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TODAY’S HEADLINES:

• Oxford NanoLabs takes in £10M for sequencing tech (PDF release)
• Alure Medical raises $4.5M for plastic-surgery implants (release)
• Bone-disease biotech Therosteon spins out of research institute, raises funds (PDF release)
• Genome-analysis toolmaker BioTrove files for $75M IPO (Edgar)
• RNAi developer Tekmira acquires Protiva, ends litigation (release)

Oxford NanoLabs takes in £10M for sequencing tech – U.K. based Oxford NanoLabs, yet another startup developing high-speed genome-sequencing technology, raised £10 million in a new funding round. The company said only that its backers included institutional and private investors.

Oxford is working on a so-called nanopore technique for DNA analysis, which typically involves chips laced with a lattice of tiny holes. The company says its process can identify the DNA “letters,” or bases, that compose the genetic code by passing DNA molecules through the pores. As each base slides past, it sticks temporarily to the side of the pore, interrupting electricity being conducted through the surface in a characteristic way that identifies whether the base is an A, C, G or T — the four letters of the DNA alphabet.

Of course, Oxford is entering a field crowded with established companies and other startups. In no particular order, we’ve recently covered fundraising and technology developments at BioNanomatrix, Intelligent Bio-Systems and Pacific Biosciences in recent months.

Alure Medical raises $4.5M for plastic-surgery implants – San Diego’s Alure Medical, a startup developing “soft-tissue” implants for cosmetic procedures, raised $4.5 million in a first funding round. Its backers include EDF Ventures and private investors.

The company is working on implants that lift sagging tissues in the breast, neck and elsewhere. Alure also named France Dixon Helfer, a former Medtronic executive and co-founder of Pegasus Biologics, as its new CEO.

TODAY’S HEADLINES:

• Compact ultrasound maker Zonare Medical raises $30M (VentureWire)
• TherOx raises $30M for hypersaturated-oxygen devices (peHUB)
• Accumetrics, antiplatelet-drug diagnostic maker, raises $29M (release)
• Population Genetics takes in £3.8M for massively parallel genome studies (GenomeWeb)
• “Brain fitness” trainer Dakim raises $11M (release)
• BioIQ, home-diagnostics maker, takes in $2.5M (release)
• Hospital med-tracker Sabal Medical raises funds (release)
• Seattle’s PharmaIN gets $400K NIH grant for nanoparticle staph drug (PDF release)
• SensiGen, molecular-diagnostics developer, receives Michigan state loan (release)
• Arcus Ventures aims for $50M fund, targets cancer (VentureWire)

Compact ultrasound maker Zonare Medical raises $30M – Zonare Medical Systems, a Mountain View, Calif., maker of ultrasound-imaging systems, raised $30 million in a recent seventh funding round, VentureWire reports. Existing investors provided the funding, a group that includes Frazier Healthcare Ventures, 3i Group, Mosaix Ventures, CB Health Ventures, Draper Fisher Jurvestson, Ascension Health Ventures, Kaiser Permanente Ventures, Earlybird, Saints Capital, Merrill Lynch Venture Capital and Texas Instruments.

The company said the funding should set it on the road to profitability and eventually to a hope-for IPO. Zonare makes compact ultrasound systems that can be used in sonography and for a variety of other medical diagnostic purposes.

TherOx raises $30M for hypersaturated-oxygen devices – TherOx, an Irvine, Calif., maker of oxygenation devices for treating heart attacks, raised $30 million in a tenth funding round, peHUB reports. Investors included Kleiner Perkins, Integral Capital Partners and New Science Ventures.

The startup makes devices that supersaturate blood with oxygen, then infuse that blood into areas of the heart at risk of damage from oxygen starvation due to a heart attack. TherOx has now raised over $120 million in venture funding.

Accumetrics, antiplatelet-drug diagnostic maker, raises $29M – San Diego’s Accumetrics, a maker of diagnostics that measure patient response to anti-platelet drugs, raised $28.8 million in a fourth round of funding. Investors included Arnerich Massena & Associates, BBT Fund, Essex Woodland Health Ventures, RiverVest, PTV Sciences, KB Partners and Kaiser Permanente Ventures.

The startup makes a system that measures how well individuals are reacting to treatment with anti-platelet drugs, which are used to prevent or help dislodge major blood clots. Since patient response can vary widely, often as a result of genetic factors (see our coverage of this sort of “personalized medicine” here), such monitoring can help doctors avoid dangerous overdoses or to switch unresponsive patients to higher doses or different drugs as necessary.

