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 www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0022572

3) Visit www.ama-assn.org 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) http://emedicine.medscape.com/genomics and also www.technologynetworks.com/Genomics

6) http://lupus.webmd.com/news/20091019/genetic-link-to-lupus

7) www.nih.gov/news/pr/sep2007/niams-06.htm

8) www.genome.gov/10001772. (2010)

9) www.ornl.gov/sci/techresources/Human_Genome/publicat/hgn/hgnarch.shtml (1995-2002)

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

11) www.biofilmcommunity.org/f4/healthy-flora-biofilms-chronic-gastrointestinal-dysbiosis-11/

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)

14) www.mercola.com/nutritionplan/index.htm

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 http://www.allergyresearchgroup.com/August-2010-Focus-Vitamin-A-sp-107.html

16) http://www.drrachelwest.com/treatments/high-dose-vitamin-a-therapy/ (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) http://lpi.oregonstate.edu/infocenter/vitamins/vitaminA/ (2007)

20) www.coconutresearchcenter.org/article red palm oil.htm (2010)

21) Veracity, Dani. “How iodine accelerates weight loss by supporting the thyroid gland.” Online at http://www.naturalnews.com/008902.html (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 www.sciencemag.org/content/296/5566/301/suppl/DC1

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 www.cell.com/immunity/abstract/S1074-7613(11)00037-9

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 www.RA-Infection-Connection.com/CancerMicrobesTable.htm

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 http://www.ntfactor.com/clinical-trials/

33) www.immed.org/illness/fatigue_illness_research.html 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 http://www.canlyme.com/patsymptoms.html

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 http://www.personal.psu.edu/faculty/j/e/jel5/biofilms/primer.html and http://www.biofilmcommunity.org/ and http://home.swipnet.se/isop/biofilms.htm and http://www.wellnessresources.com/tag/biofilms and overview at http://bacteriality.com/2008/05/26/biofilm/

38) EDSTROM. Biofilm: Understanding and Controlling Growth. White paper at www.edstrom.com/documents (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 www.erc.montana.edu.

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 http://www.springerlink.com/content/l76jh3kh552042x2/

42) See www.erc.montana.edu 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 http://www.ncbi.nlm.nih.gov/pubmed/21166710. 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 www.ncbi.nlm.nih.gov/pubmed/17948128

44) Dr. Art Ayers. “Biofilms as Human Gut Mycorrhizals.” http://coolinginflammation.blogspot.com/2009/11/biofilms-as-human-gut-mycorrhizals.html

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 http://carcin.oxfordjournals.org/content/27/9/1729.full

46) http://www.atcc.org/CulturesandProducts/Microbiology/BacteriaandPhages/tabid/176/Default.aspx

47) http://www.stanford.edu/~amatin/MatinLabHomePage/Biofilm.htm

48) http://www.medicalnewstoday.com/articles/184972.php (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 www.biofilmcommunity.org/f6/dr-scot-dowd-pathogenius-102/

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 www.biomedcentral.com/1471-2180/2/7/

52) http://www.columbia.edu/itc/hs/medical/pathophys/id/2006/PeriodontalDisease.pdf

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 http://onlinelibrary.wiley.com/doi/10.1034/j.1600-0757.2002.280102.x/full

55) http://genome.cshlp.org/content/15/6/820.full.pdf (2005)

56) Sivagnanam S and Deleu D. “Red Man Syndrome.” Crit Care. 2003; 7(2): 119–120. Online at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC270616/

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 http://pharmacy.unc.edu 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 www.ncbi.nlm.nih.gov/pubmed/20551985

60) www.nature.com/nature/journal/v428/n6978/full/nature02340.html (2004)

61) www.ncbi.nlm.nih.gov/pmc/articles/PMC1635315/

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 www.sciencemag.org/content/329/5987/52.full.

63) Vergano, Dan. “Scientists create 1st bacteria strain from man-made DNA.” USA Today. Online at www.usatoday.com/tech/science/discoveries/2010-05-21-genome21_ST_N.htm

64) Unattributed feature. “Nothing to Sneeze At.” Technology Review. November 2001, p. 21. Also see www.ornl.gov/sci/biosensors/

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 www.randox.com.

67) www.Gene-Chips.com is not associated with Affymetrix, Inc. or its GeneChip® arrays.

68) www.apbiocode.com/technology.htm (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 http://www.ncbi.nlm.nih.gov/pubmed/21871964

69) Unattributed 2008 article. “Fluorescent Nano-Barcodes Could Revolutionize Diagnostics.” Online at www.aibn.uq.edu.au/index.html?page=83259&pid=29811

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) www.nanotech-now.com/news.cgi?story_id=02063 (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 www.dsls.usra.edu/20060328.pdf.

