Binding of MetJ repressor to specific and nonspecific DNA and effect of S-adenosylmethionine on these interactions.

We have used analytical ultracentrifugation to characterize the binding of the methionine repressor protein, MetJ, to synthetic oligonucleotides containing zero to five specific recognition sites, called metboxes. For all lengths of DNA studied, MetJ binds more tightly to repeats of the consensus sequence than to naturally occurring metboxes, which exhibit a variable number of deviations from the consensus. Strong cooperative binding occurs only in the presence of two or more tandem metboxes, which facilitate protein-protein contacts between adjacent MetJ dimers, but weak affinity is detected even with DNA containing zero or one metbox. The affinity of MetJ for all of the DNA sequences studied is enhanced by the addition of SAM, the known cofactor for MetJ in the cell. This effect extends to oligos containing zero or one metbox, both of which bind two MetJ dimers. In the presence of a large excess concentration of metbox DNA, the effect of cooperativity is to favor populations of DNA oligos bound by two or more MetJ dimers rather than a stochastic redistribution of the repressor onto all available metboxes. These results illustrate the dynamic range of binding affinity and repressor assembly that MetJ can exhibit with DNA and the effect of the corepressor SAM on binding to both specific and nonspecific DNA.

Cryptococcal cell morphology affects host cell interactions and pathogenicity.

Cryptococcus neoformans is a common life-threatening human fungal pathogen. The size of cryptococcal cells is typically 5 to 10 microm. Cell enlargement was observed in vivo, producing cells up to 100 microm. These morphological changes in cell size affected pathogenicity via reducing phagocytosis by host mononuclear cells, increasing resistance to oxidative and nitrosative stress, and correlated with reduced penetration of the central nervous system. Cell enlargement was stimulated by coinfection with strains of opposite mating type, and ste3aDelta pheromone receptor mutant strains had reduced cell enlargement. Finally, analysis of DNA content in this novel cell type revealed that these enlarged cells were polyploid, uninucleate, and produced daughter cells in vivo. These results describe a novel mechanism by which C. neoformans evades host phagocytosis to allow survival of a subset of the population at early stages of infection. Thus, morphological changes play unique and specialized roles during infection.

Integrin-mediated interactions with extracellular matrix proteins for nucleus pulposus cells of the human intervertebral disc.

The extracellular matrix (ECM) of the human intervertebral disc is rich in molecules that interact with cells through integrin-mediated attachments. Porcine nucleus pulposus (NP) cells have been shown to interact with laminin (LM) isoforms LM-111 and LM-511 through select integrins that regulate biosynthesis and cell attachment. Since human NP cells lose many phenotypic characteristics with age, attachment and interaction with the ECM may be altered. Expression of LM-binding integrins was quantified for human NP cells using flow cytometry. The cell-ECM attachment mechanism was determined by quantifying cell attachment to LM-111, LM-511, or type II collagen after functionally blocking specific integrin subunits. Human NP cells express integrins β1, α3, and α5, with over 70% of cells positive for each subunit. Blocking subunit β1 inhibited NP cell attachment to all substrates. Blocking subunits α1, α2, α3, and α5 simultaneously, but not individually, inhibits NP cell attachment to laminins. While integrin α6β1 mediated porcine NP cell attachment to LM-111, we found integrins α3, α5, and β1 instead contributed to human NP cell attachment. These findings identify integrin subunits that may mediate interactions with the ECM for human NP cells and could be used to promote cell attachment, survival, and biosynthesis in cell-based therapeutics.

Computational inference of neural information flow networks.

Determining how information flows along anatomical brain pathways is a fundamental requirement for understanding how animals perceive their environments, learn, and behave. Attempts to reveal such neural information flow have been made using linear computational methods, but neural interactions are known to be nonlinear. Here, we demonstrate that a dynamic Bayesian network (DBN) inference algorithm we originally developed to infer nonlinear transcriptional regulatory networks from gene expression data collected with microarrays is also successful at inferring nonlinear neural information flow networks from electrophysiology data collected with microelectrode arrays. The inferred networks we recover from the songbird auditory pathway are correctly restricted to a subset of known anatomical paths, are consistent with timing of the system, and reveal both the importance of reciprocal feedback in auditory processing and greater information flow to higher-order auditory areas when birds hear natural as opposed to synthetic sounds. A linear method applied to the same data incorrectly produces networks with information flow to non-neural tissue and over paths known not to exist. To our knowledge, this study represents the first biologically validated demonstration of an algorithm to successfully infer neural information flow networks.

Biological and physical interactions on a tropical island coral reef: Transport and retention processes on moorea, French Polynesia

The Moorea Coral Reef Long Term Ecological Research project funded by the US National Science Foundation includes multidisciplinary studies of physical processes driving ecological dynamics across the fringing reef, back reef, and fore reef habitats of Moorea, French Polynesia. A network of oceanographic moorings and a variety of other approaches have been used to investigate the biological and biogeochemical aspects of water transport and retention processes in this system. There is evidence to support the hypothesis that a low-frequency counterclockwise flow around the island is superimposed on the relatively strong alongshore currents on each side of the island. Despite the rapid flow and flushing of the back reef, waters over the reef display chemical and biological characteristics distinct from those offshore. The patterns include higher nutrient and lower dissolved organic carbon concentrations, distinct microbial community compositions among habitats, and reef assemblages of zooplankton that exhibit migration behavior, suggesting multigenerational residence on the reef. Zooplankton consumption by planktivorous fish on the reef reflects both retention of reef-associated taxa and capture by the reef community of resources originating offshore. Coral recruitment and population genetics of reef fishes point to retention of larvae within the system and high recruitment levels from local adult populations. The combined results suggest that a broad suite of physical and biological processes contribute to high retention of externally derived and locally produced organic materials within this island coral reef system. © 2013 by The Oceanography Society. All rights reserved.

Steady flow dynamics during granular impact.

We study experimentally and computationally the dynamics of granular flow during impacts where intruders strike a collection of disks from above. In the regime where granular force dynamics are much more rapid than the intruder motion, we find that the particle flow near the intruder is proportional to the instantaneous intruder speed; it is essentially constant when normalized by that speed. The granular flow is nearly divergence free and remains in balance with the intruder, despite the latter's rapid deceleration. Simulations indicate that this observation is insensitive to grain properties, which can be explained by the separation of time scales between intergrain force dynamics and intruder dynamics. Assuming there is a comparable separation of time scales, we expect that our results are applicable to a broad class of dynamic or transient granular flows. Our results suggest that descriptions of static-in-time granular flows might be extended or modified to describe these dynamic flows. Additionally, we find that accurate grain-grain interactions are not necessary to correctly capture the granular flow in this regime.