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The U.S. Drug Enforcement Administration will reclassify marijuana as a “Schedule Three” drug on March 15, 2017, essentially legalizing medicinal cannabis in all 50 states with a doctor’s prescription, said a DEA lawyer with knowledge of the matter. http://longlivehealthtip.online/a-big-news-trump-administration-will-legalize-marijuana-and-cannabis-on-march-15-2017/
(Pick your favorite MJ StocK)! Mine is $NMUS. https://pro.agorafinancial.com/p/TEK_secretpotlife_0117/PTEKT301/?h=true Lots of people are going to get Rich$$ in this sector!!
Scientists Explore Extremophile Genome with SMRT Sequencing
Wednesday, March 1, 2017 A recent Nature publication from a large team of scientists in Europe, Canada, and the US reports the use of SMRT Sequencing to elucidate the genome of Fragilariopsis cylindrus, a single-celled eukaryotic diatom adapted to living in polar waters of the Antarctic Ocean. The work has implications for the biotechnology industry, which looks to extremophiles as a potential source of important enzymes.
“Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus” comes from lead author Thomas Mock, senior author Igor Grigoriev, and many collaborators at the University of East Anglia, Earlham Institute, Joint Genome Institute, University of California, Berkeley, and several other organizations. The project investigated how this diatom evolved to thrive in its extreme environment, frequently living in high salinity directly under sea ice.
To achieve this, the team started by sequencing the F. cylindrus genome using both Sanger and PacBio systems. For SMRT Sequencing, the scientists produced two libraries with different insert sizes (4 kb and 20 kb) and ran seven SMRT cells, which yielded 63-fold coverage of the genome. The team used the diploid-aware FALCON assembler, which generated a 59.7 Mb assembly with 745 primary contigs. In an analysis and comparison to the Sanger assembly, the scientists determined the PacBio assembly was highly accurate in sequence (ranging from 99.65% to 100%) and structure (through validation fosmid comparison).
F. cylindrus is characterized by highly divergent alleles, which represent nearly a quarter of its genome. An analysis of those genes determined that the “divergent alleles were differentially expressed across environmental conditions, including darkness, low iron, freezing, elevated temperature and increased CO2,” the scientists report. “Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most pronounced condition-dependent expression, suggesting a correlation between diversifying selection and allelic differentiation.” The team hypothesized that allele diversification took place after the last glacial period and has been maintained because the variety of gene content allows for rapid adaptation to a changing environment.
The Earlham Institute issued a press release about the project, including this comment from scientist Pirita Paajanen: “This is the first time at EI that a genome of this type was assembled into chromosomes. It is only very recently that the technology has been developed to cope with such a highly heterozygous organism and the data show that this diatom does actually have a large amount of variation within their genes.” http://www.pacb.com/blog/scientists-explore-extremophile-genome-smrt-sequencing/
PacBio Finally Makes A Move It Desperately Needed To Make
Posted on February 17, 2017 -- https://mikethemadbiologist.com/
Alaska AG says feds couldn't overturn state's pot law!! ANCHORAGE, Alaska (AP) A representative for the Alaska attorney general's office says a change in how the federal government enforces its own marijuana laws would not affect state marijuana laws.
Department of Law spokeswoman Cori Mills says Alaska's law legalizing recreational marijuana wouldn't be overturned.
She commented after White House spokesman Sean Spicer suggested during a press briefing Thursday that President Donald Trump's administration might crack down on states that have legalized marijuana for recreational use.
Mills says there is a different federal law, and it will be up to the federal government how they want to enforce that.
Cary Carrigan is executive director of the Alaska Marijuana Industry Association.
He says it's too early to get too worked up about Spicer's comments, and that this sounds like an initial overture.
Carrigan says, "You have to see something happen before you can really react to it." http://www.ktuu.com/content/news/Alaska-AG-says-feds-couldnt-overturn-states-pot-law-414678163.html
http://seekingalpha.com/article/4049512-gw-pharma-oncology-potential-underrated?source=feed_f … $NMUS $GWPH … ($NMUS mentioned in article!) $GWPH Pharma Oncology Is Potential Underrated
Feb.24.17 | About: GW Pharmaceuticals (GWPH) http://seekingalpha.com/article/4049512-gw-pharma-oncology-potential-underrated (" I wrote about one of these others back in 2015, namely Nemus Bioscience (OTCQB:NMUS).")
The administration of President Donald Trump may ramp up enforcement of federal laws against recreational marijuana use,But White House spokesman Sean Spicer said the Trump administration may distinguish between medical and recreational use of the drug.That would be great news for NMUS!! https://www.adn.com/nation-world/2017/02/23/white-house-sees-greater-enforcement-of-federal-laws-against-recreational-marijuana/ http://www.cnn.com/2017/02/23/politics/white-house-marijuana-donald-trump-pot/index.html?Sr=fbtsr0223mariijuana
Pure Cannabis Concentrate & CBD Oil Product Demand Escalates in Legal Marijuana Market
8:30 am ET February 21, 2017 (PR Newswire) Print
As the United States and Canada continues to make strides towards legalization of cannabis, the demand for pure cannabis extracts for THC & CBD oils are steadily rising at a quick pace. Cannabis operators and purveyors are acquiring advanced licenses and other assets to gain an edge on competitors in the race to improve higher grades of cannabis concentrate and CBD extraction methods as the demand rises across North America and globally.
