Введение

1 Smith B. K. Classifying animals and humans in ancient India. Man. 1991; 26: 527–548.

2 Thompson D. W. On Growth and Form. Cambridge, UK: Cambridge University Press, 1942.

3 Hayashi T., Carthew R. W. Surface mechanics mediate pattern formation in the developing retina. Nature. 2004; 431: 647–652.

4 Puklin-Faucher E., Sheetz M. P. The mechanical integrin cycle. Journal of Cell Science. 2009; 122: 179–186; del Rio A. et al. Stretching single talin rod molecules activates vinculin binding. Science. 2009; 323: 638–641.

5 Henderson D. A. The eradication of smallpox – an overview of the past, present, and future. Vaccine. 2011; 29: D7 – D9.

Глава 1. ДНК: код и спираль

1 Nelkin D., Lindee M. S. The DNA Mystique: The Gene as a Cultural Icon. W. H. Freeman, 1995.

2 Gallery puts DNA in the frame. BBC News. 2001; September 19 (http://news.bbc.co.uk/2/hi/entertainment/1550864.stm).

3 Уотсон Дж. Двойная спираль. М.: АСТ, 2019; Мукерджи С. Ген. Очень личная история. М.: Corpus, 2023; Sayre A. Rosalind Franklin and DNA. New York: W. W. Norton, 2000; Cobb M. Sexism in science: Did Watson and Crick really steal Rosalind Franklin's data? The Guardian. 2015; June 23 (http://www.theguardian.com/science/2015/jun/23/sexism-in-science-did-watson-and-crick-really-steal-rosalind-franklins-data).

4 Goldenfeld N. Lectures on Phase Transitions and the Renormalization Group. Reading, MA: Addison-Wesley, 1972; Peyrard M. Biophysics: Melting the double helix. Nat. Phys. 2006; 2: 13–14; Peyrard M. Nonlinear dynamics and statistical physics of DNA. Nonlinearity. 2004; 17: R1 – R40.

5 Mullis K. B. The unusual origin of the polymerase chain reaction. Sci. Am. 1990; 262: 56–65.

Глава 2. Белки: молекулярное оригами

1 de Chadarevian S. John Kendrew and myoglobin: Protein structure determination in the 1950s. Protein Science. 2018; 27: 1136–1143. Об истории рентгеновской кристаллографии: Brooks-Bartlett J. C., Garman E. F. The Nobel science: One hundred years of crystallography. Interdisciplinary Science Reviews. 2015; 40: 244–264; Jaskolski M. et al. A brief history of macromolecular crystallography, illustrated by a family tree and its Nobel fruits. FEBS Journal. 2014; 281: 3985–4009.

2 Изображение белка GFP основано на структуре 1EMA из Protein Data Bank: https://www.rcsb.org/structure/1EMA; Ormö M. et al. Crystal structure of the Aequorea victoria green fluorescent protein. Science. 1996; 273: 1392–1395.

3 Day R. N., Davidson M. W. The fluorescent protein palette: Tools for cellular imaging. Chem. Soc. Rev. 2009; 38: 2887–2921; Rodriguez E. A. et al. The growing and glowing toolbox of fluorescent and photoactive proteins. Trends in Biochemical Sciences. 2017; 42: 111–129; Shaner N. C. The mFruit collection of monomeric fluorescent proteins. Clin. Chem. 2013; 59: 440–441.

4 О структуре калиевых каналов: Kuang Q. et al. Structure of potassium channels. Cell Mol. Life Sci. 2015; 72: 3677–3693.

5 Изображение кинезина основано на структуре белка 1N6M из Protein Data Bank: https://www.rcsb.org/structure/1N6M; Yun M. et al. Rotation of the stalk/neck and one head in a new crystal structure of the kinesin motor protein. Ncd. EMBO Journal. 2003; 22: 5382–5389.

6 Изображение глюкокортикоидного рецептора основано на структуре белка 1R4O из Protein Data Bank: https://www.rcsb.org/structure/1R4O; Luisi B. F. et al. Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA. Nature. 1991; 352: 497–505.

7 Hartl F. U., Hayer-Hartl M. Molecular chaperones in the cytosol: From nascent chain to folded protein. Science. 2002; 295: 1852–1858.

9 Ducrot C. et al. BSE risk and the use of meat and bone meal in the feed industry: Perspectives in the context of relaxing control measures. Natures Sciences Societes. 2013; 21: 3–12.

10 Richards F. M. The protein folding problem. Scientific American. 1992; 264: 54–63; Dill K. A., MacCallum J. L. The protein-folding problem, 50 years on. Science. 2012; 338: 1042–1046.

11 Elliot A., David E. Shaw's supercomputer is uncovering secrets of human biology. Columbia Engineering. 2017; April 7 (https://engineering.columbia.edu/news/engineering-icons-david-shaw).

12 Folding@home – боремся с болезнями с помощью глобально распределенного суперкомпьютера. https://foldingathome.org/; Greene K. Folding@home takes to the lab. Science. 2002; October 21 (https://www.sciencemag.org/news/2002/10/foldinghome-takes-lab).

13 Cooper S. et al. Predicting protein structures with a multiplayer online game. Nature. 2010; 466: 756–760.

14 Service R. F. «The game has changed.» AI triumphs at protein folding. Science. 2020; 370: 1144–1145.

Глава 3. Гены и механика ДНК

1 Deeb S. S. The molecular basis of variation in human color vision. Clin. Genet. 2005; 67: 369–377; Color vision deficiency. MedlinePlus. 2020 (https://medlineplus.gov/genetics/condition/color-vision-deficiency/).

2 Kino T. et al. Noncoding RNA gas5 is a growth arrest– and starvation-associated repressor of the glucocorticoid receptor. Sci. Signal. 2010; 3: ra8; Guttman M., Rinn J. L. Modular regulatory principles of large non-coding RNAs. Nature. 2012; 482: 339–346.

3 Kyoto Encyclopedia of Genes and Genomes (KEGG), https://www.genome.jp/kegg/ (Mycobacterium tuberculosis, https://www.genome.jp/kegg-bin/show_organism?org=mtu; Vibrio cholerae, http://www.genome.jp/kegg-bin/show_organism?org=vch).

4 National Center for Biotechnology Information, https://www.ncbi.nlm.nih.gov/genome/?term=Lactobacillus%20delbrueckii /Organism/.

5 Ezkurdia I. et al. Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes. Hum. Mol. Genet. 2014; 23: 5866–5878; Willyard C. New human gene tally reignites debate. Nature. 2018; 558: 354–355.

6 Church D. M. et al. Lineage-specific biology revealed by a finished genome assembly of the mouse. PLOS Biology. 2009; 7: e1000112; Wade C. M. et al. Genome sequence, comparative analysis, and population genetics of the domestic horse. Science. 2009; 326: 865–867; Zhan X. et al. Peregrine and saker falcon genome sequences provide insights into evolution of a predatory lifestyle. Nature Genetics. 2013; 45: 563–566; Ohm R. A. et al. Genome sequence of the model mushroom Schizophyllum commune. Nature Biotechnology. 2010; 28: 957–963; Colbourne J. K. et al. The ecoresponsive genome of Daphnia pulex. Science. 2011; 331: 555–561; Rice Annotation Project database (RAP-DB): 2008 update. Nucleic Acids Res. 2008; 36: D1028 – D1033; Gramene database (http://ensembl.gramene.org/Zea_mays/Info/Annotation/); Wang H. et al. Analysis of non-coding transcriptome in rice and maize uncovers roles of conserved lncRNAs associated with agriculture traits. Plant J. 2015; 84: 404–416.