Population Genetics Technologies takes in £3.8M for massively parallel genome studies – Population Genetics Technologies, a U.K. startup devoted to technologies for studying thousands of genomes at once, raised £3.8 million ($5.9 million) in a first funding round, GenomeWeb reported. Investors included Auriga Partners, Noble Fund Managers, and Compass Genetics Investors.

The company raised £1.1 million in seed funding from the Wellcome Trust back in 2005 to aid in the development of the technology. PGT is working on a technique devised by Nobel laureate Sydney Brenner that purports to analyze genetic variation in DNA samples from thousands of individuals at once.

In this 2005 release, PGT co-founder Sam Eletr described the method as “will allow the mixing of thousands of samples in one test tube and the simultaneous interrogation [analysis] of all of them in one experiment, instead of in as many experiments as there are genomes in a population…. We expect our technology to allow handling much larger numbers of genomes than pooling does and to have the further advantage of protecting the identities of individuals involved in any population study by allocating them a code that may be kept confidential. We expect it also be applicable to any collection of DNA molecules and genomes, whether from plants, animals, micro-organisms or humans.”

PGT also named Mel Kronick, a former R&D manager at both Agilent Technologies and Applied Biosystems, as CEO.

TODAY’S HEADLINES:

• Metabolic-disease biotech NGM Biopharma raises $25M (peHUB)
• Heart, HIV drug maker Numerate acquires assets of Pharmix (release)
• Next-gen sequencer VisiGen promises $1,000 genome by late 2009 (Genome Technology)
• CalciMedica raises $5.5M for autoimmune drugs (VentureWire)
• Cancer-drug e-marketplace OneOncology raises funds (release)
• U.K. biotech Hunter-Fleming acquired by Newron for €8M (release)
• Intertek acquires Ireland’s Bioclin Labs, a contract research organization (release)

Metabolic-disease biotech NGM Biopharma raises $25M – South San Francisco-based NGM Biopharmaceuticals (Web site under construction), a biotech developing new drugs for heart and metabolic conditions, raised $25 million in a first funding round, peHUB reports. Investors included Column Group, Prospect Venture Partners and Rho Ventures.

NGM, currently helmed by Tularik founder David Goeddel on an acting basis, isn’t divulging much about its plans. According to VentureWire, the company is developing new treatments based on “post-genomic bioinformatics” (a virtually content-free buzzphrase if I’ve ever heard one) and “new approaches to human biology” (which isn’t much better). NGM plans to devote the funding to R&D spending over the next three years.

The company’s ties to the former Tularik — which was acquired by Amgen in 2004 — are worth noting. In addition to Goeddel, the company’s chief scientific officer, Jin-Long Chen, was formerly a VP of biology at Tularik, and then headed Amgen’s metabolic-disorders unit.

Heart, HIV drug maker Numerate acquires assets of Pharmix – I’ve updated this item and moved it into a standalone post here.

Next-gen sequencer VisiGen promises $1,000 genome by late 2009 – Does anyone else hear a bandwagon banging through town? Just three days after secretive Pacific Biosciences took the wraps off its high-speed sequencing effort, Houston-based VisiGen Biotechnologies laid down a new marker and said it plans to offer $1,000 sequencing of human genomes by the end of 2009 at the rate of roughly one genome a week.

The news, which comes courtesy of GenomeWeb, further turns up the pressure in the bragging-rights race to achieve the artificial “$1,000 genome” benchmark. More than a half-dozen companies have thrown their hats into the ring either explicitly or implicitly, each with its own complex approach to reading every one of the six billion DNA letters, or bases, in a human’s 23 pairs of chromosomes.

VisiGen was founded in 2000, and has received funding from Applied Biosystems and Houston’s SeqWright, as well as grants from the National Institutes of Health.

CalciMedica raises $5.5M for autoimmune drugs – San Diego’s CalciMedica, a biotech developing drugs for immune-related conditions, raised $5.5 million in a second funding round, VentureWire reports. Investors included Sanderling Ventures and SR One. We previously noted the startup’s first funding round here.

The company plans to attack autoimmune diseases such as rheumatoid arthritis and psoriasis by targeting a “calcium channel” — that is, a cellular mechanism that moves calcium in and out of cells — in immune-system components that govern the body’s adaptive immunity. That arm of the immune system sometimes goes haywire, producing autoimmune disease in which the body’s defenses attack normal tissue. CalciMedica acquired technology and drug candidates for targeting that calcium channel from TorreyPines Therapeutics in May.