Lowest short interest Since Jun 30, 2015 9,789 shares!!! http://www.otcmarkets.com/stock/NMUS/short-sales Date
Short Interest
% Change
Avg. Daily Share Volume
Days to Cover
Split
New Issue
Jan 31, 2017 6,437 -65.30 126,406 1.00 No No
Jan 13, 2017 18,549 -27.44 275,253 1.00 No No
Dec 30, 2016 25,565 28.44 133,966 1.00 No No
Dec 15, 2016 19,905 -10.57 92,289 1.00 No No
Nov 30, 2016 22,257 49.18 187,352 1.00 No No
Nov 15, 2016 14,920 9.17 346,006 1.00 No No
Oct 31, 2016 13,667 -55.58 546,750 1.00 No No
Oct 15, 2016 30,766 7.26 8,200 3.75 No No
Sept 30, 2016 28,684 -18.30 8,932 3.21 No No
Sept 15, 2016 35,108 0.00 6,311 5.56 No No
(USA should follow)!-- News story
MHRA statement on products containing Cannabidiol (CBD)
From:Medicines and Healthcare products Regulatory Agency First published:13 October 2016Last updated:30 December 2016, see all updates
The Medicines and Healthcare products Regulatory Agency has issued an opinion on the regulatory status of products containing CBD
Logo for Gov UK
An MHRA spokesperson said:
We have come to the opinion that products containing cannabidiol (CBD) used for medical purposes are a medicine. Medicinal products must have a product licence (marketing authorisation) before they can be legally sold, supplied or advertised in the UK, unless exempt. Licensed medicinal products have to meet safety, quality and efficacy standards to protect public health.
If you use CBD and if you have any questions, speak to your GP or other healthcare professional.
We have written to UK CBD stockists and manufacturers to inform them of our view. We can provide regulatory guidance to any company who may wish to apply for a licence.
Update 1 November 2016
An MHRA spokesperson said:
While MHRA has given its opinion that products containing cannabidiol (CBD) used for medical purposes are medicines, we have also carefully considered the needs of individuals using CBD products to treat or manage the symptoms of medical conditions.
Our primary concern is patient safety. In order to ensure that products remain available until individuals have the opportunity to discuss their treatment with their doctor, companies now have until 31 December 2016 to voluntarily operate within the law, by withdrawing their existing products from the market, or working with MHRA to satisfy the legal requirements of the Human Medicines Regulations 2012.
We have today written to the manufacturers of CBD to make them aware of the timeline for engagement.
It is vital that medicines meet safety, quality and efficacy standards to protect public health.
Update 30 December 2016
An MHRA spokesperson said:
Our primary concern is patient safety and we wish to reiterate that individuals using cannabidiol (CBD) products to treat or manage the symptoms of medical conditions should discuss their treatment with their doctor.
MHRA will now work with individual companies and trade bodies in relation to making sure products containing CBD, used for a medical purpose, which can be classified as medicines, satisfy the legal requirements of the Human Medicines Regulations 2012.
Background
This opinion is restricted to products containing cannabidiol (CBD).
MHRA advised manufacturers and suppliers of CBD products that we were reviewing the regulatory status of CBD products prior to this opinion being issued.
The assessment of whether a product is classified as a ‘medicinal product’ is carried out in accordance with the definition of a medicinal product and is not based on whether the product is a risk to consumers. Once a valid application is made the product will be assessed in terms of its safety quality and efficacy in the medical claims made.
Unless exempt, medicines must have a product licence (marketing authorisation) before being placed on the market. Exempt products may be supplied as ‘specials’ by an appropriate prescriber. A ‘special’ can only be supplied in order to meet the special needs of an individual patient and may not be advertised. More information about the ‘specials’ process is available on our website.
MHRA have written to 18 companies to advise them of our opinion.
MHRA is responsible for regulating all medicines and medical devices in the UK. All our work is underpinned by robust and fact-based judgments to ensure that the benefits justify any risks. MHRA is a centre of the Medicines and Healthcare products Regulatory Agency which also includes the National Institute for Biological Standards and Control (NIBSC) and the Clinical Practice Research Datalink (CPRD). The Agency is an executive agency of the Department of Health. www.mhra.gov.uk
https://www.gov.uk/government/news/mhra-statement-on-products-containing-cannabidiol-cbd
(Congressional Cannabis Caucus is discussing this)New Bill Introduced to ReClassify Cannabis.http://marijuanastocks.com/new-bill-introduced-to-reclassify-cannabis/ (This has been thrown around for awhile AUG. 10, 2016)
https://www.nytimes.com/2016/08/11/science/obama-administration-set-to-remove-barrier-to-marijuana-research.html?hp&action=click&pgtype=Homepage&clickSource=story-heading&module=second-column-region®ion=top-news&WT.nav=top-news&_r=1
Out of Congress just now. Congressional Cannabis Caucus https://blumenauer.house.gov/cannabis-caucus
NMUS compared to CNBX-(Market Cap $230.5 Million $$)!--(Shares Outstanding 114.1 Million Shares)!--(52-Week Trading Range
.0225 cents to $2.27)! No Revenues$$.NO where near as good as NMUS!!!! https://finance.yahoo.com/quote/CNBX?ltr=1 CNBX is a biotechnology pharmaceutical company. The Company is engaged in pharmaceutical development. The Company is focused on development and licensing of cannabinoid-based treatments and therapies. It develops and markets various therapies and biotechnological tools aimed at providing relief from ailments that respond to active ingredients sourced from the cannabis plant. These tools include delivery systems for cannabinoids, personalized medicine therapies and procedures based on cannabis originated compounds, and bioinformatics tools. The Company's flagship product is CANNABICS SR. CANNABICS SR is a technology for a long acting oil capsule that provides administration of cannabis. CANNABICS SR is composed solely from food grade materials and delivers effects for over 10 to 12 hours. The delivery method enables a once per day dosing regimen of medical cannabis to patients. It has not generated revenues.
