Bio Links
(09Oct2011)
BIOLOGY
GENOMICS
SEQUENCING
454 Life Sciences
454 uses "pyrosequencing" technique whereby 300-500 base ssDNA segments are read by building their complement strand via polymerase while sequentially supplying nucleotides with (luciferase based) luminescent tags
Applied Biosystems
AppliedBiosystems: SOLiD (Sequencing by Oligonucleotide Ligation and Detection) technology, uses uniquely color coded nucleotide-pair probes.
BioNanomatrix
BioNanomatrix claims to read single long (1,000's to 1,000,000's of base pair) molecules using chip based nanofluidics and flourescent tags:
Complete Genomics
CG uses their "cPAL" (combinatorial Probe Anchor Ligagtion) technology for the raw base reads. "cPAL" is based on a series of 10-position probes that are positioned relative to multiple adaptors inserted in the segments to be read. Each probe contains a single base at only one of the 10 positions (the other positions are spacers), and that single base is labled with a unique flourescent tag (i.e. for each position there are four versions of the probe, and therefore 40 different probes). Each set of 4 probes is exposed to the prepared segments and those that match a complimentary base the right number of positions away from the inserted adaptor constitutes an optically detectable read. Successive floodings of the assay with the various probes and the resulting matching builds up sequences of reads. This read methodology is complemented by proprietary preparation of the DNA molecules to be read into dense "DNA nano-balls" (DNB), a two tier library of detected patterns and associated matching and assembly algorithms.
Halcyon Molecular
"Halcyon Molecular is a Stanford area nanotech startup developing a [fast], ultra-low-cost DNA sequencing technology based on transmission electron microscopy (TEM) of heavy atom-labeled DNA. Core developments include a single DNA molecule manipulation technology that allows for the placement of megabase DNA molecules with nanometer precision."
Helicos
Helicos uses a process that they call "tSMS" (true Single Molecule Sequencing) and a device called a "Heliscope" to detect the sequential polymerization of flourescent labeled nucleotides to each of billions of 100-200base segments of the source DNA, at a rate of billions of bases/day (goal of billions/hr).
Removeable flourescent labels allow spatial identification of each strand that polymerizes a complementary nucleotide during a repeating cycle of "flood plate with polymerase and a single type of labeled nuceotides", "wash away the excess polymerase and f-labeled nucleotides", "detect flourescent label on each strand where polymerization occurred", "remove the flourescent labels from the polymerized nucleotides", "repeat the cycle with another type of nucleotide".
This process is repeated until no further polymerization is detected at any strand.
Illumina
"Illumina Sequencing technology relies on the attachment of randomly fragmented genomic DNA to a planar, optically transparent surface. Attached DNA fragments are extended and bridge amplified to create an ultra-high density sequencing flow cell with hundreds of millions of clusters, each containing ~1,000 copies of the same template. These templates are sequenced using a robust four-color DNA sequencing-by-synthesis technology that employs reversible terminators with removable fluorescent dyes. This novel approach ensures high accuracy and true base-by-base sequencing, eliminating sequence-context specific errors and enabling sequencing through homopolymers and repetitive sequences."
Ion Torrent
"Ion Torrent technology is based on the release of an H+ (Hydrogen ion) each time a nucleotide is polymerized to a ssDNA molecule. The released H+ ion causes a lower PH level of the local chemical environment.
Ion Torrent has developed a custom semi-conductor chip consisting of millions of "reaction wells" fabricated over a PH sensing layer and underlying sensor circuits. This "sequncer on a chip" allows semiconductor scale volumes with corresponding semiconductor prices.
In operation, each reaction well holds a 100-200 base fragment of ssDNA being polymerized using sequential floods of the 4 relevant nucleotides (ACGT). Within each "reaction well", if the current nucleotide is added to the DNA molecule then the resulting release of a hydrogen ion is detected through the lower PH that it causes. Apparently, the reaction well volume is such that not only is the PH difference caused by a single H+ detectable, but multiple H+ ions cause a scalable PH decrease, allowing homogeneous strings of nuceotides to be sequenced.
Claims are for a $50,000 system and the ability to sequence an entire human genome in under an hour for ~ $500 each."
LifeTechnologies
"LifeTechnologies: Single Molecule Sequencing (SMS) technology employing QDots (quantum dots) and proprietary polymerase to optically signal the addition of each successive nucleotide. They refer to a 'recursive' capability of the process alowing multiple coverage and virtually unlimited length reads. LifeTechnologies is a combination of Invitrogen and Applied Biosystems Inc."
