The Near Eastern Origin of Cat Domestication in Fredcobio

I am always amazed at the breadth and depth of scientific research going down in our own back yard. I bet you didn’t know that this 2007 paper in Science was partially done in Frederick: The Near Eastern Origin of Cat Domestication

A few weeks back I went to Olive’s, on a whim, and ended up chatting with this cat Carlos who works at the Laboratory of Genomic Diversity at NCI over a martini or two.  Fascinating stuff.   The research shows that wildcats (Felis silvestris) were initially domesticated in the Near East, probably coincident with agricultural village development in the Fertile Crescent.  Interestingly, cats differ from other domesticated animals in that they seem to provide no real benefit to humans aside from catching rodents in the early grain stores & companionship.

The Science text is a very detailed technical account and is followed up with a more elaborate, “scientifically toned down” article in the June 2009 edition of  Scientific American.

Some conclusions of this article

Unlike other domesticated creatures, the house cat contributes little to human survival.  Researchers have therefore wondered how and why cats came to live among people.

Experts traditionally thought that the Egyptians were the first to domesticate the cat, some 3,600 years ago. But recent genetic and archaeological discoveries indicate that cat domestication began in the Fertile Crescent, perhaps around 10,000 years ago, when agriculture was getting under way.

The findings suggest that cats started making themselves at home around people to take advantage of the mice and food scraps found in their settlements.

In an article published in PNAS in 2009, the authors delve into the differences between Natural vs. Artificial Selection.  Interesting stuff:

We perceive today, as did Darwin, that natural selection is the environmentally driven mechanistic process by which more advantageous traits are, on the whole, passed on to succeeding generations more often than less advantageous traits because of differential reproduction of the individuals possessing them. Sexual selection is a natural process of intraspecific competition for mating rights. Artificial selection, generally the motive force behind domestication, is often equated with selective breeding. This often amounts to prezygotic selection (where mates are chosen by humans) versus postzygotic selection (where the most fit progeny reproduce differentially) as in natural selection. Although natural selection plays a considerable role in the evolution of many traits (e.g., disease resistance) during the animal domestication process, sexual selection is effectively trumped by the human-imposed arrangements of matings and often by the human desire for particular secondary sexual characters. Artificial selection is a conscious, if unintentional, process, and therefore is generally considered to be effected only by humans.

This is exactly the kind of research we’re doing at Ft Detrick that I think would be brilliant to get out to people by a yet to be established mechanism. I wonder if The various agency “partners” at Ft Detrick even track this stuff?

My Delight, but a Germophobes Nightmare

I am always (perhaps too much) scanning the blogosphere for anything related to FredCoBio news.  This story I predict will make the Network news tonight or maybe tomorrow.

The entire article is published in Science (and will require a paid subscription to view your tax dollars at work), but ther have been a number of AP stories circulating on the blogesphere today. You can read the whole story at ScienceNOW:

Your Body Is a Wonderland … of Bacteria

By Stephanie Pappas
ScienceNOW Daily News
28 May 2009

Where can you find your skin’s most diverse community of bacteria? Not in a sweaty armpit or linty belly button. According to a new survey of the bacterial ecosystem that covers us, the diversity hot spot of the body’s exterior is the forearm. And the surprises don’t end there.

Microbes that live in and on our bodies outnumber our own cells 10 to one, but researchers have only recently begun to catalog the residents on our skin. Traditionally, scientists identified human skin bacteria by swabbing volunteers and culturing the samples, but those results skewed toward microbes that grow well in the lab. Thanks to ever-evolving gene-sequencing technology, scientists can now use microbial RNA to identify organisms. With these techniques, researchers have found an unexpectedly wide variety of bacteria on human skin (Science, 23 May 2008, p. 1001). But no one had ever systematically compared bacterial colonies from different areas on the human body.

To do so, scientists from the National Human Genome Research Institute in Bethesda, Maryland, recruited 10 volunteers and asked them to wash with mild soap for 1 week. Then, after 24 hours without bathing, the volunteers arrived at the lab, where researchers swabbed and scraped their skin in 20 places–everywhere from the nostril to the navel to that bane of low-rise jeans aficionados, the gluteal crease. The team analyzed ribosomal RNA from the samples and classified the microbes based on their genomes.

