Thousands dead in Chinese quake, todays news..


A powerful earthquake has killed at least 10,000 people in China's south-western Sichuan province, up to 5,000 of them in just one county. Many more have been killed and injured in other parts of the country after the 7.8-magnitude quake struck at 1428 local time (0628 GMT). At least 50 bodies have been recovered from the rubble of a school where an estimated 900 students were buried.

President Hu Jintao has urged "all-out" efforts to rescue victims. Search teams were sent to the area but struggled to get through because routes were blocked. The BBC's Michael Bristow, in nearby Chongqing, said torrential rains had also prevented helicopters gaining access. With communication links down, he says there is still no real indication of the death toll at the epicentre, in Wenchuan county, about 92km (57 miles) from Chengdu, Sichuan's provincial capital. Read full story on this site..




source: BBC News UK

Todays News..


Miss Earth 2008 candidates pose for photographers on the poolside of a hotel in Makati during a media presentation Tuesday.


Biotechnology and Bioinformatics

The 15 members of each Theme Panel will meet, at least twice a year, to;

  • put forward ideas for Focused Meetings
  • consider proposals from other scientists within their field of expertise (referee the proposal)
  • highlight to the Meetings Board areas of hot science that should be in the programme
  • form part of the Science Advisory Committee for each Annual Meeting (BioScience)
  • report to the Meetings Board
  • develop interdisciplinary activities and collaborate with appropriate sister societies.

The Biotechnology and Bioinformatics Theme Panel is Theme Panel VI within the Biochemical Society. The group continues to represent broad interest in the general area of biotechnology and bioinformatics and plays a major role in organizing Society Meetings across diverse areas of biotechnology and bioinformatics research and education.


The Biotechnology and Bioinformatics Theme Panel welcomes suggestions for Biochemical Society meetings from all members of the scientific community. If you have an idea for a meeting, and wish to have an informal discussion with a member of a Theme Panel, you are welcome to contact that member. If you wish to submit a formal proposal for a meeting, complete the relevant form and forward it to meetings@biochemistry.org.

Careers in bioinformatics: life after graduate qualification?

by: Andy Brass

The pharmaceutical industry and the research councils have provided very clear signals that there is a significant skills shortage in bioinformatics and that this shortage should be addressed as a matter of high priority. As a response to this the UK academic community has worked hard to provide a wide variety of bioinformatics training in a range of institutes and at a range of levels. Specific details of all the Master's courses on offer within the UK are available at the CCP11 website. Details on the various research council schemes are available from the website of the respective council (BBSRC; MRC; EPSRC; Wellcome Trust). The number of postgraduate-trained bioinformatics students is therefore beginning to rise steeply.
This raises a number of issues:

  • is there really a demand for postgraduate bionformaticians?
  • if there is a shortage is this reflected by employers paying a premium for the skills?
  • is the position likely to stay the same, at least for anyone currently contemplating entering training?

The experience we have had at the University of Manchester is that the situation for good postgraduate-trained bioinformatics students is very healthy. Companies are keen to take students for placements as part of their training. This is to the point at which we have more offers for placements than we have students to take them. As well as those in the UK and Europe, a number of companies in the USA are now offering placements. The job market is also strong. The majority of our students go directly into bioinformatics posts in industry, the rest going predominantly to PhD positions. Those who have tried to find work in the USA have found that the situation there is, if anything, better than in the UK, including one student who applied for eight jobs in the San Francisco area and was embarrassed to be offered all of them!

Protein Modification part 3 of 3

Ubiquitin in pro‑inflammatory signalling - chains of command
by:Karine Enesa and Paul C. Evans

The 2004 Nobel Prize in Chemistry was awarded to Aaron Chiechanover, Avram Hershko and Irwin Rose for their pioneering studies of ubiquitination and its role in regulating protein stability. Now, 30 years after their discovery, we are beginning to understand the pleiotropic nature of ubiquitin and its roles in diverse physiological processes. Here we review an emerging concept that the signalling pathways that control inflammation are tightly regulated by a multitude of ubiquitination and deubiquitination reactions.


