A functional proteogenomic analysis of endometrioid and clear cell carcinomas using reverse phase protein array and mutation analysis: protein expr...
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2014 Feb 22;14:120. doi: 10.07-14-120.A functional proteogenomic analysis of endometrioid and clear cell carcinomas using reverse phase protein array and mutation analysis: protein expression is histotype-specific and loss of ARID1A/BAF250a is associated with AKT phosphorylation., , , , , , , , , , , , , , , 1.1Department of Surgical Oncology, British Columbia, Cancer Agency, Vancouver, BC, Canada. mark.carey@vch.ca.AbstractBACKGROUND: Ovarian cancer is now recognized as a number of distinct diseases primarily defined by histological subtype. Both clear cell ovarian carcinomas (CCC) and ovarian endometrioid carcinomas (EC) may arise from endometriosis and frequently harbor mutations in the ARID1A tumor suppressor gene. We studied the influence of histological subtype on protein expression with reverse phase protein array (RPPA) and assessed proteomic changes associated with ARID1A mutation/BAF250a expression in EC and CCC.METHODS: Immunohistochemistry (IHC) for BAF250a expression was performed on 127 chemotherapy-naive ovarian carcinomas (33 CCC, 29 EC, and 65 high-grade serous ovarian carcinomas (HGSC)). Whole tumor lysates were prepared from frozen banked tumor samples and profiled by RPPA using 116 antibodies. ARID1A mutations were identified by exome sequencing, and PIK3CA mutations were characterized by MALDI-TOF mass spectrometry. SAM (Significance Analysis of Microarrays) was performed to determine differential protein expression by histological subtype and ARID1A mutation status. Multivariate logistic regression was used to assess the impact of ARID1A mutation status/BAF250a expression on AKT phosphorylation (pAKT). PIK3CA mutation type and PTEN expression were included in the model. BAF250a knockdown was performed in 3 clear cell lines using siRNA to ARID1A.RESULTS: Marked differences in protein expression were observed that are driven by histotype. Compared to HGSC, SAM identified over 50 proteins that are differentially expressed in CCC and EC. These included PI3K/AKT pathway proteins, those regulating the cell cycle, apoptosis, transcription, and other signaling pathways including steroid hormone signaling. Multivariate models showed that tumors with loss of BAF250a expression showed significantly higher levels of AKT-Thr308 and AKT-Ser473 phosphorylation (p & 0.05). In 31 CCC cases, pAKT was similarly significantly increased in tumors with BAF250a loss on IHC. Knockdown of BAF250a by siRNA in three CCC cell lines wild type for ARID1A showed no increase in either pAKT-Thr308 or pAKT-S473 suggesting that pAKT in tumor tissues is indirectly regulated by BAF250a expression.CONCLUSIONS: Proteomic assessment of CCC and EC demonstrates remarkable differences in protein expression that are dependent on histotype, thereby further characterizing these cancers. AKT phosphorylation is associated with ARID1A/BAF250a deficient tumors, however in ovarian cancers the mechanism remains to be elucidated.PMID:
[PubMed - indexed for MEDLINE] PMCID: PMC3941949 Hierarchical clustering of samples and proteins analyzed by RPPA. CCC and ECs form distinct clusters separated by two major high-grade serous carcinoma (HGSC) subgroups. Differential expression of proteins was examined by significance analysis of microarray data (SAM analysis) for both CCC and EC compared to HGSC as the reference group.BMC Cancer. -120.SAM Analysis of differentially expressed proteins by histotype: A. Upregulated and B. Down-regulated Proteins in Clear Cell and Endometrioid Carcinoma by SAM analysis on RPPA data, with High Grade Serous Carcinoma (HGSC) as the reference group. Proteins with FDR* of &5% are shown. Proteins that are over or under expressed in both CCC and EC are shown in the center between the two subtypes. Note: *FDR (False discovery rate): For each analysis (e.g. CCC vs. EC), the percent probability that the difference in protein expression for each comparison is attributable to chance after correcting for multiple parameter testing.BMC Cancer. -120.Heat map with samples categorized according to BAF250a IHC scores and PIK3CA mutation status. No obvious clustering patterns due to