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What do we know about the function of viruses in the microbiome?

Human ViromeThe human virome (representing human viral communities) presents greater technical challenges (1) for identification and enumeration compared to the microbiome.Technical difficulties with characterizing the human viromeWe identify bacteria in the human microbiome using conserved genomic sequences (16S rRNA). Lacking such conserved genomic regions, viral genomic sequences from human samples are compared to known virus reference sequence databases. Drawback is such databases don't include sequences from novel viruses (2) while the human virome likely harbors as-yet-undiscovered viruses and viral relics.Viruses have small genomes, and are proportionally fewer compared to bacteria. Thus, viral nucleic acids are proportionally minuscule in the total derived from human microbial communities. To detect them, we need to enrich viral nucleic acids before sequence analysis. In turn, enrichment methods could be unwittingly selective, bias against certain viruses, and lead to loss of low-abundance viruses (3).From 4The human virome constitutes viral communities all over the human body. They run the gamut from viral relics such as HERVs (Human Endogenous Retroviruses), retroviral genes internalized millions of years ago during evolution, to tissue-resident viruses such as CMV (Cytomegalovirus) in the respiratory tract. Contribution of these viral communities also runs the gamut from most essential such as HERV-W genes, necessary for placental development, to HERV-K, the most recent integrant, implicated in neurological diseases such as schizophrenia, cancers such as breast and prostate, and autoimmune diseases such as MS (multiple sclerosis), RA (rheumatoid arthritis) and SLE (systemic lupus erythematosus).Figure 1 from 5HERVs (Human Endogenous Retroviruses)Viral genetic material is either DNA or RNA. Retroviruses have RNA but use it to produce DNA, the reverse, 'retro', of the norm. When inserted into host DNA, this viral DNA replicates every time host DNA replicates. When retroviruses infect germline (eggs and sperm) cells, they acquire a vastly greater capacity to replicate. Now endogenous retroviruses (ERV), they are present not just in each and every cell of that host but also get passed on to each and every cell of the host's descendants.ERVs represent 8% of the human genome (6).How do we know we harbor such retroviral relics? By their striking structural genomic similarity consisting of gag, pro, pol and env genes flanked by two identical-at-integration non-coding long terminal repeats (LTRs), which contain the signal for transcription initiation and regulation.Over evolutionary time (~35 million years), ERVs accumulated mutations (insertions, deletions, substitutions) and/or epigenetic modifications (for e.g., DNA methylation) at the same rate as the host genome (7, 8, 9, 10), rendering them non-functional, i.e. unable to produce infectious viral particles.Recombinations between the two flanking LTRs removed the internal coding region leaving a single LTR and inactivating ERVs, which are 10–100 times more numerous than their full length counterparts (11), and many of these insertions are fixed in the host population.To date, no active ERVs have been discovered in humans. The human genome has ~100,000 ERV loci resulting from proliferations of ~50 independent invasions of the genome from free-living (exogenous) retroviruses (12, 13).Figure 2 from 14HERV classification is still a work-in-progress. Magiorkinis et al (15) classify HERV families as the typical, HERV-T; the old, HERV-L; the abundant, HERV-H; the indispensable, HERV-W; the last but not the least, HERV-K.HERV-K(HML2) or HK2, the most recent, is the only ERV lineage to still replicate in the human population within the last few million years.