NABsys
NABsys describes their approach as using "Solid State Technology" and "Electronic Detection", being "Polymerase Free", and producing "Long-Range Sequence Information" (100,000's base pair read lengths):
Oxford Nanopore
Oxford Nanopore uses a nanopore approach that they call BASE technology where a single stranded DNA molecule flows through an enzyme that successively clips off each nucleotide which is then directed into an associated nanopore in which an imbedded "cyclodextrin" senses the unique electrical resistance of each nuceotide passing through it. With tens of thousands of nanopores fabricated on a single plate and each nanopore processing about 50 nucleotides/second, potentially 100s of thousands of nucleotides/second can be sequenced per plate.
Pacific Bioscience
Pacific BioSciences uses a technology they call SMRT (Single Molecule Real Time).
Semi-conductor methods are used to build a 2 layer reaction plate. The plate consists of a transparent layer beneath a thin layer of opaque metal. Thousands of small nanopore "wells", called Zero Mode Waveguides (ZMW) are established through the metal layer.
To the bottom of each nanopore "well", on the exposed transparent layer, a polymerase enzyme is anchored which polymerizes the (long) ssDNA molecules to be sequenced.
Along with the ssDNA molecules, special nucleotides are provided for the polymerization. Each of the four nucleotide types (ATCG) have a uniquely colored flourescent tag attached to their terminal phosphate group (instead of to their base).
With the polymerization occurring at the bottom of the nanopore "well", a light detector postioned on the opposite side of the transparent layer sees millisecond pulses of colored light at each of the nanopores, corresponding to the sequence of nucleotides being added to each DNA strand.
This approach achieves read rates of 10's of bases per second per ZMW, over thousands of ZMW in parallel, with single molecule read lengths of ~1000's of bases. PacBio sets expectations of eventual $100 cost and minutes of time per complete genome sequence.
11a09 - PacBio Slashes 28% of It's Workforce to Conserve Cash
10824 - Life Technologies Buys Ion Torrent for $375M
10816 - Pacific Biosciences files for IPO
10802 - Complete Genomics files for IPO
10319 - What Seqeuncers are Where?: Sequencers and Tanks (intro article)
10319 - What Sequencers are Where?: Statistics Tables
10319 - What Sequencers are Where?: World Map
10316 - New machines from Ion Torrent, PacBio headline AGBT
10301 - Life Technologies Unveils Single Molecule Seqencing Technology
09a05 - I.B.M. Joins Pursuit of $1,000 Personal Genome
09518 - 13,000 offer up DNA to put their genomes online
08a06 - Complete Genomics $1000 genome
08611 - 3 sequencing companies join 1000 Genomes Project
08416 - James Watson's genome sequenced at high speed : Nature News
08312 - Helicos Interview
SRF - Genomic Standards Consortium; 'Sequence Read Format'
CHROMATIN STRUCTURE
Wikipedia articles:
Chromatin Diagram
,
Chromatin
NUCLEOSOMES
Wikipedia articles:
Nucleosome diagram
,
Nucleosome
,
Histone
,
Histone Octamer
,
Histone code
,
Histone Proteins (H1-H5)
Media Articles:
01b28 - Histone acetylation: a switch between repressive and permissive chromatin
66218 - An RNA-histone complex in mammalian cells
EXPRESSION/REGULATION/TRANSCRIPTION
07116 - Scientists Map positions of gene regulating nucleosomes in Human Genome
RNAi
SYSTEM EVOLUTION
human vs primate - Chromosomes.1-4
MEASUREMENTS
Genome sizes - base pair (bp) count from 3,569 to 130Billion (Wikipedia)
08124 - Longest Piece of Synthetic DNA Yet (582,970 base pairs)
06a12 - Smallest non-viral genome so far; 160,000bp (182 genes)
TOOLS & TECHNIQUES
CATEGORY
PROTEOMICS
Protein: smallest (TRP-Cage)
Protein: largest (Titin)
Cytochrome c - A Model Protein for Molecular Evolution
Enzyme groups
Protease
Protein kinase
tRNA
Essential amino acid
09218-New centres plan for healthy ageing, Ageing research, CIRM, Career View, Naturejobs
091-Sniffing out a function for prion proteins : Nature Neuroscience
088-YouTube - Folding of the Trp-cage Miniprotein
CATEGORY
CATEGORY
EPIGENETICS
CATEGORY
CATEGORY
SYNTHETIC BIOLOGY
His Corporate Strategy: The Scientific Method
CATEGORY
NEXT FIELD
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