Dahlquist:Evo-Ed Evolution of Lactase Persistence

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This page contains notes from the BioQUEST Curriculumm Consortium Summer Workshop 2015 project on the Evo-Ed Case: The Evolution of Lactase Persistence.

Other Case Studies

PowerPoint Summary

Annotated Bibliography

Reviews

  • Amiri, Mahdi, et al. (2015). The Diverse Forms of Lactose Intolerance and the Putative Linkage to Several Cancers. Nutrients, 7(9), 7209-7230. doi:10.3390/nu7095332 (Nutrients)
  • Beal, T., & Ervin, D. (2018). The Geography of Malnutrition. The Professional Geographer, 70(1), 47-59. doi: 10. 1080/00330124.2017.1310623 (Full text)
  • Blanchard, C. (2017). A history into genetic and epigenetic evolution of food tolerance. Current Opinion in Allergy and Clinical Immunology, 17(6), 460-464. doi: 10.1097/aci.0000000000000397 Ingenta])
    • Behind paywall
  • Bouwman, A., & Rühli, F. (2016). Archaeogenetics in evolutionary medicine. Journal of Molecular Medicine, 94(9), 971-977. doi:10.1007/s00109-016-1438-8 (Full text)
    • Gives brief history of emergence of LP
  • Cerny, V., Kulichova, I., Poloni, E. S., Nunes, J. M., Pereira, L., Mayor, A., & Sanchez-Mazas, A. (2018). Genetic history of the African Sahelian populations. Hla, 91(3), 153-166. doi: 10.1111/tan.13189 (Wiley)
    • Figure 2 shows allele frequencies of different SNPs associated with lactase persistence on map
  • Deng, Yanyong, et al. (2015). Lactose Intolerance in Adults: Biological Mechanism and Dietary Management. Nutrients, 7(9), 8020-8035. doi:10.3390/nu7095380 (Nutrients)
  • Fan, S., Hansen, M. E., Lo, Y., & Tishkoff, S. A. (2016). Going global by adapting local: A review of recent human adaptation. Science, 354(6308), 54-59. doi:10.1126/science.aaf5098 (PubMed Central)
  • Fassio, F., Facioni, M., & Guagnini, F. (2018). Lactose Maldigestion, Malabsorption, and Intolerance: A Comprehensive Review with a Focus on Current Management and Future Perspectives. Nutrients, 10. doi: 10.3390/nu10111599 (Nutrients)
  • Gerbault, Pascale. (2013). The onset of lactase persistence in Europe. Human heredity, 76(3-4), 154-161. doi:10.1159/000360136 (Human Heredity)
  • Goldman, A. S. (2019). Future Research in the Immune System of Human Milk. The Journal of Pediatrics, 206, 274-279. doi: 10.1016/j.jpeds.2018.11.024 (Full text)
  • Goodrich, J. K., Davenport, E. R., Clark, A. G., & Ley, R. E. (2017). The Relationship Between the Human Genome and Microbiome Comes into View. Annual Review of Genetics, 51, 413-433. doi: 10.1146/annurev-genet-110711-155532 (Full text)
  • Grand, R. J., Montgomery, R. K., Chitkara, D. K., & Hirschhorn, J. N. (2003). Changing genes; losing lactase. Gut, 52(5), 617-619. doi: 10.1136/gut.52.5.617 (Gut)
  • Hall, A. B., Tolonen, A. C., & Xavier, R. J. (2017). Human genetic variation and the gut microbiome in disease. Nature Reviews Genetics, 18(11), 690-699. doi: 10.1038/nrg.2017.63 (Nature)
  • Hartwig, Fernando Pires, et al. (2016). Association of lactase persistence genotype with milk consumption, obesity and blood pressure: a Mendelian randomization study in the 1982 Pelotas (Brazil) Birth Cohort, with a systematic review and meta-analysis. International journey of epidemiology, 45(5), 1573-1587. doi:10.1093/ije/dyw074 (Int J Epidemiol)
  • Heine, R. G., et al. (2017). Lactose intolerance and gastrointestinal cow's milk allergy in infants and children - common misconceptions revisited. World Allergy Organization Journal, 10. doi: 10.1186/s40413-017-0173-0 (WAO)
  • Ingram, C.J., Mulcare, C.A., Itan, Y., Thomas, M.G. & Swallow, D.M. (2009). Lactose digestion and the evolutionary genetics of lactase persistence. Hum. Genet. 124, 579–591. (Human Genetics)
  • Janiak, M. C. (2016). Digestive enzymes of human and nonhuman primates. Evolutionary Anthropology: Issues, News, and Reviews, 25(5). doi:10.1002/evan.21498 (Full text)
    • Good information
  • Jones, Bryony L., and Dallas M. Swallow. (2011). The impact of cis-acting polymorphisms on the human phenotype. Human genome organization, 5(1-4), 13–23. doi:10.1007/s11568-011-9155-4 (HUGO J)
  • Kimura, R. (2018). Global Landscapes of Human Phenotypic Variation in Inherited Traits. Evolution of the Human Genome I Evolutionary Studies, 217-239. doi: 10.1007/978-4-431-56603-8_11 (Full text)
  • Laland, K. N. (2015). On evolutionary causes and evolutionary processes. Behavioural Processes, 117, 97-104. doi:10.1016/j.beproc.2014.05.008 (Full text)
  • Lapides, Rebecca and Dennis Savaiano. (2018). Gender, age, race and lactose intolerance: Is there evidence to support a differential symptom response? A scoping review. Nutrients, 10(12), 1956. doi:10.3390/nu10121956 (Nutrients)
  • Lomer, M. C. E., Parkes, G. C., & Sanderson, J. D. (2008). Lactose intolerance in clinical practice–myths and realities. Alimentary pharmacology & therapeutics, 27(2), 93-103. doi:10.1111/j.1365-2036.2007.03557.x (APT)
  • Lukito, Widjaja, et al. (2015). From 'lactose intolerance' to 'lactose nutrition'. Asian pacific journal of clinical nutrition, 24(1), S1-S8. doi:10.6133/apjcn.2015.24.s1.01 (PubMed Central)
  • Marciniak, S., & Perry, G. H. (2017). Harnessing ancient genomes to study the history of human adaptation. Nature Reviews Genetics, 18, 659-674. doi: 10.1038/nrg.2017.65 (Nature)
  • Melnik, Bodo, and Gerd Schmitz. (2017). Milk’s Role as an Epigenetic Regulator in Health and Disease. Diseases, 5(1), 12. doi:10.3390/diseases5010012 (Diseases)
  • Misselwitz, Benjamin, et al. (2013). Lactose malabsorption and intolerance: pathogenesis, diagnosis and treatment. United European Gastroenterology Journal, 1(3) 151-159. doi:10.1177/2050640613484463 (PubMed Central)
  • Montinaro, F., & Capelli, C. (2018). The evolutionary history of Southern Africa. Current Opinion in Genetics & Development, 53, 157-164. doi: 10.1016/j.gde.2018.11.003 (Full text)
  • Montgomery, Robert K., et al. (2007). Lactose and lactase--who is lactose intolerant and why?. Journal of pediatric gastroenterology and nutrition, 45(2). doi:10.1097/mpg.0b013e31812e68f6 (JPGN)
  • O'Brien, M. J., & Bentley, R. A. (2015). The role of food storage in human niche construction: An example from Neolithic Europe. Environmental Archaeology, 20(4), 364-378. doi:10.1179/1749631414y.0000000053 (Taylor and Francis)
  • Pennacchio, L. A., Bickmore, W., Dean, A., Nobrega, M. A., & Bejerano, G. (2013). Enhancers: five essential questions. Nature Reviews Genetics, 14(4), 288-295. doi:10.1038/nrg3458 (Nature)
  • Schlebusch, C. M., & Jakobsson, M. (2018). Tales of Human Migration, Admixture, and Selection in Africa. Annual Review of Genomics and Human Genetics, 19, 405-428. doi: 10.1146/annurev-genom-083117-021759 (Annual Review)
  • Segurel, Laure, and Celine Bon. (2017). On the Evolution of Lactase Persistence in Humans. Annual Review of Genomics and Human Genetics, 18(1), 297-319. doi:10.1146/annurev-genom-091416-035340 (Annual Reviews)
  • Shrier, Ian, et al. (2008). Impact of lactose containing foods and the genetics of lactase on diseases: an analytical review of population data. Nutrition and cancer, 60(3), 292-300. 10.1080/01635580701745301 (PubMed Central)
  • Siggers, T., & Gordân, R. (2013). Protein–DNA binding: complexities and multi-protein codes. Nucleic acids research, gkt1112. doi: 10.1093/nar/gkt1112 (Nucleic Acids Research)
  • Storhaug, C. L., Fosse, S. K., & Fadnes, L. T. (2017). Country, regional, and global estimates for lactose malabsorption in adults: A systematic review and meta-analysis. The Lancet Gastroenterology & Hepatology, 2(10), 738-746. doi: 10.1016/s2468-1253(17)30154-1 (Full text)
  • Szilagyi, Andrew. (2015). Adaptation to Lactose in Lactase Non Persistent People: Effects on Intolerance and the Relationship between Dairy Food Consumption and Evalution of Diseases. Nutrients, 7(8), 6751-6779. doi:10.3390/nu7085309 (Nutrients)
  • Szilagyi, Andrew, and Norma Ishayek. (2018). Lactose Intolerance, Dairy Avoidance, and Treatment Options. Nutrients, 10(12), 1994. doi:10.3390/nu10121994 (Nutrients)
  • Troelsen, J. T. (2005). Adult-type hypolactasia and regulation of lactase expression. Biochimica et Biophysica Acta (BBA)-General Subjects, 1723(1), 19-32. doi: 10.1016/j.bbagen.2005.02.003 (Full text)
    • Behind paywall
  • Voss, J. D., Goodson, M. S., & Leon, J. C. (2018). Phenotype diffusion and one health: A proposed framework for investigating the plurality of obesity epidemics across many species. Zoonoses and Public Health, 65(3), 279-290. doi: 10.1111/zph.12445 (Wiley)
    • Discusses how humans benefited from milk exposure despite being exposed to the pathogens in milk
  • Wanes, Dalanda, et al. (2019). Congenital Lactase Deficiency: Mutations, Functional and Biochemical Implications, and Future Perspectives. Nutrients, 11(2), 461. doi:10.3390/nu11020461 (MDPI)
  • Wiley, A. S. (2018). The Evolution of Lactase Persistence: Milk Consumption, Insulin-Like Growth Factor I, and Human Life-History Parameters. The Quarterly Review of Biology, 93(4), 319-345. doi: 10.1086/700768 (Journals)
  • Zhang, J., Lu, Y., Wang, Y., Ren, X., & Han, J. (2018). The impact of the intestinal microbiome on bone health. Intractable & Rare Diseases Research, 7(3), 148-155. doi: 10.5582/irdr. 2018.01055 (Jstage)
    • Discusses how SNPs affect intestinal microbes

