cool stills of a hummingbird
| DNA Sequence Databases & Search Engines |
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- BR3.5 - Human Repeated DNA Database - VGC (US)
- CpG Islands Database - Human Genes and Their Associated CpG Islands - BEN (Belgium)
- dbEST - Database of Expressed Sequence Tags
- dbSTS - Database of Sequence Tagged Sites
- DDBJ - DNA Database of Japan - NIG (Japan)
- DNA Cloning Vectors Sequence Databases
- EMBL - Nuleotide Sequence Database - EMBnet-Basel (Switzerland)
- ATLAS - Keyword Search of Nucleotide Databases - MIPS (Germany)
- DBGET - Integrated Databases Sequence/Information Retreival Service - GenomeNet (Japan)
- WAIS - DNA Database (EMBL) Keyword Searching - DISC (Japan)
- EMBL-New Entries - EMBnet-Basel (Switzerland)
- EMBL Search - Search of EMBL Database - EBI (UK)
- Search by Accession No. - EBI (UK)
- ENTREZ - Nucleotide Database Search Server - NCBI (US)
- SRSWWW - Web-Based Browser of Molecular Biology Resources. (US)
- EPO - European Patent Office Nucleotide Database - CSC (Finland)
- GenBank - DNA/Protein Sequence Database - NCBI (US)
- ATLAS - Keyword Search of Nucleotide Databases - MIPS (Germany)
- DBGET - Integrated Databases Sequence/Information Retreival Service - GenomeNet (Japan)
- WAIS - DISC (Japan)
- Access GenBank - Gene Locus/Accession No. Search & Retrieval of GenBank Entry - VGC (US)
- ENTREZ - Nucleotide Database Search Server - NCBI (US)
- Network Clever - Retreive GenBank Sequence Files - IBC-WUSTL (US)
- Search GenBank Updates Database - NCBI (US)
- SRSWWW - Web-Based Browser of Molecular Biology Resources (US)
- GSDB - Genome Sequence DataBase maintained - NCGR (US)
- HOVERGEN - Vertebrate Genes Database - U Claude Bernard Lyon 1 (France)
- KEGG - Search Gene Names in KEGG Pathway Database (France)
- MPDB - Molecular Probe Database of synthetic nucleotides
- MPDB - EMBL-Heidelberg (Germany)
- MPDB - InterLab Project (Italy)
- OPD - Oligonucleotide Probe Database - MSU (US)
- PCR Primers Database - EBI (UK)
- Sequence Annotation - NCBI Sequence Annotations - BCM (US)
- TBASE - Transgenic/Targeted Mutation Database - JHU (US)
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Get one cat for you right now, isn't he so cute ?
Function
Calculates DNA RNA/DNA melting temperatureRate this post
Cat bath
Background
Staphylococcus aureus (S. aureus) is the cause of the most hospital-acquired infections worldwide. Thereby infections are particularly susceptible to being caused by Methicillin-resistant S. aureus (MRSA), for which there are only few, if any, possibilities of antibiotic therapy. It has been clearly demonstrated by various authors that Methicillin resistance is directly associated with increased mortality and morbidity with S. aureus infections. In the last 10 years an increase in the MRSA rate from 2% to approx. 25% was observed in Germany. In the Netherlands and Scandinavia a stable rate under 3% has been recorded for years. Particularly, for the Netherlands, adhering to a consequent "search and destroy" policy, MRSA felt off to very low rates and is now under control. In the Netherlands the main focus will be on isolating and controlling CA-MRSA, that are a possible danger for the open population outside hospitals.
The basis of all efforts for the fight against MRSA comprises
- Rational antibiotic therapy in order to reduce the selective pressure
- Prevention
- Real implementation of the hygiene measures according to guidelines
- Isolation of potential MRSA carriers
- Surveillance
- Early laboratory-diagnostic identification of carriers, in order to avoid nosocomial transmission as soon as possible
- Molecular classification of the MRSA isolates in order to recognize transmission chains and to gain an overview of the dynamics of the spread and persistence in the patient
- Therapy and decontamination of the infected and/or colonized persons during and after hospitalization
- Education of the population as well as further training of personnel in the health care service
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My kitten likes to, umm, air himself out when he sleeps. Looks hilarious.
RIDOM - Ribosomal Differentiation of Medical Microorganisms
Introduction
The Ribosomal Differentiation of Medical Microorganisms (RIDOM) web-server is an evolving electronic resource designed to provide microorganism (bacteria, fungi, mycobacteria) differentiation services for medical identification needs. The diagnostic procedure begins with a specimen partial small subunit (16S or SSU) ribosomal DNA sequence. Resulting from a similarity search, a species or genus name for the specimen in question will be returned. Where the first results are ambiguous or do not define to species level, hints for further molecular (internal transcribed spacer [ITS] database) and conventional differentiation will be offered
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My cat becomes spastic for no apparent reason...Then my kitten picks a fight with her.
Try our intuitive DNA sequence assembling software for automated analysis of small and medium sized (re)sequencing projects!
DNA (re)sequencing is getting more and more popular in such varied application areas like microbiology (pathogen identification [e.g., 16S rDNA], pathogen typing [e.g., MLST or SLST], resistance testing), forensics, or human genetics. Therefore, the Ridom TraceEditPro 1.0 software was designed for automated and simple analysis of such (re)sequencing data in mind (
Ridom TraceEditPro Features).
Define once for each project an assembly parameter template and analyze then automatically your ABI- or SCF-chromatogram and FASTA files. For similarity searching link seamless from within the software to Internet databases (e.g. NCBI) or create and search your own local reference sequence libraries.
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Get sh**t out of every one in office, home, any where... very nice tricks to scare them out - must watch - It's not originally developed / compiled by me
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DNA sequence analysis
<molecular biology> Determination of the nucleotide sequence of a length of DNA. Typically, this is performed by cloning the DNA of interest, so that enough can be prepared to allow the sequence to be determined, usually by the Sanger dideoxy chain temination or Maxam Gilbert chain degradation techniques. The resulting reactions are then run on a large sequencing gel, capable of resolving single nucleotide differences in chain length. Recently, PCR based methods have obviated the need to clone the DNA under some conditions and automated DNA sequencing has become widely available.
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What Does A Match Mean?
