January

Agriculture in Iraq, in the post-Saddam era - Which will be the effect of the Iraq elections, January 31, on Order 81?

The Coalition Provisional Authority at http://www.iraqcoalition.org/regulations/ - Order 81 "Patent, Industrial Design, Undiscosed Information, Integrated Circuits and Plant Variety Law (26 April 2004)

USAID - Assistance for Iraq Agriculture at http://www.usaid.gov/iraq/accomplishments/agri.html

Order 81 - by JeremySmith The ecologist (21/01/05) at http://www.theecologist.co.uk/archive_article.html?article=487&category=86

" Under the guise of helping get Iraq back on its feet, the US is setting out to totally re-engineer the country's traditional farming systems into a US-style corporate agribusiness. They've even created a new law – Order 81 – to make sure it happens. "

Agricultural dictatorship in Iraq - BC The Organic Way by Marya Skrypiczajko on Common Gound at http://www.commonground.ca/iss/0412161/cg161_marya.shtml (December 2004)

February

"In A Combat Zone"   (from Santa Cruz Sentinel, by  Doorkicker )

Just pasing through, but thought you guys might be able to chew on this a while. This is from a sniper friend of mine in Iraq, from a website support group. You will probably see it in the near future in other places, but here goes. Sorry, until the US Military gives permission for Doorkicker's identity to be disclosed, he will remain simply as Doorkicker.

I wrote, and continue to write this as an account of some of the things I have been through here in Iraq. I wasn't sure if I should post it, but decided what the hell...I can't think of a better group to share it with. It's long, but read it if you give a damn.

Well, I am still here in Iraq, and with regards to this war, I can say I have seen and done some amazing things.

