Biological chemistry

Will humans swim faster or slower in syrup?

Foreword
The scientific and engineering principles that underlie chemical engineering can also be used to understand a wide variety of other phenomena, including in areas not thought of as being central to our profession. As such applications might be of interest to our readers, we will consider brief submissions for publication in this category as R&D notes. These submissions will undergo review, and novelty will be an important factor in reaching an editorial decision.

Will humans swim faster or slower in syrup?, Gettelfinger, Brian, and Cussler E. L. , AIChE Journal, 11/2004, Volume 50, Issue 11, p.2646 - 2647, (2004)

2007 Ig Nobel Chemistry prize announced

The 2007 Ig Nobel Chemistry prize winner was Mayu Yamamoto (International Medical Centre of Japan) for developing a way to extract vanillin (vanilla fragrance and flavour) from cow dung. The 2007 Ig Nobel Prize winners were announced 5th October 2007 and prizes prizes awarded at Harvard in America. To celebrate, a local ice cream bar put on a tasting session of a new flavour, Yum-A-Moto Vanilla Twist, concocted in honour of the 2007 Ig Nobel Chemistry Prize winner Mayu Yamamoto. The mind boggles.

The 2006 Ig Nobel Chemistry prize winner was Antonio Mulet, José Javier Benedito and José Bon of the University of Valencia, Spain, and Carmen Rosselló of the University of Illes Balears, in Palma de Mallorca, Spain, for their study "Ultrasonic Velocity in Cheddar Cheese as Affected by Temperature".

Gallium Trojan horse strategy defeats drug-resistant bacteria

An article in the Journal of Clinical Investigation outlines how a new antimicrobial approach kills bacteria in laboratory experiments and eliminate life-threatening infections in mice by interfering with a key bacterial nutrient. Iron is critical for the growth of bacteria and for their ability to form biofilms, slime-encased colonies of microbes that cause many chronic infections. "Gallium acts as a Trojan horse to iron-seeking bacteria," said Pradeep Singh (senior author). "Because gallium looks like iron, invading bacteria are tricked, in a way, into taking it up. Unfortunately for the bacteria, gallium can't function like iron once it's inside bacterial cells."

The work is by by workers from the University of Iowa and the University of Cincinnati. Rather than trying to find agents that best killed bacteria in test tubes, the researchers sought to intensify the stress imposed on microbes by one of the body's own defense mechanisms. The study's senior author Singh explained "The competition for iron is critical in the struggle between bacteria and host. The body has potent defense mechanisms to keep iron away from infecting organisms, and invaders must steal some if they are to survive."

"Because iron is so important in infection, we thought infecting bacteria might be vulnerable to interventions that target iron," explained Yukihiro Kaneko, senior fellow in microbiology at the UW and the study's lead author. To accomplish this, the researchers used gallium, a metal related in some ways to iron.

The researchers showed that gallium killed microbes, and prevented the formation of biofilms. Importantly, gallium's action was intensified in low iron condition, like those that exist in the human body. Gallium was even effective against strains of Pseudomonas aeruginosa from cystic fibrosis patients that were resistant to multiple antibiotics. In mice, gallium treatment blocked both chronic and acute infections caused by this bacterium. The idea of using gallium as a substitute for iron was developed by a group led by Bradley Britigan, a researcher at the University of Cincinnati and a co-author on this study.

Nobel Chemistry Prize 2006

The Royal Swedish Academy of Sciences has decided to award the Nobel Prize in Chemistry for 2006 to Prof Roger D. Kornberg of Stanford University (Stanford, CA, USA) "for his studies of the molecular basis of eukaryotic transcription".

In order for our bodies to make use of the information stored in the genes, a copy must first be made and transferred to the outer parts of the cells. There it is used as an instruction for protein production – it is the proteins that in their turn actually construct the organism and its function. The copying process is called transcription. Roger Kornberg was the first to create an actual picture of how transcription works at a molecular level in the important group of organisms called eukaryotes (organisms whose cells have a well-defined nucleus). Mammals like ourselves are included in this group, as is ordinary yeast.

Transcription is necessary for all life. This makes the detailed description of the mechanism that Roger Kornberg provides exactly the kind of "most important chemical discovery" referred to by Alfred Nobel in his will.

If transcription stops, genetic information is no longer trans ferred into the different parts of the body. Since these are then no longer renewed, the organism dies within a few days. This is what happens in cases of poisoning by certain toadstools, like the death cap, since the toxin stops the transcription process. Understanding of how transcription works also has a fundamental medical importance. Disturbances in the transcription process are involved in many human illnesses such as cancer, heart disease and various kinds of inflammation.

The capacity of stem cells to develop into different types of specific cells with well-defined functions in different organs, is also linked to how the transcription is regulated. Understanding more about the transcription process is therefore important for the development of different therapeutic applications of stem cells.

Forty-seven years ago, the then twelve-year-old Roger Kornberg came to Stockholm to see his father, Arthur Kornberg, receive the Nobel Prize in Physiology or Medicine (1959) for his studies of how genetic information is transferred from one DNA-molecule to another. Kornberg senior had described how genetic information is transferred from a mother cell to its daughters. What Roger Kornberg himself has now done is to describe how the genetic information is copied from DNA into what is called messenger-RNA. The messenger-RNA carries the information out of the cell nucleus so that it can be used to construct the proteins.

