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Self-Correcting RNA: Is It a Missing Link?

first_imgA team of Russian scientists at Rutgers discovered a remarkable phenomenon: RNA that proofreads itself during its own synthesis.  The work was reported in Science1: “We show that during transcription elongation, the hydrolytic reaction stimulated by misincorporated nucleotides proofreads most of the misincorporation events and thus serves as an intrinsic mechanism of transcription fidelity.”  It has already been known that DNA transcription and translation includes a whole suite of error-correcting mechanisms, but this is the first instance of RNA self-correction.    The researchers did not comment on the evolution of this capability except to state that it “is likely evolutionarily conserved” (i.e., unevolved in all living organisms), and that in an RNA-protein world, a “proofreading and repair mechanism similar to the one described here could have allowed a large RNA genome of the last common universal ancestor to exist.”  This is because without an accurate proofreading mechanism even in an RNA world, duplication fidelity would have been too low for evolution: “the relatively low fidelity of RNAP-catalyzed synthesis could not have been sufficient for stable maintenance of large RNA genomes in the absence of cleavage factors.”    Patrick Cramer (Gene Center Munich), however, writing in the same issue of Science,2 launched their final, speculative paragraph into a story of how this RNA must be a missing link.  Starting with the admission that “Precision can be vital,” Cramer immediately invoked the E word: “cells have evolved processes for proofreading and correction to shut down the propagation of errors” in the DNA-to-protein pathway.  Referring to the work by Zenkin et al., he said, “This finding helps to explain the fidelity of gene transcription and suggests that self-correcting RNA was the genetic material during early evolution.”    But how, exactly, could that have come about?  In his missing-link story, notice how many times Cramer used speculation words like could, probably and suggests compared to the hard requirements of reality:The discovery of self-correcting RNA transcripts suggests a previously missing link in molecular evolution.  One prerequisite of an early RNA world (devoid of DNA) is that RNA-based genomes were stable.  Genome stability required a mechanism for RNA replication and error correction during replication, which could have been similar to the newly described RNA proofreading mechanism described by Zenkin et al.  If self-correcting replicating RNAs coexisted with an RNA-based protein synthesis activity, then an early RNA-based replicase could have been replaced by a protein-based RNA replicase.  This ancient protein-based RNA replicase could have evolved to accept DNA as a template, instead of RNA, allowing the transition from RNA to DNA genomes.  In this scenario, the resulting DNA-dependent RNA polymerase retained the ancient RNA-based RNA proofreading mechanism.    Whereas an understanding of RNA proofreading is only now emerging, DNA proofreading had long been characterized. DNA polymerases cleave misincorporated nucleotides from the growing DNA chain, but the cleavage activity resides in a protein domain distinct from the domain for synthesis.  The spatial separation of the two activities probably allowed optimization of two dedicated active sites during evolution, whereas RNA polymerase retained a single tunable active site.  This could explain how some DNA polymerases achieve very high fidelity, which is required for efficient error correction during replication of large DNA genomes.Of course, being only a “scenario” for how proofreading “could” have evolved, Cramer offered no evidence, lab or otherwise, for such a self-correcting RNA “missing link.”  For a discussion of problems with the RNA-world scenario, see the 07/11/2002 entry.1Zenkin, Yuzenkova and Severinov, “Transcript-Assisted Transcriptional Proofreading,” Science, 28 July 2006: Vol. 313. no. 5786, pp. 518 – 520, DOI: 10.1126/science.1127422.2Patrick Cramer, “Perspectives: Molecular Biology: Self-Correcting Messages,” Science, 28 July 2006: Vol. 313. no. 5786, pp. 447 – 448, DOI: 10.1126/science.1131205.Was blindness ever so dark as to look design in the eye, and attribute it to mindless chance?  The blind see naught but their own imaginations.  Cramer took an incredibly wondrous phenomenon (imagine! self-correcting code) and weaved a purely fictional tale about how it emerged from The Ancient Soup.  Yet this is the myth that our culture only allows to be heard by students in public schools, because any other explanation, such as design, is classified as “religion” (along with, presumably, rocket-launching Hezbollah terrorism).  In the same issue of Science was a very positive book review of a new work about Richard Dawkins, the rabidly atheistic Darwinist who subscribes to the Ancient Soup myth or something very like it: reviewer David C. Queller says, “Dawkins spills his own dirty, obscene secret, again no less powerful now that we have known it for 30 years.  All flesh is survival machinery, and the survival it promotes is that of our selfish genes.”    If this makes you angry, then it is time to take back science from the powers of darkness, obscenity, and selfishness that swept in like a flood after Darwin.  What would the original founders of the American Association for the Advancement of Science, like Joseph Henry, think of what has become of their honorable institution?(Visited 32 times, 1 visits today)FacebookTwitterPinterestSave分享0last_img read more