~1,000 HK2 loci in the human reference genome, apparently integrated over the last ~35 million years. Continuously replicating over this long period, most full-length integrated ERV loci (proviruses) converted to relics by recombination. Remainder acquired premature stop codons and/or frameshifts. All reference genome HK2 loci are therefore replication defective, and only 24 loci retain full-length open reading frames (ORFs) in at least one of their genes (16).RNA transcription and protein expression of HK2 and other ERVs are elevated in many cancers, some autoimmune/inflammatory diseases, and HIV infection, leading to a long and unresolved search for a causal role in disease (17, 18, 19). More recently, disease-associated elevation of HERV protein expression has driven research into their potential as immunotherapy targets for cancer and HIV treatment (20).HERV-W, the indispensable HERVs in the Placenta: Genes Syncytins 1 and 2The emergence of placentation during evolution is fundamental to human evolution.Indispensable for human fetus growth, the placenta is composed of multiple unique cell types called extravillous and villous trophoblasts. The latter differentiate into multinucleated cells called syncytiotrophoblasts, which secrete human chorionic gonadotropin (hCG) and human placental lactogen (hPL), products that help optimize mother-fetus nutrient and hormone exchange.Viral relics in the form of specific HERVs are essential for placental development (14, 21, 22).Viruses were long suspected present in placenta with virus-like particles observed in human placenta (23, 24, 25, 26). These observations faded from memory until the discovery of the Syncytin genes in the late 1990s.Two Env proteins, Syncytin-1 and Syncytin-2 proteins, encoded by two different ERV loci, i.e., ERVW-1 and ERVFRD-1, located on chromosome 7 and 6, respectively, are expressed in the placenta. Independently co-opted numerous times among placental mammals and expressed in the placenta, these genes play a crucial role in the formation of the syncytiotrophoblast, a key function that sustains the highly dynamic and metabolically demanding placenta (27, 28, 29, 30, 31, 32, 33, 34, 35).Figure 1 from 36.- Viral genes like these may actually have been central in the emergence of placental mammals from egg-laying animals (29, 37, 38, 39, 40).Box from 36.In vitro studies (41) and reduced expression in pre-eclampsia (42, 43, 44, 45, 46, 47, 48, 49) suggest these retroviral-origin genes are important in human placentation. Pre-eclampsia, 'toxemia of pregnancy', includes hypertension, liver and kidney toxicity, and if untreated, can lead to eclampsia, i.e. seizures, threatening the life of mother and child. These multiple, independent studies thus suggest that human placental syncytin expression is crucial for normal placental function and ensuing normal pregnancy.Mouse syncytin gene knockouts provide more definitive proof. Syncytin-1 knockout mouse: growth retardation, altered placental strcuture, death in utero (50). Syncytin-2 knockout mouse: impaired syncytiotrophoblasts (51).Serving a similar purpose in placentation of eutherian mammals, syncytin genes are thus a most extreme and powerful example of convergent evolution, having evolved independently multiple times through co-option of HERV genes.HERVs in the brain: No definitive proof of disease causation. Lot of correlative data for neurological diseases,Table 1 from 52.especially for schizophrenia.Tables 1 and 2 from 53HERVs and cancerHow to be sure something causes cancer? Likely causes are so numerous ranging from genetic predisposition to numerous environmental factors that pinning one or few down as causative agents is akin to the proverbial needle in a haystack. In 1965 Austin Bradford Hill proposed the famous Hill's criteria (54), essential in helping ascribe causality, as in the link between smoking and lung cancer. How does that pan out with HERVs (55, 56, 57)?Consistency of association: HERVs consistently expressed in many tumors (breast, ovarian, lymphoma, melanoma, sarcoma, bladder, prostate).Strength of association: HERVs rarely expressed in normal tissues.Temporal association: Environmental factors as in exogenous such as chemicals, UV radiation, smoking, viruses, and endogenous as in hormones and cytokines help drive HERV expression.Biological plausibility: no clear evidence yet.Experimental evidence: no clear evidence yet in humans (some mouse model data exists).Clearly work-in-progress.HERV-Breast Cancer link: 58, 59; HERV-Melanoma link: 60; HERV-prostate cancer link: 61.HERVs and autoimmunity (62, 63): MS (multiple sclerosis; 64, 65), RA (rheumatoid arthritis: 66, 67), SLE (systemic lupus erythematosus: 68), Sjogren's syndrome, Graves Disease.Association data; no