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Sunday, December 23, 2012

First goat genome sets a good example for facilitating de novo assembly of large genomes

Dec. 23, 2012 ? In a collaborative study published online today in Nature Biotechnology, researchers from Kunming Institute of Zoology, Chinese Academy of Sciences, BGI, and other institutes, have completed the first genome sequence of domestic goat by a robust approach integrated with next-generation sequencing (NGS) and whole-genome mapping (WGM) technologies. The goat genome is the first reference genome for small ruminant animals and may help to advance the understanding of distinct ruminants' genomic features from non-ruminant species. This work also yields a valuable experience for facilitating the de novo assemblies of large, complex genomes in the future.

Goats are recognized as an important member of the world livestock industry, and with many unique biological features. They are an important economic resource in many developing countries around the world, especially in China and India. However, despite their agricultural and biological importance, breeding and genetic studies of goats have been hampered by the lack of a high quality reference genome sequence. The goat genome sequence will be useful for facilitating the identification of SNP markers for marker-assisted breeding, and improving the utility of the goat as a biomedical model and bioreactor.

With the availability of next-generation sequencing (NGS), draft assemblies are easy to generate nowadays. However, to finish a sequence to the chromosome level remains a hard nut to crack. In this study, the results show that a single NGS platform, when combined with whole-genome mapping technology, could produce a finished assembly much faster and with high quality than other currently available mapping strategies such as BACs or FISH. Through this integrated approach, researchers obtained the ~2.66 Gb goat reference genome from a female Yunnan black goat.

Transposable elements (TEs) are major components of mammalian genomes and contribute to gene and/or genome evolution. The TEs in goat genome are similar to those of cattle, and contain large numbers of ruminant-specific repeats, such as SINE-tRNA and SINE-BovA. It is reported that SINE-BovA repeat expanded primarily in the cattle genome. However, in this study, researchers found the SINE-tRNA repeat expanded specifically in the goat genome.

Through constructing a phylogenetic tree among goats, cattle, horses, dogs, opossums and humans, researchers found the goat shared a common ancestor with cattle about 23 million years ago. Further comparison analysis revealed 44 rapidly evolving genes under positive selection, seven of which are immune-related genes and three are pituitary hormone or related genes. The immune-related genes identified also exist in cattle. The findings suggest that the rapid evolution of pituitary hormones may be related to the different features between goat and cattle in milk production, development rates of the fetus and/or hair variation.

The major histocompatibility complex (MHC) plays an important role in the immune system. In this study, the goat MHC was found to be located on chromosome 23 and contains two regions with length of 2.25 Mb and 360 kb, respectively. With the high quality genome assembly, further understanding of the goat MHC will be useful for immunological studies and vaccine development.

One of the distinguishing characteristics of mammals is the protective growth known as hair. It is produced by hair follicles within the skin, which could provide either protection (guard hairs) or insulation (underfur). The two major hair follicles include the primary hair follicle that produces only coat hair in all mammals, and the secondary hair follicle that can produce the cashmere or "fine hair" in certain mammals, including goats and antelopes. Despite a 2,500-year history and the extent of raw cashmere production, people are lack of understanding of the molecular mechanisms of cashmere formation and development.

Researchers conducted transcriptomic analysis on the primary and secondary follicles of a cashmere goat, revealing 51 genes that are differentially expressed between the two types of hair follicles. Keratin and keratin-associated proteins are the main structural proteins of hair fibers, determining the quality of fiber together. In the study, 29 keratin genes and 30 keratin-associated protein genes were detected in both types of follicles. Interestingly, they found two keratin genes and ten keratin-associated protein genes were consistently differentially expressed between primary and secondary hair follicles, suggesting that the keratin-associated protein genes may be more important in determining the structure of cashmere fibers. In addition to the keratin genes and keratin-associated protein genes, researchers also found several enzymes of amino acid biosynthesis, with implications in regulating primary hair growth and hair cycle.

Xun Xu, Deputy Director of BGI, said, "The goat reference genome is an important stepping stone in the molecular breeding of cashmere goats, and will help to advance the comparative studies on ruminants. The transcriptomic analysis on the primary and secondary follicles will open a new way for better improving the quality cashmere wool."

