TC_Chu's Point

Bases to Bytes Cheap sequencing technology is flooding the world with genomic data. Can we handle the deluge?

The cost of sequencing human genomes is plunging—in the most advanced genomics centers, it's falling five times faster than the cost of computing. Increasingly, people are getting their DNA sequenced by companies and research labs in a search for clues about genetic variation and disease.

But the industry must figure out how to cheaply store all the resulting data. Each of the 3.2 billion DNA base pairs in a human genome can be encoded by two bits—800 megabytes for the entire genome. But considerable data about each base is usually collected, and genes are often sequenced many times to ensure accuracy, so it's common to save around 100 gigabytes when sequencing a human genome with a machine made by industry leader Illumina. Keeping this much data about every person on the planet would require about as much digital storage as was available in the whole world in 2010.

The trick, then, will be to save less. Harvard geneticist George Church says that eventually only the differences between a newly sequenced genome and a reference genome will need to be stored. That information could be encoded in as little as four megabytes. Then your genome might be just another e-mail attachment.

via MIT Technology Review

 

DNA: The Secret of Life

via Amazon

前半段關於基因改造食物的部份差點看不下去 就算那是James D. Watson說的 後面有關基因治療的部份 我也是不是很同意 （我支持體細胞（Somatic Cell)基因治療 而不支持性細胞（Germline Cell)基因治療）因為如果你知道目前把好的基因植入你的細胞是使用反轉錄病毒而且你完全不知道會把基因植到哪邊 光是這一點就讓人不放心（對於重大的基因疾病這是兩難的選擇）Watson對基因工程的看法太過天真了 但是我同意我門應該對基因做更多的研究 甚至於找出與行為相關的基因 不是要逃避責任而是知道有這樣的缺陷才能用適當的教育或是環境來改善

The Epigenetics Revolution: How Modern Biology Is Rewriting Our Understanding of Genetics, Disease, and Inheritance

via Amazon

很有趣的書

Gene hunt is on for mental disability

Exome sequencing could help to identify the causes of intellectual disability in children such as Siebe.

...

About 2% of children experience some form of intellectual disability. Many have disorders such as Down’s syndrome and fragile X syndrome, which are linked to known genetic abnormalities and so are easily diagnosed. Others have experienced environmental risk factors, such as fetal alcohol exposure, that rule out a simple genetic explanation. However, a large proportion of intellectual disability cases are thought to be the work of single, as-yet-unidentified mutations.

Scientists estimate that about 1,000 genes are involved in the function of the healthy brain. “There are so many genes that can go wrong and give you intellectual disability,” says André Reis, a medical geneticist at Erlangen University Hospital in Germany. Reis’s group, the German Mental Retardation Network, has already sequenced the exomes — the 1–2% of the genome that contains instructions for building proteins — of about 50 patients with severe intellectual disability.

...

http://www.nature.com/news/gene-hunt-is-on-for-mental-disability-1.10463

 

Molecular Motor Coupled to High Sensitivity Nanopore Promises Cheap DNA Sequencing

"We augmented a protein nanopore we developed for this purpose with a molecular motor that moves a DNA strand through the pore a nucleotide at a time," says Jens Gundlach, a University of Washington physics professor who leads the research team, in a press release covering the research. “The motor pulls the strand through the pore at a manageable speed of tens of milliseconds per nucleotide, which is slow enough to be able to read the current signal.”

via IEEE spectrum

Cell Phone Spectrophotometer

Include all data and software to build it.

http://www.asdlib.org/onlineArticles/elabware/Scheeline_Kelly_Spectrophotometer/index.html

http://www.news.illinois.edu/news/10/1007scheeline_spectrophotometry.html

Long Term Memory Encoding in the Brain

Researchers may finally have uncovered the brain mechanism for storage of long term memories. It's long been suspected that synaptic connections between neurons were part of the mechanism. But somehow our memories survive while individual neurons die and are replaced. There's a new paper on the subject by Travis J. A. Craddock, Jack A. Tuszynski, and Stuart Hameroff, titled "Cytoskeletal Signaling: Is Memory Encoded in Microtubule Lattices by CaMKII Phosphorylation?" 

http://robots.net/article/3343.html

關於基因改造食物 (1)

如果孟山都(Monsanto)公司覺得自己的產品是那麼的值得驕傲 請在每一件使用貴公司的種子而生產的食物與沿生食品上打打上 ”Monsnto Indside" 不是很棒的一件事嗎？ 學學人家Intel and Windows 在每一臺電腦上都貼上亮晶晶的貼紙 不是很光榮的事嗎？

