text:
Listen: Filippo Beck Peccoz on Shadow Tactics: Blades of the Shogun OST
"In the end, we need to serve the game itself."
Julian Colbus / 26th December 2017
Thor Ragnarok by Mark Mothersbaugh (Soundtrack Review)
Thank you, Mr. Mothersbaugh. Humanity is forever in your debt.
Bernhard H. Heidkamp / 5th December 2017
Stranger Things Season 2 by Michael Stein & Kyle Dixon (Soundtrack Review)
"Stranger Things" sounds nice, but doesn't tell you anything which is an unforgivable pity.
Don't be afraid of being weird: Inside Elephant Music's trailer world with Vikram Gudi
Quietly yet with plenty of noise, London-based boutique agency Elephant Music has turned into one of the rising stars of the trailer scene. I got to speak with its founder and CEO...
Peter F. Ebbinghaus / 24th November 2017
The winners of the 2017 Hollywood Music and Media Awards
Over two thousand attendees including leading songwriters, composers and recording artists attended Thursday's Hollywood Music and Media Awards at the Avalon – Hollywood. The event, hosted by comedian Ron Pearson,...
Nice Folks Finish First
The fall of Harvey Weinstein has illuminated some of the longstanding practices of sexual exploitation in Hollywood. People also mention how he and his brother were bullies, routinely yelling and...
Michael A. Levine / 14th November 2017
Daniel Sadowski on his retro game score for Bloody Zombies
"I used the TK-Audio BC1 hardware compressor as well as an SSL Clone. By running the soft synths through these hardware compressors and then back into Cubase, I could get...
Patrick Doyle's film score for Murder on the Orient Express out now
Sony Classical proudly announces the release of MURDER ON THE ORIENT EXPRESS (Original Motion Picture Soundtrack) with an original score by Academy Award-nominated composer Patrick Doyle, including a song performed...
Peter F. Ebbinghaus / 6th November 2017
I am not sure ambient scores can get much better than this.
Bernhard H. Heidkamp / 5th November 2017
Diane Warren to receive Career Achievement Award at 8th HMMA
The Hollywood Music in Media Awards will present acclaimed songwriter Diane Warren with the HMMA Career Achievement award on Thursday, November 16th at Avalon – Hollywood, 1717 Vine St. The HMMA is...
Peter F. Ebbinghaus / 3rd November 2017
Mychael and Jeff Danna's film score for Alias Grace out soon
"We chose a chamber group of virtuosic musicians to lay out the complicated fabric of the musical world of ALIAS GRACE. There was interwoven string parts, often with one player...
Peter F. Ebbinghaus / 2nd November 2017
Evgueni and Sacha Galperine's about the music in Loveless
"Director Andrey Zvyagintsev's cinema always shows the invisible link between the intimate stories of human beings and the universe. And often the music personifies this link. Finding the way to...
← 1 2 3 4 … →


The five elements are foundational to understanding the basis of yogic teachings, including ayurveda, seasonal practice, and aligning one's asana practice and life with the rhythms of nature. It is understood in yoga that the five elements comprise all that is seen and unseen. With this, deepening one's relationship with the five elements will profoundly impact the way a student practices, and the way a teacher teaches. The five elements are foundational to the history and modern practice of yoga. Deepening ones understanding of these elements is to deepen ones understanding of oneself and of all of life.
These practices are ideal for an intermediate or advanced practitioner or teacher who is seeking a way in which to bring more depth and meaning to his/her mat practice.
Each practice begins with a short introduction and a unique practice designed to bring the practitioner into a deep and delicious relationship with earth, water, fire, air, and ether.
Each of the five videos builds from the foundation of living in the physical body (earth) and slowly introduces the increasingly subtle elements, culminating in ether. Practitioners are recommended to practice each element for one week 3-5 days before moving on to the next video. Element practices do stand alone and can be done independently without loss. However, the greatest benefit will come from experiencing all five element practices from earth, to water, to fire, to air, and finally to ether.


text:
Glenochrysa principissa is een insect uit de familie van de gaasvliegen (Chrysopidae), die tot de orde netvleugeligen (Neuroptera) behoort.

Glenochrysa principissa is voor het eerst wetenschappelijk beschreven door Navás in 1915.

Gaasvliegen

redpajama_set_name: RedPajamaWikipedia


LOCATION! LOCATION! LOCATION! Minutes to freeways, BART, shopping, restaurants, hiking trails, and all the best the Bay Area has to offer. Pride of ownership! Beautifully updated and maintained throughout. Gourmet's dream kitchen with granite counters and innovative custom cabinetry. Highly rated Mt Diablo Schools.
LIVING ROOM: Form and function harmonize in this fabulous room with its impressive stone fireplace, classic tile floors, and sunny seating alcove. The perfect space to relax after a long day or entertain family and friends.
KITCHEN/ DINING AREA: The well-crafted kitchen features granite tile counters and well-designed cabinetry with innovative pull-outs and abundant storage. The adjacent dining nook accommodates a large table and looks out onto the charming patio.
HALF BATH/ INDOOR LAUNDRY: Tastefully remodeled 1/2 bath with granite tile counters, shaker style vanity, contemporary lighting and indoor laundry area.
MASTER BEDROOM: Enjoy the sanctuary of this spacious master bedroom with its large wall-to-wall closet, ceiling fan, new carpets, and updated en-suite bathroom.
ADDITIONAL BEDROOMS / BATHOOM: Two additional upper level bedrooms feature sizable closets and new carpets. Conveniently located, updated hall bathroom.
OUTDOOR LIVING SPACE: The private patio is ideal for outdoor dining, couch seating, BBQ, pets, or a potted plant garden.
GARAGE/PARKING: Large 2 car garage with storage shelves and a pull down ladder for rafter storage. Additional guest parking available.
ADDITIONAL AMENITIES: New carpet and paint. Community pool and spa.