causal data yet.Certain HERVs and herpes viruses associated with MS.Circulating anti-HERV antibodies present in >50% of SLE in some studies.Those with anti-HERV antibodies more likely to have active clinical SLE.Location-wise identity of Viruses in Human bodyHuman StoolStable over time (69), unsurprisingly healthy gut virome is influenced by diet (70).Abundance of food-related (plant) viruses (71).Eneteropathogenic viruses (72) found in both healthy and in those with GI tract illnesses (73).Novel bacteriophages encode genes for antibiotic resistance and bacterial metabolic pathways (69, 70, 74). More diverse in adults, much less so in a 1-week old infant stool sample (75). Clearly, we dynamically acquire a gut bacteriophage community over time.Novel viruses. Viruses from the new genus Gyrovirus in the Circoviridae family (76) are found in both chicken meat and human samples. Open questions: Do they replicate in humans, i.e. capable of cross-species transmission, or are they harmless?Diarrhea was associated with novel viruses such as astrovirus (77), cosavirus and bocavirus (78).Human SkinPersistent colonization by papillloma, polyoma, and circoviruses(79, 80). Innocuous for the most part. Exception is Merkel cell polyomavirus associated with severe skin carcinoma (81).Human circulatory systemAnelloviridae are ubiquitous in human populations (82, 83).An intriguing heart and lung transplant study (84) tracked circulating plasma virome months post-transplant, and found circulating virome changed with post-transplant treatment. Low dose of anti-viral (valganciclovir) and immunosuppressant (tacrolimus): Herpesvirales and Caudovirales dominate; high dose, Anelloviridae dominate.Graphical Abstract from 84.LiverFlavivirus GBVC (or Hepatitis virus G), a surprising partner in human health, delays HIV disease progression (85).LungInfluenza (flu), Corona and other less well-characterized viruses (86).Bocavirus found in both healthy and in those with respiratory tract illnesses (87).Bacteriophages: Cystic Fibrosis (CF) patients have bacteriophages similar to each other while those in healthy adults are unique to each individual (88). In this study, spouse of one CF patient and an asthmatic control shared some viral genomes found in CF patients. This suggests environment strongly influences human viral genome since shared environment was associated with shared viruses between spouses, and chronic pathologies that are very different, as CF and asthma are, could still lead to establishment of similar viral communities, perhaps because they both cause impaired airway clearance of microbes.CMV (Cytomegalovirus)CMV, a herpes virus, infects majority of the world’s population.In the US, ~60% prevalence in >6 years of age and ~>90% in >80 years of age in the years 1988-1994 (89).It's usually, but not always, benign (90).Associated with immunosenescence (immune aging) in the elderly (91).CMV-schizophrenia link: In a study of >1000 subjects, 15% carried a particular benign variant of a gene involved in the stabilization of neuronal connections and in synaptic plasticity, essential to learning and memory. Carriers of this gene variant had fivefold increased probability of developing schizophrenia following maternal CMV infection (92).CMV-Flu link: CMV could help body fight off flu: CMV-seropositive young adults make stronger anti-flu antibody responses (93). Seropositive means they were likely exposed to CMV and generated an anti-CMV immune response, as revealed by presence of circulating anti-CMV antibodies. Relevance of this type of finding? The well-adjusted human super-organism is one where their mammalian and microbial components work in harmony to keep pathogens at bay.FluFlu-HERV link: The influenza virus may re-activate HERVs that are associated with neuroinflammation, and white matter and myelin degeneration (94).Such HERVs have been implicated in Bipolar disorder and Schizophrenia (95, 96).Virome BibliographyCanuti, M. "About Viruses, the Importance of Being Earnest." Austin Virol and Retrovirology 1.1 (2014): 2. http://austinpublishinggroup.com/virology/fulltext/avrv-v1-id1002.pdf.Woolhouse ME, Howey R, Gaunt E, Reilly L, Chase-Topping M, Savill N. Temporal trends in the discovery of human viruses. Proc Biol Sci 2008;275:2111–5.Thurber RV, Haynes M, Breitbart M, Wegley