Biomedicine: Resisting radiation

High doses of ionizing radiation, such as those used in radiotherapy for cancer, can cause many of the body's normal cells to self-destruct. But a tool pinched from cancer's own arsenal might keep those cells alive.

Elena Feinstein of Cleveland BioLabs in Buffalo, New York, and Andrei Gudkov of the Roswell Park Cancer Institute, also in Buffalo, developed a drug from a bacterial protein, flagellin, that activates a cell-survival pathway, known as the NF-B pathway, that is constantly active in the majority of tumours.

Mice given 0.2 milligrams per kilogram of body weight of this protein — flagellin — survived usually lethal doses of radiation, up to 13 joules per kilogram of tissue.

Science 320, 226–230 (2008)

Evolution: Lungless life

All hail the first lungless frog: Barbourula kalimantanensis of Borneo, a small, flat creature that lives in fast-flowing streams. Djoko Iskandar at the Bandung Institute of Technology in Indonesia first described the frog 30 years ago. Now he, David Bickford of the National University of Singapore and Anggraini Barlian, also at the Bandung Institute, have determined by dissection that it is entirely without lungs. Instead, it breathes through its skin.

Lunglessness among the four-limbed vertebrates is rare; only two families of salamander and one species of caecilian — a limbless amphibian — are known to have evolved this trait. Unfortunately, the frog is endangered by habitat loss and gold mining, which warms, pollutes and muddies its formerly cool and clear home streams.

Curr. Biol. doi: 10.1016/j.cub.2008.03.010 (2008)

Peacocks: Peahens vs. Sex!!



The elaborate train of the Indian peacock (Pavo cristatus) is the textbook example of a trait that is driven by female mate choice — or so everybody believed.

Mariko Takahashi at the University of Tokyo and her colleagues ran a seven-year study examining interactions between feral peahens and peacocks. They found no evidence that peahens preferred peacocks with trains that were longer, more marked or more symmetrical. They also noticed that peacocks usually actively shook their train after peahens initiated courtship, suggesting that train display is not luring females.

The train may once have been driven by sexual selection, but today it seems that the hens have grown weary of the ornament.

Anim. Behav. 75, 1209–1219 (2008)

Bacteria as a Source of Electricity

Do you know that the earth’s capacity to supply fossil fuels are decreasing day by day and if we continue to utilize our natural resources on current trends then we might have no source of natural energy in another few decades. Have you ever imagined what would happen then? There will be no oil for your cars and no electricity for your daily life!! Can you live that life?

Well this might not be a problem for developed countries that already have alternate energy sources, like nuclear energy for their power supply. But what is the solution for country like Bangladesh? Many of you already got the answer in your mind and that is solar energy. But have you ever imagined that tiny little bacteria, a microorganism that we cannot see with naked eyes could be a source of electricity.

In past few years scientific interests focused into some special group of bacteria, which can convert biochemical to electrical energy, that is during bacterial growth some products released form their body can be used to produce currents. At the beginning of this technology power production was very low but due to some development in recent years electricity production from bacteria has increased dramatically. Although most of the results are from miniature projects but the scientists are very much optimistic to produce energy from microorganisms in near future. At present the major limitations of this technology are the cost of materials used to construct microbial fuel cells. This costing problem is confined to specially those countries that already have enough power plants but may be not a problem for developing countries like Bangladesh as we are lacking of enough energy and we need more and more power plants to supply electricity. In addition we can supply the raw materials (e.g. wastewater) for such plants from our own. Therefore, if we can establish a plant where bacteria and wastewater will be the source of our future electricity, you can easily imagine how much foreign currency we can save.

So, far the bacteria which can produce electricity in microbial fuel cells (MFCs) are Geobacter and Shewanella species. In addition Pseudomonas aeruginosa also shows promising results. The recent discovery of nanowires introduces a whole new dimension in MFCs. These conductive, nanowires scientifically known as pilus-like structures, appear to be directly involved in electron transfer, an important component for electricity production.

At present some of the developed countries are planning to use microbial fuels cells for wastewater treatment. In the United States approximately $25 billion is spent annually for water and wastewater treatment and approximately 4% of the electricity produced is used for the operation of the wastewater infrastructure. A treatment system based on microbial fuel cells provides a great opportunity to develop the technology, because the substrate is free and wastewater must be treated. It has been estimated that at a modern treatment plant of MFC, the wastewater may contain nine times as much energy as is used to treat it. Energy recovery at a wastewater treatment plant could lead not only to a sustainable system based on energy requirements but also to production of a net excess of energy. MFCs would be used in a treatment system as a replacement for the existing energy-demanding bioreactor, resulting in a net energy-producing system. However, it is not known at the moment how to economically scale up a MFC or what would be the cost to replace a conventional system with a MFC-based design. But we have an advantage, as we do not have necessary treatment plants in our country to treat the wastewater; therefore, we need more and more such treatment plants to save the environment as well as save energy by using MFCs.

The MFC system could even be useful for individual homes or other small applications, although power production would probably be too low to warrant recovery of electricity on the basis of at hand technology. However, in near future it could replace the existing generator or IPS to fight against our load shedding problem. At present MFCs may be particularly useful in remote areas where little power needed to run devices, for instance, environmental sensors particularly in river and deep-water environments where it is difficult to routinely access the system to replace batteries and can routinely monitor several environmental factors. Such sensors powered by MFCs are under operations in the United States.

MFCs represent a promising technology for renewable energy production; their most likely near-term applications are as a method of simultaneous wastewater treatment and electricity production. The ability of a diverse range of bacteria to function and persist in MFC is a truly fascinating occurrence. This rapidly evolving technology will fascinate microbiologists and engineers who are challenged with waste technologies and energy production in the coming decades and could be a most suitable energy solution for developing countries like Bangladesh.