DNA identification is based on probabilities. Consider the case of just three CODIS sites. The probability that someone would match a random DNA sample at any one site is roughly one in ten (1/10). So the probability that someone would match at three sites would be about one in a thousand:
1/10 x 1/10 x 1/10 = 1/1000
Applying this probability equation to all 13 CODIS sites would mean that the chances of matching a random DNA sample are about one in ten trillion:
1/10 x 1/10 x 1/10 x 1/10 x 1/10 x 1/10 x 1/10 x 1/10 x 1/10 x 1/10 x 1/10 x 1/10 x 1/10 x = 1/10,000,000,000,000
Actual probabilities vary, depending on several factors. But the probability of two different people matching at all 13 CODIS sites is virtually zero.
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Visit the Marian Koshland Science Museum to learn more. See how DNA fingerprints are made and hear how the use of DNA evidence has affected the criminal justice system. |
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The science of identifying individuals using DNA sequences is very clear, and the probability of scientific error is extremely small. As a result, DNA evidence has been used to help identify perpetrators of crimes and to exonerate innocent people before they become suspects.
The following sections explain the science behind DNA fingerprinting in more detail.
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Reading the Sequences
The sequence of nucleotides in a gene gives it meaning by storing the instructions for building the other molecules necessary for life. These instructions are read as a string of A’s, T’s, G’s, and C’s, such as ACGGTAACT. In the sense that there are 26 letters in the English alphabet, there are four letters in the alphabet of DNA.
The four letters in the DNA alphabet are actually abbreviations for the chemicals that make up the library of instructions.
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Ever wonder what a short trip around the pattern is like in an
Quicksilver ultralight? This short film is as close as it gets
without being there. Please remember to rate this film if you more...
The Sequence On One Strand
The DNA molecule is composed of two very long strands of A’s, T’s, G’s and C’s, which are tightly paired with each other. An A on one strand is always paired with a T on the other strand, and a G is always paired with a C. This means that if the sequence of nucleotides on one strand is known, the sequence of the other strand will be automatically known as well.
One strand of DNA is like a photographic negative of the other strand. A negative can be used to make many copies of a photograph because it contains all of the information that is part of that photograph. Similarly, to read the sequence of A’s, T’s, G’s, and C’s in a genome, it is only necessary to read one strand of DNA to be able to deduce the sequence of the other strand.
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One Strand of DNA Is Like a Photographic Negative to the Other An adenine (A) on one strand is always paired with a thymine (T) on the other strand, and a guanine (G) is always paired with a cytosine (C). If the sequence of nucleotides on one strand is known, the sequence of the other strand will be automatically known as well. |
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Nice routine muscle development could usework
The DNA Sequence
The extremely long DNA molecule is actually made of a long string of chemical building blocks called “nucleotides.” There are four different nucleotides, which are labeled adenine (A), thymine (T), guanine (G), and cytosine (C). The human genome is made of a sequence of roughly three billion of these nucleotides, and it is about the same size as the genome of a chimpanzee or a mouse. In contrast, a fruit fly has 180 million, a yeast has 12 million, and the flowering weed “thale cress” has 100 million nucleotides of DNA in its genome.
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see now
DNA Sequencing
The sequence of letters within a gene is like the letters in a book of instructions. Deciphering the enormously long sequence of A’s, T’s, G’s, and C’s in an organism’s genome reveals useful information. For example, finding a difference in a gene sequence that governs muscle structure raises questions. Could the difference affect health? Just as changing one letter in a word can change its meaning – for example, mice to rice to nice – so changing one DNA letter can sometimes cause illness.
Not all of the sequences in the genes of two humans are identical. For example, because your face is unique, the precise set of sequences in the large group of genes that control the shape of your face are presumably unique too. Some special parts of the DNA sequence vary from person to person with unusually high frequency. As you will see, finding sequences in DNA samples can be used to identify individuals and help solve crimes, even when there are no eyewitnesses.
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hunter subres
The genome is like a library of instructions.
A gene is a sequence of A’s, T’s, G’s, and C’s that usually provides the instructions for a single protein component of an organism.
The letters of the genetic alphabet – A, T, G, and C – are meaningless on their own, but they are combined into useful instructions in genes. Some genes carry enough information for one complete characteristic of an organism, but most characteristics result from combinations of genes. Genes are like chapters in the books that fill the library of the genome.
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My dog has been suffering with a nasty rash on his chest for
months now and the vet can't cure the
problem...!!............................... more...
News From the Field
Dramatic Comeback of Male Butterflies in Population That Was Once Nearly Entirely Male
Researchers have documented a remarkable example of natural selection in a tropical butterfly species that fought back--genetically speaking--against a highly invasive, male-killing bacteria. Within 10 generations that spanned less than a year, the proportion of males of the Hypolimnas bolina butterfly on the South Pacific island of Savaii jumped from a meager 1 percent of the population to about 39 percent. This comeback is credited to the rise of a suppressor gene that hol
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Worlds Largest Giant Octopus WOW......!
Number of Published Science and Engineering Articles Flattens, But U.S. Influence Remains Strong
Number of published U.S. science and technology articles plateaued in the 1990s, despite continued increases in funding and personnel for research and development.
 Published U.S. science and technology articles plateaued in the 1990s. |
A new National Science Foundation (NSF) report finds the number of U.S. science and engineering (S&E) articles in major peer-reviewed journals flattened in the 1990s, after more than two decades of growth, but U.S. influence in world science and technology remains strong.
The report, Changing U.S. Output of Scientific Articles: 1988 - 2003, finds changes occurred despite continued increases in funding and personnel for research and development. Flattening occurred in nearly all U.S. research disciplines and types of institutions.
In contrast, emerging Asian nations had large increases in publication numbers, reflecting their growing expertise in science and technology. European Union totals also went up.
Numbers of articles published and their citation in S&E journals is a widely accepted indicator of research capability. When paired with trends in patenting, licensing, research and development expenditures and advanced training of personnel, publication trends may be viewed as a factor affecting a nation's ability to spur technological innovation.
Despite the leveling of articles published, researchers emphasize other evidence that indicates U.S. science and technology capability remains strong. They say the change in U.S. share of the world's S&E articles is not a surprise in view of growing S&E research capability around the world, nor do they view it as a cause for concern.