讀完“欺騙的種子”有感

濁度計 (2)

仪器工作原理、特点
1．本仪器采用积分球式浊度测定原理：
一束平行光在透明液体中传播，如果液体中无任何悬浮颗粒存在，那么光束在直线传播时不会改变方向；若有悬浮颗粒、光束在遇到颗粒时就会改变方身（不管颗粒透明与否）。这就形成所谓散射光。颗粒愈多（浊度愈高）光的散射就愈严重。

        浊度是用一种称作浊度计的仪器来测定的。浊度计发出光线，使之穿过一段样品，并从与入射光呈90°的方向上检测有多少光被水中的颗粒物所散射。这种散射光测量方法称作散射法。任何真正的浊度都必须按这种方式测量。浊度计既适用于野外和实验室内的测量，也适用于全天候的连续监测。可以设置浊度计，使之在所测浊度值超出安全标准时发出警报。
如图所示：灯源发出的白炽光经聚光镜会聚后照射在针孔上；准直物镜将针孔出射的光线变成一束平行度很好的平行光出射；平行光经样品后分解成透过光和散射光（分别记为Tp）和Td），并进入积分球内。在积分球内壁上装有二保光敏元件，它们分别接收透过光和散射光。通过光讯号和散射光讯号经电路放大和处理后按下式显示：
浊度=K×散射光通量/透过光通量
=K×Td/Tp
K:比例常数。
2．测量值不受液体色泽影响：
假定样品是无色的，进入液体的入射光通量为l0,出射光通量亦为l0。出射光通量、散射光通量和平行透过去时光通量三者关系为（不考虑比色器皿的反射、吸收等）：
l0=Tp+Td
如果样品带色，进入液体的入射光将部分被吸收，设液体透过率为T，此时出射光通量l0,、散射光通量Td,和平行透过光通量Tp,有关系。
l0,=T×l0Tp,=T×TpTd,=T×Td
也就是说：无论透过光或散射光它们的强度都衷减速了同一系数T。
此时浊度测量值仍将不变：
浊度=K×散射光通量/透过光通量
=K×Td,/Tp,=K×T×Td/T×Tp
=K×Td/Tp

http://www.hudong.com/wiki/%E6%B5%8A%E5%BA%A6%E8%AE%A1

 

利用手機做水質測試(使用手機上的相機元件）

先記著！

Why a Portable DNA Device Could Yield Better Data

The technology relies on the fact that a DNA base, or a combination of bases on a DNA strand creates a characteristic disruption in a current as it passes through the nanopore. Electrodes measure the change in current flow as DNA molecules are fed through protein nanopores; an electrical gradient drives the DNA through the pore, while molecular "controllers" attached to the molecules mechanically slow them down so that their electrical signals may be recorded.

This approach has two important advantages.

First, the system is compact and doesn't require a supply of expensive reagents. That means sequencing can come out of the lab, making it useful for personalized medicine or for use in resource-poor clinics. Indeed, the disposable sequencer the company is about to introduce is the size of a USB memory stick.

Second, the technology reads much longer stretches of DNA than other rapid sequencing approaches, which means it has the potential to be better at spotting important "structural variants" related to disease. These variants occur when a whole segment of chromosome is moved, inverted, duplicated, or otherwise changed. When DNA is chopped into shorter stretches to be sequenced and then put back together on a computer, it is easier to miss, or misinterpret, such variants.

via Technology Review

synthesis.cc 

The Machinery of Life

這是一本非常美的書 裡面很多的蛋白質機器和細胞都是用水彩話的！ 

http://www.springer.com/life+sciences/cell+biology/book/978-0-387-84924-9

http://biocurious.com/ Books's blog

MinION: a miniaturised sensing

MinION is a disposable device that contains a sensor chip, ASIC and the fluidics system that are needed to perform a complete single molecule sensing experiment. Plugging directly into a laptop or desktop computer through a USB port, it is a self contained device to deliver real time experimental data. 