• I've seen both cowards and heroes both young and oldBeen both confident and terrified, both at the same time
• I've grown to love and hate people with a fierce passion
• I've given food to the starving, and water to the thirsty
• I've seen the pain and uncertainty in a man, woman, and child's face right before they died
• I've seen the terror in a man's face when my weapon was pointed at his head
• I've looked a man in the eyes right before I put a sandbag over his head
• I've tasted the burn of OC/pepper spray as I sprayed a man in the face
• I've learned Arabic from a 12 year old girl who was my friend
• I've waved hello back at so many passing cars, I felt like I was famous
• I've been on TV 4 times, then watched the media tell lies about us
• I've been in 3 papers, and was amazed at the inaccuracy of my story
• I've seen dozens of marriages fall apart on both ends
• I've seen Iraqis cry, they were so happy that we were here
• I've had Iraqis swear me up and down because I had to search them
• I've heard the launch of mortar rounds as they left the tube
• I've seen those same mortar rounds blow up around me and my friends
• I had a friend show me pictures of his kids, and get killed the very next day
• I've heard the pop-pop-pop of gunfire, and then the ping-ping-ping as it hit around me
• I've seen people afraid to pull the trigger, and not kill...and I've seen people kill when they shouldn't have pulled the trigger
• I've seen men in the cross hairs of the scope mounted on my rifle and I've pulled the trigger so they will never ever be seen again
• I've laid countless hours on my cot trying to sleep but couldn't, because the helicopters were to loud, explosions were to close, their was to much gunfire
• I've taken prisoners, guarded prisoners, and released prisoners
• I've lost weight because my stomach couldn't handle the food here
• I've knocked on people's doors, kicked down people's doors, and almost shot off someone's door
• I've sat on a rooftop for 53 days straight looking for bad guys, and learned what patience really is
• I've lost all sense of privacy, but grew closer than a brother with my squad and platoon
• I've cleaned my weapon more than I have cleaned my clothes, because it was more important
• I've learned to appreciate all the things I once took for granted
• I've never worked so hard and got paid so little in my life, but even still worked harder
• I've watched videos of Nick Berg getting his head sawed off his body while he screamed, and never wanted to kill so bad in my life
• I remember when a young kid that called us "sadiq-i" (friend) brought us food each day at a checkpoint, and remember when a suicide bomber killed him and 18 other people days later
• I remember a crazy lady telling me lies to waste my time for no reason
• I remember a pretty girl secretly waving hello to me so nobody would see, fearing ridicule
• I remember the screams of people when a restaurant exploded with innocent people inside
• I'll never forget the smell of burning flesh for as long as I live...ever
• I've seen Iraqi people fight alongside us one minute, then fight against us the next
• I've captured dozens of weapons, some of which were gold plated
• I've been in a car accident that would've killed me if I wasn't riding in an armored hummer
• I've smiled and scowled, laughed and yelled at different crowds of people
• I've seen a 13 year old prostitute bring money home to her father to live
• I've smelled the crisp air of a new morning, and the soot and stench of cordite the next morning
• I've been so hot, that I stopped sweating and my body started to shut down
• I've been so tired and worn out, but still couldn't sleep for days at a time
• I've seen people accidentally shoot their weapons and almost kill people, and I've seen people intentionally shoot their weapons and kill people
• I've never counted or carried so much ammunition in my life, and I've been around the world more than once or twice with the military
• I've sat back and enjoyed an ice cold Coke, and other times I've called on the radio begging for a resupply of water and food because we were starving literally
• I've seen guys "baby" their weapons, and I've seen guys treat them like hell, fully knowing it was the only thing that might save their lives
• I've said "I hate here" a thousand times, and heard it said a million more times
• I've seen a platoon leader curl up in the fetal position out of terror during a firefight, and a private in that same platoon fight like a savage for his life
• I've seen a medic choke-up and not be able to do his job, and an infantryman next to him bandage up a wounded child
• I've had kids throw rocks at me because I didn't have any chocolate candy to give them
• I almost shot a 14 year old kid that pulled a gun on another kid, the toys look very real here
• I've seen kids play in a virtual minefield of explosives and ordinance like they were at Disneyland
• I've heard shots fired and hit the ground, ducked, jumped behind cover, and flat out ignored them
• I've seen "new guys" in units come here so scared they point their guns at everything they see
• I've been on missions so long, that I've come back to my FOB (base camp) with a full beard
• I've sat up late at night waiting for a friend to come back from a patrol that got hit, like a parent waits for their child who's been out all night
• I've made best of friends with a 17 year old kid, and a 47 year old man, and talked to both like we were old high school buddies
• I've cleaned my friend's blood off of his equipment, and turned it in because he was killed in an explosion hours before
• I've seen enough different people's body parts, that I could put them all together and make a completely new body with them
• I've laughed and joked with Australian soldiers, had conversations with British soldiers, and drank chi (tea) with Arab soldiers
• I've seen how well our bulletproof vest work, and they do stop bullets
• I've read the bible and figured I am in, or near the 'Garden of Eden'; but it hardly looks like paradise to me
  I've seen fisherman fishing, kids swimming, boats and dead bodies floating in the Tigris River
• I've asked myself dozens of times "Why am I here", but I know the answer, and I know if asked...I'd come back again no question
• I've missed my family and still do, and I regret not spending as much time with them as I should've before I left
  I've figured out who my real friends are back home, because they have taken the time to write me a letter or an e-mail
• I felt sold out by my chain of command because I made a decision to shoot, and sat through an 'inquisition' for making a judgment call that I would again
• I've gone on my 2 weeks of R&R and enjoyed the downtime, however was anxious to get back to this strange place
• I've been to far too many memorial services of our fallen brothers, and choked up every time, even if silently so nobody could tell
• I've seen an enemy sniper cause so much pandemonium, that without a shot being fired the sniper was winning a psychological victory over us
• I've traded 'war stories' with my best friend who worked in the private sector up north through countless e-mails
  I've been disgusted by the double standard that I have seen day in and day out
• I've lost a friend to an enemy sniper's bullet and felt helpless
• I've been given a urinalyses test because people were doing drugs over here
• I've seen the Iraqi people respect the military, and I've seen them totally disregard our presence and "walk all over us"
• I've searched a car we stopped in sector and found an Oklahoma license plate in the trunk with '04 tag stickers on it
• I've felt my stomach knot and my heart skip a beat when a vehicle speeding by, cut his wheel and came directly at me...I was going to be blown-up for sure I thought
• I've been terribly sick, but continued to work and patrol through it...mission first
• I've gotten packages and letters from people I don't know, and a smile was brought to my face each time
  I've had my comfort zone tested and violated by these people time and time again
• I've had Iraqis throw fireworks at me on New Years, thinking it was funny that I couldn't tell it wasn't a gunshot
• I've come to the conclusion that some soldiers here will return home by the grace of God, and other soldiers will come home simply because the man to the left or right of him did their job
• I've seen lousy soldiers awarded medals for no reason at all, and other soldiers who rightfully deserved recognition for gallantry under fire passed over with not even a pat on the back
• I've seen the clear difference between competence and arrogance in my leadership

This soldier sems like a true warrior to me . Just the type of man I would want wacthing my back in a combat situ

The human being in front of the Nature

How to evaluate an antivirus software

Information Skills for Problem Solving

  http://www.big6.com/showarticle.php?id=415

http://www.noodletools.com/debbie/literacies/information/1over/infolit1.html

Learning and Teaching Technology in Context using the "Big Six Skills" of Information Literacy by Michael B. Eisenberg and Doug Johnson.