text:
Articles & Updates
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360° Assessment
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Latest News Update
Daily News Roundup: Wednesday, 22nd January 2020
Daily News Roundup: Friday, 13th December 2019
Coventry facing probe after miscalculating risk
Coventry Building Society is facing possible enforcement action from the Bank of England after it admitted that it had understated its risk-weighted assets by £222m. The mistakes meant that the building society's common equity tier 1 ratio, a measure of financial strength, was 32.6%, and not 34.2% as stated in its last results. The Coventry said it had applied the wrong multiple or "scalar" and said: "We are still extremely well capitalised," adding "The society uses internal ratings based models to calculate its risk weighted assets and is seeking to update these models to ensure compliance with upcoming Basel III reforms." The Times' Patrick Hosking queries: "If the Coventry can gets its calculations wrong by 6% with no one noticing, what's to stop it being out by 26%, or 46%?"
RBS to pay out £40m over forex scam
Some £40m in compensation is to be paid out by Royal Bank of Scotland to 730,000 customers after the bank uncovered a scam where staff on the lender's foreign exchange desk manipulated the rates applied to overseas transactions - earning NatWest owner RBS tens of millions of pounds in extra profits. The employees added 0.06% to the rate applied to more than 10m foreign exchange payments. The scam was discovered in 2014 and had been running for four years.
Banks circling Sainsbury's mortgage book
Grocer Sainsbury's has received several offers for its £1.9bn mortgage book as it looks to exit the market. While Royal Bank of Scotland and Santander UK, which had previously shown an appetite, haven't tabled formal proposals, Lloyds Banking Group is understood to be among the interested parties in the auction, which is being handled by BNP Paribas.
Virgin launches its first digital account
Virgin Money has launched a digital current account and mobile app, featuring a linked, easy-access savings account. The Virgin Money Current Account pays 0.5% interest on credit balances up to £2,000.
Former lawyer bags £23m with consultancy float
Former SJ Berwin private equity partner Matthew Hudson has made a tidy £23m after the asset management consultancy he founded floated for £100m on London's junior market. Hudson founded MJ Hudson in 2010, after a career at now-defunct City firm SJ Berwin and US law firms Proskauer Rose and O'Melveny & Myers. Dankse Bank now owns 5.1% of the stock, while Canaccord Genuity, which had backed the company before, increased its holding to 16.7%. Mr Hudson and his wife, Katherine, still own a 27.9% stake in the business.
Lagarde follows Draghi's policy lead but sounds upbeat tone
Christine Lagarde has held her first rate-setting meeting as president of the European Central Bank during which she committed to maintaining Mario Draghi's bond-buying programme and keep policy rates unchanged. However, she said the €20bn a month quantitative easing programme was unlikely to push growth and inflation back to target and new stimulus measures might be needed.
StanChart sells stake in Indonesia's Permata Bank for $1.3bn
Standard Chartered shares rose 2.23% on news it has sold its stake in Indonesia's Bank Permata for $1.3bn. Shore Capital's Gary Greenwood said the stake sale appeared "to represent excellent value".
JPMorgan executive 'sickened' over racism revelations
JPMorgan Chase co-president Gordon Smith has reacted to revelations of racism at an Arizona Chase branch by saying he was "sickened" and the incidents "strike at heart of who we are".
Capital breaks for green lending 'feckless', says ex-regulator
The FT follows up on comments from former Basel committee chief Bill Coen who raises concerns about a relaxation of capital rules by US and European regulators.
Central bankers have a limited ability to tackle climate change
Harvard fellow Megan Greene says central banks need to recognise what they can and cannot do about climate change – "they have no real policy role," she says. "Their job is to contain the fallout."
Fintech: the rise of the Asian 'super app'
The FT looks at the threat to traditional banks from fintechs across Asia, such as Ant Financial, Paytm and Go-Jek, which are forging business models that could yet be used in other parts of the world.
Wizz Air to set up low-cost airline in Abu Dhabi
Hungarian low-cost airline Wizz Air plans to set up a low-cost airline in Abu Dhabi next year called Wizz Air Abu Dhabi - a joint venture with state-owned Abu Dhabi Development Holding.
Welsh road ruling derails Costain
Costain shares tanked on Thursday after it warned profit will be around £20m lower than expected following the arbitration case over its A465 Welsh motorway project. Full-year underlying profit will now be between £17m and £19m, Costain said, after previously estimating profit of between £38m and £42m. Costain's year-end order book will be about £4.2bn, with the company winning around £600m of new work in the second half of the year.
Equity release industry defends protections
The rise in popularity of equity release over the last five years has caused alarm for some campaigners who fear it could trigger a fresh financial scandal. Nearly 500,000 people have borrowed £28bn via equity release since 1991with £2.8bn accessed in the nine months to September alone. The loans come with interest rates averaging 4.91% and experts such as Baroness Altmann say this can lead to soaring debts, wiping out the value of a borrower's home when they die and leaving them with no inheritance to pass on. The Financial Conduct Authority said on Wednesday that it is undertaking "exploratory work" into lending in later life. Jim Boyd, chief executive of the Equity Release Council, said: "Our standards go beyond statutory regulation to provide the highest level of consumer protection for any type of property-based loan. Our members' customers are guaranteed qualified financial advice, face-to-face independent legal advice and clear product safeguards, including secure tenure for life and a no negative equity guarantee."
PingAn's OneConnect cuts valuation in blow for SoftBank
The fintech arm of China's biggest insurer, Ping An, has cut its expected valuation by about half ahead of a planned IPO in the US. OneConnect's announcement is a further blow for backer SoftBank's giant Vision Fund.
Big investors turn screw over climate pollution disclosure
A growing number of large asset managers, including LGIM, BNP Paribas and TCI, are threatening to vote against directors at companies that do not improve their emissions reporting.
EU confirms one-year Brexit reprieve for derivatives industry
EU nation states have approved draft plans from the European Commission to extend an existing March 2020 expiry date for access for European companies to UK clearing houses.
Securities dealing taxes: FTT would be OTT
The FT's Lex says Labour's plan for a financial transaction tax is "flawed" with derivatives "notoriously tricky" to tax and "funds and investors could relocate."
Insurance sector ripe for innovation
Lauren Jones asserts in the Scotsman that the insurance sector is ripe for the sort of disruption from technology seen in financial services, stating that data access and collaboration between insurtech providers and insurers is key to driving forward innovation.
Puregym buys Fitness World for £350m
Gym operator Puregym has acquired Fitness World from FSN Capital and Kirkbi in a £350m deal that makes Puregym the second biggest in Europe in terms of number of gyms after Basic Fit. Puregym was acquired by Leonard Green & Partners in 2017 in a deal that valued the business at £600m.
WPP agrees Goldman Sachs share buyback
WPP has agreed to buy back up to £300m in shares from Goldman Sachs, following the $4bn sale of market research firm Kantar. The advertising giant said the share buyback programme will continue to March 2020 and represents roughly a quarter of the total share buyback amount approved by shareholders, who expect to be paid out to the tune of £950m.
Five more years of Britain's Got Talent
Simon Cowell's Syco Entertainment has signed a new exclusive five-year deal with ITV. It means there will be five series of Britain's Got Talent and at least one of The X Factor.
Outsourcer Serco returns to growth
UK revenues have returned to growth for the first time since 2013 for public services outsourcer Serco with profit likely to come in at £129m on revenue of £3.2bn. The news sent shares up 5% to settle at 1% up on the previous close.
Biggest property fund withdrawals since Brexit vote
Property funds have been hit by the most investor withdrawals in a week since the Brexit vote in 2016. Data compiled by funds network Calastone reveals that savers have pulled a net £193m out of property funds in the week since M&G suspended its £2.5bn Property Portfolio following a rush of withdrawals. Around £60m was withdrawn within 24 hours of the M&G announcement, with subsequent net daily outflows ranging between £23m and £37m. The figures have fuelled concerns that other funds will be suspended.
Hammerson sells Paris site
Shopping centre owner Hammerson has sold its majority stake in Paris complex Italie Deux in the French capital to Axa Investment Managers for £362m, as it looks to turn around its fortunes. Hammerson has seen its share value slide more than 20% over the past year as it swung to a £319.8m loss in the six months to June 30 from a £55.7m profit for the same period in 2018.
Superdry slips to loss but margins improve
Superdry's first-half sales were down 11% amid a pre-tax loss of £4.2m, despite gross margins improving by 2.5 percentage points. Revenue declined in the six months to October 26th and the retailer also racked up a debt pile of £9.3m compared to a cash position of £19.2m in 2018. The group's balance sheet was hit by a £3.9m "isolated error" related to its accounting of inventory and a £6.9m charge to cover bad debts associated with its loss-making joint venture in China. Superdry said it expects second-half sales to decline by "low single digits" and that full-year sales would as a result fall by around 5%.
Dixons Carphone narrows losses despite sales drop
Dixons Carphone narrowed its losses in its latest half-year performance but a turnaround strategy took its toll on profits, the mobile phone seller said. In the six months to October 26th, the group made a pre-tax loss of £86m, an improvement on the £440m loss of a year earlier. This year's figures include a £26m charge reflecting lower "network receivables", or money owed by contract customers, and a provision of £30m to cover regulatory costs. Overall UK & Ireland electricals revenue dropped 1%, although mobile revenue in the home markets declined 18%, hurt by a 10% drop in like-for-like sales.
Championship clubs posting record losses
Championship clubs have run up "frightening" losses as they increase spending on player and staff wages in an attempt to reach the Premier League. Championship sides ran up a record high total of £307m in pre-tax losses in 2017-18 despite revenue of £749m. Separately, The Premier League has appointed interim chief executive Richard Masters on a full-time basis.
Conservatives win majority in General Election
The Conservative Party headed by Boris Johnson have won an overall majority in the UK General Election. The BBC called the result at just after 5.00am after the party passed the threshold needed to gain full control of the House of Commons. As things stand, the Tories have won 342 seats, with Labour collecting 200 seats, the SNP 46 seats, the Liberal Democrats 8 seats and other parties 22. Speaking to supporters after retaining his Uxbridge and South Ruislip constituency, Mr Johnson said the result had given him a "powerful new mandate" to deliver on its manifesto. He said: "It does look as though this One Nation Conservative government has been given a powerful new mandate to get Brexit done." He added that the Government would "recruit 50,000 more nurses and 6,000 more GPs, and we will build 40 new hospitals." Elsewhere, Jeremy Corbyn said that he will not lead Labour into the next election, saying the party's performance was "very disappointing". He said that the issue of Brexit had "polarised" politics and "overridden so much of normal political debate". The party lost seats in its Northern heartlands which have traditionally been Labour for decades including Workington, Darlington and Sedgefield – or in the case of Bishop Auckland and Blyth Valley for the first time ever. Mr Corbyn was urged to step down by some MPs within his party. Elsewhere, Jo Swinson, who only became the Lib Dem leader in July, lost her seat in Dunbartonshire East to the SNP by 149 votes. Speaking after the result, Ms Swinson blamed the national result on a "wave of nationalism" and said it would bring dread and dismay for millions of people. The SNP's leader Nicola Sturgeon, hailing her party's results, said Scotland had sent a "clear message" on a second independence referendum. Scotland's First Minister said the results had exceeded her expectations. Nigel Farage claimed that the Brexit Party has "killed the Liberal Democrats and hurt the Labour party". His party is unlikely to win any seats, but Mr Farage said he was happy that his party had killed off hopes of another referendum. In Northern Ireland, Nigel Dodds, the leader of the DUP, lost his Belfast North seat to Sinn Fein.
Minouche Shafik is favourite to succeed Carney
London School of Economics head Minouche Shafik has emerged as the favourite to succeed Mark Carney as the Governor of the Bank of England, according to a Treasury source.
Daily News Roundup: Monday, 16th December 2019
Daily News Roundup: Thursday, 12th December 2019
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redpajama_set_name: RedPajamaCommonCrawl


