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How Louisiana Lawmakers stop Residents’ Efforts to battle big Oil and gas ProPublica is a nonprofit newsroom that investigates abuses of power. check in to get hold of our greatest experiences as quickly as they’re posted. as the Bayou Bridge Pipeline was beneath building in 2018, Anne White Hat ventured deep into the Atchafalaya Swamp in St. Martin Parish to protest it. St. Martin is one in every of eleven parishes crossed by way of the pipeline, which brings crude oil from Texas to refineries in Louisiana. although White Hat had permission to be there from one of the greater than a hundred people who jointly personal the tract where she held her protest, she didn’t have permission from all. She become arrested on two criminal counts regarding trespassing. She posted a $21,000 bond and became launched. Two years later, the district attorney nevertheless hasn’t determined no matter if to proceed with the fees: two counts of unauthorized entry of a critical infrastructure. The optimum penalty is 5 years in prison, with the probability of tough labor and a excellent of as much as $1,000. Get Our precise Investigations Subscribe to the massive Story publication. “it’s intimidating for those who’re looking at facing prison in South Louisiana,” she referred to. sarcastically, a court later found that the pipeline business itself had been trespassing at the time of White Hat’s arrest. The leading proprietor, energy transfer partners, had no longer bought easement agreements with all landowners to start construction, nor had it been granted permission to accomplish that through eminent area. Its penalty: a $450 satisfactory paid to the landowners. The judge who set White Hat’s bond at $21,000 changed into the same decide who imposed power transfer companions’ high-quality.“here’s yet yet another in a long line of examples of how Louisiana laws are first made through oil and gasoline organizations and then are not noted by means of the identical businesses if they consider like it,” stated invoice Quigley, a law professor at Loyola university who’s representing White Hat pro bono. energy switch companions did not reply to calls and emails in search of remark. Louisiana has blazed a path for other states in discouraging environmental protests via elevating the criminal stakes for those who trespass on or near “important” oil and gas infrastructure — which includes refineries, chemical flora and ports. In 2004, it changed into the primary state to make that crime a legal. Louisiana’s pioneering law can also be traced to corporate lobbyists. BP and DuPont have been among the energy and chemical organizations that produced a 2003 e book disseminated to state officials, arguing that more advantageous penalties would discourage assaults by terrorists that might trigger economic disruptions. Two years in the past, legislators brought oil and gas pipelines to the checklist of infrastructure deemed critical. In White Hat’s view, the total suite of laws is anti-democratic. “They’re using the state to give protection to their corporate pursuits,” she pointed out. Residents have repeatedly pushed lower back in opposition t pipelines, proposed vegetation and latest business of their backyards. while such opposition is nearly never monolithic, it’s commonly overwhelming at the local stage. but the state’s elected leaders have historically sided with industry, in some instances passing new legal guidelines aimed at quelling opposition. a sign marks the area of a pipeline in the Atchafalaya Basin, the identical swamp where Anne White Hat protested the Bayou Bridge Pipeline in 2018. (Brett Duke/The times-Picayune and The advocate) Legislators are attempting to reduce local officials’ power to decide whether to exempt trade from local taxes. Years ago, when a native board made of experts filed an ambitious lawsuit that aimed to hold oil and fuel organizations dependable for damaging coastal wetlands, state officials undermined it. In an extra episode, they handed a legislations that barred communities from the usage of incorporation to collect property taxes from chemical flowers. And more than once they have sought to punish pupil law clinics that symbolize communities fighting business. This year’s legislative session, which starts off in March, will once more consist of bills to avoid native input into industrial tax exemptions. Some of those efforts are a part of a bigger, coordinated method. The three Louisiana lawmakers who subsidized the trespassing bill were contributors of the American Legislative alternate Council, a controversial organization