Monday, October 1, 2007

Tiny RNAs, big problems


Tiny RNAs, big problems

Spread of breast cancer to other body parts is linked to microRNA.
Ewen Callaway


The smallest bit of genetic material may cause the deadliest of tumours. Researchers have implicated a tiny RNA molecule in the invasive spread of breast cancer — the factor responsible for most deaths from the disease. In 2007, around 179,000 people in the United States will be diagnosed with invasive breast cancer and some 47,000 will probably die.RNA is one of the main players in human genetics; the most well studied type, messenger RNA (mRNA), is vital for translating the code of our DNA, allowing those instructions to be read and used to produce proteins. MicroRNAs — tiny strings of genetic code often just a couple of dozen nucleotides or 'letters' long — can block this translation process by binding to mRNAs, stopping the production of proteins. A spate of new research has found these diminutive molecules to be involved in crucial processes of development, metabolism and cell suicide.Now, a team led by Robert Weinberg at the Massachusetts Institute of Technology's Whitehead Institute in Cambridge has linked one of these up-and-coming molecules to invasive breast cancers."I think that these microRNAs are going to be involved ubiquitously in regulating a wide variety of cellular processes, and this is just the tip of the iceberg," Weinberg says.If the molecule can be confirmed as a key player in cancer migration, and targeted by drugs, the find may lead to a new preventative measure against the deadly spreading of tumours. At the moment, such cancers are normally treated through radiation and chemotherapy.On the moveA tumour's ability to hitch a ride in the bloodstream and take up residence elsewhere in the body, a process known as metastasis, is the most insidious trait of cancer. It often occurs in the later stages of the disease and precedes 90% of cancer deaths. In breast tumours, cells migrate to lymph nodes, the brain and other spots where they form deadly secondary tumours. After talking with colleagues doing microRNA research, a post-doctoral researcher in Weinberg's lab, Li Ma, wondered whether these molecules might be involved in metastasis.She and Weinberg performed a genome-wide scan of breast cancers, looking for microRNAs that are present in cases in which metastasis occurred. They found one microRNA, called miR-10b, that was highly expressed in 9 out of 18 patients with metastatic breast cancer, and not highly expressed in five women with less deadly tumours, they report today in Nature1.When the team looked at a well studied line of human breast cancer cells, extracted from another metastatic tumour, it found that the cancer cells expressed miR-10b at levels 50 times that of a non-invasive cell line.To see whether this microRNA was driving metastasis, the team implanted human cells expressing high levels of miR-10b into the fat pads of mice — a common way of testing human cancers. The tumours spread to the blood vessels and lungs of the rodents. When the team injected mice with similar cancer cells lacking miR-10b, the tumours stayed put.The researchers don't know exactly how miR-10b promotes metastasis, but one of the proteins it blocks production of, called HOXD10, has a role in embryonic development. It could be that metastatic tumours hijack the existing cellular pathway designed to turn a blob of cells into a full human, and use this to efficiently move cells around the body. "Cancer cells are not clever enough to invent these traits on their own. Instead they resurrect programmes that are in the embryo," Weinberg says.Stop the spreadIt remains to be seen whether blocking miR-10b could forestall deadly metastases in breast cancer patients. But molecules that inhibit microRNAs, called antagomirs, have already been shown to work in human cells in vitro, says Ramin Shiekhattar, a cancer biologist at the Centre for Genomic Regulation in Barcelona, Spain. Antagomirs bind microRNAs and keep them from acting on their normal mRNA targets.


Thomas Tuschl, a molecular biologist at Rockefeller University in New York, isn't yet convinced that miR-10b is so important, because it has only been found in nine metastatic tumours so far — a very small sample. "You would expect more clinical data, and it's just not there," he says.


Confirmation or refutal of the idea shouldn't be too far off. Other labs are likely to now check for miR-10b in breast cancer tissue biopsies stored in their freezers. "You will see in no time whether there's a correlation or not," Tuschl says.