7 В базе данных BioNumbers, http://bionumbers.hms.harvard.edu/search.aspx, есть информация о размере геномов, включая геномы хлебной плесени Neurospora crassa и почвенной амебы Dictyostelium discoideum; вводите в строку поиска «number of genes» или название вида.

8 Schiessel H. The physics of chromatin. J. Phys. Condens. Matter. 2003; 15: R699 – R774; Tremethick D. J. Higher-order structures of chromatin: The elusive 30 nm fiber. Cell. 2007; 128: 651–654. Изображение ДНК, намотанной на гистонный комплекс, основано на структуре 1AOI из Protein Data Bank: https://www.rcsb.org/structure/1AOI; Luger K. et al. Nature. 1997; 389: 251–260.

9 Ou H. D. et al. ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells. Science. 2017; 357: eaag0025.

10 Mirabella C. et al. Chromatin deregulation in disease. Chromosoma. 2016; 125: 75–93; DeLaurier A. et al. Histone deacetylase-4 is required during early cranial neural crest development for generation of the zebrafish palatal skeleton. BMC Developmental Biology. 2012; 12: 16.

11 Segal E. et al. A genomic code for nucleosome positioning. Nature. 2006; 442: 772–778; Brunet F. G. et al. Evidence for DNA sequence encoding of an accessible nucleosomal array across vertebrates. Biophysical Journal. 2018; 114: 2308–2316.

12 Evilevitch A. et al. Osmotic pressure inhibition of DNA ejection from phage. Proc. Natl. Acad. Sci. 2003; 100: 9292–9295; Gelbart W. M., Knobler C. M. Virology: Pressurized viruses. Science. 2009; 323: 1682–1683.

Глава 4. Хореография генов

1 Изображение lac-репрессора, прикрепленного к ДНК, основано на структуре белков 1EFA и 1TLF из Protein Data Bank и на комбинированной иллюстрации Дэвида Гудселла: https://www.rcsb.org/structure/1EFA; https://www.rcsb.org/structure/TLF; Goodsell D. Molecule of the Month: lac Repressor. PDB-101. 2003 (http://pdb101.rcsb.org/motm/39); Bell C. E., Lewis M. A closer view of the conformation of the lac repressor bound to operator. Nat. Struct. Biol. 2000; 7: 209–214.

2 Schleif R. DNA Looping. Annual Review of Biochemistry. 1992; 61: 199–223.

3 Vörös Z. et al. Proteins mediating DNA loops effectively block transcription. Protein Sci. 2017; 26: 1427–1438; Becker N. A. et al. Mechanism of promoter repression by lac repressor-DNA loops. Nucleic Acids Res. 2013; 41: 156–166.

4 История изучения генетической регуляции описана в Morange M. A History of Molecular Biology. Cambridge, MA: Harvard University Press, 2000.

5 Lambert S. A., et al. The human transcription factors. Cell. 2018; 172: 650–665.

6 Schoenfelder S., Fraser P. Long-range enhancer – promoter contacts in gene expression control. Nature Reviews Genetics. 2019; 20: 437–455.

7 Cronin C. A. et al. The lac operator-repressor system is functional in the mouse. Genes Dev. 2001; 15: 1506–1517.

8 О памяти, часах и других генетических схемах: Nelson P. C. Physical Models of Living Systems. W. H. Freeman, 2015; Alon U. An Introduction to Systems Biology: Design Principles of Biological Circuits. Boca Raton, FL: CRC Press, 2007. О циркадном ритме и его клеточных часах: Brown S. A. et al. (Re)inventing the circadian feedback loop. Dev. Cell. 2012; 22: 477–487; Maywood E. S. et al. Analysis of core circadian feedback loop in suprachiasmatic nucleus of mCry1-luc transgenic reporter mouse. Proc. Natl. Acad. Sci. 2013; 110: 9547–9552; Pett J. P. et al. Feedback loops of the mammalian circadian clock constitute repressilator. PLOS Comput. Biol. 2016; 12: e1005266.

9 Elowitz M. B., Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature. 2000; 403: 335–338.

10 Stricker J. et al. A fast, robust and tunable synthetic gene oscillator. Nature. 2008; 456: 516–519.

11 Lawrence M. et al. Lateral thinking: How histone modifications regulate gene expression. Trends in Genetics. 2016; 32: 42–56; Ho L., Crabtree G. R. Chromatin remodelling during development. Nature. 2010; 463: 474–484.

12 Allis C. D., Jenuwein T. The molecular hallmarks of epigenetic control. Nature Reviews Genetics. 2016; 17: 487–500; Boškoviс A., Rando O. J. Transgenerational epigenetic inheritance. Annual Review of Genetics. 2018; 52: 21–41; Heijmans B. T. et al. Persistent epigenetic differences associated with prenatal exposure to famine in humans. PNAS. 2008; 105: 17046–17049.

13 Painter R. C. et al. Transgenerational effects of prenatal exposure to the Dutch famine on neonatal adiposity and health in later life. BJOG: An International Journal of Obstetrics & Gynaecology. 2008; 115: 1243–1249; Veenendaal M. V. E. et al. Transgenerational effects of prenatal exposure to the 1944–45 Dutch famine. BJOG: An International Journal of Obstetrics & Gynaecology. 2013; 120: 548–554.

Глава 5. Мембраны: жидкая кожа

1 Еще больше белков отдаленно связаны с мембранами: Dobson L. et al. The human transmembrane proteome. Biol. Direct. 2015; 10: 31; Almén M. S. et al. Mapping the human membrane proteome: A majority of the human membrane proteins can be classified according to function and evolutionary origin. BMC Biology. 2009; 7: 50.

2 Grakoui A. et al. The immunological synapse: A molecular machine controlling T cell activation. Science. 1999; 285: 221–227; Bromley S. K. et al. The immunological synapse. Annu. Rev. Immunol. 2001; 19: 375–396.

3 Piguet V., Sattentau Q. Dangerous liaisons at the virological synapse. J. Clin. Invest. 2004; 114: 605–610.

4 Waksman S. A. The Conquest of Tuberculosis. Berkeley: University of California Press, 1964.

5 Leading causes of death, 1900–1998. Centers for Disease Control (USA) (https://www.cdc.gov/nchs/data/dvs/lead1900_98.pdf).

6 WHO global tuberculosis report. World Health Organization. 2017 (http://www.who.int/tb/publications/global_report/en/).

7 Twitchell D. C. The vitality of tubercle bacilli in sputum. Transactions of the National Association for the Study and Prevention of Tuberculosis, Annual Meeting. 1905; 221–230; Smith C. R. Survival of tubercle bacilli. American Review of Tuberculosis. 1942; 45: 334–345.