The Big Six Skills:

1.Task Definition

1.1 Define the task (the information problem)

1.2 Identify information needed in order to complete the task (to solve the information problem)

2.Information Seeking Strategies

2.1 Brainstorm all possible sources

2.2 Select the best sources

3.Location and Access

3.1 Locate sources

3.2 Find information within the source

4.Use of Information

4.1 Engage in the source

4.2 Extract relevant information

5.Synthesis

5.1 Organize information from multiple sources

5.2 Present the information

6.Evaluation

6.1 Judge the process (efficiency)

6.2 Judge the product (effectiveness).

Comparison with our A.S.T.I. Strategy used during the Technology Transfer Process

The A.S.T.I.  strategy includes a "mission back" approach to improve integration, innovation and performance of the targeted activities / processes and to measure  success or failure.

March

Security and intrusion 2005: The role of biology

References:

Security Supersite - "A dictionary for vulnerabilities" by Larry Seitzer at http://security.ziffdavis.com/article2/0,3973,1134336,00.asp

Common Vulnerabilities and Exposures  (CVE) at http://www.cve.mitre.org/

MITRE at http://www.mitre.org/

April

The role of synthetic peptides in the treatment of neuroimmune disorders

It is well known the effect of prolactin release on the immune system.

Our goal is focused on the characterization of antagonists and super-agonists involved in the control of prolactin secretion, using specific primary amino acid sequences as a model for the design of new compounds.

Considering the network among the immune system, the neuroendocrine system, and the olfactory system, these molecules could have a therapeutic applications on the treatment of neuroimmunology disorders (not excluded the transplant area).

Low-molecular-weight negative regulatory factors (A "cold" research project)

An immunosuppressive factor (LiF) (mol.wt. 800–1000) was purified to near homogeneity from dialysable leucocyte extracts (DLE). LiF's activity is linked to a very hydrophilic molecule with acid character. It is stable to acid / heat treatment and it contains peptidic material (although it is pronase resistant). The problem linked to the chemical structure has not been solved.

Education in protein biochemistry

MONTEGEN, as scientific education provider, is involved in a project to support and foster the education of researchers in the techniques of protein biochemistry, protein structure analysis, and proteomics. The goal is to develop the specific course electronically, on the Internet.

Italian Electronic Identification Card by Pier Carlo Montecucchi (Biometric Consortium - 22 April 2005)

The new Italian Electronic Identification Cards possess the fingerprint recognition. In addition, considering that the officer responsible for the release of the document takes the picture of the applicant, possibly a face recognition system is under development. The card can be used as a smart card because of the presence of an internal chip (access to documents,...). At present the card cannot be used for electronic signatures (possibly in the future). http://www.cartaidentita.it/cie/reader/index.html http://www.cnipa.gov.it/site/it-IT/Attivit%C3%A0/Progetti/Carta_Identit%C3%A0_Elettronica/

Some recent references on biometrics by Henry J. Boitel (Biometric Consortium - 25 April 2005)

01. Biometrics: A Grand Challenge by Anil K. Jain, Sharath Pankanti, Salil Prabhakar, Lin Hong, Arun Ross, James L. Wayman (2004) 10 pages http://biometrics.cse.msu.edu/biometricsgrandchallenge.pdf

02. Attacks on Biometric Systems: A Case Study in Fingerprints by Umut Uludag*, Anil K. Jain (2004) http://biometrics.cse.msu.edu/EI5306-62-manuscript.pdf

03. Score Normalization in Multimodal Biometric Systems by Anil Jain a Karthik Nandakumar a Arun Ross (2004) 31 pp http://biometrics.cse.msu.edu/JainNandakumarRoss_ScoreNormalization_PR05.pdf

04. An Introduction to Biometric Recognition byAnil K. Jain, Arun Ross and Salil Prabhakar (2004) 29 pp http://biometrics.cse.msu.edu/JainRossPrabhakarCSVT_v15.pdf

05. Is Computer Science Science? By Peter J. Denning (2005) 27pp http://cne.gmu.edu/pjd/PUBS/CACMcols/cacmApr05.pdf

06. BIOMETRIC AUTHENTICATION FOR WEB-BASED COURSE EXAMINATIONS by Brent Auernheimer and Max J. Tsai (2005) 7pages http://csdl.computer.org/comp/proceedings/hicss/2005/2268/09/22680294b.pdf

07. Multi-biometrics Using Facial Appearance, Shape and Temperature by Kyong I. Chang KevinW. Bowyer Patrick J. Flynn Xin Chen (2004) 6pp ~http://www.cse.nd.edu/~kwb/ChangFG04.pdf <http://www.cse.nd.edu/%7Ekwb/ChangFG04.pdf>

08. Preserving Privacy by De-Identifying Face Images by Elaine M. Newton, Latanya Sweeney, and Bradley Malin http://csdl.computer.org/comp/trans/tk/2005/02/k0232abs.htm ABSTRACT - In the context of sharing video surveillance data, a significant threat to privacy is face recognition software, which can automatically identify known people, such as from a database of drivers' license photos, and thereby track people regardless of suspicion. This paper introduces an algorithm to protect the privacy of individuals in video surveillance data by de-identifying faces such that many facial characteristics remain but the face cannot be reliably recognized. A trivial solution to de-identifying faces involves blacking out each face. This thwarts any possible face recognition, but because all facial details are obscured, the result is of limited use. Many ad hoc attempts, such as covering eyes, fail to thwart face recognition because of the robustness of face recognition methods. This paper presents a new privacy-enabling algorithm, named k-Same, that guarantees face recognition software cannot reliably recognize de-identified faces, even though many facial details are preserved. The algorithm determines similarity between faces based on a distance metric and creates new faces by averaging image components, which may be the original image pixels (k--Same-Pixel) or eigenvectors (k-Same-Eigen). Results are presented on a standard collection of real face images with varying k.