either BAF250a by IHC or PIK3CA mutation status are present. Note: capital letters for each sample histotype label (eg. CCC) indicates expression of BAF250a on IHC, small letters (e.g. ccc) indicates loss of BAF250a expression. For PIK3CA mutations, a + sign after the sample label (e.g. CCC+) indicates the presence of a PIK3CA mutation (either helical, kinase, or other) whereas a – sign indicates no mutation.BMC Cancer. -120.A) Western blot results from siRNA knockdown of BAF250a on cell lines ES2, JHOC5, and RMG1 to clarify the interaction between BAF250a expression and pAKT. Despite good knockdown of BAF250a no change in AKT phosphorylation or levels of p70S6K, a downstream signaling protein of pAKT can be seen in the ES2 and RMG1 cell lines. The baseline levels of pAKT are much higher in the JHOC5 cell line, and there is a suggestion of an increase in pAKT-Thr308 with BAF250a knockdown without obvious similar changes in pAKT-Ser473. PDK1 and PTEN levels did not change with BAF250a knockdown in any of the cell lines. B-D) Native protein AKT profiles using capillary tube isoelectric point focusing. Native AKT profiles are consistent with the western blot result in A, as little change occurs in AKT/pAKT following siRNA mediated BAF250a knockdown.BMC Cancer. -120.Publication TypesMeSH TermsSubstancesGrant SupportFull Text SourcesOther Literature Sources
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& WebMD, LLC. All rights reserved.WebMD does not provide medical advice, diagnosis or treatment. .Lawsuit Filed Today on Behalf of Chimpanzee Seeking Legal Personhood
on Monday, December 2, 2013 & &
This morning at 10.00 E.T., the Nonhuman Rights Project filed suit in Fulton County Court in the state of New York on behalf of Tommy, a chimpanzee, who is being held captive in a cage in a shed at a used trailer lot in Gloversville.
This is the first of three suits we are filing this week. The second will be filed on Tuesday in Niagara Falls on behalf of Kiko, a chimpanzee who is deaf and living in a private home. And the third will be filed on Thursday on behalf of Hercules and Leo, who are owned by a research center and are being used in locomotion experiments at Stony Brook University on Long Island.
The lawsuits ask the judge to grant the chimpanzees the right to bodily liberty and to order that they be moved to a sanctuary that’s part of the North American Primate Sanctuary Alliance (NAPSA), where they can live out their days with others of their kind in an environment as close to the wild as is possible in North America.
The legal team decided to do a clean sweep of all the chimpanzees we could find in the state of New York.
Rather than filing a single suit, the legal team decided to do a clean sweep of all the chimpanzees we could find in the state of New York. This was, in part, because we were increasingly worried about their health and welfare, in that two other chimpanzees who were originally going to be our first plaintiffs both died before we could bring the case.
Those two were Merlin and Reba, who were living in intolerable conditions at a roadside zoo, the . The day our investigative team first visited this zoo, they found Merlin living alone, next to a bear, a tiger, and other animals pacing in their cages. When they asked about Merlin’s companion, Reba, they were told that she had recently died. Three months later, we visited the zoo a second time, only to discover that Merlin’s cage was empty. He, too, had died, two days earlier, of complications from an abscessed tooth. The owner of the zoo told us that Merlin had been punching himself in the face for several weeks before they had realized that something was the matter. He died in surgery.
And then, just a few weeks ago, Kiko’s companion, Charlie, died of a heart condition that is common to chimpanzees in captivity. He was only about 28 years old.
When we visited Tommy, we found him in a small cage at the back of a dark shed at a trailer sales park that’s also home to a business called Santa’s Hitching Post that rents out reindeer for Christmas shows and other entertainment. Tommy was all by himself – his only company being a TV on a table on the opposite wall. Three years ago, to the best of our knowledge, there were four chimpanzees at Santa’s Hitching Post, and not long before that there were six.