Strange trading? Friday I tried biding as much as half point above the bid,it took awhile,but I got most of what I wanted. Monday the bid was.395,my bid of.40 did not even show up on level 2, .395 was filled before my bid of.40!!
HOPE! Feb 8, 2017 New Bill Introduced to Re-Classify Cannabis. http://marijuanastocks.com/new-bill-introduced-to-reclassify-cannabis/
Nice! Thanks.
Referring to CT order-"It means they have really obtained something very substantial,to the point the can have it excluded from disclosing."(refers to the 8K filing on 1/13/17 Nemus yesterday recorded a confidential order that was granted by the SEC called a CT Order, Confidential Treatment Order: It is recorded at the SEC as of February 6, 2017:
CT ORDER -- Documents -- Confidential treatment order
Acc-no: 9999999997-17-000586 (34 Act) Size: 11 KB 2017-02-06 000-55136 17576344
You can find it here:
https://www.sec.gov/Archives/edgar/data/1516551/999999999717000586/filename1.pdf
Inside the confidential treatment order it refers to the 8K filing on 1/13/2017 which you can find below and the pdf further states that "Nemus Bioscience, Inc. submitted an application under Rule 24b-2 REQUESTING CONFIDENTIAL TREATMENT FOR INFORMATION IT EXCLUDED FROM THE EXHIBIT to a Form 8-K filed on
January 13, 2017.... through January 10, 2027" (FOR THE NEXT TEN YEARS) which means they have really obtained something very substantial to the point the can have it excluded from disclosing. That, my friends, is very rare.
Here is the 8K filing it was excluded from:
https://www.sec.gov/Archives/edgar/data/1516551/000164033417000091/nmus_8k.htm
On January 10, 2017, Nemus Bioscience, Inc. (the “Company”) entered into a license agreement (the “License Agreement”) with the University of Mississippi, School of Pharmacy (“UM”), pursuant to which UM granted the Company an exclusive, perpetual license, including the right to sublicense, under intellectual property related to UM5070, a platform of cannabinoid-based molecules to research, develop and commercialize products for the treatment of infectious diseases. The License Agreement culminates roughly one year of screening and target molecule identification studies especially focused on therapy-resistant infectious organisms like methicillin-resistant Staphylococcus aureus (MRSA). (So it must really be something special to exclude it for ten years and apparently more important that this MRSA therapy they DID disclose.)
It's definitely a good thing. Truly a case of when no news is good news /2017)! (This,thanks to Gee, yahoo conversation board)!
The term "confidential treatment order" sounds very mysterious and forbidding. In reality, it is a fairly mundane item relegated to the backwater of the financial world. Unfortunately, sometimes it seems that the government can be inconsistent and overly broad in granting the order.
These orders are granted by the Securities and Exchange Commission (SEC) under Rule 24b-2 of the Securities Exchange Act of 1934. They allow a company to request that any filing with the SEC be treated as confidential and not disclosed to the general public. A company must make a request on paper for such treatment and state the reasons for the request. (For more on this filing, read Policing The Securities Market: An Overview Of The SEC.)
Buffett Denied
There are many reasons that companies request this treatment. Berkshire Hathaway (NYSE:BRK.A) frequently asks for confidential treatment for the 13F forms that institutional money managers must file detailing the holdings of stock and other investments.
The SEC does not always grant such requests. One famous rejection involving Berkshire occurred in 2004, when the government turned down the request saying, "Berkshire's requests do not demonstrate that the failure to grant its requests for confidential treatment would be likely to cause substantial harm to its competitive position."
What's There To Hide?
So what is contained in some of these mysterious requests? Let's take a look.
On Sept. 16, CTC Media (Nasdaq:CTCM), a Russian broadcaster, was granted confidential treatment for an exhibit in its 10-Q filed for the quarter ended July 30. A closer look at the exhibit shows the confidential information to be its "TV Channel Advertising Budget Forecast". The SEC granted confidential treatment for three years for this top-secret information.
The Sinclair Broadcast Group (Nasdaq:SBGI) is another company granted confidential treatment for an exhibit in a 10-Q filing. A close look at the exhibit shows that the confidential information excluded was the amount of money that Sinclair received from The WB Television Network and the UPN Television Network to release it from a contract. Why is this confidential? As an investor, how can I evaluate whether Sinclair received enough consideration for this release?
Sometimes relevant financial information that would help an investor analyze a company is treated as confidential. First Marblehead (NYSE:FMD) was granted such a request for information contained in an exhibit to a 10-K filed on August 28, 2007. The exhibit contains much relevant information for an investor, including the dollar amount of marketing support required by JPMorgan Chase (NYSE:JPM) and details on fees paid to First Marblehead.
Bottom Line
An overly broad and inconsistent application of the confidential treatment order procedure does not benefit investors. I feel the government should err on the side of more disclosure as a general rule.
To dig further into corporate disclosure, read Show And Tell: The Importance Of Transparency.
Read more: SEC Allowing Too Many Secrets On Wall Street | Investopedia http://www.investopedia.com/stock-analysis/2008/sec-allowing-too-many-secrets-on-wall-street-ctcm-sbgi1015.aspx#ixzz4XyYUXDm9
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Like the stock(NBUS)but,too many pumping it right now!!
After hours-1609.01 hrs. 230000 shrs. @ .358 (HMMM)???
(8 K Report) The issuance of these Shares does not involve any public offerings.
No worries!!
It is in complete control of CROOKED MARKET MAKERS (Market Manipulators)!!!!!