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South Africa’s first woman police chief

first_img13 June 2012 President Jacob Zuma has appointed South Africa’s first female national police commissioner, Mangwashi Victoria Phiyega, to replace Bheki Cele, who has been fired after a presidential board of inquiry found him unfit for office. Phiyega has been serving as chairperson of the Presidential Review Committee on State-Owned Enterprises, and deputy chair of the Independent Commission for the Remuneration of Public Office Bearers.‘Wealth of experience as senior executive’ “Ms Phiyega brings a wealth of experience as a senior executive who understands the responsibility of government in the fight against crime and the duties imposed in dealing with state assets,” Zuma told a press briefing in Pretoria on Tuesday. “I have every confidence that she will show leadership and acquit herself well as national commissioner.” Police Minister Nathi Mthethwa welcomed Phiyega’s appointment, saying she brought with her a “wealth of experience on strategic leadership and a sound management background, both from public service and the private sector”. This experience would “stand her in good stead as she steers the South African Police Service [SAPS] towards better compliance, systems integration, effective and greater accountability,” Mthethwa said.Cele ‘unfit for office’ In September last year, Zuma appointed a board of inquiry, chaired by Justice Jakes Moloi, to investigate alleged misconduct by Cele and pronounce on his fitness for office. “The board has found General Cele to be unfit for office and has recommended his removal from office in terms of the provisions of section 8(6)(b)(v) of the South African Police Service Act No. 68 of 1995,” Zuma said. “Having thoroughly considered the report of the board, and applied my mind thereto, I have decided to release General Cele from his duties.” Zuma said that Cele still had a lot to contribute to South Africa, adding that crime levels in the country had continued to drop under his tenure.Improving management, financial, security systems “However, the reports of the Public Protector and that of the board of inquiry indicate deficiencies administratively and in particular in relation to General Cele’s duties as an accounting officer,” Zuma said. Zuma said he had had a discussion with Police Minister Nathi Mthethwa about “what needs to be corrected immediately within the SAPS so that we can continue the excellent record of fighting crime”. This included management and financial systems as well as the breaches of information security which, Zuma said, had “unfortunately become common”. “We have in the past few weeks witnessed a disappointing spectacle of police officers jeopardising state security by placing information in the public domain, in contravention of their oath of office. This is unacceptable and cannot be tolerated if the fight against crime is to continue being effective.” Source: BuaNewslast_img read more

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Editing With Canon C300 Footage – Tips For When It All Goes Wrong