What is the energy of an earthquake?
We can directly measure the first of these energies, that in seismic waves. The other types of energy cannot be measured directly, but can only be indirectly inferred.
Charles Richter was one of the first scientists to propose an equation to compute the seismic wave energy from earthquakes. We can use his approach to compute the numbers in the following table, where we use Megatons of TNT as the unit of energy. The atomic bomb dropped on Hiroshima in 1945 released the equivalent of 16 Kilotons = 0.016 Megatons of TNT, about the energy equivalent of a magnitude 6 earthquake. The largest hydrogen bomb ever detonated was the Tsar bomba device exploded by the Soviet Union on October 30, 1961, with an energy equivalent of about 50 Megatons of TNT.
Two earthquakes occurred on the same day. Are they related?


text:
Q: Django 1.7 datamigration and user groups I'm trying to implement a datamigration using django 1.7 native migration system. Here is what I've done.
# -*- coding: utf-8 -*-
from __future__ import unicode_literals

from django.db import migrations

def create_basic_user_group(apps, schema_editor):
    """Forward data migration that create the basic_user group

    """
    Group = apps.get_model('auth', 'Group')
    Permission = apps.get_model('auth', 'Permission')
    group = Group(name='basic_user')
    group.save()

    perm_codenames = (
        'add_stuff',
        '...',
    )

    # we prefere looping over all these in order to be sure to fetch them all
    perms = [Permission.objects.get(codename=codename)
             for codename in perm_codenames]

    group.permissions.add(*perms)
    group.save()

def remove_basic_user_group(apps, schema_editor):
    """Backward data migration that remove the basic_user group

    """
    group = Group.objects.get(name='basic_user')
    group.delete()

class Migration(migrations.Migration):
    """This migrations automatically create the basic_user group.

    """

    dependencies = [
    ]

    operations = [
        migrations.RunPython(create_basic_user_group, remove_basic_user_group),
    ]

But when I try to run the migration, I got a LookupError exception telling me that no app with label 'auth' could be found.
How can I create my groups in a clean way that could also be used in unit tests ?

A: I've done what you are trying to do. The problems are:

*

*The documentation for 1.7 and 1.8 is quite clear: If you want to access a model from another app, you must list this app as a dependency:

When writing a RunPython function that uses models from apps other than the one in which the migration is located, the migration's dependencies attribute should include the latest migration of each app that is involved, otherwise you may get an error similar to: LookupError: No installed app with label 'myappname' when you try to retrieve the model in the RunPython function using apps.get_model().

So you should have a dependency on the latest migration in auth.

*As you mentioned in a comment you will run into an issue whereby the permissions you want to use are not created yet. The problem is that the permissions are created by signal handler attached to the post_migrate signal. So the permissions associated with any new model created in a migration are not available until the migration is finished.
You can fix this by doing this at the start of create_basic_user_group:
from django.contrib.contenttypes.management import update_contenttypes
from django.apps import apps as configured_apps
from django.contrib.auth.management import create_permissions

for app in configured_apps.get_app_configs():
    update_contenttypes(app, interactive=True, verbosity=0)

for app in configured_apps.get_app_configs():
    create_permissions(app, verbosity=0)

This will also create the content types for each model (which are also created after the migration), see below as to why you should care about that.
Perhaps you could be more selective than I am in the code above: update just some key apps rather than update all apps. I've not tried to be selective. Also, it is possible that both loop could be merged into one. I've not tried it with a single loop.

*You get your Permission objects by searching by codename but codename is not guaranteed to be unique. Two apps can have models called Stuff and so you could have an add_stuff permission associated with two different apps. If this happens, your code will fail. What you should do is search by codename and content_type, which are guaranteed to be unique together. A unique content_type is associated with each model in the project: two models with the same name but in different apps will get two different content types.
This means adding a dependency on the contenttypes app, and using the ContentType model: ContentType = apps.get_model("contenttypes", "ContentType").

A: As said in https://code.djangoproject.com/ticket/23422, the signal post_migrate should be sent before dealing with Permission objects.
But there is a helper function already on Django to sent the needed signal: django.core.management.sql.emit_post_migrate_signal
Here, it worked this way:
# -*- coding: utf-8 -*-
from __future__ import unicode_literals

from django.db import models, migrations
from django.core.management.sql import emit_post_migrate_signal

PERMISSIONS_TO_ADD = [
    'view_my_stuff',
    ...
]

def create_group(apps, schema_editor):
    # Workarounds a Django bug: https://code.djangoproject.com/ticket/23422
    db_alias = schema_editor.connection.alias
    try:
        emit_post_migrate_signal(2, False, 'default', db_alias)
    except TypeError:  # Django < 1.8
        emit_post_migrate_signal([], 2, False, 'default', db_alias)

    Group = apps.get_model('auth', 'Group')
    Permission = apps.get_model('auth', 'Permission')

    group, created = Group.objects.get_or_create(name='MyGroup')
    permissions = [Permission.objects.get(codename=i) for i in PERMISSIONS_TO_ADD]
    group.permissions.add(*permissions)

class Migration(migrations.Migration):

    dependencies = [
        ('auth', '0001_initial'),
        ('myapp', '0002_mymigration'),
    ]

    operations = [
        migrations.RunPython(create_group),
    ]

A: So, I figure out how to solve this problem and I get the following exit: get_model will only fetch Your model apps. I don't have sure about if this would be a good pratice, but it worked for me.
I just invoked the model Directly and made the changes.
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
from django.contrib.auth.models import Group

def create_groups(apps, schema_editor):
    g = Group(name='My New Group')
    g.save()

class Migration(migrations.Migration):

    operations = [
        migrations.RunPython(create_groups)
    ]

And then, just apply a /manage.py migrate to finish.
I hope it helps.

redpajama_set_name: RedPajamaStackExchange


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Fitted with jack and indicator for each line. The connections are made by mean of pairs of plugs and cords, with a ring-off indicator in series on each pair. A service plug is provided for ringing the subscriber required and telling him that his attention is sought. Lightning protectors, night bell with plug switch, hand micro-telephone, and generator are included in the equipment. Also provided with all the necessary terminals.


text:
This Might Be Scott Pruitt's Most Destructive Move Yet
"He's changing the internal rules of the game by which [the] EPA plays in order to rig it."
Rebecca Leber
AP Photo/Susan Walsh
Adopting a strategy successfully employed by the tobacco industry, Environmental Protection Agency Administrator Scott Pruitt announced a sweeping new regulation that would restrict the kinds of scientific studies the agency can use in developing its regulations.
The EPA administrator, who has come under fire from both parties for his personal conduct and ethical scandals, announced the changes at an EPA event Tuesday, where he was surrounded by conservative allies and pollution skeptics. "I know many of you here have supported this through a number of years," he told his audience, which did not include any reporters.
For years, EPA critics have pushed Congress to forbid the agency from relying on the studies that comprise the bulk of the independent research on fossil fuels on public health. Their strategy aims to sow doubt about the health effects of air pollution, while slowing down or weakening future rules targeting particulate matter and ozone. The proposed rule is modeled after bills introduced by Rep. Lamar Smith (R-Texas) in the House, which Pruitt described as the "codification of an approach."
The centerpiece proposal—restricting the EPA's use of the best available science in crafting policy—has been tried before. The tobacco industry laid out its strategy to combat "secret science" in the EPA's work to rein in cigarette smoke in a 1996 memo, according to The Intercept, claiming that it was impossible to know the accuracy of studies in which the researcher didn't make all their raw data public. The fossil fuel industry later borrowed the same strategy in an attempt to undermine the landmark 1993 Harvard "Six Cities" public health study on air pollution.
Many scientists note that, in practice, the policy will prove to be unworkable. It would drastically limit the kinds of studies available to regulators crafting the agency's air and water regulations, because many of these studies rely on sensitive medical records that cannot be made public, or may be owned by private institutions not keen on publishing proprietary information.
"The irony is whenever the industry does these studies from their own angle, do they reveal all the data? No. It becomes this very disingenuous cry of someone playing dirty."
The EPA's critics "are forever trying to cut this data and saying the broad scientific community aren't giving them all the information they need to disprove this data," says Dan Costa, former director of the EPA's Air, Climate, and Energy Research Program, who recently retired. "The irony is whenever the industry does these studies from their own angle, do they reveal all the data? No. It becomes this very disingenuous cry of someone playing dirty."
According to emails obtained by the Union of Concerned Scientists through FOIA requests, Nancy Beck, a top political appointee at the agency, had noted her concern about this approach in January to Richard Yamada, the top political appointee in the Office of Research and Development. She suggested that industry studies also would be affected by the changes. "Such a requirement would be incredibly burdensome," she wrote, "not practical."
The proposed rule that will be published in the Federal Register appears to get around this obstacle for industry studies by granting Pruitt the power to personally decide what exemptions can be made. The generous carveout allows the "Administrator to exempt significant regulatory decisions on a case-by-case basis if he or she determines that compliance is impracticable because it is not feasible…"
Once implemented, the rule would have a far-reaching impact on the agency's future policymaking and its rules on lead in drinking water and air pollution. For example, the agency is due to review regulations on particulate matter small enough to lodge into the lungs and cause serious health problems. "This is very transparently a way to attack the ozone and particulate matter standards," Gretchen Goldman, lead analyst with the Union of Concerned Scientists says. "It's written very prescriptively, focused on getting down to the inconvenient studies for those being regulated." Every five years the EPA is supposed to assess the best available science on ozone and particulate matter and decide action from there, but with this policy in place, the work would either be slowed down to a crawl as researchers try to obtain the raw data, or it would end up being based on a skewed sample of studies.
For the "Secret Science Reform" bill introduced by Rep. Smith in 2014, the Congressional Budget Office estimated the implementation costs would be $250 million a year—half of the Office of Research and Development's research budget. Though the EPA proposal is not as far-reaching, applying to economically significant regulations only, it is still burdensome for a cash-strapped agency. The CBO report estimated the cost would go up $10,000 to $30,000 for each study the agency uses; one way it suggests reducing costs is for the EPA to rely on "significantly fewer studies each year in support of its mission."
The most effective way Pruitt can hollow out the EPA, besides gutting its staff, is to attack the heart of how the agency uses and studies science—the bedrock of the EPA's work. And he's taken aim at science in other ways, as he highlighted in Tuesday's speech, such as changing the composition of the agency's independent science advisory boards. He claimed that he was removing advisers because they had a "conflict of interest" because they received EPA grants. But by removing them, he paved the way for more industry-sympathetic views on the boards that are designed to serve as an independent check on the agency's science.
Tuesday's move advances that goal. Joseph Goffman, a former EPA attorney who is now director of the Harvard Environmental Law program, told me he was especially struck by "how transparent Pruitt is about rigging the process: Rigging the membership of the science boards, rigging the range of studies that will be incorporated in agency decision-making. And in both cases [he's] excluding sources of information or expertise that would lead to outcomes that Pruitt doesn't prefer."
Goffman thinks Pruitt's predecessors never went as far as Pruitt to change the agency's internal processes to suit their political purposes. "He's changing the internal rules of the game by which [the] EPA plays in order to rig it."
Internal Emails Show How EPA Officials Lobby For Their Former Employers
Megan Jula
New Lawsuit Targets EPA Over Audit Scott Pruitt Has Tried to Keep Secret