09. Recent advances in ear biometrics by Pun, K.H. Moon, Y.S http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?isNumber=28919&prod=CNF&arnumber=1301525&arSt=+164&ared=+1 70&arNumber=1301525 < http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?isNumber=28919&prod=CNF&arnumber=1301525&arSt=+164&ared=+ 170&arNumber=1301525 > Abstract: In this paper, a relatively new form of biometrics - ear biometrics - is introduced and compared with popular forms of biometrics such as face and fingerprint. A review of the leading works including those, which appear in the research world very lately, is given. In the end, a proposal for possible future research directions is discussed.

10. Fuzzy Identity-Based Encryption by Amit Sahai and Brent Waters (2004) 15 pp http://eprint.iacr.org/2004/086.pdf

11. A Biometric Identity Based Signature Scheme by Andrew Burnett, Adam Duffy and Tom Dowling (2004) 15 pp http://eprint.iacr.org/2004/176.pdf

12. U.S. Visa Policy: Securing Borders and Opening Doors by Maura Harty is U.S. Assistant Secretary of State for Consular Affairs. (2005) 12pp http://www.twq.com/05spring/docs/05spring_harty.pdf

13. Learning Motion Patterns of People for Compliant Robot Motion by Maren Bennewitz, Wolfram Burgard, Grzegorz Cielniak and Sebastian Thrun (2004) 30 pp ~http://www.informatik.uni-freiburg.de/~burgard/postscripts/bennewitz_ijrr05.pdf

14. WiCTP: A Token-based\ Access Control Mechanism for Wireless Networks by Raal Goff (2004) 50pp http://undergraduate.csse.uwa.edu.au/year4/Current/Students/Files/2004/RaalGoff/CorrectedDissertation.pdf

15. Recent advances in visual and infrared face recognition--a review by Seong G. Kong,* Jingu Heo, Besma R. Abidi, Joonki Paik, and Mongi A. Abidi (2004) 33pp ~ http://www.ece.utk.edu/~kong/Paper_PDF/2005-CVIU.pdf

16. AnSVMclassifier incorporating simultaneous noise reduction and feature selection: illustrative case examples by R. Kumar,V.K. Jayaraman, B.D. Kulkarni?(2005) http://sci2s.ugr.es/keel/monografia/feature_selection/Kumar_An_SVM_2005.pdf

17. A statistical model for signature verification by Ian W. McKeague = May 14, 2004 25pp Abstract ~http://stat.fsu.edu/~mckeague/ps/sig-rev1.pdf <http://stat.fsu.edu/%7Emckeague/ps/sig-rev1.pdf>

18. A Generative Framework for Real Time Object Detection and Classification by Ian Fasel a,b Bret Fortenberry a Javier Movellan a (2005) 9 pp http://mplab.ucsd.edu/grants/project1/publications/pdfs/FaselFortenberryMovellan-CVIU2005.pdf

19. Identity Related White Papers - Digitial ID World http://www.digitalidworld.com/modules.php?op=modload&name=News&file=article&sid=131 <http://www.digitalidworld.com/modules.php?op=modload&name=News&file=article&sid=131 > The National Electronic Commerce Coordinating Council - Identity Management - A White Paper (2002) 68pp http://www.ec3.org/Downloads/2002/id_management.pdf

20. Efficient Search and Retrieval in Biometric Databases by Amit Mhatre, Srinivasa Palla, Sharat Chikkerur and Venu Govindaraju - Center for Unified Biometrics and Sensors, University at Buffalo, NY (2005) 4pp ~http://www.eng.buffalo.edu/~ssc5/research/papers/spie_binning.pdf

21 On U.S. Homeland Security and Database Technology by Won Kim, Cyber Database Solutions, USA (2005) 17pp http://www.igi-online.com/downloads/pdf/ITJ2670_ZccdK6NHZF.pdf

22. Learning Motion Patterns of People for Compliant Robot Motion by Maren Bennewitz, Wolfram Burgard, Grzegorz Cielniak and Sebastian Thrun

(2004) 30pp ~ http://www.informatik.uni-freiburg.de/~burgard/postscripts/bennewitz_ijrr05.pdf

Fingerprinting cell lines

We have open a discussion on the paper "Cell line fingerprinting using retroelement insertion polymorphism" by Svetlana V. Ustyugova, Anna L. Amosova, Yuri B. Lebedev, and Eugene D. Sverdlov, BioTechniques 38 (4),  561 - 565 (2005).