L, Rohwer F. Laboratory procedures to generate viral metagenomes. Nat Protoc 2009;4:470–83.Delwart, Eric. "A roadmap to the human virome." PLoS pathogens 9.2 (2013): e1003146. A Roadmap to the Human ViromeWylie, Kristine M., George M. Weinstock, and Gregory A. Storch. "Emerging view of the human virome." Translational Research 160.4 (2012): 283-290. Page on els-cdn.comLander ES, Linton LM, Birren B, Nusbaum C, Zody MC, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409: 860–921.Blikstad V, Benachenhou F, Sperber GO, Blomberg J (2008) Evolution of human endogenous retroviral sequences: a conceptual account. Cellular and Molecular Life Sciences 65: 3348–3365.Dewannieux, M.; Heidmann, T. Endogenous retroviruses: Acquisition, amplification and taming of genome invaders. Curr. Opin. Virol. 2013, 3, 646–656.Stoye, J.P. Studies of endogenous retroviruses reveal a continuing evolutionary saga. Nat. Rev. Microbiol. 2012, 10, 395–406.Magiorkinis, G.; Gifford, R.J.; Katzourakis, A.; de Ranter, J.; Belshaw, R. Env-less endogenous retroviruses are genomic superspreaders. Proc. Natl. Acad. Sci. USA 2012, 109, 7385–7390.Stoye JP (2001) Endogenous retroviruses: still active after all these years? Curr Biol 11: R914–916.Belshaw R, Pereira V, Katzourakis A, Talbot G, Pa?es J, Burt A, Tristem M. 2004. Long-term reinfection of the human genome by endogenous retroviruses. Proc. Natl. Acad. Sci. U. S. A. 101:4894 – 4899.Mayer J, Blomberg J, Seal RL. 2011. A revised nomenclature for transcribed human endogenous retroviral loci. Mobile DNA 2:7.Young, George R., Jonathan P. Stoye, and George Kassiotis. "Are human endogenous retroviruses pathogenic? An approach to testing the hypothesis." Bioessays 35.9 (2013): 794-803. Are human endogenous retroviruses pathogenic? An approach to testing the hypothesisMagiorkinis, Gkikas, Robert Belshaw, and Aris Katzourakis. "‘There and back again’: revisiting the pathophysiological roles of human endogenous retroviruses in the post-genomic era." Philosophical Transactions of the Royal Society B: Biological Sciences 368.1626 (2013): 20120504. revisiting the pathophysiological roles of human endogenous retroviruses in the post-genomic eraSubramanian RP, Wildschutte JH, Russo C, Coffin JM. 2011. Identification, characterization, and comparative genomic distribution of the HERV-K (HML-2) group of human endogenous retroviruses. Retrovirology 8:90.Voisset C, Weiss RA, Griffiths DJ. 2008. Human RNA “rumor” viruses: the search for novel human retroviruses in chronic disease. Microbiol. Mol. Biol. Rev. 72:157–196.Young GR, Stoye JP, Kassiotis G. 2013. Are human endogenous retro- viruses pathogenic? An approach to testing the hypothesis. Bioessays 35: 794 – 803.Jern P, Coffin JM. 2008. Effects of retroviruses on host genome function. Annu. Rev. Genet. 42:709 –732.Marchi, Emanuele, et al. "Unfixed endogenous retroviral insertions in the human population." Journal of virology 88.17 (2014): 9529-9537. Unfixed Endogenous Retroviral Insertions in the Human PopulationMangeney M, Renard M, Schlecht-Louf G, Bouallaga I, et al. 2007. Placental syncytins: genetic disjunction between the fusogenic and immunosuppressive activity of retroviral envelope proteins. Proc Natl Acad Sci USA 104: 20534–9.Dupressoir A, Lavialle C, Heidmann T. 2012. From ancestral infectious retroviruses to bona fide cellular genes: role of the captured syncytins in placentation. Placenta 33: 663–71.Kalter SS, Helmke RJ, Heberling RL, Panigel M, et al. 1973. Brief communication: C-type particles in normal human placentas. J Natl Cancer Inst 50: 1081–4.Vernon ML, McMahon JM, Hackett JJ. 1974. Additional evidence of type-C particles in human placentas. J Natl Cancer Inst 52: 987–9.Kalter SS, Heberling RL, Helmke RJ, Panigel M, Smith GC, Kraemer DC, Hellman A, Fowler AK, Strickland JE (1975) A comparative study on the presence of C-type viral particles in placentas from primates and other animals. Bibl Haematol 1975(40):391–40.Dirksen ER, Levy JA. 1977. Virus-like particles in placentas from normal individuals and patients with systemic lupus erythematosus. J Natl Cancer Inst 59: 1187–92.Blond, J.L.; Beseme, F.; Duret, L.; Bouton, O.; Bedin, F.; Perron, H.; Mandrand, B.; Mallet, F. Molecular characterization and placental expression of herv-w, a new human endogenous retrovirus family. J. Virol. 