Alpha and Omega Semiconductor Ltd. (AOSL) Upgraded to “Buy” by TheStreet
from a “hold” rating to a “buy” rating and set a $15.00 ----------- The stock has a consensus rating of “Buy” and a consensus price target of $12.88. http://www.americanbankingnews.com/2016/08/13/alpha-and-omega-semiconductor-ltd-aosl-upgraded-to-buy-by-thestreet/
MCRB As of 6/30/16 they had $370 MILLION in cash on hand, which is almost close to what their current market cap is!!! If I was short,I don`t think I could SLEEP?? (monday,monday,just wait)!
Your holding Short? Brave Trader!!? I`m holding long,if it goes down, I have a little room to get out!!
July 29, 2016- "Currently, the analyst consensus on Seres Therapeutics is Strong Buy and the average price target is $46.50, representing a 445.8% upside." -According to The Fly, cowen & Co. analyst Ritu Baral reiterated a Buy rating on Seres Therapeutics (NASDAQ: MCRB) today. The company’s shares opened today at $8.52.
Ritu Baral, 4 star ranked analyst.
According to TipRanks.com, Baral is a 4-star analyst with an average return of 4.6% and a 44.6% success rate. Baral covers the Healthcare sector, focusing on stocks such as Global Blood Therapeutics, Protalix Biotherapeutics, and Intra-Cellular Therapies.
http://www.analystratings.com/2016/07/29/seres-therapeutics-receives-a-buy-from-cowen-co-2/448028/
July 29th, 2016-- Research analysts at HC Wainwright started coverage on shares of Seres Therapeutics Inc. (NASDAQ:MCRB) in a research report issued to clients and investors on Friday. The brokerage set a “buy” rating and a $50.00 price target on the stock. HC Wainwright’s price target points to a potential upside of 39.78% from the company’s previous close. -- http://www.com-unik.info/hc-wainwright-begins-coverage-on-seres-therapeutics-inc-mcrb/
Tuesday, July 26, 2016-- Mitochondrial Genome Analysis Yields Novel Findings in Antiretroviral-Treated HIV Patients---- Scientists from Yale University and Memorial Sloan Kettering Cancer Center used SMRT Sequencing to determine whether antiretroviral therapies were triggering mitochondrial genome mutations in HIV patients. The results were recently published in HIV Medicine (“High frequency of mitochondrial DNA mutations in HIV-infected treatment-experienced individuals”).
The publication, from lead author Min Li, senior author Elijah Paintsil, and collaborators, reports results from an analysis of 71 people, including 47 HIV patients who had received antiretroviral therapy (about half had mitochondrial toxicity) and 24 healthy controls. DNA was isolated from peripheral blood mononuclear cells and mitochondrial genome sequencing performed on a PacBio System.
SMRT Sequencing was chosen for its long reads and accuracy, according to the authors. “PacBio technology overcomes some of the limitations of current next-generation sequencing platforms by providing significantly longer reads (> 1 kb), single molecule sequencing, and a single-pass error rate of < 15%,” Li et al. write. “Moreover, SMRT sequencing exceeds the consensus accuracy achieved by other sequencing methods because of the random nature of the errors. The SMRT sequencing achieves results with > 99.999% accuracy.”
The team found that HIV-infected patients, regardless of whether they experienced mitochondrial toxicity or not, had a higher frequency of mitochondrial mutations — in particular, large-scale deletions — than their healthy counterparts. However, they did not find statistically significant differences in mutation load between HIV patients with and without mitochondrial toxicity. “We did not observe mtDNA depletion in HIV-infected treatment-experienced patients with toxicity as expected,” the scientists report. “To our surprise, HIV-infected treatment-experienced patients with toxicity had significantly higher mRNA expression of Pol-? in comparison with HIV-infected treatment-experienced patients without toxicity (P < 0.05) and HIV-uninfected controls (P < 0.01). This contradicts the Pol-? inhibition theory.”
The authors attribute some of these novel findings to sequencing and analyzing the whole mitochondrial genome, whereas previous studies have taken less comprehensive approaches. The work also paves the way for increased use of peripheral blood mononuclear cells to characterize the biology of HIV patients, compared to the more commonly used invasive tissue biopsies.
