Chapter 8 Endnotes for Arthritis and Autoimmune Disease: The Infection Connection

Trends in Infection Research

1)      Mattman (2000)

2)      Rider TH, Zook CE, Boettcher TL, Wick ST, Pancoast JS, et al. (2011) “Broad-Spectrum Antiviral Therapeutics.” PLoS ONE 6(7): e22572. Online at

3)      Visit and use the term “proteomics” in the search window.

4)      Lemonick, Michael; Cray, Dan; Park, Alice; Song, Sora, and Thompson, Dick. “The Genome is Mapped. Now What?” TIME, July 3, 2000.

5) and also



8) (2010)

9) (1995-2002)

10)   Medzhitov, R. “Inflammation 2010: new adventures of an old flame.” Cell. 2010 Mar 19:140(6):771-6.


12)   Kozul, CD, et al. “Laboratory diet profoundly alters gene expression and confounds genomic analysis in mouse liver and lung.” Chem Biol Interact. 2008 May 28;173(2):129-40.

13)   Maslowski KM. “Diet, gut microbiota and immune responses.Nat Immunol 12:5 (2011)


15)   Michael Ash, B.Sc. (Hons) D.O. N.D. F.Dip ION. “Vitamin A: The Key to a Tolerant Immune System?” FOCUS, the Allergy Research Group Newsletter, August 2010. Online at

16) (2004)

17)   Pangborn and Baker (2002) pages 216-220

18)   Semba RD. “Vitamin A and human immunodeficiency virus infection.” Nutr Soc. 1997;56(1B):459-469.

19)  (2007)

20) red palm oil.htm  (2010)

21)   Veracity, Dani. “How iodine accelerates weight loss by supporting the thyroid gland.” Online at (2005)

22)   This section includes insights from the 2011 International Symposium on Functional Medicine in Seattle, WA, notably Michael Ash’s presentation “Living with the Host: Immune Programming and Clinical Implications.”

23)   Matzinger, P. “Tolerance, Danger and the Extended Family.” Annual Reviews in Immunology, 1994. 12:991-1045. Dr. Matzinger’s now famous “Danger Model” is described in layman’s terms in Science, April 2002: vol. 296 no. 5566 pp. 301-305. Online at

24)   Matzinger, P. Annu. Rev. Immunol. 12, 991 (1994).

25)   Matzinger, P and Kamala, T. Nature Reviews Immunology 11, 221-30. (2011)

26)   Eberi, G. “A new vision of immunity: homeostasis of the superorganism. Mucosal Immunol. 2010; 3(5): 450-60

27)   Op cit. presentation by Dr. Michael Ash. Also see Hadis, U., et al. “Intestinal Tolerance Requires Gut Homing and Expansion of FoxP3+ Regulatory T Cells in the Lamina Propria.” Immunity 34, Issue 2, pp. 237-246 (2011). Online at

28)   Cerf-Bensussan1, N., Gaboriau-Routhiau, V. “The immune system and the gut microbiota: friends or foes?” Nature Reviews Immunology 10, 735-744 (October 2010). Also Mazmanian1 SK, Round JL & Kasper, DL. “A microbial symbiosis factor prevents intestinal inflammatory disease.” Nature 453, 620-625 (2008).

29)   Many of the insights in this section are based on a presentation by Dr. Paul Ewald at the 2011 IFM international conference in Bellevue, WA.

30)   For detailed tables of specific cancer versus microbe(s) and cause(s), see

31)   From a presentation by Professor Garth Nicolson at the 2011 IFM international conference in Bellevue, WA.

32)   Conversation with Professor Garth Nicolson, 2011. He recommends NT Factor, for CFS, Metabolic Syndrome, and as a co-therapy to improve immune system function. See

33) describes this therapy.

34)   Presentation by Dr. Neil Nathan at the 2011 International IFM conference in Bellevue, WA. “Evaluation of Chronic Infections in Complex Patients.” Also see

35)   Jaenisch, R, Bird, A. "Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals." Nature genetics 33 Suppl (3s): 245–254 (2003)

36)   Nathan (2010)

37)   Find a wealth of information on biofilms at and and and and overview at

38)   EDSTROM. Biofilm: Understanding and Controlling Growth. White paper at (2011)

39)   The way biofilms develop, thrive, and spread are described in detail at the homepage of the National Science Foundation’s Center for Biofilm Engineering, Montana State University, at

40)   O'May GA, et al. “Effect of pH and antibiotics on microbial overgrowth in the stomachs and duodena of patients undergoing percutaneous endoscopic gastrostomy feeding.” J Clin Microbiol. 2005 Jul;43(7):3059-65.