first_imgEditing Canon C300 MXF footage? Follow our tips to make video editing with C300 MXF footage go as smoothly as possible.Working with Canon C300 footage – which is XDCAM 422 50/Mbs footage in a .MXF wrapper – should ordinarily be quite straight forward. MXF files will work natively in Adobe Premiere and ingest quite happily through a free plugin in Final Cut Pro 7 and FCPX.  You can also bring this footage in through AMA into Avid Media Composer 6. AbelCine has an excellent step by step guide to importing C300 footage in Adobe Premiere CS6, Final Cut Pro X, FCP 7 and Avid Media Composer 6. You can check it out here.Everything will work seamlessly, that is, if your cards have been copied correctly to the hard drive with their entire folder structure intact. Without that folder structure you are effectively locked out of accessing your footage and an editing application like FCP7 will give you an error message like this one:How to Copy MXF Files CorrectlySo how do you copy cards correctly?Well first, and this may go without saying, but if you’re going to get an intern or producer to do it make sure they know what they’re doing. Essentially you must copy the entire card structure (preferably not through dragging and dropping in the finder).Sony and Canon both have free browser apps that will let you back up your media. Or you could invest in something like Shotput Pro to duplicate your cards to multiple drives simultaneously. You are backing them up as you go, right?If that’s not enough detail, just watch this great tutorial on a correct tapeless media workflow from Shane Ross. Although the tutorial winds up in Final Cut Pro 7, the initial principles are the same for any system. If you want even more tips, check out this great video from Chase Jarvis on his complete tapeless workflow.What To Do If Your C300 Card Structure Is BrokenIf for whatever reason your card structure doesn’t come across intact, what can you do?Depending on your NLE you have various options. If you’re in Adobe Premiere it doesn’t matter, as it will read the MXF files just fine.First, you can try to ‘fake it’ out by recreating the C300 card structure (which should look like the example below). In the past I’m sure I’ve gotten lucky with it but its a pretty slim chance of actually working.  FCPX needs a correct card structure so if you have to, transcoding in a 3rd party app is a feasible workaround.Free App For Converting C300 MXF FilesMiro is a great free app (one of the few free apps I found) that actually works and works well. Miro Video Converter will allow you to grab the .MXF files and transcode them into Pro Res 422, DNxHD and AVC Intra 1080p and 720p. You can batch transcode as many of them as you like and it works pretty quickly. The files look great and were a higher quality than files I created using the demo of MXF Converter for Mac from Pavtube. But as Miro is a free app, there are a few catches.First, you cannot specify the output folder and it defaults to your MacHD > User > Movies folder. So you need to have enough space on your boot drive to transcode the footage too. This is also a problem if you have multiple files with the same name, (which I had on this edit with a two camera shoot) as this means you have to transcode one set at a time and move them out of the folder so as not to overwrite them with the next batch. Annoying.Also the original camera footage I was working with had two audio tracks in it where as Miro would only export a single mono track. This was not helpful either as I needed to be able to mix each track individually.Paid Apps for Working With C300 MXF FilesAs I was editing on an FCP7 system I had to find a way to get my C300 MXF files to play nice with Final Cut Pro 7, while getting around the broken file structure. A cry for help on Twitter led to this great recommendation from Andy Mees who saved the day by suggesting I check out both MXF Import from Calibrated {Q} or MXF4Mac from Hamburg Pro Media. Both plugins essentially do the same thing which is to allow Quicktime (and any apps that make use of the Quicktime architecture) to work with MXF files, just like any other file.Calibrated{Q} MXF Import for OSX is a QuickTime Import component for NATIVE Importing and Editing of MXF Files within Final Cut Pro 6, 7, and X without using Log and Transfer.And you’re not just limited to Final Cut Pro, you can also natively import and work with MXF files in CatDV, Compressor, Motion, Sound Track Pro, QuickTime Player and Shake.You can download a free demo of MXF Import from Calibrated {Q} to test that it will work on your system. The demos only restriction is that it only allows you to view the first 30 seconds of the clip, other than that it’s the same as the full app. After installing the plugin I could drop the C300 MXF files directly onto the timeline in FCP7 and get editing – and with the dual audio tracks in the original files! Huzzah.Hopefully these tips will save you some time, effort and frustration with broken MXF file structures.  And next time you’ll just copy the cards structure correctly…and get to editing!last_img read more

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Serena Williams Is Some Kind Of Clutch

