Posts Tagged by technology

NuGEN Launches BaseSpace Cloud App to Help Streamline NGS Analysis

 Sequence data generated with NuGEN’s target enrichment technology can be processed in BaseSpace using new app to mark duplicates and perform quality trimming
San Carlos, CA -OCT. 6– NuGEN Technologies is pleased to announce that scientists and clinicians using its Ovation Target Enrichment System to prepare biologic samples for genomic analysis can now process resulting sequence data in BaseSpace–a cloud computing platform, hosted by Illumina, Inc.
“NuGEN’s new Ovation Target Enrichment System Data Processing Application will allow the large community of Illumina sequence platform users to further streamline the rapid and convenient workflow of our Ovation Target Enrichment System products,” said Alan Dance, VP of Marketing at NuGEN.

The Ovation Target Enrichment product line employs Single Primer Enrichment Technology (SPET), a novel approach for enrichment of genomic DNA targets or cDNA for RNA target regions. SPET products allow researchers and clinicians to quickly and accurately enrich biologic samples for sensitive detection of a wide range of genomic markers including mutations, SNPs, indels, gene fusions, alternately spliced transcripts and copy number variants.

The new NuGEN-application, published on BaseSpace on September 30, provides an intuitive user interface for uploading sequence data. The application performs quality trimming and probe trimming on the parsed data – removing data derived from bases with low sequencing quality scores and aligning high quality data to the UCSC human reference genome.
Subsequently, PCR duplicate reads created during the library amplification process are identified using a random N6 sequence, unique to the Ovation Target Enrichment System workflow positioned adjacent to the barcode index.

Output files from the Ovation Target Enrichment System Data Processing Application for BaseSpace include processed BAM files with PCR duplicates removed or marked, processed FASTQ files with duplicates removed, and UCSC bigWig tracks with duplicates removed for visualization using the UCSC human genome browser.

For full details, visit
NuGEN Technologies Inc. is a rapidly-growing, privately-held company providing innovative products and systems for the preparation of biologic samples for targeted genomic analysis. Founded in 2000 and based in San Carlos, CA, NuGEN has long been at the cutting edge of genomic technology, with accurate, cost-effective reagent kits for even the most challenging sample types. NuGEN products are used in more than 1000 leading life science institutes and in diagnostic and pharmaceutical companies in 40 countries.
Media Contact:
Anita Harris, Harris Communications Group

The Harris Communications Group is an award-winning PR and marketing firm specializing in outreach for health care, life sciences and technology, worldwide.


Clarifying CIC Venture Cafe’s New Policy

Just spoke with Venture Cafe manager Chris Myles, who said he’ll  be providing more information about Venture Cafe’s new incarnation shortly–including the list of affiliated organizations whose members may attend without applying.   Those do include the Cambridge Innovation Center and various entrepreneurial groups…

Chris said the The Cafe’s new incarnation is not meant to be elite or exclusionary–but rather to encourage participation from the innovation community. More to follow.


–Anita Harris


Anita Harris is the founder and president of the Harris Communications Group of Cambridge, MA. HarrisCom is a strategic communications firm specializing in public relations, thought leadership, marketing communications and social media for emerging companies and research institutes in health, science, technology and energy, worldwide.   She also blogs at New Cambridge Observer.  

Update: CIC’s Venture Cafe Now Less of a Free-For-All

Note: This blog has been updated based on new information-also posted at  Clarifying Venture Cafe’s New Policy. 

Cambridge Innovation Center (CIC)  leaders founded Venture Cafe almost two years ago with the idea of opening  a Kendall Square restaurant where entrepreneurs and funders could walk in and meet one another over drinks or a meal.

In the economic downturn, the CIC turned that beta version into an alpha version–in which just about anyone was welcome for free drinks and networking on Thursday afternoons on the CIC’s fifth floor.

Yesterday, the CIC launched a new model in which members of the innovation community will be welcome as guests–but after three visits, anyone not affiliated with certain yet-to-be named entrepreneurial groups must formally apply to become  “contributors”… who actively aid others to pursue their innovative and entrepreneurial goals.” CIC clients and members of many other innovation-oriented groups will not need to apply.

In a letter to guests, Tim Rowe, a founder of both the CIC and Venture Cafe, and Chris Myles, Venture Cafe’s Executive Director, explain that “an analysis of the attendance of the Cafe has led us to conclude that we….have space for only 120 Contributors. As a consequence, becoming a Contributor is selective, similar to applying to a university, and is by application.  Applicants must also provide up to three references (these maybe Venture Cafe Volunteers, Contributors, or a well-known member of the innovation community…”

The new model is an “ongoing experiment,” they write,  aimed at creating “a more focused, committed core of regular attendees while preserving plenty of space and opportunity for new participants.”

As a frequent participant, I do think it’s a good idea to limit the numbers and to impose some structure on the Cafe. At times, the room gets overcrowded and chaotic;  it’s sometimes difficult to find the people one hopes to meet.   But I hope the new plan allows Venture Cafe to maintain the spontaneity, excitement, and sharing  and openness that participants have enjoyed in its earlier incarnations.


