The Fox and the Rabbits—Environmental Variables and Population Genetics (1) Replication Problems in Association Studies and the Untapped Power of GWAS (2) Vitamin A Deficiency, Herpes Simplex Reactivation and Other Causes of Alzheimer's Disease

Table 3

Viral, bacterial, and fungal protein homology with beta-amyloid; beta-amyloid segments were compared with Borrelia Burgdorferi, C. Neoformans, C. Pneumoniae, H. Pylori, P. Gingivalis, and herpes viruses (HSV1, HHV6, and cytomegalovirus) proteomes by BLAST analysis. The B cell and T cell antigenicity indices are shown, and those above the server set threshold of 0.35 (B cell epitope) or 0.5 (T cell epitope) are highlighted in bold. The first column shows the amino acid sequence of beta-amyloid_1-42 and the alignments with pathogen proteins are shown. Spaces represent nonidentical amino acids and + signs amino acids with similar physicochemical properties. Only highly antigenic regions of pentapeptides or more were processed. The VGGVV sequence, antibodies to which label beta-amyloid in brain tissue, despite relatively low antigenicity, has already been reported to be identical to proteins expressed by 69 viruses including HSV-1, HSV-2, and HHV6 [230].

	B cell	T cell	Alignments
D	0.41	0.04	+AE HDSG+ C. Neoformans DAE F H+SG EV Borrelia burgdorferi DAEF H. Pylori DA FRH H. Pylori +AE RH HSV-1 D FR DS HHV-6 +AEFR P. Gingivalis DA EFRHD and +AEFR +SG C. Pneumoniae
A	0.35	0.78	AEFR D GY+V C. Neoformans AEF D S YE H. pylori AE+RH+ H. pylori AEF H+ Borrelia burgdorferi AEFR HD Cytomegalovirus AE R SG HSV-1 AE+ HD HHV-6 A+F H+S and AEFR P. Gingivalis AEF DSG C. Pneumoniae
E	0.62	0.02	EFRHD H. Pylori EF DSG HHV-6 EFR DS Borrelia Burgdorferi EF R DS YE C. Neoformans E R DSGY V P. Gingivalis EF SGYEV C. Pneumoniae
F	0.73	0.93	FRHDS C. Neoformans +RH SGY++ Borrelia burgdorferi F HD EV H. Pylori F H+SG H. Pylori FR SGY Cytomegalovirus +RHDS P. Gingivalis F H+SGY C. Pneumonia
R	0.85	0.05	R D GYEV C. Neoformans R SGYE H. pylori RHDS Y V H. pylori RH+ GY Borrelia burgdorferi RHDSG Cytomegalovirus RHD YE cytomegalovirus RH SG HSV-1 RHDS HHV-6 R+DS Y+ P. Gingivalis
H	0.57	0.14	HDSGY C. Neoformans HD G EV H. pylori +DSGY H. pylori H+SG Y+V Borrelia burgdorferi H+SG HSV-1 HDSG P. Gingivalis ++SGY+V C. Pneumoniae
D	0.69	0.03	DSGY+V C. Neoformans +SG+EV H. pylori DSGY HSV-1 DSG+EV P. Gingivalis DSGY V C. Pneumoniae
S	0.38	0.02	SGYEV P. Gingivalis SGYE H. pylori SGY++ C. Neoformans SG+EV C. Pneumoniae
G	0.63	0.04	GYEVH H. pylori GYE V KL+ Borrelia Burgdorferi GYE LV and GY++ + LV C. Neoformans GYEV P. Gingivalis GYEV and GY HH C. Pneumoniae
Y	0.56	0.96	YE HH and YE+ HQ and Y++H Q and YE HHQ H. pylori YEVH Cytomegalovirus YE+ KL Borrelia Burgdorferi YE + QK FC. Neoformans Y++H H+K P. Gingivalis Y+V +Q LV C. Pneumoniae
E	0.58	0.02	EV +QK H. pylori EV HQ L Cytomegalovirus EV +KL Borrelia Burgdorferi EV Q LV C. Neoformans EV KLV P. Gingivalis EV QKLV C. Pneumoniae
V	0.35	0.90	.+H QK H. pylori V HQ LV Cytomegalovirus VH QK+V HHV-6 VH KL Borrelia Burgdorferi +HH LV C. Neoformans VH + LV P. Gingivalis V HQKL C. Pneumoniae
H	−0.17	0.10	HHQK H. pylori and C. Pneumoniae HH KL Cytomegalovirus HH KL P. Gingivalis
H	−0.66	0.11	HQKL+ Borreli Burgdorferi HQKL C. Pneumoniae and HSV-1 +QKLV P. Gingivalis
Q	−1.03	0.03	QKLV C. Neoformans and P. Gingivalisand C. Pneumoniae
K	−1.47	0.93	KLVFF H. pylori: Cryptococcus neoformans Borrelia Burgdorferi Chlamydophila pneumoniae KLVF Human herpesvirus 1
L	−1.34	0.95	LVFF Human herpesvirus 5: Human herpesvirus 6
V	−1.20	0.68
F	−0.93	0.69
F	−0.98	0.74
A	−0.82	0.05
E	−0.31	0.05
D	0.23	0.11
V	0.81	0.88	VGSNK Borrelia burgdorferi Cryptococcus neoformans Porphyromonas gingivalis +GSNK Cytomegalovirus VGSN Helicobacter pylori Chlamydophila pneumoniae
G	1.24	0.03	GSNK Helicobacter Pylori Chlamydophila pneumoniae
S	1.22	0.03
N	0.90	0.03
K	0.36	0.30
G	0.30	0.10
A	−0.24	0.05
I	−0.58	0.07
I	−1.00	0.13
G	−1.14	0.03
L	−1.19	0.72
M	−1.23	0.13
V	−1.16	0.23	VGGVV 69 viruses/phages
G	−0.97	0.03
G	−1.02	0.03
V	−0.63	0.23
V	−0.45	0.33
I	−0.80	0.95
A	−1.06	0.83