8 Crowe J. H. et al. Anhydrobiosis. Annu. Rev. Physiol. 1992; 54: 579–599.

9 О работе над трегалозными липидами в моей лаборатории: Harland C. W. et al. The M. tuberculosis virulence factor trehalose dimycolate imparts desiccation resistance to model mycobacterial membranes. Biophys. J. 2008; 94: 4718–4724; Harland C. W. et al. Synthetic trehalose glycolipids confer desiccation resistance to supported lipid monolayers. Langmuir. 2009; 25: 5193–5198.

10 Baumgart T. et al. Large-scale fluid/fluid phase separation of proteins and lipids in giant plasma membrane vesicles. Proc. Natl. Acad. Sci. 2007; 104: 3165–3170.

11 Rayermann S. P. et al. Hallmarks of reversible separation of living, unperturbed cell membranes into two liquid phases. Biophys. J. 2017; 113: 2425–2432.

12 Seo A. Y. et al. AMPK and vacuole-associated Atg14p orchestrate μ-lipophagy for energy production and long-term survival under glucose starvation. eLife. 2017; 6: e21690.

13 Singer S. J., Nicolson G. L. The fluid mosaic model of the structure of cell membranes. Science. 1972; 175: 720–731.

Глава 6. Предсказуемая случайность

1 Mazo R. M. Brownian Motion: Fluctuations, Dynamics, and Applications. Oxford, UK: Clarendon Press, 2002; Hänggi P., Marchesoni F. 100 years of Brownian motion. Chaos. 2005; 15: 026101–026105.

2 Berg H. C. Random Walks in Biology. Princeton, NJ: Princeton University Press, 1993.

3 Luo L. Why is the human brain so efficient? Nautilus. 2018 (http://nautil.us/issue/59/connections/why-is-the-human-brain-so-efficient).

4 Redner S. A Guide to First-Passage Processes. Cambridge, UK: Cambridge University Press, 2007.

5 О моторных белках и транспортировке грузов в нейронах см. Yagensky O. et al. The roles of microtubule-based transport at presynaptic nerve terminals. Front. Synaptic Neurosci. 2016; 8: 3.

6 Purcell E. M. Life at low Reynolds number. American Journal of Physics. 1977; 45: 3–11.

Глава 7. Сборка эмбрионов

1 Pinto-Correia C. The Ovary of Eve. Chicago: University of Chicago Press, 1998.

2 Gilbert S. F. Developmental Biology (6th ed.). Sunderland, MA: Sinauer Associates, 2000.

3 Nüsslein-Volhard C., Wieschaus E. Mutations affecting segment number and polarity in Drosophila. Nature. 1980; 287: 795–801; Haskett D. R. Hedgehog signaling pathway. Embryo Project Encyclopedia. 2015 (http://embryo.asu.edu/handle/10776/8685).

4 Изображение белка Hedgehog мушки Drosophila melanogaster основано на структуре 2IBG из Protein Data Bank: https://www.rcsb.org/structure/2IBG; McLellan J. S. et al. Structure of a heparin-dependent complex of hedgehog and ihog. Proc. Natl. Acad. Sci. 2006; 103: 17208–17213. Изображение человеческого белка Sonic hedgehog основано на структуре 3MXW из Protein Data Bank: https://www.rcsb.org/structure/3MXW; Maun H. R. et al. Hedgehog pathway antagonist 5E1 binds hedgehog at the pseudo-active site. J. Biol. Chem. 2010; 285: 26570–26580.

5 Towers M. et al. Insights into bird wing evolution and digit specification from polarizing region fate maps. Nature Communications. 2011; 2: 426.

6 Tarazona O. A. et al. Evolution of limb development in cephalopod mollusks. eLife. 2019; 8: e43828.

7 Kim S. et al. Epigenetic regulation of mammalian hedgehog signaling to the stroma determines the molecular suptype of bladder cancer. eLife. 2019; 8: e43024.

8 Turing A. The chemical basis of morphogenesis. Philosophical Transactions of the Royal Society London, B: Biological Sciences. 1952; 237: 37–72.

9 Forrest K. M., Gavis E. R. Live imaging of endogenous RNA reveals a diffusion and entrapment mechanism for nanos mRNA localization in Drosophila. Current Biology. 2003; 13: 1159–1168; Lucas T. et al. 3 minutes to precisely measure morphogen concentration. PLOS Genetics. 2018; 14: e1007676.

10 Ilsley G. R. et al. Cellular resolution models for even skipped regulation in the entire Drosophila embryo. eLife. 2013; 2: e00522; Petkova M. D. et al. Optimal decoding of cellular identities in a genetic network. Cell. 2019; 176: 844–855.e15.

11 Dubuis J. O. et al. Positional information, in bits. Proc. Natl. Acad. Sci. 2013; 110: 16301–16308.

12 Eddison M. et al. Notch signaling in the development of the inner ear: Lessons from Drosophila. Proc. Natl. Acad. Sci. 2000; 97: 11692–11699.

13 Doe C. Q., Goodman C. S. Early events in insect neurogenesis: II. The role of cell interactions and cell lineage in the determination of neuronal precursor cells. Developmental Biology. 1985; 111: 206–219.

14 Об открытии роли латерального торможения в структурировании развивающегося организма см. Bussell K. Milestone 3 (1937): Inhibit thy neighbour. Nat. Rev. Neurosci. 2004. О белке Notch, его расщеплении и роли в клеточной сигнализации и в латеральном торможении: Gordon W. R. et al. The molecular logic of Notch signaling – a structural and biochemical perspective. Journal of Cell Science. 2008; 121: 3109–3119; Sjöqvist M., Andersson E. R. Do as I say, Not (ch) as I do: Lateral control of cell fate. Developmental Biology. 2019; 447: 58–70.

15 Gomez C. et al. Control of segment number in vertebrate embryos. Nature. 2008; 454: 335–339.

16 Cooke J., Zeeman E. C. A clock and wavefront model for control of the number of repeated structures during animal morphogenesis. J. Theor. Biol. 1976; 58: 455–476.

17 Palmeirim I. et al. Avian hairy gene expression identifies a molecular clock linked to vertebrate segmentation and somitogenesis. Cell. 1997; 91: 639–648; Oates A. C. et al. Patterning embryos with oscillations: Structure, function and dynamics of the vertebrate segmentation clock. Development. 2012; 139: 625–639.

18 What is the future of developmental biology? Cell. 2017; 170: 6–7.

Глава 8. Конструирование органов

1 Potten C. S., Morris R. J. Epithelial stem cells in vivo. J. Cell Sci. 1988; 45–62. Считают, что в день теряется около 10¹¹ клеток при массе каждой около 11^–12 килограммов, а это соответствует потере около 3 тысяч килограммов в течение жизни.

2 Engler J. et al. Matrix elasticity directs stem cell lineage specification. Cell. 2006; 126: 677–689.

3 Keung J. et al. Presentation counts: Microenvironmental regulation of stem cells by biophysical and material cues. Annual Review of Cell and Developmental Biology. 2010; 26: 533–556.

4 Haswell E. S. et al. Mechanosensitive channels: What can they do and how do they do it? Structure. 2011; 19: 1356–1369; Peyronnet R. et al. Mechanosensitive channels: Feeling tension in a world under pressure. Front. Plant Sci. 2014; 5: 558.