that brings lawmakers and corporate lobbyists collectively to draft “model legislation” that they then shop to different states. Louisiana’s 2004 trespassing legislation became simply such a template. Fifteen years later, 10 states have an identical legal guidelines. “Louisiana become a very essential state,” spoke of Connor Gibson, an investigator with Greenpeace. The addition of pipelines to the law two years in the past came according to protests that garnered country wide consideration, principally these at Standing Rock in North Dakota, which became the focal factor of indigenous protests of the Dakota entry Pipeline. “This simply protects in opposition t people that need to inhibit commerce,” bill sponsor Rep. main Thibaut noted as he delivered the invoice in 2018. Thibaut, now president of Pointe Coupee Parish, pointed out the legislation protects people and would-be protesters from defense issues on work websites with heavy device. When asked no matter if protesters should be arrested in the event that they don’t interfere with worker’s, he spoke of, “That’s up to the courts to check.” In a organized observation, Louisiana Mid-Continent Oil and gasoline association President Tyler gray said the law “doesn’t infringe on a person’s constitutional rights.” up to now, 15 people were arrested for violating Louisiana’s new legislation: 14 protesters and a journalist covering them. a few of them filed a swimsuit in might also, claiming the law chills free speech and is as a consequence unconstitutional. The suit is pending. Mounting Political force For a long time, an vague Louisiana board doled out 10-12 months property tax exemptions to nearly each predominant manufacturer that become building or expanding a plant in the state. It became the definition of a rubber stamp. Between 1997 and 2016, the board rejected simply eight of the 16,931 functions for reduction during the Industrial Tax Exemption program, for an approval cost of ninety nine.ninety five%, in keeping with an analysis by together Louisiana, a grassroots firm that has pushed to rein in the software. That modified when Gov. John Bel Edwards signed an govt order in 2016 that gave native governing our bodies plagued by the exemptions a say over them for the primary time. The breaks can have a large impact on native executive’s base line. study greater in view that the 2016 government order, the native agencies that would forgo money on industrial tax exemptions have gotten to vote on them. The East Baton Rouge Parish college Board last 12 months rejected a tax spoil for a variety Exxon Mobil had completed two years prior. That induced heavy pushback from trade. Unsuccessful law ultimate yr would have required parishes to create a single board that votes up or down on the tax breaks, rather than letting the sheriff, the faculty board and the parish govt approve or deny them piecemeal. Explaining his invoice, Sen. Bodi White, R-Baton Rouge, noted, “I didn’t elect my college board for financial building to deliver organizations to this state.” A vast swath of local officers fought to kill White’s bill, together with associations of sheriffs, school boards and parish governments. “A parish governing authority should still be able to make a decision no matter if they could have enough money to supply an exemption and make sure the company getting the exemption is keeping up their end of the deal,” referred to guy Cormier, govt director of the lobby for parish governments. A failed invoice filed by way of Rep. Barry Ivey, R-significant, would have long past even extra, putting the exemption again in the state’s arms. Ivey, who observed producers want extra walk in the park, is already working on an identical invoice this 12 months. “I intend to birth off where I left off at the conclusion of the 2019 session,” he referred to. despite a recent boom in industrial plant life moving to Louisiana, Edwards’ modest reforms had been used via his Republican challengers in last year’s gubernatorial race as proof of the Democrat’s hostility toward trade. Baton Rouge businessman Eddie Rispone — who garnered 49% of the vote in November — made undoing Edwards’ tweaks a big a part of his platform. Edwards, now in his second time period, looks to have heard the complaints. he’s attempting to get native governments, including those in New Orleans and Baton Rouge, to dump new rules that bar exemptions for tasks, like Exxon’s, that were accomplished by the time the destroy was requested. Louisiana’s Love Affair With business As Louisiana’s wetlands vanish, coastal communities have turn into ever greater susceptible to storm surges and sea