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Complete Genome Sequence of Treponema pallidum, the Syphilis Spirochete Claire M. Fraser et al. Science 281, 375 (1998); DOI: 10.1126/science.281.5375.375
This copy is for your personal, non-commercial use only.
If you wish to distribute this article to others, you can order high-quality copies for your
colleagues, clients, or customers by clicking here.
Permission to republish or repurpose articles or portions of articles can be obtained by
following the guidelines here.
The following resources related to this article are available online at
www.sciencemag.org (this information is current as of March 30, 2014 ):
Updated information and services, including high-resolution figures, can be found in the online
version of this article at:
http://www.sciencemag.org/content/281/5375/375.full.html
This article cites 77 articles, 42 of which can be accessed free:
http://www.sciencemag.org/content/281/5375/375.full.html#ref-list-1
This article has been cited by 525 article(s) on the ISI Web of Science
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Science (print ISSN 0036-8075; online ISSN 1095-9203) is published weekly, except the last week in December, by the
American Association for the Advancement of Science, 1200 New York Avenue NW, Washington, DC 20005. Copyright
1998 by the American Association for the Advancement of Science; all rights reserved. The title Science is a
registered trademark of AAAS.
R ESEARCH
A RTICLES
Complete Genome Sequence of Treponema pallidum, the Syphilis Spirochete
Claire M. Fraser,* Steven J. Norris, George M. Weinstock,
Owen White, Granger G. Sutton, Robert Dodson,
Michelle Gwinn, Erin K. Hickey, Rebecca Clayton,
Karen A. Ketchum, Erica Sodergren, John M. Hardham,
Michael P. McLeod, Steven Salzberg, Jeremy Peterson,
Hanif Khalak, Delwood Richardson, Jerrilyn K. Howell,
Monjula Chidambaram, Teresa Utterback, Lisa McDonald,
Patricia Artiach, Cheryl Bowman, Matthew D. Cotton,
Claire Fujii, Stacey Garland, Bonnie Hatch, Kurt Horst,
Kevin Roberts, Mina Sandusky, Janice Weidman,
Hamilton O. Smith, J. Craig Venter
The complete genome sequence of Treponema pallidum was determined and shown to be 1,138,006 base pairs containing 1041 predicted coding sequences (open reading frames). Systems for DNA replication, transcription, translation, and repair are intact, but catabolic and biosynthetic activities are minimized. The number of identifiable transporters is small, and no phosphoenolpyruvate:
phosphotransferase carbohydrate transporters were found. Potential virulence factors include a family of 12 potential membrane proteins and several putative hemolysins. Comparison of the T. pallidum genome sequence with that of another pathogenic spirochete, Borrelia burgdorferi, the agent of Lyme disease, identified unique and common genes and substantiates the considerable di- versity observed among pathogenic spirochetes.
Venereal syphilis was first reported in Europe in the late 1400s (1), coincident with the return of Columbus from the New World. The disease quickly reached epidemic pro- portions in Europe and spread across the world during the early 16th century with the age of exploration. Syphilis was ubiquitous by the 19th century and has been called the acquired immune deficiency syndrome of that era (2). Syphilis is characterized by mul- tiple clinical stages and long periods of latent, asymptomatic infection. The primary infec- tion is localized, but organisms rapidly dis- seminate and cause manifestations through- out the body, including the cardiovascular
C. M. Fraser, O. White, G. G. Sutton, R. Dodson, M. Gwinn, E. K. Hickey, R. Clayton, K. A. Ketchum, S. Salzberg, J. Peterson, H. Khalak, D. Richardson, T. Utterback, L. McDonald, P. Artiach, C. Bowman, M. D. Cotton, C. Fujii, S. Garland, B. Hatch, K. Horst, K. Roberts, M. Sandusky, J. Weidman, H. O. Smith, and J. C. Venter are with The Institute for Genomic Re- search, 9712 Medical Center Drive, Rockville, MD 20850, USA. S. J. Norris, G. M. Weinstock, E. Soder- gren, J. M. Hardham, M. P. McLeod, J. K. Howell, and M. Chidambaram are at the University of Texas Health Science Center, Departments of Microbiology and Molecular Genetics, Pathology and Laboratory Medi- cine, and the Center for the Study of Emerging and Reemerging Pathogens, Post Office Box 20708, Hous- ton, TX 77225, USA.
*To whom correspondence should be addressed. E- mail: tpdb@tigr.org
and nervous systems (3). Although effective therapies have been available since the intro- duction of penicillin in the mid-20th century, syphilis remains an important global health problem. Treponema pallidum is the causative agent of syphilis. It is a spirochete, a helical to sinusoidal bacterium with outer and cyto- plasmic membranes, a thin peptidoglycan layer, and flagella that lie in the periplasmic space and extend from both ends toward the middle of the organism. Recent pulsed-field gel electrophoresis studies (4) have shown that T. pallidum contains a circular chromo- some of about 1000 kilobase pairs, making it
one of the smallest prokaryotic genomes. De- spite its importance as an infectious agent, relatively little is known about T. pallidum in comparison with other bacterial pathogens (5). The organism is an obligate human par- asite that cannot be cultured continuously in vitro (6 ). Mechanisms of T. pallidum patho- genesis are poorly understood. No known virulence factors have been identified, and the outer membrane is mostly lipid with a paucity of proteins (7 ). Consequently, exist- ing diagnostic tests for syphilis are subopti- mal, and no vaccine against T. pallidum is available. Spirochetes represent a phylogenetically ancient and distinct bacterial group. Both T.
pallidum and Borrelia burgdorferi, the caus- ative agent of Lyme disease, are similar in having relatively small genomes and surviv- ing only in association with a host. However, they are not closely related and probably evolved independently from a more complex ancestor by loss of unnecessary genes and acquisition of new functions that promoted survival in the host environment. Comparison of the T. pallidum and B. burgdorferi ge- nomes (8) allows assessment of biological diversity within this group of bacteria. Genome analysis. The genome of T. pal- lidum subsp. pallidum (Nichols) was se- quenced by the whole genome random se- quencing method as described (8–10). The T. pallidum genome is a circular chromosome of 1,138,006 base pairs with an average G C content of 52.8% (Figs. 1 and 2). There are a total of 1041 predicted open reading frames (ORFs), with an average size of 1023 bp, representing 92.9% of total genomic DNA. Predicted biological roles were assigned to 577 ORFs (55%) by the classification scheme adopted from Riley (11); 177 ORFs (17%) match hypothetical proteins from other spe- cies, and 287 ORFs (28%) have no database match and presumably represent novel genes (Fig. 1 and Table 1). Ninety T. pallidum ORFs of unknown function match chromo- some-encoded proteins in B. burgdorferi (8); however, no T. pallidum ORFs match B. burgdorferi plasmid-encoded proteins, sug- gesting that the plasmid proteins may be unique to Borrelia species (8). The average size of the predicted proteins in T. pallidum is 37,771 daltons, ranging from 3235 to 172,869 daltons, and the mean isoelectric point for all predicted proteins is 8.1, ranging from 3.9 to 12.3, values similar to those observed in other bacterial species (8, 9). Forty-two paralogous gene families con- taining a total of 129 ORFs (12%) were identified in T. pallidum (Fig. 1). Fifteen families contain 44 genes that have no as- signed biological role. Thirty families have only two members. The largest family, with 14 members, consists of proteins with aden- osine triphosphate (ATP)–binding cassettes in ABC transport systems. Within 13 gene families are 16 clusters of adjacent genes that may represent duplications in the T. pallidum genome. All 61 triplet codons are used in T. palli- dum. There is a bias for G or C in the third codon position in T. pallidum, in contrast to an A or T bias in this position in B. burgdor- feri. This observation is consistent with the G C content in the T. pallidum genome being almost twice that in the B. burgdorferi ge- nome. The disparate G C content between the spirochete genomes creates a bias in over- all codon usage, resulting in a difference in amino acid composition in the predicted cod- ing sequences.
Origin of replication. Two criteria were used to identify a replication origin in T. pallidum: the co-localization of genes (dnaA, dnaN, recF, and gyrA) often found near the origin in prokaryotic genomes and GC skew (12) (Fig. 2). On the basis of these results, we designated base pair 1 of the T. pallidum ge- nome in an intergenic region of the chromo- some that is located within the putative origin of replication. Sixty-four percent of the coding se- quences in the T. pallidum genome are aligned in the direction of replication, with the point of transcriptional divergence lo- cated near the putative origin between clpP and dnaA (Figs. 1 and 2). A number of codons occur in coding sequences aligned in the direction of replication at significant- ly higher frequencies than expected ( P 5.3 e 27 ), including TTG (Leu), GCG (Ala), CGT (Arg), GTG (Val), and TGT (Cys). Codons that are overrepresented are also found in the most highly skewed oligomers (GGAGCGTG, TGTGTGTG, GTGTGTGC, TTTTTTGT, and GGTGTGTG). Codon adaptation index (CAI), which is designed to be a relative measure of transla- tional efficiency (13), was computed for T. pallidum with the codon frequencies from the ribosomal proteins, the translation elongation factors, and glyceraldehyde-3-phosphate de- hydrogenase. Proteins with a high CAI are presumably highly expressed in exponential growth (13). The distribution of CAI scores in T. pallidum ORFs (13) exhibits a strand- dependent switch in magnitude around the origin of replication (Fig. 2). In both T. pal- lidum and B. burgdorferi, there is a marked difference in CAI values (high versus low) for genes on opposite strands of the chromo- some, with genes transcribed in the direction of replication exhibiting a high CAI. Transcription and translation. Trepo- nema pallidum contains a basic set of genes for transcription and translation that includes homologs to the , , and subunits of the core RNA polymerase, five sigma factors ( 24 , 28 , 43 , 54 , and 70 ), and five genes that encode proteins involved in transcript elongation and termination (nusA, nusB, nusG, greA, and rho). Treponema pallidum is missing both a recognizable 38 (rpoS), which is the major sigma factor in stationary phase activated in response to oxidative and osmotic stress, and a 32 , which is involved in transcription of heat shock proteins. Forty-four tRNA species, organized into eight clusters containing 25 genes plus 19 single genes, were identified (Figs. 1 and 2). Two ribosomal RNA (rRNA) operons are present in the genome. Their organization is the same as that commonly found in eubac- teria (16S-tRNA-23S-5S) (14), in contrast with the unusual arrangement seen in B. burgdorferi (8, 15). Both T. pallidum rRNA
operons are transcribed in the direction of replication. All tRNA synthetase genes were identi- fied with the exception of glutaminyl-tRNA synthetase, similar to B. burgdorferi (8). It is likely that glutamyl-tRNA synthetase amino- acylates tRNA Gln with glutamate followed by transamidation by Glu-tRNA amidotrans- ferase (16 ). Two distinct lysyl-tRNA syn- thetase (LysS) species are present in T. pal- lidum, a class I type most similar to those in euryarchaea and B. burgdorferi (17 ) and a class II type most similar to those in eubac- teria and eukaryotes. The class II LysS in T. pallidum represents a COOH-terminal frag- ment of Escherichia coli LysS. A region near the NH 2 -terminus of LysS binds the antico- don of the tRNA and is crucial for its activity (18). Thus, it is likely that the class II LysS is nonfunctional and may be in the process of being lost from the genome. Replication, repair, recombination, and restriction-modification systems. The com- plement of genes for DNA replication in T. pallidum is similar to that in other minimal genomes such as Mycoplasma genitalium and B. burgdorferi. Orthologs for the , , , , and subunits of E. coli DNA polymerase III are present. Treponema pallidum has ho- mologs of one type I topoisomerase (topA) and one type II topoisomerase (gyrAB), but unlike B. burgdorferi, it is missing topoisom- erase IV, which is involved in chromosome segregation. However, chromosome segrega- tion in T. pallidum may proceed by an alter- native mechanism that involves the binding of hemimethylated DNA to the cytoplasmic membrane. This idea is supported by the presence of DNA adenine methyltransferase (dam) in T. pallidum but not in B. burgdorferi
