life inspired

"Your DNA is not a blueprint. Day by day, week by week, your genes are in a conversation with your surroundings. Your neighbors, your family, your feelings of loneliness: They don’t just get under your skin, they get into the control rooms of your cells. Inside the new social science of genetics." News article @ Pacific Standard

Labels: dna, gene regulation

Conducting research on sea urchins at the Naples Zoological Station, 19th century developmental biologist Hans Driesch demonstrated the totipotent nature of early embryonic cells, contributing significantly to the then-nascent field of “developmental mechanics.” [...] As developmental biology moves into its third century of existence as a modern science, we find that major advances are bringing us full-circle to approach central questions posed by early pioneers[...]. In PNAS, Peter et al. (2) describe a quantitative model to describe at a molecular level the processes of cellular differentiation that have fascinated generations of biologists, providing a means to link developmental and systems biology. See full letter @ PNAS. See original reference:

Peter IS, Faure E, Davidson EH (2012) "Predictive computation of genomic logic processing functions in embryonic development". PNAS 109:16434–16442.

Labels: boolean networks, complex networks, gene regulation

"The spatial organization of cell fates during development involves the interpretation of morphogen gradients by cellular signaling cascades and transcriptional networks. Recent studies use biophysical models, genetics, and quantitative imaging to unravel how tissue-level morphogen behavior arises from subcellular events. Moreover, data from several systems show that morphogen gradients, downstream signaling, and the activity of cell-intrinsic transcriptional networks change dynamically during pattern formation. Studies from Drosophila and now also vertebrates suggest that transcriptional network dynamics are central to the generation of gene expression patterns. Together, this leads to the view that pattern formation is an emergent behavior that results from the coordination of events occurring across molecular, cellular, and tissue scales. The development of novel approaches to study this complex process remains a challenge." Full review @ Science

Labels: development, gene regulation, morphogenesis

"Combining transcriptomic and signaling data, we develop an evolutionary computational procedure that allows obtaining alternative genomic transcriptional regulatory network (GTRN) that still maintains its adaptability to dynamic environments. We apply our methodology to an E. coli GTRN and show that it could be rewired to simpler transcriptional regulatory structures." Full paper @
PNAA

Labels: evolutionary algorithms, gene regulation, synthetic biology, systems biology

"Although long-studied, the underlying basis of mammalian coat patterns remains unclear. By studying a large number of cat species and varieties, Kaelin et al. identified two genes, Taqpep and Edn3, as critical factors in the development of feline pigment patterns."

See news piece @ NYTimes. Paper: Kaelin et al [2012]. "Specifying and Sustaining Pigmentation Patterns in Domestic and Wild Cats." Science. 337 (6101), 1536-1541.

Labels: gene regulation, genotype-phenotype map

Mapping the Mind: Online Interactive Atlas Shows Activity of 20,000 Brain-Related Genes. A meticulously constructed atlas of the human brain reveals the molecular roots of mental illness—and of everyday behavior. Full article @ Scientific American

Labels: brain, gene regulation, imaging

"To convert the encoded genetic information from eukaryotic DNA into proteins, base sequences of genes are first transcribed into RNA by RNA polymerase II. To produce functional RNA molecules, dozens of accessory factors are needed to define the proper locations for RNA polymerase II to begin and end transcription. Although we have some basic knowledge about how these factors work, it is still not possible to take a eukaryotic genome sequence and accurately predict what RNA species it will produce. Recent efforts to map and sequence "transcriptomes" have only increased the challenge by revealing a much more complex set of RNAs than expected, including many that do not produce proteins". Full article @ Science

Labels: gene regulation, genomics, RNA

"The known world of RNA is expanding faster than that of any other cellular building block. The latest additions are types of long and short non-coding RNAs formed by bidirectional transcription and unusual processing. The relationship between DNA, RNA and protein is no longer as simple as we once thought — that specific genomic sequences are transcribed into messenger RNAs, which are then translated into proteins. In recent years, a flurry of studies has reported the existence of a large and growing family of non-protein-coding RNAs (ncRNAs), describing the different mechanisms of their transcription and their role in regulating gene expression." Full article @ Nature

Labels: complexity, gene regulation, RNA