Pneumococcus forks out…

New research in the EMBO Journal
provides a first molecular insight into
how Streptococcus pneumoniae binds
to and invades human epithelial cells
— the first step in the pneumococcal
pathogenic process.
Currently, S. pneumoniae infects
approximately 100 million people
each year,with a fatality rate of more
than 10%. In the initial stages of
infection the bacterium adheres to
and enters human nasopharyngeal
epithelial cells and subsequently
escapes to the bloodstream. The
mode of attachment of S. pneumoniae
utilizes a protein on the bacterial
cell surface called choline binding protein
A (CbpA). This adhesin is secreted
by the microorganism and is recaptured
onto the bacterial surface
through interaction with choline moieties.
To invade epithelial cells,CbpA
interacts with a protein — the polymeric
immunoglobulin receptor
(pIgR) — located on the epithelial cell
surface. Although the participation of
CbpA in this process has been known
for some time, the molecular details of
the interaction were not understood.
Now, Elaine Tuomanen, Richard
Kriwacki and colleagues report the
solution structure of one of two
‘repeated’ adhesion domains (R1 and
R2) of CbpA, which are essential for
interaction with pIgR. As these
domains have 78% identity and
exhibit similar biochemical properties,
the authors were also able to use the
solved structure of R2 to model that of
R1. Their analysis of the domains
reveals that both adopt a unique threehelical
raft-like structure with a novel
‘tyrosine fork’ motif positioned in a
loop sequence connecting helices 1
and 2. Phylogenetic analysis of CbpA
sequences from 47 S. pneumoniae
strains revealed that 22 conserved
residues are located in, or in close
proximity to, this loop region. To
further investigate the role of the
R domains in the interaction with
pIgR and the significance of the tyrosine
fork structure, the authors used
surface plasmon resonance and
isothermal titration calorimetry
techniques to analyse the binding
activity of wild-type and sitedirected
mutants of CbpA. These
data confirmed the importance of
some of these conserved residues for
high-affinity binding.
These biochemical data, combined
with the structural-based analysis,
provide an initial insight into a molecular
understanding of CbpA-mediated
bacterial adhesion to pIgR. Future
work will be required to further our
understanding of the mechanism and
to exploit this knowledge in the search
for new antibacterial therapies.
David O’Connell
References and links
ORIGINAL RESEARCH PAPER Lou, R. et al.
Solution structure of choline binding protein A, the
major adhesin of Streptococcus pneumoniae.
EMBO J. 16 December 2004
(doi:10.10138/sj.emboj.7600490)

How Cars Recovered In Ierland!!











Sacrifice

Sacrifice
(Elton John)

--------------------------------------------------------------------------------
Hot tip:You can sing this song with a PC karaoke player!
With Microke you can sing Elton John songs and much more
See www.microke.com for details.

Lyric:

It's a human sign when things go wrong,
when the scent of her lingers
and temptation's strong.
Into the boundary of each married man,
sweet deceit comes callin' and negativity lands.
Cold, cold heart hard done by you.
Some things lookin' better, baby,
just passin' through.
And it's no sacrifice, just a simple word.
It's two hearts living in two separate worlds.
But it's no sacrifice, no sacrifice,
it's no sacrifice at all.
Mutual misunderstanding after the fact.
Sensitivity builds a prison in the final act.
We lose direction, no stone unturned.
No tears to damn you, when jealousy burns.
Cold, cold heart hard done by you.
Some things lookin' better, baby,
just passin' through.
And it's no sacrifice, just a simple word.
It's two hearts living in two separate worlds.
But it's no sacrifice, no sacrifice,
it's no sacrifice at all.
Cold, cold heart hard done by you.
Some things lookin' better, baby,
just passin' through.
And it's no sacrifice, just a simple word.
It's two hearts living in two separate worlds.
But it's no sacrifice, no sacrifice,
it's no sacrifice at all, no sacrifice at all,
no sacrifice at all.

Door

--- When one door of happiness closes ... another opens ... but often we look so long at the closed door that we do not see the one which has been opened for us ---

Cricket

An article from Sydney Morning Herald (about the ODI between Australia & Bangladesh on June 18, 2005)
Australia's world champion cricket team now has another place in history, and its Ashes tour a place in the doghouse.
Its five-wicket, tri-series loss to Bangladesh - the poorest cousin of cricket's first family - sparked pandemonium at Sophia Gardens in Cardiff, wild celebration in Dhaka and humiliation across Australia.
Australia lost to a side that was ranked 33-1 underdogs with nine wins from 107 one-dayers beforehand, among them victories over Scotland, Hong Kong and Zimbabwe (four times).
Bangladesh's win is one of cricket's biggest upsets, possibly rivalling the Test that created the Ashes, when Australia beat England at The Oval in 1882, and Australia's loss to Zimbabwe in the 1983 World Cup.
Ricky Ponting said the defeat was "easily" the worst of his stint at Australian captain and said his side had to accept the unthinkable.
"It's probably one of the biggest upsets in the history of the game, today, and we've got to be made aware of that and if that doesn't click us into gear and into shape then nothing will," he said.
While Australia can make amends - of sorts - against England in today's tri-series match in Bristol, the loss to the lowest-ranked one-day side in the world continued a shocking start to Australia's Ashes defence.
Advertisement
The sorry tale reads three beatings in six days, to England (Twenty20), county side Somerset and Bangladesh, with allrounder Andrew Symonds likely to face further suspension for drinking the night before the Cardiff match.
Symonds is understood to have been drinking early into yesterday morning and it was only revealed during the side's warm-up that he was in no fit state to play.
Australian team management met late into last night to discuss further sanctions, and it is expected that Symonds, 30, will also be suspended from today's match against England - the first real contest this winter of the Ashes combatants.
In another shabby effort, Australia laboured to 5-249 after Ponting misread the wicket and seaming conditions and the batsmen struggled against the accurate Bangladeshi attack.
Even worse, Australia was powerless to prevent 20-year-old batsman Mohammad Ashraful and his captain Habibul Bashar putting on 130 to spearhead their side to victory.
Ashraful struck a glorious 100 from 101 balls, Habibul 47 and Aftab Ahmed a quickfire 21 not out.
Needing seven runs off Jason Gillespie's final over, Aftab blasted the first delivery over mid-wicket for six to level the scores before he and partner Mohammad Rafique pinched a single next ball to give their nation its greatest-ever victory.
Australia started the day unbackable - one bookie offered odds of 1-500 - and although the first Ashes Test against England is still over four weeks away, Ponting admitted to some worries, especially over how Bangladesh dictated terms.
"That's a bit of a worry - the No.1 ranked team in the world against Bangladesh, it's reasonably worrying," he said.
"That's why it's going to be difficult for us to sort of work out what's going on - it's not that we're not training well or training hard.
"It's just that when the games are coming around we're not performing."
Bangladesh coach Dav Whatmore said the win would have huge repercussions in the Asian nation, and had come less than two years after his players spent the winter putting players like Steve Waugh, Ponting, Glenn McGrath and Adam Gilchrist on pedestal.
"[That] didn't didn't please me too much, but to get them again in a different country and to win was wonderful," Whatmore said.
Bangladesh's 2005 includes its first Test win (over Zimbabwe) and one-day wins over India and Australia.
To add to Australia's woes, batsman Mike Hussey could be interviewed by match referee Jeff Crowe today about a large sticker on the back of his bat, which exceeds International Cricket Council (ICC) guidelines that say advertising material must not take up more than 50 per cent of the back of the blade.
A Cricket Australia spokeswoman said Crowe had not formally spoken with management, and that Hussey's bat and its graphite stickers - similar to the ones on Ponting's bats - had been approved until an ICC review later this year





