Thursday, April 11, 2013

Join me at RNA-Seq 2013



Paul Kayne
11:05 AM (1 hour ago)

to me
  Dear MUTOMBO,







If one was so inclined, RNA-seq could be considered in the context of a symphony. The first movement, as with Beethoven’s Symphony No. 5 in C minor, started with an Allegro con brio, “with vigor”. The advent of next generation sequencing empowered pioneers to look into the life of cells with unprecedented resolution. 

Details of new species of RNA, allele specific expression, and more began to emerge, with a new discovery almost every day. That we were only in the first movement likewise became clear. How to prepare samples, what platform to choose, how to work with the data, were questions without easy answers. Just as conductors fought over the correct interpretation of Beethoven’s score, so scientists brought their individual perspective to RNA-seq.

Second movements in symphonies are typically slower, but Beethoven chose an Andante con moto, “with movement and certain quickness”, describing well the state of RNA-seq today. Our field is moving forward deliberately now, towards answers as to how best to use these new capabilities, with exciting discoveries along the way.

And you have the opportunity to further your part in the symphony. I invite you to join me at RNA-Seq 2013 in Boston, June 18-20, 2013. You will hear from leaders using this technology to drive research and make decisions.

Presentations will address sample prep methods, analysis methods, platform choices, characterizing complicated expression patterns, choosing solution providers, application to drug discovery and more. Add your voice to our panel discussion on customizing analysis to meet your needs. Join us as we move towards the next movement in RNA-seq.

I understand that early registration closes in a month so book soon to get the best prices. You can see the full agenda and speaker line up here: www.rna-seqsummit.com

I look forward to seeing you there.

Kind regards,

Paul

Paul Kayne
Senior Principal Scientist,
Head of Genomic Technologies
Bristol Myers-Squibb





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JUST PURE BIOLOGICAL SCIENCE!

WE ESCAPED SMARTLY IN THE MELI-MELO OF AGING JUST TO DIVERT OUR ATTENTION ON GENES INVOLVED IN ALZHEIMER. DON'T ASK ME WHY, BUT WE DID. WE CAME OUT MORE PUZZLED THEN ANYTHING ELSE!

MANY QUESTIONS THOUGH:

Many of the striking things and questions

1.Can calcium inhibitors slow down Alzheimer progression?
2. Is Namenda's role to slow down apoptosis in neurons by giving non specific stimulation to Glutamate receptors ?  Or this really by counterbalancing or increasing the effect of cholinesterase inhibitors? We know that when the disease is advanced and cell death has occurred, Namenda does not do much.
3. Can S100B be a more reliable way of monitoring Alzheimer's progression?
4. Does Alzheimer reflects a deficiency of Macrophage function and therefore Colony stimulating factors a way of treatment?
5. What is the effect of GM-CSF on NG2 glial cell and can this slow down Alzheimer?
6. What can slow down tau-protein phosphorylation, will ubiquitination work in detoxifying cells ?
7. What is the effect of disrupting the exosome, could this cause abnormal cell to be cleaned up earlier...? ....before plaque build up!
8. What is the real relation between Vit. D and DAG (diacyl glycerol), the phosphorylator, APOE and Presenilin?

Many question to struggle with...but the challenge is thrown at you, let's go to work!

FYN, A CRAZY GENE...

IT DOES NOT KNOW WHEN TO STOP INTERACTING
IT IS INVOLVED IN CRAZINESS (ALZHEIMER'S)
BUT YET IT KEEPS DOING ITS THING.
CAN WE STOP IT ELECTIVELY?
WE ARE WORKING HARD!

FYN

From Wikipedia, the free encyclopedia
Jump to: navigation, search
FYN oncogene related to SRC, FGR, YES

PDB rendering based on 1a0n.
Available structures
PDB Ortholog search: PDBe, RCSB
Identifiers
Symbols FYN; SLK; SYN; p59-FYN
External IDs OMIM137025 MGI95602 HomoloGene48068 ChEMBL: 1841 GeneCards: FYN Gene
EC number 2.7.10.2
RNA expression pattern
PBB GE FYN 210105 s at tn.png
PBB GE FYN 212486 s at tn.png
PBB GE FYN 216033 s at tn.png
More reference expression data
Orthologs
Species Human Mouse
Entrez 2534 14360
Ensembl ENSG00000010810 ENSMUSG00000019843
UniProt P06241 P39688
RefSeq (mRNA) NM_001242779 NM_001122892
RefSeq (protein) NP_002028 NP_001116364
Location (UCSC) Chr 6:
111.98 – 112.19 Mb
Chr 10:
39.37 – 39.57 Mb

PubMed search [1] [2]
Proto-oncogene tyrosine-protein kinase Fyn is an enzyme that in humans is encoded by the FYN gene.[1]
This gene is a member of the protein-tyrosine kinase oncogene family. It encodes a membrane-associated tyrosine kinase that has been implicated in the control of cell growth. The protein associates with the p85 subunit of phosphatidylinositol 3-kinase and interacts with the fyn-binding protein.