DNA repair in T. pallidum includes the major known pathways of uvr excision re- pair, mutL/mutS mismatch repair, mutY, and dat. The T. pallidum genome encodes ho- mologs of the recF pathway of recombination (recFGJNR) but lacks homologs to sbcB (exoI) as well as recB, recC, and recD. Thus, homologous recombination resembles the recF pathway of E. coli. The converse is true in B. burgdorferi, where there are homologs of recBCD but not the recF pathway genes (8). Treponema pallidum contains an A- or G-specific adenine glycosylase (mutY), rec- ognizes GA mismatches in duplex DNA, and excises adenine. No enzyme with similar ac- tivity has been identified in either M. geni- talium or B. burgdorferi. This difference may, in part, explain the lower G C content of the B. burgdorferi and M. genitalium ge- nomes as compared with T. pallidum. No recognizable genes encoding restriction or modification enzymes were found. Biosynthetic pathways. Treponema pal- lidum is an obligate parasite of humans. Con-
sistent with this property, previous physio- logic studies have shown that it has limited biosynthetic capabilities and requires multi-
ple nutrients from the host (20) (Fig. 3). The
T. pallidum genome encodes a pathway for
the conversion of phosphoenolpyruvate or pyruvate through oxaloacetate to aspartate (at the expense of glutamate), in accordance with the previous observation that most of the [ 14 C]glucose incorporated into amino acids was in the form of aspartate (21). Predicted pathways for the interconversion of aspartate and glutamine to glutamate, aspartate to as- paragine, glutamate to proline, and serine to glycine are also present. Treponema pallidum is unable to synthesize enzyme co-factors, fatty acids, and nucleotides de novo, similar to M. genitalium and B. burgdorferi. Deoxy- ribonucleotides can be obtained by reduction of ribonucleoside diphosphates through the action of ribonucleotide diphosphate reduc- tase and thioredoxin reductase. Transport. An organism such as T. pal- lidum, with limited biosynthetic capabilities, must have a repertoire of transport proteins with broad substrate specificity to obtain the necessary nutrients from the environment. The T. pallidum genome contains 57 ORFs (5% of the total) that encode 18 distinct transporters with predicted specificity for
amino acids, carbohydrates, and cations (Fig. 3 and Table 1). For the most part, these transport systems are of similar specificity to those found in M. genitalium and B. burgdor- feri (8); however, several important differ- ences are seen. Treponema pallidum has a broad spec- trum of amino acid transporters, although these transporters are different from those in
B. burgdorferi. For example, a transporter for
glutamate or aspartate in T. pallidum is most
similar to mammalian glutamate transporters. There are no phosphoenolpyruvate:phospho- transferase (PTS) systems in T. pallidum for the import of carbohydrates, in contrast to other bacterial species whose genome se- quences have been determined (8, 9). Ge- nome analysis predicts that T. pallidum has three ATP-binding cassette transporters with specificity for galactose (mglBAC) (22, 23), ribose (rbsAC), and multiple sugars (y4oQRS), respectively; however, these three transporters may display a broader substrate specificity. In E. coli, the mgl transporter displays affinity not only for galactose but also for glucose (24), and its expression is up-regulated in glucose-limiting conditions but repressed at high glucose concentrations (24). Treponema pallidum may also require an environment with limiting glucose con- centrations for maximal expression of this transporter. Treponema pallidum has no rec- ognizable inorganic phosphate (P i ) uptake system, unlike other bacteria studied by whole-genome analysis to date; therefore, up-
376 17 JULY 1998
take of glycerol-3-phosphate through the multiple sugar transporter may represent the primary means whereby T. pallidum obtains P i (Fig. 3). Treponema pallidum contains an ATP- binding cassette transporter with specificity for thiamine. Both thiamine and thiamine pyrophosphate (TPP) are substrates for the thiamine transporter in E. coli (25). This find- ing is of interest because T. denticola, T. vincentii, and Leptospira species require TPP for growth in vitro (26 ), which suggests that T. pallidum may also exhibit a growth de- pendency on TPP. The only recognizable TPP-dependent enzyme present in T. palli- dum is transketolase, which creates a link between the pentose phosphate pathway and glycolysis. Energy metabolism. The complement of transport proteins in T. pallidum suggests that it may use several carbohydrates as energy sources, including glucose, galactose, mal-
tose, and glycerol. Experimental evidence has demonstrated that only glucose, mannose, and maltose support the multiplication of T. pallidum in a tissue culture system (27). It is not known whether T. pallidum can use ami- no acids as a source of carbon and energy; however, the lack of necessary catabolic and anabolic pathway genes suggests that it would not be able to use such alternative compounds. Metabolic pathway analysis reveals that genes encoding all of the enzymes of the glycolytic pathway are present in T. pallidum, including hexokinase, which phosphorylates glucose and other hexose sugars (Fig. 3). Both M. genitalium and B. burgdorferi lack hexokinase; however, in these organisms, phosphorylation of hexoses is an integral part of the PTS uptake mechanism. Instead of the typical eubacterial phosphofructokinase and pyruvate kinase, T. pallidum contains ho- mologs of these enzymes that use pyro-
phosphate. Similar inorganic pyrophosphate (PP i )–dependent enzymes have been de- scribed in some bacteria, protists, protozoa, and plants (28). None of the genes encoding components of the tricarboxylic acid cycle or oxidative phosphorylation were identified, contrary to previous reports of the presence of cytochromes, flavoproteins, and some of the tricarboxylic acid cycle enzymes (20, 29); these may have represented contaminating rabbit components. Reducing power is prob- ably generated through the oxidative branch of the pentose phosphate pathway. This sim- plified metabolic strategy is similar to that seen in both M. genitalium (9) and B. burg- dorferi (8). Treponema pallidum, like B. burgdorferi, lacks a respiratory electron transport chain; therefore, ATP production must be accom- plished by substrate-level phosphorylation. As a result, membrane potential must be es- tablished by the reverse reaction of the ATP
P-type ATPase
K +
Cu +
ntpJ
glutamate/aspartate
TpF1
spermidine /putrescine
potABCD
troABCD
Mg ++
neutral amino acids
mgtCE
Ribose-5-P
D-alanine/glycine
Glucose-6-P
Na +
Ribulose-5-P
oadAB
Glyc-3-P
PENTOSE PHOSPHATE
6-P-gluconate
GLYCOLYSIS
L-glutamate
ADP + P i
Oxaloacetate
NUCLEOSIDES/NUCLEOTIDES
L-aspartate + -ketoglutarate
L-asparagine
dAMP, dCMP, dTMP
rAMP, rCMP, rUMP
MUREIN SYNTHESIS
Acetyl P
N-acetyl-Gln-1-P
dNDPs
rNDPs
UDP-N-acetyl-D-Gln
Phosphatidic acid
8 murein synthesis genes
dNTPs
rNTPs
ribose/
Phosphatidyl glyc -P
UDP-N-acetyl-Gln
rbsAC
D-glutamate
Phosphatidyl glycerol
D-alanine
mglABC
D-alanyl-D-alanine
Glycerol-3-P
PROTEIN SECRETION
malate /succinate/
fumarate
sec protein excretion
dctM
H +
glucose/ galactose/
leader peptidases
glycerol-P(?)
22 putative lipoproteins
Fig. 3. Solute transport and metabolic pathways in T. pallidum. A schematic diagram of a T. pallidum cell providing an integrated view of the transporters and the main components of the metabolism of this organism, as deduced from the genes identified in the genome. Presumed transporter specificity is indicated. Question marks indicate where particular uncertainties exist or
expected activities were not found. r, ribo; d, deoxy; AMP, adenosine mono- phosphate; CMP, cytosine monophosphate; NDP, nucleotide diphosphate; NTP, nucleotide triphosphate; TMP, thymidine monophosphate; UMP, uri- dine monophosphate; ADP, adenosine diphosphate; CoA, coenzyme A; UDP, uridine diphosphate; PRPP, phosphoribosyl-pyrophosphate.
synthase. In both spirochetes, the ATP syn- thase is of the V 1 V 0 type, most similar to those found in eukaryotic vacuoles and in archaea (30). Treponema pallidum has two V 1 V 0 -type ATP synthase operons, each con- taining seven genes (Table 1). The gene order in one operon (subunit E–ORF–subunit A–subunit B–subunit D–subunit I–subunit K) is identical to that seen in the ATP synthase operon in B. burgdorferi (8). The second operon in T. pallidum contains ATP synthase subunits A, B, D, E, F, I, and K. The differ- ence in subunit gene composition between these operons suggests that the ATP syn- thases may have different functions in the cell. One clue as to the functional role for the two ATP synthases is the presence of an oxaloacetate decarboxylase transporter that may be involved in extrusion of Na from the cell, creating a Na gradient (31). Such a gradient can be used to drive Na -dependent transporters similar to the amino acid trans- porters that are found in T. pallidum. Alter- natively, the Na gradient could be used to synthesize ATP in the same manner as the H gradient is used by an F 1 F 0 -type ATP synthase. Two ATP synthases have been identified in Enterococcus hirae, with speci- ficity for Na and H , respectively (32). Cellular processes. Treponema pallidum is microaerophilic and grows only at reduced concentrations of molecular oxygen (33). This most likely reflects a balance between an oxygen requirement for energy production and defects in protective mechanisms against reactive oxygen intermediates. Unlike B. burgdorferi, which is also microaerophilic, T. pallidum apparently lacks genes encoding su- peroxide dismutase, catalase, or peroxidase
Fig. 4. Dendrogram of members of the tpr protein family of T. pallidum. This unrooted distance dendrogram was generated from a multiple sequence alignment of the 12 T. pal- lidum tpr paralogs described herein and Msp sequences from three Treponema denticola strains (tdA, T. denticola OTK; tdB, T. denticola 35405; tdC, T. denticola 33520) (42).
activities that protect against oxygen toxicity. NADH oxidase is the only enzyme identified thus far that can account for O 2 utilization by T. pallidum. Treponema pallidum contains a basic set of heat shock proteins but lacks 32 , which is responsible for transcription of heat shock genes in other bacteria. This lack is consistent with previous reports that T. pallidum lacks a detectable heat shock response. There is no change in the amounts of GroEL or other proteins at increased temperatures (34). At least two heat shock proteins in T. pallidum (GroEL and DnaK) appear to be constitutive- ly expressed at high levels, which may miti- gate the need for a typical heat shock re- sponse (35). However, the observed thermal sensitivity of T. pallidum (6 ) may reflect the absence of a robust heat shock response in this organism. It is of interest that B. burg- dorferi, which also lacks a recognizable 32 , exhibits a heat shock response. The differen- tial response of the two spirochetes to in- creased temperatures suggests that a protein or proteins of unknown biological func- tion may be involved in this process in B. burgdorferi. Regulatory functions. Treponema palli- dum contains a minimal set of regulatory genes that encode two response-regulator two-component systems and several puta- tive transcriptional repressors of unknown specificity. Although T. pallidum does not have a sugar-specific PTS system, it does contain a homolog of enzyme I ( ptsI), a phosphocarrier protein HPr ( ptsH), an HPr(Ser) kinase ( ptsK), and two ptsN genes, which suggests that these proteins may function mainly as regulators. Gram-positive bacteria have a specific ATP-dependent protein kinase ( ptsK) that phosphorylates HPr on a serine residue (36 ). HPr(Ser P) and a DNA-bind-
ing protein then interact to mediate repression by binding specifically to DNA sequences, catabolite responsive elements found in the control regions of catabolite-sensitive oper- ons (36 ). These proteins in T. pallidum may function in a manner similar to that observed in Gram-positive bacteria. Escherichia coli and other Gram-negative organisms coordinate nitrogen and carbon utilization so that mechanisms of carbon re- pression do not block the uptake and use of organic nitrogen sources. Nitrogen-carbon utilization in E. coli is modulated by a regu- latory protein, PtsN, that displays similarity to the PTS enzymes IIA specific for fruc- tose and mannitol (37 ). Biochemical data suggest that PtsN does not phosphorylate car- bohydrates but instead serves as a positive regulator of organic nitrogen metabolism. Under such conditions, phosphoenolpyruvate (PEP)-dependent phosphorylation of PtsN occurs through the transfer of a phosphate group from PEP to enzyme I, then to a histi- dine residue on HPr, and finally to PtsN (37 ). The gene content of T. pallidum suggests that both ATP- and PEP-dependent protein phos- phorylation of HPr may integrate intracellular signals reflecting the metabolic state of the cell. However, these hypotheses remain to be demonstrated experimentally. These proteins may play alternative regulatory roles in T. pallidum as this organism displays limited transport and metabolic capacities. Motility and chemotaxis. Motility-asso- ciated genes are highly conserved in both T. pallidum and B. burgdorferi, consistent with the importance of this activity in these highly invasive spirochetes (23, 38). The 36 genes encoding proteins involved in flagellar struc- ture and function in T. pallidum are most similar to those in B. burgdorferi (8). They differ only in the number of proteins in the periplasmic flagellar filaments; T. pallidum