With so many deaths having occurred so recently, we were now deeply concerned that Tommy, too, could die at any time before he could ever have a chance to walk on grass and climb in trees with others of his own kind. The same could also happen to Kiko, who has inner ear problems and suffers from motion-type sickness due to abuse early in his life. (We have no insight into the condition of Hercules and Leo since there is no way for us to gain access to the laboratory at Stony Brook.)
So, the conclusion of the legal team was to move as quickly as possible and to file suit on behalf of all the chimpanzees we could locate in the state. (There may, in fact, be more than these four, but no official record exists in New York State of chimpanzees who are being owned by humans.)
The Writ of Habeas Corpus
The legal cause of action that we are using is the common law writ of habeas corpus, through which somebody who is being held captive, for example in prison, seeks relief by having a judge call upon his captors to show cause as to why they have the right to hold him.
More specifically, our suits are based on a case that was fought in England in 1772, when an American slave, James Somerset, who had been taken to London by his owner, escaped, was recaptured and was being held in chains on a ship that was about to set sail for the slave markets of Jamaica. With help from a group of abolitionist attorneys, Somerset’s godparents filed a writ of habeas corpus on Somerset’s behalf in order to challenge Somerset’s classification as a legal thing, and the case went before the Chief Justice of the Court of King’s Bench, Lord Mansfield. In what became one of the most important trials in Anglo-American history, Lord Mansfield ruled that Somerset was not a piece of property, but instead a legal person, and he .
A clear case as to why these cognitively complex, autonomous beings have the basic legal right to not be imprisoned.
New York State recognizes the continuing viability of the common law writ of habeas corpus. New York case law permitted slaves to use the writ to challenge their status as legal things and establish their right to freedom. And the state also adopted Lord Mansfield’s celebrated habeas corpus ruling in the Somerset case.
While our legal petitions and memoranda, along with affidavits from some of the world’s most respected scientists, lay out a clear case as to why these cognitively complex, autonomous beings have the basic legal right to not be imprisoned, we cannot, of course, predict how each of the judges in the three county courts will respond. Habeas corpus cases are usually heard soon after being filed since the person is being held captive. So it’s possible that the judges in any or all of these cases could move quickly to a hearing – or to deny the petition altogether. On the other hand, considering that this is new legal territory, they could slow the proceedings down. And each judge could rule in a different way.
Whatever happens in the trial court, however, New York allows for an automatic appeal of an adverse habeas corpus decision. And either side can appeal the ruling. So our case will be heard, sooner or later, by New York’s intermediate appellate court, and quite possibly by New York’s highest court, the State Court of Appeals. And, from many points of view, that’s where we would like the case to be heard, since what happens at the appellate level has much wider reach than at the trial level.
Future suits
When, in 1772, Chief Justice Lord Mansfield ruled that James Somerset was a “legal person” who could not be held as another person’s property, this did not bring an end to slavery in the American colonies. Rather, it set the stage for numerous similar suits to be filed in courts across the newly formed states. In some cases, mainly in the north, judges ruled that the petitioners were “legal persons” with fundamental rights and set them free. In other cases, they did not.
Our goal is to breach the legal wall that separates all humans from all nonhuman animals.
Several states in the south, which considered slaves to be simply chattel, not legal persons, simply barred them altogether from using habeas corpus to challenge their enslavement. (Ultimately, it took almost a full century and then a civil war for the matter to be resolved.) And with rulings of that kind still in place in several states, the Nonhuman Rights Project would likely have a hard time demonstrating that any nonhuman animals are anything but chattel, too.
Our strategy, then, is to file as many suits as we have the funds to be able to pursue, and in the states where we have the best chance of winning them. We will also encourage other animal rights attorneys and legal experts to file similar cases, modeled on the ones that have been successful.
section of this website you can check out an interactive map that includes a brief synopsis of how previous rulings and subsequent laws may or may not favor our suits.)
Our goal is, very simply, to breach the legal wall that separates all humans from all nonhuman animals. Once this wall is breached, the first nonhuman animals on earth will gain legal “personhood” and finally get their day in court — a day they so clearly deserve.