Additional studies will be needed to follow up on these discoveries, the scientists note. “There are currently two proposed mechanisms to explain the association between mtDNA mutations and [antiretroviral therapy (ART)],” they write, “ART directly or indirectly provides a permissive environment for sporadic mtDNA mutagenesis; and ART pressure leads to clonal expansion of existing mutations.” http://www.pacb.com/blog/mitochondrial-genome-analysis-yields-novel-findings-antiretroviral-treated-hiv-patients/?platform=hootsuite
Posted July 19, 2016.-- SMRT Genome Assembly Corrects Reference Errors, Resolving the Genetic Basis of Virulence in Mycobacterium tuberculosis-- Abstract
The genetic basis of virulence in Mycobacterium tuberculosis has been investigated through genome comparisons of its virulent (H37Rv) and attenuated (H37Ra) sister strains. Such analysis, however, relies heavily on the accuracy of the sequences. While the H37Rv reference genome has had several corrections to date, that of H37Ra is unmodified since its original publication. Here, we report the assembly and finishing of the H37Ra genome from single-molecule, real-time (SMRT) sequencing. Our assembly reveals that the number of H37Ra-specific variants is less than half of what the Sanger-based H37Ra reference sequence indicates, undermining and, in some cases, invalidating the conclusions of several studies. PE_PPE family genes, which are intractable to commonly-used sequencing platforms because of their repetitive and GC-rich nature, are overrepresented in the set of genes in which all reported H37Ra-specific variants are contradicted. We discuss how our results change the picture of virulence attenuation and the power of SMRT sequencing for producing high-quality reference genomes.-- Tweets referencing this article:
Logan Fink
@logan_d_fink
RT @ZaminIqbal: PacBio sequencing of virulence-attenuated strain of M. tuberculosis to fix previously-studied assembly https://t.co/D8hmV6…
05:47PM
Afif Elghraoui
@afif_elghraoui
We @Valafarlab used @PacBio to correct attenuated Mtb strain reference genome. Much clearer genetics of virulence! https://t.co/ffMey7wv6p
05:40PM
Pacific Biosciences
@PacBio
RT @ZaminIqbal: PacBio sequencing of virulence-attenuated strain of M. tuberculosis to fix previously-studied assembly https://t.co/D8hmV6…
04:24PM
Dan
@danielkein
RT @ZaminIqbal: PacBio sequencing of virulence-attenuated strain of M. tuberculosis to fix previously-studied assembly https://t.co/D8hmV6…
04:00PM
Literature Bot
@litscraper
SMRT Genome Assembly Corrects Reference Errors, Resolving the Genetic Basis of Virulence in Mycobacterium… https://t.co/18vichfXdE
02:33PM
Keith Robison
@OmicsOmicsBlog
RT @ZaminIqbal: PacBio sequencing of virulence-attenuated strain of M. tuberculosis to fix previously-studied assembly https://t.co/D8hmV6…
12:42PM
Lei ZHANG
@jameslz
RT @ZaminIqbal: PacBio sequencing of virulence-attenuated strain of M. tuberculosis to fix previously-studied assembly https://t.co/D8hmV6…
11:59AM
Zamin Iqbal
@ZaminIqbal
PacBio sequencing of virulence-attenuated strain of M. tuberculosis to fix previously-studied assembly https://t.co/D8hmV6i67T
11:48AM
Carlos Magalhães
@CarlosARMagal
RT @PhilippBayer: SMRT Assembly Corrects Reference Errors, Resolving the Genetic Basis of Virulence in Mycobacterium tuberculosis https://t…
11:07AM
madhu
@madhubioinfo
RT @PhilippBayer: SMRT Assembly Corrects Reference Errors, Resolving the Genetic Basis of Virulence in Mycobacterium tuberculosis https://t…
10:44AM
Jan-Jaap Wesselink
@janjwesselink
RT @PhilippBayer: SMRT Assembly Corrects Reference Errors, Resolving the Genetic Basis of Virulence in Mycobacterium tuberculosis https://t…
10:26AM
Afonso Henriques
@AfonsoHenriques
RT @PhilippBayer: SMRT Assembly Corrects Reference Errors, Resolving the Genetic Basis of Virulence in Mycobacterium tuberculosis https://t…
10:25AM
Nick Loman
@pathogenomenick
RT @PhilippBayer: SMRT Assembly Corrects Reference Errors, Resolving the Genetic Basis of Virulence in Mycobacterium tuberculosis https://t…
10:23AM
Nouri Ben Zakour
@genomiss
RT @PhilippBayer: SMRT Assembly Corrects Reference Errors, Resolving the Genetic Basis of Virulence in Mycobacterium tuberculosis https://t…
10:18AM
Brian Forde
@fordebm
RT @biorxivpreprint: SMRT Genome Assembly Corrects Reference Errors, Resolving the Genetic Basis of ... https://t.co/zwqKLkCl2A #bioRxiv
10:04AM
Paul R Johnston
@Paul_R_Johnston
RT @PhilippBayer: SMRT Assembly Corrects Reference Errors, Resolving the Genetic Basis of Virulence in Mycobacterium tuberculosis https://t…
09:58AM
Philipp Bayer
@PhilippBayer
SMRT Assembly Corrects Reference Errors, Resolving the Genetic Basis of Virulence in Mycobacterium tuberculosis https://t.co/DBGJqqdSVP
09:51AM
Tim Stinear
@tstinear
RT @biorxivpreprint: SMRT Genome Assembly Corrects Reference Errors, Resolving the Genetic Basis of ... https://t.co/zwqKLkCl2A #bioRxiv
09:01AM
Anders G da Silva
@drandersgs
RT @biorxivpreprint: SMRT Genome Assembly Corrects Reference Errors, Resolving the Genetic Basis of ... https://t.co/zwqKLkCl2A #bioRxiv
06:47AM
Matteo Floris
@babamatteo
RT @biorxivpreprint: SMRT Genome Assembly Corrects Reference Errors, Resolving the Genetic Basis of ... https://t.co/zwqKLkCl2A #bioRxiv
06:05AM
Russell Orr
@RJSOrr77
RT @biorxivpreprint: SMRT Genome Assembly Corrects Reference Errors, Resolving the Genetic Basis of ... https://t.co/zwqKLkCl2A #bioRxiv
06:04AM
Biswapriya Misra
@BiswapriyaMisra
RT @biorxivpreprint: SMRT Genome Assembly Corrects Reference Errors, Resolving the Genetic Basis of ... https://t.co/zwqKLkCl2A #bioRxiv
04:51AM
Pooled Sequencing
@pooledseq
bioArXiv_ SMRT Genome Assembly Corrects Reference Errors, Resolving the Genetic Basis of Virulence in Mycobacterium… https://t.co/WpeikUJLC6
04:46AM
bxv_genomics
@bxv_genomics
SMRT Genome Assembly Corrects Reference Errors, Resolving the Genetic Basis of Virulence in Mycobacterium… https://t.co/zspgZEvd0S #genomics
04:17AM
bioRxiv
@biorxivpreprint
SMRT Genome Assembly Corrects Reference Errors, Resolving the Genetic Basis of ... https://t.co/zwqKLkCl2A #bioRxiv
04:00AM
bioRxiv Genomics
@biorxiv_genomic
SMRT Genome Assembly Corrects Reference Errors, Resolving the Genetic ... https://t.co/zYF3YdMK8g #biorxiv_genomic
04:00AM
http://biorxiv.org/content/early/2016/07/19/064840
Front End Developer
Pacific Biosciences, Menlo Park, CA, USA
Opening expires in 29 days 23:54:03
100 - 499 employees
PacBio develops comprehensive solutions for scientists that propel the field of genomics, improve science and research, and create positive impact globally.
