China Science & Technology Forum

[JSCh]

A 100-year-old physics problem has been solved at EPFL

23.06.17 - EPFL researchers have found a way around what was considered a fundamental limitation of physics for over 100 years. They were able to conceive resonant systems that can store electromagnetic waves over a long period of time while maintaining a broad bandwidth. Their study, which has just been published in Science, opens up a number of doors, particularly in telecommunications.

At EPFL, researchers challenge a fundamental law and discover that more electromagnetic energy can be stored in wave-guiding systems than previously thought. The discovery has implications in telecommunications. Working around the fundamental law, they conceived resonant and wave-guiding systems capable of storing energy over a prolonged period while keeping a broad bandwidth. Their trick was to create asymmetric resonant or wave-guiding systems using magnetic fields.

The study, which has just been published in Science, was led by Kosmas Tsakmakidis, first at the University of Ottawa and then at EPFL’s Bionanophotonic Systems Laboratory run by Hatice Altug, where the researcher is now doing post-doctoral research.

This breakthrough could have a major impact on many fields in engineering and physics. The number of potential applications is close to infinite, with telecommunications, optical detection systems and broadband energy harvesting representing just a few examples.

Casting aside reciprocity
Resonant and wave-guiding systems are present in the vast majority of optical and electronic systems. Their role is to temporarily store energy in the form of electromagnetic waves and then release them. For more than 100 hundred years, these systems were held back by a limitation that was considered to be fundamental: the length of time a wave could be stored was inversely proportional to its bandwidth. This relationship was interpreted to mean that it was impossible to store large amounts of data in resonant or wave-guiding systems over a long period of time because increasing the bandwidth meant decreasing the storage time and quality of storage.

This law was first formulated by K. S. Johnson in 1914, at Western Electric Company (the forerunner of Bell Telephone Laboratories). He introduced the concept of the Q factor, according to which a resonator can either store energy for a long time or have a broad bandwidth, but not both at the same time. Increasing the storage time meant decreasing the bandwidth, and vice versa. A small bandwidth means a limited range of frequencies (or ‘colors’) and therefore a limited amount of data.

Until now, this concept had never been challenged. Physicists and engineers had always built resonant systems – like those to produce lasers, make electronic circuits and conduct medical diagnoses – with this constraint in mind.

But that limitation is now a thing of the past. The researchers came up with a hybrid resonant / wave-guiding system made of a magneto-optic material that, when a magnetic field is applied, is able to stop the wave and store it for a prolonged period, thereby accumulating large amounts of energy. Then when the magnetic field is switched off, the trapped pulse is released.

With such asymmetric and non-reciprocal systems, it was possible to store a wave for a very long period of time while also maintaining a large bandwidth. The conventional time-bandwidth limit was even beaten by a factor of 1,000. The scientists further showed that, theoretically, there is no upper ceiling to this limit at all in these asymmetric (non-reciprocal) systems.

“It was a moment of revelation when we discovered that these new structures did not feature any time-bandwidth restriction at all. These systems are unlike what we have all been accustomed to for decades, and possibly hundreds of years», says Tsakmakidis, the study’s lead author. "Their superior wave-storage capacity performance could really be an enabler for a range of exciting applications in diverse contemporary and more traditional fields of research.” Hatice Altug adds.

Medicine, the environment and telecommunications
One possible application is in the design of extremely quick and efficient all-optical buffers in telecommunication networks. The role of the buffers is to temporarily store data arriving in the form of light through optical fibers. By slowing the mass of data, it is easier to process. Up to now, the storage quality had been limited.+

With this new technique, it should be possible to improve the process and store large bandwidths of data for prolonged times. Other potential applications include on-chip spectroscopy, broadband light harvesting and energy storage, and broadband optical camouflaging (“invisibility cloaking”). “The reported breakthrough is completely fundamental – we’re giving researchers a new tool. And the number of applications is limited only by one’s imagination,” sums up Tsakmakidis.

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Source: Breaking Lorentz reciprocity to overcome the time-bandwidth limit in physics and engineering

Cover image capture: Generic image illustrating wave-interference and resonant energy transfer from one source to another distant source or object, pertaining to the fundamental concept of resonances.