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This is absolutely great news and I look forward to seeing the NHrP present its reasoned argument for legal personhood and standing for release from confinement in a court of law. It is time to confront this issue.
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The Nonhuman Rights Project is the only civil rights organization in the United States working to achieve actual LEGAL rights for members of species other than our own.
Our mission is to change the legal status of appropriate nonhuman animals from mere “things,” which lack the capacity to possess any legal right, to “persons,” who possess such fundamental rights as bodily integrity and bodily liberty.
Our first cases were filed in 2013 on behalf of we plan to continue to file as many lawsuits as we have funds available. Your support of this work is deeply appreciated!
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＞＞＞Washoe is a young chimpanzee(黑猩猩). She is no ___1___ chi..
Washoe is a young chimpanzee(黑猩猩). She is no ___1___ chimpanzee, though. Scientists are doing a research ___2___ her. They want to see how civilized(驯化) she can ___3___. Already she does many things a human being can do. For example, she has been learning how to exchange ___4___ with people. The scientists are teaching her ___5___ language. When she wants to be picked ___6___, Washoe points up with one finger. She rubs her teeth with her finger ___7___ she wants to brush her teeth. This is done after every meal. Washoe has also been ___8___ to think out and find answers to problems. Once she was put in a ___9___ with food hanging from the ceiling. It was too high to ___10___. After she considered the ___11___, she got a tall box to stand ___12___. The food was still too high to be reached. Washoe found a ___13___ pole. Then she climbed onto the ___14___, grasped the pole, and ___15___ down the food with the pole. Washoe ___16___ like a human, too. The scientists keep her in a fully furnished(家具齐全的) house. After a hard ___17___ in the laboratory, she goes home. ___18___ she plays with her toys. She ___19___ enjoys watching television before going to bed. Scientists hope to ___20___ more about people by studying our closest relative(亲属) — chimpanzee. 