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The above story is reprinted from materials provided by BGI Shenzhen, via EurekAlert!, a service of AAAS.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.

Journal Reference:

Yang Dong, Min Xie, Yu Jiang, Nianqing Xiao, Xiaoyong Du, Wenguang Zhang, Gwenola Tosser-Klopp, Jinhuan Wang, Shuang Yang, Jie Liang, Wenbin Chen, Jing Chen, Peng Zeng, Yong Hou, Chao Bian, Shengkai Pan, Yuxiang Li, Xin Liu, Wenliang Wang, Bertrand Servin, Brian Sayre, Bin Zhu, Deacon Sweeney, Rich Moore, Wenhui Nie, Yongyi Shen, Ruoping Zhao, Guojie Zhang, Jinquan Li, Thomas Faraut, James Womack, Yaping Zhang, James Kijas, Noelle Cockett, Xun Xu, Shuhong Zhao, Jun Wang, Wen Wang. Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nature Biotechnology, 2012; DOI: 10.1038/nbt.2478

Note: If no author is given, the source is cited instead.

Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.

Source: http://feeds.sciencedaily.com/~r/sciencedaily/~3/CNn97tXK9DU/121223152629.htm

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The Tyee ? An Early Holiday Gift: Steve Burgess's Poignant Family ...

The tale begins with a crisis and a Dickensian voyage though Christmas Past. The first installment in an 11-segment series.

Steve Burgess, writer, former CBC radio host and deliquent son.

Welcome to the first of what we hope will become a regular feature on The Tyee. Audio books! But first, a quick word about how this came about.

It started with Tyee regular contributor, Steve Burgess. As you may be aware, in 2011 Steve wrote a humorous and heartfelt memoir last year called, Who Killed Mom: A Delinquent Son?s Meditation on Family, Mortality, and Very Tacky Candles. The story begins at Christmas at Steve's parent's house in Manitoba. So, we thought, how can we package it up as a gift for our loyal Tyee readers this Christmas? That's where our able and enthusiastic intern, Stacey Sellars, stepped in a few months ago. She approached a local audiobook company, Post Hypnotic Press, to find out how much it might cost to produce an audio version of Steve's book.

Post Hypnotic Press is a relatively new audiobook company, one of only three in Canada, publishing a variety of titles, but with a core of strong, intelligent books by thoughtful, and thought-provoking, Canadian authors. When they heard what we had in mind, they saw an opportunity. "Why stop at offering Steve's book?" they said. "We're offering some really great non-fiction books, many by local authors, some of them Tyee builders, and we're huge fans of The Tyee. Couldn't we work together to make something happen?"

And so, this is what we're doing. We're starting with Steve's touching memoir, audio-book-style, in full, for free, for you. We're publishing two chapters a day for the next 11 days. But, if you like it and want the full version, not broken into chunks, do consider buying it from Post-Hypnotic books or the print version from Douglas & McIntyre.

Once those are done, we're we're going to offer individual chapters of other great Post Hypnotic Press audio books in the weeks and months to come. Sometimes, we'll offer the whole book, in pieces, as with Who Killed Mom. Sometimes, we'll offer a chapter or two (Post Hypnotic does have to pay the writers, actors, and other staff that work to produce the audiobooks).

Speaking of which, to learn more about Post Hypnotic Press, browse their catalogue and perhaps buy some audio books in time for Christmas, go here:

If you want to set up your system to automatically download these books as they are published, do this:

? For those using iTunes, go here: https://itunes.apple.com/ca/podcast/podcasts-from-the-tyee/id557209921?mt=2

? For those using other subscription services, here's the raw RSS feed: http://feeds.feedblitz.com/tyee-podcasts

? And the mobile version of that raw RSS feed: http://m.feedblitz.com/tyee-podcasts

Enjoy!

Dear readers and commenters, you may notice that comments are not enabled for this story. In what has become a Tyee tradition, we're closing the commenting system for the holidays to allow our hardworking team a brief respite and chance to recharge. Thanks for all the insightful, informative comments in 2012. We look forward with happy anticipation to more of the same in 2013.