"In addition to numbers published, one should look at another very important indicator -- article quality," said Derek Hill, senior analyst and a coauthor of the report. "The more often an article is cited by other publications, the higher quality it's believed to have. While citation is not a perfect indicator, U.S. publications are more highly cited than those from other countries."
In raw numbers, the United States continues to publish far more articles than any other country and remains a major force in world S&E. However its overall share of published articles has declined while other nations produce more.
Four Asian societies--China, Singapore, South Korea, and Taiwan--out-distanced all others in the world between 1992 and 2003 with an average annual growth rate of 15.9 percent in publications.
According to the report, Japan's article output rose at an average annual rate of 3.1 percent, five times faster than the United States.
The European Union, which passed the U.S. several years ago in total numbers of articles published, posted an average annual growth rate of 2.8 percent during the same period, more than four times faster than the United States.
The report is part of a larger study of trends in scientific publication by NSF's Division of Science Resources Statistics (SRS). Along with the report, SRS is releasing a workshop summary and working paper called "The Changing Research and Publication Environment in American Research Universities (SRS 07-204)."
These two reports explore the contexts and causes of the initial publication's findings and report on the perspectives of practitioners and experts regarding how S&E research and publication are changing.
A second working paper, "U.S. Academic Scientific Publishing," reporting statistical analysis of trends in the U.S. academic sector is scheduled to be released later this year
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This Bird Is Trained Enough . Amazing !!
About the Office of Legislative & Public Affairs
MISSION
The Office of Legislative and Public Affairs (OLPA) communicates information about the activities, programs, research results and policies of the National Science Foundation. OLPA employs a wide variety of tools and techniques to engage the general public and selected audiences including Congress, the news media, state and local governments, other Federal agencies, and the research and education communities.
Jeff Nesbit is the director of OLPA.
OLPA has five sections that provide information about the NSF's science and engineering research and education: Congressional Affairs, Media and Public Information, Communications Resources, Issues Development, and Special Projects.
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Celebrity makeup artist shows you how to get that red carpet look in 3 minutes with just 3 products.
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In 4 minutes learn to calculate faster than the calculator. You can power-up your weak Math muscle and turn it into a bulging bicep.
Tri-Pedic Mattress Brings Further Innovation To NASA's Technology
The advancement I am referring to is what many people have come to know as memory foam, a technological advancement that NASA developed in the 1970s that allows foam to mould to your body and then return to its original shape once your body moves to a new position.
I have been coveting one of these mattresses for years, but like many consumers was not ready to shell out the extra dollars for a new mattress, let alone one that I knew was bound to cost much more than a traditional spring mattress.
However, one recent uncomfortable and sleepless night, I found myself spending hours researching all there was to know about memory foam mattresses. While I may be a professional researcher by trade, I have to admit that at first I was a bit confused as to which company produced the best memory foam mattress.
I had already heard about the Tempur-Pedic. They were the first company to use NASA's technology for the purposes of consumer bedding. However, I had read that the use of their five pound density foam was too temperature sensitive, and the overall feeling of the mattress was too hot.
From what I could gather, due to the high viscosity of the memory foam that Tempur-Pedic uses, it could feel too firm in cooler temperatures and even too soft for some people when it was heated up. Not being one to be easily discouraged, I continued my investigation and learned that there was a new innovation that solved this dilemma, but more on this in a moment.
What I did readily notice during my investigation was that there were other companies producing memory foam mattresses that were reported to be just like Tempur-Pedic, but a bit less costly. However, upon further examination many of these companies were using inferior quality foam and I did not feel comfortable that it would stand the test of time.
Then I came upon a new mattress that didn't just try to use NASA's technology and copy Tempur-Pedic. Rather, they were using innovation to improve upon the use of NASA's technology in a design that could answer the concerns that Tempur-Pedic and other memory foam mattress consumers seemed to want addressed.
This new mattress is called the Tri-Pedic. The mattress is relatively new on the market when compared to some of the older and well established names out there, but it was actually developed about five years ago. What makes the Tri-Pedic more innovative than the competition, is that it found a way to address some of the previously mentioned Tempur-Pedic and other five pound density memory foam mattress concerns.
It did this by creating the first three layer memory foam mattress with two different densities. The top layer uses a softer four pound density memory foam that was not nearly as temperature sensitive, and had a more instantly plush feel to it.
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Their confidence in the longevity of the mattresses they sell on Selectabed.com has lead them to offer a 30-year warranty. They also offer a 4-month sleep trial to ensure that your are completely satisfied with your mattress. Selectabed.com is a division of the actual manufacture, Relief-Mart, Inc.
On behalf of Space Daily I ordered Tri-Pedic mattresses for myself, as well as a member of my staff. I will readily admit that I selfishly was hoping to improve my own sleep while testing this mattress on a personal level and rendering an opinion.
Fortunately for Selectabed.com, my staff and I have been thoroughly impressed by how the mattress feels and the level of support that it gives. Therefore, we unanimously decided to give the Tri-Pedic mattress our Space Daily product innovation award for finding a way to improve upon the use of NASA's technology and literally helping to make dreams come true.
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Monster Truk Crash, verry beautiful
Floods And Fires Across Europe Captured From Space
Paris, France (ESA) Jul 29 - Highlighting the extreme weather conditions hitting Europe, space sensors aboard ESA's Envisat satellite have detected the worst floodwaters to hit Britain for 60 years and deadly fires raging through southern Europe. Heavy rains caused the River Thames to burst its banks on Wednesday, forcing the evacuation of hundreds of homes in Britain's university city of Oxford. The flooding across England and Wales has left tens of thousands without electricity and water.
The Environment Agency still has three severe flood warnings in place - two on the Thames around Oxford and one on the Ock River near Oxfordshire. In areas where flooding is beginning to recede, sanitation officials are warning of health risks posed by stagnant waters.
Flooding is estimated to be the world's most costly kind of natural disaster. The flooding of June and July in the UK is expected to cost the insurance industry at least pound2 billion, according to the Association of British Insurers (ABI). Floods Minister John Healey said recovery and clean-up efforts could take a number of months.
One of the biggest problems during flooding emergencies is obtaining an overall view of the phenomenon, with a clear idea of the extent of the flooded area. Aerial observation is often very difficult due to prohibitive weather conditions and, if the phenomenon is widespread, would be very time-consuming and expensive.