Cell lines are an indispensable rosource for numerous studies in various fields of modern biology and medicine. It is highly desirable to have reliable cell line identification techniques to make sure that the cell line to be used in experiments are exactly what is expected. To this end, the Authors have developed a set of infiormative markers based on insertion polymorphism of human retroelements. Using locus-specific PCR assays, the Authors have genotyped 10 human cell lines of various origins. For each of these cell lines, characteristics fingerprints were obtained. An estimated probability that two different cell lines posses the same marker genotype is about 10 ^-18. Therefore, the proposed set of markers provides a reliable tool for cell line identification. The analysis could be extended to includeadditional human lines, as well as hybrids and cell lines from other species.

May

The RNAi technology.

Discussion on the article: " The Prospect of Silencing Disease Using RNA Interference" by Premlata Shankar, MD; N. Manjunath, MD; Judy Lieberman, MD, PhD , JAMA. 293:1367-1373. (2005)

In vivo demonstrations of RNAi therapeutic efficacy in rodents.

The discovery of RNA interference (RNAi), an endogenous cellular gene-silencing mechanism, has already provided a powerful tool for basic science researchers to study gene function. The subsequent finding that RNAi also operates in mammalian cells has generated excitement regarding potential therapeutic applications. In this article we discuss the basic mechanism of RNAi and the therapeutic opportunities and obstacles for harnessing RNAi for therapy of human disease.

Nano-bio convergence

From biosensors and disease detectors to novel drug delivery systems and tissue engineering techniques, biological applications of nanotechnology already has begun to transform medicine.

The MIT 's Synthetic Biology Working Group. Synthetic biology can create new biological devices.

Reverse-engineering diatoms to build precise nanostructures (UC, San Diego: UC, Berkeley; other laboratories)

Bacteria to build nanostructures (circuits). -  Altered proteins in bacteriophages so that the viruses assembled themselves into the building blocks of liquid crystal displays (by Angela Belcher, MIT- Semzyme). Recently, she has produced a virus (a nanowire virus) that coats itself with semiconducting material and forms a bridge between two electrodes. The nanowire virus is just a precursor to a microbe she's developing that self-assembles into a transistor (proposed application: electronics, sensors, displays, magnetic storage).

DNA robot. Individual DNA strands can be "programmed" with complementary bases that bind together to form specific shapes (Nadrian Seeman and William Sherman of the New York University). Seeman recently reported that he had built a DNA "robot" (= nanowalker), just 10 nanometers long (nanoscale devices capable of bipedal motion).

Reference: "Nano-bio convergence could evolve from work in progress to a link that makes nanotech work" by David Pescovitz, SmallTimes 4 (4)  64 (2004)