Use Angular.js 2.0 to develop user-interfaces for designing and executing scientific analyses and managing the associated data. • Engage in an unusually multi-disciplinary organization of software and hardware engineers, bioinformaticians, chemists and molecular biologists.
https://www.workshape.io/p/pacific-biosciences/d494065b-129b-45df-8eeb-521d17286dbf
First Comprehensive View of Alternative Splicing in Sorghum Powered by SMRT Sequencing
Monday, July 11, 2016
A paper from scientists at Colorado State University and the National Center for Genome Resources provides an in-depth view of the transcriptome of sorghum, a crop that’s important for human and animal food and also shows potential as a biofuel. Through this project, the team produced a new isoform analysis pipeline for community use and identified novel genes, as well as far more alternative splicing than had been expected for this plant.
The publication, “A survey of the sorghum transcriptome using single-molecule long reads,” comes from lead author Salah Abdel-Ghany, senior author Anireddy Reddy, and collaborators. The researchers were particularly interested in alternative splicing and alternative polyadenylation, two mechanisms that increase transcript diversity and may help plants adapt to stress. “Despite the fact that several large-scale RNA-seq studies have been performed in plants to analyse [alternative splicing], currently it is not known how many distinct splice isoforms are produced,” the team writes. “This is primarily due to challenges associated with short-read sequencing in accurately reconstructing full-length splice variants.”
To directly observe full-length splice isoforms, they turned to long-read SMRT Sequencing to characterize the transcriptome of sorghum seedlings. The scientists also developed the Transcriptome Analysis Pipeline for Isoform Sequencing, or TAPIS, to identify alternative splicing events and evidence of alternative polyadenylation. “The analysis of sorghum Iso-Seq data uncovered over 7,000 novel [alternative splicing] events, ~11,000 novel splice isoforms, over 2,100 novel genes and several thousand transcripts that differ in 3' untranslated regions due to [alternative polyadenylation],” the team reports, noting that many of the novel genes are putative long non-coding transcripts. The total number of unique transcripts was nearly 28,000, covering more than 14,000 genes.
The scientists discovered a significantly higher rate of alternative splicing than had been expected for sorghum. “Previously, it was reported that pre-mRNAs of ~1,500 genes undergo [alternative splicing] in sorghum,” they note. “In this work, we demonstrate that this number is much higher.” Indeed, they found more than 10,000 alternative splicing events, compared with fewer than 3,000 included in existing gene models. The scientists performed a number of validation studies to confirm these and other novel findings and have made their TAPIS tool available for use in other organisms.
“Pacific Biosciences single-molecule long reads obtained using the Iso-Seq protocol offer a considerable advantage in transcriptome-wide identification of full-length splice isoforms and other forms of post-transcriptional regulatory events such as [alternative polyadenylation],” the team writes.--http://www.pacb.com/blog/first-comprehensive-view-alternative-splicing-sorghum-powered-smrt-sequencing/?platform=hootsuite
Wednesday, July 6, 2016- A paper just out in Nature Communications reports the de novo genome assembly and transcriptome of a Chinese individual, generated from long-read SMRT Sequencing and other technologies. The effort revealed nearly 13 Mb of sequence not included in the GRCh38 reference genome as well as novel gene and alternative splicing content not annotated in GENCODE.
“Long-read sequencing and de novo assembly of a Chinese genome” comes from lead author Lingling Shi at Jinan University and senior author Kai Wang from the University of Southern California, as well as many other collaborators in China and the US. The team was particularly interested in finding population-specific variants, including structural variants, which required the use of long-read sequencing. Assemblies based on short-read sequence data “may have inherent technical limitations in characterizing repeat elements that span longer than the read length, yet repeats and segmental duplications are known to cover approximately half of the human genome,” the scientists write. Using SMRT Sequencing and mapping technology from BioNano Genomics, “we perform detailed characterization of the HX1 genome and demonstrate that long-read sequencing can detect functional elements in human genomes that are missed by short-read sequencing.”
For the genome assembly, the team sequenced DNA from an anonymous Chinese individual (HX1) to 103x coverage, producing a 2.93 Gb genome with a contig N50 of 8.3 Mb. Included in the results were 206 Mb of alternative haplotypes that “were constructed along with the primary contigs,” Shi et al. write. Consensus accuracy for the assembly was 99.73%, matching the accuracy of the well-known NA12878 genome assembly. In an analysis of structural variants, the team found about 20,000 insertions and deletions, with half of them classified as short tandem repeats or mobile elements. Nearly 50 exonic deletions or insertions were specific to the HX1 genome, including one previously characterized deletion that has only been seen in the Asian population.
The team also developed a new gap-filling method to make use of all this sequence data. They determined that nearly 30% of gaps in the GRCh38 reference genome could be addressed with data from HX1. “The total length of filled or shortened gaps amounts to 7.1?Mb,” they report. “We further evaluated the repeat contents within the gaps that can be closed by us, and found that simple repeats and satellite sequences were significantly enriched within the closed gaps compared with GRCh38.”