Study conducted by:

Kosmas Tsakmakidis, lead author, former researcher at the University of Ottawa and currently an EPFL Fellow in EPFL's Bionanophotonic Systems Laboratory
Linfang Shen and collaborators, Institute of Space Science and Technology, Nanchang University, Nanchang, China and State Key Laboratory of Modern Optical Instrumentation, Zhejiang University, Hangzhou, China
Prof. Robert Boyd and collaborators, University of Ottawa
Prof. Hatice Altug, director of EPFL's Bionanophotonic Systems Laboratory
Prof. Alexandre Vakakis, University of Illinois at Urbana-Champaign

Author:Laure-Anne Pessina



A 100-year-old physics problem has been solved at EPFL

K. L. Tsakmakidis, L. Shen, S. A. Schulz, X. Zheng, J. Upham, X. Deng, H. Altug, A. F. Vakakis, R. W. Boyd. "Breaking Lorentz reciprocity to overcome the time-bandwidth limit in physics and engineering". Science (2017). DOI: 10.1126/science.aam6662

 

[JSCh]

New form of carbon discovered that is harder than diamond but flexible as rubber
June 24, 2017 1.40am AEST
Timothy Strobel

Scientists have found a way to make carbon both very hard and very stretchy by heating it under high pressure. This “compressed glassy carbon”, developed by researchers in China and the US, is also lightweight and could potentially be made in very large quantities. This means it might be a good fit for several sorts of applications, from bulletproof vests to new kinds of electronic devices.

Carbon is a special element because of the way its atoms can form different types of bonds with each other and so form different structures. For example, carbon atoms joined entirely by “sp³” bonds produce diamond, and those joined entirely by “sp²” bonds produce graphite, which can also be separated into single layers of atoms known as graphene. Another form of carbon, known as glassy carbon, is also made from sp² and has properties of both graphite and ceramics.

But the new compressed glassy carbon has a mix of sp³ and sp² bonds, which is what gives it its unusual properties. To make atomic bonds you need some additional energy. When the researchers squeezed several sheets of graphene together at high temperatures, they found certain carbon atoms were exactly in the right position to form sp³ bonds between the layers.

Bond, sp³ bond. Timothy Strobel​

By studying the new material in detail, they found that just over one in five of all its bonds were sp³. This means that most of the atoms are still arranged in a graphene-like structure, but the new bonds make it look more like a large, interconnected network and give it greater strength. Over the small scale of individual graphene sheets, the atoms are arranged in an orderly, hexagonal pattern. But on a larger scale, the sheets are arranged in a disorderly fashion. This is probably what gives it the combined properties of hardness and flexibility.

The researchers made the compressed glassy carbon using a relatively simple method that could be reproduced on a large scale easily and cheaply. In simple terms, they used a sort of machine press that applies high-pressure loads to the carbon. But this must have involved several tricks to control the pressure and temperature in exactly the right way. This would have been a time-consuming process but should still be achievable for other people replicate the results.

New surprises
Carbon materials are continually surprising us – and the emphasis of research has been to find or cook things in between its natural forms of diamond and graphite. This new form is the latest of what seem like limitless ways you can bond carbon atoms, following on from the discovery of graphene, cylindrical carbon nanotubes and spherical buckminsterfullerene molecules.

A material like this – that is strong, hard, lightweight and flexible – will be in high demand and could be used for all sorts of applications. For example, military uses could involve shields for jets and helicopters. In electronics, lightweight, cheaply manufactured materials with similar properties to silicon that could also have new abilities could provide a way to overcome the limitations of existing microchips.

The dream is to find a carbon material that could replace silicon altogether. What is needed is something that allows electrons to move through it quickly and whose electrons can easily be placed into an excited state to represent the on and off functions of a transistor. The researchers behind glassy carbon haven’t studied these properties in the new material so we don’t yet know how suitable it might be. But it might not be that long until another of carbon is found. So far, decades of hunting hasn’t turned up what we need, but maybe we just have to look deep down to find it.

http://theconversation.com/new-form...der-than-diamond-but-flexible-as-rubber-79879

Meng Hu, Julong He, Zhisheng Zhao, Timothy A. Strobel, Wentao Hu, Dongli Yu, Hao Sun, Lingyu Liu, Zihe Li, Mengdong Ma, Yoshio Kono, Jinfu Shu, Ho-kwang Mao, Yingwei Fei, Guoyin Shen, Yanbin Wang, Stephen J. Juhl, Jian Yu Huang, Zhongyuan Liu, Bo Xu and Yongjun Tian. Compressed glassy carbon: An ultrastrong and elastic interpenetrating graphene network. Science Advances, June 2017 DOI: 10.1126/sciadv.1603213

 

[Clutch]

 

[cirr]

China’s genomics giant to make stock-market debut

Once the world's biggest DNA sequencer for research, BGI is now looking to medical applications to boost profits.