5 Aragona M. et al. Mechanisms of stretch-mediated skin expansion at single-cell resolution. Nature. 2020; 584: 268–273.

6 Yamamoto K. et al. Fluid shear stress induces differentiation of Flk-1-positive embryonic stem cells into vascular endothelial cells in vitro. American Journal of Physiology-Heart and Circulatory Physiology. 2005; 288: H1915 – H1924 (2005); Wang H. et al. Shear stress induces endothelial differentiation from a murine embryonic mesenchymal progenitor cell line. Arteriosclerosis, Thrombosis, and Vascular Biology. 2005; 25: 1817–1823.

7 Landecker H. Culturing Life: How Cells Became Technologies. Cambridge, MA: Harvard University Press, 2010; Steinberg M. S., Takeichi M. Experimental specification of cell sorting, tissue spreading, and specific spatial patterning by quantitative differences in cadherin expression. Proc. Natl. Acad. Sci. 1994; 91: 206–209.

8 Simian M., Bissell M. J. Organoids: A historical perspective of thinking in three dimensions. J. Cell Biol. 2017; 216: 31–40.

9 Sato T. et al. Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche. Nature. 2009; 459: 262–265.

10 Eiraku M. et al. Self-organizing optic-cup morphogenesis in three-dimensional culture. Nature. 2011; 472: 51–56.

11 Eiraku M. et al. Self-organized formation of polarized cortical tissues from ESCs and its active manipulation by extrinsic signals. Cell Stem Cell. 2008; 3: 519–532.

12 Lancaster M. A. et al. Cerebral organoids model human brain development and microcephaly. Nature. 2013; 501: 373–379.

13 Cepelewicz J. An ethical future for brain organoids takes shape. Quanta Magazine. 2020; January 13 (https://www.quantamagazine.org/an-ethical-future-for-brain-organoids-takes-shape-20200123/).

14 Huh D. et al. Reconstituting organ-level lung functions on a chip. Science. 2010; 328: 1662–1668.

15 McAleer C. W. et al. Multi-organ system for the evaluation of efficacy and off-target toxicity of anticancer therapeutics. Science Translational Medicine. 2019; 11: eaav1386; Edington C. D. et al. Interconnected microphysiological systems for quantitative biology and pharmacology studies. Sci. Rep. 2018; 8: 1–18.

Глава 9. Экосистема внутри вас

1 Sender R. et al. Revised estimates for the number of human and bacteria cells in the body. PLOS Biology. 2016; 14: e1002533.

2 Venter J. C. et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science. 2004; 304: 66–74.

3 Schlomann B. H., Parthasarathy R. Timescales of gut microbiome dynamics. Current Opinion in Microbiology. 2019; 50: 56–63.

4 Durack J., Lynch S. V. The gut microbiome: Relationships with disease and opportunities for therapy. Journal of Experimental Medicine. 2019; 216: 20–40; Douglas A. E. Fundamentals of Microbiome Science: How Microbes Shape Animal Biology. Princeton, NJ: Princeton University Press, 2018; The Gut Microbiome in Health and Disease / Haller D. (ed.). Cham, Switzerland: Springer, 2018; Tremlett H. et al. The gut microbiome in human neurological disease: A review. Ann. Neurol. 2017; 81: 369–382; Griffiths J. A., Mazmanian S. K. Emerging evidence linking the gut microbiome to neurologic disorders. Genome Medicine. 2018; 10: 98.

5 Drew L. Microbiota: Reseeding the gut. Nature. 2016; 540: S109 – S112; van Nood E. et al. Duodenal infusion of donor feces for recurrent clostridium difficile. New England Journal of Medicine. 2013; 368: 407–415; Colman R. J., Rubin D. T. Fecal microbiota transplantation as therapy for inflammatory bowel disease: A systematic review and meta-analysis. J. Crohns Colitis. 2014; 8: 1569–1581.

6 Zmora N. et al. Personalized gut mucosal colonization resistance to empiric probiotics is associated with unique host and microbiome features. Cell. 2018; 174: 1388–1405.e21.

7 Round J. L., Mazmanian S. K. The gut microbiota shapes intestinal immune responses during health and disease. Nat. Rev. Immunol. 2009; 9: 313–323; Hooper L. V. et al. Interactions between the microbiota and the immune system. Science. 2012; 336: 1268–1273; Jones T. A., Guillemin K. Racing to stay put: How resident microbiota stimulate intestinal epithelial cell proliferation. Curr. Pathobiol. Rep. 2018; 6: 23–28.

8 Hill J. H. et al. A conserved bacterial protein induces pancreatic beta cell expansion during zebrafish development. eLife. 2016; 5: e20145.

9 Schwarzer M. et al. Lactobacillus plantarum strain maintains growth of infant mice during chronic undernutrition. Science. 2016; 351: 854–857.

10 Finucane M. M. et al. A taxonomic signature of obesity in the microbiome? Getting to the guts of the matter. PLoS ONE. 2014; 9: e84689; Sze M. A., Schloss P. D. Looking for a signal in the noise: Revisiting obesity and the microbiome. mBio. 2016; 7: e01018– e01016.

11 О заболеваемости холерой и ее лечении см. статьи на сайтах ВОЗ (https://www.who.int/news-room/fact-sheets/detail/cholera) и Центров по контролю и профилактике заболеваний США (https://www.cdc.gov/cholera/treatment/index.html).

12 Russell B. et al. Type VI secretion system effectors: Poisons with a purpose. Nat. Rev. Micro. 2014; 12: 137–148.

13 Об экспериментах с холерным вибрионом и его T6SS в моей лаборатории: Logan S. L. et al. The Vibrio cholerae type VI secretion system can modulate host intestinal mechanics to displace gut bacterial symbionts. Proc. Natl. Acad. Sci. 2018; 115: E3779 – E3787.

14 Wiles T. J. et al. Swimming motility of a gut bacterial symbiont promotes resistance to intestinal expulsion and enhances inflammation. PLOS Biology. 2020; 18: e3000661.

15 Kotula J. W. et al. Programmable bacteria detect and record an environmental signal in the mammalian gut. Proc. Natl. Acad. Sci. 2014; 111: 4838–4843.

16 Cremer J. et al. Effect of flow and peristaltic mixing on bacterial growth in a gut-like channel. Proc. Natl. Acad. Sci. 2016; 113: 11414–11419.

17 Shin W. et al. Human intestinal morphogenesis Controlled by Transepithelial Morphogen Gradient and Flow-Dependent Physical Cues in a microengineered gut-on-a-chip. iScience. 2019; 15: 391–406.

18 Goldford J. E. et al. Emergent simplicity in microbial community assembly. Science. 2018; 361: 469–474.

19 May R. M. Stability and Complexity in Model Ecosystems (reprint ed.). Princeton, NJ: Princeton University Press, 2001; May R. M. Will a large complex system be stable? Nature. 1972; 238: 413–414.

20 Cui W. et al. Diverse communities behave like typical random ecosystems. bioRxiv. 2019 (https://doi.org/10.1101/596551); Marsland III R. et al. Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities. PLOS Computational Biology. 2019; 15: e1006793.