Palmitoylation - putting on fat Marie-
by:José Bijlmakers

The modification of proteins by the attachment of palmitate is a reversible process that has profound effects on protein function. Although palmitoylation was first documented almost 30 years ago, it is still poorly understood. Progress in this field has been hampered by the elusive nature of the enzymes involved and the absence of an obvious consensus palmitoylation motif. However, major steps forward have recently been made. The cloning of two yeast enzymes revealed the existence of a family of palmitoyltransferases, and new techniques have been developed for the large-scale detection and identification of the palmitoyl-proteome.


Macromolecular crystallography - new light on protein structure
by: Armin Wagner

X‑ray diffraction is the method of choice to determine structural information from biological macromolecules to atomic resolution. This technique depends on the availability of single crystals of protein, which are notoriously difficult to produce. It can take months or even years to find crystallization conditions capable of producing crystals with sufficient diffraction quality. During the last few years the field of MX (macromolecular crystallography) has undergone considerable change and most of the steps from protein expression to structure solution have been automated, speeding up the process significantly. Facilities such as Diamond Light Source, the new UK synchrotron radiation source in Oxfordshire, have been developed to incorporate new automation technologies and Diamond will provide an important user resource for XRD (X‑ray diffraction) experiments on crystals of biological macromolecules. Furthermore, in collaboration with Professor So Iwata (Imperial College and Diamond Light Source) and funded by the Wellcome Trust, Diamond Light Source is developing a laboratory dedicated specifically to solving the structure of membrane proteins, the crystallization of which poses a particular problem to the crystallographer.

Protein Modification part 2 of 3

Histone methylation -making binding relationships
by: Andrew J Bannister

The nucleosome is the fundamental unit of chromatin and its high‑resolution X‑ray crystal structure was solved in 19971. This remarkable achievement showed the elegant and highly ordered packing of histones within 1.75 turns of DNA and it hinted at ways in which histones may be involved in regulating higher‑order chromatin structure. Perhaps most striking is the way in which histone N‑terminal tails protrude from their own nucleosome and, in some cases, make contact with adjacent nucleosomes. Simple extrapolation from this observation has implicated these interactions in higher‑order chromatin regulation and many considered it likely that PTM (post‑translational modification) of the tails would affect inter‑nucleosomal stability and hence DNA processes such as transcription. Histone tails actually support multiple PTMs, including acetylation, phosphorylation and methylation. This brief overview considers histone methylation and discusses what we understand concerning its role.

Protein phosphorylation -
by: Dario R. Alessi and Elton Zeqiraj

At first glance, the odds that the introduction of a diminutive and unsuspicious phosphoryl group on to a hydroxy‑containing side chain of a much larger protein molecule would be selected by Nature as the most widely deployed mechanism to control biological processes, and be responsible for many major diseases, seems unlikely. However, this process termed protein phosphorylation is a vital regulator of almost all events that take place in eukaryotic organisms. This review outlines what phosphorylation is, how it is regulated and why disruptions of the network of enzymes and proteins that regulate the phosphorylation are a principal cause of many maladies. It also discusses how advances are leading to exciting strategies to develop drugs to treat diseases caused by disruptions of protein phosphorylation.

Protein modification part1 of 3

Introduction - protein post-translational modifications

by:Andrew J. Bannister and Colyn Crane-Robinso

Organisms exist in a continually changing environment: they are constantly bombarded and challenged with stimuli to which they must respond in order to survive. Such responses require three essential steps: detection/initiation, transmission and read-out. In practice, a cell detects a particular signal, such as the presence of a hormone or the appearance of a potentially damaging free radical, and activates a series of enzymes in a signalling cascade that ultimately determines the appropriate biological outcome. These responses are largely achieved via PTMs (post-translational modifications) of pre-existing proteins by specific enzymes. In this series of articles, experts in the relevant subject areas review our current understanding of the major PTMs and how they affect their target proteins.

Histone acetylation -
by: playing tag Colyn Crane-Robinson
Acetylation of the e-amino group of specific lysine residues of core histones – principally but not exclusively in their unstructured N-terminal tails – is a key biochemical modification for establishing the transcriptional competence of genes bound by such histones. High resolution mapping of acetylated core histones by chromatin IPs (ChIPs) has shown them to be preferentially located at the promoters and enhancers of active genes rather than throughout the transcribed regions. Particular distributions of acetylated lysines are part of the nucleosomal ‘histone code’ that defines and to a considerable extent determines the functional status of the local chromatin. HHe istone acetylation is deposited and removed by numerous histone acetyltransferases (HATs) and deacetylases (HDACs) and acetyl-lysines are recognized (i.e. the histone code is ‘read’) by bromodomain-containing proteins.