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 www.popsci.com/technology

80) http://www.msnbc.msn.com/id/19230748/ns/health-health_care/t/bogus-ingredients-put-consumers-health-risk/#.TuJyGVuyVPE (2007).

81) http://articles.latimes.com/2011/jun/26/world/la-fg-china-food-20110627.

82) http://health.usnews.com/usnews/health/healthday/080115/us-food-safety-the-import-alarm-keeps-sounding.htm (2008).

83) FDA information at http://www.foodsafetynews.com/2011/02/fsma-import-rules-may-foster-global-food-safety/ (2011)

84) http://www.foodsafetynews.com/2011/11/tests-show-most-store-honey-isnt-honey/ (2011)

85) http://www.ra-infection-connection.com/NutritionURLs.htm

86) http://www.ra-infection-connection.com/PaulingAngina.htm

87) http://herpes-coldsores.com/lysine-safety.htm

88) http://www.elmhurst.edu/~chm/vchembook/561aminostructure.html

89) http://www.bio.davidson.edu/courses/genomics/jmol/aatable.html

90) http://www.townsendletter.com/Klenner/KlennerProtocol_forMS.pdf

91) www.whale.to/vaccine/megson.pdf

92) http://www.ra-infection-connection.com/KalokerinosAA-VaccinesRefs.htm

93) http://www.crnusa.org/about_recs3.html and http://www.crnusa.org/about_recs2.html

94) http://www.ra-infection-connection.com/coq10andstatins.htm

95) http://www.ra-infection-connection.com/LecithinGutBacteria.htm

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 http://www.nutritionjrnl.com/article/S0899-9007%2810%2900280-7/abstract

98) Atkins (1998, 2002, 2004)

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

100) http://www.ra-infection-connection.com/CaseHistories.htm

101) Wu GD, et al. “Linking long-term dietary patterns with gut microbial enterotypes.” Science. 2011 Oct 7;334(6052):105-8. Online at http://www.ncbi.nlm.nih.gov/pubmed/21885731

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. http://www.low-carb.com/atarfatfa.html 2011)

104) Dr. Joseph Brasco. “Low Grain and Carbohydrate Diets Treat Hypoglycemia, Heart Disease, Diabetes Cancer and Nearly ALL Chronic Illness.” Online at http://www.mercola.com/article/carbohydrates/scientific_evidence_low_grains.htm

105) Malik, VS, et al. “Sugar-Sweetened Beverages, Obesity, Type 2 Diabetes Mellitus, and Cardiovascular Disease Risk.” Circulation. 2010; 121: 1356-1364 Online at http://circ.ahajournals.org/content/121/11/1356.long

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 http://circ.ahajournals.org/content/120/11/1011

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 http://circ.ahajournals.org/content/116/5/480.full

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 http://care.diabetesjournals.org/content/32/4/688.full

109) Krikorian R, et al. “Dietary ketosis enhances memory in mild cognitive impairment.” Neurobiology of Aging, Volume 33, Issue 2. http://www.neurobiologyofaging.org/article/S0197-4580%2810%2900439-2/abstract

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 http://www.ncbi.nlm.nih.gov/pubmed/20071471

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 http://www.nature.com/oby/journal/v16/n10/abs/oby2008351a.html

112) National Institute of Diabetes and Digestive and Kidney Diseases, 2008. http://diabetes.niddk.nih.gov/DM/PUBS/statistics/

113) Society for Neuroscience. “Diabetes, the Brain, and Cognition.” (2008) Online at http://www.sfn.org/index.aspx?pagename=brainbriefings_diabetes

114) http://www.anh-usa.org/coconut-oil-and-alzheimer%E2%80%99s-disease/ (2010). Also Newport (2011). Dr. Newport’s website is http://www.coconutketones.com/

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 www.AlzheimersWeekly.com

117) http://alzheimersweekly.com/content/keto-dementia-diet

118) Henderson ST. “Ketone bodies as a therapeutic for Alzheimer's disease.” Neurotherapeutics. 2008 Jul;5(3):470-80.Online at http://www.ncbi.nlm.nih.gov/pubmed/18625458

119) Unattributed article. “Vitamins, Omega-3s May Keep Brain From Shrinking: Study.” Online at http://www.nlm.nih.gov/medlineplus/news/fullstory_120199.html (2011)

120) http://alzheimersweekly.com/content/saying-no-antipsychotics-seroquel-dementia

121) http://www.brenda-enzymes.org/php/result_flat.php4?ecno=5.2.1.8

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 http://www.ncbi.nlm.nih.gov/pubmed/16554819

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 http://www.jci.org/articles/view/34308

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 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655545/?tool=pubmed

125) A comprehensive and informative website covering many illnesses, including cancer and Alzheimer’s, in www.savvypatients.com. Use the search window on the site to learn about integrative medicine options. Also see http://www.ra-infection-connection.com/DiagnosisChecker.htm

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