More than a half-dozen startups and established companies are in hot pursuit of the “$1,000 genome,” a Holy Grail for those who believe fast, cheap genome sequencing will revolutionize medicine. The latest is Pacific Biosciences, a formerly secretive Menlo Park, Calif., company that just spilled its guts to the NYT over the weekend. We take a look at the company, its technology and the competitive landscape in this piece over at VentureBeat Life Sciences.

Competition to analyze human genomes faster and cheaper — a subject I’ve discussed at length here and here — keeps heating up. The latest shot came yesterday, when Menlo Park, Calif.-based Pacific Biosciences granted the NYT an exclusive look at technology it says should eventually make it possible to sequence a genome in just a few minutes for under $1,000.

Although the “$1,000 genome” is a purely arbitrary goal, it’s become a Holy Grail of sorts for the genomics field. (The startup Knome, which we covered here, currently offers full-genome sequencing for $350,000.) Cheap, fast sequencing of all six billion DNA “letters,” or bases, in humans could make it possible, for instance, for doctors to better tailor treatments to a patient’s own genetic quirks or to identify the specific weaknesses of tumor cells. More broadly, it would also vastly increase our understanding of the genome, which has turned out to be a much more mysterious realm than just about anyone expected only a decade ago, and illuminate the ways DNA varies between individuals, groups and even among cells and tissues within a single individual.

PacBio has long been secretive about its work, although it’s been clear that the company has some heavy hitters backing it, including Kleiner Perkins Caufield & Byers, Alloy Ventures and Mohr-Davidow Ventures. (Our earlier coverage of the company’s $50 million financing last year is here.) A research team including scientists from PacBio — then known as NanoFluidics — and Cornell did publish a 2003 paper in Science describing some of the company’s work, but it’s a fairly abstruse piece even by the standards of the scientific literature, unless ploughing through mathematical descriptions of zero-mode waveguides is your idea of fun.

Before getting into the PacBio technology, however, a word of caution. The high-speed sequencing race is pretty crowded, with more than a half-dozen companies pushing forward with new technological approachs and making grand claims for their speed, accuracy and ultimate utility. None of these claims are really possible to evaluate at the moment, and of course the companies involved have every incentive to play up their strengths. PacBio is no different in this respect, and while the NYT story focuses on this particular startup, reporter Andrew Pollack is careful to quote several skeptics who raise perfectly reasonable concerns about the company’s expansive claims.

According to a sidebar to the main NYT story, PacBio’s basic approach involves trapping individual DNA molecules in thousands of tiny holes, or “wells,” fabricated in a thin sheet of metal. These holes are only 70 nanometers wide, or about one-thousandth the width of a human hair — small enough to hold a single stretch of DNA, but large enough for various biochemical reactions to take place inside.

Once inside the wells, the double-helix structure of DNA “unzips” into two single strands, each of which then rebuilds a complementary strand from chemical bases floating in the wells with the help of an enzyme called DNA polymerase. Those bases are tagged with fluorescent molecules that make it possible to identify them under a microscope. PacBio’s system uses digital-camera technology to observe the process in real time, allowing it to analyze and “read” the order in which the bases are strung together.

PacBio claims several advantages over other high-speed sequencing techniques, all of which involve chopping up DNA into short pieces that can be read more easily and then reassembled into a full genome. PacBio says it can read 1,000 bases of DNA in one go — several times greater than other high-speed techniques, which are capable of analyzing stretches of only 30 to 450 bases at once.

By observing the same reaction across thousands of wells, the PacBio sequencing system should read genomes with great speed. The company is currently able to read about 10 bases a second in any given well, so if 1,000 wells all worked at once — itself something of a tall order — the system should run about twice as fast as existing sequencers.

The company certainly doesn’t lack self-confidence. “If we ever make this work, there would be no other technology applicable in the sequencing field,” Hugh Martin, the company’s CEO, told the NYT. Martin went on to discuss the Archon X Prize for Genomics, which offers $10 million to anyone who can sequence 100 genomes in ten days. “When we’re ready,” Martin said, “we’re just going to win the X Prize.” (PacBio hasn’t even officially entered the contest yet.)

PacBio, however, doesn’t plan to release a commercial version of its system until early 2010, and won’t have a model capable of sequencing a full genome until 2013. Some of its competitors could leapfrog it in the meantime — Intelligent BioSystems, for instance, claims it will have a machine that can sequence a full genome in 24 hours for $5,000 by the end of this year. (The NYT says it will cost $10,000, presumably reflecting the difference between the full six billion bases in our 23 pairs of chromosomes and the three billion bases that make up just one set of chromosomes.) Complete Genomics and BioNanomatrix, who haven’t disclosed details of their technological approach except to say they plan to read a stunning 100,000 bases at a time, assert they’ll be able to decode a full genome in eight hours for $100, although it’s not clear by when.