The cloning revolution - DNA cloning and biochemistry

According to the online reference source Wikipedia (www.wikipedia.org), biochemistry is “the study of the chemical processes and transformations in living organisms. It deals with the structure and function of cellular components, such as proteins, carbohydrates, lipids, nucleic acids and other biomolecules.” It seems appropriate to start with a definition from the World Wide Web, which has changed information retrieval as much as DNA cloning has changed biochemistry.

by: James L. Hartley (Protein Expression Laboratory, USA)

The protein world - evolution of protein architecture

Contemporary protein architectures can be regarded as molecular fossils, historical imprints that mark important milestones in the history of life. A census of protein structure in proteomes and novel bioinformatics methods uncovered patterns and processes linked to the evolution of both proteins and proteomes that are described here. Timelines of discovery of protein architectures revealed episodes of specialization, reductive evolutionary tendencies of architectural repertoires in proteomes and the rise of modularity in the protein world. Some of these tendencies were driven by recruitment of structures and functions. Our observations have important implications for origins of modern biochemistry, modules in the protein world, and diversification of life.


by: Gustavo Caetano-Anollés and Minglei Wang (University of Illinois, USA)

How DDT metabolite disrupts breast cancer cells

Research has shown that the main metabolite of the insecticide DDT could be associated with aggressive breast cancer tumours, but there has been no explanation for this observation to date.
Now a report published in the open access journal Breast Cancer Research shows how DDT could act to disrupt hormone-sensitive breast cancer cells.Michel Aubé and colleagues from Université Laval and Institut national de santé publique in Québec, Canada have published findings suggesting that DDT’s main metabolite, 1,1-dichloro-2,2-bis(p-chlorophenyl)ethylene (p,p’-DDE), could increase breast cancer progression. They suggest a mechanism whereby p,p’-DDE opposes the androgen signalling pathway that inhibits growth in hormone-responsive breast cancer cells. The team tested the effect of p,p’-DDE on the proliferation of CAMA-1 cells, a human breast cancer cell line that expresses the estrogen receptor alpha (ERa) and the androgen receptor (AR), either with or without physiological concentrations of estrogens and androgens.
They also assessed p,p’-DDE-induced modifications in cell cycle entry and the expression of sex-steroid dependent genes including ESR1 and CCND1, the latter coding for a key protein involved in cell proliferation.When estrogens and androgens were present in the cell culture medium, increasing concentrations of p,p’-DDE accelerated the growth of CAMA-1 breast cancer cells. p,p’-DDE had a similar effect on the proliferation of MCF7-AR1 cells, an estrogen responsive cell line genetically engineered to over express the AR. Adding the potent androgen dihydrotestosterone together with estradiol to the cell culture medium decreased the recruitment of CAMA-1 cells in the S phase and the expression of ESR1 and CCND1, by comparison with cells treated with estradiol alone.
These androgen-mediated effects were blocked with similar efficacy by p,p’-DDE and the potent antiandrogen hydroxyflutamide.“Our results suggest that in addition to estrogenic compounds, which have been the main focus of researchers over the past decades, chemicals that block the AR could favour breast cancer progression” says Pierre Ayotte, who is leading the research team.Ayotte’s team had previously linked concentrations of p,p’-DDE with tumour aggressiveness in women with breast cancer.
They are now investigating the effect on breast cancer cell proliferation of a complex mixture of environmental chemicals, similar to that found in the blood of women, which comprises compounds with estrogenic and antiandrogenic activities

BI-D1870 is a specific inhibitor of the p90 RSK (ribosomal S6 kinase) isoforms in vitro and in vivo