Kornberg's contribution has culminated in his creation of detailed crystallographic pictures describing the transcription apparatus in full action in a eukaryotic cell. In his pictures (all of them created since 2000) we can see the new RNA-strand gradually developing, as well as the role of several other molecules necessary for the transcription process. The pictures are so detailed that separate atoms can be distinguished and this makes it possible to understand the mechanisms of transcription and how it is regulated.

Manganese blocks hydrogen sulphide in water systems

Trace amounts of manganese is essential to human health. Now, a team of scientists from the University of Delaware, Scripps Institution of Oceanography, the University of Hawaii, and Oregon Health and Science University has found that a dissolved form of manganese, Mn(III), is important in waterways such as the Black Sea and Chesapeake Bay. It can keep toxic hydrogen sulfide (sulphide) zones in check.1

The research is based on research conducted in 2003 that explored the chemistry of the Black Sea. Nearly 90% of the mile-deep system is a no-oxygen "dead zone," containing large amounts of naturally produced hydrogen sulfide (sulphide), which is lethal to most marine life. Only specialized microbes can survive in this underwater region.

Above this "dead zone" in the Black Sea lies another aquatic layer, the "suboxic zone,". This has both minimal amounts of oxygen and minimal amounts of hydrogen sulfide. This layer may be up to 40 metres (130 feet) deep in the Black Sea, but only 4 metres (13 feet) deep in the Chesapeake Bay.

The research team found that a chemical form of dissolved manganese, Mn(III), can maintain the existence of the suboxic zone by reacting as a reductant with oxygen and as an oxidant with hydrogen sulfide, preventing deadly hydrogen sulfide from reaching the surface layer of water, which is where most fish, algae and microscopic plants live. The scientists used an electrochemical analyzer to locate and map the chemistry of the suboxic zone in real time under changing salinity, temperature and depth.

The finding is surprising, George Luther (Delaware) said, because dissolved manganese as Mn(III) was assumed not to form in the environment and thus was largely ignored by scientists. The research team conclude that "Manganese in natural oxygen-poor waters can persist in a +3 oxidation state, a state previously seen only in the lab, necessitating a major revision of the current understanding of manganese aqueous geochemistry".

"Now we've learned that this form of dissolved manganese [Mn(III)] can constitute almost all the dissolved manganese in suboxic water columns and can react with hydrogen sulfide and other compounds that only solid manganese(IV) phases were thought to be doing," Luther noted. "It is also more reactive than the solid phases."

"Our research shows that the impact of dissolved manganese(III) is significant in any aquatic environment, including lakes, plus sediments on the seafloor and soils on land," Luther said. "And for the public who live near the water, dissolved manganese(III) actually helps prevent naturally occurring hydrogen sulfide from getting to the surface, so it prevents both fish kills and the foul odours from this compound's telltale 'rotten egg' smell."

Athlete's foot drug: treatment for Alzheimer's

The Daily Telegraph web site is carrying a story indicating a possible treatment for Alzheimer's.

Quote:"A drug that is used in the treatment of athlete's foot could be used to treat Alzheimer's disease, according to a new study by British doctors.

The study, by a team from University College, London, found that clioquinol, a drug that is also used to treat ear infections and indigestion, can almost halt the progression of Alzheimer's.

It discovered that clioquinol, which was developed 100 years ago, is able to absorb the zinc and copper atoms that concentrate in the brains of Alzheimer's sufferers before dementia sets in.
....
Prana Technology, an Australian drug firm, provided clioquinol for the first small trial. "

Buildings Blocks of life found in deep space

An amino acid, one of the building blocks of life, has been spotted in deep space, signalling that alien life forms could indeed exist on other planets. If the find stands up to scutiny, it means that the sorts of chemistry needed to create life are not unique to Earth, verifying one of astrobiology's cherished theories. This would add weight to the idea that life exists on other planets, or that molecules from outer space kick-started life on Earth.

According to the New Scientist, more than 130 molecules have been identified in interstellar space so far, including sugars and ethanol. But amino acids are a particular important find because they link up to form proteins, the molecule that run, and to large extend make up, human cells.1

quoted from The Straits Times: Monday, July 29, 2002

Screensaver lifesaver

Anyone, anywhere with access to a personal computer, could help find a cure for cancer by giving 'screensaver time' from their computers to the world's largest ever computational project, which will screen 250 million molecules for cancer-fighting potential.

The project is being carried out by Oxford University's Centre for Computational Drug Discovery - a unique 'virtual centre' funded by the National Foundation for Cancer Research (NFCR), which is based in the Department of Chemistry and linked with international research groups via the world-wide web - in collaboration with United Devices, a US-based distributed computing technology company, and Intel, who are sponsoring the project.

Update: On Friday 27 April the Screensaver Project finally came to a close. The project, developed with the National Foundation for Cancer Research has run for six years and has at various times been funded by Intel, Microsoft and by IBM, but was chiefly a collaboration with United Devices Inc of Austin Texas.

It has been an enormous success, involving over 3.5 million personal computers in more than 200 countries. Only the SETI [Search for Extraterrestrial Intelligence] project has had more participants, but none has involved as much data transmission as this research.

The project built a database of billions of small drug-like molecules with known routes to synthesis. These compounds have been screened virtually to see if they might make potent inhibitors of proteins of known crystal structure and biological significance.

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Copyright 1993-2011 Mark Winter [The University of Sheffield and WebElements Ltd, UK]. All rights reserved.