About DNA sequence industry: Welcome to the $1,000 genome: on Illumina and next-gen sequencing
Recently I found a news from Illumina, the leading DNA sequencing technology provider about two new sequencing machines. In the article, Mark Wation from The Roslin Institute, University of Edinburgh, gives his insight about the state-of-art of DNA sequencing and its future tends: Welcome to the $1,000 genome: on Illumina and next-gen sequencing
<More about Mick Watson>
I extracted a small part of the article below:
The future for Illumina’s competitors
It will be really interesting to see how Life Technologies responds to Illumina’s latest developments. Their key advantage is speed, with the Ion Torrent platforms carrying out the sequencing component in hours rather than days. However, the throughput and cost-per-base do not match current Illumina platforms, never mind the new ones. To remain a viable business, Life Technologies, and its Ion Torrent platforms, must respond.
Pacific Biosciences’ SMRT technology has evolved significantly too and has become an essential tool for those wishing to close genomes, or sequence de novo new genomes. Intriguingly, Roche, a global health-care company, announced an agreement with Pacific Biosciences to develop DNA sequencing products for clinical diagnostics. This is not a space that Pacific Biosciences have been in up until now, and it is difficult to see how their RS II system can compete with Illumina and Ion Torrent in the clinic. Because of this, rumors of a new (benchtop?) PacBio machine abound on social media.
For many, Oxford Nanopore Technologies, heir apparent to the sequencing crown, remain the future. The company recently opened up an early-access program for their USB sequencer, the MinION. At the AGBT conference, David Jaffe showed the first data from this platform. These are exciting times for nanopore-based sequencing, but there remain challenges – particularly in interpreting the signal and turning it into the ‘bases + quality scores’ paradigm that many are used to. In fact, to get the best out of the platform, many think a change to the above paradigm will need to happen, and software may need to interpret the raw signal rather than the traditional 4 bases. On his blog, Yaniv Erlich commented that ‘MinION is not a sequencing platform. It is a sequencing sensor.’ (his italics) and I think this is a key differentiator of the platform. It is the only platform that detects an actual single strand of DNA (rather than incorporation events as a template strand is copied), and it still astounds me to think that we are soon to have in our hands the very first mobile device capable of sequencing DNA – surely an historic moment. With that idea in mind, it is hard not to believe that nanopore-based sequencing is the future. Of course, Oxford Nanopore have competitors, but one look at their management team, followed by a look at their IP portfolio, and it is hard to imagine anyone being better placed to deliver on the promises of nanopore-based sequencing.
image source: All Things Illumina Sequencing Methods
Imaging technologies from bench to bedside
Corresponding author: Ravinder Reddy krr@mail.med.upenn.edu
Author Affiliations
Center for Magnetic Resonance and Optical Imaging, Perelman School of Medicine, Department of Radiology, University of Pennsylvania
Journal of Translational Medicine 2015, 13:97 doi:10.1186/s12967-015-0449-5
More about author
Editorial
The last few decades have seen tremendous advances in medicine that have enhanced understanding of pathophysiological processes at the cellular and molecular level, and led to the development of increasingly sophisticated diagnostic imaging technologies. Early detection of disease induced molecular and functional changes before induction of irreversible structural changes is key for optimal treatment efficacy. Non-invasive imaging modalities, such as positron emission tomography (PET) [1], single photon emission computed tomography (SPECT) [2], computed tomography (CT) [3], optical tomographic technologies [4], magnetic resonance imaging (MRI) [5], ultrasound (US) [6], and X-rays play a vital role in both the diagnosis and monitoring of disease in response to therapy. These techniques cover a broad range of spatio-temporal resolution and varying degrees of sensitivity and specificity to different molecular changes, and in many cases provide complementary information [7],[8]. Recently discovered molecular targets of various disease states, including oncology, neurodegenerative and neuropsychiatric, cardiovascular, and musculoskeletal pathologies, drive further developments in the imaging field to detect these new molecular markers. Ultimately, these technologies contribute to improved disease management and personalized patient care.
Standard-of-care medical imaging techniques such as X-rays, US, CT and MRI provide exquisite structural details of human anatomy. These methods are the first-line techniques in clinic for diagnosis and characterization of disease, based primarily on structure/morphology such as size, texture and tissue attenuation [8]. In addition to providing diagnostic information, the US modality has the additional benefit of use as a therapeutic tool [6],[7],[9].