SONDESH SANDESH
Mumbai, June 23, 2005


I have noted with full empathy the hurt sentiments and national pride of the people of Bangladesh by the article written by Deputy Editor of CricketNext.com, Tapan Joshi. Ironically, instead of celebrating Bangladesh's extraordinary achievement in trouncing the formidable World Cup champions and increasingly cocky Australian team, the author perhaps got too carried away by painting a dark side to the economic and social environment of Bangladesh, which was highly exaggerated, extremely inaccurate and totally inappropriate. I have since ensured that the relevant piece has been removed from our content pages forthwith.
CricketNext's launch in Y 2000 and Bangldesh's entry into international cricket by getting ICC recognition go hand-in-hand. I am sure all cricket lovers will never forget the ICC Cricket Week 2000 which was completely sponsored by CricketNext.com, culminating in that sensational last-ball finish to the CricketNext.com Cup match between the first Asia XI vs Rest of the World XI. At that point, Jagmohan Dalmiya, then President, ICC had categorically told me of how CricketNext's sponsorship support would help in getting Bangladesh into the world-map. I am glad that finally we had played an instrumental role by getting Bangladesh cricket the requisite global attention, and the Bangladesh government with due humility recognized our contribution by issuing a prestigious stamp in our honour. We remain touched by the gesture.
I would like to place on record the wonderful time I had there along with my wife and the rest of the CricketNext team. On a hot sultry day in early April, there were over 40,000 passionate cricket lovers trying to get into the Bangabandhu stadium, and yet there was such immaculate lane discipline and admirable crowd behaviour, appreciative of every nuance of the game, and full of bustling energy. And people in Dhaka loved Sachin Tendulkar as if like their own. And the teeming crowds in the bazaar streets, the genteel modest behaviour of all we met, the aroma of mutton curry and the palpable simplicity of the people of Bangladesh has remained a memorable experience.
I would like to reiterate that people have expected miracles from Bangladesh from the time they have got recognition (unfairly enough, perhaps), and many (including us) were naturally frustrated by the continuing humiliating defeats. When Bangladesh defeated India in the ODI last year, believe me, we were genuinely happy for an outstanding performance by our opponents, despite our patriotic commitments and feelings.
Right now, I am happy that Bangladesh is making all its critics and cynics, eat humble apple pie with cinnamon flavoured vanilla ice cream. This is a moment to rejoice, to celebrate! This could be the turning point for Bangladesh cricket, as red-faced Ricky Ponting and his gum-chewing supercilious bunch retreat into their dressing room to recuperate from the ravaging attack of the Bangladesh typhoon!
Every citizen of Bangladesh must feel proud of this spectacular show by its cricketers. So are we all in India. And at CricketNext.
SANJAY JHA
Managing Editor

Feedback to CricketNext

Is Joshi afraid of Bangladeshi Tigers!!!! As in recent times they beat the two finalist of the 2003 World Cup. The first victim was the runners-up India (a reflection of how fortunate the Tigers) and the second was the champion Australia (again the Tigers were very fortunate).

We wont mind if our Tigers continuously win with the help of fortune and conquer the World Cup some day, so did the Sri Lankans, when they won the 1995/96 World Cup (fortunately!!!).

I hope like Joshi all Indians remember the ODI#1081, Wills World Cup, 1995/96, 1st Semi Final: India v Sri Lanka, Eden Gardens, Calcutta (day/night), 13 March 1996. In the history of World cricket it was a nightmare. Do you remember Joshi!! Sri Lanka won by default!! At the fall of the 8th Indian wicket, sections of the crowd vented their disgust with the state of the match by setting fire to some areas of the stands and throwing fruit and water bottles onto the field. The match was briefly stopped and when play was about to resume, the crowd again threw bottles at the deep fielders. The match referee (CH Lloyd) stopped the game and the game was awarded to Sri Lanka by default. Thanks God Joshi as we beat you at Dhaka otherwise who knows you might repeat the same performance and place your name in the history book again.

I guess from your fear whether Tigers beat India again in India, is the only reason why you wrote the article titled THE CUBS ARE LEARNING TO ROAR where the subject heading completely mismatched with inside text, where you write about poverty, fundamentalism, natural disasters and multitude social and economical problems of Bangladesh and many other things. But Dear Sir!! Is India free from above-mentioned problems?