As I noted earlier, however, it’s best to take all such projections with a grain of salt. Hitting goals like these are best-case scenarios that could be tripped up by any number of unexpected wrinkles in the engineering and technology-development process. Still, it’s a heck of a lot of fun to watch.

PacBio has raised a total of $78 million to date, and will probably need another $80 million to bring its systems to market, the company’s CEO told the NYT.

TODAY’S HEADLINES:

• Joint-implant maker Ascension Orthopedics raises $21M (release)
• High-speed sequencer Genome Corp. draws another $250K (GenomeWeb News)
• Bausch & Lomb acquires implantable lens maker Eyeonics (release)
• Bederra buys up Houston’s Diagnos and its PET-scan diagnostics (release)

High-speed sequencer Genome Corp. draws another $250K — Genome Corp., a Providence, R.I., tool-maker focused on a new type of high-speed genome sequencing, raised another $250,000, GenomeWeb News reports. The Slater Technology Fund, a venture-capital entity backed by the Rhode Island state government, provided the funding.

Genome doesn’t appear to have said much publicly about its technology — its Web site is a stub and it doesn’t appear to have put out any of its own news releases. GenomeWeb, however, reports that the company is taking a different approach from many other new genome-sequencing concerns, which typically chop DNA into tiny pieces, sequence them quickly and then rely on sophisticated software to “stitch” the sequence back together. Genome, by contrast, is reportedly pursuing a “massively parallel” version of a standard technique known as Sanger dideoxy sequencing, which will involve much longer DNA stretches of 1,200 genetic “letters,” or base pairs.

The startup previously raised $250,000 from the Slater Fund back in September. Our coverage is here.

Bausch & Lomb acquires implantable lens maker Eyeonics — Eyeonics, an Aliso Viejo, Calif., medical-device company focused on implantable lenses, sold itself to Bausch & Lomb for an undisclosed sum. The release is here. Eyeonics’ operations will become part of Bausch & Lomb’s surgical business.

Eyeonics currently makes and sells the Crystalens implant, which replaces the eye’s natural lens in patients with severe cataracts. While many implantable intraocular lenses only permit the treated eye to focus at fixed distance, Eyeonics claims that the Crystalens can adjust and change shape in response to the movement of eye muscles, allowing it to fcous in a manner similar to that of a natural human lens. As a result, the implanted lens can also correct presbyopia, or age-releated far-sightedness.

We covered another implantable-lens maker, Belmont, Calif.-based PowerVision, here.

Joint-implant maker Ascension Orthopedics raises $21M — Austin, Tex.-based Ascension Orthopedics, a device company developing joint-replacement and other surgical implants, raised $21 million in a fourth funding round. Frazier Healthcare Ventures provided the funding.

Ascension’s first marketed product, which it released in 2001, was a total joint-replacement implant for the knuckle joint of the hand. The company has since launched several other joint replacements for the shoulder, elbow, wrist, fingers and toes.

The cost of sequencing human genomes is dropping steadily, from several hundred million dollars a decade ago to $100,000 or so today, thanks to a bevy of entrepreneurial companies that have attacked the problem of making the process faster and cheaper with gusto. We’ve looked at several of the newer upstarts in the field, most recently Complete Genomics and Bionanomatrix, Genome Corp. (seventh item), and Genomic Diagnostics (fourth item).

Now another startup is preparing to establish a new benchmark in the fast, cheap and out-of-control gene-sequencing race. Intelligent Bio-Systems, a Waltham, Mass., sequencer, says that by late next year, its new technology should make it possible to sequence a full genome in 24 hours at a cost of just $5,000, according to this VentureWire story (subscription required). Not only is that a jaw-dropping reduction compared to today’s costs, it potentially brings the Holy Grail of the $1,000 genome far closer than than even many optimistic forecasts.

Of course, talk is cheap. IBS, however, says it’s already placed one of its sequencing systems with an undisclosed institution as part of its beta testing, and plans to distribute three more systems next year, with a full launch by the end of 2008. The company’s CEO, Steven Gordon, says the system should be able to sequence five billion DNA “letters” — technically, DNA base pairs — in a day. A full human genome consisting of 23 pairs of chromosomes — such as Craig Venter’s new high-resolution genome — contains six billion base pairs, although many sequencing efforts to date have settled for only one set of chromosomes, or three billion base pairs.

The details of sequencing technology are generally of interest only to experts, so anyone interested in the guts of the IBS approach is welcome to check out the company’s description here. This GenomeWeb story from late last year offers some additional technical analysis.