21 Posfai A. et al. Metabolic trade-offs promote diversity in a model ecosystem. Phys. Rev. Lett. 2017; 118: 028103.

Глава 10. Восприятие масштаба

1 Темы этой главы развиваются в таких увлекательных книгах, как Vogel S. Life's Devices: The Physical World of Animals and Plants. Princeton, NJ: Princeton University Press, 1988; Schmidt-Nielsen K. How Animals Work. Cambridge, UK: Cambridge University Press, 1972; Haldane J. B. S. On Being the Right Size and Other Essays. Oxford, UK: Oxford University Press, 1985.

2 O'Connor J. J., Robertson E. F. Osborne Reynolds – biography. Maths History. 2003 (https://mathshistory.st-andrews.ac.uk/Biographies/Reynolds/).

3 Low Reynolds Number Flow на сайте Национального комитета фильмов по механике жидкостей, http://web.mit.edu/hml/ncfmf.html; а также https://www.youtube.com/watch?v=51-6QCJTAjU (начиная с 13:40).

4 Prange H. D. The scaling and mechanics of arthropod exoskeletons // Scale Effects in Animal Locomotion / Pedley T. J. (ed.). London: Academic Press, 1997.

5 Tenney S. M., Remmer J. E. Comparative quantitative morphology of the mammalian lung: Diffusing area. Nature. 1963; 197: 54–56.

6 McMahon T. A., Bonner J. T. On Size and Life. NY: Scientific American Library, 1983.

7 Cooper M. The elephant in the room. Oregon Quarterly. 2014; Spring 2014: 34–38; Lynn C. The time Tusko the elephant was abandoned at the Oregon State Fair. Salem Statesman Journal. 2017; August 25.

8 Vogel S. Life's Devices: The Physical World of Animals and Plants.

Глава 11. Жизнь на поверхности

1 Klowden M. J. Physiological Systems in Insects. Amsterdam: Academic Press, 2010.

2 Than K. Why giant bugs once roamed the earth. National Geographic. 2011; August 9 (https://www.nationalgeographic.com/news/2011/8/110808-ancient-insects-bugs-giants-oxygen-animals-science/).

3 Mlot N. J. et al. Fire ants self-assemble into waterproof rafts to survive floods. Proc. Natl. Acad. Sci. 2011; 108: 7669–7673.

4 Altman L. K. A Kennedy baby's life and death. New York Times. 2013; July 30 (https://www.nytimes.com/2013/07/30/health/a-kennedy-babys-life-and-death.html); Schraufnagel D. Breathing in America: Diseases, Progress, and Hope (1st ed.). NY: American Thoracic Society, 2010.

5 Clements J. A. Surface tension in the lungs. Scientific American. 1962; 207: 120–130; Clements J. A. Lung surfactant: A personal perspective. Annual Review of Physiology. 1997; 59: 1–21; Dobbs L. G. Pulmonary surfactant. Annu. Rev. Med. 1989; 40: 431–446.

Гдава 12. Загадки размера и формы

1 McMahon T. A., Bonner J. T. On Size and Life; Gazzola M. et al. Scaling macroscopic aquatic locomotion. Nat. Phys. 2014; 10: 758–761; Baumgart J., Friedrich B. M. Fluid dynamics: Swimming across scales. Nat. Phys. 2014; 10: 711–712; Willmer P. et al. Environmental Physiology of Animals. Malden, MA: Wiley-Blackwell, 2004; Bale R. et al. Energy efficiency and allometry of movement of swimming and flying animals. Proc. Natl. Acad. Sci. 2014; 111: 7517–7521; Hedrick T. L. et al. Wingbeat time and the scaling of passive rotational damping in flapping flight. Science. 2009; 324: 252–255.

2 Лэйн Н. Энергия, секс, самоубийство. Митохондрии и смысл жизни. СПб.: Питер, 2016.

3 Kleiber M. Body size and metabolism. Hilgardia. 1932; 6: 315–353.

4 White C. R., Seymour R. S. Mammalian basal metabolic rate is proportional to body mass^2/3. Proc. Natl. Acad. Sci. 2003; 100: 4046–4049.

5 Rubner M. Ueber den einfluss der korpergrosse auf stoffund kaftwechsel. Zeitschrift fur Biologie. 1883; 19: 535–562; McMahon T. A., Bonner J. T. On Size and Life. NY: Scientific American Library, 1983.

6 Dodds P. S. et al. Re-examination of the «¾-law» of metabolism. Journal of Theoretical Biology. 2001; 209: 9–27.

7 Bennett P. M., Harvey P. H. Active and resting metabolism in birds: Allometry, phylogeny and ecology. Journal of Zoology. 1987; 213: 327–344.

8 West G. B. et al. A general model for the origin of allometric scaling laws in biology. Science. 1997; 276: 122–126.

9 Dodds P. S. et al. Re-examination of the «¾-law» of metabolism. Journal of Theoretical Biology. 2001; 209: 9–27; Etienne R. S. et al. Demystifying the West, Brown & Enquist model of the allometry of metabolism. Functional Ecology. 2006; 20: 394–399.

10 Banavar J. R. et al. Size and form in efficient transportation networks. Nature. 1999; 399: 130–132.

11 Лэйн Н. Энергия, секс, самоубийство; Darveau C.-A. et al. Allometric cascade as a unifying principle of body mass effects on metabolism. Nature. 2002; 417: 166–170.

12 Brown J. H. et al. Toward a metabolic theory of ecology. Ecology. 2004; 85: 1771–1789.

13 Bettencourt L. M. A. et al. Growth, innovation, scaling, and the pace of life in cities. Proc. Natl. Acad. Sci. 2007; 104: 7301–7306; Bettencourt L. M. A. The origins of scaling in cities. Science. 2013; 340: 1438–1441.

14 Shalizi C. R. Scaling and hierarchy in urban economies. arXiv. 2011 (http://arxiv.org/abs/1102.4101); Arcaute E. et al. Constructing cities, deconstructing scaling laws. Journal of the Royal Society Interface. 2015; 12: 20140745.

15 Thommen A. et al. Body size-dependent energy storage causes Kleiber's law scaling of the metabolic rate in planarians. eLife. 2019; 8: e38187.

Глава 13. Как мы читаем ДНК

1 Shendure J. et al. DNA sequencing at 40: Past, present and future. Nature. 2017; 550: 345–353; Heather J. M., Chain B. The sequence of sequencers: The history of sequencing DNA. Genomics. 2016; 107: 1–8.

2 Muthukumar M. Theory of electrophoretic mobility of polyelectrolyte chains. Macromolecular Theory and Simulations. 1994; 3: 61–71; Viovy J.-L. Electrophoresis of DNA and other polyelectrolytes: Physical mechanisms. Rev. Mod. Phys. 2000; 72: 813–872.

3 О первом секвенировании генома человека: Carvalho T., Zhu T. The Human genome project (1990–2003). Embryo Project Encyclopedia. 2014 (http://embryo.asu.edu/handle/10776/7829); International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature. 2001; 409: 860–921; Venter J. C. et al. The sequence of the human genome. Science. 2001; 291: 1304–1351. О завершении проекта «Геном человека»: Pennisi E. Reaching their goal early, sequencing labs celebrate. Science. 2003; 300: 409; Genome.gov, Human Genome Project FAQ (https://www.genome.gov/human-genome-project/Completion-FAQ).