Molecular Biology

  • Arnold, Jason W., et al. (2018). Prebiotics for Lactose Intolerance: Variability in Galacto-Oligosaccharide Utilization by Intestinal Lactobacillus rhamnosus. Nutrients, 10(10), 1517. doi:10.3390/nu10101517 (Nutrients)
  • Boll, Werner, et al. (1991). Structure of the Chromosomal Gene and cDNAs Coding for Lactase-Phlorizin Hydrolase in Humans with Adult-Type Hypolactasia or Persistence of Lactase. American Journal of Human Genetics, 48(5), 889-902. (PubMed Central)
  • Boyd, M., Bressendorff, S., Møller, J., Olsen, J., & Troelsen, J. T. (2009). Mapping of HNF4α target genes in intestinal epithelial cells. BMC gastroenterology, 9(1), 68. doi: 10.1186/1471-230X-9-68 (BMC Gastroenterology)
  • Brasen, C. L., Frischknecht, L., Ørnskov, D., Andreasen, L., & Madsen, J. S. (2017). Combination of real-time PCR and sequencing to detect multiple clinically relevant genetic variations in the lactase gene. Scandinavian Journal of Clinical and Laboratory Investigation, 77(1), 60-65. doi:10.1080/00365513.2016.1261408 (Taylor and Francis)
    • Behind paywall
  • Diekmann, Lena, et al. (2015). Congenital lactose intolerance is triggered by severe mutations on both alleles of the lactase gene. BMC Gastroenterology, 15(36). doi:10.1186/s12876-015-0261-y (BMC)
  • Elliott, G. et al. (2015). Intermediate DNA methylation is a conserved signature of genome regulation. Nat. Commun. 6, 6363. (Nature Comm.)
  • Escher, J. C., et al. (1992). Molecular basis of lactase levels in adult humans. Journal of clinical investigation, 89(2), 480-483. doi:10.1172/jci115609 (JCI)
  • Fajardo, Osvaldo, et al. (1994). The polymorphic expression of lactase in adults is regulated at the messenger RNA level. Gastroenterology, 106(5), 1233-1241. doi:10.1016/0016-5085(94)90014-0 (Science Direct)
  • Fang, R., Santiago, N. A., Olds, L. C., & Sibley, E. (2000). The homeodomain protein Cdx2 regulates lactase gene promoter activity during enterocyte differentiation. Gastroenterology, 118(1), 115-127. doi:10.1016/S0016-5085(00)70420-3 (Gastroenterology)
    • Behind paywall
  • Fang, R., Olds, L.C. & Sibley, E. (2006). Spatio-temporal patterns of intestine-specific transcription factor expression during postnatal mouse gut development. Gene Expr. Patterns 6, 426–432. (ScienceDirect)
  • Fitzgerald, Kevin, et al. (1998). GATA-6 stimulates a cell line-specific activation element in the human lactase promoter. American journal of physiology-gastrointestinal and liver physiology, 274(2), 314-324. doi:10.1152/ajpgi.1998.274.2.g314 (Am J Physiology)
  • Gerstein, M. B., Kundaje, A., Hariharan, M., Landt, S. G., Yan, K. K., Cheng, C., ... & Zilberman-Schapira, G. (2012). Architecture of the human regulatory network derived from ENCODE data. Nature, 489(7414), 91-100. (Nature)
  • Goda, T., Yasutake, H., Tanaka, T. & Takase, S. (1999). Lactase-phlorizin hydrolase and sucrase-isomaltase genes are expressed differently along the villus-crypt axis of rat jejunum. J. Nutr. 129, 1107–1113. (JN)
  • Grand, R. J., et al. (2003). Changing genes; losing lactase. Gut, 52(5), 617–619. doi:10.1136/gut.52.5.617 (Gut)
  • Harvey, W. B., et al. (1995). Studies on the expression of intestinal lactase in different individuals. Gut, 36(1), 28-33. doi:10.1136/gut.36.1.28 (BMJ)
  • Huang, M., et al. (2016). Evolutionary triangulation: Informing genetic association studies with evolutionary evidence. BioData Mining, 9. doi:10.1186/s13040-016-0091-7 (BioData Mining)
  • Kuranuki, Sachi, et al. (2007). The possible roles of homeobox protein, Cdx-2 for the expression of LPH gene during postnatal development. Life sciences, 80(8), 795-799. doi:10.1016/j.lfs.2006.11.007 (Science Direct)
  • Labrie, Viviane, et al. (2016). Lactase non-persistence is directed by DNA variation-dependent epigenetic aging. Nature structural & molecular biology, 23(6), 566-573. doi:10.1038/nsmb.3227 (NSMB)
    • Discusses aging as a factor
  • Lacey, S. W., et al. (1994). Expression of lactase-phlorizin hydrolase in sheep is regulated at the RNA level. Biochemical journal, 302(3), 929-935. doi:10.1042/bj3020929 (BMC)
  • Leseva, Milena N., et al. (2018). Differences in DNA Methylation and Functional Expression in Lactase Persistent and Non-persistent Individuals. Scientific Reports, 8(1). doi:10.1038/s41598-018-23957-4 (Scientific Reports)
  • Lewinsky, R. H., Jensen, T. G., Møller, J., Stensballe, A., Olsen, J., & Troelsen, J. T. (2005). T− 13910 DNA variant associated with lactase persistence interacts with Oct-1 and stimulates lactase promoter activity in vitro. Human Molecular Genetics, 14(24), 3945-3953. doi:10.1093/hmg/ddi418 (Human Molecular Genetics)
  • Linnell, J., Mott, R., Field, S., Kwiatkowski, D. P., Ragoussis, J., & Udalova, I. A. (2004). Quantitative high‐throughput analysis of transcription factor binding specificities. Nucleic Acids Research, 32(4), e44-e44. doi:10.1093/nar/gnh042 (Nucleic Acids Research)
  • Motohashi, Yasuko, et al. (1997). Lactase decline in weaning rats is regulated at the transcriptional level and not caused by termination of milk ingestion. The journal of nutrition, 127(9), 1737-43. doi:10.1093/jn/127.9.1737 (JN)
  • Olds, L.C. & Sibley, E. (2003). Lactase persistence DNA variant enhances lactase promoter activity in vitro: functional role as a cis regulatory element. Hum. Mol. Genet. 12, 2333–2340. (HMG)
  • Perissinato, Aline G., et al. (2018). Simple Strategy to Protect Lactase Activity in Solid Formulation. Current Drug Delivery, 15(2), 215-218. doi:10.2174/1567201814666170518125802 (PubMed Central)
    • Behind paywall
  • Roder, Pia V., et al. (2014). The Role of SGLT1 and GLUT2 in Intestinal Glucose Transport and Sensing. PLoS ONE, 9(2). doi:10.1371/journal.pone.0089977 (PLoS)
  • Rossi, M., et al. (1997). Lactase persistence versus decline in human adults: multifactorial events are involved in down-regulation after weaning. Gastroenterology, 112(5), 1506–1514. doi:10.1016/s0016-5085(97)70031-3 (PubMed Central)
  • Schrider, D. R., & Kern, A. D. (2016). S/HIC: Robust Identification of Soft and Hard Sweeps Using Machine Learning. PLOS Genetics, 12(3). doi:10.1371/journal.pgen.1005928 (PLOS Genetics)
    • Brief mention of lactase
  • Stegmann, Anders, et al. (2006). Metabolome, transcriptome, and bioinformatic cis-element analyses point to HNF-4 as a central regulator of gene expression during enterocyte differentiation. Physiological Genomics, 27(2), 141-155. doi:10.1152/physiolgenomics.00314.200 (Physiol Genomics)
  • Strand, Harald, et al. Lactase persistence genotyping: rapid detection of seven sequence variants in a single tube with melting curve analyses. Clinical chemistry and laboratory medicine, 52(9). doi: 10.1515/cclm-2014-0123 (PubMed Central)
  • Swallow, D. M., & Troelsen, J. T. (2016). Escape from epigenetic silencing of lactase expression is triggered by a single-nucleotide change. Nature Structural & Molecular Biology, 23(6), 505-507. doi:10.1038/nsmb.3238 (Nature)
    • Behind paywall
  • Tjalling, Bosse, et al. (2007). Gata4 and Hnf1alpha are partially required for the expression of specific intestinal genes during development. American journal of physiology-gastrointestinal and liver physiology, 292(5), 1302-1314. doi:10.1152/ajpgi.00418.2006 (Am J Physiology)
  • Troelsen, J.T., Olsen, J., Møller, J. & Sjöström, H. (2003). An upstream polymorphism associated with lactase persistence has increased enhancer activity. Gastroenterology 125, 1686–1694. (ScienceDirect)
  • Troelsen, J., Mitchelmore, C., Spodsberg, N., Jensen, A., Noren, O., & Sjostrom, H. (1997). Regulation of lactase–phlorizin hydrolase gene expression by the caudal-related homoeodomain protein Cdx-2. Biochem. J, 322, 833-838. doi: 10.1042/bj3220833 (PubMedCentral)
  • Wang, Z., Fang, R., Olds, L. C., & Sibley, E. (2004). Transcriptional regulation of the lactase-phlorizin hydrolase promoter by PDX-1. American Journal of Physiology-Gastrointestinal and Liver Physiology, 287(3), G555-G561. doi: 10.1152/ajpgi.00011.2004 (Physiology)
  • Wering, Herbert M. Van, et al. (2002). Novel interaction at the Cdx-2 binding sites of the lactase-phlorizin hydrolase promoter. Biochemical and biophysical research communications, 299(4), 587-593. doi:10.1016/s0006-291x(02)02697-9 (Science Direct)
  • Yeh, K.Y., Yeh, M. & Holt, P.R. (1991). Intestinal lactase expression and epithelial cell transit in hormone-treated suckling rats. Am. J. Physiol. 260, G379–G384. (AJPGI)
    • behind paywall