Steve Burgess is a freelance writer, regular contributor to The Tyee, and author of Who Killed Mom?, published in 2011 by Greystone Books.

Source: http://thetyee.ca/Books/2012/12/22/Burgess-Audiobook-Memoir/

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WWII vet's remains return 66 years after death

Perinchief Chapels

SSGT Zoltan Dobovich, an Allentown native, was one of eight men who were killed while on board a B-17G Flying Fortress back on Nov. 1, 1946.

By David Chang, NBC10

It's a journey over six decades in the making. But 66 years after his death, a World War II army staff sergeant is finally returning home.

SSGT Zoltan Dobovich, an Allentown native, was one of eight men who were killed while on board a B-17G Flying Fortress back on November 1, 1946. The heavy bomber aircraft was flying from Naples, Italy to Bovingdon, England when it crashed into the French Alps. He was 21-years-old.

After the fatal accident, several attempts were made to locate the men. While some initial remains were recovered in 1947, none of the soldiers were individually identified. The recovered remains were buried in a single grave at the Arlington National Cemetery in Virginia. Between 1972 and 1975 as well as 1979, more remains were recovered at the crash site, primarily by Italian military authorities, but were still unidentified.

A NEW TEACH YOURSELF AFAAN OROMOO BOOK - Ayyaantuu ...

teachyourself

A NEW TEACH YOURSELF

AFAAN OROMOO BOOK

Title

?LEARN TO READ, WRITE AND SPEAK THE OROMO LANGUAGE?

Author: Dr. Mohammed Badasso

Why this book?

It is the first of its kind book written for Oromo Diaspora both for those who do not read and write their language, and the expatriates who want to learn the Oromo language. This is an OROMO ? ENGLISH teach yourself handbook not only made available for the Diaspora but soon will be published in Oromia where it is needed the most. As you all are aware, there is no single book of this sort that you can buy or an expatriate buys from a bookstore to learn the Oromo language completely. For the first time English speaking Oromo Diaspora and those Oromo at home who speak English can now benefit from it. The Oromo in Diaspora can now learn to read, write and speak their own language, be at their own home comfort, at their work places, at their community centers, and elsewhere. This has been a problem that I have seen existed while I was at home that you could not buy a single complete handbook to learn the Oromo language unless you go to school to learn, and this has been true for the Diaspora as well. Now this gap has been fulfilled, the next major tasks are to produce Oromo language books in other major world languages such as, Oromo ? German, Oromo ? Arabic, Oromo ? French?etc. I hope this work will give some guidance for those who will endeavor these timely tasks.

I say, this is a must have book. It has all the ingredients required to learn the Oromo language. It consists of ? the alphabet, essential grammar to learn the system of the language, personal introductions and descriptions, numerous dialogues, questions and answers, positives and negatives, imperative forms and commands, knowing Oromo family, what is the homes, foods and related words, Oromo time reckoning, counting in Oromo, money matters, health matters, important phrases and vocabularies, and miscellaneous exercises for each chapter. The book is written exactly the way the Oromo speak to one another based on their culture. Every sentence in this book is written carefully to reflect the culture of the people. So, it is a living book, and when you talk to the book, you can feel one another and engage in real communication, thus you will learn proper usage of words and speak the language properly.

For the first time in this book, the rules of writing the Oromo language are precisely described and presented with appropriate examples. All un wanted complications that make harder to learn the alphabet such as the so-called ?combined letters?, ?hudhaa? and? ?irra-butaa? are either eliminated from the alphabet or described exactly what it is, to make as simple as possible to learn the alphabet in a very short time. Various examples and adequate exercises are provide to enable you master the alphabet in no time. Furthermore, the grammar of the language has been described in such a way to make the learning very interesting by providing examples and numerous exercises to navigate through the language easily. The book is also written in chapters to be read consecutively, so at the end you can challenge yourself with miscellaneous exercises based on the entire book.

I CHALLENGE YOU TO READ IT! THIS IS A GIFT TO ALL OF YOU!