4 Mardis E. R. Next-generation DNA sequencing methods. Annual Review of Genomics and Human Genetics. 2008; 9: 387–402; Metzker M. L. Sequencing technologies – the next generation. Nature Reviews Genetics. 2010; 11: 31–46.

5 Margulies M. et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature. 2005; 437: 376–380; Nyren P. et al. Solid phase DNA minisequencing by an enzymatic luminometric inorganic pyrophosphate detection assay. Analytical Biochemistry. 1993; 208: 171–175.

6 Davies K. The $ 1,000 Genome: The Revolution in DNA Sequencing and the New Era of Personalized Medicine. NY: Free Press, 2010.

7 Pennisi E. Semiconductors inspire new sequencing technologies. Science. 2010; 327: 1190; Rothberg J. M. et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature. 2011; 475: 348–352.

8 Herper M. Gene machine. Forbes. 2010; December 30 (https://www.forbes.com/forbes/2011/0117/features-jonathan-rothberg-medicine-tech-gene-machine.html#12c8a7ed2711).

9 Draven1983101. Illumina Solexa sequencing. YouTube. 2010 (https://www.youtube.com/watch?v=77r5p8IBwJk).

10 Eid J. et al. Real-time DNA sequencing from single polymerase molecules. Science. 2009; 323: 133–138.

11 Bayle H. Nanopore sequencing: From imagination to reality. Clin. Chem. 2015; 61: 25–31: Deamer D. et al. Three decades of nanopore sequencing. Nat. Biotechnol. 2016; 34: 518–524.

12 Изображение нанопорового канального белка основано на структуре 3X2R из Protein Data Bank: https://www.rcsb.org/structure/3X2R; Cao B. et al. Structure of the nonameric bacterial amyloid secretion channel. Proc. Natl. Acad. Sci. 2014; 111: E5439 – E5444. Изображение полимеразы, прикрепленной к нанопоровому канальному белку, основано на структуре 3BDP из Protein Data Bank: https://www.rcsb.org/structure/3BDP; Kiefer J. R. et al. Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal. Nature. 1998; 391: 304–307.

13 Информация из базы данных Национальных институтов здоровья США: Wetterstrand K. A. DNA sequencing costs: Data. National Human Genome Research Institute. 2023 (www.genome.gov/sequencingcostsdata).

14 См., например, https://www.nih.gov/news-events/news-releases/nhgri-funds-development-third-generation-dna-sequencing-technologies.

15 Coffin J. M., Fan H. The discovery of reverse transcriptase. Annual Review of Virology. 2016; 3: 29–51.

16 Zheng G. X. Y. et al. Massively parallel digital transcriptional profiling of single cells. Nature Communications. 2017; 8: 14049; Kotliar D. et al. Identifying gene expression programs of cell-type identity and cellular activity with single-cell RNA-Seq. eLife. 2019; 8: e43803; Wagner D. E. et al. Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo. Science. 2018; 360: 981–987.

Глава 14. Генетические комбинации

1 Roser M. et al. Human height. Our World in Data. 2013 (https://ourworldindata.org/human-height); Roser M., Ritchie H. Food supply. Our World in Data. 2013 (https://ourworldindata.org/food-supply).

2 О наследуемости роста, питании и полногеномных исследованиях: Lai C.-Q. How much of human height is genetic and how much is due to nutrition? Scientific American. 2006; December 11 (https://www.scientificamerican.com/article/how-much-of-human-height/).

3 Lello L. et al. Accurate genomic prediction of human height. Genetics. 2018; 210: 477–497.

4 Wainschtein P. et al. Recovery of trait heritability from whole genome sequence data. bioRxiv. 2019; 588020; Geddes L. Genetic study homes in on height's heritability mystery. Nature. 2019; 568: 444–445.

5 Hesser L. F. The Man Who Fed the World: Nobel Peace Prize Laureate Norman Borlaug and His Battle to End World Hunger. Dallas, TX: Durban House Publishing, 2006; Easterbrook G. Forgotten benefactor of humanity. The Atlantic. 1997; January (https://www.theatlantic.com/magazine/archive/1997/01/forgotten-benefactor-of-humanity/306101/).

6 Zuidhof M. J. et al. Growth, efficiency, and yield of commercial broilers from 1957, 1978, and 2005. Poultry Science. 2014; 93: 2970–2982.

7 Activity reports. Council on Dairy Cattle Breeding (https://uscdcb.com/activity-reports/).

8 Strauss M. The 5,000-year secret history of the watermelon. National Geographic. 2015; August 21 (https://www.nationalgeographic.com/news/2015/08/150821-watermelon-fruit-history-agriculture/); Jayakodi M. et al. Sweet genes in melon and watermelon. Nature Genetics.2019; 51: 1572–1573; Guo S. et al. Resequencing of 414 cultivated and wild watermelon accessions identifies selection for fruit quality traits. Nature Genetics. 2019; 51: 1616–1623.

9 Antoniou A. et al. Average risks of breast and ovarian cancer associated with BRCA1 or BRCA2 mutations detected in case series unselected for family history: A combined analysis of 22 studies. American Journal of Human Genetics. 2003; 72: 1117–1130.

10 Edwards R. G. et al. Early stages of fertilization in vitro of human oocytes matured in vitro. Nature. 1969; 221: 632–635.

11 Подробный разбор научного, исторического и социального контекстов искусственного оплодотворения см. в Ball P. Unnatural: The Heretical Idea of Making People. London, first edition: Bodley Head, 2011.

12 Harris L. The Life poll. Life. 1969; 66 (23): 52–55.

13 Kiefer H. M. Gallup brain: The birth of in vitro fertilization. Gallup.com. 2003; August 5 (https://news.gallup.com/poll/8983/Gallup-Brain-Birth-Vitro-Fertilization.aspx).

14 European Society of Human Reproduction and Embryology. Science Daily 2018; July 3 (https://www.sciencedaily.com/releases/2018/07/180703084127.htm).

15 Danish Health and Medicines Authority, 2017 assisted reproduction report.

16 Cimadomo D. et al. The impact of biopsy on human embryo developmental potential during preimplantation genetic diagnosis. BioMed Research International. 2016; e7193075; Stern H. J. Preimplantation genetic diagnosis: Prenatal testing for embryos finally achieving its potential. Journal of Clinical Medicine. 2014; 3: 280–309.

17 Karavani E. et al. Screening human embryos for polygenic traits has limited utility. Cell. 2019; 179: 1424–1435.e8.

18 Wills M. When forced sterilization was legal in the U. S. JSTOR Daily. 2017; August 3 (https://daily.jstor.org/when-forced-sterilization-was-legal-in-the-u-s/).

19 DenHoed A. The forgotten lessons of the American eugenics movement. New Yorker. 2016; April 27 (https://www.newyorker.com/books/page-turner/the-forgotten-lessons-of-the-american-eugenics-movement); Zimmer C. She Has Her Mother's Laugh: The Powers, Perversions, and Potential of Heredity (1st ed.). New York: Dutton, 2018.