Assuming that IBS isn’t being wildly over-optimistic, which wouldn’t exactly come as a stunning surprise in this field, the new technology raises the possibility that a sufficiently motivated group might capture the Archon X Prize for Genomics within the next year or so. The $10 million award, offered by the X Prize Foundation, will go to anyone who can sequence 100 genomes in ten days.

Since that challenge amounts to sequencing 60 billion base pairs in 240 hours, anyone who ponies up for a dozen IBS sequencing systems could just barely knock off the requisite 100 genomes in that time period — assuming nothing goes wrong. In actuality, though, this strategy probably wouldn’t qualify for the prize, since the rules require the use of a single “device” in the challenge.

Still, it’s fun to play with the numbers, since this approach — were it legal — could even be profitable. IBS estimates that each system will cost $250,000 to $275,000, or just $3.4 million for the dozen. It’s a fascinating indication of just how fast the whole genomics revolution is moving.

On the far more mundane business front, VentureWire reports that IBS raised an undisclosed amount of first-round venture funding in June from angels and angel groups. The company will be looking for another $10 million to $20 million for commercial launch unless it finds a distribution partner.

Things are starting to get crowded in the race to sequence entire human genomes quickly and relatively cheaply — usually meaning somewhere in the territory of $1,000 per genome, compared to the $100,000+ it costs with current technology. At least four startups have taken on the $1,000 genome challenge, two of which have already been acquired by larger companies. (See details at the end of the first item here.)

Last week, two relatively new venture-backed startups — Complete Genomics, of Menlo Park, Calif., and Philadelphia’s BioNanomatrix — considerably upped the ante in what I’ve started to think of as the “fast, cheap and out-of-control” genome race when they announced a joint venture that aims to sequence an entire human genome in eight hours for less than $100. (Technically, it appears that this figure applies only to a single set of the 23 paired chromosomes every individual carries, so a spiffy new high-resolution “diploid” genome like Craig Venter’s would presumably take more like 16 hours and cost somewhere around $200. That’s still dirt cheap, of course.)

This is, of course, some mighty big talk from companies that virtually no one had heard of until recently. (See our coverage of Complete Genomics here.) The companies still aren’t saying exactly how they hope to pull off this feat, although they’ve disclosed a bit more detail in their latest announcement. Apparently they plan to adapt a “novel DNA sequencing chemistry” (presumably from Complete Genomics) and combine it with a “linearized nanoscale DNA imaging” scheme (BioNanomatrix’s technology, it appears) in a way that allows them to read up to long DNA stretches of up to 100,000 nucleotide bases — those DNA “letters” we’re always carrying on about — at a time.

What, exactly, that means and whether it’s possible is something the experts will have to hash out. The best I can figure at the moment is that since BioNanomatrix specializes in “nanofluidics” systems — little gizmos that are essentially labs-on-a-chip at near-atomic dimensions — it might somehow be possible to snake long stretches of DNA into a tiny channel on a chip, where having the molecule laid out end-to-end might make it easier to tag and read out the bases in one fell swoop. But that’s just a guess at this point.

Another interesting element here is that these companies bluntly acknowledge the direct threat they pose to today’s genetic-testing industry. Existing genetic tests usually rely on antibodies or other probes that identify a single gene variant; newer varieties examine a handful of single-base variations that have been correlated with something like your risk of heart disease. The ability to read out an individual’s entire genome, however, would effectively demolish the need for such tests, as any the information the tests could turn up would be right there in your genome. (The same issue arises, albeit in somewhat less-dramatic form, with the SNP genome “outlines” that startups like 23andMe and Navigenics would like to provide — our coverage is here, here and here.) This is a potentially huge problem for companies like DNA Direct, one of the first consumer-oriented genetic-testing startups. Expect to see some fireworks on this front before it’s all settled.

The joint venture recently received an $8.8 million grant from the National Institute of Standards and Technology, which for some reason got virtually no attention at the time but for the noble exception of the Philadelphia Business Journal.