Do you know in which country the world’s largest numbers of poor people live? I am sorry to say but the answer is INDIA. India still has the world’s largest number of poor people in a single country. Of its nearly 1 billion inhabitants, an estimated 350-400 million are below the poverty line, 75 per cent of them in the rural areas [http://www.indiaonestop.com/povertyindia.htm]. Do you know in India, one household in two is without electricity, two in three without running water and six in ten without indoor toilet facilities!!! What an example of rich country!! Hey, I suppose you live in Mumbai. Do you want me to write something interesting about Mumbai? Okay just tell me where you find “Asia's largest slums”, the answer would be definitely Mumbai, the Maharashtrian capital, where you will find the heat, humidity, hassle, traffic fumes, relentless crowds, appalling poverty, beggars, jostled by coolies, and hand-cart pullers (definitely better than cycle rickshaws)!!! And cow!! Yes hundreds of free floating cows and cow dung all over the streets. However, these scenarios are not only in Mumbai, you will find all the interesting things in all big and small cities in India, including the capital New Delhi. Hey are you still living in India!!

Do you know in which country world’s largest number of fundamentalist live? Again it’s INDIA. Indian experience with fundamentalism has been bloody and traumatic. Mahatma Gandhi (father of the Indian nation), fell victim to a Hindu fundamentalist's bullets. The Sikh fundamentalist gunned down Prime Minister Indira Gandhi and her son Prime Minister Rajiv Gandhi also blew up by a female suicide bomber of the Tamil fundamentalist group.

Now natural disasters. Do you know what is call tsunami? Is any part of South India affected by the recent devastating tsunami? Aren’t hundreds of Indian people died? Hey man it is called natural disaster, i.e. naturally occurring disaster which is beyond the control of human being (till now) but you could control the Bhopal (Human) disaster where 3,500 were killed by a gas leak from a pesticide plant in Bhopal in 1984 and many are suffering still now.

You are also not free from social and economical problem. Do you know how many people mugged or killed, or how many women raped, in a day in India? The reported cases are in the column of thousands but unreported cases in millions!! Do you know which country gave birth of the bandit queen, Fulon (Phulan) Devi, the most dreaded bandit, poacher and smuggler, Veerappan, the Mumbai mafia don Daud Ibrahim? I assume they are all from India.

You described Bangladesh as a nation of chaotic, and blamed government for that and compares general peoples life with animals. I assume you did not know before reading my article that India harbors world’s largest number of poor people and fundamentalist, continuously giving birth of world famous bandit kings and queens as well as millions of malnourished children, and facing devastating social and economical problems daily, burning people live inside train and Church. So, please let us know: How you will describe your own country? To whom you will blame for it? and; With whom/which you will compare general peoples life?

You also said Bangladesh has no heroes on the world stage. But why your government awarded Indira Gandhi peace prize to Grameen Bank chairman Dr Mohammad Younus in 1998. I know why. Because the concept of Micro credit was invented by Dr. Mohammed Younus, and first implemented in the Grameen Bank, Bangladesh. Since its inception in 1976, the Grameen Bank has provided billions of dollars worth of loans to millions of Bangladeshis, most of them women for poverty alleviation. And his concept of Microcredit for poverty alleviation is widely accepted and implemented worldwide including India.

Dear Mr. Joshi Bangladesh is emerging so did the Bangladeshi Tigers and we believe that we will defeat the Indian Cricket Team again in India in near future. So pleases don’t waste your time writing weird articles and start collecting fruit and water bottles for throwing onto the field to bring to an end that match by chaos!!

ABBA: Chiquitita

Chiquitita

Chiquitita, tell me what’s wrong
you’re enchained by
your own sorrow
in your eyes
there is no hope for tomorrow
how I hate to see you like this
there is no way you can deny it
I can see that you’re
oh so sad, so quiet

Chiquitita, tell me the truth
I’m a shoulder you can cry on
your best friend
I’m the one you must rely on
you were always sure of yourself
now I see you’ve broken a feather
I hope we can
patch it up together

Chiquitita
you and I know
how the heartaches
come and they go
and the scars they’re leavin’
you’ll be dancin’ once again
and the pain will end
you will have no time for grievin’
Chiquitita
you and I cry
but the sun is still in the sky
and shining above you
let me hear you sing once more
like you did before
sing a new song
Chiquitita
try once more
like you did before
sing a new song
Chiquitita

So the walls came tumblin’ down
and your love’s a blown out candle
all is gone and it seems
too hard to handle
Chiquitita, tell me the truth
there is no way you can deny it
I see that you’re
oh so sad, so quiet

Chiquitita
you and I know
how the heartaches
come and they go
and the scars they’re leavin’
you’ll be dancin’ once again
and the pain will end
you will have no time for grievin’
Chiquitita
you and I cry
but the sun is still in the sky
and shining above you
let me hear you sing once more
like you did before
sing a new song
Chiquitita
try once more
like you did before
sing a new song
Chiquitita

Friends: I'LL BE THERE FOR YOU

I'LL BE THERE FOR YOU

So no one told you life was gonna be this way [four claps]
Your job's a joke, you're broke, your love life's D.O.A.
It's like you're always stuck in second gear
When it hasn't been your day, your week, your month, or even your year, but

CHORUS
I'll be there for you
(When the rain starts to pour)
I'll be there for you
(Like I've been there before)
I'll be there for you
('Cause you're there for me too)

You're still in bed at ten and work began at eight
You've burned your breakfast so far, things are going great
Your mother warned you there'd be days like these
But she didn't tell when the world has brought you down to your knees

CHORUS

No one could ever know me, no one could ever see me
Seems you're the only one who knows what it's like to be me
Someone to face the day with, make it through all the rest with
Someone I'll always laugh with
Even at my worst, I'm best with you
Yeah!

It's like you're always stuck in second gear
When it hasn't been your day, your week, your month, or even your year, but

CHORUS

Ashraful heating England

Article on Bangladesh Today: Peptic Ulcer and Helicobacter pylori

Part 1



Part 2

Scientists discover way to reverse loss of memory

By Jeremy Laurance, Health Editor
Wednesday, 30 January 2008


Scientists performing experimental brain surgery on a man aged 50 have stumbled across a mechanism that could unlock how memory works.