David Cyranoski

21 June 2017

Daniele Mattioli/Anzenberger/eyevine
BGI in Shenzhen has shifted its focus from serving researchers to medical applications of genome sequencing.

China’s genomics giant BGI, once the world leader in DNA sequencing for basic science, is going public — capping off a dramatic transformation into a mainly biomedical firm with a focus on reproductive health.

A financial prospectus document released to support the initial public offering (IPO) details how BGI, squeezed by its rivals and the plummeting cost of sequencing, has been drawn to more-profitable pursuits, such as prenatal genetic testing, in China’s expanding medical market. The shift is also in line with the Chinese government’s multibillion-yuan drive to promote precision medicine, an effort to use the reams of genomic and other medical data being created to tailor treatments.

China’s bid to be a DNA superpower

BGI is currently working out the details of the IPO, which was years in the making and approved by China’s financial regulators in late May. The IPO is expected within a month and the firm hopes to raise 1.7 billion yuan (US$250 million).

As the first genomics company to be listed in China, BGI will be a pioneer in the country’s precision-medicine market, which is estimated to be worth 20 billion yuan by 2020. “It's a milestone for both BGI and the field,” says Ruiqiang Li, who used to work for BGI and is now chief executive of competing genomics firm Beijing-based Novogene, which Li hopes to take public.

Income shift

BGI was established in 1999 as the Beijing Genomics Institute and the force behind China’s contribution to the Human Genome Project — it sequenced a small, but symbolic, 1% of the genome.

Over the next decade, it produced a series of high-profile sequencing breakthroughs, including the genomes of rice, the giant panda, the cucumber, an ancient human and more than 1,000 species of gut bacteria. In 2010 — now based in Shenzhen and known simply as BGI — the company purchased 128 of the world’s most-advanced genome-sequencing machines. Overnight it became the industry’s most prolific player.

The firm gained a reputation as a genome factory. The number of studies based on BGI-sequenced genomes — paid for by scientists from all over the world, who acknowledged BGI scientists’ contributions by making them co-authors — jumped from a handful to hundreds per year.

But that number has plateaued, and it looks set to drop this year. According to the prospectus, BGI’s income from research-driven sequencing dropped by more than one-quarter between 2014 and 2016, and now accounts for less than 20% of its business, down from 40% in 2014. Reproductive-health screening makes up the lion’s share of the company's income, at 55% (see ‘Focus on health’). Services related to complex diseases — those caused by a combination of genetic and environmental factors — brings in 23%.

The company would not comment on its operations, citing a “quiet” period mandated by the financial regulator before its stock-market debut. But its prospectus says that the move away from research-based sequencing is the result of the falling price of sequencing machines, which has allowed research institutes to set up their own facilities.

China embraces precision medicine on a massive scale

Li says, however, that even though some institutions are trying to build their own facilities, the market for third-party research sequencing is growing. “It’s not efficient and cost effective to maintain a small-scale sequencing lab,” he says. “Most such labs in China decided to discontinue their own platform operation and outsource sequencing to centralized sequencing centres.”

Still, sequencing for researchers isn’t the business it used to be. The prospectus points out that in the early days, there was more low-hanging fruit — sequencing the whole genome of a plant or animal, for example, were large projects with big profit margins. Now, projects are smaller and less lucrative. And competition has intensified from companies such as Novogene, which says it has the largest sequencing capacity in the world.

Prenatal testing

“This shift seems to be market driven,” says Dorret Boomsma of the VU University Amsterdam, who has used BGI sequences in studies of Dutch twins. “Apparently facilities for large-scale research sequencing are available on a more-competitive pricing, or nearer by, elsewhere.”

BGI’s ability to keep pace in the research was also affected by its failure to develop an advanced sequencer based on technology that it bought in 2013 from Complete Genomics in Mountain View, California. It also suffered after the departure of its chief executive Jun Wang, who spearheaded many of BGI’s research projects, but left in 2015 to start his own company.

Clinical sequencing in China, however, is booming, fuelled by the country’s growing middle class, expanding health-care system and focus on precision medicine. Sales of BGI’s non-invasive prenatal testing kit, NIFTY — which screens maternal blood to determine whether a fetus has chromosomal abnormalities such as Down’s syndrome — passed the million mark in March 2016. And China’smove from a one-child to two-child policy in 2016 increased the birth rate among NIFTY’s target demographic: women in their late 30s who are considered to be high risk for chromosomal abnormalities. According to an analysis by Chinese investment bank CITIC Securities, BGI has nearly 50% of the prenatal screening market in China, far ahead of its closest competitor.