With inundated areas typically visible from space, Earth Observation (EO) is increasingly being used for flood response and mitigation. In October 2000, ESA and the French space agency (CNES) initiated the International Charter on 'Space and Major Disasters', a joint initiative for providing emergency response satellite data free of charge to those affected by disasters anywhere in the world. On 24 July, the UK Environment Agency requested the aid of the Charter.
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KTFO
Security Solution Extended for Desktop Threats 
Enterprises, businesses, and customers have put forward their demand and concern for the need of a Unified Threat Management (UTM) solution to safeguard their desktops and businesses from various threats - such as anti-virus, spyware, etc.
A new product, launched by SonicWALL, promises to provides similar client side protection capabilities as its Enforced Client Anti-Virus and Anti-Spyware software solution for non-SonicWALL UTM customers. It enables users to safeguard their desktops from internet threats, without replacing their current UTM appliance. The solution can be deployed and managed via MySonicWall.com web portal.
The company has also introduced some other enhancements to its Enforced Client Anti-Virus and Anti-Spyware Software version 4.5, which include support for Windows Vista - a centralized desktop firewall feature that acts as a blockade against malicious intrusions and browser protection. It aims to protect users from various web sites that cause malware. The new version comprises client firewall settings and browser protection.
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Cars
TJSB Enjoys CBS Benefits 
In September 2006, the Thane Janata Sahakari Bank (TJSB) deployed OMNIEnterprise Core Banking Solution (CBS) from Infrasoft Technologies. This strategy allowed the bank to enhance its market share and profitability through organic and inorganic growth.
According to R.G. Karve, CEO of TJSB, a transition from the decentralized branch banking approach to a contemporary technology-based CBS was adopted. The approach resulted in low cost of operations, focus on business development, and market-share enhancement. Additionally, the bank has gained competitive advantage by implementing customer-centric operations at branches, and by moving all back-office data processing to a common data processing centre.
The centralized service delivery is a strategy that provides services such as anywhere, anytime banking, internet, phone and SMS banking, automated cheque book dispensing, and cheque depository facility to its increasing clientele base. "Due to the establishment of these business units, TJSB has saved manpower to the tune of 70%. Today, the centralized operations of the bank are managed by 15 employees, as against 55 persons working earlier in the branches," said Subodh Nagwekar, CIO of TJSB.
TJSB was initially using the Betrive DOS-based system and moving data from this system to the CBS was a major challenge faced during the transitional phase. "The IT team developed a standard checklist, made trial conversions, and tested and verified all the branch migrations with expected results of the standard checklist. Deviations observed were rectified immediately," said Nagwekar.
TJSB established its data center in November 2005, which is capable of supporting 100 branches. It has 3 layers of physical security including biometric access control, fire detection, and a suppression system. Maintaining the Automated Teller Machine (ATM) connectivity during the migration process, network shifting to the new data centre from old premises, centralized process implementation, and training the staff were some other challenges faced during and post deployment. The bank's area covers 28 locations spread across Mumbai, Navi Mumbai, Thane, Pune, and Nashik. The network integration was made under the guidance of Datacraft India- through the installation of CISCO routers, switches, firewalls, and network intrusion detection and prevention systems.
The IT team gave special emphasis on a CBS training program to all staff members. The training centre was equipped with the required infrastructure. Windows-based software functional training was imparted to the branch staff, 2 days before moving the branch to the new CBS software.
The bank has established a helpdesk to give support to the CBS application branch users, and all calls for application support are handled by the IT team centrally. The managers independently handle functions like database and server administration, delivery channel management, application support and release, data centre infrastructure management and control, and network management.
28 ATMs are running with the anywhere banking transaction routed through the ATM Switch. The IT team has made an Asset Classification with the risks associated, and has taken adequate countermeasures to mitigate the risks.
With the implementation of CBS, TJSB benefits with extended business hours, connectivity to the ATM Switch, instantaneous credit and access to account for inter-branch transaction and term deposits, and reduction in transaction and operating cost.
The bank is maintaining its customer relationship through 24 x 7 delivery channels. To keep the communication lines between the bank and its customers open, various notices are generated by the banking application software - such as term deposit maturity notices, loan installment due notice, etc. Apart from the above, the customer is able to monitor transactions through SMS Banking.
Speaking about the present bottlenecks and plans to overcome them, Nagwekar said, "TJSB has already established a near recovery site, and data log shipment is done using the processes." The recovery time as of today is 2 hours, which is quite high. Therefore, the bank has decided to achieve recovery time of less than 30 minutes. For this, they're taking steps to establish a Data Recovery (DR) Site with cluster base and host-base replication. Data will then be updated at the DR Site, and in case of disaster, the operations can be streamlined within the desired time of 30 minutes. TJSB also plans on introducing the Internet Banking Facility. To build the knowledge repository of the bank's employees, an Intranet Setup is under process.
The IT expenditure budget for the current financial year is Rs.2 crore, considering the fact that the bank is in the process of acquiring 2 co-operative banks.
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Video from Slovenian spray artist Sprayman
Clayton at Executive Board Position of Sage 
Sage group has appointed David Clayton as its group strategy, and mergers and acquisitions director. Clayton is currently a non-executive director of Sage and a senior independent director.
He was, previously, the managing director and the head of European Technology Research at Credit Suisse until 2004, and has held a number of senior industry positions in the technology sector.
Clayton will step down from the Sage board, effective immediately. He will take up his new position and join the board as an executive director 1 October, 2007 onwards.
Tim Ingram, non-executive director of Sage since 2002, and chairman of the remuneration committee becomes senior independent director, effective immediately, taking over from Clayton.
Paul Walker, chief executive of Sage said, "David will concentrate on long-term trends in the industry, and help position Sage for continued success in our global markets."
The appointment of 2 new independent non-executive directors is underway.
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nice gymnastic skills shown by a guy called tye hill
Drip, Drip Of Global Warming Spells Change In Northern Russia
 While there are fears for wildlife, there is growing optimism about the Arctic maritime passage that runs across the top of Russia from the Bering Straits to the north Atlantic. |
As he tries to work out the effects of rising temperatures on his 32,000 reindeer, questions are being asked about global warming across northern Russia, from Chukotka region in the east, where Kanchalan is located, to Murmansk in the west.
While there are fears for wildlife, there is growing optimism about the Arctic maritime passage that runs across the top of Russia from the Bering Straits to the north Atlantic.