Platinum® Pfx DNA Polymerase


Platinum® Pfx DNA Polymerase
Cat. No. 11708-013
Size: 100 reactions 11708-021
250 reactions11708-039
500 reactions
Conc: 2.5 U/μl
Store at -20°C
Note: Read and follow reaction conditions carefully to ensureoptimal performance.
Description Platinum® Pfx DNA Polymerase is a proprietary enzyme preparation containing recombinant DNA polymerase from Thermococcus sp. strainKOD (1,2). Platinum® Pfx DNA Polymerase possesses proofreading3′ to 5′ exonuclease activity and provides higher fidelity than Pfu DNApolymerase (3). It is a highly processive enzyme with fast chainextension capability.Platinum® Pfx DNA Polymerase is provided in inactive form, due tospecific binding of the Platinum® antibody. Polymerase activity isrestored after a PCR denaturation step at 94°C, providing an automatic.hot start. and increasing specificity, sensitivity, and yield (4). Thehigh accuracy, specificity, and yield of Platinum® Pfx DNA Polymerasemake it ideal for demanding PCR applications such as site-directedmutagenesis and PCR expression cloning.For problematic and/or GC-rich templates, PCRx Enhancer Solution isincluded with each kit (see the guidelines for use on page 2). The number of reactions per kit is based on a standard reaction size of 50 μl.Kit SizeComponents 100 Rxns 250 Rxns 500 RxnsPlatinum Pfx DNA Polymerase 100 units 250 units 500 units50 mM Magnesium Sulfate 1 ml 1 ml 1 ml10X Pfx Amplification Buffer 1 ml 2 × 1 ml 3 × 1 ml10X PCRx Enhancer Solution 1 ml 2 × 1 ml 3 × 1 mlPart no. 11708.pps Rev. date 07/11/03T his product is distributed for laboratory research only.

CAUTION: Not for diagnostic use. The safety and efficacy of this product in diagnostic orother clinical uses has not been established.For technical questions about this product, call the Invitrogen Tech-LineSM U.S.A. 800 955 6288Page 2 of 4Platinum® Pfx DNA Polymerase Storage Buffer50 mM Tris-HCl (pH 8.0), 50 mM KCl, 1 mM DTT, 0.1 mM EDTA,stabilizers, and 50% (v/v) glycerol.Unit DefinitionOne unit of Platinum Pfx DNA Polymerase incorporates 10 nmol ofdeoxyribonucleotide into acid-precipitable material in 30 min at 74°C.Quality ControlThe DNA polymerase:antibody complex is evaluated in a DNApolymerization activity assay that measures the percent of DNApolymerase inhibition versus an uninhibited control. Platinum® PfxDNA Polymerase is functionally tested in an amplification using 100 ngof K562 genomic DNA as a template.Guidelines for Using PCRx Enhancer SolutionFor problematic and/or GC-rich templates, PCRx Enhancer Solutionprovides higher primer specificity, a broader range of optimalmagnesium concentrations, broad annealing temperatures, andimproved thermostability.Use of PCRx Enhancer Solution is optional; use in combination with10X Pfx Amplification Buffer, not as a substitute. PCRx EnhancerSolution lowers the DNA melting temperature (Tm), reducing themaximum primer annealing temperature approximately 2°C per 1XPCRx Enhancer Solution concentration, while at the same timeexpanding the effective annealing temperature over a much broaderrange. To determine the optimal reaction concentrations andconditions, we recommend starting with an annealing temperature of55°C to 60°C and varying the amount of 10X PCRx EnhancerSolution. For targets with higher GC content (60 to 90%), werecommend testing 10X PCRx Enhancer Solution at final concentrationsof 0.5X, 1X, 2X, and 3X.Page 3 of 4PCR ProtocolThe following procedure is suggested as a guideline and starting pointwhen using Platinum Pfx DNA Polymerase in any PCR amplification.1. Add the following components to an autoclaved microcentrifuge tubeeither at ambient temperature or on ice:Component Volume Final Concentration10X Pfx Amplification Buffer 5 μl 1X10 mM dNTP mixture* 1.5 μl 0.3 mM each50 mM MgSO4 1 μl 1 mMPrimer mix (10 μM each)* 1.5 μl 0.3 μM eachTemplate DNA (10 pg - 200 ng) ≥1 μl As requiredPlatinum® Pfx DNA Polymerase** 0.4.1 μl 1.0.2.5 unitsAutoclaved, distilled water to 50 μl*Platinum® Pfx DNA Polymerase will not function in reactionsthat contain dUTP in either the dNTP mix or the primers.**For most targets 1 unit is sufficient. When amplifying targetsabove 3 kb, more enzyme may be required.2. Mix tube contents and overlay with mineral or silicone oil, if necessary.3. Cap the tube and centrifuge briefly to collect the contents.4. Denature the template for 2 min at 94°C. Perform 25.35 cycles of PCRamplification as follows:Three-step cycling Two-step cyclingDenature: 94°C for 15 s Denature: 94°C for 15 sAnneal: 55°C for 30 s Extend: 68°C for 1 min per kbExtend: 68°C for 1 min per kbNote: Two-step cycling can be used for long primers with highTm.5. Maintain the reaction at 4°C after cycling. Samples can be stored at-20°C until use.6. Analyze the products by agarose gel electrophoresis.