With the money raised from its IPO, the firm hopes to improve its reproductive and cancer-diagnosis technologies, and add other, similar, sequencing-based diagnostic services for other health conditions. It also plans to expand genetic consulting services and establish cloud-computing platforms to crunch genomic data for precision medicine. Earlier this year, BGI struck a deal with Foxconn — the Taiwanese company that manufactures iPhones at its base in Shenzhen — to mass-produce sequencers, which BGI plans to sell to hospitals throughout China.

Other sequencing companies will be watching closely to see how BGI fares in the nascent market. “We don’t know the level of interest from investors. The industry is still relatively small, but it’s fast growing and has a lot of potential,” says Li.

Nature 546,461 22 June 2017) doi:10.1038/546461

http://www.nature.com/news/china-s-genomics-giant-to-make-stock-market-debut-1.22171

 

[Bussard Ramjet]

This has already been posted in Science and Technology thread.

I think we can discuss here the failure of BGI to get into the sequencing equipment business. That is dominated by Illumina. In fact it seems its acquisition of Complete Genomics was a waste.

 

[Keel]

What has the report above missed out on?

How about combustible ice?
The discovery of new materials harder than diamond but as bouncy as rubber!
How about making artificial cornea?
How about genome techniques to improve infertility?

How about the heavy lift rocket CZ-5; capable of lifting 14T material/spacecraft/satellites to GTO and 8T+ to GEO (lifting our Shijian 17 precisely into GEO on first try!)
http://spaceflight101.com/cz-5-maiden-flight/shijian-17-settles-in-geostationary-orbit/

Our research and discovery in fighting cancer:

http://www.nature.com/news/chinese-scientists-to-pioneer-first-human-crispr-trial-1.20302
http://www.scmp.com/lifestyle/healt...l-chinese-medicine-have-role-helping-patients
http://www.collective-evolution.com...ls-12000-cancer-cells-for-every-healthy-cell/
http://www.cpr.cuhk.edu.hk/en/press_detail.php?id=2486

Chinese researchers achieve major breakthrough in nuclear energy
chinadaily.com.cn | Updated: 2017-06-09
http://www.chinadaily.com.cn/china/2017-06/09/content_29686492.htm

and plenty plenty more ...and forthcoming!!
Search and read the contributions from @JSCh et al to get an idea here

https://defence.pk/pdf/threads/china-science-technology-forum.249386/page-101

 

[Han Patriot]

This has already been posted in Science and Technology thread.

I think we can discuss here the failure of BGI to get into the sequencing equipment business. That is dominated by Illumina. In fact it seems its acquisition of Complete Genomics was a waste.

Can you explain to me the failure and why it is a waste?

 

[Bussard Ramjet]

Can you explain to me the failure and why it is a waste?

It is a failure because it has won no commercial success. Even novogene the company founded by ex BGI people uses Illumina machines.

 

[Shotgunner51]

Week In Review: Shenzhen's BGI Plans $250 Million China IPO To Support Genomics Operations
Jun. 25, 2017 11:02 AM ET
ChinaBio Today

Deals and Financings

BGI Genomics, the contract sequencing and diagnostics divisions of China genomic company BGI, is edging closer to an IPO. The company expects to raise $250 million on Shenzhen's Chi-Next Exchange sometime in July, following all-but-final approvals from China's Securities Regulatory Commission. Known as a world leader in basic science sequencing, BGI Genomics now generates 55% of its income from clinical genomic tests, especially its NIFTY prenatal test for hereditary illnesses such as Down's syndrome. The business is very profitable: BGI's IPO prospectus puts gross profit margin for reproductive services at 76%.

ShangPharma will merge its Shanghai ChemPartner division, which includes all of the company's CRO/CMO operations, into Quantum Hi-Tech China Biological (SZE: 300149). The transaction, a reverse merger, allows ChemPartner access to China's capital markets rather than spending years waiting for the China IPO approval. ShangPharma said ChemPartner will continue to operate as a stand-alone company even after the merger. Quantum, which is listed on the Shenzhen exchange with a market capitalization of $1.2 billion, produces fructooligosaccharide products as a probiotic for nutritional snacks. Specific terms, including ChemPartner's merger valuation, were not disclosed.