In May President Vladimir Putin called for greater attention to this passage, which is known as the Northern Sea Route and now operates only piecemeal. It could potentially cut thousands of kilometres (miles) off sea travel between Europe and Asia.
In an address on a nuclear ice-breaker in Murmansk, he urged more effort in the area to secure Russia's "strategic, economic, scientific and defence interests."
In Chukotka, regional governor Roman Abramovich, the oil tycoon and owner of Britain's Chelsea football club, has given at least symbolic backing to this goal.
He sponsored a successful search for the steamship Chelyuskin, which sank off Chukotka's coast in 1933 while trying to prove the viability of the Northern Sea Route. The operation rescued from the ice almost all those who were on board, and salvaged some items from the ship.
The administration now plans to build a floating nuclear power station off Chukotka's north coast as part of the bid to revive the region.
In addition, explorer and parliament member Artur Chilingarov is leading a survey of the Arctic seabed this summer, with a view to extending Moscow's territorial claims and developing new energy deposits.
Referring to prospects for the Northern Sea Route, Chilingarov told AFP: "No one except Russia can do this.... We have our own ice-breakers. We had a system in Soviet times. We need to restore it."
A British yachtsman, Adrian Flanagan, is due shortly to head off from Chukotka to attempt the first solo sail through the Northern Sea Route.
While one Chukotka port official described this as "kamikaze," Flanagan too is optimistic. Contacted by AFP he said that the ice looked set to recede at least as far as in 2005, which was a record year.
But while some see opportunities, others are already counting the costs of climate change.
In Kanchalan, some 70 kilometres (45 miles) northwest of the regional capital Anadyr, teachers at the local school blamed global warming for cracks that have appeared in the building due to melting of the permafrost below ground.
And while Makhushkin worries about his reindeer, receding ice is also proving troublesome for sea mammal hunters.
In coastal districts members of the Chukchi ethnic group are struggling to adapt as whales head for cooler waters even further north, says Eduard Zdor, secretary of Chukotka's Association of Traditional Marine Mammal Hunters.
Also along the coast there is growing conflict between people and polar bears.
The bears have been forced ashore as their normal habitat, the polar ice sheets, now recedes as much as 1,000 kilometres (620 miles) north of Chukotka in summer.
In the last five years two people have been killed and another maimed by polar bears in Chukotka as the animals have taken to approaching villages, desperate for food, says Anatoly Kochnev, a fisheries researcher with the agriculture ministry.
"Whereas before people wanted to feed them, tolerated them and considered them beautiful, now they are seen as enemies and are getting killed more and more," he said.
"We can't maintain nature in absolutely the same state but we need to reduce our influence on the animal world, not help them to die," he said.
There is little sign of environmental decline from the Anadyr seashore, where visitors can see fish jumping from the water and seals and white whales surfacing for air.
In Chukotka, where the 1991 collapse of the Soviet Union brought many people close to starvation, it may be the quality of government rather than climate change that will most preoccupy residents in coming years.
While the whales are retreating farther north, the longer summer fishing season is so far not having much effect on other sea life, said Anatoly Zaitsev, head of a local fishing team.
"As long there isn't over-fishing, we'll continue to have fish," he said as he breakfasted on salmon caviar spread thickly on hunks of bread.
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These fish look like extraterrestrials! Too weird for earth.
Southern Europe Braces For More Fires As Arson Suspected
 The sun is seen through thick smoke in the town of Nafplion, eastern Peloponese, 26 July 2007. The fire department said 99 blazes had broken out around Greece since 24 July 2007, added to hundreds of fires that have burned thousands of hectares of forest and agricultural land since a first heat wave last month. Photo courtesy AFP. |
Three heat-related deaths were reported in Greece Thursday as southern Europe blistered under a devastating heatwave and environmentalists blamed many of the fires raging in Italy on arsonists. Greek authorities said two elderly women were found dead Thursday in the Peloponnese village of Diakofto where a fire was raging for a third day. A 76-year-old man died Wednesday evening in another fire in the village of Mamoussia.
The blaze destroyed homes there and in two other towns, Pyrgaki and Melissia. All the residents were evacuated.
The inferno broke out in the area some 200 kilometers (120 miles) from Athens on Tuesday and has yet to be brought under control.
A dozen other fires were still burning across the country, much of which wilted under temperatures of 45 degrees Celsius (113 Fahrenheit).
There were major blazes on the islands of Kefalonia and Zakynthos in the Ionian sea, at Chios island in the Aegean, Hydra south of Athens and in Kastoria and Kozani, in the north.
Russian President Vladimir Putin said Moscow would send firefighting aircraft to Greece on Friday following a request from the Greek prime minister.
Two Greek Canadair pilots have already died while trying to douse a forest fire, as well as three firefighters.
In Italy, at least 4,500 hectares (11,000 acres) of protected areas have burned in the past three weeks, according to the environmental group WWF, which charged widespread arson.
"Most of the fires of the past few days have been of a criminal nature," the WWF said in a statement. "It is well known that fire almost always serves to get rid of trees and other natural obstacles to make way for new hotels, villas or pastures."
Public safety chief Guido Bertolaso accused "many cities" of failing to update the property records of areas that are burned. Under Italian law, no new construction is allowed on burned land until 15 years after a fire.
WWF said the hardest hit regions were Campania around Naples, in addition to Abruzzo, Calabria, Sicily and Apulia.
Meanwhile, the Italian cabinet was due on Friday to proclaim the level of the disaster, a government official said.
The Italian Farmers Confederation said that more than 5,000 hectares of farmland had also been destroyed, worth some one billion euros (1.4 billion dollars).
In Bulgaria, some 9,500 hectares in the centre and northeast were on fire Thursday, prompting Sofia to seek aid from the European Union, NATO and Russia.
A state of emergency was declared Wednesday in the central Kazanlak region and northeastern Dabovo.
Temperatures have dropped, but winds are still fanning the fires.
In Slovakia, a fire sparked by lightning raged Thursday through the Slovensky Raj national park in the country's east. Authorities have estimated that the damage caused by fires nationwide is about 1.8 million euros.
Croatia's Dalmatian coast was ablaze with dozens of fires, and 1,400 tourists and residents were evacuated Wednesday from the island of Solta, where some 400 hectares of forest and olive groves burned down and homes were threatened.