level rise. And whereas there are disagreements over the way to apportion blame for the erosion, it’s undisputed that oil and gasoline exploration has played a key position — partly, via dredging 10,000 miles of canals. A gas transmission pipeline cuts during the wetlands in St. Bernard Parish, Louisiana. Canals alter the drainage patterns of wetlands, inflicting the loss of the marshes and flood protection. (Bonnie Jo Mount/The Washington put up by way of Getty images) And so, in 2013, the board that oversees flood insurance plan in most of metropolitan New Orleans filed an audacious lawsuit that sought to grasp 97 oil and fuel companies in charge for harmful the location’s herbal flood defenses. It activate an instantaneous firestorm. The board’s lawsuit right away earned it rogue status — even though, after the levee screw ups of hurricane Katrina, levee board contributors for the first time have been required to have specific skills. as a result of those adjustments, the board that filed the suit turned into made from participants nominated by using expert groups, appointed with the aid of Gov. Kathleen Blanco and verified with the aid of the Senate. Historian and creator John Barry, who turned into vice chairman of the board, estimated the Legislature filed 20 separate expenses in 2014 to intestine the lawsuit. “The Legislature made a extremely honest effort to kill the lawsuit after it had already been filed,” he spoke of. “within the end, we defeated all but one piece of law.” The surviving bill, authored with the aid of former state Sens. Robert Adley and Bret Allain, retroactively voided the suit. Adley said his pork changed into that the board didn’t give the proper authorities a heads-up earlier than filing swimsuit. A state judge later found the brand new legislations to be unconstitutional, in three alternative ways. That wasn’t the end of the assault. Then-Gov. Bobby Jindal, a Republican who opposed the swimsuit, tried to swap out the authority’s board. He replaced 4 of the nine board members, dumping coastal consultants in favor of political appointees. Even then, a slender majority of the board backed the suit. finally, the lawsuit was thrown out with the aid of U.S. District judge Nannette Jolivette Brown, who spoke of oil and fuel corporations had no legal obligation to pay the levee authority for wetland hurt, a view upheld by means of an appeals court. The U.S. Supreme court refused to listen to the case. considering the fact that then, seven coastal parishes, together with New Orleans, have filed identical court cases against oil and gas businesses over land loss in their communities, and Edwards has urged different coastal parishes to follow suit. none of the situations were decided. The Chilling impact people that push back towards business in Louisiana frequently find themselves outmaneuvered. In 1994, residents of Geismar, in Ascension Parish, have been hoping to observe in the footsteps of their upriver neighbors in St. Gabriel by incorporating into a town. The stream would supply residents greater political clout — including the potential to assert no to new flora — and produce in tax greenbacks from local industrial facilities. The late Amos favorite Sr., who was seventy one at the time, was a leading advocate. “These plant life pay a lot of money to Ascension Parish. We (in Geismar) don’t see anything else however pollution,” favorite stated in 1994. Amos favourite Sr. speaks at a meeting about racial discrimination within the River region plant life in 1997. favorite, an environmental activist, led an incorporation effort within the community of Geismar. (Tim Mueller/The recommend) but the following yr, eleven chemical plants in Ascension Parish filed a lawsuit to quash the incorporation. With that case pending, state Rep. Jerry Luke LeBlanc, a Democrat, backed a bill to ban new municipalities from including industrial areas into their boundaries. Then-Gov. Edwin Edwards signed it into legislation in 1995. Citing the brand new law, the court docket sided with the plant life. the new legislations intended the planned city would have a a good deal smaller tax base and plenty less say over the polluters in its midst. Geismar’s pressure for incorporation misplaced steam. favorite’s daughter, Malaika favourite, an artist who nevertheless lives in Geismar, said the episode took an emotional toll on her father. “It was definitely disappointing to him,” she talked about. “The flowers have so tons vigor.” proscribing illustration New legal guidelines are rarely the best formula Louisiana elected officers have used to stifle residents’ opposition to business. In 