Previous Special Features | PNAS
Gene Regulatory Networks Special Feature. April 5, 2005; 102 (14) [List of Papers]. Long-Range Electron Transfer Special ... Gene Networks in Development and Evolution Special Feature. December 23, 2008; 105 (51) [List of Papers]. Movement Ecology ...
The topological relationship between the large-scale attributes and local interaction patterns of complex networks | PNAS
In contrast, in transcriptional regulatory networks information flow between a transcription factor and the operon (gene) ... Subgraph distributions in cellular networks. a and b show all nodes in the S. cerevisiae transcription regulatory network that ... transcriptional regulatory networks of cells (1, 2, 5, 6), neural networks of C. elegans (2), and some electronic circuits (2) ... the number of transcription factors regulating a target gene) of regulatory networks, which decays faster than a power law, ...
Embryology of a planktonic tunicate reveals traces of sessility | PNAS
... culminating in the deciphering of the first metazoan whole-embryo gene regulatory network (13, 14), lack of comparable ... Journal Club: Gene isolated that triggers asexual births in dandelions. Researchers found a gene that could pave the way toward ... 2001) Brachyury (T) gene expression and notochord development in Oikopleura longicauda (Appendicularia, Urochordata). Dev Genes ... 1996) Requirement of the Manx gene for expression of chordate features in a tailless ascidian larva. Science 274:1205-1208. ...
Spontaneous spatiotemporal waves of gene expression from biological clocks in the leaf | PNAS
gene regulatory networks. Footnotes. *. ↵1B.W. and D.L.K.T. contributed equally to this work. ... Spontaneous spatiotemporal waves of gene expression from biological clocks in the leaf. Bénédicte Wenden, David L. K. Toner, ... We used luciferase reporter gene imaging to monitor circadian rhythms in leaves of Arabidopsis thaliana plants, achieving ... Leaves grown without environmental cycles for up to 3 wk reproducibly showed spatiotemporal waves of gene expression consistent ...
Mapping posttranscriptional regulation of the human glycome uncovers microRNA defining the glycocode | PNAS
Little is known about the regulatory networks controlling this complex biosynthetic process. Recent work points to a role for ... Journal Club: Gene isolated that triggers asexual births in dandelions. Researchers found a gene that could pave the way toward ... We validate three of these predicted miRNA/glycogene regulatory networks: high mannose, fucose, and terminal β-GalNAc, ... We identify and validate several miRNA-glycan networks, including a major decision point in N-linked glycan biosynthesis. ...
Human skin long noncoding RNA WAKMAR1 regulates wound healing by enhancing keratinocyte migration | PNAS
... we constructed a functional protein association network with the WAKMAR1-regulated genes (Fig. 4B). Of note, many genes within ... Further exploration of the epigenetic regulatory network in human skin wound healing will open exciting opportunities for ... S9). Gene set enrichment analysis (GSEA) (30) revealed that a set of cell migration-related genes (Gene Ontology accession GO: ... WAKMAR1 Regulates a Gene Network Mediating Its Promigratory Function in Keratinocytes.. To gain more insight into the ...
Determining the factors driving selective effects of new nonsynonymous mutations | PNAS
... the mutational robustness model predicts that more complex species will have more robust regulatory networks that will better ... Assuming that broadly expressed genes are more pleotropic than tissue-specific genes, we observe that tissue-specific genes ... We filtered for genes that are strictly orthologous between humans and Drosophila, and also required gene sets to have similar ... Furthermore, genes showing greater pleiotropy, as inferred from breadth of gene expression, tend to have a DFE that is less ...
Phosphoproteins in extracellular vesicles as candidate markers for breast cancer | PNAS
... using STRING to identify enriched gene ontology categories and signaling networks (21). We found that several crucial functions ... 2014) Ultradeep human phosphoproteome reveals a distinct regulatory nature of Tyr and Ser/Thr-based signaling. Cell Reports 8(5 ... 2000) STRING: A web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. Nucleic Acids Res 28(18): ... 2003) Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res 13(11):2498-2504 ...
The regulatory utilization of genetic redundancy through responsive backup circuits | PNAS
Such conditional coregulation or partial coregulation of these genes within the transcriptional network was shown to be very ... Regulatory Designs.. What regulatory design could account for a gene sensing and responding to its redundant partners ... For each RBC, a diagram is shown describing the regulatory interactions between the responsive and controlling gene. The plots ... Duplicate genes and paralogous gene families long have been perceived as genomic sources of genetics robustness (1-5). The ...
Molecular basis of Tank-binding kinase 1 activation by transautophosphorylation | PNAS
Journal Club: Gene isolated that triggers asexual births in dandelions. Researchers found a gene that could pave the way toward ... 2007) Interferon regulatory factor 3 is regulated by a dual phosphorylation-dependent switch. J Biol Chem 282:22816-22822. ... 2011) Mapping a dynamic innate immunity protein interaction network regulating type I interferon production. Immunity 35:426- ... E-mail: erind{at}gene.com.. *. Author contributions: X.M., E.H., Q.T.P., and E.C.D. designed research; X.M., E.H., Q.T.P., R.S. ...
Elucidation of tonic and activated B-cell receptor signaling in Burkitt's lymphoma provides insights into regulation of cell...
S3A). Because most annotation databases [e.g., Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), and ... BCR signaling networks. (A and B) Enlarged versions of cluster "b" (A) and cluster "a" (B) of the heatmap shown in Fig. 2E ... 3A). Such p-sites were found on proteins such as tyrosine kinase LYN and regulatory subunits of PI3K, both of which are known ... Among these genes were several that have not yet been described as relevant for BL pathophysiology, including ADP ribosylation ...
Disintermediating your friends: How online dating in the United States displaces other ways of meeting | PNAS
Journal Club: Gene isolated that triggers asexual births in dandelions. Researchers found a gene that could pave the way toward ... Frustrated or engaged? Regulatory focus predicts experiences with online dating. Sue Song, Penelope Lockwood ... Digital networks: Elements of a theoretical framework. Kevin Lewis. Social Networks 2021 ...
Theory of prokaryotic genome evolution | PNAS
... regulators and signaling proteins that enhance regulatory circuits (32), and defense genes (33). However, much more research is ... 2009) Toolbox model of evolution of prokaryotic metabolic networks and their regulation. Proc Natl Acad Sci USA 106(24):9743- ... genes over an individual with x. genes. Conveniently, selection coefficients associated with gene acquisition and gene deletion ... genes, and the variation in genome size is attributed to stochastic gain and loss of genes (Fig. 2). New genes are assumed to ...
Edaravone alleviates Alzheimer's disease-type pathologies and cognitive deficits | PNAS
Journal Club: Gene isolated that triggers asexual births in dandelions. Researchers found a gene that could pave the way toward ... 2012) Neurotoxicity of amyloid β-protein: Synaptic and network dysfunction. Cold Spring Harb Perspect Med 2(7):a006338. ... One approach is to screen current drugs approved by regulatory bodies for other indications and reposition them for AD (12). In ...