Sanovas, a Bay-Area medical device maker, will start a venture capital fund in Suzhou's BioBay park, which will invest "upwards" of $75 million in Suzhou technologies. Sanovas makes innovative micro-invasive devices, and its fund will seek investments in procedures that treat unmet medical conditions at affordable prices. The company will establish an Innovation Center in the Suzhou Institute of Nano-Tech and Nano-Bionics (SINANO). Sanovas' Suzhou center will also serve as a sales/learning base for China.

GlaxoSmithKline (NYSE:GSK) will form a big data partnership with Guangzhou Institute of Respiratory Diseases (GIRD) to develop a respiratory disease management system that will target both asthma and chronic obstructive pulmonary disease (COPD) (see story). The goal will be to optimize care plans, especially for rural settings. The studies will include reimbursement systems, and they will also pay attention to China's tiered healthcare system, apparently allocating specific tasks to the appropriate levels.

https://seekingalpha.com/article/40...million-china-ipo-support-genomics-operations

 

[Speeder 2]

Japan's Science&Technology Ministry just published a new research paper concluding that global science & technology has stepped into the era of Sino-American competition.

This Japanese govenment research has ranked top 10% of globally quoted sci-tech research papers as a measure of one's sci-tech research quality,therefore one's future sci-tech powess, from the global top 6 industrial powers, namely America, UK, France, Germany, China and Japan (not in a particular order).

The ranking results are that China and America together lead in all 8 key basic industries, with each holding 1st place in 4 industries, ahead of the rest --

China (1st place):
Computer Science and Mathematics,
Chemistry,
Materials Science,
Engineering

America (1st place):
Physics,
The Environment and Earth science,
Basic Life Sciences,
Clinical Medicine

Paper also states that China is very likely to become world's centre in the field of Particle Physics - the very forefront of Physics Science.

The paper reasecher states that it has caught him by surprise to have found out that China has surpassed America in many areas.

The paper concludes that China's rapid development of science and technology has been assisted by 2 major factors: abundant capital & talents.

科研論文是技術創新的源泉，日本文部科學省下屬的科學技術振興機構實施的調查顯示，在計算機科學與數學、化學等4個領域，中國的論文數量位居全球首位，在主要8大領域中與美國平分秋色，進入了「中美兩強」時代。擴充研究經費和人才招攬政策等發揮了功效。

該機構此次以被其他論文引用次數為指標對其影響力進行了調查。根據被引用次數排名前10%的論文來評價美國、英國、德國、法國、中國和日本等國的研究人員水平。中國在計算機科學與數學、化學、材料科學、工學4個領域排在首位。美國在物理學、環境與地球科學、基礎生命科學、臨床醫學4個領域排在第一。連續3年獲得諾貝爾物理學獎的日本只排在5～６位。

( America: Blue lines. China: Red lines. Japan: Black lines)


中國進步神速的象徵是計算機科學領域。在這個領域，中國被引用次數排名前10%的論文所佔的比例2000年時為3%，但2015年達到了21%。中國超級計算機的性能也從2013年起保持世界第一。2016年還獨攬前兩位。

在美國擅長的物理領域，中國也正在加速追趕。中國投入了60億美元以上建設全球最大的加速器，在最前端的粒子物理學領域，中國也有可能成為世界的中心。

帶動中國科研飛快發展的是充裕的資金和人才爭奪戰略。在研究經費方面，2000年前後中國政府和企業合計投入5萬億日元左右，但到2014年迅速擴大到了38萬億日元。相當於一直徘徊在18萬億～19萬億日元左右的日本的2倍，緊追美國的46萬億日元。除了積極呼籲在已開發國家求學的中國研究人員回國之外，還通過留學和派遣等，來構築海外的研究人脈和豐富的渠道。

日本的科學技術振興機構的研究員伊藤裕子指出，「中國在多個領域超過美國，實屬意料之外」。美國總統川普日前提出大幅削減科技預算的方針，中國的存在感估計會日漸增強。

https://zh.cn.nikkei.com/industry/scienceatechnology/25550-2017-06-13-00-42-11.html


Finally, China is catching up on quality and innovation!

 

[Dungeness]

This has already been posted in Science and Technology thread.

I think we can discuss here the failure of BGI to get into the sequencing equipment business. That is dominated by Illumina. In fact it seems its acquisition of Complete Genomics was a waste.

Just a request, can you start an India S/T thread so we can appreciate India's achievements beyond MoM and 104, which have been cited by almost every PDF Indian members repeatedly? Thanks.