Hormones and growth factors induce the activation of a number of protein kinases that belong to the AGC subfamily, including isoforms of PKA, protein kinase B (also known as Akt), PKC, S6K p70 (ribosomal S6 kinase), RSK (p90 ribosomal S6 kinase) and MSK (mitogen- and stress-activated protein kinase), which then mediate many of the physiological processes that are regulated by these extracellular agonists. It can be difficult to assess the individual functions of each AGC kinase because their substrate specificities are similar. Here we describe the small molecule BI-D1870, which inhibits RSK1, RSK2, RSK3 and RSK4 in vitro with an IC50 of 10–30 nM, but does not signi-ficantly inhibit ten other AGC kinase members and over 40 other protein kinases tested at 100-fold higher concentrations. BI-D1870 is cell permeant and prevents the RSK-mediated phorbol ester- and EGF (epidermal growth factor)-induced phosphoryl-ation of glycogen synthase kinase-3β and LKB1 in human embry-onic kidney 293 cells and Rat-2 cells. In contrast, BI-D1870 does not affect the agonist-triggered phosphorylation of substrates for six other AGC kinases. Moreover, BI-D1870 does not suppress the phorbol ester- or EGF-induced phosphorylation of CREB (cAMP-response-element-binding protein), consistent with the genetic evidence indicating that MSK, and not RSK, isoforms mediate the mitogen-induced phosphorylation of this transcription factor.

Bio-Chemical Tests in Alaska Whitewashed By Government, todays featrured articles

President Bush extended holiday greetings to military troops this Christmas, but one gift he’ll never open is the executive order he signed, which keeps sensitive documents secret about biological and chemical testing at Fort Greely near Fairbanks, Alaska.
The president, by sealing important documents, obviously feels military health concerns were of secondary importance to protecting the Department of Defense (DOD) against potential exposure for injuries resulting from chemical testing and dumping.
What little is known about chemical and biological testing at Fort Greely has surfaced from leaked documents, eyewitness accounts and other general information provided reluctantly by the DOD after health problems began to surface by those living near the base.
Other information, scratching the surface of what really happened, has also appeared in Seymour Hersh’s book Chemical and Biological Testing: America’s Hidden Arsenal, a historical account of the base by Norman Chase and a March 2003 article entitled “Northern Exposure” in The Nation magazine by Korey Capozza.
“The real story of what went on is in the classified documents kept secret by the DOD and President Bush,” said Capozza, a critic of the recent executive order signed by Bush. “They have yet to give veterans a clear definition of possible causes of their health problems. The DOD also refuses to grant any of the veterans health care based on exposure to agents used in the secret site’s experiments.”
Records show that Fort Greely, as far back as 1952 and continuing to at least 1970, was used for the explicit purpose of testing chemical and biological weapons. The base, located 100 miles southwest of Fairbanks on 640,000 acres, originally began operating in 1942 as a staging area for planes ferried to the Soviet Union during World War II.
However, seven years later a nuclear reactor was built to serve as the military’s power plant. Then in 1966, the Army began testing biological, chemical and various other weapons. The reactor was dismantled in 1973, and in 1995 the base was scheduled for closure.
But recently, under the Bush administration, the DOD proposed Fort Greely be used as a storage site for interceptor missiles in support of the space-based missile defense program.
However, what transpired on the base during the 1960s and 1970s is still heavily debated as veterans are now surfacing with what amounts to “chemical horror” stories.
According to several veterans who spoke to VA officials, between 1962 and 1967, the Army blasted hundreds of rockets and bombs containing sarin and VX nerve gas into the region which is densely populated by forests and wildlife.
Veterans recall canisters of VX nerve agents being indiscriminately buried approximately a mile from the Alaskan highway or tossed in a nearby frozen lake in the winter of 1966, where the canisters later sank to the bottom when the ice melted in the spring. Regular dumping expeditions were reportedly carried out until 1970, when the testing discontinued.
Now, 30 years later, veterans and civilians are coming forward with serious health concerns, but since no records are available due to Fort Greely’s top-secret status, VA officials at first had a hard time believing the veterans’ credibility.
After heavy pressure was applied by watchdog groups, the DOD has released some documents revealing the test site may have been operated with blatant disregard for human and environmental safety.
The documents also suggest that some of the deadly materials used may still be unaccounted for and buried somewhere beneath the pristine Alaskan wilderness.
Critics suggest the executive order signed by Bush was designed to protect the DOD against conclusive evidence, hiding a massive cover-up of illegal chemical and biological testing.