Fig. 5. Gene clusters found in both the T. pallidum and B. burgdorferi genomes. Graph values represent the number of T. pallidum gene clusters in which orthologous genes have the same organization in B. burgdorferi.
has three core proteins (FlaB1, FlaB2, and FlaB3), a sheath protein (FlaA), and two uncharacterized proteins (39), and B. burg- dorferi has a single core protein and sheath protein, whereas most other bacteria have only a core protein. Both spirochetes contain two copies of the flagellar motor switch pro- tein, FliG; however, the importance of this gene duplication is not known. Most of the flagellar genes in T. pallidum are found in four operons that contain between 2 and 16 genes, most similar to the arrangement seen
in B. burgdorferi. Treponema pallidum has retained a 28 ortholog and class II and class III motility promoters, whereas motility genes in B. burgdorferi appear to be transcribed through 70 initiation (8, 40). Treponema pal- lidum contains 13 chemotaxis genes that in- clude four methyl-accepting chemotaxis pro- teins with putative specificity for amino acids (aspartate, glutamate, and histidine) or carbohy- drates (glucose, ribose, and galactose).
Membrane proteins and lipoproteins. Freeze fracture studies (7 ) have shown that the outer membrane of T. pallidum contains a relatively small number of integral membrane proteins, a feature that may permit the organ- ism to evade the human immune response. Two candidate outer membrane proteins have been identified, but the cellular location and function of these proteins are a subject of some controversy (41). Although it is diffi- cult to identify outer membrane proteins with certainty, genome analysis of T. pallidum indicates the presence of only 22 putative lipoproteins, as compared with 105 in B. burgdorferi, consistent with results from ul- trastructural studies. Potential virulence factors. Treponema pallidum contains a large family of duplicat- ed genes (paralogs) (tprA-L) that encode pu- tative membrane proteins that may function as porins and adhesins (Figs. 2 and 4). This hypothesis is based on pair-wise and multiple sequence alignments of the T. pallidum gene family to a major outer sheath protein (Msp) from T. denticola that represents an abundant, highly immunogenic, pore-forming adhesin in the outer membrane (42). It is not yet known whether the tpr genes are expressed individually or coordinately or to what extent each gene is expressed. This gene family in T. pallidum is reminiscent of a 32-member paralogous gene family encoding outer mem- brane proteins in Helicobacter pylori (omp) (9). The two gene families share features besides possible porin and adhesin functions, the most striking being that both have mem- bers with regions of extensive sequence iden- tity. However, in both organisms, the homol- ogous regions do not always encompass the entire gene, so that some regions are identi- cal, but others are variable. As in the H. pylori family, one of the T. pallidum genes (tprA and L) contains a frameshift within a
small dinucleotide repeat that might be cor-
rected by slipped-strand mispairing. Multiple copies of the tpr genes may represent a mech- anism for generation of antigenic variation in
T. pallidum as is found in other pathogenic
bacteria, including Neisseria gonorrhoeae,
M. genitalium, relapsing fever borreliae, and
B. burgdorferi. Identification of the tpr fam-
ily of putative outer membrane proteins may provide new targets for vaccine development. Previous studies have indicated that T. pallidum does not produce lipopolysaccha- ride or potent exotoxins, although cytotoxic activity against neuroblasts and other cell types has been observed at extremely high concentrations of the bacterium (43). Ge- nome analysis has revealed five genes encod- ing proteins similar to bacterial hemolysins. These putative hemolysin orthologs also share varying degrees of amino acid sequence similarity with B. burgdorferi predicted pro- teins (8). None of the predicted hemolysins with similarity to T. pallidum sequences have been shown to be cytolytic in their purified
state, and it will be necessary to perform such studies with the T. pallidum proteins before a cytotoxic function can be assigned definitive- ly. A B. burgdorferi protein with hemolytic activity (BlyA) was described recently (44), but orthologous sequences are not present in
T. pallidum.
Comparative genomics. Four hundred seventy-six ORFs in T. pallidum (46%) have orthologs in B. burgdorferi; 76% of these ORFs have a predicted biological function. More than 40% of the orthologous genes in T. pallidum and B. burgdorferi are highly con- served in other bacteria (8, 9) and are in- volved in housekeeping functions such as transcription, translation, DNA replication, basic energy metabolism, flagellar structure and function, cell division, and protein secre- tion. Some of the genes of unknown function that are conserved in the spirochetes but not recognized in the other available genome se- quences are likely to represent "spirochete- specific" genes that contribute to the unusual structural properties of these bacteria. One hundred fifteen ORFs shared by T. pallidum and B. burgdorferi encode proteins of unknown biological function; and almost 50% of these appear to be unique to the spirochete group. This set of proteins with a limited phylogenetic distribution may include important determinants of spirochete struc- ture and physiology and may, for example, be involved in the ability of both T. pallidum and B. burgdorferi to infect humans and cause chronic, disseminated disease. Three hundred four of the ORFs shared by the two spirochetes are located in gene clus- ters with conserved gene order (Fig. 5). Sev- eral conserved clusters contain ORFs encod- ing ribosomal proteins, including the largest cluster containing 27 ORFs, whereas other
important clusters encode proteins for the flagella, adenosine triphosphatases (ATPases), and cell division, as well as groups of pro- teins that are not obviously related. Further
study of the arrangement of these clusters in the two genomes may provide insight into
the evolution of the chromosomes of these
organisms. Of the 572 T. pallidum ORFs (54% of total) that are not shared with B. burgdorferi, more than 80% are of unknown biological function. This finding lends support to the concept of diversity within a single group of bacteria and underscores the fact that a con- siderable amount of T. pallidum biology is yet to be elucidated. Conclusion. Treponema pallidum has been a difficult organism to study experimen- tally because of its absolute dependence on a mammalian host for sustained growth and viability. The genomic sequence of T. palli- dum offers a wealth of basic information that would be difficult, if not impossible, to obtain by any other approach. A more complete understanding of the biochemstry of this or- ganism derived from genome analysis may provide a foundation for the development of a culture medium for T. pallidum, which opens up the possibility of future genetic studies.
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chloroform:isoamyl alcohol until the interface was free of visible debris. After a final extraction with chloroform and addition of 1 M ammonium acetate, the nucleic acid was precipitated from the aqueous phase by addition of two volumes of ethanol, pel- leted by centrifugation, washed once with 70% eth- anol, air-dried for 15 min at 37°C, resuspended in 100 l of TE buffer (10:1), and stored at 4°C. DNA concentration was determined by fluorometry. Elec- trophoresis of the DNA in 0.6% agarose gel (0.5 tris–boric acid–EDTA buffer) indicated that the DNA was 23 kb in size. Purity of the T. pallidum DNA was assessed by treatment of 3 l of the sample with Sal I, electrophoresis, Southern (DNA) blotting, and hybridization with a rabbit mitochondrial DNA probe. Although hybridizing bands were detectable, the amount of contaminating rabbit mitochondrial DNA was estimated to be 1% of the total DNA. For preparation of a small insert library in pUC 18 vector, 10 g of purified T. pallidum DNA was sheared by nebulization at 1.5 10 3 N/m 2 for 2 min and size fractionated on a 1.2% agarose gel. A library with an average insert size between 1.6 and 2.0 kb was prepared, and the T. pallidum genome was sequenced by a whole-genome random sequencing method pre- viously applied to other microbial genomes (8, 9). An about sevenfold genome coverage was achieved by generating 14,464 sequences with an average edited length of 525 bases. Sequences were assembled with TIGR Assembler, resulting in a total of 130 assemblies containing at least two sequences, which were clus- tered into 30 groups on the basis of linking informa- tion from forward and reverse sequence reads. All T. pallidum sequences that had been mapped previously were searched against the assemblies in an attempt to order the contig groups. Sequence and physical gaps for the chromosome were closed as previously described (8, 9). A total of 676 sequencing reactions were necessary to complete genome closure. At the completion of the project, less than 1% of the chro- mosome had single-fold coverage. Coding regions (ORFs) were identified with compositional analysis that used an interpolated Markov model based on variable length oligomers [S. Salzberg, A. Delcher, S. Kasif, O. White, Nucleic Acids Res. 26, 544 (1998)]. ORFs of 600 bp were used to train the Markov model, as well as T. pallidum ORFs from GenBank. Once trained, the model was applied to the complete T. pallidum genome sequence. ORFs that overlapped were visually inspected and, in some cases, removed. All putative ORFs were searched against a nonredun-
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We thank A. R. Kerlavage for preparation of Fig. 2;
D. Soll and M. H. Saier Jr. for helpful discussions; M.
Heaney, J. Scott, and A. Saeed for software and
database support; and B. Vincent, D. Maas, and V.
Sapiro for computer system support. Supported by
NIH grant AI31068 to GMW. Requests for reprints
should be sent to C.M.F. (e-mail: tpdb@tigr.org).
The annotated genome sequence and gene family
alignments are available on the World Wide Web
at www.tigr.org/tdb/mdb/tpdb/tpdb.html. Addi- tional information regarding the T. pallidum ge-
nome is available at utmmg.med.uth.tmc.edu/
treponema/tpall.html. The genome sequence has
been deposited with GenBank under accession
number AE000520.
6 March 1998; accepted 6 May 1998
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BackSt. Petersburg results
Ponce De Leon Hotel
95 Central Ave, St. Petersburg, FL, 33701, United States of America
A stay at Ponce De Leon Hotel places you in the heart of St. Petersburg, within a 15-minute walk of Museum of Fine Arts and Salvador Dali Museum. This hotel is 0.7 mi (1.1 km) from University of South Florida-St. Petersburg and 1.3 mi (2.2 km) from Tropicana Field.
Make yourself at home in one of the 74 air-conditioned rooms featuring flat-screen televisions. Complimentary wired and wireless Internet access keeps you connected, and satellite programming provides entertainment. Private bathrooms with shower/tub combinations feature complimentary toiletries and hair dryers. Conveniences include desks and coffee/tea makers, as well as phones with free local calls.
Take advantage of recreation opportunities such as a nightclub, or other amenities including complimentary wireless Internet access and a television in a common area.
Enjoy a satisfying meal at Ceviche serving guests of Ponce De Leon Hotel. Quench your thirst with your favorite drink at the bar/lounge.
Featured amenities include a 24-hour front desk, multilingual staff, and laundry facilities. Limited parking is available onsite.
Tampa Bay - 0.1 km / 0.1 mi
Pioneer Park - 0.1 km / 0.1 mi
The James Museum of Western & Wildlife Art - 0.1 km / 0.1 mi
Al Lang Stadium - 0.3 km / 0.2 mi
Jannus Live - 0.3 km / 0.2 mi
Sundial St. Pete - 0.4 km / 0.2 mi
Museum of Fine Arts - 0.4 km / 0.3 mi
St. Petersburg Museum of History - 0.5 km / 0.3 mi
Mahaffey Theater - 0.6 km / 0.3 mi
Demens Landing Park - 0.6 km / 0.4 mi
Florida Holocaust Museum - 0.7 km / 0.4 mi
Chihuly Collection - 0.7 km / 0.4 mi
Salvador Dali Museum - 0.9 km / 0.6 mi
Palladium Theater - 1 km / 0.6 mi
University of South Florida-St. Petersburg - 1.1 km / 0.7 mi
St. Petersburg, FL (SPG-Albert Whitted) - 0.8 km / 0.5 mi
St. Petersburg, FL (PIE-St. Petersburg-Clearwater Intl.) - 20.7 km / 12.9 mi
Tampa, FL (TPA-Tampa Intl.) - 33.8 km / 21 mi
Tampa, FL (TPF-Peter O. Knight) - 41.5 km / 25.8 mi
Sarasota, FL (SRQ-Sarasota-Bradenton Intl.) - 57.3 km / 35.6 mi
The preferred airport for Ponce De Leon Hotel is Tampa, FL (TPA-Tampa Intl.).
This property doesn't offer after-hours check-in. Guests arriving late won't be able to check in until the next morning. Early check-in is available prior to noon for a nominal fee. Please contact the hotel using the number listed on the reservation for more information.
Deposit: USD 109.00 per night
Nearby parking fee: USD 15.00 per night
-Parking (limited spaces)
-Total number of rooms - 74
-Nightclub