—Anita M. Harris
Anita Harris is President of the Harris Communications Group, a  public relations firm specializing in marketing communications, thought leadership and social media for companies in health, science, and technology, worldwide. HarrisCom is located in the Cambridge Innovation Center at 1 Broadway in Cambridge, MA. Anita also blogs at New Cambridge Observer





Despite fracking concerns, experts predict growth in shale gas extraction

Despite environmental, cost and market concerns, fracking–the hydraulic extraction of natural gas from shale–is here to stay.  That was the consensus of  experts who spoke  at the British Consulate in Boston on Dec 15 2011.

Sponsored by the British American Business Council and National Grid, the panel included  moderator Daniel Goldman, executive vice president and chief financial  officer of Great Point Energy;  David Hobbes, chief energy strategist for the information/strategy firm IHS CERA;  Dr. Elizabeth Kane, first secretary and head of the energy team at the British Embassy in Washington, DC, and Dr. Francis O’Sullivan, research engineer and executivedDirector of the Energy Sustainability Challenge Program, MIT Energy Initiative.

Hobbes described the complexity of shifting international energy markets–pointing out the need to include the costs of extraction and transportation of what otherwise appears to be a low-cost source of energy.  He challenged as “shoddy” a recent Cornell University report that extracting natural gas  from shale could do more to aggravate global warming than mining coal, and said that it is unfortunate that the study is being used as a basis for US shale extraction policy.  He predicted, jokingly,  that the UK will come up with “an even stupider policy,” because, as a friend to the US,  his homeland “tries to make the US look good,” by comparison.

According to Kane,  incentives to invest in shale gas extraction are limited in the UK because the Crown holds mineral rights,  because most shale fields are located in densely populated areas (such as under London), and because England does not have the road structure needed to support the fracking industry.  Fracking in England was temporarily halted after it was determined that the practice had caused two  small earthquakes–but resumed after experts found  it was unlikely to cause major quakes, she said.  Environmental concerns remain, however;  members of a group calling itself “frack off” have chained themselves to fracking equipment to keep it from being operated.

O’Sullivan explained that despite significant shale reserves,  few fracking operations are currently profitable because extraction costs are relatively high–but that this will change as technology improves.   Regarding environmental concerns, he said it’s unlikely that chemicals used in fracking will leak from pipes into drinking water. In part, that’s because  leaky pipes diminish wells’ performance , which provides the industry with incentives to make sure that fracking equipment and wells are tightly sealed. A greater concern is highly polluted “return” water. In Texas, he said,  this water is injected into deep sealed aquifer but in Pennsylvania and Western New York State, which have different geologic underpinnings, companies must use other methods to prevent pollution.

O’Sullivan also pointed out that there’s shale to be mined in China, Australia and Argentina–and that the abundance of shale and the possibilities it presents as a source of relatively inexpensive fuel (compared with oil) will impact the global energy market in coming years.

Regarding future markets for natural gas, Hobbes said it’s not likely to be widely used for hybrid electric cars, which are expensive to produce and therefore not popular with consumers. He predicted that the market for shale gas will increase “in little bits and pieces over the next 20-30 years.”  Over that period, energy consumption will go down, the US and Canada will add as much oil production as Iran possesses, and Chinese energy demands will optimize the market for natural gas producers in the US, he said.

O’Sullivan predicted growth markets for shale gas  in commercial, residential, power, industrial and feed stock uses in the US and elsewhere, and– in light of the recent nuclear reactor failures–in Japan.


–Anita M. Harris
Anita Harris is president of the Harris Communications Group, an award-winning public relations firm located in  Cambridge, MA.  HarrisCom specializes in integrated strategic communications, thought leadership and content strategy for companies and organizations in health, science, technology and energy, worldwide.   She also blogs at   New Cambridge Observer.

PhotOral launched to develop “blue light” consumer device to combat gum disease

[Disclosure:  please see below]

Two Forsyth Institute scientists and a Lexington, MA entrepreneur have launched PhotOral (TM)to develop and market the first consumer device using  blue light to combat gum sisease.

Scientists Nikos Soukos, director of Forsyth’s  Applied Molecular Photomedicine Laboratory and J. Max Goodson, senior member of the staff,  found when testing the effectiveness of blue light in tooth whitening equipment,  their patients’ gum health improved.  They determined through research published in 2005 (see below)  that such light can selectively kill pathogenic oral bacteria–without harming so-called “good bacteria” that exist in normal mouths–and began work on a device.

This year, Forsyth received a patent for the proposed blue-light treatment method;  Soukos, Goodson and entrepreneur Stamatis Astra founded PhotOral; and, in September, PhotOral received an exclusive license from Forsyth to commercialize the technology.

The device  will  look  “either like a mouth guard or a lollipop,”   Soukos said.

It will work by shining certain light wavelengths onto the teeth, which act as mirrors to deliver the light to dental pockets between the teeth.  Inserted into the mouth twice a day for 30-60 seconds, it should selectively target pathogenic bacteria and, as a cumulative effect, suppress them to prevent periodontal disease. It will not replace brushing or flossing–but, rather, will allow consumers an additional method for improving their oral health.