1997, former Gov. Mike Foster compelled the Louisiana Supreme court to trim the sails of scholar law clinics after the Tulane Environmental law health center helped St. James Parish residents fight a polyvinyl chloride plant the chemical gigantic Shintech wanted to build in Convent. Foster badly desired to look the Shintech plant developed. He mocked the plant’s two most vocal opponents, Emelda West and Pat Melancon of Convent, as “a bunch of housewives.” Calls to Shintech searching for remark had been no longer again. Former Louisiana Gov. Mike Foster pushed for Tulane university to be defunded after students in the Tulane Environmental legislations health center helped Convent residents challenge air and water makes it possible for for a proposed polyvinyl chloride plant. (Bryan S. Berteaux/The times-Picayune) moreover challenging Shintech’s air and water enables, Convent residents — with the aid of Tulane — filed a criticism with the U.S. Environmental protection company claiming the state violated the landmark 1964 Civil Rights Act when it accredited the undertaking. The complaint grew to become the first key examine of an executive order signed by way of former President bill Clinton in 1994 that aimed to address the indisputable fact that communities of colour bore a disproportionate burden of pollution. Foster become apoplectic. He inspired Tulane alumni and business leaders to rethink their economic guide for the tuition. a few business lobbying organizations, meanwhile, entreated the Louisiana Supreme court docket, which oversees student legislation practice within the state, to investigate the legislations health center. scholar legislation apply enables prison beginners to gain hands-on journey, while providing legal information to those who would not in any other case have access. The Louisiana affiliation of enterprise and business, the state’s most powerful business lobby, had recently helped three pro-enterprise justices win seats on the Supreme court. the executive justice, Pascal Calogero, changed into up for election here 12 months. At LABI’s urging, the courtroom all started investigating the Tulane hospital in 1997. as the election heated up, Calogero — and all but one justice — voted to avert pupil legislation tips. the brand new rules banned the illustration of any group corporation affiliated with a countrywide corporation — like Greenpeace, the Sierra club or the NAACP and prohibited college students and supervising legal professionals from initiating contact with expertise clients. the brand new suggestions also placed limits on how an awful lot residents might earn and nevertheless receive pupil representation. A family unit of three, for example, could not get assistance if they made greater than $13,650 annually. the top of the affiliation of american law colleges known as the new requirements “essentially the most restrictive student practice rule within the nation.” Emelda West, of the St. James citizens for Jobs and the atmosphere, speaks in front of the Governor’s Mansion throughout a protest against the governor’s threats in opposition t the Tulane Environmental legislations health facility in 1997. (Tim Mueller/The suggest) ironically, the new suggestions — which have considering the fact that been relaxed some — got here too late to store Shintech’s plant. The company introduced in 1998 it had scratched its plan, opting as an alternative for a an awful lot smaller facility in Iberville Parish. The Tulane health facility has persevered to garner the ire of business over the ultimate two a long time. In 2010, Adley brought a different bill geared toward stopping the hospital from going after chemical plants. it might have yanked state funding from Tulane if its legislation clinic sued a government company. because the bill become brought, Dan Borné, then head of Louisiana Chemical association, stated: “My board acted on taking an aggressive method toward the Tulane Environmental legislation health center. here is a part of that method.” but Adley’s bill to defund Tulane became unwell-timed. One month past, the Deepwater Horizon oil rig exploded within the Gulf of Mexico. Lawmakers have been involved that if the bill passed, residents littered with the spill wouldn’t be in a position to get prison advice from Tulane. The bill failed. Lisa Jordan, director of the hospital, co-wrote the civil rights petition to the EPA on behalf of Convent residents two decades in the past. besides the fact that the case put a crimp on the health facility, she’s pleased with taking up the battle. “It changed into complicated, and it had a really good result for the