pipette science


পিপেটিং...সাবধান!
আজকে একটা ইন্টারেস্টিং লেখা পড়লাম...পিপেটিং নিয়ে। এরা বলছে ঠান্ডা স্যাম্পল আর গরম স্যাম্পল দুইটাই সঠিক ভাবে আয়তন মাপতে বাঁধা সৃষ্টি করে।ধর একটা ঠান্ডা স্যাম্পল ৪ ডিগ্রীতে আছে ।টিপস বদল না করে একই টিপস দিয়ে কাজ করলে প্রথম বার আসল আয়তনের থেকে বেশি স্যাম্পল উঠবে। কারণ তরল অংশের উপরের ফাঁকা জায়গাটুকুর বাতাস ঠান্ডা হয়ে সংকুচিত হয়ে যাবে , ফলে আসলের চেয়ে বেশি তরল উঠে। যখন দ্বিতীয় বার উঠাব তখন ফাঁকা অংশের বাতাস প্রথমে টিপসের অলরেডি ঠান্ডা অংশ দিয়ে পাস করে এবং তারপর আরো উপরে উঠে ..যেই অংশটা (টেপেড অঞ্চল) গরম ফলে তাপমাত্রা বাড়ে.....বাতাস প্রসারিত হয় এবং স্যাম্পল কম উঠে। এবং এর পর থেকে প্রতিবারই কম পরিমাণ উঠে। অর্থাৎ ঠান্ডা স্যাম্পেল প্রথমবার বেশি উঠে এবং এর পর থেকে কম উঠে।
একইভাবে গরম স্যাম্পলে প্রথমে বেশি উঠে এবং পরে ২য সাইকেল থেকে প্রতিবারই বেশি উঠে। ঠিক বিপরীত কারণে।
এই সমস্যার সমাধান হল স্যাম্পল তোলার সময়ে প্রথমটাই না নিয়ে কয়েকবার উঠানামা করে তারপর নেয়া। এতে তাপমাত্রাটা অ্যাডজাস্ট হবে।
এছাড়া একটা কারেকশন ফ্যাক্টর তারা দিয়েছেন। ভল্যুম সেটিং= টার্গেট ভল্যুম x {১-ক(স্যাম্পলের তাপমাত্রা - রুমের তাপমাত্রা)} এখানে ক=০.০০২ ডিগ্রী পার সেন্টিগ্রেড। তাহলে ১০০ মাইক্রো উঠাতে আমাকে পিপেট সেটিং করা লাগবে ৯৬ তে। যখন রুম তাপমাত্রা ২০ ডিগ্রী আর স্যাম্পল তাপমাত্রা ৪০ ডিগ্রী।
http://www.nature.com/nmeth/journal/v4/n9/full/nmeth1086.html