The researchers found about 1000 species total, which were fairly consistent from person to person; it turns out we all have similar tenants in our noses and on our backs. The number suggests that our skin is as variegated as our guts, which house anywhere from 500 to 1000 bacterial species. The team also found vast differences across the skin, according to the study published in tomorrow’s issue of Science. Contrary to what acne-prone teenagers might expect, oily areas such as the forehead and scalp are actually less diverse than dry areas such as the forearm (though one is enough for grief: Propionibacterium acnes thrives in oily spots). The most barren region was behind the ear, with a median diversity of 15 species. In comparison, the forearm teemed with a median 44 species. A follow-up with five of the volunteers months later found that bacterial makeup changed little over time.

The link to FredCoBio is simple. Alice Y. and I worked together in at Molecular Diagnostic Division of Life Tech, which is now known as Digene/Qiagen.  She used to give us so many clothes passed down from her daughter, Rachel, to our oldest (now 20, yikes!).  And Bob B. is an original BRL guy who lives in Frederick.  I remember his wife worked the cash register at Martins on 7th street when we used to live in the city.  Anyway, they are both at NHGRI now, along with a number of other former Life Tech people.

Pretty cool research and yet another deep tie into the FredCoBio community.

FredCoBio joins the Personal Genome Project

Laura Rauch for The New York Times
George Church leads the Personal Genome Project and is one of its first 10 participants.

In another non-local story, today the Harvard’s Personal Genome Project released the results of the so-called “PGP 10″ (see this NY Times story, which I think requires free registration).  I met a number of the PGP 10 at Scifoo.  I even ate lunch one day with George Church.  I had no clue who he was, but he was a nice enough introverted science guy.  His hair is a bit lighter whiter than in the picture on his bio.

Anyway, I registered myself today.  They are looking to sequence DNA from 100,000 people, assemble the data in a public data base “to speed medical research by dispensing with the elaborate precautions traditionally taken to protect the privacy of human subjects. The more genetic information can be made open and publicly available, nearly everyone agrees, the faster research will progress.  In exchange for the decoding of their DNA, participants agree to make it available to all — along with photographs, their disease histories, allergies, medications, ethnic backgrounds and a trove of other traits, called phenotypes, from food preferences to television viewing habits.”

I am not a nudist, but you take take a peek at my DNA if you’d like.  You show me yours and I’ll show you mine.

So what are you waiting for?  REGISTER TODAY!

UPDATE 10/22:  Another good story on topic from Nature

USAMRIID Publications

I was surfing around a few web sites of Ft Detrick “Tennants” and came across something I’ve been looking for.  This web site lists all of the publications produced by Ft Detrick, USAMRIID laboratories.

Here’s the impressive collection of publications in 2008 (for earlier dates, back to 2000, see the web site).  Most of these will grant access to the abstract only and you’ll have to pay to get the whole text.  Funny how you have to pay to read publications made by our own Government employees.  So much for Science in the Open:

Blow JA, Mores CN, Dyer J, Dohm DJ. Viral nucleic acid stabilization by RNA extraction reagent. Journal of virological methods Jun 2008, 150(1-2):41-4 Bradfute SB, Warfield KL, Bavari S. Functional CD8+ T Cell Responses in Lethal Ebola Virus Infection. Journal of immunology Mar 15 2008, 180(6):  4058-66 Cote CK, DiMezzo TL, Banks DJ, France B, Bradley KA, Welkos SL. Early interactions between fully virulent Bacillus anthracis and macrophages that influence the balance between spore clearance and development of a lethal infection. Microbes and infection May 2008, 10(6):613-9 Cote CK, Bozue J, Moody KL, Dimezzo TL, Chapman CE, Welkos SL. Analysis of a novel spore antigen in Bacillus anthracis that contributes to spore opsonization. Microbiology (Reading, England)  Feb 2008, 154(Pt 2):619-32 Golden JW, Hooper JW. Heterogeneity in the A33 protein impacts the cross-protective efficacy of a candidate smallpox DNA vaccine. Virology Jul 20 2008, 377(1):19-29 Golden JW, Josleyn MD, Hooper JW. Targeting the vaccinia virus L1 protein to the cell surface enhances production of neutralizing antibodies. Vaccine   Jun 25 2008, 26(27-28):3507-15 Groves SS, Turell MJ, Bailey CL, Morozov VN. Rapid active assay for the detection of antibodies to West Nile virus in chickens American Journal of Tropical Medicine and Hygiene JAN 2008, 78(1):63-69 Hewetson JF, Little SF, Ivins BE, Johnson WM, Pittman PR, Brown JE, Norris SL, Nielsen CJ. An in vivo passive protection assay for the evaluation of immunity in AVA-vaccinated individuals. Vaccine Aug 5 2008, 26(33):4262-6 Hooper JW, Ferro AM, Wahl-Jensen V. Immune serum produced by DNA vaccination protects hamsters against lethal respiratory challenge with Andes virus. Journal of virology Feb 2008, 82(3): 1332-8 Kortepeter MG, Martin JW, Rusnak JM, Cieslak TJ, Warfield KL, Anderson EL, Ranadive MV. Managing potential laboratory exposure to ebola virus by using a patient biocontainment care unit. Emerging infectious diseases Jun 2008, 14(6):881-7 Krakauer T, Buckley M. The potency of anti-oxidants in attenuating superantigen-induced proinflammatory cytokines correlates with inactivation of NF-kappaB. Immunopharmacology and immunotoxicology  2008, 30(1): 163-79 Lebeda FJ, Adler M, Erickson K, Chushak Y. Onset dynamics of type A botulinum neurotoxin-induced paralysis. Journal of pharmacokinetics and pharmacodynamics Jun 2008, 35(3):251-67 McCall S, Vilensky JA, Gilman S, Taubenberger JK. The relationship between encephalitis lethargica and influenza: a critical analysis. Journal of neurovirology May 2008, 14(3):177-85 Nalca A, Hatkin JM, Garza NL, Nichols DK, Norris SW, Hruby DE, Jordan R. Evaluation of orally delivered ST-246 as postexposure prophylactic and antiviral therapeutic in an aerosolized rabbitpox rabbit model. Antiviral research Aug 2008, 79(2):121-7 Nuss JE, Choksi KB, DeFord JH, Papaconstantinou J. Decreased enzyme activities of chaperones PDI and BiP in aged mouse livers. Biochemical and biophysical research communications  Jan 11 2008, 365 (2): 355-61 Page JE, Murphy WJ. Construction of radiation hybrid panels. Methods in molecular biology 2008, 422:51-64 Peyser BD, Irizarry R, Spencer FA. Statistical analysis of fitness data determined by TAG hybridization on microarrays. Methods in molecular biology (Clifton, N.J.) 2008, 416:369-81 Raab R, Swietnicki W.. Yersinia pestis YopD 150-287 fragment is partially unfolded in the native state Protein Expression and Purification MAR 2008, 58(1):53-60 Rozak D, Rozak A. Simplicity, function, and legibility in an enhanced ambigraphic nucleic acid notation. BioTechniques May 2008, 44(6):811-3 Spurgers KB, Sharkey CM, Warfield KL, Bavari S Oligonucleotide antiviral therapeutics: Antisense and RNA interference for highly pathogenic RNA viruses. Antiviral research  Apr 2008, 78(1): 26-36 Swenson DL, Wang D, Luo Min; Warfield KL, Woraratanadharm J, Holman DH, Dong JY, Pratt WD Vaccine to confer to nonhuman primates complete protection against multistrain Ebola and Marburg virus infections. Clinical and vaccine immunology  Mar 2008, 15(3): 460-7 Turell MJ, Linthicum KJ, Patrican LA, Davies FG; Kairo A, Bailey CL. Vector competence of selected African mosquito (Diptera: Culicidae) species for Rift Valley fever virus. Journal of medical entomology Jan 2008, 45(1) 102-8 Turell MJ, Parker MD. Protection of Hamsters by Venezuelan Equine Encephalitis Virus Candidate Vaccine V3526 against Lethal Challenge by Mosquito Bite and Intraperitoneal Injection. American journal of tropical medicine and hygiene Feb 2008,78(2):328-32 Turell MJ, Whitehouse CA, Butler A, Baldwin C, Hottel H, Mores CN. Assay for and replication of Karshi (mammalian tick-borne flavivirus group) virus in mice. American journal of tropical medicine and hygiene  Feb 2008, 78(2): 344-7 Twenhafel NA, Whitehouse CA, Stevens EL, Hottel HE; Foster CD, Gamble S; Abbott S, Janda JM, Kreiselmeier N, Steele KE. Multisystemic abscesses in African green monkeys (Chlorocebus aethiops) with invasive Klebsiella pneumoniae–identification of the hypermucoviscosity phenotype. Veterinary pathology Mar 2008, 45(2):226-31 Welkos S, Norris S, Adamovicz J.Modified caspase-3 assay indicates correlation of caspase-3 activity with immunity of nonhuman primates to Yersinia pestis infection. Clinical and vaccine immunology Jul 2008, 15(7):1134-7 2007 • 2006 • 2005• 2004 • 2003 • 2002 • 2001 • 2000 Last updated: 28 July, 2008