Two water-dropping planes were backing up 300 firefighters in that battle.
Worst-hit Hungary, where up to 500 people may have died last week from heat-related causes, was enjoying a significant drop in temperatures with the welcome arrival of a cool front.
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a lizzard jumps on this guy's jaket and he freaks funny
Bureaucratic tangle worsens problem
As with many land disputes in Cambodia, the Trapeang Krasaing case highlights the near total lack of documentation -- common in countries where landownership has largely been historic and traditional -- to determine who owns what property.
Land records in Cambodia were largely destroyed during the 1975-79 rule of the communist Khmer Rouge, which abolished private ownership.
A land titling programme has made little headway in restoring ownership records, which even when they do exist are often simply ignored by those handing out eviction notices.
Tangled bureaucracies elsewhere have also exacerbated the problem, making land grabs easier to pull off and harder to resolve.
In Indonesia, the grabbing of long-neglected plots of land has led to a mushrooming of disputes that are only made worse by rampant corruption and a poor registration system.
One particular type of grabbing on the rise involves the encroachment of agricultural fields and settlements into protected forest areas and parks, a serious cause of environmental degradation.
Chalid Mohammad, executive director of Walhi, the country's leading environmental watchdog, said the grabs have become "a major problem found in almost all forested areas in Indonesia".
In the densely-populated province of Lampung at the south end of Indonesia's Sumatra island, illegal encroachment has reached critical levels, said Sutono, the deputy chief of the Lampung forestry office.
"In Lampung, this encroachment has been going on for a long time, even back 30 to 40 years," he said, adding there were now even registered official villages inside what should have been protected natural forest areas.
He estimates about 65 percent of a million hectares of protected forest area in Lampung has been grabbed and converted to settlements and farmland.
"The root cause of this illegal occupation is the absence of work opportunities, and most of the people involved in this usually are willing to leave the forest if they can get jobs or livelihoods elsewhere," Sutono said.
Ownership disputes have also led to an explosion of court cases in Thailand after the 2004 tsunami displaced thousands of villagers from the Andaman coast.
Many either had no documents to prove they owned the land, or lost their property deeds in the waves.
Some 387 court cases have been filed by companies against villagers since the tsunami, with more than 200 still before the courts.
Another 800 eviction notices are in mediation, according to Suttipong Lyetip of the National Human Rights Commission.
Most of the cases that have been settled were resolved through compromise, often with the companies paying out some compensation.
But that is an unlikely outcome elsewhere.
Worsening violence has come to characterise the growing number of disputes that erupt in China, where at least half of all land deals are thought to be illegal and the victims get nothing from the transaction.
"The crux of the issue is that governments at all levels plunder the land resources, the commoners see little if any of the money," said Hou Guoyan, a retired professor from the China University of Political Science and Law.
"Violators get off scot-free and the (central) government is at a loss to solve the problem."
Beijing has issued a series of regulations aimed at increasing scrutiny over land deals, experts say, but has little power to enforce the law in the provinces.
"The main problem is that standard compensation levels for villagers are too low," said Liu Xiaoying, a rural issues researcher at the China Academy of Social Sciences. "This is very difficult to solve."
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I've never seen another cat do this! Have you? He does it every day! (Even though he's neutered...)
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Cool time lapse of Barrett the boa having a lil snack. (don't watch if you love rats!!)
Smog To Accelerate Global Warming As a result, more CO2 will build in the atmosphere instead of being taken up by the land, which in turn will stoke global warming and thus worsen climate change. In the stratosphere, a thin, naturally-occurring level of ozone is a vital shield for life on Earth, providing a shield against DNA-damaging ultraviolet. But at ground level, it is a man-made pollutant, brewed in a reaction between fossil-fuel gases and sunlight. Ozone has long been known to be a risk to health by damaging the airways, but recent research has also highlighted its damaging effect on vegetation. The gas enters plants through respiratory pores, called stomata, in the leaves. It then produces byproducts that crimp efficiency in photosynthesis, leaving a plant that is weak and undersized. Efforts to figure out how fast-rising levels of ozone will affect forests have been hampered by a nasty confounding factor. High levels of CO2 and ozone cause stomata to close, which means the plant takes in less of the CO2 that it needs to grow -- but also less of the ozone that damages it. Published in the British scientific journal Nature, the new study seeks to unravel these intertwining factors. British researchers built a computer model to simulate the response of carbon sinks around the world in response to ozone levels, on a timescale running from 1901 to 2100. They used two scenarios, depending on whether plants were deemed to have high or low sensitivity to ozone. These scenarios were vetted for reliability by comparison with an experiment in which trees and shrubs in a Swiss field were exposed to artificially high levels of CO2 and ozone for seven years. Under the "high" plant-sensitivity scenario, ozone diminished land carbon capture by a massive 23 percent over the two centuries. Under the "low" scenario, the fall was 14 percent. Lead researcher Stephen Sitch of the Hadley Centre, part of Britain's Met Office, told AFP that the study did not estimate the effect of ozone for the 21st century specifically. But, he said, it was clear that there would be a major contributory effect to global warming by 2100 as less airborne CO2 will be captured by the land. "Existing calculations of the carbon cycle haven't factored in the negative effect of ozone," he said. A rough calculation is that ozone could indirectly add "somewhere in the range of 0.5 to 1.25 degrees Celsius" (0.9-2.25 degrees Fahrenheit) in warming, according to Sitch. By comparison, global surface temperatures rose by 0.74 C (1.33 F) from 1906 to 2005, eroding glaciers and alpine snow cover and forcing permafrost into retreat, according to the latest report, issued this year, by the UN's Intergovernmental Panel on Climate Change (IPCC). By 2100, global average surface temperatures could rise by between 1.1 C (1.98 F) and 6.4 C (11.52 F) compared to 1980-99 levels, the IPCC calculates. But this prediction is based on concentrations of greenhouse-gases and does not factor in the indirect effect of ozone. Unlike CO2, which spreads around the planet's atmosphere, ground-level ozone pools nearer to its source, with North America, Europe, China and India high on the list of polluted regions. In pre-industrial times, ozone was 17 parts per billion (ppb). Today, it is 35 ppb and is on course for 54 ppb by the end of the century, said Sitch. Damage to plants starts to occur from 40-50 ppb but the levels vary greatly depending on the season, local topography and weather. Observational research in the US grainbelt has found spikes as high as 120 ppb.