Universities & companies involved in medical and pharmaceutical applications of nano-biotech
A	B	C	D	E	F	G	H	I	L
M	N	O	P	Q	R	S	T	U / V	Z / W
A
Accelrys (genomics & proteomics)					Princeton, NJ, U.S.A.
Acrongenomics  ( http://www.acrongen.com ) (sector: detection and diagnosis cancer)					Athens, Greece
Advion Biosciences (proteomic analysis)					Ithaca, NY, U.S.A.
Agilent Technologies (genomics)					Palo Alto, CA, U.S.A.
American Bioscience					Santa Monica, CA, U.S.A.
American Pharmaceutical Partners					Schaumburg, IL, U.S.A.
Asylum Research (3D resolution of biomolecules)					Santa Barbara, CA, U.S.A.
B
BioForce Nanosciences, Inc					Ames, Iowa - U.S.A.
BioNanomatrix (genomics) (Borne of a multi-million dollar Department of Defense project funded by DARPA (Defense Advanced Research Project Agency) at Princeton University)					Princeton , NJ, U.S.A.
BioSante Pharmaceutical Inc					Illinois - U.S.A.
BioTraces  (nanoproteomics)					Herndon, VA, USA
BioTrove (gnomics, proteomics)					Woburn, MA, U.S.A.
C
C Sixty, Inc. (sector: therapeutics)					Houston, TX, U.S.A
Caliper Life Sciences (Genomics)					Mountain View, CA, U.S.A.
CeNTech (proteomics)					Gievenbecker Weg 11 - D – 48149 Münster (Germany)
Crystalplex (proteomics)					Pittsburgh, PA, U.S.A.
D
Dendritic NanoTechnologies					Mount Pleasant, MI, U.S.A
E
eMembrane (proteomics, viral vectors)					Providence, RI, U.S.A.
Elan Pharmaceuticals (NanoCrystal Technology)  (sector: drug deliverys)					Dublin, Ireland
Evident Technologies [ http://www.evidenttech.com (in partnering with Upstate ( http://www.upstate.com ) ] (sector: detection & diagnosis cancer)					Troy, New York, U.S.A.
F
FEI Company ( http://www.feicompany.com ) (protein tomography)					Hillsboro, Oregon . U.S.A.
Five Star Technologies ("Controlled Flow Cavitation"), working in collaboration with the Illinois Institute of Technology					Cleveland , OH, U.S.A.
Flamel Technologies (sector: drug deliverys)					Lyon, France
G
GE Global Research Center (sector: diagnostics and molecular imaging)
Georgia Institute of Technology (FIRAT, Force sensing Integrated Readout and Active Tip)
I
IBM (Zurich Research Laboratory) (genomics)					Zurich, Switzerland)
IMedd					Foster City, CA, U.S.A.
Immunicon (sector: diagnostics and imaging)					Huntingdon Valley, PA, U.S.A.
Insert Therapeutics ( http://www.inserttherapeutics.com ) (sector: detection and diagnosis cancer)					Pasadena, CA, U.S.A.
Institute for Bioengineering and Nanoscience in Advanced Medicine (sector: tissue reconstruction)					Northwestern University, Chicago, IL, U.S.A.
Invitrogen (genomics)					Carlsbad, CA, U.S.A.
L
Lumera (proteomics, protein-DNA interactions)					Bothell, WA, U.S.A.
Lux Research Inc.					New York, NY, U.S.A.
N
National Cancer Institute (NCI) Alliance for Nanotechnology in camcer
NanoCure (Avidimer Therapeutics)					Ann Arbor, MI, U.S.A.
Nanogen ( http://www.nanogen.com ) (sector: detection and diagnosis cancer)					San Diego, CA, U.S.A.
Nanometrix (proteomics)					Montreal, Quebec, Canada
Nanopharma					Boston, MA, U.S.A.
Nanoplex Technologies, Inc					Menlo Park, California - U.S.A.
Nanospectra Biosciences  (sector: therapeutics)					Houston, TX, U.S.A.
Nanosphere (sector: diagnostics and imaging) ( http://www.nanosphere-inc.com )					Northbrook, IL, U.S.A.
NanoString Technologies (genomics, proteomics)					Seattle, WA, U.S.A.
Nanosys (proteomics)					Palo Alto, CA, U.S.A.
Nanoxis (membrane proteins)					Kemivägen 9, SE-412 96 Gothenburg, Sweden
NEC (proteomics) ( http://www.nec.co.jp/ )					Japan
O
Oxonica (DNA-protein interaction, genomics, proteomics)					Yarnton, Kidlington , Oxfordshire OX5 1PF, United Kingdom
P
Pfizer Global Research & Development (Sector: contrast agents for studying vascular walls)
PharmaSeq  (genomics, proteomics)					Monmouth Junction, NJ, U.S.A.
PlasmaChem (human genomics)					Berlin, Germany
pSivida					Australia
Q
Quantum Dot Corp.(sector: imaging) ( http://www.qdots.com )					Hayward, California - U.S.A
S
StarPharma (sector: nanotechnology drugs; VivaGel, a nanotechnology drug to prevent the sexual transmission of HIV)					Melborne, Australia
SurModics (sector: drug delivery matrix)					Eden Prairie, MN, U.S.A.
T
Triton Biosciences  (sector: therapeutics)					Chelmsford, Mass.,  U.S.A.
U
UCLA (nanoproteomics)
W
Winship Cancer Institute at Emory University (sector: imaging)					Atlanta, GA, U.S.A.
Source: "The ups and downs of nanobiotech" by Jeffrey M. Perkel, The Scientist 18 (16), 14 - 18 (2004); "Recruiting nanobiotech for attacking cancer" by Lynne Lederman, Genetic Engineering News 24 (10), 18 - 19 (2004);  "Using nanotechnologies in biotech and medicine" by Patricia F. Dimond, Genetic Enginnering News 25 (6), 1,21 (2005); Lux Research report at http://www.luxresearchinc.com/testimony.pdf

June

Deciphering the messaging systems connecting mammalian cells

Proteomics allows to identify the diverse protein messages cells send to each other. Deconding the significance of the message itself is another question. Deciphering these cryptic messages will permit to understand  the inteaction between the biological compartments into the cell and , possibly, the identification of biomarkers specific for normal and pathological conditions. It is necessary to make a screening of all protein signals and then to correlate their presence to some specific conditions. The epigenetic factors need to be taken into consideration. . This will be useful for synthetic biology and for the identification of new biomarkers.

Scientific terminology: the genetic code is not a synonym for genome sequence

Scientific confusion between "genetic code" and "genome".

The dictionary defines "code" as "a system of signals used to represent letters or numbers in transmitting messages" .or "a system of words or symbols arbitrarily used to represent words".

