Простое начало. Как четыре закона физики формируют живой мир
Шрифт:
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 –
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.