1999, 73, 1175–1185.Blond, J.L.; Lavillette, D.; Cheynet, V.; Bouton, O.; Oriol, G.; Chapel-Fernandes, S.; Mandrand, B.; Mallet, F.; Cosset, F.L. An envelope glycoprotein of the human endogenous retrovirus herv-w is expressed in the human placenta and fuses cells expressing the type d mammalian retrovirus receptor. J. Virol. 2000, 74, 3321–3329.Mi, S.; Lee, X.; Li, X.; Veldman, G.M.; Finnerty, H.; Racie, L.; LaVallie, E.; Tang, X.Y.; Edouard, P.; Howes, S.; et al. Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis. Nature 2000, 403, 785–789.Frendo, J.L.; Olivier, D.; Cheynet, V.; Blond, J.L.; Bouton, O.; Vidaud, M.; Rabreau, M.; Evain-Brion, D.; Mallet, F. Direct involvement of herv-w env glycoprotein in human trophoblast cell fusion and differentiation. Mol. Cell. Biol. 2003, 23, 3566–3574.Blaise, S.; de Parseval, N.; Benit, L.; Heidmann, T. Genomewide screening for fusogenic human endogenous retrovirus envelopes identifies syncytin 2, a gene conserved on primate evolution. Proc. Natl. Acad. Sci. USA 2003, 100, 13013–13018.Malassine, A.; Dupressoir A, Marceau G, Vernochet C, Benit L, Kanellopoulos C, Sapin V, Heidmann T. 2005 Syncytin-A and syncytin-B, two fusogenic placenta- specific murine envelope genes of retroviral origin conserved in Muridae. Proc. Natl Acad. Sci. USA 102, 725 – 730.Handschuh, K.; Tsatsaris, V.; Gerbaud, P.; Cheynet, V.; Oriol, G.; Mallet, F.; Evain-Brion, D. Expression of herv-w env glycoprotein (syncytin) in the extravillous trophoblast of first trimester human placenta. Placenta 2005, 26, 556–562.Muir, A.; Lever, A.M.; Moffett, A. Human endogenous retrovirus-w envelope (syncytin) is expressed in both villous and extravillous trophoblast populations. J. Gen. Virol. 2006, 87, 2067–2071.Hayward, M.D.; Potgens, A.J.; Drewlo, S.; Kaufmann, P.; Rasko, J.E. Distribution of human endogenous retrovirus type w receptor in normal human villous placenta. Pathology 2007, 39, 406–412.Cornelis, Guillaume, et al. "Retroviral envelope gene captures and syncytin exaptation for placentation in marsupials." Proceedings of the National Academy of Sciences (2015): 201417000.Heidmann O, Vernochet C, Dupressoir A, Heidmann T. 2009 Identification of an endogenous retroviral envelope gene with fusogenic activity and placenta- specific expression in the rabbit: a new “syncytin” in a third order of mammals. Retrovirology 6, 107.Cornelis G, Heidmann O, Bernard-Stoecklin S, Reynaud K, Veron G, Mulot B, Dupressoir A, Heidmann T. 2012 Ancestral capture of syncytin- Car1, a fusogenic endogenous retroviral envelope gene involved in placentation and conserved in Carnivora. Proc. Natl Acad. Sci. USA 109, E432 – E441.Lavialle, C., Cornelis, G., Dupressoir, A., Esnault, C., Heidmann, O., Vernochet, C., & Heidmann, T. (2013). Paleovirology of 'syncytins', retroviral env genes exapted for a role in placentation. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 368(1626), 1471-2970.Lokossou, Adjimon Gatien, Caroline Toudic, and Benoit Barbeau. "Implication of Human Endogenous Retrovirus Envelope Proteins in Placental Functions." Viruses 6.11 (2014): 4609-4627. Implication of Human Endogenous Retrovirus Envelope Proteins in Placental FunctionsVargas, Amandine, et al. "Syncytin-2 plays an important role in the fusion of human trophoblast cells." Journal of molecular biology 392.2 (2009): 301-318. Syncytin-2 Plays an Important Role in the Fusion of Human Trophoblast CellsLee, X., Keith Jr., J.C., Stumm, N., Moutsatsos, I., McCoy, J.M., Crum, C.P., Genest, D., Chin, D., Ehrenfels, C., Pijnenborg, R., van Assche, F.A., Mi, S., 2001. Downregulation of placental syncytin expression and abnormal protein localization in pre- eclampsia. Placenta 22, 808–812.Keith Jr., J.C., Pijnenborg, R., Van Assche, F.A., 2002. Placental syncytin expression in normal and preeclamptic pregnancies. Am. J. Obstet. Gynecol. 187, 1122–1123 author reply 1123–1124.Knerr, I., Beinder, E., Rascher, W., 2002. Syncytin, a novel human endogenous retroviral gene in human placenta: evidence for its dysregulation in preeclampsia and HELLP syndrome. Am. J. Obstet. Gynecol. 186, 210–213.Chen, C.P., Wang, K.G., Chen, C.Y., Yu, C., Chuang, H.C., Chen, H., 2006. Altered placental syncytin and its receptor ASCT2 expression in placental development and pre- eclampsia. BJOG 113, 152–158.Chen, C.P., Chen, L.F., Yang, S.R., Chen, C.Y., Ko, C.C., Chang, G.D., Chen, H., 2008. Functional characterization of the human placental fusogenic membrane protein syncytin 2. Biol. Reprod. 