Ozone smog will accentuate global warming this century, for it will damage plants and trees that help soak up carbon emissions, a study to be published on Thursday says. Its authors fear a major factor in the climate-change equation has been badly overlooked. "Carbon sinks" -- the famous ability of vegetation to absorb carbon dioxide (CO2), the principal greenhouse gas -- are being damaged by ozone, they say.
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Jelly fish at the Monterey Bay Aquarium
Screenshots
Here are few screen shots of DNA Baser interface.
The interface is skinable so you can change in depth the way it looks. More skins are available to download for free.
Click a window to enlarge it.
Click to enlarge it.
Main window and the Reverse Complement tool
DNA Baser showing a SCF chromatogram
The log of an assembly process
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For Head Two Animals
How to use DNA Baser
Part 3
How to assemble using a reference sequence
This tutorial will show you how to assemble contigs using reference sequence files.
DNA Baser uses the reference sequence to:
- give the contig orientation
- crop the contig
The reference sequence is not used for calculating the consensus sequence of the contig.
1. Open DNA Baser by clicking its icon on your desktop. When DNA Baser starts, the Project Manager should be opened by default. Navigate to the folder where your files are.
2. Choose a name for this current project. DNA Baser will automatically choose a name for you but you can change it. Use this box to choose/change project's name:
3. Next step is to choose a reference sequence. Drag and drop the desired sequence file in this panel: .
The check box must be activated in order to assemble using a reference sequence.
4. Select the two or more files that are going to be assembled by adding them to the JOB LIST. DNA Baser supports SCF, ABI, FASTA and SEQ.
You can add files to the Job List in several ways:
-use the button to add selected file/files to the Job List.
-use the button to add all files to the Job List.
-using your mouse, drag and drop files one by one from File List to the Job List.
If you want to remove files from the Job List, than use button.
5. The final step is to press the START button. In this moment, DNA Baser should begin the assembling process.
If something is wrong, the START button will be disabled:
This can be caused by:
-less than 2 files in the Job List
-invalid combinations of file types in the Job List
-one or more files in the Job List are invalid or it has been removed from your computer's hard disk meanwhile.
6. After the assembly process, you can check the log file. If DNA Baser has not already opened the log window for you, then press this button to display it.
7. The reference sequence will be placed in the contig grid (click here to read more about the contig grid) on the first position and it will have a light-pink background.
Read the next tutorial to find out how to assemble using the batch mode. If you have any questions, don't hesitate to write an email to us or to use our forum for support.
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poor penguin
How to use DNA Baser
Part 4
How to assemble using the batch mode
This tutorial will show you how to assemble contigs from chromatogram/fasta/seq files using the batch mode.
During the batch assembly, the following steps are automatically performed for each individual assembling process:
- cleaning of the bad ends
- assembling into a contig
- error correction
- vector removal using primer sequences (if option is checked)
- assembly using a reference sequence (if option is checked)
Example: you have a clone library with 500 clones and you use two primers (Forward and Reverse) to sequence each clone. At the end, you will have a folder with 1000 sequences, which need to be assembled in 500 contigs. If you would assemble each contig at a time, it would be rather tedious. A faster option is to assemble in one-step, using the batch mode button. The prerequisite is that the sequences are named after a pattern that will help DNA Baser recognize the sequences that belong to the same contig.
1. Open DNA Baser by clicking its icon on your desktop. When DNA Baser starts, the Project Manager should be opened by default. Navigate to the folder with your sequences (sample's folder).
2. Open the Settings window and navigate to the Manager tab, where the settings for the batch assembly mode are.
Here you instruct DNA Baser about the name pattern. The name pattern means that the files belonging to the same contig have first letters of the name identical (to signal the contig) and the last ones different (to signal each sequence).
In this case, the sequences belonging to same contig have the same name, except for the last letter. For example: E10B082TF and E10B082TR belong to the same contig. The first 8 letters are identical to both sequences (E10B082T), enabling DNA Baser to assign them to the same contig.
In this window, you can also set DNA Baser to either move or copy the sequences that cannot be assembled in separate folders.
At the end, press OK and go the Project manager window.
3. Next, press the START BATCH ASSEMBLY button. DNA Baser will start assembling the sequences into contigs.
4. During the assembly process, a log file is generated and automatically saved in the same folder with the sequences used. If DNA Baser has not already showed the log window for you, then press this button to display it. The log contains: information about each individual assembling process, a batch job summary, the list of parameters used for assembling.
5. DNA Baser creates the following folders (located in the sample's folder):
.../Output - this is the folder were the contigs are saved. Two types of files are here: individual contig files (in fasta format) and a file with all the generated contigs, in multifasta format. The individual contig files are named with the prefix "contig" and a suffix indicating the invariable part of the original sequence names (in this example, the contig from E10B082TF and E10B082TR will be named "Contig - E10B081T"). The multifasta file is saved with the name deriving from the name of the sample's folder.
.../Unassembled - here are moved/copied the sequences which do not fulfill the assembly parameters, and hence cannot be assembled to contigs. In order to assemble them the assembling parameters must be relaxed. Click here to see were you can change the assembling parameters.
.../Unpaired - here are moved/copied the sequences which do not have pairs.
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http://broadband-tech.blogspot.com/ --Sent via http://heyspread.com
Now you can download a free, functional version for testing! No limitations, no nag screens, no crippled functionality! DNA Baser is the only software on the market that allows you to save your work while you are in the trial period.
After the trial period ends, you can still use DNA Baser's internal tools to view chromatogram files, cut primers, make contig assembly, reverse complement, etc but you won't be able to save the contig.
If you need help installing DNA Baser, please visit this page or ask for support on our dedicated forum.
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Our black lab thinks he's a superstar. He's not, but he thinks he is.
Phylogenetic tree
A phylogenetic tree is a tree showing the evolutionary interrelationships among various species or other entities that are believed to have a common ancestor. A phylogenetic tree is a form of a cladogram. In a phylogenetic tree, each node with descendants represents the most recent common ancestor of the descendants, and edge lengths correspond to time estimates. Each node in a phylogenetic tree is called a taxonomic unit. Internal nodes are generally referred to as Hypothetical Taxonomic Units (HTUs) as they cannot be directly observed.