Physiology

  • Abildgaard, A., Tovbjerg, S. K., Giltay, A., Detemmerman, L., & Nissen, P. H. (2018). Lactase persistence genotyping on whole blood by loop-mediated isothermal amplification and melting curve analysis. Clinica Chimica Acta, 482, 50-56. doi: 10.1016/j.cca.2018.03.029 (Full text)
  • Blekhman, R., Goodrich, J. K., Huang, K., Sun, Q., Bukowski, R., Bell, J. T., . . . Clark, A. G. (2015). Host genetic variation impacts microbiome composition across human body sites. Genome Biology, 16. doi:10.1186/s13059-015-0759-1 (GenomeBiology)
  • Bonder, M. J., et al. (2016). The effect of host genetics on the gut microbiome. Nature Genetics, 48, 1407-1412. doi:10.1038/ng.3663 (Nature Genetics)
  • Buning, Carsten, et al. (2005). Introducing Genetic Testing for Adult-Type Hypolactasia. Digestion, 71(4), 245-250. doi:10.1159/000087050 (Karger)
  • Davenport, E. R., Goodrich, J. K., Bell, J. T., Spector, T. D., Ley, R. E., & Clark, A. G. (2016). ABO antigen and secretor statuses are not associated with gut microbiota composition in 1,500 twins. BMC Genomics, 17. doi:10.1186/s12864-016-3290-1 (BMC Genomics)
  • Fang, L., Ahn, J. K., Wodziak, D., & Sibley, E. (2012). The human lactase persistence-associated SNP− 13910* T enables in vivo functional persistence of lactase promoter–reporter transgene expression. Human genetics, 131(7), 1153-1159. doi: 10.1007/s00439-012-1140-z (PubMedCentral)
  • Gencdal, G., Salman, E., Ozutemiz, O., & Akarca, U. S. (2017). Association of LCT-13910 C/T Polymorphism and Colorectal Cancer. Annals of Coloproctology, 33(5), 169-172. doi: 10.3393/ac.2017.33.5.169 (Coloproctol)
  • Hoang, T. T., et al. (2019). Maternal Lactase Polymorphism (rs4988235) Is Associated with Neural Tube Defects in Offspring in the National Birth Defects Prevention Study. The Journal of Nutrition, 149(2), 295-303. doi: 10.1093/jn/nxy246 (Academic)
  • Malek, Adil J., et al. Associations of the lactase persistence allele and lactose intake with body composition among multiethnic children. Genes & nutrition, 8(5), 487-494. doi:10.1007/s12263-013-0335-9 (PubMed Central)
    • discusses LP allele with obesity in children in America; Hispanic Americans, African Americans, and European Americans.
  • Manco, L., Dias, H., Muc, M., & Padez, C. (2016). The lactase −13910CT polymorphism (rs4988235) is associated with overweight/obesity and obesity-related variables in a population sample of Portuguese young adults. European Journal of Clinical Nutrition, 71, 21-24. doi:10.1038/ejcn.2016.164 (Nature)
    • Behind paywall
  • Mattar, R., de Campos Mazo, D. F., & Carrilho, F. J. (2012). Lactose intolerance: diagnosis, genetic, and clinical factors. PubMedCentral, NCBI, 5, 113. doi:10.2147/CEG.S32368 (PubMedCentral)
    • Table 1 has countries and populations as well as the 13910 allele frequency for each and the reference in which they got the data
    • Table 2 has frequencies of 13910 allele in African countries
    • Table 3 has countries and populations as well as the frequency of other LP alleles and references in which they got the data
      • this article cited a separate article where they got their US data (Utah only) from
        • Enattah, N. S., et al. (2007). Evidence of Still-Ongoing Convergence Evolution of the Lactase Persistence T-13910 Alleles in Humans. The American Journal of Human Genetics, 81(3), 615–625. doi: 10.1086/520705 ([1])
          • examined 37 countries and took 1,611 samples total; the places did not have a uniform number of samples taken, meaning the data could be under or over-represented in some areas
  • Oh, E., et al. (2017). Transcriptional heterogeneity in the lactase gene within cell-type is linked to the epigenome. Scientific Reports, 7. doi: 10.1038/srep41843 (Nature)
  • Petruski-Ivleva, N., Kucharska-Newton, A., Palta, P., Couper, D., Meyer, K., Graff, M.,... Heiss, G. (2017). Milk Intake at Midlife and Cognitive Decline over 20 Years. The Atherosclerosis Risk in Communities (ARIC) Study. Nutrients, 9. doi: 10.3390/nu9101134 (Nutrients)
  • Physicians Committee for Responsible Medicine. (2019). Health Concerns About Dairy: Avoid the Dangers of Dairy with a Plant-Based Diet. (Physicians Committee for Responsible Medicine)
  • Pruimboom, L., Fox, T., & Muskiet, F. A. (2014). Lactase persistence and augmented salivary alpha-amylase gene copy numbers might have been selected by the combined toxic effects of gluten and (food born) pathogens. Medical Hypotheses, 82(3), 326-334. doi:10.1016/j.mehy.2013.12.020 (Science Direct)
  • Rusynyk, R. Alexander and Still, Christopher D. (2001). Lactose Intolerance. The Journal of American Osteopathic Association 101: S10-S12. (JAOA)
  • Sahi, T., Launiala, K. & Laitinen, H. (1983). Hypolactasia in a fixed cohort of young Finnish adults: a follow-up study. Scand. J. Gastroenterol., 18, 865–870. (Taylor and Francis)
  • Smith, C. E., et al. (2017). Genome-wide association studies of body mass index. Molecular Nutrition Food Research, 62(3), 69-78. doi: 10.1017/cbo9781107337459.007 (Wiley)
    • Table 2 has a list of 26 SNPs that they considered, but selected 6 to test that they put in table 3
  • Stegmann, A., Hansen, M., Wang, Y., Larsen, J. B., Lund, L. R., Ritié, L., ... & Olsen, J. (2006). Metabolome, transcriptome, and bioinformatic cis-element analyses point to HNF-4 as a central regulator of gene expression during enterocyte differentiation. Physiological genomics, 27(2), 141-155. doi: 10.1152/physiolgenomics.00314.2005 (Physiology)
  • Szilagyi, Andrew, and Norma Ishayek. (2018). Lactose Intolerance, Dairy Avoidance, and Treatment Options. Nutrients, 10(12), 1994. doi:10.3390/nu10121994 (PubMed Central)
    • Table 4 and 5 have good dairy alternative data and recommendations
  • Wang, Z., Maravelias, C., & Sibley, E. (2006). Lactase gene promoter fragments mediate differential spatial and temporal expression patterns in transgenic mice. DNA and cell biology, 25(4), 215-222. doi:10.1089/dna.2006.25.215 (Liebert)
    • Behind paywall
  • Wilt, T. J., Shaukat, A., Shamliyan, T., Taylor, B. C., MacDonald, R., Tacklind, J., ... & Levitt, M. (2010). Lactose intolerance and health. Evidence Reports/Technology Assessments, No. 192 (NCBI)
    • Looks at how LI influences bones in relations to age and race
  • U.S. National Library of Medicine (NIH). (2019). Lactose Intolerance. (NIH)
  • Zheng, X., Chu, H., Cong, Y., Deng, Y., Long, Y., Zhu, Y., . . . Fox, M. (2015). Self-reported lactose intolerance in clinic patients with functional gastrointestinal symptoms: Prevalence, risk factors, and impact on food choices. Neurogastroenterology & Motility, 27(8), 1138-1146. doi:10.1111/nmo.12602 (Full text)