1. A. foolish&& B. ordinary&&&& C. special&&&&&& D. simple2. A. for& B. by&&&&& C. to&&&&&& D. on3. A. experience&&&& B. change&&&&&& C. develop&&&&& D. become4. A. actions&& B. views& C. messages&&& D. feelings5. A. sign&&&&&& B. human&&&&&& C. spoken&&&&&& D. foreign6. A. out B. at&&&&&& C. on&&&&& D. up7. A. when&&&& B. until&& C. since&& D. while8. A. raised&&&& B. trained&&&&&& C. ordered&&&&& D. led9. A. cave&&&&&& B. zoo&&&& C. room& D. museum10. A. pull&&&&& B. see&&&&& C. eat&&&&& D. reach11. A. problem&&&&&& B. position&&&&& C. food&& D. ceiling12. A. by B. on&&&&& C. up&&&&& D. with13. A. straight B. strong C. long&&& D. big14. A. wall&&&& B. box&&&& C. ceiling&&&&&& D. pole15. A. knocked&&&&& B. picked C. took&&& D. shocked16. A. lives&&&& B. acts&&&& C. thinks D. plays17. A. task&&&&& B. lesson C. day&&&& D. time18. A. Here&&& B. There& C. So&&&&& D. Then19. A. quite&&& B. already&&&&&& C. even&& D. still20. A. observe&&&&&& B. discover&&&& C. gain&&& D. learn
题型：完形填空难度：偏易来源：不详
1---20&&& BDDCA&& DABCD&& ABCBA&& ACBCD&&科学家通过实验测试黑猩猩所能驯化的程度。1. B。句中的 though 是副词，意为“可是”，根据下文描述的实验情况可知“这只黑猩猩不是一只 ordinary(普通的)黑猩猩”。2. D。do a research on 意为“对…进行研究”。3. D。四个选项中只有 become 是连系动词，其后接形容词 civilized 作表语。4. C。下文说到：当黑猩猩想要被抱起时，她将手指向上指；当她想要刷牙时，则用手指刮牙齿。这说明她与人们交换的是“信息”，即 message。5. A。根据下文：当黑猩猩想要被抱起时，她将手指向上指；当她想要刷牙时，她则用手指刮牙齿。这说明黑猩猩用的是“手势语”，即 sign language。6. D。pick up 有很多意思，如表示：拿起，捡起；收拾，整理；学会；(用车)来接，去取；改进，改善；重新开始，继续；感染(疾病、坏习惯)等。它在本句中的意思是“抱起”。7. A。根据上一句的结构可推知。8. B。根据下文的语境可推知。9. C。注意本句后面的信息词 ceiling(天花板)。根据常识，四个选项中只有 C 才具备有 ceiling。10.D。根据后面的 The food was still too high to be reached 可推知答案。11. A。根据上文的 ... to think out and find answers to problems 可知此处应填 problems。12. B。黑猩猩弄来盒子是为了增加高度，所以她应站在箱子之上，即填介词 on。13. C。站在箱子上，高度仍不够，故又弄来一根 pole(竿)。根据常识，在此情况下，这 pole 的特征应是 long。14. B。根据上文可知。15. A。根据常识和语境，黑猩猩此时应是用竿 knock 食物。16. A。从本段后面内容可知，这只黑猩猩是像人一样在“生活”(live)。17. C。根据下文语境用排除法可推知答案。18. B。根据上文可知这里的 there 指“在家里”。19. C。对于黑猩猩来说，enjoys watching television before going to bed 显然比 play with toys 更不常见，故用even(甚至)强调后者。20. D。learn 的意思是“了解”，即指通过研究黑猩猩来“了解”人类自己。
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据魔方格专家权威分析，试题“Washoe is a young chimpanzee(黑猩猩). She is no ___1___ chi..”主要考查你对&&科教类阅读，健康环保类阅读&&等考点的理解。关于这些考点的“档案”如下：
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因为篇幅有限，只列出部分考点，详细请访问。
科教类阅读健康环保类阅读
科教类阅读的概念：
科教类阅读主要考查考生对书面语篇的整体领悟能力和接受及处理具体信息的能力。试题的取材，密切联系当前我国和世界经济、科技等方面的变化，有关数据的来源真实可信。科教类文章阅读技巧：