20 Robinson M. R. et al. Genetic evidence of assortative mating in humans. Nature Human Behaviour. 2017; 1: 1–13.

Глава 15. Как мы пишем ДНК

1 Wendt D. Two tons of pig parts: Making insulin in the 1920s. O Say Can You See? (blog for the National Museum of American History). 2013; November 1 (https://americanhistory.si.edu/blog/2013/11/two-tons-of-pig-parts-making-insulin-in-the-1920s.html); Cloning insulin. Genentech. 2016 (https://www.gene.com/stories/cloning-insulin).

2 Простое иллюстрированное объяснение бактериальной трансформации можно найти на сайте «Академии Хана»: https://www.khanacademy.org/science/biology/biotech-dna-technology/dna-cloning-tutorial/a/bacterial-transformation-selection. Более подробные протоколы этапов трансформации, позволяющие понять, как эти процедуры выглядят в реальности, можно найти на сайтах поставщиков расходных материалов и реактивов – например, https://www.thermofisher.com/us/en/home/life-science/cloning/cloning-learning-center/invitrogen-school-of-molecular-biology/molecular-cloning/transformation.html.

3 Cohen S. N. et al. Construction of biologically functional bacterial plasmids in vitro. Proc. Natl. Acad. Sci. 1973; 70: 3240–3244.

4 Culliton B. J. Recombinant DNA: Cambridge City Council votes moratorium. Science. 1976; 193: 300–301.

5 Hughes S. S. Genentech: The Beginnings of Biotech (reprint ed.). Chicago: University of Chicago Press, 2013; Mukherjee S. The Gene: An Intimate History. New York: Scribner, 2016.

6 Nielsen J. Production of biopharmaceutical proteins by yeast. Bioengineered. 2013; 4: 207–211.

7 Behringer R. et al. Manipulating the Mouse Embryo: A Laboratory Manual (4th ed.). Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 2013.

8 Tzfira T., et al. Agrobacterium T-DNA integration: Molecules and models. Trends in Genetics 20, 375–383 (2004).

9 Micronutrient deficiencies: Vitamin A deficiency. World Health Organization. 2009 (https://www.who.int/data/nutrition/nlis/info/vitamin-a-deficiency).

10 Ye X. et al. Engineering the provitamin A (b-carotene) biosynthetic pathway into (carotenoid-free) rice endosperm. Science. 2000; 287: 303–305.

11 Researchers determine that golden rice is an effective source of vitamin A. American Society of Nutrition. 2009 (http://www.goldenrice.org/PDFs/ASNonGR.pdf); Tang G. et al. Golden rice is an effective source of vitamin A. Am. J. Clin. Nutr. 2009; 89: 1776–1783. Массу информации о золотом рисе, в том числе подробное описание его генетики и результаты его проверки на безопасность, можно найти в Golden Rice Humanitarian Board. Golden Rice Project (http://www.goldenrice.org/).

12 Regis E. Golden Rice: The Imperiled Birth of a GMO Superfood. Baltimore: Johns Hopkins University Press, 2019; Regis E. The true story of the genetically modified superfood that almost saved millions. Foreign Policy. 2019; October 17 (https://foreignpolicy.com/2019/10/17/golden-rice-genetically-modified-superfood-almost-saved-millions/).

13 Stokstad E. After 20 years, golden rice nears approval. Science. 2019; 366: 934–934.

14 Gaj T. et al. ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends in Biotechnology. 2013; 31: 397–405.

15 Ishino Y. et al. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. Journal of Bacteriology. 1987; 169: 5429–5433.

16 Mojica F. J. M. et al. Transcription at different salinities of Haloferax mediterranei sequences adjacent to partially modified PstI sites. Molecular Microbiology. 1993; 9: 613–621.

17 Mojica F. J. M. et al. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J. Mol. Evol. 2005; 60: 174–182; Pourcel C. et al. CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. Microbiology. 2005; 151: 653–663; Bolotin A. et al. Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin. Microbiology. 2005; 151: 2551–2561.

18 Ledford H. Five big mysteries about CRISPR's origins. Nature News. 2017; 541: 280; Sorek R. et al. CRISPR-mediated adaptive immune systems in bacteria and archaea. Annual Review of Biochemistry. 2013; 82: 237–266.

19 Palermo G. et al. The invisible dance of CRISPR-Cas9. Physics Today. 2019; 72: 30–36; CRISPR: Gene editing and beyond. Nature Video. 2017 (https://youtu.be/4YKFw2KZA5o); Jiang F., Doudna J. A. CRISPR – Cas9 structures and mechanisms. Annual Review of Biophysics. 2017; 46: 505–529. Эту статью сопровождает информативная компьютерная анимация структурных изменений Cas9, доступная на платформе YouTube: https://www.youtube.com/watch?v=XAtZEIyzd7g, https://www.youtube.com/watch?v=YaXoom7YAY.

20 О ранней истории CRISPR: Campbell M. Francis Mojica: The modest microbiologist who discovered and named CRISPR. Genomics Research from Technology Networks. 2019; October 14 (https://www.technologynetworks.com/genomics/articles/francis-mojica-the-modest-microbiologist-who-discovered-and-named-crispr-325093); Ishino Y. et al. History of CRISPR-Cas from encounter with a mysterious repeated sequence to genome editing technology. Journal of Bacteriology. 2018; 200: e00580-17; Lander E. S. The heroes of CRISPR. Cell. 2016; 164: 18–28. Последняя статья вызывает немало споров – см., например: Vence T. «Heroes of CRISPR» disputed. Scientist Magazine. 2016; January 19 (https://www.the-scientist.com/news-opinion/heroes-of-crispr-disputed-34188) и Morange M. Why Eric Lander's controversial paper «The Heroes of CRISPR» is not solid historical research. American Scientist. 2016; February 17 (https://www.americanscientist.org/blog/macroscope/why-eric-lander%E2 %80 %99s-controversial-paper-%E2 %80 %9Cthe – heroes-of-crispr%E2 %80 %9D-is-not-solid-historical).

21 Jinek M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012; 337: 816–821.

22 Zimmer C. CRISPR natural history in bacteria. Quanta Magazine. 2015; February 6 (https://www.quantamagazine.org/crispr-natural-history-in-bacteria-20150206/).

23 Gasiunas G. et al. Cas9 – crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. PNAS. 2012; 109: E2579 – E2586.

24 Begley S. Who gets credit for CRISPR? Prestigious award singles out three. STAT. 2018; May 31 (https://www.statnews.com/2018/05/31/crispr-scientists-kavli-prize-nanoscience/); Bichell R. Science rewards eureka moments, except when it doesn't. NPR.org. 2016; November 2 (https://www.npr.org/sections/health-shots/2016/11/02/500331130/science-rewards-eureka-moments-except-when-it-doesn't); Guglielmi G. Million-dollar Kavli Prize recognizes scientist scooped on CRISPR. Nature. 2018; 558: 17–18.

25 Cong L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science. 2013; 339: 819–823; Mali P. et al. RNA-guided human genome engineering via Cas9. Science. 2013; 339: 823–826.