SNPs and Population Genetics

  • Antelope, C. X., Marnetto, D., Casey, F., & Huerta-Sanchez, E. (2017). Leveraging Multiple Populations across Time Helps Define Accurate Models of Human Evolution: A Reanalysis of the Lactase Persistence Adaptation. Human Biology, 89(1). doi: 10.13110/humanbiology.89.1.05 (MUSE)
  • Baffour-Awuah, Nana Yaa, et al. (2015). Functional significance of single nucleotide polymorphisms in the lactase gene in diverse US patients and evidence for a novel lactase persistence allele at -13909 in those of European ancestry. Journal of pediatric gastroenterology and nutrition, 60(2), 182-191. doi:10.1097/mpg.0000000000000595 (PubMed Central)
    • -13909C>A SNP (European ancestry)
  • Bayoumi, R., et al. (2016). Positive selection of lactase persistence among people of Southern Arabia. American Journal of Physical Anthropology, 161(4). doi:10.1002/ajpa.23072 (Full text)
    • −13,915G SNP (Arabian LP‐related variation was found in Dhofaris and Yemenis)
  • Bersaglieri, Todd, et al. (2004). Genetic Signatures of Strong Recent Positive Selection at the Lactase Gene. American journal of human genetics, 74(6), 1111–1120. doi:10.1086/421051 (PubMed Central)
  • Blant, A., Kwong, M., Szpiech, Z. A., & Pemberton, T. J. (2017). Weighted likelihood interference of genomic autozygosity patterns in dense genotype data. BMC Genomics, 18(1). doi: 10.1186/s12864-017-4312-3 (BMC)
    • Discusses autozygosity hotspots in relation to lactase persistence
  • Boschmann, Stefanie Epp., et al. (2015). The Frequency of the LCT*-13910C>T Polymorphism Associated with Lactase Persistence Diverges among Euro-Descendant Groups from Brazil. Medical Principles and Practice, 25(1), 18–20. doi:10.1159/000440807 (MPP)
  • Brasen, Claus Lohman, et al. (2016). Combination of real-time PCR and sequencing to detect multiple clinically relevant genetic variations in the lactase gene. Scandinavian journal of clinical and laboratory investigation, 77(1), 60-65. doi:10.1080/00365513.2016.1261408 (PubMed Central)
  • Burger, J., et al. (2007). Absence of the lactase-persistence-associated allele in early Neolithic Europeans. Proceedings of the National Academy of Sciences, 104(10). doi:10.1073/pnas.0607187104 (PNAS)
  • Charati, H., et al. (2019). The evolutionary genetics of lactase persistence in seven ethnic groups across the Iranian plateau. Human Genomics, 13(7). doi: 10.1186/s40246-019-0195-5 (Human Genomics)
  • Chin, E. L., et al. (2019). Association of Lactase Persistence Genotypes (rs4988235) and Ethnicity with Dairy Intake in a Healthy U.S. Population. Nutrients, 11(8), 1860. doi: 10.3390/nu11081860 ([file:///C:/Users/aweisbla/Downloads/nutrients-11-01860.pdf])
    • discusses LP in US and examines ethnicity in US
  • Corella, Dolores, et al. (2010). Association of the LCT-13910C>T polymorphism with obesity and its modulation by dairy products in a Mediterranean population. Obesity, 19(8), 1707-1714. doi:10.1038/oby.2010.320 (Wiley)
  • Enattah, N. S., et al. (2007). Evidence of still-ongoing convergence evolution of the lactase persistence T-13910 alleles in humans. The American journal of human genetics, 81(3), 615-625. doi:10.1086/520705 (Science Direct)
    • SNP frequencies analyzed in 37 worldwide populations
  • Enattah, N. S., et al. (2008). Independent Introduction of Two Lactase-Persistence Alleles into Human Populations Reflects Different History of Adaptation to Milk Culture. The American journal of human genetics, 82(1), 57-72. doi:10.1016/j.ajhg.2007.09.012 (AJHG)
    • Analyzed 124 samples from Saudi Arabia looking for European SNP
      • G-13915 has complete co-occurence with C-3712
      • Determined that A/G-12962 is NOT an LP causative SNP
  • Enattah, N. S., Sahi, T., Savilahti, E., Terwilliger, J. D., Peltonen, L., & Järvelä, I. (2002). Identification of a variant associated with adult-type hypolactasia. Nature genetics, 30(2), 233-237. doi: 10.1038/ng826 (Nature)
  • Fanti, Sarah De, et al. (2015). Inferring the genetic history of lactase persistence along the Italian peninsula from a large genomic interval surrounding the LCT gene. American journal of physical anthropology, 158(4), 708-18. doi:10.1002/ajpa.22814 (Wiley)
  • Fernández, C. I., & Flores, S. V. (2014). Brief Communication: Lactase persistence and dairy intake in Mapuche and Mestizo populations from southern Chile. American journal of physical anthropology, 155(3), 482-487. doi:10.1002/ajpa.22594 (AJPA)
  • Fernández, C. I., Montalva, N., Arias, M., Hevia, M., Moraga, M. L., & Flores, S. V. (2015). Lactase non-persistence and general patterns of dairy intake in indigenous and mestizo chilean populations. American Journal of Human Biology, 28(2), 213-219. doi:10.1002/ajhb.22775 (Full text)
  • Friedrich, Deise C., et al. (2012). Several Different Lactase Persistence Associated Alleles and High Diversity of the Lactase Gene in the Admixed Brazilian Population. PLoS ONE, 8(10). doi:10.1371/journal.pone.0046520 (PLoS)
  • Gallego Romero, I. et al. (2012). Herders of Indian and European cattle share their predominant allele for lactase persistence. Mol. Biol. Evol. 29, 249–260. (MBE)
  • Gamba, C. et al. (2014). Genome flux and stasis in a five millennium transect of European prehistory. Nat. Commun. 5, 5257. (Nature Communications)
  • Gerbault, P., et al. (2011). Evolution of lactase persistence: an example of human niche construction. Philosophical Transactions of the Royal Society B: Biological Sciences, 366(1566), 863-877. doi:10.1098/rstb.2010.0268 (Royal Society B)