My 100th Post: Marligen Makes a Deal

It’s been a while since I’ve heard anything about Marligen, the only Biotech company in my home town of Ijamsville. And even though they are less than a mile from the Montgomery County line, they’re still a FredCoBio member. That’s like having a semi-sterile cell culture flask, I guess. Here’s the news clip, via businesswire.com:

Marligen Exclusively Licenses Genisphere Labeling Technology for the Detection of microRNAs on the xMAP® Platform

Marligen Launches Vantage™ Line for the Purification, Labeling and Detection of microRNAs

IJAMSVILLE, Md.–(BUSINESS WIRE)–Marligen Biosciences, Inc., a supplier of innovative products for the life sciences research market, will become the exclusive provider of Genisphere’s biotinylated labeling kits for detection of microRNAs on the xMAP^® multiplex platform. The microRNA labeling kits using Genisphere Inc.’s 3DNA^™ dendrimer signal amplification technology will be an integral product to Marligen’s new offering supporting researchers studying microRNAs. The Vantage™ product line includes reagent kits for purifying, labeling and detecting microRNA species.

Genisphere’s unique 3DNA^™ dendrimer technology is based on highly branched DNA structures serving as scaffolds for multiple biotins. The use of Genisphere’s signal amplification technology in combination with the Vantage™ microRNA detection panels offers researchers a fast and cost-effective system to directly profile multiple microRNAs in a single sample. The complete system offers exceptional sensitivity and throughput capabilities of greater than 100 samples in a single day and is compatible with total RNA or enriched RNA including degraded RNA from archived tissues. The initial Vantage™ microRNA Detection Panels are designed for profiling the relative abundance of different microRNA species known to be relevant in oncology. The Vantage™ Products will be launched at the upcoming annual meeting of the American Association of Cancer Research.

“High throughput profiling of MicroRNAs presents a challenge when combining rapid, effective labeling with improved detection sensitivity,” said Dr. Robert Getts, Director of R&D at Genisphere. “The complete Vantage™ package, having integrated our rapid 3DNA™ dendrimer microRNA labeling method with Marligen’s carefully designed detection panels, provides an optimized solution with consistent performance and much needed sensitivity on the xMAP® high-throughput detection platform.”

“Because microRNA play such an important role in tumor development and progression, it is vital we offer researchers innovative tools that allow them to profile these biological markers in archived samples. Our collaboration with Genisphere allows us to provide one of the most rapid and sensitive methods to screen directly from such samples,” said James Lazar, Chief Scientific Officer of Marligen Biosciences. “This will not only advance basic research but should expedite the application of microRNA detection in the diagnosis of cancer.”

It’s strange, because this article couldn’t be more timely. The Founder & CEO, Sherry Challberg, was the one who hired me in April 1988 to move South to Maryland. It’s hard to believe that it has been 20 years ago to this day.