The accidental breakthrough came during an experiment originally intended to suppress the obese man's appetite, using the increasingly successful technique of deep-brain stimulation. Electrodes were pushed into the man's brain and stimulated with an electric current. Instead of losing appetite, the patient instead had an intense experience of déjà vu. He recalled, in intricate detail, a scene from 30 years earlier. More tests showed his ability to learn was dramatically improved when the current was switched on and his brain stimulated.

Scientists are now applying the technique in the first trial of the treatment in patients with Alzheimer's disease. If successful, it could offer hope to sufferers from the degenerative condition, which affects 450,000 people in Britain alone, by providing a "pacemaker" for the brain.

Three patients have been treated and initial results are promising, according to Andres Lozano, a professor of neurosurgery at the Toronto Western Hospital, Ontario, who is leading the research.

more....

Epidemic community-associated methicillin-resistant Staphylococcus aureus: Recent clonal expansion and diversification

Emerging and re-emerging infectious diseases, especially those caused by drug-resistant bacteria, are a major problem worldwide. Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) appeared rapidly and unexpectedly in the United States, resulting in an epidemic caused primarily by isolates classified as USA300. The evolutionary and molecular underpinnings of this epidemic are poorly understood. Specifically, it is unclear whether there has been clonal emergence of USA300 isolates or evolutionary convergence toward a hypervirulent phenotype resulting in the independent appearance of similar organisms. To definitively resolve this issue and understand the phylogeny of USA300 isolates, we used comparative whole-genome sequencing to analyze 10 USA300 patient isolates from eight states in diverse geographic regions of the United States and multiple types of human infection. Eight of 10 isolates analyzed had very few single nucleotide polymorphisms (SNPs) and thus were closely related, indicating recent diversification rather than convergence. Unexpectedly, 2 of the clonal isolates had significantly reduced mortality in a mouse sepsis model compared with the reference isolate (P = 0.0002), providing strong support to the idea that minimal genetic change in the bacterial genome can have profound effects on virulence. Taken together, our results demonstrate that there has been recent clonal expansion and diversification of a subset of isolates classified as USA300. The findings add an evolutionary dimension to the epidemiology and emergence of USA300 and suggest a similar mechanism for the pandemic occurrence and spread of penicillin-resistant S. aureus (known as phage-type 80/81 S. aureus) in the 1950s.

Adam D. Kennedy*, Michael Otto*, Kevin R. Braughton*, Adeline R. Whitney*, Liang Chen, Barun Mathema, Jose R. Mediavilla, Kelly A. Byrne*, Larye D. Parkins*, Fred C. Tenover, Barry N. Kreiswirth, James M. Musser, and Frank R. DeLeo*,¶

*Laboratory of Human Bacterial Pathogenesis, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840; International Center for Public Health, Public Health Research Institute, 225 Warren Street, Newark, NJ 07103; Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA 30333; and Center for Molecular and Translational Human Infectious Diseases Research, Methodist Hospital Research Institute and Department of Pathology, 6565 Fannin Street, B490, Houston, TX 77030

Edited by Richard M. Krause, National Institutes of Health, Bethesda, MD, and approved December 10, 2007 (received for review October 26, 2007)

Microbial Diagnostic Microarrays

A powerpoint presentati on microbial diagnostic microarrays

Enhanced hydrogen production from glucose by metabolically engineered Escherichia coli.

To utilize fermentative bacteria for producing the alternative fuel hydrogen, we performed successive rounds of P1 transduction from the Keio Escherichia coli K-12 library to introduce multiple, stable mutations into a single bacterium to direct the metabolic flux toward hydrogen production. E. coli cells convert glucose to various organic acids (such as succinate, pyruvate, lactate, formate, and acetate) to synthesize energy and hydrogen from formate by the formate hydrogen-lyase (FHL) system that consists of hydrogenase 3 and formate dehydrogenase-H. We altered the regulation of FHL by inactivating the repressor encoded by hycA and by overexpressing the activator encoded by fhlA, removed hydrogen uptake activity by deleting hyaB (hydrogenase 1) and hybC (hydrogenase 2), redirected glucose metabolism to formate by using the fdnG, fdoG, narG, focA, focB, poxB, and aceE mutations, and inactivated the succinate and lactate synthesis pathways by deleting frdC and ldhA, respectively. The best of the metabolically engineered strains, BW25113 hyaB hybC hycA fdoG frdC ldhA aceE, increased hydrogen production 4.6-fold from glucose and increased the hydrogen yield twofold from 0.65 to 1.3 mol H(2)/mol glucose (maximum, 2 mol H(2)/mol glucose).


Maeda T, Sanchez-Torres V, Wood TK.
Artie McFerrin Department of Chemical Engineering, Texas A & M University, 220 Jack E. Brown Building, College Station, TX, 77843-3122, USA.

Ultrafast DNA sequencing on a microchip by a hybrid separation mechanism that gives 600 bases in 6.5 minutes

To realize the immense potential of large-scale genomic sequencing after the completion of the second human genome (Venter's), the costs for the complete sequencing of additional genomes must be dramatically reduced. Among the technologies being developed to reduce sequencing costs, microchip electrophoresis is the only new technology ready to produce the long reads most suitable for the de novo sequencing and assembly of large and complex genomes. Compared with the current paradigm of capillary electrophoresis, microchip systems promise to reduce sequencing costs dramatically by increasing throughput, reducing reagent consumption, and integrating the many steps of the sequencing pipeline onto a single platform. Although capillary-based systems require 70 min to deliver 650 bases of contiguous sequence, we report sequencing up to 600 bases in just 6.5 min by microchip electrophoresis with a unique polymer matrix/adsorbed polymer wall coating combination. This represents a two-thirds reduction in sequencing time over any previously published chip sequencing result, with comparable read length and sequence quality. We hypothesize that these ultrafast long reads on chips can be achieved because the combined polymer system engenders a recently discovered "hybrid" mechanism of DNA electromigration, in which DNA molecules alternate rapidly between reptating through the intact polymer network and disrupting network entanglements to drag polymers through the solution, similar to dsDNA dynamics we observe in single-molecule DNA imaging studies. Most importantly, these results reveal the surprisingly powerful ability of microchip electrophoresis to provide ultrafast Sanger sequencing, which will translate to increased system throughput and reduced costs.