Here’s some additional detail from the press release:

“We tried to approach this project from the perspective of the clinician, looking at the requirements and opportunities associated with incorporating genetics into routine clinical diagnostics,” said Dr. Radoje (Rade) Drmanac, chief science officer and co-founder of Complete Genomics. “Accuracy, speed and low cost were paramount considerations. While there are a number of powerful and elegant sequencing strategies available or under development, we determined that we needed a completely novel approach to overcome their inherent limitations and achieve our $100 cost objective. We are optimistic that the combination of our two highly innovative approaches has a good chance of success. ”

The joint venture has proposed adapting a novel DNA sequencing chemistry combined with linearized nanoscale DNA imaging to create a system that can “read” very long DNA sequences of greater than 100,000 bases at high speed and with accuracy exceeding the current industry standard. By condensing a wide range of genetic tests into a single, cost-effective platform, the proposed technology has the potential to enable improvements in the diagnosis and personalized treatment of a wide variety of health conditions, as well as the ability to deliver individually tailored preventive medicine. The $100 genome would also have important applications in medical research and drug development.

Featured companies: CG Therapeutics, Complete Genomics, ConforMIS, Flexible Medical Systems, LeMaitre Vascular, MAP Pharmaceuticals, ParaPro, Vascular Architects, Zars Pharma

(UPDATED on 10/1/07: See below.)

[NOTE: Posting has been slow recently for personal reasons. I'll be doing my best to catch up today.]

Complete Genomics raises funding for high-speed sequencing — Complete Genomics, a Mountain View, Calif., developer of high-speed genome sequencing technology, said it raised an undisclosed sum in a second funding round, VentureWire reports (subscription required). The company said the funding was significantly larger than its $6 million first round last year, but declined to say by how much. Investors included OVP Venture Partners and Enterprise Partners Venture Capital.

Complete Genomics is one of several companies aiming to bring down the cost of genome sequencing in order to, among other things, eventually make it possible for individuals to base medical and lifestyle decisions on their individual genetic profiles. The company, founded in 2005, hasn’t disclosed many details about its technological approach, although its Web site vaguely describes it as “a novel combination of high-density DNA nanoarrays, sequencing-by-hybridization and combinatorial probe-ligation chemistry, and high-performance computing techniques.”

The high-speed sequencing market has been in a state of flux recently. Cambridge, Mass.-based Helicos Biosciences, went public in May. Solexa, a U.K.-based sequencer that later moved to the U.S., also went public in 2005 via a reverse merger and then was acquired earlier this year by Illumina. 454 Life Sciences was acquired by Roche earlier this year. VentureWire also lists Pacific Biosciences as a recent venture-backed sequencing company.

UPDATE: Complete Genomics announced an interesting new joint venture with BioNanomatrix of Philadelphia ten days after this funding; see our coverage here.

MAP Pharma prices IPO, looks to raise $92M — Mountain View, Calif.-based MAP Pharmaceuticals said it plans to price its initial-offering shares at $14 to $16 apiece, a range that could potentially raise $92 million. That’s up from the $86 million take MAP estimated in June (see our coverage at the time).

MAP makes reformulated versions of existing drugs for delivery via inhalers. Its lead candidate is a new inhaled version of budesonide, a corticosteroid used to treat pediatric asthma.

Implant maker ConforMIS ponders new funding, possible IPO — ConforMIS, a Lexington, Mass., medical-device company, is raising a “mezzanine” round of financing while it plans for an IPO within two years, VentureWire reports. The company, which makes personalized knee implants, raised a $10 million “debt facility” in August (see our coverage in the second item here).

LeMaitre acquires Vascular Architects for $2.8M — LeMaitre Vascular, a publicly traded maker of devices and implants for vascular surgery based in Burlington, Mass., acquired venture-backed Vascular Architects of San Jose, Calif., for $2.8 million in cash. Vascular Architects makes devices for the removal of plaque deposits that can clog arteries and cause life-threatening blood clots. The company had previously raised more than $42 million in equity and $5 million in debt, according to VentureWire.

Lice-drug maker ParaPro gets $2.1M grant — ParaPro, a Carmel, Ind., specialty pharmaceutical company developing a topical cream for treating head lice, received a $2.1 million grant from Indiana’s 21st Century Research and Technology Fund. The company said the funding will finance late-stage trials of its lice treatment, which it calls Spinosad.

CG Therapeutics names Christopher Henney chairman, seeks funding — Chris Henney, who co-founded three of Seattle’s most successful biotechs — Immunex, Icos and Dendreon — is now also the new chairman (PDF link) of CG Therapeutics, a new cancer-vaccine company in Seattle. The company said Henney will play a key role in lining up corporate partners and seeking new funding. CG Therapeutics is currently working on a first funding round intended to support mid-stage trials of its cancer vaccine in lung and colon cancer.

Zars Pharma delays IPO — Salt Lake City’s Zars Pharma, a developer of topical drugs, postponed its IPO until next week. Zars priced its IPO at $14 to $16 a share in August, and was slated to hit the market this week. See our previous coverage here and in the third item here.