I was working in a lab at the University of Rochester doing papilloma virus research (which supported research leading to a Nobel prize for Micheal Bishop in 1989 and in support of research into Open Reading Frames, which lead to the 1993 Nobel Prize for Sharp & Roberts and also 1989 Nobel prize in Chemistry for Thomas Cech’s discovery of Ribozymes) and steroid hormone modulation of gene expression (in support of research into Protein Phosphorylation as a regulatory mechanism of proteins leading to the 1992 Nobel prize for Edmund Fisher and Edwin Krebs and leading to the discovery of COX-2 enzyme and COX-2 inhibitors in 1991 which was subsequently “borrowed” by Pfizer and made into the blockbuster drug Celebrex, reaffirming Dr Young’s assertion that I was leaving academia to go work in the “Evil Empire” that is Industrial research).

But enough name dropping, lest you think this blog is just about shameless self-promotion.

Back to the story. We moved down here in 1988 to work in the Molecular Diagnostics Division of Life Technologies. This was sold in 1990 or ’91 to become Digene. To the left you see the 25 year old version of yours truly, pretending I am doing lab work. This is from the front page of the Baltimore Sun’s Business section on Dec. 21, 1988. The story was about our pending FDA approval for (one of?) the first clinically approved DNA test on the market. You may notice that the paper has a tinge of orange from age, and if you look closely, you’ll see my beard was still orange, too. By the way, the Dow closed at a mere 2,166 that day, a 1-year CD would yield 9.00 % and the Prime was 10.5%.

Genome Projector

I ran across this neat little tool called the Genome Projector via My BioTech Life. It’s a Google Maps based graphics program which contains 320 bacterial genomes and gives you a zoomable view of circular DNA sequences, pathways and a DNA walk. It’s pretty cool and I’ll link it in the Gene Jockey section later. Why don’t you give it a try?

More Tales About Cats and Virus

I picked up another story from the same group at NCI/SAIC-Frederick from GenomeWeb Daily News feed.

It would appear that if you have any questions about the feline genome, then Dr SJ O’Brien would be the person to speak with. I have always found it interesting, and quite different than myself, that people can get so deep and specific about a topic such as the cat genome. And this morning I have festered away quite a few hours on the topic myself. I find it fascinating that the authors are able to draw analogies between African Lion FIV and modes of transmission of HIV in humans.

The most recent article is actually available on from an “Open Access”, peer-reviewed journal, BMC Genomics. So, here’s the skinny on this publication (or should I say, just scratching the surface):

Conclusions

This study demonstrates the necessity of whole-genome analysis to complement population/gene-based studies, which are of limited utility in uncovering complex events such as recombination that may lead to functional differences in virulence and pathogenicity. These full-length lion lentiviruses are integral to the advancement of comparative genomics of human pathogens, as well as emerging disease in wild populations of endangered species.

Interestingly, in another featured article in the same publication, yet another “Frederick Connection”. One of the authors of the paper “A large-scale proteomic analysis of human embryonic stem cells“, Mahendra S Rao, was working closely with SuperArray on their Stem Cell platforms and then left to go to work across the street at Invitrogen.  I think that’s pretty cool!

Genetic Characterization of Feline Leukemia Virus from Florida Panthers

I ran across an interesting bit of research this morning while surfing. An article in the CDC Publication “Emerging Infectious Diseases”, authored by Meredith A. Brown, from NCI and Stephen J. O’Brien, SAIC-Frederick et al.

The suggested citation: Brown MA, Cunningham MW, Roca AL, Troyer JL, Johnson WE, O’Brien SJ. Genetic characterization of feline leukemia virus from Florida panthers. Emerg Infect Dis [serial on the Internet]. 2008 Feb [date cited]. Available from http://www.cdc.gov/EID/content/14/2/252.htm

Being in industry for the past 20 some odd years, I am not real hip on current publications and don’t even subscribe to PubMed. I get a lot out of the abstracts and turn to my more research-minded partners if I need to pull up a publication.