Functional nuclear medicine techniques (PET and SPECT) provide a unique, non-invasive assessment of intracellular processes and enzyme trafficking, receptors and gene expression, and serve as the underpinnings of molecular medicine. These techniques provide non-invasive diagnostic information about biochemical and physiological process ranging from glucose metabolism to gene expression by evaluating the kinetics of short-lived radioisotope tracers. While many promising tracers have been synthesized that target a variety of metabolic pathways or specific markers 18F-fluorodeoxyglucose (FDG), a glucose analogue is the main radiotracer in clinical practice today. In addition, these functional nuclear medicine techniques are also being used in research and clinical settings to detect and evaluate Alzheimer’s disease, metabolic viability of cardiac tissues, in vivo gene expression, and in tracking of cancer metastasis to different organs [7],[8],[10]-[12].
MRI is one of the most powerful and versatile non-invasive techniques. The major advantage of MRI is that it provides high-resolution, three-dimensional images of tissue structure, as well as functional and metabolic information. Furthermore, MRI is performed in vivo without the use of any ionizing radiation, allowing for repeated study. Several advanced MRI methods have been introduced to monitor the structural [13], functional [14],[15] as well as biochemical changes in various diseases. Magnetic resonance spectroscopy (MRS), which provides the information about the biochemical signatures, is an additional important clinical research tool to assess and characterize disease pathophysiology [16],[17].
Using MRS, enriched metabolites (e.g. 13C enriched) can be used to probe endogenous reaction kinetics. Latest advances in chemical exchange saturation transfer (CEST) MRI show promise in detecting several endogenous metabolites and proteins with substantially enhanced sensitivity (at least an order of magnitude) compared to conventional MRS [18]-[25]. Recent developments in hyperpolarized imaging based on dynamic nuclear polarization (DNP) of 13C enriched pyruvate are yielding highly promising preclinical results [26],[27] exploring in vivo reactions in oncology and other disease conditions. Some very preliminary results showing the promise of these methods in addressing clinical problems in patients have been demonstrated [28].
Optical imaging is another emerging imaging modality with high potential for improving diseases diagnosis and treatment, which can be readily set up at the patient’s bedside or in the operating room [4],[29]-[31]. Optical imaging uses non-ionizing radiation and offers potentially to image organs, tissues as well as smaller structures including cells and molecules using their unique photon absorption or scattering profiles. It also differentiates between native soft tissue and tissue labeled with endogenous or exogenous probes based on their wavelength dependent photon absorption or scattering pattern [32]-[35]. Despite limitations in their spatial resolution, optical imaging methods offer capabilities for studying functional and molecular events in different pathophysiological conditions. There are several techniques in optical imaging that are currently being used both in research and clinical setting for evaluating various diseases and therapeutic responses [30],[36]-[38]. Potentially, optical imaging can also be combined with other imaging modalities to improve the patient’s clinical management.
PET, SPECT and near-infrared reflectance fluorescence optical imaging techniques have relatively high sensitivity and can detect compounds with concentrations in micro- to pico-molar range [7]. Despite the high sensitivity these methods are beset by a relatively low spatial resolution (5 to 10 mm in clinical setting). Also, in many cases the emitting ligands may lose the specificity. One issue with nuclear medicine techniques is the use of nuclear radiation, which precludes their repeat use in short time spans. On the other hand, MRI provides high spatial resolution (in hundreds of micrometers range), but is relatively insensitive, in comparison to nuclear medicine techniques mentioned above; it requires concentrations of metabolites to be detected to be in the millimolar range and few endogenous molecules or metabolites can be imaged [39].
A milestone in the field of diagnostic imaging is the emergence of integrated structural and functional modalities such as combined PET-CT and PET-MRI [40],[41]. These integrated modalities provide concurrent structural, molecular and functional information, improve the multimodal imaging correlations and ease the patient burden for multiple imaging sessions.
Combining these advanced imaging techniques will result in improved precision of the data that are intrinsically more sensitive to the underlying pathophysiology than the morphological features available in routine structural imaging. Over the years, all these powerful imaging techniques have been improving the way the diseases are diagnosed, therapeutic responses are monitored and dramatically enhancing the practice of medicine making it more prognostic, preventative and personalized. Despite these advances, many technological innovations in these imaging modalities are still in research setting. Transferring these technologies into clinical setting requires an intense collaborative effort between researchers in imaging physics, instrumentation, image processing, biologists, chemists, and regulatory bodies as well as clinicians from all branches of medicine. This journal section facilitates communication of advances in translating the imaging modalities from mere research tools to clinical setting. We welcome research articles from all the stakeholders in this field.