Fig. 1: A speculatively rooted tree for rRNA genes
[Enlarge]
A rooted phylogenetic tree is a directed tree with a unique node corresponding to the (usually imputed) most recent common ancestor of all the entities at the leaves of the tree. Figure 1 depicts a rooted phylogenetic tree, which has been colored according to the three-domain system. The most common method for rooting trees is the use of an uncontroversial outgroup - close enough to allow inference from sequence or trait data, but far enough to be a clear outgroup.
While unrooted phylogenetic trees can be generated from rooted ones by omitting the root from a rooted tree, a root cannot be inferred on an unrooted tree without either an outgroup or additional assumptions (for instance, about relative rates of divergence). Figure 2 depicts an unrooted phylogenetic tree for myosin, a superfamily of proteins. Links to other pictures are given in the pictures on the web subsection below.
Fig. 2: Unrooted tree of the myosin supergene family
[Enlarge]
There are three main methods of constructing phylogenetic trees: distance-based methods such as neighbour-joining, parsimony-based methods such as maximum parsimony, and character-based methods such as maximum likelihood or Bayesian inference.
Tree-building methods can be assessed on the basis of several criteria:
* efficiency (how long does it take to compute the answer, how much memory does it need?)
* power (does it make good use of the data, or is information being wasted?)
* consistency (will it converge on the same answer repeatedly, if each time given different data for the same model problem?)
* robustness (does it cope well with violations of the assumptions of the underlying model?)
* falsifiability (does it alert us when it is not good to use, i.e. when assumptions are violated?)
Caveats
* By their very nature, phylogenetic trees cannot represent actual evolutionary patterns and are in fact distorted by, any lateral gene transfer[5] or hybridisation between species that are not nearest neighbours on the tree before hybridisation takes place. For these reasons, the proposed PhyloCode (see external links below) does not assume a tree structure.
* The phylogenetic tree of a single gene or protein taken from a group of species often differs from similar trees for the same group of species, and therefore great care is needed in inferring phylogenetic relationships amongst species. This is most true of genetic material that is subject to lateral gene transfer and recombination, where different haplotype blocks can have different histories.
* When extinct species are included in a tree, they should always be terminal nodes, as it is unlikely that they are direct ancestors of any extant species. Scepticism must apply when extinct species are included in trees that are wholly or partly based on DNA sequence data, due to evidence that DNA is not preserved intact for longer than 100,000 years.
References
1. Hodge, T. & M. J. T. V. Cope. 2000. A Myosin Family Tree. Journal of Cell Science 113: 3353-3354. See also the Myosin external link below.
2. Woese, C. R. 1998. The Universal Ancestor. Proceedings of the National Academy of Sciences 95: 6854-6859.
3. Maher, B. A. 2002. Uprooting the Tree of Life. The Scientist 16: 18 (Sep. 16, 2002); subscription only
4. Penny, D., Hendy, M. D. & M. A. Steel. 1992. Progress with methods for constructing evolutionary trees. Trends in Ecology and Evolution 7: 73-79.
5. Woese, C. R. 2002. On the evolution of cells. Proceedings of the National Academy of Sciences 99: 8742-8747. The owner of this article is: Wikipedia.
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AJ practicing his basketball skills.
About QV
High quality reads:
- no ambiguities
- no noise
- peaks very well spaced
Good quality reads:
- no ambiguities
- some noise (notice baselines)
- peaks very well spaced
Medium quality regions:
- some ambiguities
- no noise
- peaks well spaced
- some homopolymeric stretches are not well resolved
Poor quality reads:
- some ambiguities
- bad noise (notice baselines)
- overlaping peaks
- low confidence in bases assignment (low QV)
As you can see, this abi file contains no information about QV.
Why my alignments are wrong?
The problem with wrong alignments often appears when the bad ends of the chromatograms have not been properly cleaned.
DNA Baser is doing the cleaning automatically before assembly. However, how much it cleans depends on the parameters the user gave it. There are three parameters, which can be set for the end cleaning. The most important one is the QV value, which can be increased or decreased to provide a good end cleaning. Another thing would be to change the default scores for alignments.
By default, the gap opening = gap extension. If you want to favor the introduction of more gaps, than the scores need to be changed. We could recommend the following: match 20, non-match -15, gap opening -30, gap extension -6. The percent identity between the sequences also is important for the alignment. The algorithm is made to assemble contigs, therefore starting with sequences with high similarity (after end cleaning). If the identity between the sequences is low, than the multiple alignment is faulty.
The alignment can be manually edited at the end of the process, in the sense that bases can be changed, inserted and deleted. However, there is no dragging feature, to rearrange the assembled sequences, since we figure out that the alignment should work for properly cleaned sequences.
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more funny photos with animals.
What is DNA Baser?
An easy to use software package providing batch DNA sequence assembly, contig editing, chromatogram viewer/editor and rapid detection of mutations in DNA sequences. We have created a fast assembly engine with a range of features that greatly speeds the process of sequence assembly and mutation analysis.
DNA BASER provides automated end trimming (clipping) so there is no need to manually trim the low quality bases from the ends of the trace files before contig assembly. This saves considerable time, especially when assembling many DNA sequences.
DNA BASER offers a smart navigation system that takes you to the location of each sequence ambiguity (mutation) with only a single click. Our proprietary sequencing error correction algorithm provides further timesavings.
The truly user-friendly interface makes DNA Baser the best choice for DNA contig assembly. For more details, see the DNA BASER Features page.
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It is ideal for assembly of all sequence types, including the SSU rRNA genes (16S and 18S rRNA), LSU rRNA genes (23S and 28S rRNA), protein genes, and/or genomic fragments. The DNA BASER package is offered at a very affordable price (590$ for academic/ 690$ for business), making it an ideal for universities, research institutions, or private companies performing DNA sequencing. Discounts apply if you purchase more than one license.
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Starting with version 2.7, DNA Baser can Rate this post
The lizard which runs over water
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Coding Regions |
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GeneChip expression arrays enable researchers to simultaneously monitor genome-wide expression profiles. This global view helps scientists understand biological mechanisms of complex diseases and processes, and identify new drug targets in ways never before possible. Utilizing gene expression profiles as novel "biomarkers," for conditions such as cancer or lupus, scientists are able to more accurately classify disease, predict clinical progression, and determine likelihoods of treatment success. |
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