26 Anzalone V. et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature. 2019; 576: 149–157; Ledford H. Super-precise new CRISPR tool could tackle a plethora of genetic diseases. Nature. 2019; 574: 464–465.

27 Zsögön A. et al. De novo domestication of wild tomato using genome editing. Nature Biotechnology. 2018; 36: 1211–1216.

28 Tebas P. et al. Gene editing of CCR5 in autologous CD4 T cells of persons infected with HIV. New England Journal of Medicine. 2014; 370: 901–910.

29 Reardon S. Leukaemia success heralds wave of gene-editing therapies. Nature News. 2015; 527: 146.

30 Ledford H. CRISPR treatment inserted directly into the body for first time. Nature. 2020; 579: 185–185; Maeder M. L. et al. Development of a gene-editing approach to restore vision loss in Leber congenital amaurosis type 10. Nature Medicine. 2019; 25: 229–233.

31 Bondy-Denomy J. et al. Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system. Nature. 2013; 493: 429–432; Dolgin E. The kill-switch for CRISPR that could make gene-editing safer. Nature. 2020; 577: 308–310.

32 Marino N. D. et al. Anti-CRISPR protein applications: Natural brakes for CRISPR-Cas technologies. Nature Methods. 2020; 17: 471–479; Liu L. et al. Phage AcrIIA2 DNA mimicry: Structural basis of the CRISPR and anti-CRISPR arms race. Molecular Cell. 2019; 73: 611–620.e3; Shin J. et al. Disabling Cas9 by an anti-CRISPR DNA mimic. Science Advances. 2017; 3: e1701620.

33 Nakamura M. et al. Anti-CRISPR-mediated control of gene editing and synthetic circuits in eukaryotic cells. Nature Communications. 2019; 10: 194.

Глава 16. Конструирование будущего

1 White T. H. The Book of Beasts: Being a Translation from a Latin Bestiary of the Twelfth Century. Madison, WI: UW-Madison Libraries Parallel Press, 2002.

2 Carroll S. B. The Serengeti Rules. Princeton, NJ: Princeton University Press, 2016.

3 Wang H. et al. One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell. 2013; 153: 910–918; Hwang W. Y. et al. Efficient genome editing in zebrafish using a CRISPR-Cas system. Nature Biotechnology. 2013; 31: 227–229; Niu Y. et al. Generation of gene-modified cynomolgus monkey via Cas9/RNA-mediated gene targeting in one-cell embryos. Cell. 2014; 156: 836–843.

4 Cyranoski D. The CRISPR-baby scandal: What's next for human gene-editing. Nature. 2019; 566: 440–442; Outrage intensifies over claims of gene-edited babies. NPR.org. 2018; December 7 (https://www.npr.org/sections/health-shots/2018/12/07/673878474/outrage-intensifies-over-claims-of-gene-edited-babies); Normile D. Chinese scientist who produced genetically altered babies sentenced to 3 years in jail. Science. 2019; December 31 (https://www.sciencemag.org/news/2019/12/chinese-scientist-who-produced-genetically-altered-babies-sentenced-3-years-jail).

5 Jiang S. et al. China suspends scientists who claim to have produced gene-edited babies. CNN. 2018; November 29 (https://www.cnn.com/2018/11/29/health/china-gene-editing-he-jiankui-intl/index.html).

6 Ferdman R. A. Admit it, you didn't know this about baby carrots. The Independent. 2016; January 13 (http://www.independent.co.uk/life-style/food-and-drink/news/admit-it-you-didn-t-know-this-about-baby-carrots-a6810651.html).

7 Erisman J. W. et al. How a century of ammonia synthesis changed the world. Nature Geoscience. 2008; 1: 636–639; Ritter S. K. The Haber-Bosch reaction: An early chemical impact on sustainability. Chemical & Engineering News. 2008; 86 (33) (https://cen.acs.org/articles/86/i33/Haber-Bosch-Reaction-Early-Chemical.html).

8 Owen J. Farming claims almost half earth's land, new maps show. National Geographic. 2005; December 8 (https://www.nationalgeographic.com/news/2005/12/agriculture-food-crops-land/).

9 Cane toad. National Geographic. 2010 (https://www.nationalgeographic.com/animals/amphibians/c/cane-toad/); Butler T. Cane toads increasingly a problem in Australia. Mongabay. 2005 (https://news.mongabay.com/2005/04/cane-toads-increasingly-a-problem-in-australia/).

10 О генных драйвах: Champer J. et al. Cheating evolution: Engineering gene drives to manipulate the fate of wild populations. Nature Reviews Genetics. 2016; 17: 146–159; Wedell N. et al. Gene drive: Progress and prospects. Proceedings of the Royal Society B: Biological Sciences. 2019; 286: 20192709; Scudellari M. Self-destructing mosquitoes and sterilized rodents: The promise of gene drives. Nature. 2019; 571: 160; Kyrou K. et al. A CRISPR – Cas9 gene drive targeting doublesex causes complete population suppression in caged Anopheles gambiae mosquitoes. Nature Biotechnology. 2018; 36: 1062–1066.

11 World malaria report. World Health Organization. 2018 (https://www.who.int/malaria/publications/world-malaria-report-2018/report/en/).

12 Milius S. Genetically modified mosquitoes have been OK'd for a first U. S. test flight. Science News. 2020; August 22 (https://www.sciencenews.org/article/genetically-modified-mosquitoes-florida-test-release); Winter L. 750 Million GM mosquitoes will be released in the Florida Keys. Scientist Magazine. 2020; August 21 (https://www.the-scientist.com/news-opinion/750-million-gm-mosquitoes-will-be-released-in-the-florida-keys-67855); Lacroix R. et al. Open field release of genetically engineered sterile male Aedes aegypti in Malaysia. PLOS ONE. 2012; 7: e42771.

13 Gilbert N. GM mosquitoes wipe out dengue fever in trial. Nature. 2010; November 11 (http://blogs.nature.com/news/2010/11/gm_mosquitoes_wipe_out_dengue.html); Servick K. Study on DNA spread by genetically modified mosquitoes prompts backlash. Science. 2019; September 17 (https://www.sciencemag.org/news/2019/09/study-dna-spread-genetically-modified-mosquitoes-prompts-backlash).

14 Waltz E. First genetically modified mosquitoes released in the United States. Nature. 2021; 591: 175–176; Coffey D. First genetically modified mosquitoes released in U. S. are hatching now. Scientific American. 2021; May 14 (https://www.scientificamerican.com/article/first-genetically-modified-mosquitoes-released-in-u-s-are-hatching-now/).

15 Servick K. Brazil will release billions of lab-grown mosquitoes to combat infectious disease. Will it work? Science. 2016; October 13 (https://www.sciencemag.org/news/2016/10/brazil-will-release-billions-lab-grown-mosquitoes-combat-infectious-disease-will-it).

16 Vella M. R. et al. Evaluating strategies for reversing CRISPR-Cas9 gene drives. Scientific Reports. 2017; 7: 11038.

17 Ledford H. Garage biotech: Life hackers. Nature. 2010; 467: 650–652.

18 О проекте «Открытый инсулин»: https:.//openinsulin.org/