  • Goh, Li-Han, et al. (2018). Lactase deficiency and lactose intolerance in a multiracial Asian population in Malaysia. Journal of Gastroenterology and Hepatology, 2(6), 307-310. doi:10.1002/jgh3.12089 (JGH Open)
  • Halima, Y. B., et al. (2017). Lactase persistence in Tunisia as a result of admixture with other Mediterranean populations. Genes & Nutrition, 12. doi: 10.1186/s12263-017-0573-3 (Genes & Nutrition)
  • Hassan, Hisham Y., et al. (2016). Genetic diversity of lactase persistence in East African populations. BMC Research Notes, 9(1). doi:10.1186/s13104-015-1833-1 (PubMed Central)
  • Hermisson, J., & Pennings, P. S. (2017). Soft sweeps and beyond: Understanding the patterns and probabilities of selection footprints under rapid adaptation. Methods in Ecology and Evolution, 8, 700-716. doi: 10.1111/2041-210x.12808 (BES)
    • Look at Box 2
  • Hilliard, C. B. (2016). High osteoporosis risk among East Africans linked to lactase persistence genotype. BoneKEy Reports, 5. doi:10.1038/bonekey.2016.30 (PubMed Central)
  • Imtiaz, F., et al. (2005). The T/G−13915 variant upstream of the lactase gene (LCT) is the founder allele of lactase persistence in an urban Saudi population. Journal of medical genetics, 40(10). doi:10.1136/jmg.2007.051631 (PubMed Central)
  • Itan, Yuval, et al. (2009). The Origins of Lactase Persistence in Europe. PLoS Computational Biology, 5(8). doi:10.1371/journal.pcbi.1000491 (PLoS)
  • Itan, Y., Jones, B. L., Ingram, C. J., Swallow, D. M., & Thomas, M. G. (2010). A worldwide correlation of lactase persistence phenotype and genotypes. BMC evolutionary biology, 10(1), 36. doi:10.1186/1471-2148-10-36 (BMC)
  • Jensen, T. G., Liebert, A., Lewinsky, R., Swallow, D. M., Olsen, J., & Troelsen, J. T. (2011). The− 14010* C variant associated with lactase persistence is located between an Oct-1 and HNF1α binding site and increases lactase promoter activity. Human genetics, 130(4), 483-493. (Human Genetics)
  • Jones, Bryony L., et al. (2015). Diversity of lactase persistence in African milk drinkers. Human genetics, 134(8), 917-925. doi:10.1007/s00439-015-1573-2 (PubMed Central)
  • Kasimov, S., Nazarova, G., Kasimova, D., Yunusova, Z., & Rakhmatova, M. (2015). A Single Nucleotide Polymorphism C/T - 13910 And Consumption Of Dairy Products In Uzbek Population. Journal of Evolution of Medical and Dental Sciences, 4(86), 15042-15050. doi:10.14260/jemds/2015/2134 (JEMDS)
  • Khabarova, Yulia, et al. (2009). Prevalence of lactase persistent/non-persistent genotypes and milk consumption in a young population in north-west Russia. World journal of gastroenterology, 15(15), 1849. doi:10.3748/wjg.15.1849 (WJG)
  • Khabarova, Yulia, et al. (2010). The -13914G>A variant upstream of the lactase gene (LCT) is associated with lactase persistence/non-persistence. Scandanavian journal of clinical and laboratory investigation, 70(5), 354-357. doi:10.3109/00365513.2010.491554 (PubMed Central)
  • Kuchay, Raja A. H., et al. (2012). Correlation of G/A -22018 single-nucleotide polymorphism with lactase activity and its usefulness in improving the diagnosis of adult-type hypolactasia among North Indian children. Genes and nutrition, 8(1) 145-151. doi:10.1007/s12263-012-0305-7 (Springer)
  • Kulichova, I., et al. (2017). Internal diversification of non-Sub-Saharan haplogroups in Sahelian populations and the spread of pastoralism beyond the Sahara. American Journal of Physical Anthropology, 164(2). doi: 10.1002/ajpa.23285 (Wiley)
  • Kuokkanen, M., Enattah, N. S., Oksanen, et al (2003). Transcriptional regulation of the lactase-phlorizin hydrolase gene by polymorphisms associated with adult-type hypolactasia. Gut, 52(5), 647-652. (Gut)
  • Laso-Jadart, R., Harmant, C., Quanch, H., Zidane, N., Tyler-Smith, C., Mehdi, Q., ...Patin, E. (2017). The Genetic Legacy of the Indian Ocean Slave Trade: Recent Admixture and Post-admixture Selection in the Makranis of Pakistan. The American Journal of Human Genetics, 101(6), 977-984. doi: 10.1016/j.ajhg.2017.09.025 (PubMed Central)
    • Table 1 has relevance to lactose tolerance
  • Lember, Margus. (2006). Lactase non-persistence and milk consumption in Estonia. World journal of gastroenterology, 12(45), 7329. doi:10.3748/wjg.v12.i45.7329 (WJG)
  • Liebert, Anke, et al. (2013). In vitro functional analyses of infrequent nucleotide variants in the lactase enhancer reveal different molecular routes to increased lactase promoter activity and lactase persistence. Annals of Human Genetics, 80(6), 307-318. doi: doi:10.1111/ahg.12167 (PubMed Central)
  • Liebert, Anke, et al. (2017). World-wide distributions of lactase persistence alleles and the complex effects of recombination and selection. Human genetics, 136(11). (PubMed Central)
  • Montalva, N., Adhikari, K., Liebert, A., Mendoza-Revilla, J., Flores, S. V., Mace, R., & Swallow, D. M. (2018). Adaptation to milking agropastoralism in Chilean goat herders and nutritional benefit of lactase persistence. Annals of Human Genetics, 83(1), 11-22. doi: 10.1111/ahg. 12277 (Wiley)
  • Morales, E., Azocar, L., Maul, X., et al (2011). The European lactase persistence genotype determines the lactase persistence state and correlates with gastrointestinal symptoms in the Hispanic and Amerindian Chilean population: a case–control and population-based study. BMJ, 1(1), e000125. doi:10.1136/bmjopen-2011-000125 (BMJ)