The MinION is adaptable for DNA sequencing, protein sensing and other nanopore sensing techniques. 

via nanopore_tech

 

What is nanopore

MIT duo successfully tests wireless drug-delivery microchips, more consistent than injections

 This past week, researchers in Cambridge -- alongside scientists from MicroCHIPS, Inc. -- announced that they have successfully used the aforementioned chip to give osteoporosis patients their daily allotment of teriparatide. "You can do remote control delivery, you can do pulsatile drug delivery, and you can deliver multiple drugs,"

via engadget

Device Brings $1,000 Genome Within Reach

At $149,000, the new machine is about three times the price of the Personal Genome Machine, the sequencer that the company debuted about a year ago. But the DNA-reading chip inside it is 1,000 times more powerful, according to Rothberg, allowing the device to sequence an entire human genome in a day for $1,000—a price the biotech industry has been working toward for years because it would bring the cost down to the level of a medical test.

via MIT Technology Review

 

Find Your Inner Neanderthal

In the last few years, scientists have uncovered clues not just to what the lives of Neanderthals may have been like, but also clues that tell us more about what it means to be a modern human.

Most interesting of all is that, although Neanderthals disappeared long ago, their DNA lives on in all non-African people.

http://spittoon.23andme.com/2011/12/15/find-your-inner-neanderthal/

PS.我在網路上的看過那個分析資料 蠻有趣的 因為收集到的尼安德塔人的基因量真的很少 如何分析這些資料和方法很有趣 (沒記錯的話是MIT Bioinformatics的課　一個很cool的年輕教授）

 

 

Is Autoimmunity a Result of Genetic Adaptation to Pathogens?

Although about 95% of the observed human genetic diversity appeared to be due to non-selective processes, a finding that was not surprising, adaptation to local environments—and specifically to pathogens—also accounted for a significant amount of genetic diversity. Viruses, bacteria, protozoan organisms that cause malaria and leishmaniasis, and parasitic worms are all examples of pathogens.

The study’s findings suggest that about 100 human genes have been strongly influenced by pathogenic organisms. Parasitic worms seem to have posed the most pressure on human genes. Because worms are complex organisms with longer lifespans than more simple pathogens, they may have co-evolved with people and exerted more pressure on the human genome.

...

This study offers new evidence for the hygiene hypothesis, a currently unproven theory suggesting that ramped up immune systems originally evolved to protect people from infectious organisms. As societies devised ways to keep pathogens at bay, however, their immune systems failed to adjust and they began to suffer from immune diseases characterized by too much inflammation.

http://spittoon.23andme.com/2011/11/30/is-autoimmunity-a-result-of-genetic-adaptation-to-pathogens/

 

Roboticists Learn from the Dragonflies

a 14-channel digital wireless neural/EMG telemetry system, suitable for in-flight neural recording from flying insects such as dragonflies. It has a system mass of only 38 milligrams. The IC is powered by RF energy harvesting and consumes less than 1.23mW. It digitizes 10 neural and 4 EMG signals with 11 bit resolution as a 5 Mbps backscattered data stream at UHF (902-928 MHz). It has been fabricated in a 0.35um 4M1P CMOS process.

http://robots.net/article/3269.html

Glucose Necessary For Cancer Growth May Prove To Be Its Weak Link

Researchers at Albert Einstein College of Medicine of Yeshiva University have discovered that cancer cells tap into a natural recycling system to obtain the energy they need to keep dividing. In a study with potential implications for cancer treatments, Einstein researchers used genetic manipulation to turn off this recycling system within the walls of cells and stop both tumor growth and metastasis (cancer spread). The findings were published in the online edition of Science Translational Medicine.

Scientists have known that cancer cells require a large amount of energy in the form of glucose (sugar) to support their abnormally rapid growth. But it wasn't clear how cancer cells met those energy needs. The study shows that cancer cells fuel their growth by revving up autophagy, a recycling process that occurs in cell compartments called lysosomes.

http://www.medicalnewstoday.com/releases/237837.php

How The Brain's Structure And Genes Affect Autism And Fragile X Syndrome

Research just released shows that scientists are finding new tools to help understand neurodevelopmental disorders like autism and fragile X syndrome. These studies show in new detail how the brain's connections, chemicals, and genes interact to affect behavior. The research findings were presented at Neuroscience 2011, the Society for Neuroscience's annual meeting and the world's largest source of emerging news about brain science health.

http://www.medicalnewstoday.com/releases/237823.php

 

Human Brain Cells' Genetic Make-Up Changes During A Lifetime

Investigators from The Roslin Institute, at the University of Edinburgh have discovered that during the lifetime of an individual, brain cells change their genetic make-up. This finding could offer new insight into neurological diseases. The study is published in the journal Nature and was conduced together with researchers from Italy, The Netherlands, the United States, Japan and Australia.