Christopher P. Fredlake*, Daniel G. Hert*, Cheuk-Wai Kan*, Thomas N. Chiesl*, Brian E. Root, Ryan E. Forster, and Annelise E. Barron*,,

Departments of *Chemical and Biological Engineering, Chemistry, and Materials Science and Engineering, Northwestern University, Evanston, IL 60208

New Mode of Cell Communication Discovered

By Steve Mitchell
ScienceNOW Daily News
9 January 2008

Like teenagers, cells in our bodies constantly chatter back and forth. But instead of zapping text messages, they relay signals with molecules. Now, researchers have discovered a surprisingly tiny new messenger in worms: protons. The find raises the possibility that the subatomic particle plays the same role in humans, the researchers say.
Research in mice has hinted that protons--hydrogen atoms stripped of their electrons--might act as messengers, but until now direct evidence has been lacking. A team led by biologist Erik Jorgensen of the University of Utah, Salt Lake City, made the discovery while investigating how the worm Caenorhabditis elegans contracts certain muscles around its intestines to squeeze out waste. Previous experiments had ruled out several neurotransmitters known to aid defecation, suggesting that a novel molecule might be playing a role.

After sequencing the DNA of worms with defects in muscle contraction, the team identified mutations in a gene called PBO4. This gene encodes a protein located on the outer surface of intestinal cells, where it brings sodium ions into the cell while pumping protons out. This hinted that protons might play a role in making the muscles contract.

more....http://sciencenow.sciencemag.org

Why We're Different: Probing the Gap Between Apes and Humans

Science 25 January 2008: Vol. 319. no. 5862, pp. 404 - 405
Michael Balter

We sometimes see apes and monkeys in the movies, but we never see them at the movies. Although nonhuman primates can do remarkable things--chimps have rudimentary cultures, and some monkeys have highly complex social systems--none shows the kind of creativity and innovation that are the hallmarks of Homo sapiens. Researchers have long puzzled about which human behaviors stem from our primate roots and which are unique to the hominid line.
Beginning in the 1960s, scientists focused on the similarities, as lab and field studies revealed that the cognitive talents of other primates had been underestimated. But during the past decade or so, researchers say, there has been renewed interest in the traits that set us apart. At a recent meeting* here, anthropologist Carel van Schaik of the University of Zurich, Switzerland, emphasized this evolutionary divergence. "Mind the gap!" he said in a keynote talk. "Humans have a huge number of [novel] characteristics." Indeed, participants at the meeting, which was designed to compare and contrast humans and nonhuman primates, demonstrated several of these seemingly unique human behaviors: advanced planning (the conference was months in the making), social organization and cooperation (everyone showed up at the same time and place), and culture and teaching through language.

At the conference, researchers heard evidence that many of these behaviors, such as planning, may have deep evolutionary roots. But some talents, such as cultural innovation, seem unique to our species, and others, including altruism, may represent a novel blend of old and new characteristics. The challenge now, says van Schaik, "is to figure out how one ape among many--humans--could become so radically different."

more....http://www.sciencemag.org

Biofuels on a Big Scale

By Robert F. Service
ScienceNOW Daily News
7 January 2008

On paper, making biofuels from switchgrass and other perennials that need not be replanted seems like a no-brainer. Use the sun's energy to grow the crop, and then convert it to liquid fuels to power our cars without the need for gasoline. But so far, experiments with these "cellulosic" crop-based fuels have only been conducted on small scales, leaving open the question of how feasible the strategy is. Now, the first large-scale study shows that switchgrass yields more than five times the energy needed to grow, harvest, and transport the grass and convert it to ethanol. The results could propel efforts to sow millions of hectares of marginal farmland with biofuel crops.
Previous studies on switchgrass plots suggested that ethanol made from the plant would yield anywhere from 343% to 700% of the energy put into growing the crop and processing it into biofuel. But these studies were based on lab-scale plots of about 5 square meters. So 6 years ago, Kenneth Vogel, a geneticist with the U.S. Department of Agriculture in Lincoln, Nebraska, and colleagues set out to enlist farmers for a much larger evaluation. Farmers planted switchgrass on 10 farms, each of which was between 3 and 9 hectares. They then tracked the inputs they used--diesel for farm equipment and transporting the harvested grasses, for example--as well as the amount of grass they raised over a 5-year period. After crunching the numbers, Vogel and his colleagues found that ethanol produced from switchgrass yields 540% of the energy used to grow, harvest, and process it into ethanol. Equally important, the researchers found that the switchgrass is carbon neutral, as it absorbs essentially the same amount of greenhouse gases while it's growing as it emits when burned as fuel.

more...http://sciencenow.sciencemag.org

Another Big Bang for Biology

By Phil Berardelli
ScienceNOW Daily News
3 January 2008

Researchers have uncovered what they think is a sudden diversification of life at least 30 million years before the Cambrian period, the time when most of the major living groups of animals emerged. If confirmed, the find reinforces the idea that major evolutionary innovations occurred in bursts.


The main points of Charles Darwin's theory of evolution, which he carefully laid out in The Origin of Species 149 years ago, have stood the test of time. But where Darwin assumed that natural selection proceeds slowly and orderly--much the way Isaac Newton imagined a clockwork universe--modern investigations have shown that the process more resembles the chaotic world of quantum physics. Scores of new groups of species can appear within a few million years. By far the biggest and most famous of these events is the Cambrian explosion, a period between 542 million and 520 million years ago, when due to some still-unknown cause, the ancestors of nearly all extant groups, or phyla, of animals appeared.

more....www.sciencenow.sciencemag.org

Scientists Synthesize a Genome From Scratch

By Elizabeth Pennisi
ScienceNOW Daily News
24 January 2008

Researchers have rebuilt an entire genome from scratch, they report online today in Science. Although the team has yet to demonstrate that this DNA can substitute for the real thing, the work paves the way for customized bacteria that could efficiently produce drugs, biofuels, and other molecules useful to humankind.
Ever since his group decoded the genome of Mycoplasma genitalium, a parasitic bacterium that lives in the human urogenital tract, sequencing maverick J. Craig Venter has wanted to remake the bug's genome in the lab. At just under 600,000 bases, M. genitalium sports the smallest known genome for a free-living organism, and Venter hoped that an artificial genome could be modified to turn the bacterium into a living chemical-manufacturing plant.