Francis Crick led the team that deciphered the code 1n 1961 [F.H.C. Crick et al. "General nature of the genetic code for proteins" Nature, 192 : 227 - 232 (1961) ]. The same codons specify the same amino acids in all the living organisms.

As a consequence, "decifering the genetic code"  and "sequencing the genome" are not the same things: the code is the correspondence not the sequence.

June 15 (2000), it was published the article "Breaking the code" ( http://www.pbs.org/newshour/bb/health/jan-june00/genome_6-15.html )

July 3 (2000), Time Magazine reported the title "Cracking the code" on the cover , with reference to the article "The men who mapped the genome" (J.Craig Venter and Francis Collins) on page 18 ( http://www.grg.org/breakingnews2999.htm ).

The error (code insted of genome) persists:  for example, David Malakoff published a comment on Science with the title: "Report upholds public access to genetic codes" [ Science 305 (5691) :  692 (2004) ]. The title itself implies the existence of more than one code. In the same article, it is reported that "since scientists sequenced the first viral genome in 1975, they have released the genetic codes of more than 1100 viruses and 150 bacteria, including those of the dangerous pathogens that cause smallpox,...".

Fortunately a report published on Nature has finally put usage of the term "genetic code" on the right track,  expanding the rules of the genetic code estalished nearly half a century ago.

References:

1) "The 22nd Amino Acid" by John F. Atkins and Ray Gesteland, Science 296 (5572), 1409 - 1410 (2002)

• 21st amino acid        selenocysteine   (UGA is the "stiop codon" encoding selenocysteine)
• 22nd amino acid       UAG     pyrrolysine (UAG is the codon encoding pyrrolysine)

Two models of codon redefinition:

(i) mRNA context-dependent redefinition of stop codons

(ii) mRNA context-independent redefinition of stop codons

2) "Pyrrolysine encoded by UAG in Archaea: charging of a UAG-decoding specialized tRNA" by Gayathri Srinivasan, Carey M. James, Joseph A. Krzycki, Science 296 (5572), 1459 - 1462 (2002)

3) "A new UAG-encoded residue in the structure of a methanogen methyltransferase" by Bing Hao et al, Science 296 (5572), 1462 - 1466 (2002) [L-pyrrolysine is a naturally occurring amino acid so far only found in some archaeal proteins; pyrrolysine is a lysine in amide-linkage to (4R,5R)-4-substituted-pyrroline-5-carboxylate].

 4) "In search of the human genetic code - It is not a synonym for genome sequence! " by Ricki Lewis , The Scientist 18 (20) , 68 (2004)

5) "Genetic code seizes pyrrolysine" by Paul Schimmel and Kirk Beebe, Nature 431 (7006), 257 - 259 (2004) - The genetic code requires for its implementation a set of 20 universal enzymes  [aminoacyl tRNA synthetases (one for each amino acid)]. But  Blight et al (2004) show that in certain archea an unusual , natural amino acid is read by the code using a novel twenty-first amionoacyl t-RNA synthetase. The novelty of the work by Blight et al. rests on ther identification of a natural  twenty-first synthetase that directly activates pyrrolysine (pLys), both in vitro and in vivo. A natural synthetase tRNA pair brings a new amino acid into the genetic code. UAG is the codon for pLys.

6) "Direct charging of tRNACUA with pyrrolysine in vitro and in vivo" by Sherry K. Blight et al, Nature 431 (7006), 333 - 335 (2004).  The authors establish that synthetic L-pyrrolysine is attached as a free molecule to to tRNA CUA  by PyIS, an archeal class II aminoacyl-tRNA synthetase. PyIS activates pyrrolysine with ATP and ligates pyrrolysine to tRNACUA in vitro in reactions specific for pyrrolysine. The addition of pyrrolysine to E. coli cells expressing pyIT (encoding tRNACUA) and pyIS results in the translation of UAG in vivo as a sense codon. This is the first example from nature of direct amynoacylation of a tRNA with a non-canonical amino acid and shows that the genetic code of E.coli can be expanded to include UAG-directed pyrrolysine incorporation into proteins.

July

"Why politicized science is dangerous" - Open discussion about science and politics, starting from the artcle written by Michael Crichton, enclosed as Appendix 1 on the book "State of Fear" (HarperCollinsPulishers, New York, NY, U.S.A.; 2004)

• The theory of eugenics. "The eugenics movement was really a social program masquerading as a scientific one"
• Vernalization  , by Trofim Denisovich Lysenko (1928).
• Global warming - The science of climate change

"When the search for the truth is confused with political advocacy, the pursuit of knowledge is reduced to the quest for power" (Alston Chase).

Knowledge must be disinterested and honest.