Some praises for the book

This book is an excellent companion for those interested in learning the Oromo language. It is a book you will refer to again and again to read, write and speak the Oromo language. The book consists of all fundamental elements required to learn the language properly ? starting with the alphabet followed by essential grammar, dialogues, vocabularies and numerous examples and exercises to help you with. In short, the book surpasses all Oromo language books to date. It is therefore, a must have reference book that you should have by you all the time, and if you want to learn the language in an entirely new way or approach read this book now.

Furthermore, this beautifully written book is a gift to all Oromo and others, who want to learn the language without many un necessary or un wanted complications ? avoiding such things as ?combined letters? (digraphs), ?irra-butaa,? confusion with ?hudhaa? and many more making the road map much more easier to learn the Oromo language. I call it a ?one stop? shopping where everything you need to learn this language is in one package.

Having read the book, I am also compelled to tell you that, those who can read, write and speak the Oromo language, can learn more, with so much obvious further additions added to this book, such as the use of ?fi?, ?dha?, ?the definite article? and the emphasis put to write what is said in Oromo to mention a few. Above all, I admire the clarity and how it is made simply to learn the language. The book speaks to me and I speak to it. I felt the interconnections of the entire sections of the book. Finally, this is a single book that one can rely on to learn Afan Oromo. The time to buy many different and confusing books to learn how to read, write and speak the Oromo language has gone by. I definitely say, well done, and this is a worthwhile contribution to the ongoing development of the Oromo language.

Ibrahim Hajii Ali Boru

Editor-in-chief of Radio Fana

Oromo language Program, Finfinne

This book is a great guide for people who want to learn, revisit or refresh their knowledge of the Oromo language. Written by an educator whose love for the language and the culture of the Oromo people, it incites readers to research and explore their own journey into the communication and history of this fascinating Cushitic language.

Antu Yacob

Actor, Teacher

New Jersey

A wonderful resource for people to learn the Oromo language. Whether you are a beginner or fluent, this book will help deepen your understanding of the language and enable you to strengthen you conversation skills. It also serves as a great lifelong reference book.

Sara, Graduate Student

New York

A great resource for people who want to learn the Oromo language

Dr. Abdusamd Mohammed

Minneapolis, Minnesota

An excellent resource and reference book for learning the Oromo language

Mahdi Hamid Muude

Atlanta, Georgia

WHERE YOU CAN FIND THE BOOK

1.?? Gada.com
2.?? ?Local Oromo shops in most major USA cities, most countries in Europe and Australia

For further information please contact the author at the following

?e-mail address: mbaddaso@yahoo.com

Source: http://ayyaantuu.com/horn-of-africa-news/oromia/a-new-teach-yourself-afaan-oromoo-book/

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Research shows Acne Success stories in over 16,577 customer ...

It would shock you to realize how insanely true this is. I stumbled on this about 7 months ago on another blog and set my mind to find out what the rave was about. ?Are you guilty of buying several bottles of toners, cleansers, Spot clearing creams, Acne medications, without exactly having any tangible results?

I have had my own fair share of Acne, Pimples and spots problems, buying products, soaps, creams, cleansers again and again with no success till i went the natural route. So it was even more refreshing to realize that what the Acne Experts offered was indeed a natural approach to dealing with Acne and Pimples
Isn?t it remarkable that the major success stories of clearing Acne completely come from people who decided to go the natural route?

The Acne Experts reveal a tried and trusted way to deal with skin problems and Acne, Naturally.

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Free instant Access to the Acne Experts.

This is where my interest lies and this is what gets me excited. Just knowing that they are available to help you through whatever skin issues you have for Free, and show you methods and techniques to completely get back to youthful glowing, clear Skin in Days.

The answers are in Nature! And it could be anything as simple as changing your pillowcases as often as every 3days, drinking lots of water, Eating more fibre, eating plenty of fresh vegetables.

Every year, in Africa alone, the cosmetics and Skin care industries rake in billions of dollars. Half of that alone come from people dealing with all forms of Acne/Pimples or surface skin issues. Imagine that!
What they do not tell you obviously is how so easy it could be to actually heal your skin problems. They also refuse to tell you that you could?in fact?clear all skin issues, naturally!