41)   Amir S, et al. “Acanthamoeba castellanii an environmental host for Shigella dysenteriae and Shigella sonnei.” Archives of Microbiology. Volume 191, Number 1, 83-88. Online at

42)   See Center for Biofilm Engineering

43)   Puttamreddy S, Minion FC. “Linkage between cellular adherence and biofilm formation in Escherichia coli.” FEMS Microbiol Lett. 2011 Feb;315(1):46-53. Online at Also see Xicohtencatl-Cortes J, et al. “Intestinal adherence associated with type IV pili of enterohemorrhagic Escherichia coli.” J Clin Invest. 2007 Nov;117(11):3519-29.  Online at

44)   Dr. Art Ayers. “Biofilms as Human Gut Mycorrhizals.”

45)   Shayan R, Achen MG, and Stacker, SA. “Lymphatic vessels in cancer metastasis: bridging the gaps.” Carcinogenesis vol.27 no.9 pp.1729–1738, 2006. Online at



48) (2010)

49)   Presentation by Dr. Sandra Macfarlane at the 2011 International IFM conference in Bellevue, WA. Also Macfarlane S, Bahrami B, Macfarlane GT.  “Mucosal biofilm communities in the human intestinal tract.” Adv Appl Microbiol. 2011;75:111-43.

50)   An expert interview with Dr. Scot Dowd of PathoGenius labs (Lubbock, TX) explaining biofilms and testing methods can be found at

51)   Murphy TF, Kirkham C. “Biofilm formation by nontypeable Haemophilus influenzae: strain variability, outer membrane antigen expression and role of pili.” BMC Microbiology 2002, 2:7 at


53)   Hajishengallis G, et al. “Low-Abundance Biofilm Species Orchestrates Inflammatory Periodontal Disease through the Commensal Microbiota and Complement.”  Cell Host & Microbe. Volume 10, Issue 5, 17 November 2011, Pages 497–506.

54)   Socransky SS and Haffaje AD. “Dental biofilms: difficult therapeutic targets.” Periodontology 2000. Vol. 28, No. 1, pages 12–55, January 2002. Online at

55) (2005)

56)   Sivagnanam S and Deleu D. “Red Man Syndrome.” Crit Care. 2003; 7(2): 119–120. Online at

57)   Clardy J, Fischbach MA, Walsh CT. “New antibiotics from bacterial natural products.” Nature Biotechnology 24, 1541 - 1550 (2006).

58)   Singleton S. “Innovative Antibiotic Development: New Strategies, Targets, and Drugs.”   At enter “antibiotic” in the search window

59)   Donadio S, et. Al. “Antibiotic discovery in the twenty-first century: current trends and future perspectives.” J Antibiot (Tokyo). 2010 Aug;63(8):423-30. Abstract at

60) (2004)


62)   Gibson DG, et al. “Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome.” Science 2 July 2010: Vol. 329 no. 5987 pp. 52-56 . Online at

63)   Vergano, Dan. “Scientists create 1st bacteria strain from man-made DNA.” USA Today. Online at

64)   Unattributed feature. “Nothing to Sneeze At.” Technology Review. November 2001, p. 21. Also see

65)   Dimov IK, Basabe-Desmonts L, et al. “Stand-alone self-powered integrated microfluidic blood analysis system (SIMBAS) Lab Chip, 2011, Vol. 11, pp. 845-850.

66)   One such company is RANDOX. See

67) is not associated with Affymetrix, Inc. or its GeneChip® arrays.

68) (2011). Also see Sheikholvaezin A, et al. “Rational recombinant XMRV antigen preparation and bead coupling for multiplex serology in a suspension array.” Protein Expr Purif. 2011 Dec;80(2):176-84. Online at

69)   Unattributed 2008 article. “Fluorescent Nano-Barcodes Could Revolutionize Diagnostics.” Online at

70)   Stikeman, Alexandra. “Bar-Coding Life: Tiny tags to decode disease.” Technology Review, January/February 2002, p. 22. SurroMed, a CA-based company, is working with the Institute for Nanotechnology at Northwestern University to perform experimental studies.

71)   Webb, Carol. “Chip Shots.” IEEE Spectrum, October 2004.

72)   Voss, David. “Protein Chips.” Technology Review, May 2001.

73) (2003)

74)   Wood, Christina. “Implications: Medicine on a Microchip.” PC Magazine, August 2001.

75)   This research is being done at MicroChips in Cambridge, MA. Dr. Santini is the president of MicroChips.

76)   Ferrari, Mauro. “Biomedical Nanotechnologies And Space Medicine.” NASA presentation, 2006. Online at

77)   Even vitamin C cannot get past the gut lining if there is already sufficient ascorbate in the blood stream.