Last year, Venter and his colleagues developed a technique for replacing M. genitalium's genome with another natural genome from a different species (Science, 3 August 2007, p. 632). But synthesizing the M. genitalium genome from the ground up proved challenging, in part because long strands of DNA are quite fragile.

Japanese researchers have built a large genome from two existing bacterial chromosomes. But Venter, Hamilton Smith, and their colleagues at the J. Craig Venter Institute in Rockville, Maryland, started with short pieces of DNA that a company had manufactured base by base. About 6000 bases long, these pieces represented overlapping bits of the microbe's only chromosome. Some of the pieces also contained "watermarks": a few extra or different bases here and there that distinguish an artificial chromosome from a natural one.

To link the pieces, Smith and Venter's team used enzymes that allowed them to join longer and longer DNA strands until they had just four, each representing one-quarter of the genome. Finally, the team inserted these quarters into yeast, which copied and combined them into a complete chromosome. The researchers sequenced their newly constructed genome and, except for the watermarks, it matched M. genitalium's exactly. The work is "a technical tour de force" and a "monumental effort," says yeast biologist Jef Boeke of Johns Hopkins University School of Medicine in Baltimore, Maryland. However, to be sure this genome works as it should, the researchers must still put it into a DNA-less M. genitalium, notes Eckard Wimmer, a molecular virologist at Stony Brook University in New York state: "Proof is biological function, and that's missing in this paper."

http://sciencenow.sciencemag.org/cgi/content/full/2008/124/3?etoc

Universal Influenza Vaccine Tested Successfully In Humans

ScienceDaily (Jan. 25, 2008) — The British-American biotech company Acambis reports the successful conclusion of Phase I trials of the universal flu vaccine in humans. The universal influenza vaccine has been pioneered by researchers from VIB and Ghent University. This vaccine is intended to provide protection against all ‘A’ strains of the virus that causes human influenza, including pandemic strains. Therefore, this vaccine will not need to be renewed annually.


Flanders Institute for Biotechnology (2008, January 25). Universal Influenza Vaccine Tested Successfully In Humans. ScienceDaily. Retrieved January 28, 2008, from http://www.sciencedaily.com­ /releases/2008/01/080124185522.htm

International Team to Sequence 1000 Genomes

By Jocelyn Kaiser
ScienceNOW Daily News
22 January 2008

Just a year after the first individual human genomes were sequenced, an international team announced today that it will probe the entire genomes of about 1000 people. The aim is to create the most detailed catalog yet of human genetic diversity to help biomedical researchers home in on disease genes.
The 1000 Genomes Project will delve much deeper than the three celebrity genomes completed last year, including those of genome researcher J. Craig Venter and DNA co-discoverer James Watson (ScienceNOW, 4 September 2007). It will build on the recently completed HapMap, which describes how blocks of DNA tagged by common variants, called single-nucleotide polymorphisms (SNPs), vary in different populations (ScienceNOW, 26 October 2005). These SNPs have turned up more than 100 new DNA markers associated with common illnesses such as diabetes and heart disease (Science, 21 December 2007, p. 1842). But the HapMap includes only the most common markers, those present in at least 5% of the population.

To find rarer SNPs that occur at 1% frequency, genome leaders say, they need to sequence about 1000 genomes. The 3-year project, which will cost $30 million to $50 million, will take advantage of new technologies that have slashed the cost of sequencing. The work will be funded by the U.S. National Human Genome Research Institute (NHGRI) in Bethesda, Maryland, the Sanger Institute in Hinxton, U.K., and the Beijing Genomics Institute in Shenzhen, China.

The consortium will start with three pilot projects. One will exhaustively sequence the entire genome of six individuals: two adults and both sets of their parents. A second project will sequence 180 individual genomes at light coverage, leaving gaps. The third project will fully sequence the protein-coding regions of 1000 genes (5% of the total) in about 1000 genomes. The samples, all anonymous and with no clinical information, will mainly be drawn from those collected for the HapMap, which includes people of European, Asian, and African descent. The first data from the pilot projects should become public later this year.

The new catalog could help disease gene hunters in several ways. It will potentially eliminate the need to sequence around a newly discovered disease SNP to find the variant that actually alters the gene product, says NHGRI Director Francis Collins. The project will also catalog genes that are sometimes lost or duplicated--such copy-number variants can cause disease. By compiling rarer variants, the project should also help resolve a debate about the relative contribution of these mutations to disease risks. Most disease SNPs found so far raise risk only 50% or less, for example, and some researchers suspect that there are rarer SNPs that raise risk twofold, threefold, or more. "There's no question it's going to be a tremendous resource," says Yale University's Judy Cho, who has used the HapMap to find a new gene for Crohn's disease.

