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.