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Veterinary Clinic, no later than 1934, viewed from the north. Photo Credit: M.S.U. Physical Plant, whose site mistakenly claims it was "demolished around 1935," perhaps confusing it with the older Veterinary Laboratory.
This building should be considered notable among Edwyn Bowd's works, even though its form has been almost entirely obscured by later modification. Its long horizontal lines, flat roofs with broad overhangs, and a touch of stylized ornament in the pilaster caps (all of which are lost except for one fragment noted below), are elements borrowed from the Prairie School. Yet in this era Bowd was mainly working in the Neoclassical and Beaux-Arts styles, and this author cannot name another Bowd design that is at all similar to this one.
Anatomy Building, no later than 1934. Frame building to right is a poultry house.
Veterinary Clinic addition of 1939, viewed from the west in an undated photo prior to 1949. Anatomy Building is in the distance at left. At right beyond the vehicles is the west wing and center pavilion of the original 1915 construction, the latter topped with a new upper story and hipped roof. Photo Credit: M.S.U. Archives.
Main entrance of Giltner Hall, part of the 1952 addition, with its original oak doors and Collegiate Gothic detailing, August 2006. The brick-edged sidewalk with grassy median strip meets the entrance at an angle because it extends from the main axis of the center pavilion of the Natural Science building, across Farm Lane. Photo Credit: Kevin S. Forsyth.
A portion of the original Veterinary Clinic still exists within Giltner Hall, although it is difficult to recognize the century-old building that appears in the image at the top of this page. The Vet Clinic's west wing, now the westernmost part of Giltner, is topped with an additional story and gable-ended roof, and its window openings have been altered. Its east wing is hidden behind a loading dock and newer additions. Only one distinctive wall, the second floor east wall with its keystone arch and four decorative pilasters, is visible from the exterior—and is the only face of the center pavilion of the clinic not obscured by later additions.
This 3D Google Maps rendering shows a portion of Giltner Hall, viewed from the southeast. Behind the 8-fan cooling unit (which happens to be sitting on the roof of the Vet Clinic's east wing) is the east wall of the original two-story pavilion.