Interactions

FYN has been shown to interact with:

References (WIKIPEDIA)

WITH THIS MANY INTERACTIONS, IT IS A CRITICAL GENE, BUT WATCH OUT NOW, IT NEEDS TO BE HANDLED WITH CARE.  HIT IT ONLY IN A VERY SELECTIVE FASHION NOW! OR YOU LOSE THE HOST!

 

another crazy gene

 

Androgen receptor has been shown to interact with:

 wikipedia! remember what we said about short stature

this one also is that kind, lack of it lead to short stature so it it is a powerful gene, suppression here cures prostate cancers!

Medscape Medical News from the:

NCCN Issues New Treatment Guidelines for Penile Cancer

Roxanne Nelson
Mar 22, 2013
Hollywood, Florida — The National Comprehensive Cancer Network (NCCN) has issued new treatment guidelines for penile cancer.
"The first thing people ask me is why develop guidelines for such a rare cancer," said Philippe  E. Spiess, MD, genitourinary oncologist at the H. Lee Moffitt Cancer Center in Tampa, Florida.
In 2010, an estimated 1250 new cases of penile cancer were diagnosed in the United States and there were about 310 related deaths. Penile cancer accounts for 0.4% to 0.6% of all malignant neoplasms in the United States and Europe.
Dr. Philippe Spiess
Dr. Spiess presented highlights of the guidelines here at the NCCN 18th Annual Conference.
There is a high degree of heterogeneity in the way penile cancer is treated in North America and globally, he explained. "The standard of care remains complete tumor excision and eradication of negative margins."
However, there has been increasing consideration of less or noninvasive management of primary penile tumors, based on stage and grade, he added.
Less and Noninvasive Therapy
For carcinoma in situ and superficial verrucous carcinoma, a British study showed that 5-fluorouracil or imiquimod produced response rates of 60% to 70% at 5 years (World J Urol. 2009;27:179-187). In this setting, CO2 and Nd:YAG laser ablation can also be used, although retreatment rates are quite high (about 20% to 30%), explained Dr. Spiess.
Total gland resurfacing and wide local excision with circumcision are also options.
There is some evidence for the use of topical therapies. In a recent retrospective review of all primary and recurrent cases of penile carcinoma in situ treated with topical 5-fluorouracil and imiquimod over a 10-year period (Eur Urol. 2012;62:923-928), "the response rates were excellent," said Dr. Spiess. "A complete response was seen in 57% of the patients, with a partial response in 14%."
No response was seen in the remaining 29.5% of patients, but none of the patients recurred or progressed. Toxicity was also low; 10% of patients reported local toxicity and 12% reported an adverse event.
Another study, looking at penile-preserving surgery for patients with penile Tis and PT1 tumors, found that there was a recurrence rate of 21.4% in both subgroups (J Urol. 2011;186:1303-1307). At 5 years, 13.8% of patients had a late recurrence, but none of the patients with pTis tumors had progressed to invasive or metastatic disease.
"These patients can recur fairly late, so it is important to follow them for at least 10 years," Dr. Spiess pointed out.
"As far as penile-preserving therapy, the take-home message is that clinical stage is everything," Dr. Spiess explained. However, he went on to emphasize that "it has to be a patient with a small superficial lesion, where you can obtain negative margins. If you can't, then you need to look at more radical options in surgery."
Another treatment option is brachytherapy. A recent French study found a 10-year penile recurrence rate of 20% and a 10-year inguinal recurrence rate of 11% (Int J Radiat Oncol Biol Phys. 2009;74:1150-1156). However, "centers of excellence that have experience with penile brachytherapy are few and far between," he cautioned. "That's why the guidelines...are somewhat cautious in making recommendations until we see a wider experience using penile brachytherapy."
He emphasized the importance of stringent surveillance after radiotherapy to the penis; up to 40% of patients who receive radical radiotherapy will eventually need surgery for disease recurrence. Surgery in this population can be challenging because irradiated tissues are brittle and poorly vascularized, making them less than ideal for grafting.
Sentinel Node Biopsy
Dr. Spiess discussed the concept of sentinel lymph node biopsy in penile cancer, which was proposed more than 30 years ago. One study reported a false-negative rate of 18% using a combined preoperative injection of technetium-99m labeled sulfur colloid and isosulfan blue dye (J Urol. 2002;168:76-80).
A more recent prospective study found a sensitivity of only 71%, with 2 false-negative results reported (J Urol. 2007;177:2157-2161). But a review found that false-positive results can be minimized with preoperative ultrasound and fine-needle aspiration cytology on suspicious nodes (World J Urol. 2009;27:197-203).
However, this technique has not yet been embraced in this setting. "We are somewhat cautious about promoting this technique, although clearly it is something very interesting and something that can be used at a center that has high expertise in sentinel lymph node biopsy," said Dr. Spiess. "At this point, it is not being widely used in North American centers."
National Comprehensive Cancer Network (NCCN) 18th Annual Conference.
 

