"These findings are important because identifying a new mutation that affects HIV drug resistance allows physicians to make better decisions and prescribe the proper drugs," Sarafianos said. "Without that knowledge, therapy can be suboptimal and lead to early failure."
Patients with HIV are routinely tested to track the levels of the virus and immune cells in their body. Results of the tests help physicians gauge the health of their patients and prescribe the right mix of antiviral drugs. The drugs help prevent the spread of HIV in patients by inhibiting the virus' ability to replicate.
Sarafianos' lab determined the biochemical properties that allow strains of HIV with a specific mutation -- the N348I mutation -- to escape inhibition despite treatment with Nevirapine. The drug is commonly used in combination with other antiviral medications to decrease the amount of HIV in the blood. As a result of Sarafianos' discovery, at least one major company that manufactures HIV mutation-testing kits has modified its test to detect the N348I mutation.
Sarafianos' recent findings resulted from research supported by five National Institutes of Health grants. He recently received another $417,000 award from the NIH to assist him in developing modified antibodies for HIV therapy.
"Our latest efforts to design broadly neutralizing antibodies against HIV will hopefully expand our toolbox against the virus, which remains a constantly moving target," Sarafianos said.
Disclaimer: This article is not intended to provide medical advice, diagnosis or treatment. Views expressed here do not necessarily reflect those of ScienceDaily or its staff.

Tuesday, September 28, 2010

TLR3 Receptor

TLRs are believed to function as dimers. Though most TLRs appear to function as homodimers, TLR2 forms heterodimers with TLR1 or TLR6, each dimer having a different ligand specificity. TLRs may also depend on other co-receptors for full ligand sensitivity, such as in the case of TLR4's recognition of LPS, which requires MD-2. CD14 and LPS Binding Protein (LBP) are known to facilitate the presentation of LPS to MD-2.


The adapter proteins and kinases that mediate TLR signaling have also been targeted. In addition, random germline mutagenesis with ENU has been used to decipher the TLR signaling pathways. When activated, TLRs recruit adapter molecules within the cytoplasm of cells in order to propagate a signal. Four adapter molecules are known to be involved in signaling. These proteins are known as MyD88, Tirap (also called Mal), Trif, and Tram.[15][16][17] The adapters activate other molecules within the cell, including certain protein kinases (IRAK1, IRAK4, TBK1, and IKKi) that amplify the signal, and ultimately lead to the induction or suppression of genes that orchestrate the inflammatory response. In all, thousands of genes are activated by TLR signaling, and collectively, the TLRs constitute one of the most pleiotropic yet tightly regulated gateways for gene modulation.

Signaling pathway of Toll-like receptors. Dashed grey lines represent unknown associations.

Saturday, September 4, 2010

Biosynthesis of Fatty acid

Fatty acid are monocarboxylic acid (R-COOH) with hydrocarbon side chain of 4 to 36 carbon.

Some important feature of fatty acid biosynthesis

1. Fatty acid are degraded and synthesized by different pathway
2. Synthesis occur in cytoplasm in contrast with degardation, which occur in mitochrondria
3. Intermediates in fatty acid synthesis are attached to an acyl carrier proteins (ACP)
4. The enzyme catalyzes the reaction in fatty acid biosynthesis in higher organisms are joined in a single peptide chain called fatty acid synthase (FAS)
5. Fatty acid is built up by successive addition of 2 carbon units derived from acetyl CoA in each cycle.
6. After addition of 2-C unit, the intermediates are reduced by NADPH.

Citrate Shuttle (Click for large picture)

Citrate Shuttle


• FAs are synthesized in the cytoplasm from acetylCoA

• AcetylCoA generated from pyruvate by the action of PDH

and by β-oxidation of fatty acids is in the mitochondria.

• For fatty acid biosynthesis, acetylCoA has to be transported

from the mitochondria to the cytoplasm. This is done via a

shuttle system called the Citrate Shuttle.

• AcetylCoA reacts with oxaloacetate to give citrate. A

tricarboxylate translocase transports citrate from

mitochondria to cytosol.

• In the cytosol, citrate is cleaved back to oxaloacetate and

acetylCoA. This reaction is catalyzed by ATP-citrate lyase

and requires the hydrolysis of one molecule of ATP.


Citrate shuttle + fatty acid synthesis (Click for large picture)

Monday, August 30, 2010

Cellular Energy Metabolism

1.IntroductiontoMetabolism



2.Thermodynamics and Bioenergitics


3.EnergyMetabolism

-Carbohydrate metabolism

-GlycolyticPathway

-Fermentation

-TCAcycle

-Pentose PhosphatePathway(PPP)
 
-β-oxidation of fatty acids


-electron transport system and oxidative phosphorylation

4. Other Energy Metabolism

-amino acid oxidation
 

What is metabolism?


An organized sequence of metabolic reactions is

termeda metabolic pathway.

Saturday, August 7, 2010

Cellular and Molecular Physiology

Some Characteristics of Living Things
•Growth
•Reproduce
•Process information
•Response to stimuli
•Maintenance of complex structure –resistance to entropy.