  • Nilsson Torbjorn K., and Lovisa A. Olssen. (2008). Simultaneous genotyping of the three lactose tolerance-linked polymorphisms LCT -13907C>G, LCT -13910C>T and LCT -13915T>G with Pyrosequencing technology. Clinical chemistry and laboratory medicine, 46(1). doi:10.1515/cclm.2008.015 (PubMed Central)
  • Ojeda-Granados, C., Panduro, A., Pinho, J. R. R., Ramos-Lopez, O., Gleyzer, K., de Mello Malta, F., ... & Roman, S. (2016). Association of lactase persistence genotypes with high intake of dairy saturated fat and high prevalence of lactase non-persistence among the Mexican population. Lifestyle Genomics, 9(2-4), 83-94. doi:10.1159/000446241 (Karger)
  • Olds, L. C., Ahn, J. K., & Sibley, E. (2011). − 13915* G DNA polymorphism associated with lactase persistence in Africa interacts with Oct-1. Human genetics, 129(1), 111-113. doi:10.1007/s00439-010-0898-0 (PubMedCentral)
  • Paz-Y-Miño, C., Burgos, G., López-Cortés, A., Herrera, C., Gaviria, A., Tejera, E., & Cabrera-Andrade, A. (2016). A study of the molecular variants associated with lactase persistence in different Ecuadorian ethnic groups. American Journal of Human Biology, 28(6). doi:10.1002/ajhb.22865 (Full text)
  • Peltonen, Leena, et al. (2018). Identification of a DNA Variant Associated with Adult-Type Hypolactasia. (U.S. Patents)
  • Pinto, J. C., Oliveira, S., Teixeira, S., Martins, D., Fehn, A., Aço, T., . . . Rocha, J. (2016). Food and pathogen adaptations in the Angolan Namib desert: Tracing the spread of lactase persistence and human African trypanosomiasis resistance into southwestern Africa. American Journal of Physical Anthropology, 161(3), 436-447. doi:10.1002/ajpa.23042 (Full text)
  • Plantinga, Theo S., et al. (2012). Low prevalence of lactase persistence in Neolithic South-West Europe. European journal of human genetics, 20(7), 778-782. doi:10.1038/ejhg.2011.254 (PubMed Central)
  • Poulter, M., et al. (2003). The causal element for the lactase persistence/non-persistence polymorphism is located in a 1 Mb region of linkage disequilibrium in Europeans. Annals of human genetics, 67(4), 298-311. doi:10.1046/j.1469-1809.2003.00048.x (PubMed Central)
  • Priehodová, E., et al. (2017). The historical spread of Arabian Pastoralists to the eastern African Sahel evidenced by the lactase persistence −13,915*G allele and mitochondrial DNA. American Journal of Human Biology, 29(3). doi: 10.1002/ajhb.22950 (Full text)
  • Ranciaro, Alessia, et al. (2014). Genetic Origins of Lactase Persistence and the Spread of Pastoralism in Africa. The American Journal of Human Genetics, 94(4), 496-510. doi:10.1016/j.ajhg.2014.02.009 (PubMed Central).
  • Rasinpera, H., et al. (2005). Transcriptional downregulation of the lactase (LCT) gene during childhood. Gut, 54(11), 1660–1661. doi:10.1136/gut.2005.077404 (Gut)
  • Raz, Maytal, et al. (2013). Frequency of LCT-13910C/T and LCT-22018G/A single nucleotide polymorphisms associated with adult-type hypolactasia/lactase persistence among Israelis of different ethnic groups. Gene, 519(1), 67-70. doi:10.1016/j.gene.2013.01.049 (Science Direct)
  • Seppo, Leena, et al. (2008). Can primary hypolactasia manifest itself after the age of 20 years? A two-decade follow-up study. Scandinavian journal of gastroenterology, 43(9), 1082-7. doi:10.1080/00365520802095485 (PubMed Central)
  • Sibley, E., & Ahn, J. K. (2011). Theodore E. Woodward Award: lactase persistence SNPs in African populations regulate promoter activity in intestinal cell culture. Transactions of the American Clinical and Climatological Association, 122, 155. (PubMedCentral)
  • Smith, George Davey, et al. (2008). Lactase persistence-related genetic variant: population substructure and health outcomes. European journal of human genetics, 17(3), 357-367. doi:10.1038/ejhg.2008.156 (PubMed Central)
  • Szilagyi, A., & Xue, X. (2016). Geographic associations between lactase phenotype, multiple sclerosis, and inflammatory bowel diseases; Does obesity trump geography? Medical Hypotheses, 96, 68-72. doi:10.1016/j.mehy.2016.10.001 (Full text)
  • Tishkoff, S. A., Reed, F. A., Ranciaro, A., Voight, B. F., Babbitt, C. C., Silverman, J. S., ... & Ibrahim, M. (2007). Convergent adaptation of human lactase persistence in Africa and Europe. Nature genetics, 39(1), 31. doi:10.1038/ng1946 (Nature)
  • Torniainen, Suvi, et al. (2009). Screening of variants for lactase persistence/non-persistence in populations from South Africa and Ghana. BMC genetics, 10(31). doi:10.1186/1471-2156-10-31 (PubMed Central)
  • Tournebize, R., Poncet, V., Jakobsson, M., Vigouroux, Y., & Manel, S. (2018). McSwan: A joint site frequency spectrum method to detect and date selective sweeps across multiple population genomes. Molecular Ecology Resources, 19(1), 283-295. doi: 10.1111/1755-0998.12957 (Wiley)
  • Valencia, L., et al. (2017). Identification of novel genetic variants in the mutational hotspot region 14 kb upstream of the LCT gene in a Mexican population. Scandinavian Journal of Clinical and Laboratory Investigation, 77(5), 311-314. doi:10.1080/00365513.2017.1318445 (Taylor & Francis)
    • Behind paywall
  • Williamson, S. H., Hubisz, M. J., Clark, A. G., Payseur, B. A., Bustamante, C. D., & Nielsen, R. (2007). Localizing recent adaptive evolution in the human genome. PLoS genetics, 3(6), e90. doi:10.1371/journal.pgen.0030090 (PLoS)