clients,” she noted. “and because it advised me here is such essential work, even should you don’t always be triumphant … to provide people a felony voice that they otherwise couldn’t have had.” Monique Harden, of the Deep South center for Environmental Justice who co-wrote the civil rights petition, mentioned the repeated assaults on the hospital exemplify how Louisiana officials tend to react to environmental uprisings. “There is that this systemwide hostility to americans fighting lower back,” Harden referred to. “They wish to reduce support. but not simply cut guide, cut your cure.” Share Your Story Do you reside in one of these affected parishes? Share your story with us. ProPublica and The instances-Picayune and The recommend are investigating the huge chemical vegetation within the industrial stretch between New Orleans and Baton Rouge, and hearing from you will assist us tell more experiences. confer with us if: you work or have labored in an industrial facility in Louisiana, and you may tell us what your journey has been like. There’s a new plant for your local, and you may inform us how your neighborhood has been responding to it. You’ve been in touch with the DEQ and/or your parish executive about a plant and can share with us what the responses from these entities has been. that you can confer with us in regards to the influence of these plants in your community, including sharing evidence like signage, emails, residue or different anecdotes with us. here’s a way to discuss with us: examine greater Sara Sneath is an environmental reporter with The times-Picayune and The advocate. e-mail her information at [email protected] and observe her on Twitter @sarasneath. CME 323: dispensed Algorithms and Optimization Spring 2015, Stanford institution Mon, Wed 12:35 PM – 1:50 PM at 530-127 instructor: Reza Zadeh The emergence of large distributed clusters of commodity machines has brought with it a slew of recent algorithms and equipment. Many fields equivalent to computing device studying and Optimization have tailored their algorithms to deal with such clusters. The type will cowl commonplace disbursed algorithms in academia and trade. we can cover distributed algorithms for: Convex Optimization Matrix Factorization desktop getting to know Neural Networks The Bootstrap Numerical Linear Algebra tremendous Graph evaluation Streaming and online algorithms A shorter edition of this class turned into given at Spark Summit 2015: [slides] category format throughout the class, topics might be illustrated with arms-on workout routines the use of the excessive-speed cluster programming framework, Spark, with computing substances supplied via the instructor. The design of allotted algorithms primarily differs from common algorithms within the requirement to trust communication cost, so there can be evaluation of communication charge. Pre-requisites: focused on graduate college students having taken Algorithms on the level of CME 305 or CS 261. Being able to properly application in any main-circulate excessive stage language. There may be three homeworks, one scribed lecture, and a challenge. students taking the type for credit score/no credit in its place of letter grade can pass the assignment. non-compulsory textbooks:Convex Optimization by Boyd and Vandenberghe [BV]Randomized Algorithms by way of Rajeev Motwani and Prabakhar Raghavan [MR]aspects of Statistical studying by using Trevor Hastie, Robert Tibshirani, Jerome Friedman [HTF] Homework Homework 1 [pdf] [tex] [solutions], accumulated Monday April 20th in class Homework 2 [pdf] [tex] [solutions], amassed Monday may 4th in classHomework three [pdf] [tex] [solutions], accrued Monday can also 18th in class Scribe template Lectures and References Lecture 1: disbursed Computing with Spark [slides] [typical cluster] Lecture 2: disbursed Optimization Overview [slides] [SQL guide] [RDD guide] [PairRDD API] Lecture 3: Complexity measures for clusters [notes] [last reducer] Lecture 4: Shuffling statistics to do be part of, Groupby, and different all-to-all conversation patterns [slides] [notes] [timsort] Lecture 5: fingers-on a true cluster in classification, half 1 [slides] [streaming demo] Lecture 6: fingers-on a true cluster in type, part 2 [slides] [parquet] [guide] Lecture 7: Partitioning for repeated joins and Pagerank [slides] [notes] Lecture eight: The Pregel information movement paradigm [slides] [notes] [pregel] [graphx] Lecture 9: Matrix Computations: Multiplication, Singular value Decomposition (Tall and thin, rectangular), PCA [slides] [notes] Lecture 10: Covariance Matrix and All-pairs Similarity [slides] [notes] Lecture