79, 815–823.Kudaka, W., Oda, T., Jinno, Y., Yoshimi, N., Aoki, Y., 2008. Cellular localization of placenta-specific human endogenous retrovirus (HERV) transcripts and their possible implication in pregnancy-induced hypertension. Placenta 29, 282–289.Langbein, M., Strick, R., Strissel, P.L., Vogt, N., Parsch, H., Beckmann, M.W., Schild, R.L., 2008. Impaired cytotrophoblast cell–cell fusion is associated with reduced Syncytin and increased apoptosis in patients with placental dysfunction. Mol. Reprod. Dev. 75, 175–183.Vargas, A., Toufaily, C., Lebellego, F., Rassart, E., Lafond, J., Barbeau, B., 2011. Reduced expression of both Syncytin 1 and Syncytin 2 correlates with severity of pre-eclampsia. Reprod. Sci. 18, 1085–1091.Dupressoir, Anne, et al. "Syncytin-A knockout mice demonstrate the critical role in placentation of a fusogenic, endogenous retrovirus-derived, envelope gene." Proceedings of the National Academy of Sciences 106.29 (2009): 12127-12132. http://www.pnas.org/content/106/29/12127.full.pdf?sid=91dd4002-9a0e-4639-b244-3efa6df52d5fDupressoir A, Vernochet C, Harper F, Guegan J, Dessen P, Pierron G, Heidmann T (2011) A pair of co-opted retroviral envelope syncytin genes is required for formation of the two-layered murine placental syncytiotrophoblast. Proc Natl Acad Sci USA 108:E1164–E1173.Manghera, Mamneet, Jennifer Ferguson, and Renée Douville. "Endogenous retrovirus-K and nervous system diseases." Current neurology and neuroscience reports 14.10 (2014): 1-10.Raúl, Alelú-Paz, and Iturrieta-Zuazo Ignacio. "Human endogenous retroviruses: Their possible role in the molecular etiology of the schizophrenia." Open Journal of Genetics 2012 (2012). Their possible role in the molecular etiology of the schizophreniaHill, Austin Bradford. "The environment and disease: association or causation?." Proceedings of the Royal Society of Medicine 58.5 (1965): 295. The Environment and Disease: Association or Causation?Cegolon, Luca, et al. "Human endogenous retroviruses and cancer prevention: evidence and prospects." BMC cancer 13.1 (2013): 4. Page on biomedcentral.com.Downey, Ronan F., et al. "Human endogenous retrovirus K and cancer: innocent bystander or tumorigenic accomplice?." International Journal of Cancer (2014). Page on wiley.comKassiotis, George. "Endogenous retroviruses and the development of cancer." The Journal of Immunology 192.4 (2014): 1343-1349. Endogenous Retroviruses and the Development of CancerSalmons, Brian, James S. Lawson, and Walter H. Günzburg. "Recent developments linking retroviruses to human breast cancer: infectious agent, enemy within or both?." Journal of General Virology Page on 95.pt 12 (2014): 2589-2593.Fimereli, Danai, et al. "No significant viral transcription detected in whole breast cancer transcriptomes." BMC cancer 15.1 (2015): 147. Page on biomedcentral.comRincon, Liliana, et al. "K-type human endogenous retroviral elements in human melanoma." Advances in Genomics & Genetics 4 (2014). Page on dovepress.comWallace, Tiffany A., et al. "Elevated HERV-K mRNA expression in PBMC is associated with a prostate cancer diagnosis particularly in older men and smokers." Carcinogenesis (2014): bgu114.Balada, Eva, Miquel Vilardell-Tarrés, and Josep Ordi-Ros. "Implication of human endogenous retroviruses in the development of autoimmune diseases." International reviews of immunology 29.4 (2010): 351-370.Fierabracci, A. "Unravelling the role of infectious agents in the pathogenesis of human autoimmunity: the hypothesis of the retroviral involvement revisited." Current molecular medicine 9.9 (2009): 1024-1033. Page on researchgate.netKrone, Bernd, and John M. Grange. "Paradigms in multiple sclerosis: time for a change, time for a unifying concept." Inflammopharmacology 19.4 (2011): 187-195. Paradigms in multiple sclerosis: time for a change, time for a unifying concept.Antony, Joseph M., et al. "Human endogenous retroviruses and multiple sclerosis: innocent bystanders or disease determinants?." Biochimica et Biophysica Acta (BBA)-Molecular Basis of Disease 1812.2 (2011): 162-176. Innocent bystanders or disease determinants?Tugnet, Nicola, et al. "Human endogenous retroviruses (HERVs) and