At that, Zars is in far better shape than Cumberland Pharmaceuticals, which has been expected to go public on a day-to-day basis since mid-August. We last wrote about Cumberland here.

Flexible Medical Systems raises $1.2M for remote diagnostics — Rockville, Md.-based Flexible Medical Systems, a device and diagnostics maker focused on non-invasive devices that continuously monitor vital signs, raised $1.2 million in a seed financing. “Accredited investors” provided the funding.

FMS is developing diagnostic monitors that continuously draw “interstitial fluid” through the skin without a needle or other punctures. This fluid can theoretically be used to monitor protein levels in blood, although it’s also worth noting that other attempts to do this sort of thing — especially continuous blood-sugar monitoring for diabetics — have had a mixed history.

(UPDATED at 5:55pm PT: See below.)

Featured companies: Sierra Surgical Technologies, HerbalScience Nutraceuticals, Topigen Pharmaceuticals, EKR Therapeutics, Molecular Partners, Celsense, Glucose Sensing Technologies, Falcon Genomics, Waters, Calorimetry Sciences, Parion Sciences, Gilead Sciences, Isto Technologies, Fluidnet, NABsys

Sierra Surgical raises $7.1M — Palo Alto, Calif.-based Sierra Surgical Technologies, a developer of female sterilization technology, raised $7.1 million in a first funding round, PE Hub reports, citing a regulatory filing. Alta Partners and De Novo Ventures provided the funding.

Singapore’s HerbalScience raises $28M for natural extracts — HerbalScience Nutraceuticals, a Singapore-based natural-extracts company with offices in Naples, Fla., raised $28 million from the private-equity firms Aisling Capital and Weston Presidio, VentureWire reports (subscription required). The investment purchased a 25 percent stake in HerbalSciences, which makes purified extracts from various natural substances, valuing the company at $112 million.

Topigen Pharma pulls in $25M against lung disease — Montreal’s Topigen Pharmaceuticals, a biotech developing inhalable drugs to treat asthma and other lung diseases, raised $25 million (C$26 million) in a third funding round. Investors included NovaQuest, MMV Financial, BDC Venture Capital, Desjardins Venture Capital, Caisse de Dépot et Placement du Québec (Caisse), T2C2/BIO 2000 and Lothian Partners 27 (sarl) SICAR.

The funding will “accelerate” mid-stage human trials for Topigen’s leading drug candidates, a small-molecule treatment for chronic obstructive pulmonary disease and an RNA inhibitor for asthma.

EKR receives over $13M, licenses opiod drug — EKR Therapeutics, a Cedar Knolls, N.J., specialty pharmaceutical company, raised more than $13 million in a private placement. Investors included Quaker BioVentures, NewSpring Capital, and ESP Equity Partners. EKR also acquired rights to DepoDur, an extended-release opioid, from Pacira Pharmaceuticals.

Switzerland’s Molecular Partners gets $15.6M for novel binding proteins — Zurich-based Molecular Partners, a biotech developing drugs based on a new class of binding proteins, raised $15.6 million (CHF18.5 million) in a first funding round. Investors included Index Ventures, BB Biotech Ventures, Johnson & Johnson Development Corp. and Endeavour.

Molecular Partners is focused on developing therapeutics proteins it calls “DARPins,” which the company says offer the same ability to stick selectively to other molecules as monoclonal antibodies, but with greater stability and ease of manufacturing. DARPins are based on the notion of “repeat proteins,” which as the name suggests are modular proteins that contain repeated elements — something like posts spaced at regular intervals along a barbed-wire fence. (See the image at left.) The protein itself ends up looking something like a string that’s been knotted at regular intervals, only much more complicated.

Repeat proteins are found in almost all species, and in nature serve to bind other proteins in order to facilitate protein-protein reactions. By shuffling the modular elements in these proteins, they can be engineered to stick to specific molecules such as cell-surface proteins, potentially making them useful as drugs. The company has a more detailed description here.

Although Molecular Partners likes to play up the advantages of DARPins (the acronym stands for “designed ankyrin repeat proteins”) over antibodies — here, for instance — there are a few disadvantages the company doesn’t mention. As large molecules, DARPins most likely won’t get inside cells, limiting their potential as drugs to interactions with free-floating and cell-surface proteins. (Monoclonal antibodies have the same limitation.) Potentially more important, however, is the fact that the effectiveness of many antibody-based drugs results from their ability to stimulate a particular immune response, not just to stick to the appropriate target. DARPins, which aren’t immune-system molecules the way antibodies are, seem unlikely to do the same.