eleven: Streaming Stochastic Gradient Descent for Generalized Linear fashions, Streaming okay-capability [notes] [hogwild] [parallel SGD] [SGD convergence] Lecture 12: Streaming gadgets via a cluster with Spark Streaming, Perceptron Introduction [slides] [notes] [streaming examples] Lecture 13: Streaming Proof, Alternating course formulation of Multipliers (ADMM), concept/observe interface, AllReduce [notes] [ADMM resources] [ADMM on Spark] [Slide 37] Lecture 14: Matrix Completion, Alternating Least Squares, Generalized Low Rank models [notes] [slides] [paper summary] [GLRM] [FastALS] Lecture 15: Neural Networks [notes] [DistBelief] Lecture sixteen: allotted resolution timber, Bag of little Bootstraps [notes] [PLANET] [BLB] projects Swaroop Indra Ramaswamy and Rohit Patki: dispensed minimum spanning bushes. [slides] [report] Carlos Riquelme, Lan Nguyen and Sven Schmit: Cascading vector machines. [slides] [report] [Github] Benoit Dancoisne, Emilien Dupont and William Zhang: disbursed Max-movement in Spark. [slides] [report] [Github] Kevin Chavez, Hao Yi Ong and Augustus Hong: disbursed Deep Q-discovering. [slides] [report] [Github] Zi Yin and Zhiang Hu (Harvy): Parallelized Union find Set, with an software in discovering linked accessories in a Graph. [slides] [report] Charles Y. Zheng, Jingshu Wang and Arzav Jain: All-Pairs Shortest Paths in Spark. [slides] [report] [Github] Haoming Li and Bangzheng He: A disbursed Solver for Kernalized SVM. [slides] [report] Yilong Geng and Mingyu Gao: disbursed solid Marriage with Incomplete record and Ties using Spark. [slides] [report] [Github] David Daniels, Eric Liu and Charles Zhang: distributed Structural Estimation of Graph part-class Weights from Noisy PageRank Orders. [slides] [report] [Github] Yifan Jin and Shaun Benjamin: Monte Carlos Tree Search. [slides] [report] [Code] Orren Karniol-Tambour: data Parallel EM for estimating the Genome Relative Abundance (GRA) in Metagenomic Samples. [slides] [report] [Github] Supplementary materials advanced records Science on Spark: [slides] Spark Intro Tutorial: [slides] [code and data – 1 GB] Spark Devops Slides: Spark Summit slides Tutorial: Stanford Spark Workshop exercises Tutorial: movie suggestion with MLlib Tutorial: Graph Analytics with GraphX Contact Reza: rezab at stanford.eduOffice hours: by way of appointment TA Dieterich Lawson: jdlawson at stanford.eduOffice hours: Tuesdays four-6pm Simon Anastasiadis: simonsa at stanford.eduOffice hours: Wednesdays 2:15-four:15pm TA office hours will be held within the Huang Engineering center basement (in entrance of the ICME workplace) Pyro Q-CpG™: quantitative evaluation of methylation in varied CpG websites by way of Pyrosequencing® Methylation of cytosines in CpG dinucleotides is a crucial regulator of gene expression in the human genome. adjustments in methylation are now time-honored to have a fundamental role in the development of numerous tumors. Quantitative measurement of variation of methylation over time and amongst tissues will exhibit critical correlations with different organic phenomena. Pyro Q-CpG is attractive for the analysis of CpG methylation because it is capable of quantifying methylation in explicit sequence context, and is speedy and straightforward to function. Assay design is flexible, because the distance from the first base to be sequenced can be distinct, and hence, the primer can usually be positioned in a place free of CpG websites. moreover, there are 4 options for design: the assay may also be performed in ahead or reverse orientations, and on both the proper or the bottom strands. The approach uses bisulfite treatment and PCR to distinguish methylated cytosine (mC) from unmethylated cytosine (C), and Pyrosequencing to quantify the ratio mC:C at each site1,2,three,4,5. It was first mentioned in 2002 (ref. 1) and independently developed via other groups2,3,4,5. Quantification by way of Pyrosequencing Pyrosequencing analyzes single-stranded DNA templates by using synthesizing complementary strands. in brief, the 4 nucleotides (A, T, G and C) are introduced sequentially by using a Pyrosequencing instrument to DNA templates. For each a success nucleotide incorporation, pyrophosphate (PPi) is launched. PPi is transformed in enzyme-catalyzed reactions to force gentle emission in a volume that’s proportional to the variety of incorporations6 (Fig. 1). for this reason, height heights in the Pyrogram™ inform on homopolymeric sequences and allele frequencies. determine 1: The precept of Pyrosequencing and the output Pyrogram™. Double top heights indicate incorporations of two nucleotides in a row. precept of analysis As with