 

[Han Patriot]

It is a failure because it has won no commercial success. Even novogene the company founded by ex BGI people uses Illumina machines.

But why there is no commercial success? Is it because it was not advanced enough? Buying that company led BGI to gain valuable IPs. Its too early to call it a failure. I think it's good to have competition. At least China is trying to change the status quo instead of just importing like India.

https://www.wired.com/2017/05/chinese-genome-giant-sets-sights-uitimate-sequencer/

In 2013, BGI purchased Illumina’s main competitor: Complete Genomics in Mountain View, California. Its first attempt was a flop. BGI suspended sales after just three orders. The next machine, a sequencer called the BGISEQ-500, launched in late 2015, and according to BGI, can now sequence an entire human genome for $600. That’s about 40 percent cheaper than the going street price on the Illumina platform.

Just a request, can you start an India S/T thread so we can appreciate India's achievements beyond MoM and 104, which have been cited by almost every PDF Indian members repeatedly? Thanks.

True, I have not seen any grounbreaking research from Supapowans. Maybe it's time to create such a thread for us to appreciate the geniusity.

 

[JSCh]

Harnessing Cancer’s Methylation Footprint for More Precise Diagnosis and Prognosis
A bit of basic genetic machinery could help identify malignant tumors more easily and with greater accuracy
June 27, 2017 | Scott LaFee

In a new study, published online in the July 26 issue of PNAS, researchers at University of California San Diego School of Medicine, with colleagues in Xijing Hospital and Sun Yat-sen Cancer Center in China, report that DNA methylation can provide effective markers for at least four major cancers, not only correctly differentiating malignant tissues from normal, but also providing information on prognosis and survival.

DNA methylation occurs when methyl groups — one carbon atom bonded to three hydrogen atoms — attach to DNA molecules, changing gene function without changing DNA sequence.

“Choosing the proper cancer treatment with the best chance of recovery and survival depends greatly upon accurately diagnosing the specific type or subtype of cancer,” said Kang Zhang, MD, PhD, founding director of the Institute for Genomic Medicine and co-director of biomaterials and tissue engineering at the Institute of Engineering in Medicine, both at UC San Diego School of Medicine. “If you can do that using a minimally invasive biopsy, it has significant implications for cancer science and medicine. Using DNA methylation markers may be a new and more effective a way forward.”

DNA methylation involves methyl groups — one carbon atom bonded to three hydrogen atoms — attaching to DNA molecules. It is a fundamental epigenetic process that regulates gene function without changing the DNA sequence of a gene, essential to normal development and associated with numerous key processes, including initiation and progression of cancer.

Zhang and colleagues looked at DNA methylation for differentiating tumor tissue and normal tissue for the four most common cancers (lung, breast, colon and liver) in three different databases: a training cohort of 1,619 tumor samples and 173 matched adjacent normal tissue samples; a testing cohort of 791 tumor samples from The Cancer Genome Atlas and 93 matched adjacent normal tissue samples and another independent testing Chinese cohort of 394 tumor samples; and 324 matched adjacent normal tissue samples.

They found that DNA methylation analysis could predict cancer versus normal tissue with more than 95 percent accuracy in the three cohorts, comparable to typical diagnostic methods, according to Zhang.

In addition, the analysis correctly identified 97 percent colorectal cancer metastases to the liver and 94 percent colorectal cancer metastases to the lung. “Since 10 percent of cancers present as metastatic lesions or cancers of unknown primary origin, identification of tissue of origin is critical for choosing a correct therapy. This new simple method will be of great value to pinpoint the primary source of the tumor,” said Michael Karin, co-senior author of the study and Distinguished Professor of Pharmacology, also at UC San Diego School of Medicine.

Zhang suggested DNA methylation has the potential to improve outcomes by providing more accurate diagnoses, particularly of relatively indolent or aggressive tumors that may require more or less aggressive treatment.

“Although we focused on just four common cancers here, we expect that DNA methylation analysis could be easily expanded to aid diagnoses of a much larger number of cancers,” said Zhang. “A great benefit is that this approach requires only a small amount of tissue to obtain adequate DNA for analysis, potentially allowing the use of less invasive biopsies or biopsies of metastatic lesions where the tumor is of unknown primary cancer type.”

He said more studies have been planned to fully explore the clinical applications and potential of DNA methylation and its role in future personalized cancer care.