By Greg Szymanski

Not Copyrighted. Readers can reprint and are free to redistribute - as long as full credit is given to American Free Press - 645 Pennsylvania Avenue SE, Suite 100 Washington, D.C. 20003

Biochemical Simulation

What is Gepasi?
Gepasi is a software package for modeling biochemical systems. It simulates the kinetics of systems of biochemical reactions and provides a number of tools to fit models to data, optimize any function of the model, perform metabolic control analysis and linear stability analysis.
Gepasi simplifies the task of model building by assisting the user in translating the language of chemistry (reactions) to mathematics (matrices and differential equations) in a transparent way. This is combined with a set of sophisticated numerical algorithms that assure the results are obtained fast and accurate.

Bioreactor design

Bioreactor design is a complex engineering task. Under optimum conditions, the microorganisms or cells are able to perform their desired function with 100 percent rate of success. The bioreactor's environmental conditions like gas (i.e., air, oxygen, nitrogen, carbon dioxide) flow rates, temperature, pH and dissolved oxygen levels, and agitation speed/circulation rate need to be closely monitored and controlled.
Most industrial bioreactor manufacturers use vessels, sensors and a control system networked together.
Fouling can harm the overall sterility and efficiency of the bioreactor, especially the heat exchangers. To avoid it, the bioreactor must be easily cleaned and as smooth as possible (therefore the round shape).
A heat exchanger is needed to maintain the bioprocess at a constant temperature. Biological fermentation is a major source of heat, therefore in most cases bioreactors need refrigeration. They can be refrigerated with an external jacket or, for very large vessels, with internal coils.
In an aerobic process, optimal oxygen transfer is perhaps the most difficult task to accomplish. Oxygen is poorly soluble in water--even less in fermentation broths--and is relatively scarce in air (20.8%). Oxygen transfer is usually helped by agitation, which is also needed to mix nutrients and to keep the fermentation homogeneous. There are, however, limits to the speed of agitation, due both to high power consumption (which is proportional to the cube of the speed of the electric motor) and to the damage to organisms caused by excessive tip speed causing shear stress.
Industrial bioreactors usually employ bacteria or other simple organisms that can withstand the forces of agitation. They are also simple to sustain, requiring only simple nutrient solutions, and can grow at astounding rates.
Sewage Treatment: Bioreactors are also designed to treat sewage and wastewater. In the most efficent of these systems there is a supply of free-flowing, chemically inert media that acts as a receptacle for the bacteria that breaks down the raw sewage. Examples of these bioreactors often have separate, sequential tanks and a mechanical separator or cyclone to speed the division of water and biosolids. In the process, the liquids Biochemical Oxygen Demand BOD is reduced sufficiently to render the contaminated water fit for reuse. The biosolids can be collected for further processing or dried and used as fertilizer.
In bioreactors where the goal is grow cells or tissues for experimental or therapeutic purposes, the design is significantly different from industrial bioreactors. Many cells and tissues, especially mammalian ones, must have a surface or other structural support in order to grow, and agitated environments are often destructive to these cell types and tissues. Higher organisms also need more complex growth medium.

Bioreactor

A bioreactor may refer to any device or system that supports a biologically active environment. In one case, a bioreactor is a vessel in which is carried out a chemical process which involves organisms or biochemically active substances derived from such organisms. This process can either be aerobic or anaerobic. These bioreactors are commonly cylindrical, ranging in size from liters to cube meters, and are often made of stainless steel.
A bioreactor may also refer to a device or system meant to grow cells or tissues in the context of cell culture. These devices are being developed for use in tissue engineering.
On the basis of mode of operation, a bioreactor may be classified as batch, fed batch or continuous (e.g. Continuous stirred-tank reactor model). An example of a bioreactor is the chemostat.
Organisms growing in bioreactors may be suspended or immobilized . The simplest, where cells are immobilized, is a Petri dish with agar gel.
Large scale immobilized cell bioreactors are:

  • moving media
  • packed bed
  • fibrous bed
  • membrane

What is biochemical engineering?

Biochemical engineering is a branch of chemical engineering or biological engineering that mainly deals with the design and construction of unit processes that involve biological organisms or molecules. Biochemical engineering is often taught as a supplementary option to chemical engineering or biological engineering due to the similarities in both the background subject curriculum and problem-solving techniques used by both professions. Its applications are used in the food, feed, pharmaceutical, biotechnology, and water treatment industries.


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