Education

  • Boguski, M. S., Boguski, R. M., & Berman, M. R. (2013). Personal genotypes are teachable moments. Genome medicine, 5(3), 22. doi:10.1186/gm426 (Full text
  • Daley, L. A. A., Wagner, J. K., Himmel, T. L., McPartland, K. A., Katsanis, S. H., Shriver, M. D., & Royal, C. D. (2013). Personal DNA testing in college classrooms: perspectives of students and professors. Genetic testing and molecular biomarkers, 17(6), 446-452. doi: 10.1089/gtmb.2012.0404 (Full text)
  • Garber, K. B., Hyland, K. M., & Dasgupta, S. (2016). Participatory genomic testing as an educational experience. Trends in Genetics, 32(6), 317-320.10.1016/j.tig.2016.03.008 (Full text)
  • Haga, S. B., Barry, W. T., Mills, R., Ginsburg, G. S., Svetkey, L., Sullivan, J., & Willard, H. F. (2013). Public knowledge of and attitudes toward genetics and genetic testing. Genetic testing and molecular biomarkers, 17(4), 327-335. doi: 10.1089/gtmb.2012.0350 (Full text)
  • Hill, R. W., Wyse, G. A., & Anderson, M. (2016). Nutrition, Feeding, and Digestion. In Animal Physiology (3rd ed., pp. 127-128). Sunderland, MA: Sinauer Association. (Full text)
  • Leksmono, Cattleya S., et al. (2018). Measuring Lactase Enzymatic Activity in the Teaching Lab. Journal of Visualized Experiments, (138), 54377. doi:10.3791/54377. (Jove)
  • Mavroidopoulou, V., Xera, E., & Mollaki, V. (2015). Awareness, attitudes and perspectives of direct-to-consumer genetic testing in Greece: a survey of potential consumers. Journal of human genetics, 60(9), 515. (Full text)
  • Michigan State University. (2019). Evo Ed Project: Molecular Biology of Lactase Persistence. (Evo-Ed)
  • Ormond, K. E., Hudgins, L., Ladd, J. M., Magnus, D. M., Greely, H. T., & Cho, M. K. (2011). Medical and graduate students' attitudes toward personal genomics. Genetics in Medicine, 13(5), 400. (Full text)
  • Pearson, Y. E., & Liu-Thompkins, Y. (2012). Consuming direct-to-consumer genetic tests: the role of genetic literacy and knowledge calibration. Journal of Public Policy & Marketing, 31(1), 42-57. doi: 10.1509/jppm.10.066 (Full text)
  • Salari, K., Karczewski, K. J., Hudgins, L., & Ormond, K. E. (2013). Evidence that personal genome testing enhances student learning in a course on genomics and personalized medicine. PLoS One, 8(7), e68853. doi: 10.1371/journal.pone.0068853 (Full text)
  • Sanderson, S. C., Linderman, M. D., Kasarskis, A., Bashir, A., Diaz, G. A., Mahajan, M. C., ... & Schadt, E. E. (2013). Informed decision-making among students analyzing their personal genomes on a whole genome sequencing course: a longitudinal cohort study. Genome medicine, 5(12), 113. doi:10.1186/gm518 (Full text)
  • Sanderson, S. C., Linderman, M. D., Zinberg, R., Bashir, A., Kasarskis, A., Zweig, M., ... & Schadt, E. E. (2015). How do students react to analyzing their own genomes in a whole-genome sequencing course?: outcomes of a longitudinal cohort study. Genetics in Medicine, 17(11), 866. (Full text)
  • Schultheis, P. J., & Bowling, B. V. (2011). Analysis of a SNP linked to lactase persistence: An exercise for teaching molecular biology techniques to undergraduates. Biochemistry and Molecular Biology Education, 39(2), 133-140. doi:10.1002/bmb.20456 (IUBMB)
  • Stourman, N., & Moore, J. (2018). Analysis of lactase in lactose intolerance supplements. Biochemistry and Molecular Biology Education, 46(6), 652-662. doi: 10.1002/bmb.21185 (Full text)
  • Vernez, S. L., Salari, K., Ormond, K. E., & Lee, S. S. J. (2013). Personal genome testing in medical education: student experiences with genotyping in the classroom. Genome medicine, 5(3), 24. doi:10.1186/gm428 [(Full text)
  • Weinlander, K. M., Hall, D. J., & De Stasio, E. A. (2010). RFLP analysis and allelic discrimination with real‐time PCR using the human lactase persistence trait. Biochemistry and Molecular Biology Education, 38(3), 167-171. doi: 10.1002/bmb.20357 (IUBMB)

