Evolutionary analyses of the human genome

Li, Wen-Hsiung; Gu, Zhenglong; Wang, Haidong; Nekrutenko, Anton

doi:10.1038/35057039

Cited by 426 publications

(256 citation statements)

References 5 publications

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“…Finally, the experimental FRET efficiency can be calculated using Eq 4: (4) where F D and F DA are the fluorescence of the donor in the absence and presence of acceptor, respectively.…”

Section: Binary Probe Designmentioning

confidence: 99%

“…The elucidation of the human genome at the beginning of this century opened the door to new possibilities for treatment and diagnosis of disease, 1 a better understanding of memory and behaviors, 2,3 and the study of our genetic evolution as a species, 4 among other important, little understood areas of study. However, this achievement also poses a challenge for the development of new and improved methods for the detection and monitoring of DNA or RNA either in vitro or in vivo.…”

Section: Introductionmentioning

confidence: 99%

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Design and characterization of two-dye and three-dye binary fluorescent probes for mRNA detection

Martí

Jockusch

et al. 2007

Tetrahedron

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We report the design, synthesis and characterization of binary oligonucleotide probes for mRNA detection. The probes were designed to avoid common problems found in standard binary probes such as direct excitation of the acceptor fluorophore and overlap between the donor and acceptor emission spectra. Two different probes were constructed that contained an array of either two or three dyes and that were characterized using steady-state fluorescence spectroscopy, time-resolved fluorescence spectroscopy and fluorescence depolarization measurements. The three-dye binary probe (BP-3d) consists of a Fam fluorophore which acts as a donor, collecting light and transferring it as energy to Tamra, which subsequently transfers energy to Cy5 when the two probes are hybridized to mRNA. This design allows the use of 488 nm excitation, which avoids the direct excitation of Cy5 and at the same time provides a good fluorescence resonance energy transfer (FRET) efficiency. The two-dye binary probe system (BP-2d) was constructed of Alexa488 and Cy5 fluorophores. Although the overlap between the fluorescence of Alexa488 and the absorption of Cy5 is relatively low, FRET still occurs due to their close physical proximity when the probes are hybridized to mRNA. This framework also decreases the direct excitation of Cy5 and reduces the fluorescence overlap between the donor and the acceptor. Picosecond time-resolved spectroscopy showed a reduction in the fluorescence lifetime of donor fluorophores after the formation of the hybrid between the probes and target mRNA. Interestingly, BP-2d in the presence of mRNA shows a slow rise in the fluorescence decay of Cy5 due to a relatively low FRET rate, which together with the reduction in the Alexa488 lifetime provides a way to improve the signal to background ratio using time-resolved fluorescence spectra (TRES). In addition, fluorescence depolarization measurements showed complete depolarization of the acceptor dyes (Cy5) for both BP-3d (due to sequential FRET steps) and BP-2d (due to the relatively low FRET rate) in the presence of the mRNA target.

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“…Finally, the experimental FRET efficiency can be calculated using Eq 4: (4) where F D and F DA are the fluorescence of the donor in the absence and presence of acceptor, respectively.…”

Section: Binary Probe Designmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Design and characterization of two-dye and three-dye binary fluorescent probes for mRNA detection

Martí

Jockusch

et al. 2007

Tetrahedron

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“…First, gene number is not as low as it seems because 2 about 40% of human genes are alternatively spliced. Second, human proteins contain novel combinations of domains, which allow for increased protein-protein interactions, compared to invertebrate proteins [1][2][3]. Third, posttranslational modification of proteins adds complexity.…”

Section: Introductionmentioning

confidence: 99%

Evolution of adrenal and sex steroid action in vertebrates: a ligand‐based mechanism for complexity

Baker

2003

BioEssays

105

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SummaryVarious explanations have been proposed to account for complex differentiation and development in humans, despite the human genome containing only two to three times the number of genes in invertebrates. Ignored are the actions of adrenal and sex steroids-androgens, estrogens, glucocorticoids, mineralocorticoids, and progestins-which act through receptors that arose from an ancestral nuclear receptor in a protochordate. This ligand-based mechanism is unique to vertebrates and was integrated into the already robust network of transcription factors in invertebrates. Adrenal and sex steroids influence almost all aspects of vertebrate differentiation and development. I propose that evolution of this ligand-based mechanism in a primitive vertebrate was an important contribution to vertebrate complexity. Sequencing of genomes from a cephalochordate, such as amphioxus, and from hagfish and lamprey will establish early events in the evolution of steroid hormone signaling, and also allow genetic studies to elucidate how vertebrate complexity depends on steroid hormones.

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“…Gene duplication plays a leading role in the generation of novel gene function [23]. Under the driving force of adaptive evolution, vast majority of duplicated genes are deleted or degrade into pseudogenes [24,25]. More rarely, some new copies acquire novel functions and contribute to organism complexity and adaptability [26].…”

Section: Discussionmentioning

confidence: 99%

Expression and function analysis of two naturally truncated MyD88 variants in the Pacific oyster Crassostrea gigas

Xu¹,

Zhang²,

Li³

et al. 2015

Fish & Shellfish Immunology

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Evolutionary analyses of the human genome

Cited by 426 publications

References 5 publications

Design and characterization of two-dye and three-dye binary fluorescent probes for mRNA detection

Design and characterization of two-dye and three-dye binary fluorescent probes for mRNA detection

Evolution of adrenal and sex steroid action in vertebrates: a ligand‐based mechanism for complexity

Expression and function analysis of two naturally truncated MyD88 variants in the Pacific oyster Crassostrea gigas

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