Single-order-parameter description of glass-forming liquids:A one-frequency test

Thermo-viscoelastic linear-response functions are calculated from the master equation describing viscous liquid inherent dynamics. From the imaginary parts of the frequency-dependent isobaric specific heat, isothermal compressibility, and isobaric thermal expansion coefficient, we define a "linear dynamic Prigogine-Defay ratio" with the property that if this quantity is unity atone frequency, then it is unity at all frequencies. This happens if and only if there is a single-order-parameter description of the thermo-viscoelastic linear responses via an order parameter (which may be non-exponential in time). Generalizations to other cases of thermodynamic control parameters than temperature and pressure are treated in an Appendix.Comment: Replaces arXiv:cond-mat/040570

Genomic SELEX for Hfq-binding RNAs identifies genomic aptamers predominantly in antisense transcripts

An unexpectedly high number of regulatory RNAs have been recently discovered that fine-tune the function of genes at all levels of expression. We employed Genomic SELEX, a method to identify protein-binding RNAs encoded in the genome, to search for further regulatory RNAs in Escherichia coli. We used the global regulator protein Hfq as bait, because it can interact with a large number of RNAs, promoting their interaction. The enriched SELEX pool was subjected to deep sequencing, and 8865 sequences were mapped to the E. coli genome. These short sequences represent genomic Hfq-aptamers and are part of potential regulatory elements within RNA molecules. The motif 5′-AAYAAYAA-3′ was enriched in the selected RNAs and confers low-nanomolar affinity to Hfq. The motif was confirmed to bind Hfq by DMS footprinting. The Hfq aptamers are 4-fold more frequent on the antisense strand of protein coding genes than on the sense strand. They were enriched opposite to translation start sites or opposite to intervening sequences between ORFs in operons. These results expand the repertoire of Hfq targets and also suggest that Hfq might regulate the expression of a large number of genes via interaction with cis-antisense RNAs

Complexity Theory for a New Managerial Paradigm: A Research Framework

In this work, we supply a theoretical framework of how organizations can embed complexity management and sustainable development into their policies and actions. The proposed framework may lead to a new management paradigm, attempting to link the main concepts of complexity theory, change management, knowledge management, sustainable development, and cybernetics. We highlight how the processes of organizational change have occurred as a result of the move to adapt to the changes in the various global and international business environments and how this transformation has led to the shift toward the present innovation economy. We also point how organizational change needs to deal with sustainability, so that the change may be consistent with present needs, without compromising the future

The Peter Pan paradigm

Genetic and environmental agents that disrupt organogenesis are numerous and well described. Less well established, however, is the role of delay in the developmental processes that yield functionally immature tissues at birth. Evidence is mounting that organs do not continue to develop postnatally in the context of these organogenesis insults, condemning the patient to utilize under-developed tissues for adult processes. These poorly differentiated organs may appear histologically normal at birth but with age may deteriorate revealing progressive or adult-onset pathology. The genetic and molecular underpinning of the proposed paradigm reveals the need for a comprehensive systems biology approach to evaluate the role of maternal-fetal environment on organogenesis

Heat capacity changes associated with nucleic acid folding

Abstract: Whereas heat capacity changes (DC P s) associated with folding transitions are commonplace in the literature of protein folding, they have long been considered a minor energetic contributor in nucleic acid folding. Recent advances in the understanding of nucleic acid folding and improved technology for measuring the energetics of folding transitions have allowed a greater experimental window for measuring these effects. We present in this review a survey of current literature that confronts the issue of DC P s associated with nucleic acid folding transitions. This work helps to gather the molecular insights that can be gleaned from analysis of DC P s and points toward the challenges that will need to be overcome if the energetic contribution of DC P terms are to be put to use in improving free energy calculations for nucleic acid structure prediction.