autoimmune rheumatic disease: Is there a link?." The open rheumatology journal 7 (2013): 13. Human Endogenous Retroviruses (HERVs) and Autoimmune Rheumatic Disease: Is There a Link?.Nelson, Paul N., et al. "Rheumatoid Arthritis is Associated with IgG Antibodies to Human Endogenous Retrovirus Gag Matrix: A Potential Pathogenic Mechanism of Disease?." The Journal of rheumatology 41.10 (2014): 1952-1960.Nelson, P., et al. "Viruses as potential pathogenic agents in systemic lupus erythematosus." Lupus 23.6 (2014): 596-605. Wu, Zhouwei, et al. "DNA methylation modulates HERV-E expression in CD4+ T cells from systemic lupus erythematosus patients." Journal of dermatological science (2015).Reyes, A., Haynes, M., Hanson, N., Angly, F.E., Heath, A.C., Rohwer, F., and Gordon, J.I. (2010). Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 466, 334–338.Minot, S., Sinha, R., Chen, J., Li, H., Keilbaugh, S.A., Wu, G.D., Lewis, J.D., and Bushman, F.D. (2011). The human gut virome: inter-individual variation and dynamic response to diet. Genome Res. 21, 1616–1625.Zhang T, Breitbart M, Lee WH, Run JQ, Wei CL, Soh SW, et al. RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS Biol. 2006; 4: e3. RNA viral community in human feces: prevalence of plant pathogenic viruses.Lagier JC, Million M, Hugon P, Armougom F, Raoult D. Human gut microbiota: repertoire and variations. Front Cell Infect Microbiol. 2012; 2: 136).Witsø E, Palacios G, Cinek O, Stene LC, Grinde B, Janowitz D, et al. 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If I lived with a man as his partner for over 30 years, what right do I have to his house when he dies?

If you no longer live with him, I am not sure what your rights are. If he dies while living with him states vary according to their laws, but if he died and did not create a will naming you, you really need a lawyer to navigate this. These states may offer some hope. Historically, marriage has carried with it religious, cultural, and legal purposes.States that recognize Common Law Marriage?These states have common law marriage in their statutes, while others do so through court decisions. The common law states are:Colorado—(Colo. Rev. Stat. Ann. §14-2-109.5.)Iowa—(Iowa Code Ann. §§252A.3 and 1A.)Kansas—(Kan. Stat. §§23-2502 and 23-2714.)Montana—(Mont. Code Ann. §40-1-403.)New Hampshire—(N.H. Rev. Stat. Ann. §457:39.)OklahomaRhode IslandTexas —(Tex. Fam. Code §2.401.)Utah—(Utah Code Ann. §30-1-4.5.)Note that the District of Columbia, although not a state, also permits common law marriages.Regarding the above list, there are a few things you should be aware of. In New Hampshire, the way the law is written, the state only recognizes common law marriage for estate purposes. In other words, the marriage doesn’t legally exist until one of the couple dies, which then allows the surviving spouse to claim any inheritance.In Oklahoma, the state statutes and state case law appear to clash as to the legality of common law marriage. The statutes, on their face, would seem to permit only formalized marriages. But despite the statutes’ wording, the courts have upheld common law marriages. At this point, how this conflict resolves itself is up in the air.In Rhode Island, the courts have made it very clear that they believe common law marriage is an “outmoded doctrine”, and they have practically begged the legislature to abolish it. (Luis v. Gaugler, 185 A.3d 497 (2018).) So that situation is one to keep an eye on.States Recognizing Prior Common Law MarriagesSome states that formerly allowed common law marriages if they validly existed prior to the prohibition date.These states are:Alabama (if the marriage was before January 1, 2017)—(Ala. Code § 30-1-20 (2018).)Florida (if the marriage was before January 1, 1968)—(Fla. Stat. Ann. § 741.21.)Georgia (if the marriage was before January 1, 1997)—(Ga. Code Ann. § 19-3-1.1.)Idaho (if the marriage was before January 1, 1996)—(Idaho Code Ann. - Title 32 - Chapter 02 §32-201.)Indiana (if the marriage was before January 1, 1958)—(Ind. Code Ann. § 31-11-8-5.)Ohio (if the marriage was before October 10, 1991)—(Ohio Rev. Code Ann.§ 3105.12.)Pennsylvania (if the marriage was before January 1, 2005)—(23 Pa. Cons. Stat. § 1103.)South Carolina (if the marriage was before July 24, 2019)—(Stone v. Thompson, 426 S.C. 291 (2019).)