With Sunday’s U.S. Open victory, 32-year-old Serena Williams gathered her 18th major singles title — tying her with Chris Evert and Martina Navratilova for second on the all-time open-era list, behind only Steffi Graf’s 22. Remarkably, this was only Williams’s 22nd appearance in a final. Graf won her 18th Grand Slam title in her 26th final (at age 26). Navratilova didn’t win her 18th slam title until her 30th final (age 33), and Evert won her 18th (age 31) in her 33rd appearance (though, in fairness, those two had to play each other in 14 finals).Combined with her 22-3 record in semifinals, Williams’s career win rate in the last two rounds of major tournaments stands at 85.1 percent, easily topping the list of women with five or more slam titles:Second and third place go to Margaret Court and Graf, respectively — and then it’s daylight down to Monica Seles.But it’s also clear in the above chart that Williams’s performance prior to the semifinals is less remarkable: She ranks only 10th of 12 on that list in win percentage in the earlier rounds (despite not yet experiencing end-of-career decline). She has more exits in the first four rounds of majors (18) than Navratilova and Evert had, combined (16).In fact, Williams’s early-round performance is fairly similar to that of contemporary Maria Sharapova, particularly after we adjust for relative player strength. Both Williams and Sharapova have a reputation for dropping the occasional early-rounder against lower-ranked opponents. To see how often they lost to what kind of opponent, I broke the following chart down by “degree of mismatch” (techy mumbo-jumbo: the x-axis metric is the difference between the log of Williams’s/Sharapova’s seed and the log of their opponent’s seed. I treated all unseeded players like they had the No. 32 seed. This is just a better way of establishing relative strength than raw ranking difference):Williams does a little bit better, particularly in situations where she’s the lower seed (that’s not surprising considering her volatility), but then she takes a turn for the incredible at the semis:Williams is deadly when she makes it deep, regardless of ranking. Sharapova — the second-winningest player since Wimbledon 2004 — not so much.Of course, that Sharapova has been Williams’s main competition for so long is one of the reasons to be skeptical of Williams’s finishing skills: She hasn’t had to face a Seles or an Evert, as Graf and Navratilova did (or vice versa). So using the data from the 13 women with five or more major wins, I created a model to determine some basic odds of one of these top players beating an opponent based on each player’s ranking (actually, the model ends up using both the relative seeds and the absolute seed of the opponent — apparently, for top players, their own seed is much less important). From that, we can evaluate each player’s performance not just as a percentage, but against expectation considering the relative strength of their opponents.In this case, Williams has an even larger advantage than above when it comes to semifinals and finals, with a nearly 10 percent gap between herself and sister Venus Williams, with Court dropping to third, and Justine Henin taking the No. 4 spot.Yet, prior to the semifinals, Serena Williams is almost exactly at expectation: She’s ahead of it by two one-hundredths of 1 percent.To some degree, this has made me reconsider Williams’s career. Of course, we’ve always known she is brilliant, clearly the class of this generation and quite possibly the greatest female player of all time. But I have always assumed that she was reverse clutch — meaning that she was demonstrating clutchlike performance, but that it was probably a result of playing poorly in less-“clutch” situations (for example, if she didn’t try very hard in earlier rounds).This may still be the case. Or perhaps some other factor explains the findings — for instance, maybe Williams’s form entering Grand Slam events varies wildly, so she either loses early or wins the title. But the longer and more consistently this phenomenon persists, the more I’m forced to consider (at least conceptually) that perhaps Williams is really just a typical great player most of the time, but actually does possess the ability to summon something extra when the pressure is on. read more

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Former Supreme Court Justice John Paul Stevens has died at age 99

first_img Updated: 5:46 PM July 16, 2019 Posted: July 16, 2019 AP Former Supreme Court Justice John Paul Stevens has died at age 99 Categories: Local San Diego News, National & International News AP, WASHINGTON (AP) — John Paul Stevens, who served on the Supreme Court for nearly 35 years and became its leading liberal, has died. He was 99.Stevens’ influence was felt on issues including abortion rights, protecting consumers and placing limits on the death penalty. He led the high court’s decision to allow terrorism suspects held at Guantanamo Bay to plead for their freedom in U.S. courts.As a federal appeals court judge in Chicago, Stevens was considered a moderate when Republican President Gerald Ford nominated him. On the Supreme Court he became known as an independent thinker and a voice for ordinary people against powerful interests.He retired in June 2010 at age 90, the second oldest justice in the court’s history. FacebookTwitterlast_img read more