Royalty free music played on Yamaha drums. This groove is in 4/4 funky beat, and on a tempo of 100 BPM. The drums are accompanied by congas which adds a little extra to this music. The final recording was processed by a compressor (with high compression ratio) and a limiter to give a very energetic sound.
Tags: Drums, congas, drums, groove, loop, funk,..


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1957 Porsche 356A 1500 GS Carrera
2dr Speedster
Following the success of the original 356 (now known as the "Pre-A"), the 356A was introduced. It was part of factory designation "Technical Program 1" (T1), followed by a revision in 1957 that resulted in T2. An open Speedster version aimed at the U.S. market along with a high-performance four-cam Carrera GS model were offered in addition to the standard coupe, cabriolet and later Convertible D models.
Changes to the outside of the 356 were minimal, but a larger 1600cc engine was introduced along with revised suspension and wider tires. A keener eye will notice the addition of a rub strip below the doors and the use of enamel paint in place of lacquer. Interior changes were similarly minor with a flat-face dashboard following the contour of the now curved instead of bent windscreen. Other options were the provision for a modern radio, courtesy lighting and a dash clock.
For the 1957 model year, a revised T2 model was released with the exhausts now routing through the rear bumper over-riders. Mechanically, carburation was changed to Zeniths from the previous Solexes.
The 356A was available with a total of five different four-cylinder engines, ranging from the 1300cc unit with 44bhp to the 1500cc Carrera GS that made 100bhp. From its inception, the Porsche 356 was engineered and constructed to make the most of its competition pedigree. This shows in abundance in the road manners and handling. Whilst other manufacturers were using increased capacity engines to gain performance, Porsche concentrated on lightness and engineering balance to achieve these aims, in many cases out-performing comparative machinery with sometimes twice the horsepower.
Rust is the principle consideration of Porsche 356 purchase and ownership. Complex body construction methods ensured plenty of hidden areas where serious structural rust can take hold. Consequently, properly restored or sound original cars command a high premium. Any 356A is a desirable car. The car's long-standing appeal has been enhanced over the years by competition success and the growth of the Porsche brand as a whole.
Vehicle Length: 155.5 in
Wheelbase - Inches: 82.7 in
More 1957 Porsche 356A 1500 GS Carrera values
Protect your 1957 Porsche 356A from the unexpected.