And so the spending continues. Year in, Year out, millions of women across Africa and the world in general spend lump sums off their income on skin care products and Acne medications hoping to get the magazine-model skin they so desire. And as soon as there is talk of a new product that could maybe work the wonders, you are off again to spend money, regardless of how many other many products you have bought before.?A friend asked me some weeks ago,

?Really how did you get rid of all that Acne and Pimples, and get your skin so spotless and smooth??? ?Big deal question? No way. Not when the answer lies in all the natural ingredients and resources lying all around us, available at our disposal at prices 95% less than what our cosmetics and skin care range would cost. I wish i had found out about the Acne Experts years ago. I probably would have a lot more in my savings today.?Visit the Acne Experts , Get instant Free Access?and begin to enjoy the values of knowing exactly what Natural resources at your disposal could be very useful in your journey to Clear, Acne/Spot free skin.

Comments

comments

Source: http://www.360nobs.com/2012/12/acne-pimples-cleared-naturally/

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Saturday, December 22, 2012

Damage To The Inner Ear Spotted On A Hearing Test

One of the things that a hearing test can show is that there is damage to the inner ear. The ear?s various structures work together to bring in sound and to deliver the meaning of that sound to the brain. When even one portion does not work well, the entire remaining parts of the ear cannot work properly. That leads to a loss of the ability to hear in many cases. If you have any damage to this portion of your ear, chances are good you are going to need to manage the condition to improve quality of life.

What Happens to the Inner Ear?

Damage to the inner ear is actually quite common. Most often, aging is the reason for this to occur. However, if you are exposed to noise on a regular basis, this can cause wear and tear on the nerve cells and the hairs located in this portion of the ear. These nerve cells, located in the cochlea, have the job of sending sound signals from the ear to the brain. Often times, these hairs are missing or they become damaged. As a result, they are unable to transmit those electrical signals effectively. When this happens, there is some loss of the ability to hear.

In many people who have this condition, the higher pitched tones may seem like they are muffled. Over time, the condition worsens and it leaves you with difficulty picking out specific words against any type of background noise that may be present. This further worsens your ability to hear. A hearing test can pick up this damage and provide information to your doctor about what may be happening.

Why Is This Happening?

Many people suffer this type of damage due to hereditary factors. If your parents or grandparents suffered from this type of damage and loss, it is more likely that you will as well. Additionally, when you have this type of loss, it is often due to prolonged exposure to the louder-than-normal sounds in your work or other environment. This type of loss, which is known as sensorineural loss, is a permanent form. However, it may be improved on when you use a device that can make sounds louder for you.

If you have a hearing test and it reveals damage to the inner ear, you may become worried about what this may mean for you and your future. Though the damage can become worse over time, it is unlikely to be something doctors cannot improve on with the use of devices. Still, it can seem frustrating that you are experiencing this, since it is such a significant change in lifestyle.

Don?t take chances with such an important aspect of your sensory health. If you live in the area and are concerned about possible loss, schedule a tacoma, wa hearing test with the trusted professionals at http://www.miracle-ear-tacoma.com today.

Source: http://www.articlesrx.com/damage-to-the-inner-ear-spotted-on-a-hearing-test/9966

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Bernard Madoff's brother gets 10-year sentence

NEW YORK (AP) ? The brother of imprisoned financier Bernard Madoff was sentenced Thursday to 10 years in prison for crimes committed in the shadow of his notorious sibling by a judge who said she disbelieved his claims that he did not know about the epic fraud.

Peter Madoff, 67, had agreed when he pleaded guilty in June to serve the maximum sentence allowable to the charges of conspiracy and falsifying the books and records of an investment adviser. He follows to prison his 74-year-old brother, who is serving a 150-year sentence after admitting he created a fraud so large decades ago that thousands of people lost $20 billion.

U.S. District Judge Laura Taylor Swain urged Peter Madoff, of Old Westbury, to tell the truth even now.

The judge said Peter Madoff, wearing a well-tailored charcoal suit, was "frankly not believable" when he claimed at his plea that he only learned of the fraud when his brother revealed it to him just before he surrendered to authorities.

Peter Madoff spoke briefly Thursday and less emotionally than in June, saying: "I am deeply ashamed of my conduct and have tried to atone by pleading guilty and have agreed to forfeit all of my present and future assets."