The researchers identified genes known as retrotransponsons - which are responsible for thousands of tiny alterations in the DNA of brain tissue. They discovered that the genes were especially active in areas of the brain associated with cell regeneration.

http://www.medicalnewstoday.com/articles/236929.php

What European DNA Can Say About Ancestry, Disease Risk, and Cultural Traits

All the drama in the European Union right now — the debt crisis, the North-South divide and the kvetching over the wisdom of a common currency — has reignited talk about the cultural divide between people on the continent.

But is the divide more than a political and cultural one? Is there a deeper difference among the people of Europe or those of European ancestry than whether Germans have a firmer handshake or are more punctual, or which nationality prefers a kielbasa to köttbulla?

There may be, and those differences can be seen in people’s DNA.

Although all humans are over 99 percent identical genetically, even in the tight geographic confines of Europe there is enough genetic variation that 23andMe researchers can use it to determine from where in Europe a person, or a person’s ancestors, came.

http://spittoon.23andme.com/2011/10/21/genes-and-geography/

Open Spectrometer

Beginning with the Open Spectrometer, we aim to produce a line of low-cost, high-value scientific instrumentation. Plans for everything will be freely available under open license, and kits and assembled devices will be fairly priced.Hardware Specifications:

• Toshiba TCD1304AP- 3648 pixel CCD array
• 16-bit ADC
• Texas Instruments Stellaris Microcontroller - 9000 series - 80mhz, 96kb RAM, ethernet, USB, microSD, and other hackable buses
• Possible Arduino UNO/DUE shield

Optical Specifications:

• Fiber coupled
• Reflective grating (configurable based on range/resolution needs)
• Option to replace the glass CCD window with Fused Silica for UV operation (>200nm)

http://www.kickstarter.com/projects/makerhaus/open-spectrometer

Gamers solve decade-long simian AIDS protein conundrum

For over a decade, researchers have been arduously attempting to reconstruct the folded shape of M-PMV with the aid of the task-specific Rosetta software, but to no avail. Now, in what they're calling a possible first, gamers were able to do what scientific brains and algorithms could not, creating a sufficient model for molecular replacement -- all in just three weeks. Feel like dedicating your leisure hours to this worthwhile cause? Then be sure to hit up the source link below, and transform yourself from couch potato to couch crusader.

via Engadget

把蛋白質折疊當成Game來玩 請Game玩家來解決科學家一直找不出來的方法 (玩家們只花了3星期 兒科學家花了10年)

http://fold.it/portal/

Mining Data for Better Medicine

The spread of electronic patient records, with their computer-readable entries, is opening new possibilities for medical data mining. Instead of being limited to carefully planned studies on volunteers, scientists can increasingly carry out research virtually by sifting through troves of data collected from the unplanned experiments of real life, as preserved in medical records from scores of hospitals.

Such techniques are allowing researchers to ask questions never envisioned at the time of a drug's approval, such as how a medicine might affect particular ethnicities. They are also being used to uncover evidence of economic problems, such as overbilling and unnecessary procedures. Mining of health records "is going to build advancements in research, but also efficiencies in the health delivery system," says Margaret Anderson, executive director of FasterCures, a think tank in Washington, D.C.

via MIT Technology Review

Your Heartbeat on an iPhone

ECGs are used to diagnose irregular heartbeats, or arrhythmias, a common type of medical problem that can also be the result of a heart attack. AliveCor's monitor is built into a case that slips onto an iPhone. It has two electrodes that pick up voltage changes on the skin—the ECG signal—produced by the contraction of the heart. A low-power wireless transmitter sends the signal to the phone. Power comes from a lithium watch battery that Albert claims will last for 180 hours of continuous use.

via MIT Technology Review <--- Check the video!

An RNA Switch for Stem Cells

Mitchell Guttman, first author of the study and a graduate student at MIT and the Broad Institute, says that when the Broad team discovered more than 3,500 unique lincRNAs in the human and mouse genomes in 2009, "the potential was enormous, and we wanted to know what they could be doing."