Using the Iso-Seq method, the scientists also analyzed the transcriptome of this individual and detected more than 58,000 isoforms, including “57 isoforms at 42 loci that do not overlap with any GENCODE transcript,” they write. Follow-up studies for some of the more complex data — such as “a novel transcribed element with at least five exons and six isoforms” — validated these predicted splicing events. They also found at least two genes that have never been identified with short-read data. The team looked for disease-causing variants, finding two that were classified in ClinVar as pathogenic. However, “manual review of the literature cited in the two ClinVar records indicated that both of them represented erroneous database records,” the scientists report. “This analysis highlights the need for extreme caution in interpreting ‘pathogenic’ variants documented in variant databases.”
“In summary, while short-read-based alignment and variant calling based on reference genome remain a common practice to assay personal genomes, de novo assembly by long-read sequencing may reveal novel and complementary biological insights,” Shi et al. conclude. “Furthermore, long-read RNA sequencing may identify novel transcripts that can be missed by short-read RNA sequencing.”
http://www.pacb.com/blog/chinese-genome-assembly-smrt-sequencing-finds-novel-genes-recovers-missing-sequence/
Something new coming out! @ PACBIO CHAT,(koala genome)??!! 50x PacBio koala genome coming soon! Various koala genome assemblies show vast improvements with Pacbio sequencing. HMMM!!
University of Washington PacBio Sequencing Services--Notice: prices effective July 1, 2016--- Single Molecule Sequencing
The single molecule real-time (SMRT) sequencing is a third generation sequencing that allows for long-read sequencing. With the RSII technology, we are able to get an average of 4-6 Kb read length with 3-20 Kb library preparations, generating about 1200 Mb per SMRT cell. We are an HHMI-designated Pacific Biosciences (PacBio) sequencing site offering services for library preparation as well as sample sequencing.
https://pacbio.gs.washington.edu/
Published 30 June 2016--("PacBio reads generally had high coverage in a large proportion of regions that are poorly covered (≤5 ×) in Illumina data (Fig. 4b).") ("compared with the Illumina platform that enabled $1000 genomes, PacBio long-read sequencing is still relatively cost-prohibitive to be applied to personal genomes at large scale. With the continued decline in sequencing cost and the improvement in sequencing throughput per flow cell, this problem may be reduced in the future.") Once this improves,it will make the difference! (http://www.nature.com/ncomms/2016/160630/ncomms12065/full/ncomms12065.html?platform=hootsuite
Long-Read Assembly of the Aedes aegypti Aag2 Cell Line
Genome Resolves Ancient Endogenous Viral Elements
1PacBio, 1380 Willow Road, Menlo Park, CA 94025
2Department of Microbiology and Immunology, University of California, San Francisco, CA.-- http://www.pacb.com/wp-content/uploads/long-read-assembly-aedes-aegypti-aag2-cell-line-genome-resolves-ancient-endogenous-viral-elements.pdf
PacBio Sequencing Systems provide an unmatched depth of genetic information through exceptionally long sequencing reads (average > 10,000 bp) and the highest consensus accuracy available today. http://players.brightcove.net/61995988001/default_default/index.html?videoId=4925054467001
Wednesday, June 22, 2016
East Coast UGM: SMRT Sequencing Data for Carnivorous Plants, Hummingbirds, Mammalian Methylation, Repeat Expansions, and More--- Many thanks to the nearly 200 scientists who signed up for our East Coast User Group Meeting, and to the Institute for Genome Sciences for hosting us! The event was a hit with customers and PacBio staff alike, and discussions we heard in the hallways and during breaks told us there was some great knowledge exchange that should give labs inspiration for generating and analyzing their SMRT Sequencing data.
The day kicked off with a talk from our own Marty Badgett, senior product manager for the PacBio RS II System and Sequel System. He offered some historical perspective on throughput improvements over time for the SMRT Sequencing platforms (believe it or not, throughput has increased 100x in the past five years) and shared some data produced by the Sequel System. He spoke about the newly released SMRT Link software, which brings existing modules into an integrated workflow and adds components for data management. Badgett also alerted users to four upcoming enhancements: spin column size selection, on-chip additive cleanup, asymmetric SMRTbell templates, and active loading. With these and other changes, Badgett predicted that a 3 Gb genome could be assembled de novo with the Sequel System for $9,000 by next year and as little as $1,500 in 2018.
The event focused on our customers and the impressive results they’ve achieved with SMRT Sequencing. Jerry Jenkins from HudsonAlpha talked about high-quality de novo plant genomes — his team has released six FALCON-assembled plant genomes already, with more coming soon. The simple sequences and repetitive elements common to plant genomes are a major challenge, he said, noting that “it gives Illumina a fit and with PacBio it works well.” He said SMRT Sequencing has been “a game-changer” for his team when it comes to contiguity and completeness of assemblies. He gave several examples, including the bean Phaseolus vulgaris, for which a Sanger/454 assembly had a contig N50 of 39.5 kb while PacBio yielded 1.9 Mb. An analysis of cotton showed that a short-read assembly was missing nearly 500 Mb of sequence, which was recovered in the PacBio assembly.
Another plant presentation came from Victor Albert of the University at Buffalo, who intrigued attendees with his description of the carnivorous aquatic plant Utricularia gibba. Its genome was originally published in 2013 sporting 82 Mb in a fragmented assembly, but a new PacBio assembly shows the genome size is actually about 100 Mb and captures the data in fewer than 600 contigs. One challenge for this plant is its 3 Mb of rDNA repeats. “You can never assemble rDNA repeats,” Albert said of other sequencing platforms. “PacBio zips right through them.” He was delighted to find that the largest contig contained a full chromosome, and noted that the accuracy was excellent. “There’s no sense in doing any polishing with Illumina,” he added. With the new assembly, he’s able to explore telomeres, centromeres, and retrotransposons; he can also separate tandem duplication events from artifacts of previous whole genome duplications.