The electronic version of this article is the complete one and can be found online at: http://www.translational-medicine.com/content/13/1/97
Image source: National Institute of Biomedical Imaging and Bioengineering
Still 0 and 1? Check this out: Memory leads the way to better computing
Correspondence: H.-S. Philip Wong & Sayeef Salahuddin
H.-S. Philip Wong - Department of Electrical Engineering and the Stanford SystemX Alliance, Stanford University, Stanford, California 94305, USA
Sayeef Salahuddin - Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California 94720, USA
Nature Nanotechnology 10, 191–194 (2015) doi:10.1038/nnano.2015.29
More about Authors:
http://web.stanford.edu/~hspwong/
https://www.eecs.berkeley.edu/Faculty/Homepages/salahuddin.html
Introduction
Current memory devices store information in the charge state of a capacitor; the presence or absence of charges represents logic 1's or 0's. Several technologies are emerging to build memory devices in which other mechanisms are used for information storage. They may allow the monolithic integration of memories and computation units in three-dimensional chips for future computing systems1. Among those promising candidates are spin-transfer-torque magnetic random access memory (STT-MRAM) devices, which store information in the magnetization of a nanoscale magnet. Other candidates that are approaching commercialization include phase change memory (PCM), metal oxide resistive random access memory (RRAM) and conductive bridge random access memory (CBRAM).
Today's computing systems use a hierarchy of volatile and non-volatile data storage devices to achieve an optimal trade-off between cost and performance2. The portion of the memory that is the closest to the processor core is accessed frequently, and therefore it requires the fastest operation speed possible; it is also the most expensive memory because of the large chip area required. Other levels in the memory hierarchy are optimized for storage capacity and speed (Fig. 1). The main memory is often located in a separate chip because it is fabricated with a different technology from that of the microprocessor.
For over 30 years, static random access memory (SRAM)3 and dynamic random access memory (DRAM)3 have been the workhorses of this memory hierarchy4. Both SRAM and DRAM are volatile memories — that is, they lose the stored information once the power is cut off. For non-volatile data storage, magnetic hard disk drives (HDDs) have been in use for over five decades5, 6, 7. Since the advent of portable electronic devices such as music players and mobile phones, however, solid-state non-volatile memory known as Flash memory8 has been introduced into the information storage hierarchy between the DRAM and the HDD. Flash has become the dominant data storage device for mobile electronics; increasingly, even enterprise-scale computing systems and cloud data storage systems are using Flash to complement the storage capabilities of HDD.
For complete FREE article for:
- Electrical manipulation of magnetism in ferromagnets
- Electrical control of magnetization in multiferroics
image source: Controlling size and helicity of a spin-vortex skyrmion
the Year of goat, NOT ‘any ruminant horned animal’ ??
An interesting article:
also see here:
"The Chinese word yang in oracle-bone script - the ancient characters found on bones used for divination in the Bronze Age - looked like an animal with two horns and a pointy face, said Professor Ho Che-wah, head of the department of Chinese literature at Chinese University.
But the character could be translated to goat, sheep or ram in English.
Ho said that while sheep had a long history in Chinese society, the country's culinary past suggested the goat as the most likely animal to have been included in the zodiac.
"In ancient China, people ate six types of animals - horse, cow, goat, pig, dog and chicken. Goat is therefore included in the zodiac, too," Ho said.
Goats also had a higher status among the six animals in Chinese society, as in the past, only rich people and the aristocracy could afford to eat them.
The Chinese word for "envy" originally referred to a person salivating over a goat, Ho added."
“gung1 hei2 faat3 coi4”
Tag :
general,
Geoengineering - technology against our nature?
There is an interesting article on BBC-science/environment recently titled "'Next Pinatubo' a test of geoengineering" and Prof. Alan Robock from Rutgers University shared his viewpoints about this.
One topic being discussed is to take advantage of next big volcanic eruption to study sulphur dioxide how it could help against global warming. Enjoy it.
The article also points out that this is a plan Z in case there is no remarkable outcome to reduce greenhouse gas emission.
About Prof. Alan Robock
related infographcis:
Youtube about Geoengineering:
image source: The pros and cons of geoengineering
biochemistry or chemical biology?
What is Chemical Biology? and
What is Biochemistry?
I extracted the following description from a RSC book, New Frontiers in Chemical Biology
"Chemical biology is an emerging field at the interface between chemistry and biology. It utilises the tools and techniques of chemical synthesis to study and influence biological systems. Recent developments in this area have great potential in addressing the productivity challenges expressed above. For example, chemical biology studies have already led to the identification of novel targets with exciting therapeutic potential and it is clear that the field will prove a key enabler of target discovery in the future. Moreover, the precise synthetic manipulation of biological molecules involved in many chemical biology approaches is now fuelling a new wave of chemically-modified biologics, 'chemologics', with unique properties. In these, and many other ways, chemical biology is a key discipline within 21st century drug discovery and the purpose of this book is to highlight the most important developments. It provides a valuable resource for scientists in academia and industry who are looking to build their knowledge of this hot topic."
You may get more ideas from the following:
Institute of Chemical Biology, Imperial College.
Chemical Biology Graduate @ UC Berkeley
Chemical Biology PHD Program
To review what is biochemistry, try Biochemical Society.