78)   Wimmer E, et al. “Synthetic viruses: a new opportunity to understand and prevent viral disease.” Nat Biotechnol. 2009 Dec;27(12):1163-72.

79)   Boyle, R. “Government Says Biotech Companies Can Be Their Own Safety Testers.” April 2011 at

80) (2007).


82) (2008).

83)   FDA information at (2011)

84) (2011)









93) and



96)   Combine Dr. Klenner's AA guidelines and Dr. Brown’s Appendix II protocol.

97)   Cunnane S, et al. “Brain fuel metabolism, aging, and Alzheimer’s disease.” Nutrition. Volume 27, Issue 1 , Pages 3-20, January 2011. Online at

98)   Atkins (1998, 2002, 2004)

99)   Another excellent book on the topic is Smith, MD (2002)


101)   Wu GD, et al. “Linking long-term dietary patterns with gut microbial enterotypes.” Science. 2011 Oct 7;334(6052):105-8. Online at

102)   Tilg H and Kaser A. “Gut microbiome, obesity, and metabolic dysfunction.”  J Clin Invest. 2011 June 1; 121(6): 2126–2132.

103)   Atkins Article: The Fat Fast. 2011)

104)   Dr. Joseph Brasco. “Low Grain and Carbohydrate Diets Treat Hypoglycemia, Heart Disease, Diabetes Cancer and Nearly ALL Chronic Illness.” Online at

105)   Malik, VS, et al. “Sugar-Sweetened Beverages, Obesity, Type 2 Diabetes Mellitus, and Cardiovascular Disease Risk.” Circulation. 2010; 121: 1356-1364 Online at

106)   Johnson RK, et al, for the American Heart Association Nutrition Committee of the Council on Nutrition, Physical Activity and Metabolism and the Council on Epidemiology and Prevention. “Dietary sugars intake and cardiovascular health: a scientific statement from the American Heart Association.” Circulation. 2009; 120: 1011–1020. Online at

107)   Dhingra R, et al. “Soft drink consumption and risk of developing cardiometabolic risk factors and the metabolic syndrome in middle-aged adults in the community.” Circulation. 2007; 116: 480–488. Online at

108)   Nettleton JA, et al. “Diet soda intake and risk of incident metabolic syndrome and type 2 diabetes in the Multi-Ethnic Study of Atherosclerosis (MESA).” Diabetes Care. 2009; 32: 688–694. Online at

109)   Krikorian R, et al. “Dietary ketosis enhances memory in mild cognitive impairment.” Neurobiology of Aging, Volume 33, Issue 2.

110)   Flegal KM, et al. “Prevalence and trends in obesity among US adults, 1999-2008.” JAMA. 2010 Jan 20;303(3):235-41. Online at

111)   Wang, Y, et al. “Will All Americans Become Overweight or Obese? Estimating the Progression and Cost of the US Obesity Epidemic.” Obesity (2008) 16 10, 2323–2330. Online at

112)   National Institute of Diabetes and Digestive and Kidney Diseases, 2008.

113)   Society for Neuroscience. “Diabetes, the Brain, and Cognition.” (2008) Online at

114) (2010). Also Newport (2011). Dr. Newport’s website is

115)   Lieberman S, Enig MG, and Preuss, HG. “A Review of Monolaurin and Lauric Acid: Natural Virucidal and Bactericidal Agents.” Alternative and Complementary Therapies. December 2006, 12(6): 310-314

116)   Their very comprehensive and helpful website is


118)   Henderson ST. “Ketone bodies as a therapeutic for Alzheimer's disease.” Neurotherapeutics. 2008 Jul;5(3):470-80.Online at

119)   Unattributed article. “Vitamins, Omega-3s May Keep Brain From Shrinking: Study.” Online at (2011)



122)   Pastorino L, et al. “The prolyl isomerase Pin1 regulates amyloid precursor protein processing and amyloid-beta production.” Nature. 2006 Mar 23;440(7083):528-34. Online at 

123)   Lim J, et al. “Pin1 has opposite effects on wild-type and P301L tau stability and tauopathy.” J Clin Invest. 2008;118(5):1877–1889. Online at

124)   Peloponese JM, et al.  “Peptidylproline cis-trans-isomerase Pin1 interacts with human T-cell leukemia virus type 1 tax and modulates its activation of NF-kappaB.” J Virol. 2009 Apr;83(7):3238-48. Online at

125)   A comprehensive and informative website covering many illnesses, including cancer and Alzheimer’s, in Use the search window on the site to learn about integrative medicine options. Also see


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