Co-authors include: Xiaoke Hao, Fourth Military Medical University, Xi’an, China; Huiyan Luo and Rui-hua Xu, Sun Yat-sen University Cancer Center, Guangzhou, China; Michal Krawczyk, Wei Wei, Ken Flagg, Jiayi Hou, Shaohua Yi, Maryam Jafari, Danni Lin, Christopher Chung, Bennett A. Caughey, William Shi, Jie Zhu, Xin Fu, Edward Zhang, Charlotte Zhang, and Debanjan Dhar, UC San Diego; Heng Zhang, Lianghong Zheng, and Rui Hou, Chinese Academy of Sciences, Shanghai, China; and Gen Li and Liang Zhao, Guangzhou Youze Biological Pharmaceutical Technology Company, Guangzhou, China.

Funding for this research came, in part, from the Carol and Dick Hertzberg Fund, the Richard Annesser Fund and the Michael Martin Fund.


https://health.ucsd.edu/news/releas...on-footprint-for-diagnosis-and-prognosis.aspx

Xiaoke Hao et al, DNA methylation markers for diagnosis and prognosis of common cancers, Proceedings of the National Academy of Sciences (2017). DOI: 10.1073/pnas.1703577114

 

[JSCh]

New research may be cure to Huntington’s Disease
By Meng Yaping
2017-06-28 09:52 GMT+8

There may be new hope for those suffering from a fatal brain disorder called Huntington’s Disease. Researchers at Emory University, are using a groundbreaking gene editing tool called CRISPR-Cas9 to provide new insight into how the disease works, and possible ways to reverse its devastating effects.

Huntington’s Disease is a genetically inherited condition that leads to nerve cell destruction in the brain. Symptoms which usually appear in mid-life, include uncontrolled muscle movement, balance issues, mood swings and cognitive decline.

While there is no known cure for Huntington’s, a recent study by Chinese scientists at Emory University in Atlanta, Georgia is showing promise. Early results suggest possible treatments for the disease and a path to preventing its occurrence in the first place.

Emory School of Medicine /emory.edu Photo‍

The research is part of an ongoing medical collaboration between the US National Institute of Health (NIH) and the National Natural Science Foundation of China. Under this program, both the US and China contribute funds and scientists for research in both countries.

Using the revolutionary gene editing technique known as CRISPR-Cas9, researchers at Emory were able to reverse the effects of Huntington’s in test mice. The mice had been genetically modified to carry a human version of the huntingtin gene that causes the disease. While considered essential for nervous system development in early life, a mutated huntingtin gene can also produce toxic proteins that cause neural generation.

After nine months, when the mice developed the animal version of Huntington’s Disease, researchers used CRISPR-Cas9 to replace the mutant gene with a normal one and then reintroduce the repaired DNA into mice.

CRISPR is a technology that employs a DNA-splitting enzyme along with a highly focused molecular guide that tell those enzymes where to split. /McGovern Institute Photo

Weeks after treatment, the brain-damaging proteins had almost disappeared and motor functions of the mice dramatically improved, though not to the same level in healthy control mice in which Huntington’s hadn’t been induced.

While the results show promise for future human trials involving humans, clinical trials remain a long way off. The long term effectiveness and safety of CRISPR-Cas9 are still under review.

The study’s senior author Dr. Li Xiaojiang, PhD, is optimistic. “The findings open up an avenue for treating Huntington’s as well as other inherited neurodegenerative diseases, although more testing of safety and long-term effects is needed,” said Li.

In addition to developing a treatment for victims of Huntington’s, the Sino-US research group hopes to develop ways to reduce the risk for people who are genetically predisposed to developing Huntington’s.

Last year, the same group of Emory researchers found they could delete the huntingtin gene in mice older than four months without any known adverse effects. Younger mice without this gene developed fatal pancreatitis. The findings suggest it may someday be possible to safely shut off the gene in adult humans, as well.

Full results of the group’s research were published in the Journal of Clinical Investigation on June 19, 2017.

 

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New photoacoustic technique detects gases at parts-per-quadrillion level
June 27, 2017 Media contact: Kevin Stacey 401-863-3766
The technique enables the detection of gases, such as atmospheric pollutants, present in extremely small quantities that are otherwise difficult or impossible to detect.

Detection device Using a new technique a device can detect gases, such as environmental pollutants, in extremely minute concentrations. Gerald Diebold

PROVIDENCE, R.I. [Brown University] — A team of researchers has found a way to detect trace gases down to concentrations at the parts-per-quadrillion level using a new variation on the photoacoustic effect, a technique that measures the sound generated when light interacts with molecules.