Most current consumer treatments–such as flossing, tooth brushing and antiseptics–seek to eliminate all sorts of the 700 bacteria found in the mouth,  Soukos explained.  But some of those bacteria are beneficial.  “Our device aims to selectively target ‘bad bacteria’ in order to restore a healthy balance in the mouth.”

By doing so,  the team hopes to help prevent or treat gingivitis, which occurs in 90% of adults, and periodontitis, which affects some 34% of adults in the US over 30.  Severe periodontitis, which may be treated with medication, by scaling and planning or surgically,  affects 13% of all adults. It can lead to loss of bone and teeth and is suggested as a risk factor for coronary based heart disease, atherosclerosis, pre-term births and chronic kidney disease.

Stamatis, the PhotOral CEO,  said he  is currently raising funds  to support prototype production, clinical trials and marketing operations. “The potential market for the device is  greater than $7B”


Scientific background: 

Soukos and Goodson’s research, published in the April, 2005 Journal of Antimicrobial Agents and Chemotherapy, suggested that light in the blue region of the visible spectrum might be useful in preventing, controlling or treating periodontitis-an oral infection that can lead to loss of bone and teeth.

Among the most destructive oral bacteria are the so-called  “black-pigmented” bacteria  (BPB), which are implicated as pathogens associated with periodontitis. Such bacteria accumulate black pigment consisting mainly of organic compounds called porphyrins . Some porphyrins are photosensitive and, when activated  by light, induce a photodynamic reaction that kills the microorganism within seconds.

Before starting their research, Soukos and Goodson knew that other  researchers had used lasers to deliver red or green light, which partially inactivated certain oral bacterial. The team also knew, from published reports, that porphyrins absorb blue light more readily than light that is red or green.

The Forsyth scientists employed a halogen lamp source commonly used for tooth whitening to shine broadband light composed mainly of  blue and a small percentage of green light on pure cultures of BPB and on dental plaque samples obtained from individuals with chronic periodontitis. They found that the light rapidly killed BPB in pure cultures and that it selectively eliminated BPB in plaque samples containing 50o0-6000 different bacteria. They also found that certain species were more readily inactivated by the light than others and that varying the intensity and exposure time had different impacts on different bacterial species. The researchers concluded that intraoral light exposure can selectively reduce pathogens in dental plaque.


–Anita M. Harris

Anita Harris is president of the Harris Communications Group, a Cambridge, MA public relations firm specializing in strategic communications,  thought leadership and content strategy for companies and organizations in health, science and technology, worldwide.  The Forsyth Institute and Goodson are former clients; Soukos serves on her advisory board, and she is an unpaid advisor to PhotOral.  Harris won a 2006 International Communicator Award for her work in publicizing  the Forsyth “Blue Light ” paper.  She also blogs at New Cambridge Observer.






Vishwa Robotics’ military surveillance ‘bird’ drones to diminish civilian deaths

Recently, at the Cambridge Innovation Center, I happened to meet  Bhargav  Gajjar,  who founded Vishwa Robotics two years ago, while still a grad student at MIT.    I  was blown away by the product for which he’s received NASA funding:  a battery-powered robot, the size and shape of a bird, which, if successful, will serve as a surveillance drone that can be perched, undetected, on a windowsill or statue to provide information about activities in its purview.

Today, Gajjar  explains,  most drones are the size of automobiles, which means they can easily be seen and shot down. He   and his team are currently developing designs for the birds–which will be made to look like species native to particular areas of the world.  Operators wearing special goggles will be able to see what the “birds” see and to guide the birds’ movement–having them walk, fly and perch–from miles away.  Vishwa’s robotic birds hold larger batteries  than recently publicized robotic hummingbirds and, thus, can be used for longer periods of time than the tinier drones.

The immediate goal is to  help the military prevent unintended civilian deaths in war zones. And,  Gajjar says, the devices should also be useful in industrial or other situations to assess environmental, human or other hazards.

I do wonder how much the devices will cost–and whether they could make it too easy for the wrong people to snoop.  Gajjar says the bird/drones will be owned by the military and regulated by the FAA, which will prohibit their use in civilian areas (except with specific permission in times of disaster) in the US.  He’s not speculating about how they will be used in foreign nations.

Vishwa Robotics offers consulting and design services in a range of fields, including mechanical design, simulation, advanced control systems and prototyping of complex electromechanical and robotic systems.

According to company materials: “In a world where radical technological advances are taken for granted, Vishwa’s goal is to revolutionize industrial and consumer robotics through applications of new concepts and cutting-edge technologies and to create a better future for mankind.

“Leveraging their experience from Massachusetts Institute of Technology’s famed Media Lab, MIT Leg Lab, MIT Artificial Intelligence (AI) Lab and other advanced research organizations like NASA and US Air Force Research Lab, Vishwa works with a diverse array of experts from various fields.
Vishwa can  reached at info “a-t” .  A Website is under construction at


—–Anita M. Harris
Anita Harris is the president of the Harris Communications Group of Cambridge, MA,  which specializes in strategic outreach for companies and organizations in health, science and technology, worldwide.  HarrisCom also publishes New Cambridge Observer,  offering commentary on art, science, technology and community.