一、材料特点：这类文章的总体特点是：科技词汇多，句子结构复杂，理论性强，逻辑严谨。具体说来它有以下几个特点：　1、文章中词汇的意义比较单一、稳定、简明，不带感情色彩，具有单一性和准确性的特点。这类文章通常不会出现文学英语中采用的排比、比喻、夸张等修辞手法，一词多义的现象也不多见。　2、句子结构较复杂，语法分析较困难。为了描述一个客观事物，严密地表达自己的思想，作者经常会使用集多种语法现象于一体的长句。　3、常使用被动语态，尤其是一些惯用被动句式。二、命题特点：科普类阅读的主要命题形式有事实细节题、词义猜测题、推理判断题以及主旨概括题等，其中推理判断题居多。三、应对策略：1、要想做好科普英语阅读理解题，同学们就要注意平时多读科普知识类文章，学习科普知识，积累常见的科普词汇，从根本上提高科普英语的阅读能力。 2、要熟悉科普类文章的结构特点。科普类文章一般由标题(Head line)，导语(Introduction)，背景(Back ground)，主体(Main body)和结尾(End)五部分构成。标题是文章中心思想高度而又精辟的概括，但根据历年的高考情况来看，这类阅读理解材料一般不给标题，而要同学们选择标题。导语一般位于整篇文章的首段。背景交待一个事实的起因。主体则对导语概括的事实进行详细叙述，这一部分命题往往最多，因此，阅读时，同学们要把这部分作为重点。结尾往往也是中心思想的概括，并与导语相呼应，命题者常在此要设计一道推理判断题。　　3、在进行推理判断时，同学们一定要以阅读材料所提供的科学事实为依据，同时所得出的结论还应符合基本的科普常识。科普类阅读应试策略：
【命题趋势】阅读理解题主要考查考生对书面语篇的整体领悟能力和接受及处理具体信息的能力。试题的取材，密切联系当前我国和世界经济、科技等方面的变化，有关数据的来源真实可信。因此科普知识类文章是每年的必考题。分析历年的科普类文章我们不难发现以下特点： 1、文章逻辑性强，条理清楚，语法结构简单，用语通俗。 2、文章内容注重科技领域的新发现。内容新颖，从而使文章显得陌生，内容抽象复杂。 3、命题方面注意对具体细节的准确理解和以之为依据的推理判断。 4、以人们的日常行为或饮食健康入手，探讨利弊，诠释过程，阐述概念。【应试对策】许多考生在考试时感到困惑的是：为什么一些没有超越中学语法和词汇范围的篇章，读起来却不能正确理解，或者要花费很多时间才能读懂呢？这种现象的产生与阅读方法有很大的关系。例如，有的考生在考试时一见到文章就立刻开始读，结果读了半天，还不知道短文讲的是什么，试题要求了些什么，结果浪费了大量的时间，而阅读效果并不好。那么，怎样读效果才好呢？任何一种阅读方法或技巧的使用，都是由篇章特点和试题本身的要求决定的，应根据不同的体裁和试题要求采取不同的策略。 1、浏览。浏览的主要目的就是确定文章的体裁。如果文章属于人物传记、记叙文、故事、科普小品和有关社会文化、文史知识的文章，一般来说，应该先看看文章的试题考查内容，对题目类型做到心中有数，针对不同问题，在通读时有粗有细地去阅读，这样不仅能把握篇章的基本结构和逻辑线索，也能做好有关具体事实信息考查的试题。 2、挖掘寓意，掌握中心思想，推出结论。任何文章，作者在行文时都有一定的写作目的和主要话题。在通读篇章时应该吃透作者的写作意图，抓住文章的主题句，充分发挥自己的想象力和概括力，作出对中心思想的归纳和结论的推断。 3、把握篇章结构，利用上下文进行推测。高考中的阅读理解篇章往往是一个较完整的短文，其结构、思想，前后上下连贯统一。考试时应充分利用这一特点推测一些生词、短语在句中的含义，切莫盲目孤立猜测。 4、综观全篇，前后呼应。这是阅读理解的最后一步，在做完阅读理解题后，要立足于文章整体，再迅速读一遍短文，短文中的问题和答案的设置前后都是相关联的，有着一定的连续性，体现着文章的基本脉络。健康环保累阅读概念：
健康环保类文章常是介绍科学知识、生活常识和环境保护方面的短文。体裁有记叙文、 说明文、议论文和各种应用文。 健康环保类文章阅读技巧：
&&&&&&&健康环保类文章常是介绍科学知识、生活常识和环境保护方面的短文。阅读此类短文要以现象或事物为中心进行思考，理解现象产生的原因、条件和客观规律等。同时要抓住事物的特征、用途和相互关系等。科普环保类文章一般为说明文，从结构上看大致可分为三个部分：&&&&&& 第一部分一般是文章的首段，主要用来提出文章的主题，即文章想要阐述、说明的主要内容；&&&&&& 第二部分是文章的主体，可由若干个段落组成，对文章的主题进行展开说明；&&&&&& 第三部分是结尾段，对文章的主题进行归纳总结。这类文章多用一般现在时，而且一般多使用客观性词语表述。有时为了强调客观性，也常使用被动语态。&&&&&& 从近几年的考试题来看，科普环保类的文章越来越与人们的实际生活相接近。由于此类文章缺乏故事情节，很多同学对此类文章感到费解。但一般的科普类文章都是就事论事，需要逻辑推理和想象的时候较少，因此此类阅读题也没有同学们想象中的那么难，只要多加训练，就能较好地答题。【阅读策略】 1、概要(Summarizing)：&&&&&&阅完材料后，将所阅材料浓缩，摘要，做出所阅材料的书面或口头梗概。 2、组织(Organization)：&&&&& 阅读后根据阅读内容，识别观点、人物、事件之间的关系以及文章的结构关系。如：时间关系、比较或对比关系、相关关系及因果关系等。
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