“In many ways, the photoacoustic effect is already the most practical method available for detecting pollutants in the atmosphere,” said Gerald Diebold, a professor of chemistry at Brown University and coauthor of a new paper describing his lab’s research. “But when the concentration of the molecules you’re trying to detect gets down to the parts-per-trillion level, the signal become too weak to detect. We’ve developed a new photoacoustic technique that boosts the signal and enables us to get down to the parts-per-quadrillion level, which to our knowledge is a record.”

The study, which was a collaboration between Diebold’s lab at Brown and the lab of Fapeng Yu at Shandong University in China, is published in the Proceedings of the National Academy of Sciences.

The photoacoustic effect takes place when a beam of light is absorbed by a gas, liquid or solid causing it to expand. The expansion is a mechanical motion that results in the launching of a sound wave. The effect was first discovered by Alexander Graham Bell in the 1880s but was of little practical value until the invention of the laser, which — as a result of its typically narrow linewidth and high power — made photoacoustic signals large enough to be easily detectable.

Photoacoustic detectors work by zapping a material with a laser tuned to a wavelength that is absorbed by the molecule of interest. In a typical photoacoustic experiment, the laser beam is switched on and off at a frequency that can be detected by a sensitive microphone to listen for any sound waves produced. Different molecules absorb light at different frequencies, so by adjusting the frequency of the laser, it’s possible to fine-tune a detector for specific substances. So to look for ammonia in air, for example, the laser would be tuned to the specific absorption frequency of ammonia molecules. One would then zap an air sample, and if the microphone picks up sound waves, that means the sample contains ammonia.

But the smaller the concentration of the target substance, the quieter the signal. So Diebold and his colleagues used an unconventional technique to boost the signal amplitude.

“What we’ve done is devise a method that relies on three different resonances,” Diebold said. “The signal gets bigger with each resonance.”

Instead of a single laser beam, Diebold and his colleagues combine two beams at a specific frequency and angle. The joining of the beams creates a grating — a pattern of interference between the two beams. When the laser frequencies are tuned just right, the grating travels in a detection cell at the speed of sound, creating an amplification effect at each of the peaks in the grating.

The second resonance is created by a piezoelectric crystal used in the experiment, which vibrates precisely at the frequency of the combined laser beams. The small compressive forces in the pressure waves gradually induce motion in a crystal much in the same way that small, repeated pushes of a playground swing eventually lead to a large amplitude motion of the swing.

The third resonance is generated by adjusting the length of the cavity in which the crystal is mounted so that it resonates when an integral number of half wavelengths of the sound exactly matches the cavity length. The output of the crystal, which is piezoelectric so that it generates a voltage proportional to its oscillatory motion, is sent to amplifiers and sensitive electronic devices to record the acoustic signal.

“One of the reasons that the moving grating method worked so well is that Professor Yu’s group at Shandong University grew a special crystal that gives very large signals in response to the pressure waves,” Diebold said. “We were told that it took them three months to synthesize the crystal.”

In their experiments, the researchers showed that by using those three resonances, they were able to detect the gas sulfur hexafluoride in amounts down to the parts per quadrillion.

Diebold thinks the technique will be useful in developing detectors that are sensitive to very low pollutant gas concentrations, or for detecting molecules that have weak absorptions that make them inherently difficult to detect.

Diebold noted that in carrying out the experiments, he and his colleagues were “amazed to find that because the frequencies are so high — in the hundreds of kilohertz range — that there is virtually no background interference, either from electrical pickup or from acoustic sources such as room noise, wind or vibrations of a building. That means we can do experiments in an open cavity without having to block outside noise. So if you have a landfill and you’re trying to detect methane, for example, you just take this detector, sit it there in the open air and continuously monitor the output.”

There remains some work on engineering a compact instrument before this technique can be used outdoors, but this study offers a convincing proof of concept, the researchers say.

Diebold’s coauthors on the paper were Brown graduate students Lian Xiong and Wenyu Bai, along with Feifei Chen, Xian Zhao and Fapeng Yu from Shandong University in China. The research was funded in part by the U.S. Department of Energy (DE-SC0001082).


New photoacoustic technique detects gases at parts-per-quadrillion level | News from Brown

Lian Xiong et al, Photoacoustic trace detection of gases at the parts-per-quadrillion level with a moving optical grating, Proceedings of the National Academy of Sciences (2017). DOI: 10.1073/pnas.1706040114