Wednesday, April 10, 2013

ON THE CPRIT FRONT THE DANCE GOES ON!
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04/09/2013 08:11 PM

CPRIT executives grilled by lawmakers


Executives for the Cancer Prevention and Research Institute of Texas were being grilled by state lawmakers Tuesday. The organization is currently under criminal investigation and an audit showed millions of dollars in scientific grant funds went out, but results weren't coming in.
For House committee members, Tuesday’s meeting was all about trust, transparency, and accountability.
"How can we expect public trust to be reaffirmed?" Republican committee member Dan Flynn said.
Four months after a criminal investigation began on the Cancer Prevention and Research Institute of Texas, Transparency Committee members continue to look for answers.
Questions surrounded the non-scientific grant approval for Dallas-based Pelaton Therapeutics, worth $11 million dollar.
Suspicions of grant-rigging went public in November of last year.
"When it appeared that the grant report was missing information or inaccurate, I immediately called for an investigation,” Jimmy Mansour, CPRIT chairman, said.
The CPRIT chief told the committee that $3 million dollars of that public money grant will not be recovered.
"And that is regrettable that much is lost," Mansour said.
To date three people have left CPRIT while under criminal investigation. Committee members want to know if only those three misled the entire agency.
Committee members also wanted to know how public trust could be restored in the CPRIT executives, the same executives who brought scrutiny to the cancer agency.
They also criticized the renaming of the fundraising entity of CPRIT, the CPRIT Foundation. That name change came about two weeks ago. Committee members said any money raised by the foundation needs to be returned to the state.

==============================================
How can this organization survive such a lengthy, protracted war and come out winning?
One thing for sure it will never be the same and will come out weaker and slim!  another win for cancer and another impediment to the CURE.   The cure is with us, we just complicate our minds with politics and favoritism.  What a waste!  I still pray for CPRIT...SAVIOR PLEASE COME UPON THIS ORGANIZATION!...
ACTIVITIES AT CRBCM

*COMPLETED INDIANA WORK
BACK IN EL PASO, TX
Initiated therapy for Angiosarcoma with trial of Avastin alone at this point thanks to drug company help.
will try 3-4 infusions and reassess.  Votrient still an option.  But remember (OUR PT developed severe skin reaction to taxanes and had received MAID)
-------------------------------------------------------------------------------
J Am Acad Dermatol. 2010 Oct;63(4):e83-4. doi: 10.1016/j.jaad.2009.09.035.

Dramatic improvement of inoperable angiosarcoma with combination paclitaxel and bevacizumab chemotherapy.

--------------------------------------------------------------------------------------------
 
Avastin alone has proven to be effective.
 
 Case Report"Scalp Angiosarcoma Remission with Bevacizumab and Radiotherapy without Surgery: A Case Report and Review of the Literature, " DE YAO et al.
=========================================================================

*Also we are searching for a surgeon who would consider resecting a Pancreatic cancer with mesenteric VEIN NOT ARTERY involvement.  we are shrinking the tumor with chemotherapy and Radiation, will reassess result radiologically.  Call me if you can help!

=============================================

DON'T LOOK FOR ME THIS WEEK-END
WILL BE HARD AT WORK!

  Prostate Symposium

Dear Dr.Mutombo Kankonde,

Below is the link for the agenda for the Prostate Symposium research event on April 13, 2013 in Las Vegas.  Below you will find the agenda link and hotel information:  
Meeting Information:

Mandarin Oriental
3752 Las Vegas Blvd South
Las Vegas, Nevada 89158
(702) 590 8888
Meeting: Ballroom B, 3rd Floor
WILL LOSE SOME MONEY BUT THAT COMES WITH THE TERRITORY!  BELIEVE ME IT'S HARD TO MISS THE ACTION, WILL TRY TO BE GOOD COLLECTED AND UNDER CONTROL.
THANKING THE ORGANIZER FOR INVITING ME, WILL LEARN PLENTY OF GOOD STUFF FOR THE BLOG AND FURTHER RESEARCH!
==================================================

WILL PUBLISH OUR BLOG STATISTICS AS SOON AS WE HIT 15000 REVIEWS WHICH WE PROJECT WILL BE IN 2-3 DAYS AT CURRENT PACE OF ATTENDANCE!  CRBCM, WE ARE HARD AT WORK!