To answer that question, the researchers focused on understanding lincRNAs' role in embryonic stem cells. Using a technique called RNA interference, they systematically shut down the function of each of more than 200 lincRNAs previously identified as playing a role in embryonic stem cells. They then profiled the genes expressed in the cells and studied their functions. They found that most lincRNAs have widespread effects on cells, and that they help control the fate of stem cells. The team identified about two dozen lincRNAs that help maintain the cell's pluripotency—its ability to beget all other kinds of cells—and a similar number of lincRNAs that repress genes involved in differentiating into other cell types.

via MIT Technology Review

Glucose sensor skin implant glows when blood sugar spikes

Checking blood glucose levels used to mean a finger prick and a test-strip, but researchers at the University of Tokyo are offering a different approach: a glowing skin implant. After being injected with the 1 mm wide filament, it monitors your blood sugar by glowing when your level changes. Based on existing glowing glucose sensor technology, this hydrogel fiber is considered more accurate and stable than its predecessors, plus it requires no oxygen to function. So far, it's worked in mice for up to 140 days. Note to future human patients: don't eat a candy bar before you go to bed unless you want your arm looking like a nightlight.

via Engadget

就是把一種東西直入你的皮下 當你的血糖飆高的時候會發出螢光來警告你

j5 DNA Construction Software

Researchers at the Joint BioEnergy Institute (JBEI) have developed j5, a technology that automates and optimizes the design of the molecular biological process of cloning/constructing DNA. j5 enables users to benefit from multi-part scar-less SLIC, Gibson, CPEC, (combinatorial) Golden-gate assembly, or variants thereof, where automation software does not exist, without the current level of intense labor associated with the process. The j5 manual provides a step-by-step user’s guide and describes the software’s feature set in greater detail.

http://j5.jbei.org/index.php/Main_Page <--- j5 main page

USB Pregnancy Test (USB驗孕機)

Features:

• USB 2.0 compatible

•Plug-and-play, easy operation

•No batteries required — draws power from USB

•Operating Systems: Win 98, ME, 2000, XP, Vista, Linux 2.4 or higher, Mac OS 8.6 or higher

•20 test strips included

•99% accuracy*

While most home tests can detect a level of 15-50 mIU/mL of hCG, the enhanced methodology of the USB Pregnancy Test Kit can detect 5-50 mIU/mL, and will show you the exact concentration via its friendly onscreen interface. In addition, the LCD display on the device itself will light up and show you the symbol of a baby, no baby, or multiples and your Estimated Delivery Date based on the concentration of hCG, hCG-H, and LH in your urine. So you can clear your calendar in advance.

via bookofjoe

 

Science DNA-based artificial neural network is a primitive brain in a test tube

via Engadget

Tiny Plastic Card IDs HIV in Minutes

The awesome science of microfluidics has the potential to revolutionize diagnostics, particularly in developing countries where well-equipped labs are hard to come by. Small, inexpensive and accurate diagnostic tools like this one from Columbia University researchers could save countless lives by detecting deadly diseases like HIV without the need for complicated equipment.

via gajitz.com

Massive Project to Study the Link between Genetics and Health

Now Kaiser Permanente, the nation's largest nonprofit health plan, has announced that it's finished the first phase of a massive project to compile genetic, medical, and environmental information for 100,000 of its members. Researchers also analyzed the length of participants' telomeres—a molecule structure at the tip of the chromosome that has been linked to aging. This represents the largest telomere study to date.

The resulting data, gathered in collaboration with the University of California, San Francisco, will soon be available to outside researchers who study how different genetic and environmental factors influence disease. It took about 15 months for the team to collect and analyze the genomes of 100,000 people ranging in age from 18 to 107. The team used gene microarrays—small chips designed to quickly detect hundreds of thousands of genetic variations across the genome.

via MIT Technology Review

Modelling chemical reactions using an FPGA

[Bruce Land] is a professor at Cornell University who was looking for a way to quickly solve chemical kinetic systems. He had used MATLAB but longed for a faster method. His upgrade achieves a 100 times speed increase by using an FPGA as a parallel stochastic solver.

via Hack a Day

DNA is now DIY: OpenPCR ships worldwide

The eagerly awaited OpenPCR kit is now shipping! UPS picked up the first batch of kits and OpenPCRs are on their way to users in 5 continents and 13 countries around the world. For $512, every OpenPCR kit includes all the parts, tools, and beautiful printed instructions – you ONLY need a set of screwdrivers.

A PCR machine is basically a copy machine for DNA. It is essential for most work with DNA, things like exposing fraud at a sushi restaurant, diagnosing diseases including HIV and H1N1, or exploring your own genome. The guy who discovered the PCR process earned a Nobel Prize in 1993, and OpenPCR is now the first open source PCR machine.

...

OpenPCR is designed for labs, classrooms, and garages. Tell your science-y friends about OpenPCR, “Like” us on Facebook, or write us and tell us that you stopped by! You can also get your own OpenPCR kit!

http://openpcr.org/2011/07/dna-is-now-diy-openpcr-ships-worldwide/