"We desperately need a nonpartisan , blinded funding mechanism to conduct research to determine appropriate policy. Scientists are only too aware whom they are working for. Those who fund research - whether a drug company, a government agency, or an environmental organization - always have a particular outcome in mind. Research funding is almost never open-ended or open-minded. Scientists know that continued funding depends on delivering the results the funders desire....No faction should be given a free pass." (Michael Crichton, 2004)

Human nature and human interaction with  the natural world. "The greatest problem for all observers of the world is to determine whether their perceptions are genuine and verifiable or whether they are merely the projections of inner feeling" (M. Criichton, 2004)

August

Can one person have two types of DNA in different parts of his body? The Chimeras

People with two types of DNA are called chimeras after a mythical creature with a lion's head, a goat's body, and a serpent's tail (individuals are also called mosaics). These people have two different sets of DNA in different parts of the body.
How does someone become a chimera? There are a number of ways this can happen: http://www.thetech.org/genetics/ask.php?id=23

September

Psycological operations related to the intelligence process [Reference: " Doctrine for Joint Psycological Operations " (September 5, 2003)]

October

OGM soldiers - Program of human enhancement [under: Harvesting Biology for Defense Technology (Defense Advanced Researc Projects Agency (DARPA)]:

Brain Interface Program: translation of cerebral signals into electrical signals that should be understood by sistems made with electronic prosthesis [developed by John Donoghue, of the Neuroscience Department at the Brown University, Providence, RI, U.S.A. ( http://www.brainscience.brown.edu/departments/faculty/donoghue.html ).

Human Assisted Neural Devices (HAND)

Neural interfaces : BrainGate, a neural interface system ( http://www.cyberkineticsinc.com/content/medicalproducts/braingate.jsp ) developed by the company CyberKinetics [( http://www.cyberkineticsinc.com/content/technology/platformtechnology.jsp ) Foxborough, Massachusetts, U.S.A.,  and Salt Lake City, Utah, U.S.A.]

Persistence in combat:

a program to develop new molecules against pain [ anti-NGF Antibody for Acute and Chronic Pain (RN 624) at RINAT Neuroscience (South San Francisco, CA, U.S.A.) RN 624 is a novel humanized monoclonal antibody that blocks nerve growth factor (NGF), a key mediator of acute and chronic pain. RI 624 is being developed by Rinat and is currently in Phase I clinical trials ( http://www.rinatneuro.com/ )

Laser Therapy & Nerve Regeneration ( a research program developed by prof. Harry Whelan http://www.thorlaser.com/nerve/harry.htm

Portable ventilators for respiratory emergency under stress or injury [ Impact Instrumentation Inc. (West Caldwell, NJ, U.S.A.) http://www.impactinstrumentation.com/ ]

Repair of tissue injury (University of California, Davis, U.S.A.)

Continuous Assisted Performance (Sleep deprived soldiers)

Possible treatment for behavior and cognition [Ampakine http://www.cortexpharm.com/html/research/tech.html ;  new molecules starting from a research on the biochemical switch that regulates the waking and sleeping patterns in migrant birds  (mechanisms affecting circadian rhtyhms)]

November

Forensic DNA - A review on the principal aspects concerning forensic DNA analysis, with respect  to scientific, legal, ethic, and human rules.

December

Stem cells and cancer

The tumor initiating cell (T-IC).

• The stochastic theory
• The hierarchical model

http://www.genomenewsnetwork.org/articles/03_03/stem_c.shtml

http://www.med.umich.edu/medschool/orgs/biopathways/Pathways_Aug2005.pdf

http://www.cancerdecisions.com/042603_page.html

Reference:

"Prospective identification of tumorigenic breast cancer cells" by Muhammad Al-Hajj, Max S. Wicha, Adalberto Benito-Hernandez, Sean J. Morrison, and Michael F. Clarke PNAS  100 (7).  3983-3988 (2003)

Entire cancerous tumors may arise from the multiplication of only a small minority of malignant cells. In an article published this week in PNAS, scientists identify markers of these cancer "stem cells," a finding that may lead to novel therapeutics. Michael Clarke (University of Michigan - Medical School)  and colleagues investigated cells from breast cancer tumors recently removed from human patients. Using cell surface markers, proteins expressed on the outer cell membrane, to sort the cells into types, the scientists injected cells of a single marker type into mouse mammary pads. One cell type consistently caused tumors to develop: cells that expressed a marker called CD44 and had either no or low levels of a marker called CD24. Because only large injections of unsorted cancer cells were able to prompt tumors, the scientists surmised that CD44+/CD24- cells were a small but powerful minority within cancer cell populations. Further tests showed that these cell types were able to generate the diverse array of other cells seen in tumors, a quality reminiscent of stem cells. Stem cells are often resistant to chemotherapy, and the authors suggest that understanding why these cells are able to create tumors could lead to more productive cancer therapies.

http://www.genetics.wisc.edu/courses/spring05/707/readings/alexander3.pdf