most methods for quantitative analysis of CpG methylation, CpG sites of genomic DNA are first chemically transformed by bisulfite treatment and then amplified through PCR. in this technique, C is converted to uracil (U), whereas mC is still unchanged. within the subsequent PCR, U is amplified as thymine (T), and mC is amplified as C. in the Pyrogram, mC and C are hence represented as C and T peaks, respectively. These top heights are proportional to the variety of methylated alleles at every CpG website (Fig. 2). determine 2: precept of evaluation. Unmethylated C (purple) and methylated C (green) are differentiated via bisulfite remedy and PCR. The ratio C:mC at each CpG site (peaks in orange column) is measured in sequence context. C not followed by means of G acts as control for the bisulfite step (blue column). Experimental issues Sequence context is a crucial handle as a result of bisulfite-treated, PCR-amplified DNA is A-T-rich, which decreases sequence version. Pyro Q-CpG hence guarantees that the relevant sequence turned into analysed. Pyro Q-CpG assays can include an inner manage for bisulfite treatment. C that isn’t adopted via G in sequence isn’t methylated, and should be completely transformed to T through bisulfite and PCR. To ascertain this, all templates may still exhibit only T and zero C in this place (Fig. 2). Pyro Q-CpG is functional in terms of beginning fabric and throughput. DNA is with ease analyzed from both fresh frozen tissue as well because the brief PCR fragments that are commonplace of paraffin-embedded tissue, by which restriction fragment analysis could be elaborate. The analysis takes about one hour for ninety six specimens in parallel, at a fraction of the cost and time of equivalent dideoxy sequencing reactions. Workflow commercial reagent kits are available for bisulfite remedy of human genomic DNA. The PCR is carried out with one of the crucial PCR primers biotinylated. this is required for the conversion of the PCR product to single-stranded DNA templates. A sequencing primer is then introduced, which anneals to the single-stranded DNA template. Analyses are automated, permitting routine processing of 96 samples in parallel. Pyro Q-CpG Pyro Q-CpG is an entire answer from Biotage for methylation evaluation that exploits the advantages of Pyrosequencing technology. Pyro Q-CpG includes PyroMark™ instrumentation and optimized application for CpG methylation analysis, as well as validated analysis-Use-most effective (RUO) tests for measuring methylation in particular genes. The PyroMark RUO exams include assays for methylation in p16INK4A (CDKN2A), MLH1, MGMT, RASSF1A, in addition to Prader-Willi and Angelman syndromes, with more checks in the pipeline. Instrument users can entry over 1,000 assays in the PyroMark on-line assay database, which incorporates assays for single nucleotide polymorphism (SNP), mutation and methylation analysis. For researchers who choose to outsource methylation evaluation, Biotage presents session for customized methylation assay design and laboratory functions for pattern analysis, including bisulfite treatment. summary Pyro Q-CpG from Biotage presents a few merits for methylation analysis. basically, reproducible quantification of consecutive CpG websites is convenient and speedy on 96 samples in parallel. Assay design is flexible. The components is flexible for a number analyses, from single and distinct consecutive CpGs to estimations of world methylation. As methylation of each website is measured within the context of the DNA sequence, software instantly performs fine handle of the uncooked records to make sure that the expected sites had been analyzed. furthermore, Cs no longer followed by a G are used as high-quality handle to evaluate even if the bisulfite medication went to completion, thereby making certain reliable facts. The method is proper for analysis of sparkling -frozen, mounted and paraffin-embedded specimens. Pyro Q-CpG is a valuable strategy for acquiring quantitative methylation information which are related over time. Pyro Q-CpG can as a result further our understanding on the variability of methylation with exterior variables reminiscent of medication, individual and tissue pattern (Fig. three), which is a prerequisite for establishing models describing methylation, gene expression and drug response. determine 3: facts output from evaluation of seven CpG sites within the p16INK4A promoter. Methylation tiers in simple tumor ( a ) and metastatic lymphnodes ( b ) in head and neck melanoma. facts courtesy of R. Krahe, M.D. Anderson melanoma middle..

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