Transgenic expression of Helicobacter pylori CagA induces gastrointestinal and hematopoietic neoplasms in mouse: PNAS | January 22, 2008 | vol. 105 |

Infection with cagA-positive Helicobacter pylori is associated with gastric adenocarcinoma and gastric mucosa-associated lymphoid tissue (MALT) lymphoma of B cell origin. The cagA-encoded CagA protein is delivered into gastric epithelial cells via the bacterial type IV secretion system and, upon tyrosine phosphorylation by Src family kinases, specifically binds to and aberrantly activates SHP-2 tyrosine phosphatase, a bona fide oncoprotein in human malignancies. CagA also elicits junctional and polarity defects in epithelial cells by interacting with and inhibiting partitioning-defective 1 (PAR1)/microtubule affinity-regulating kinase (MARK) independently of CagA tyrosine phosphorylation. Despite these CagA activities that contribute to neoplastic transformation, a causal link between CagA and in vivo oncogenesis remains unknown. Here, we generated transgenic mice expressing wild-type or phosphorylation-resistant CagA throughout the body or predominantly in the stomach. Wild-type CagA transgenic mice showed gastric epithelial hyperplasia and some of the mice developed gastric polyps and adenocarcinomas of the stomach and small intestine. Systemic expression of wild-type CagA further induced leukocytosis with IL-3/GM-CSF hypersensitivity and some mice developed myeloid leukemias and B cell lymphomas, the hematological malignancies also caused by gain-of-function SHP-2 mutations. Such pathological abnormalities were not observed in transgenic mice expressing phosphorylation-resistant CagA. These results provide first direct evidence for the role of CagA as a bacterium-derived oncoprotein (bacterial oncoprotein) that acts in mammals and further indicate the importance of CagA tyrosine phosphorylation, which enables CagA to deregulate SHP-2, in the development of H. pylori-associated neoplasms.

[Naomi Ohnishi*, Hitomi Yuasa*, Shinya Tanaka, Hirofumi Sawa, Motohiro Miura*, Atsushi Matsui*, Hideaki Higashi*, Manabu Musashi, Kazuya Iwabuchi¶, Misao Suzuki||, Gen Yamada||, Takeshi Azuma**, and Masanori Hatakeyama*,

*Division of Molecular Oncology, Institute for Genetic Medicine and Division of Chemistry, Graduate School of Science, Health Administration Center, and ¶Division of Immunobiology, Institute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan; Laboratory of Molecular and Cellular Pathology, Hokkaido University Graduate School of Medicine, Sapporo 060-8638, Japan; Department of Molecular Pathobiology, Hokkaido University Research Center for Zoonosis Control, Sapporo 001-0020, Japan; ||Center for Animal Resources and Development, Graduate School of Medical and Pharmaceutical Sciences, Kumamoto University, Kumamoto 860-0811, Japan; and **Department of Gastroenterology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan]

Hypertension: Pass on the Salt

John F. Foley

Science Signaling, AAAS, Washington, DC 20005, USA

Salt is well known to promote hypertension, but the mechanisms involved in regulating the tone of arterial smooth muscle are poorly characterized. This is particularly true with regard to our understanding of whether similar or distinct mechanisms are responsible for regulating both basal blood pressure and salt-induced hypertension. Phosphorylation of myosin light chain (MLC) is critical for the vascular constriction that is associated with hypertension. Many receptors promote the phosphorylation of MLC either by stimulating MLC kinase, through the activation of heterotrimeric GTP-binding proteins (G proteins) of the Gq and G11 families, or by inhibiting, through G12 and G13 G proteins, the phosphatase that returns MLC to its inactive form. Wirth et al. produced mice that could be induced by treatment with tamoxifen to lack both Gq and G11 (Gq-G11 KO) or both G12 and G13 (G12-G13 KO) in smooth muscle cells. Treatment with tamoxifen caused an increase in blood pressure in all mice, but whereas the blood pressure of wild-type and G12-G13 KO mice soon returned to basal levels, that of Gq-G11 KO mice became 10 to 15% lower than normal, implicating Gq and G11 in the regulation of basal blood pressure. Treatment of wild-type mice with a salt preparation increased their blood pressure, but Gq-G11 KO and G12-G13 KO mice were unaffected, showing that both sets of G proteins mediate salt-induced hypertension. Mice deficient in LARG, an effector of G12 and G13 found in smooth muscle cells that mediates the inhibition of myosin phosphatase, responded to salt treatment similarly to G12-G13 KO mice. As Schoner discusses in commentary, this study makes possible the development of therapies that could interfere with salt-induced hypertension while leaving basal blood pressure regulation intact.

A. Wirth, Z. Benyó, M. Lukasova, B. Leutgeb, N. Wettschureck, S. Gorbey, P. rsy, B. Horváth, C. Maser-Gluth, E. Greiner, B. Lemmer, G. Schütz, J. S. Gutkind, S. Offermanns, G12-G13-LARG-mediated signaling in vascular smooth muscle is required for salt-induced hypertension. Nat. Med. 14, 64-68 (2008). [PubMed]

W. Schoner, Salt abuse: The path to hypertension. Nat. Med. 14, 16-17 (2008). [PubMed]


Citation: J. F. Foley, Pass on the Salt. Science Signaling 1, ec23 (2008).

HIV-positive blood donors set record in '07

Blood donors who tested positive for HIV numbered a record 102 in 2007, surpassing 100 for the first time since the HIV antibody test for blood donors began in 1986, according to a Japanese Red Cross Society report Wednesday.

The society's preliminary data found the number of blood donors per 100,000 with HIV also marked a record high of 2.06 in 2007. Meanwhile, the number of total donors recorded its lowest level of 4.94 million in 2007.

Because the tests are only designed to prevent the virus from spreading through donated blood products, the society does not inform donors of the results.

However, a health ministry official said an increasing number of people are donating blood as a free and easy way of getting an HIV test, unaware they will not get the results.

"To prevent the possibility of the virus from spreading, the ministry is urging the public to refrain from blood donation for such purposes," the official said, adding that people should get HIV tests at public health centers or at medical institutions.

The 102 included six people who tested negative for the virus in the society's ordinary blood antibody tests, but ended up being diagnosed as HIV-positive in the society's more highly sensitive virus test.

The number of HIV-positive donors in 2007 was up 15 from the preceding year.

(Source: Japan Times)

Croatia opens Tokyo office to promote tourism, ties

The Croatian government has set up a tourism promotion office in Tokyo to meet a sharp increase in Japanese tourists and to deepen bilateral friendship.

According to the Croatia National Tourist Board, which opened the branch, 64,751 Japanese visited the nation in 2006, almost double the previous year's 32,748. The figure rose to 83,346 between last January and November.

The tourism board has set its sights on raising the number by 10 percent from the current level by 2010, the office said in a statement.

The branch will engage in a tourism promotion campaign and provide up-to-date information for visitors.

(Source: Japan Times)