Does everything that exists have a cause? Is there anything that exists (even in regard to quantum mechanics) that doesn’t have a cause?

Causality is a cognitive thing, Bondi.The Heisenberg Uncertainty Principle, the most misunderstood thing in all of physics, refers ONLY TO WAVE FUNCTIONS PRIOR TO DETECTION. At the moment of detection, the HUP is rendered non-sequitur.see Bill Bray's answer to The double slit experiment proved that direct observation altered results. What would happen if the sensors recorded results but the results weren't accessible by humans? For example, what if a computer put an impossible password on the results?The result is that time exists in a state of superposition. This is a fact in QM with too many references to list. Nonetheless, here is a list, most are freely available:Note that time being in superposition is not ‘causality violation,’ it is a statement that makes it clear that the order of events is not fixed. This is best explained in the following papers:R. D. 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Philosophical Library: New York.6.Black, Max (1950-1951). “Achilles and the Tortoise,” Analysis 11, pp. 91-101.7.Cajori, Florian (1920). “The Purpose of Zeno’s Arguments on Motion,” Isis, vol. 3, no. 1, pp. 7-20.8.Cantor, Georg (1887). "Über die verschiedenen Ansichten in Bezug auf die actualunendlichen Zahlen." Bihang till Kongl. Svenska Vetenskaps-Akademien Handlingar , Bd. 11 (1886-7), article 19. P. A. Norstedt & Sôner: Stockholm.9.Chihara, Charles S. (1965). “On the Possibility of Completing an Infinite Process,” Philosophical Review 74, no. 1, p. 74-87.10.Copleston, Frederick, S.J. (1962). “The Dialectic of Zeno,” chapter 7 of A History of Philosophy, Volume I, Greece and Rome, Part I, Image Books: Garden City.11.Dainton, Barry. (2010). Time and Space, Second Edition, McGill-Queens University Press: Ithaca.12.Dauben, J. (1990). Georg Cantor, Princeton University Press: Princeton.13.De Boer, Jesse (1953). “A Critique of Continuity, Infinity, and Allied Concepts in the Natural Philosophy of Bergson and Russell,” in Return to Reason: Essays in Realistic Philosophy, John Wild, ed., Henry Regnery Company: Chicago, pp. 92-124.14.Diels, Hermann and W. Kranz (1951). Die Fragmente der Vorsokratiker, sixth ed., Weidmannsche Buchhandlung: Berlin.15.Dummett, Michael (2000). “Is Time a Continuum of Instants?,” Philosophy, 2000, Cambridge University Press: Cambridge, pp. 497-515.16.Earman J. and J. D. Norton (1996). “Infinite Pains: The Trouble with Supertasks,” in Paul Benacerraf: the Philosopher and His Critics, A. Morton and S. Stich (eds.), Blackwell: Cambridge, MA, pp. 231-261.17.Feferman, Solomon (1998). In the Light of Logic, Oxford University Press, New York.18.Freeman, Kathleen (1948). Ancilla to the Pre-Socratic Philosophers, Harvard University Press: Cambridge, MA. Reprinted in paperback in 1983.19.Grünbaum, Adolf (1967). Modern Science and Zeno’s Paradoxes, Wesleyan University Press: Middletown, Connecticut.20.Grünbaum, Adolf (1970). “Modern Science and Zeno’s Paradoxes of Motion,” in (Salmon, 1970), pp. 200-250.21.Hamilton, Edith and Huntington Cairns (1961). The Collected Dialogues of Plato Including the Letters, Princeton University Press: Princeton.22.Harrison, Craig (1996). “The Three Arrows of Zeno: Cantorian and Non-Cantorian Concepts of the Continuum and of Motion,” Synthese, Volume 107, Number 2, pp. 271-292.23.Heath, T. L. (1921). A History of Greek Mathematics, Vol. I, Clarendon Press: Oxford. Reprinted 1981.24.Hintikka, Jaakko, David Gruender and Evandro Agazzi. Theory Change, Ancient Axiomatics, and Galileo’s Methodology, D. Reidel Publishing Company, Dordrecht.25.Kirk, G. S., J. E. Raven, and M. Schofield, eds. (1983). 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