Here’s the abstract

Abstract
From 2002 through 2005, an outbreak of feline leukemia virus (FeLV) occurred in Florida panthers (Puma concolor coryi). Clinical signs included lymphadenopathy, anemia, septicemia, and weight loss; 5 panthers died. Not associated with FeLV outcome were the genetic heritage of the panthers (pure Florida vs. Texas/Florida crosses) and co-infection with feline immunodeficiency virus. Genetic analysis of panther FeLV, designated FeLV-Pco, determined that the outbreak likely came from 1 cross-species transmission from a domestic cat. The FeLV-Pco virus was closely related to the domestic cat exogenous FeLV-A subgroup in lacking recombinant segments derived from endogenous FeLV. FeLV-Pco sequences were most similar to the well-characterized FeLV-945 strain, which is highly virulent and strongly pathogenic in domestic cats because of unique long terminal repeat and envelope sequences. These unique features may also account for the severity of the outbreak after cross-species transmission to the panther.

Does anyone know if there is a central site for Publications coming out of NCI, NIAD, SAIC or any of the other Agencies at Ft Detrick? Drop me a line if you do. This is the kind of research I would like to give more publicity to in my little space on the web.

And don’t forget to check out the entire Calendar of seminars, all open to the public, hosted by NCI. I’ll stick them on the Calendar page since it’s a pretty long list.

NCI-Frederick November events

I lifted this table off NCI-Frederick’s web site and included it as a new link on the Calendar page:

Tuesday, November 06, 2007
8:30:00 AM	Michael Dean, PhD	Bldg 549 Conf. Rm B
	Cancer, Inflammation, and Stem Cells	Details Series
Wednesday, November 07, 2007
12:00:00 PM	Sina Bavari	Bldg 549 Auditorium
	Innate Immune Responses to Highly Pathogenic Microbes	Details Series
Friday, November 09, 2007
12:00:00 PM	Dr. Hal Broxmeyer	Bldg 549 Auditorium
	Regulation of Hematopoietic and Embryonic Stem Cells	Details Series
Tuesday, November 13, 2007
8:30:00 AM	Jacques Banchereau, PhD	Bldg 549 Conf. Rm B
	Harnessing Dendritic Cells to Build Cancer Vaccines	Details Series
Wednesday, November 14, 2007
12:00:00 PM	James Kelley	Bldg 549 Auditorium
	Getting a Charge Out of Chemistry: Making and Using Ions for Bioanalysis	Details Series
Friday, November 16, 2007
11:00:00 AM	Dr. Joseph Lakowicz, Director	Bldg 549 Auditorium
	Plasmon-Controlled Fluorescence: A New Paradigm in Biological Fluorescence	Details Series
12:00:00 PM	Dr. Licia Selleri	Bldg 426 Conf. Rm
	A First Step Towards a Genetic and Transcriptional Control of Spleen Development	Details Series
Tuesday, November 20, 2007
8:30:00 AM	Ian F. Tannock, MD, PhD,FRCPC	Bldg 549 Conf. Rm B
	Limited Drug Distribution and Repopulation as Important and Neglected Causes of Drug Resistance in Solid Tumors	Details Series
Tuesday, November 27, 2007
8:30:00 AM	Catherine M. Handy, PhD, RN, AOCN	Bldg 549 Conf. Rm B
	The Future is Bright Yet so Small: Nanotechnology and Cancer Therapy	Details Series
Wednesday, November 28, 2007
12:00:00 PM	Steven Hou	Bldg 549 Auditorium
	Molecular Genetic Study of Stem Cell Regulation in Drosophila and Mice	Details Series
Thursday, November 29, 2007
9:00:00 AM	Various Speakers	Bldg 10 Lipsett
	The IL-10 Cytokine Family: IL-10, IL-19, IL-20, IL-24 and IL-28/IL-29	Details
Friday, November 30, 2007
12:00:00 PM	Dr. William Paul	Bldg 549 Auditorium
	The2 Cells: Differentiation and Repertoire-dependent Immunopathology	Details Series

I think that these would be open to the public, but am awaiting verification from someone at NCI. This is the type of information I’ve been looking for that would benefit everyone in the Frederick County Biotech community. I was delighted and surprised to see Dr Harold Broxmeyer speaking 11/9. He is a giant in the field of hematopoeitic stem cell research and transplantation.