Pittsburgh-area biotechs, device makers get $350K — The Pittsburgh Life Sciences Greenhouse, a public-private life-sciences investment partnership, invested $350,000 in three Pittsburgh-area life-science startups. Falcon Genomics, a developer of chip-based cancer-detection diagnostics, received $150,000. Another $100,000 went to Celsense, which uses an MRI tracing agent to image transplanted cells. The final $100,000 was invested in Glucose Sensing Technologies, which is developing a catheter-based glucose sensor for continuous blood-sugar monitoring in intensive-care units.

Waters acquires Calorimetry Sciences — Milford, Mass.-based Waters, a laboratory-instrument maker, acquired Calorimetry Sciences of Linden, Utah. Terms of the deal weren’t announced. Calorimetry Sciences, which makes high-performance devices intended to measure the heat produced or absorbed by chemical reactions, will be merged into Waters’ TA Instruments division.

Fedora Commons wins $4.9M grant for open collaboration software — Fedora Commons, a non-profit organization devoted to open-source technologies for creating and sharing digital content, received a $4.9 million grant from the Gordon and Betty Moore Foundation. From the release:

With this funding, Fedora Commons will foster an open community to support the development and deployment of open source software, which facilitates open collaboration and open access to scholarly, scientific, cultural, and educational materials in digital form. The software platform developed by Fedora Commons with Gordon and Betty Moore Foundation funding will support a networked model of intellectual activity, whereby scientists, scholars, teachers, and students will use the Internet to collaboratively create new ideas, and build on, annotate, and refine the ideas of their colleagues worldwide. With its roots in the Fedora open-source repository system, developed since 2001 with support from the Andrew W. Mellon Foundation, the new software will continue to focus on the integrity and longevity of the intellectual products that underlie this new form of knowledge work. The result will be an open source software platform that both enables collaborative models of information creation and sharing, and provides sustainable repositories to secure the digital materials that constitute our intellectual, scientific, and cultural history.

Parion licenses lung-disease drug to Gilead for up to $146M — Parion Sciences, a Durham, N.C., biotech focused on diseases of the mucous membranes, struck a licensing and co-development deal with Gilead Sciences for its drug P-680 worth up to $146 million. The drug, an epithelial sodium-channel inhibitor, could potentially be useful in a variety of lung diseases, including cystic fibrosis. The companies will also work to identify other similar drug candidates.

Isto Tech raises $8.8M, prepares to launch synthetic bone grafts — St. Louis’ Isto Technologies, a developer of cell-based cartilage and bone regeneration technology, raised $8.8 million in a fifth funding round as it prepares for its first product launch, VentureWire reports. Investors included Ascension Health Ventures, Alafi Capital, Life Sciences Partners, Mid-America Transplant Services and private individuals. Isto’s leading product, InQu, is a synthetic biomaterial intended to help tissues heal and bones to regenerate; Isto expects FDA approval later this year.

Fluidnet rises from ashes, raises $6.4M for IV pumps — Portsmouth, N.H.-based Fluidnet, a “reincarnation” of its bankrupt predecessor FluidSense, raised $6.4 million in a first funding round to launch a new intravenous-infusion pump next year, VentureWire reports. Cardinal Partners and Rockport Venture Partners provided the funding.

NABsys raises $750K for high-speed genome sequencing — NABsys, a Providence, R.I., startup focused on high-speed gene-sequencing technologies, raised $750,000 in seed funding, VentureWire reports. Slater Technology Fund and individual investors provided the funding, which closely follows a $1.3 million grant from the National Institutes of Health.

UPDATE (10:55am PT): Added items on Molecular Partners and the Pittsburgh Life-Sciences Greenhouse investments.

UPDATE REDUX (5:55 pm PT): Added items on Waters/Calorimetry Sciences, Fedora Commons, Isto Technologies, Fluidnet, NABsys.

Helicos BioSciences, a Cambridge, Mass., maker of high-speed genome-sequencing equipment, raised $48.6 million in an IPO, well under the $81 million it had hoped to raise. My earlier item on the Helicos IPO is here.

Helicos is the latest biotechnology company to find itself at the mercy of unforgiving IPO investors. The company cut its estimated per-share offering range to $10 to $11 from its earlier estimate of $13 to $15, then found itself forced to price the shares at $9. It did, however, manage to sell all 5.4 million shares it had intended to offer. Adding insult to injury, the stock has slumped ever since the offering, falling to a recent low of $8.40 earlier today.

Helicos plans to offer its first product, a rapid single-molecule sequencer called HeliScope, later this year. (Hat tip: VentureWire.) The company’s IPO release is here.