Its booklet describes what is biochemistry:
http://www.biochemistry.org/Portals/0/Education/Docs/Biochem_Booklet_web.pdf
"explore the chemical process that take place inside all living things, from bacteria to plants and animals"
image source: The Chemistry-Biology Interface Training Program
Tag :
general,
Tips: For all Scientists: Starting up a career
Start up a career:
Tips extracted from the articles:
Lesson 1: Write a business plan.
Lesson 2: Get the right patent.
Lesson 3: Enter a contest.
Lesson 4: Funding comes in many forms.
Lesson 5: The science isn't everything
Lesson 6: Rent a bench.
Lesson 7: Assemble a good team.
Lesson 8: Biotech companies can be virtual.
Lesson 9: Entrepreneurship = experience
You will find the technology you are developing is only a tiny factor in your entrepreneurial journey.
image source: 10 Entrepreneur Lessons Not Taught in Classroom
Cars without Driver
There is an interesting article about driverless cars in Nature recently - Autonomous vehicles: No drivers required. In the first line, it states that:
"This summer, people will cruise through the streets of Greenwich, UK, in electric shuttles with no one's hands on the steering wheel — or any steering wheel at all."
No need to be scare when you find a moving car without a driver.
Btw, this is not a new things. Google Driverless Project may give you more confident on driverless technology. Take a look here:
A Ride in the Google Self Driving Car
A First Drive
related news:
Ten ways that driverless cars will change the world, the Telegraph
There is a good academic reference for you, edited by Prof. Azim Eskandarian:
I hope the test in UK works and it will be a good news for all travelers without driving licence. Anyway, this news remind me the Google Driverless project.
image source: Autonomous vehicles: No drivers required
Tag :
general,
Open questions: seeking a holistic approach for mitochondrial research
Correspondence: Heidi M McBride heidi.mcbride@mcgill.ca
Montreal Neurological Institute, McGill University, 3801 University Avenue, Rm 622C H3A 2B4, Montreal H3A 0G4, QC, Canada
BMC Biology 2015, 13:8 doi:10.1186/s12915-015-0120-x
[More about author]
Collaborate
Most of us are not geniuses, and cannot operate with an encyclopaedic knowledge of metabolism, calcium homeostasis, tissue physiology, bioenergetics and lipid chemistry. On the other hand, clinician scientists or physiologists who hope to incorporate mitochondria into their signalling paradigms feel overwhelmed with the complexity of the organelle, the experimental approaches, and sometimes, the dogma common to such established fields. The first step is an obvious one - forge meaningful collaborations that will truly push the field forward. I think we are finally past the point where non-mitochondrial scientists simply write us off, assuming that the mitochondria are a known entity, uninteresting, boring. Indeed the potential for fundamental new concepts in mitochondrial function has never been higher, and the disease relevance is clear. Mitochondrial pathways are practically untouched as a therapeutic target, for example.
For those of us working on the fundamental aspects of mitochondrial function, we must work harder to consider the physiology of real tissues. I’m not suggesting we abandon our fundamental projects, certainly not! Basic discoveries will remain the lifeblood of clinical development. But with collaborations we can extend our studies simultaneously and move into ‘real’ cells. Adapting these models will more rapidly push our discoveries up the ladder of biomedical translation. My own collaborations have provided me with confidence and helped me to understand complex physiologies that would otherwise have not crossed my radar screen. It sounds obvious, but funding agencies and promotion mechanisms do not always reward collaborations enough. Grants need a single principal applicant and team grants can be more political than functional. It is also clear that collaborations are more difficult than simply continuing along a successful, independent track. However, understanding the complexities of mitochondrial function and signalling will require open, and sometimes challenging, collaborations.
The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1741-7007/13/8
There is an interesting video on Youtube about mitochondria!! - "Power Pack - The Mitochondria Rock Song"
image source: Blame it On Your Mother
Nanyang Technological University produced a 3D printed concept car
Of course this is not the first 3D printer car, but it is good to see a group of students from Nanyang Technological University to get it done.
They are NTU Venture 8 & NTU Venture 9, both with round 150 parts are 3D-pritned.
For the NTU Venture 8, honeycomb structure and a unique joint design was employed, to ensure the car doesn't come apart. Also, the car chassis is see-through when hit by the light at the right angle. Presumably, most of the light will be absorbed by the solar cells so that the inside of the car doesn't heat up overmuch during summer.
NTU Venture (NV) 9, a slick three-wheeled racer which can take sharp corners with little loss in speed due to its unique tilting ability inspired by motorcycle racing.
NTU unveils Singapore’s first 3D-printed concept car
3D-printed green vehicle to blaze a trail for future car technology
This first 3D printed car is like this:
image source: straitstimes