Other

  • Allentoft, Morten E., et al. (2015). Population genomics of Bronze Age Eurasia. Nature, 522, 167-172. (Nature)
  • American Dairy Association. (2019). Dietary Recommendations. (Drink Milk)
  • Brock, W. A., O’Brien, M. J., & Bentley, R. A. (2016). Validating niche-construction theory through path analysis. Archaeological and Anthropological Sciences, 8(4), 819-837. doi:10.1007/s12520-015-0257-0 (Full text)
    • Good path analysis and mathematics
  • Cohen, Mathilde. (2017). Animal Colonialism: The Case of Milk. AJIL Unbound, 111, 267-271. (AJIL)
  • Curry, Andrew. (2013). Archaeology: The Milk Revolution. Nature, 500(7460). doi:10.1038/500020a (Nature)
  • Dairy Council of California. (2019). Health Benefits of Dairy. (Healthy Eating)
  • Food and Agriculture Organization. (2012). Milk and Dairy Products in Human Nutrition: Questions and Answers. FAO Milk. (FAO)
  • Food Empowerment Project. (2019). Lactose Intolerance. (FEP)
  • Food Empowerment Project. (2010). Shining a Light on the Valley of Heart’s Delight: Taking a Look at Access to Healthy Foods in Santa Clara County’s Communities of Color and Low-Income Communities. (FEP)
  • Freeman, A. (2013). The unbearable whiteness of milk: Food oppression and the USDA. UC Irvine L. Rev., 3, 1251. (HeinOnline)
  • Friedman, Mendel. (2015). Antibiotic-Resistant Bacteria: Prevalence in Food and Inactivation by Food-Compatible Compounds and Plant Extracts. Journal of Agricultural and Food Chemistry 63 (15), 3805-3822. doi: 10.1021/acs.jafc.5b00778 (ACS)
  • Gaard, Greta. (2013). Toward a Feminist Postcolonial Milk Studies. American Quarterly, 65(3), 595-618. doi:10.1353/aq.2013.0040 (JSTOR)
  • Hagenkord J, Funke B, Qian E, Hegde M, Jacobs KB, Ferber M, Lebo M, Buchanan AH, Bick D. 2019. Design and reporting considerations for genetic screening tests. PeerJ Preprints 7:e27922v4 https://doi.org/10.7287/peerj.preprints.27922v4
    • Preprint; may or may not be relevant
  • Henry, A. G. (2016). The Evolution of Human Diets. Ernahrungs Umschau, 63(6), M350-M358. doi:10.4455/eu.2016.030 (Ernaehrungs Umschau)
    • Abstract had to be translated and behind paywall
  • Hertzler, S., Savaiano, D. A., Dilk, A., Jackson, K. A., Bhriain, S. N., & Suarez, F. L. (2017). Nutrient Considerations in Lactose Intolerance. In A. M. Coulston, C. J. Boushey, M. G. Ferruzzi, & L. M. Delahanty (Eds.), Nutrition in the prevention and treatment of disease (4th ed., pp. 875-892). Amsterdam: Academic Press. (Full text)
  • Jennings, Kerri-Ann. Health Line. (2018). Top 15 Calcium-Rich Foods (Many Are Non-Dairy). (Calcium-Rich Foods)
  • Montalva, Nicolas, et al. (2018). Adaptation to milking agropastoralism in Chilean goat herders and nutritional benefit of lactase persistence. Annals of human genetics, 83(1), 11-22. doi:10.1111/ahg.12277 (PubMedCentral)
  • Moshfegh A, Goldman J, Ahuja J, Rhodes D, LaComb R. US Department of Agriculture. (2009). What we eat in America, NHANES 2005-2006: Usual Intakes from Food and Water compared to 1997 Dietary Reference Intakes for Vitamin D, Calcium, Phosphorus and Magnesium. (U.S. ARS)
  • Office of Disease Prevention and Health Promotion. (2019). Dietary Guidelines for Americans 2015-2020, 8th edition. (Dietary Guidelines)
  • SELF Nutrition Data. (2018). Milk, whole, 3.25% milkfat Nutrition Facts & Calories (SELF)
  • Silanikove, Nissim, et al. (2015). The Interrelationships between Lactose Intolerance and the Modern Dairy Industry: Global Perspectives in Evolutional and Historical Backgrounds. Nutrients, 7(9), 7312-7331. doi:10.3390/nu7095340 (PubMed Central)
  • Smith, J., Coop, G., Stephens, M., & Novembre, J. (2018). Estimating Time to the Common Ancestor for a Beneficial Allele. Molecular Biology and Evolution, 35(4), 1003-1017. doi: 10.1093/molbev/msy006 (Full text)
  • Vegetarian Nation. (2019). Getting Protein, Calcium & Iron. (Vegetarian)
  • Investigating the racial bias in genetic research (Biotechniques news article) based on Perez-Ramos JG, Dye TD, Fernandez ID et al. Variation in intention to participate in genetic research among Hispanic/Latinx populations by Latin America birth-residency concurrence: A global study. Presented at: American Society of Human Genetics 2019 Annual Meeting. Houston, TX, USA, 15 – 19 October 2019

Protein Structure Exercises

POU2F1 (aka OCT-1)

Background

In this exercise, you will explore the structure of a the regulatory transcription factor POU2F1 (OCT-1) from human, bound to its regulatory DNA. The binding of POU2F1 to an enhancer upstream of the LCT gene that encodes lactase activates lactase expression. Variants in the enhancer motif are responsible for lactase persistence, which enables humans to digest the milk sugar, lactose, after weaning.

Learning objectives

At the end of this exercise, the student should be able to

  • define and show the differences between different levels of protein structure: primary, secondary, tertiary, and quaternary.
  • locate a domain and explain its relationship to the levels of structure mentioned above
  • identify the types of amino acid side chains that interact with the DNA and name the types of weak, noncovalent bonds responsible for the interaction
  • describe the relationship of structure to function for POU2F1 and how this relates to lactase persistence

SNP Data and Human Genome Browser

Excel Sheet with SNPs

LMU Box