Rachael Workman from Johns Hopkins presented transcriptome data generated through the Most Interesting Genome SMRT Grant program for the ruby-throated hummingbird, Archilochus colubris. The team used the Iso-Seq method to analyze liver tissue to better understand this bird’s remarkable metabolism, finding 450,000 unique isoforms. While the full analysis is still underway, Workman shared some interesting examples, such as the complete coverage of a glucose transporter gene that shows quite a bit of divergence across avian species.
Continuing the avian theme, Duke’s Erich Jarvis spoke about the B10K project, an effort to sequence every species of bird on the planet. Jarvis’s area of interest is vocal learning, a trait shared by few organisms. His lab has found that PacBio sequencing produces genome assemblies of much higher quality than those from short-read data (in some cases increasing the contig N50 from as little as 30 kb to as much as 10 Mb, and reducing contig counts from more than 120,000 to about 1,000). In one example, he showed that a dopamine receptor that appeared to be lost by many bird species was actually conserved across them; it just wasn’t included in the short-read draft assemblies. Another example was of Egr1, with a promoter region that scientists had long wanted to study but wasn’t assembled in any existing bird genome. With PacBio sequencing, the region is fully assembled for the first time.
Tao Wu from Yale presented findings of A-base methylation in mouse embryonic stem cells (if you missed the seminal Nature paper on this previously unsuspected form of methylation in a mammal, check out our recap). Wu and team developed SMRT ChIP, a method for conducting ChIP-seq on a PacBio sequencer, and discovered N6-methyladenine throughout the genome. “Without PacBio, I think we could not get this done,” he said. The findings were confirmed by mass spec. Wu also tracked down the Alkbh1 demethylase and conducted functional studies that showed the methylation suppressed genes and transposons.
After lunch, the topic shifted to studies of primate and human genomes. Julie Karl from the University of Wisconsin analyzed the MHC locus in macaques, which have a more complex allele assortment than humans do. Using PacBio amplicon sequencing to span the full 1.1 kb locus, she was able to resolve full-length alleles unambiguously and phase haplotypes, finding many novel alleles to contribute to community databases. Karl is now working to expand her immunology investigation to KIR and FCGR, two other complex regions.
NIAID’s Brandon DeKosky spoke about sequencing antibody repertoires, which requires analyzing both heavy chain and light chain elements. Previous protocols involved analyzing three separate amplicons to cover these regions, but with the PacBio system his team has been able to sequence full-length amplicons covering both elements in B cells. “I certainly am in favor of moving everything over to the PacBio,” he said. “We can see this entire molecule at once.” DeKosky and his colleagues have studied cells from humans and rhesus macaque, and are now using transgenic mice to model antibody response to knocked-in precursor genes to determine whether this approach could be used towards developing a vaccine.
In a clinically oriented research presentation, Tetsuo Ashizawa from the Houston Methodist Research Institute reported the analysis of the ATXN10 gene responsible for spinocerebellar ataxia type 10. The gene harbors a pentanucleotide repeat in intron 9, characterized by an ATTCT repeat sometimes interrupted by other five-nucleotide repeats that lead to three broad disease phenotypes. Since the full region can’t be amplified, Ashizawa used CRISPR/Cas9 for target enrichment, making a double-strand break near the region and attaching a SMRTbell adapter for PacBio sequencing . This allowed the team to assess the motifs associated with different subtypes, in one example studying brothers with different phenotypes of the disorder and finding that the difference lay in repeat content.
Maria Nattestad from Cold Spring Harbor spoke about her genome and transcriptome analysis of SK-BR-3, one of the most widely studied breast cancer cell lines with a Her2 amplification. Long-read SMRT Sequencing was able to characterize the whole genome. Nattestad’s Assemblytics tool, which she used to call variants ranging from single-base changes to large structural changes, is now available as a web app. She discussed her reconstruction of how variants worked together to amplify the Her2 oncogene (an effort we profiled in-depth). Using the Iso-Seq method to produce full-length transcripts, she was also able to detect and explain complex gene fusions for which there was previously no DNA evidence.
Our CSO Jonas Korlach wrapped up the day with a talk highlighting some of the biggest advances we’ve seen from SMRT Sequencing, noting that there are now nearly 1,500 papers describing the use and value of this technology. Particularly productive topics include hospital-associated infections, base modifications in bacteria, and phylogenetic profiling of microbial communities. He also spoke about the recent wave of de novo human assemblies from PacBio data, noting that a shift toward diploid assemblies will be important as the community deepens its understanding of human genetic variation. Korlach also cautioned attendees about confusing contigs with scaffolds; while some assemblies boast impressive scaffold N50s, they may be missing a lot of important information if contigs are short and disconnected.
We’d like to thank our partners, who helped us put on this great event: Advanced Analytical Technologies, Covaris, Diagenode, DNAnexus, PerkinElmer, and Sage Science. With their support, we were able to host the full-day user group meeting, but also half-day workshops on sample prep and bioinformatics as well.
http://www.pacb.com/blog/east-coast-ugm-smrt-sequencing-data-carnivorous-plants-hummingbirds-mammalian-methylation-repeat-expansions/?platform=hootsuite
Anthera
Craig Thompson, President and COO of $ANTH, to present update next Wednesday, June 22 at 2:00 PM at JMP Securities Life Sciences Conference. http://stocktwits.com/Anthera