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NBC may launch Netflixlike streaming service in 2019 says report

first_img Digital Media Tech Industry Internet Services Post a comment NBC Universal CEO Steve Burke is also executive vice president of the Comcast division.  Alexander Tamargo/Telemundo/NBCU Photo Bank via Getty Images NBC Universal may launch its own on-demand video platform next year.CEO Steve Burke, who heads the Comcast division, unveiled in a holiday greeting to employees that a streaming service may come soon, according to Bloomberg’s report on Tuesday. The message was reportedly written in the rhyming style of Dr. Seuss.”While you all go off to relax, swim or ski,” Burke reportedly wrote. “Maybe, just maybe, next year we will announce our plan for OTT.”OTT means “over-the-top” services that stream videos online, like Netflix. NBC Universal didn’t immediately respond to a request for comment. Traditional cable TV giants are racing to compete with Netflix, which in October unveiled that the company had accumulated over 137.1 million subscribers worldwide. US subscribers nearly doubled what Netflix had predicted.Disney plans to launch its own streaming service, called Disney+, in 2019, which would become the new home for films from Walt Disney Studios, Pixar and other studios under its umbrella.AT&T is also brewing its own on-demand streaming service. The carrier’s WarnerMedia in November said the company planned to offer a three-tier video subscription service in the fourth quarter of next year. CNET’s Holiday Gift Guide: The place to find the best tech gifts for 2018.Best Netflix series: There’s no shortage of original Netflix series to binge. Tags NBC 0 Share your voicelast_img read more

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Video Mapping Refugee Healthcare In Houston Chapter 2

first_img Share It’s our final chapter in a two-part video series following Weijie Violet Lin, a young Baylor College of Medicine student and Albert Schweitzer Fellow, aiming to make it easier for refugees to access basic healthcare in Houston.Watch as she takes her next big step: getting feedback on her web portal directly from refugees.If you need to catch up, take a look at chapter 1.New videos drop every Monday for Imaginarium on YouTube. Subscribe to our channel.last_img

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Pinch interface can link displays of multiple screens w Video

first_img Samsung tablet concept shows a see-through, bendable future (w/ video) Citation: Pinch interface can link displays of multiple screens (w/ Video) (2012, November 2) retrieved 18 August 2019 from https://phys.org/news/2012-11-interface-link-multiple-screens-video.html Explore further © 2012 Phys.org (Phys.org)—A research group from Tokyo gives new meaning to the word pinch—newer than a notion of gripping two pieces of skin, or throwing a little salt into a stew, or, of course, referring to a multitouch gesture for touchscreens, but not only that. They have worked up a Pinch interface that puts the user into another display environment where screens serve as visual-display tiles, working together. Even if your smart device screens are of different sizes, the Pinch interface allows them to join forces, resulting in one single display, like a slick, if out of joint, tile puzzle.center_img Pinch is an interface that connects the displays from multiple touch devices and it is under development by a research group at the Tokyo University of Technology. When the user places a thumb and index finger on two adjacent screens and pinches, the screens link up. The screens can be lined up freely, vertical or horizontal. The connected devices share each other’s position and screen size via Wi-Fi. Devices with different-sized screens, such as smartphones and tablets, can go together to form a display interface. According to Takashi Ohta, Associate Professor at Tokyo University of Technology, who appeared in a video demo, “This Pinch interface we’ve developed is used to create applications that make devices react when they’ve both been pinched, so they work together. In the case of a graphics application, when the devices recognize they’ve been pinched, they can show the whole picture as if it’s on one screen.”He said that Pinch can be the foundation of a musical experience, where you connect the different devices you have horizontally, with the result that “you could keep playing music for a long time.” Ohta sees Pinch as enabling “fun” communications, where people gather, place their devices next to one another, and communicate ideas and images in novel ways. Other avenues, too, could include mobile music, advertising, and photo-sharing experiences.The Pinch team said it was offering Pinch to developers, hoping they could “do something with it.”In 2010, Ohta co-wrote a paper that cast some light on the present research. In that paper, titled “Automatic configuration of display ordering for multi-display environments,” Ohta and Jun Tanaka said, “We designed and built a system that configures the information of how displays are arranged as a multi-display environment. The system automatically matches the physical location of displays and network addresses. It uses a web camera for capturing a real-time video to observe each display to flash its screens one by one. The timing and relative locations of the flashing screens are recognized using an image processing technique. Furthermore, the correspondence of the displays and the network addresses can be deduced from these data.” The team concluded, based on their results, that the “system works perfectly, with various configurations of display dispositions.” This document is subject to copyright. Apart from any fair dealing for the purpose of private study or research, no part may be reproduced without the written permission. The content is provided for information purposes only.last_img read more

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