He added: "I am profoundly sorry that my failures let many people down, including my loved ones."

Two investors, among 40 who wrote victim impact statements, spoke during the proceeding, each describing the financial ruins of their extended family.

Investor Michael T. De Vita, 62, also called for truth, saying he believed "it to be physically impossible for a single person to carry out such a gargantuan task all by himself."

De Vita said investors "have waited four years for others to accept responsibility for this massive crime. We are still waiting for that today."

"All of this was preventable if only one person was willing to do the right thing and stop this in its tracks years ago. Peter Madoff could have been that person," he said.

Amy Luria Nissenbaum, 49, choking up at times, also complained that Peter Madoff had chosen even after his plea to "turn a blind eye," saying her home was in foreclosure and some days she struggles to "clothe and feed my children."

Nissenbaum said Peter Madoff was part of his brother's fraud for more than 30 years and he should serve the same amount of time in prison.

When Swain announced that Peter Madoff will not have to report to prison until Feb. 6, Nissenbaum laughed out loud bitterly. The delay in reporting to prison will let Peter Madoff attend his granddaughter's Bat Mitzvah on Jan. 19. He got into a BMW after he left the courthouse.

The judge noted that 10 years was the maximum sentence allowed by the charges to which Madoff had pled and repeatedly urged Madoff to relieve the pain of investors by revealing more about the Madoff business.

"I challenge you to be honest about all that you have done and all that you have seen. In other words, all that you know," she said.

The magnitude of the damage done by the Madoffs cannot be underestimated, she said.

"Trust in financial institutions, thousands of individual lives and numerous charitable organizations have been blown apart," she said.

Assistant U.S. Attorney Lisa Baroni said it would have been easy for Peter Madoff to blow the whistle if he had even minimally carried out his duties. Instead, she said, he even teamed up with his brother to distribute the remaining $300 million in the company's accounts to family, friends and favored clients before the FBI put an end to that scheme by arresting his brother.

The sentencing comes four years and a week after Bernard Madoff first revealed the fraud, which occurred as the former NASDAQ chairman built a reputation for delivering unparalleled investment results, even in bad times. The revelation came only days after the business sent out statements that made investors think their investments had grown to a total of more than $65 billion.

Peter Madoff said at his plea that he had no idea his brother was running a massive Ponzi scheme, paying off longtime investors at times with money from newer investors.

"My family was torn apart as a result of my brother's atrocious conduct," he said. "I was reviled by strangers as well as friends who assumed that I knew about the Ponzi scheme."

Peter Madoff, who joined his brother's firm after graduating from Fordham Law School in 1970, has been free on $5 million bail after he agreed to surrender all assets. He has conceded he was paid more than $40 million by the Madoff firm in the final years of the fraud.

Prior to sentencing, his lawyer, John Wing, said in a memorandum that Peter Madoff will "almost certainly live out his remaining days as a jobless pariah, in or out of prison." He called him a victim of his loyalty to his brother, saying he had been mistreated by the sibling who was eight years older and was viewed as "the prince" by his mother.

As part of a forfeiture agreement, Madoff's wife, Marion, and daughter Shana must forfeit nearly all of their assets. The government said those assets and assets that will be forfeited by other family members include several homes, a Ferrari and more than $10 million in cash and securities. It said his wife will be left with $771,733. Besides the Madoff brothers, no other family members have been arrested.

Though Madoff had been the firm's chief compliance officer for nearly four decades, the government marked his start in the conspiracy as 1996, when he created false and misleading compliance documents and false reports for the Securities and Exchange Commission.

Since the fraud was revealed, a court-appointed trustee has reached agreements to recover approximately $9.3 billion and is hoping to recover another $3 billion over the next 18 months. About $3 billion has been approved for redistribution to victims through an ongoing claims process.

Besides his brother, Peter Madoff is among six who have pleaded guilty in the case, including the former finance chief, a payroll manager, an accountant, a comptroller and a securities trader.

Five others face trial next year, including Bernard Madoff's longtime secretary. All have pleaded not guilty.

Source: http://news.yahoo.com/bernard-madoffs-brother-gets-10-sentence-224213417--finance.html

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