The effect of fiddler crab burrowing on sediment mixing and radionuclide profiles along a topographic gradient in a southeastern salt marsh

Fiddler crabs are one of the principal agents of bioturbation in intertidal salt marshes. The physical, chemical, and biological properties of sediments can be modified by fiddler crab burrowing activity. This study examined the effect of fiddler crab burrowing on sediment reworking and the distributions of 210Pb and 137Cs in salt marsh sediments at North Inlet Estuary, South Carolina. Fiddler crab burrow density, turnover, and volume were measured along a transect from the forest to the creek bank. Burrow density ranged between 40 and 300 burrows m-2 with highest densities at the creek bank. Sediment reworking is related to burrow turnover, density and size. Sediment reworking rates ranged between 4.4 × 103 and 5.7 × 104 cm3 m-2 y-1. Excess 210Pb and 137Cs profiles indicated that fiddler crab burrowing mixed the top 8 to 15 cm of sediment. Direct field measurements of burrow density, turnover, and size were used as input to a modified version of the regeneration model of Gardner et al. (1987) to assess the effect of fiddler crab bioturbation on 210Pb profiles. The modification takes into account the filling of abandoned fiddler crab burrows from both the infilling of surface sediment and the collapse of burrow walls. Model results were in good agreement with the observed 210Pb distributions in the sediments. Overall the results of this study suggest that fiddler crabs directly influence sediment composition and biogeochemical cycles in salt marsh systems

Material temperature effects on final product size for new profile ring mill forming technology

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 1999.Includes bibliographical references (leaf 72).by Andrew D. McCraith.S.M

Using graph concepts to understand the organization of complex systems

Complex networks are universal, arising in fields as disparate as sociology, physics, and biology. In the past decade, extensive research into the properties and behaviors of complex systems has uncovered surprising commonalities among the topologies of different systems. Attempts to explain these similarities have led to the ongoing development and refinement of network models and graph-theoretical analysis techniques with which to characterize and understand complexity. In this tutorial, we demonstrate through illustrative examples, how network measures and models have contributed to the elucidation of the organization of complex systems.Comment: v(1) 38 pages, 7 figures, to appear in the International Journal of Bifurcation and Chaos v(2) Line spacing changed; now 23 pages, 7 figures, to appear in the Special Issue "Complex Networks' Structure and Dynamics'' of the International Journal of Bifurcation and Chaos (Volume 17, Issue 7, July 2007) edited by S. Boccaletti and V. Lator

A systematic analysis of host factors reveals a Med23-interferon-λ regulatory axis against herpes simplex virus type 1 replication

Herpes simplex virus type 1 (HSV-1) is a neurotropic virus causing vesicular oral or genital skin lesions, meningitis and other diseases particularly harmful in immunocompromised individuals. To comprehensively investigate the complex interaction between HSV-1 and its host we combined two genome-scale screens for host factors (HFs) involved in virus replication. A yeast two-hybrid screen for protein interactions and a RNA interference (RNAi) screen with a druggable genome small interfering RNA (siRNA) library confirmed existing and identified novel HFs which functionally influence HSV-1 infection. Bioinformatic analyses found the 358 HFs were enriched for several pathways and multi-protein complexes. Of particular interest was the identification of Med23 as a strongly anti-viral component of the largely pro-viral Mediator complex, which links specific transcription factors to RNA polymerase II. The anti-viral effect of Med23 on HSV-1 replication was confirmed in gain-of-function gene overexpression experiments, and this inhibitory effect was specific to HSV-1, as a range of other viruses including Vaccinia virus and Semliki Forest virus were unaffected by Med23 depletion. We found Med23 significantly upregulated expression of the type III interferon family (IFN-λ) at the mRNA and protein level by directly interacting with the transcription factor IRF7. The synergistic effect of Med23 and IRF7 on IFN-λ induction suggests this is the major transcription factor for IFN-λ expression. Genotypic analysis of patients suffering recurrent orofacial HSV-1 outbreaks, previously shown to be deficient in IFN-λ secretion, found a significant correlation with a single nucleotide polymorphism in the IFN-λ3 (IL28b) promoter strongly linked to Hepatitis C disease and treatment outcome. This paper describes a link between Med23 and IFN-λ, provides evidence for the crucial role of IFN-λ in HSV-1 immune control, and highlights the power of integrative genome-scale approaches to identify HFs critical for disease progression and outcome

Vaccinia Virus G8R Protein: A Structural Ortholog of Proliferating Cell Nuclear Antigen (PCNA)

BACKGROUND: Eukaryotic DNA replication involves the synthesis of both a DNA leading and lagging strand, the latter requiring several additional proteins including flap endonuclease (FEN-1) and proliferating cell nuclear antigen (PCNA) in order to remove RNA primers used in the synthesis of Okazaki fragments. Poxviruses are complex viruses (dsDNA genomes) that infect eukaryotes, but surprisingly little is known about the process of DNA replication. Given our previous results that the vaccinia virus (VACV) G5R protein may be structurally similar to a FEN-1-like protein and a recent finding that poxviruses encode a primase function, we undertook a series of in silico analyses to identify whether VACV also encodes a PCNA-like protein. RESULTS: An InterProScan of all VACV proteins using the JIPS software package was used to identify any PCNA-like proteins. The VACV G8R protein was identified as the only vaccinia protein that contained a PCNA-like sliding clamp motif. The VACV G8R protein plays a role in poxvirus late transcription and is known to interact with several other poxvirus proteins including itself. The secondary and tertiary structure of the VACV G8R protein was predicted and compared to the secondary and tertiary structure of both human and yeast PCNA proteins, and a high degree of similarity between all three proteins was noted. CONCLUSIONS: The structure of the VACV G8R protein is predicted to closely resemble the eukaryotic PCNA protein; it possesses several other features including a conserved ubiquitylation and SUMOylation site that suggest that, like its counterpart in T4 bacteriophage (gp45), it may function as a sliding clamp ushering transcription factors to RNA polymerase during late transcription

A Human Protein Interaction Network Shows Conservation of Aging Processes between Human and Invertebrate Species

We have mapped a protein interaction network of human homologs of proteins that modify longevity in invertebrate species. This network is derived from a proteome-scale human protein interaction Core Network generated through unbiased high-throughput yeast two-hybrid searches. The longevity network is composed of 175 human homologs of proteins known to confer increased longevity through loss of function in yeast, nematode, or fly, and 2,163 additional human proteins that interact with these homologs. Overall, the network consists of 3,271 binary interactions among 2,338 unique proteins. A comparison of the average node degree of the human longevity homologs with random sets of proteins in the Core Network indicates that human homologs of longevity proteins are highly connected hubs with a mean node degree of 18.8 partners. Shortest path length analysis shows that proteins in this network are significantly more connected than would be expected by chance. To examine the relationship of this network to human aging phenotypes, we compared the genes encoding longevity network proteins to genes known to be changed transcriptionally during aging in human muscle. In the case of both the longevity protein homologs and their interactors, we observed enrichments for differentially expressed genes in the network. To determine whether homologs of human longevity interacting proteins can modulate life span in invertebrates, homologs of 18 human FRAP1 interacting proteins showing significant changes in human aging muscle were tested for effects on nematode life span using RNAi. Of 18 genes tested, 33% extended life span when knocked-down in Caenorhabditis elegans. These observations indicate that a broad class of longevity genes identified in invertebrate models of aging have relevance to human aging. They also indicate that the longevity protein interaction network presented here is enriched for novel conserved longevity proteins