Biologically inspired sensing: infrared spectroscopic analysis of cell responses to an inhalation health hazard

This work describes the development of a biologically based sensing technique to quantify chemical agents that pose inhalation health hazards. The approach utilizes cultured epithelial cells (A549 human type II pneumocytes) of the lung, exposed to potential toxins and monitored through the noninvasive means of infrared spectroscopy to quantify changes to cell physiology and function. Cell response to Streptolysin O, a cholesterol-binding cytolysin, is investigated here. Infrared spectra display changes in cell physiology indicative of membrane damage, altered proteins, and some nucleic acid damage. Methods to improve cell adhesion through modification of support surface properties are detailed. This spectroscopic approach not only provides a robust means to detect potential toxins but also provides information on modes of damage and mechanisms of cellular response.     

Chromatin remodeling by ISW2 and SWI/SNF requires DNA translocation inside the nucleosome

Chromatin-remodeling complexes regulate access to nucleosomal DNA by mobilizing nucleosomes in an ATP-dependent manner. In this study, we find that chromatin remodeling by SWI/SNF and ISW2 involves DNA translocation inside nucleosomes two helical turns from the dyad axis at superhelical location-2. DNA translocation at this internal position does not require the propagation of a DNA twist from the site of translocation to the entry/exit sites for nucleosome movement. Nucleosomes are moved in 9- to 11- or approximately 50-base-pair increments by ISW2 or SWI/SNF, respectively, presumably through the formation of DNA loops on the nucleosome surface. Remodeling by ISW2 but not SWI/SNF requires DNA torsional strain near the site of translocation, which may work in conjunction with conformational changes of ISW2 to promote nucleosome movement on DNA. The difference in step size of nucleosome movement by SWI/SNF and ISW2 demonstrates how SWI/SNF may be more disruptive to nucleosome structure than ISW2.     

Investigating the role of native propionyl‐CoA and methylmalonyl‐CoA metabolism on heterologous polyketide production in Escherichia coli

6‐Deoxyerythronolide B (6dEB) is the macrocyclic aglycone precursor of the antibiotic natural product erythromycin. Heterologous production of 6dEB in Escherichia coli was accomplished, in part, by designed over‐expression of a native prpE gene (encoding a propionyl‐CoA synthetase) and heterologous pcc genes (encoding a propionyl‐CoA carboxylase) to supply the needed propionyl‐CoA and (2S)‐methylmalonyl‐CoA biosynthetic substrates. Separate E. coli metabolism includes three enzymes, Sbm (a methylmalonyl‐CoA mutase), YgfG (a methylmalonyl‐CoA decarboxylase), and YgfH (a propionyl‐CoA:succinate CoA transferase), also involved in propionyl‐CoA and methylmalonyl‐CoA metabolism. In this study, the sbm, ygfG, and ygfH genes were individually deleted and over‐expressed to investigate their effect on heterologous 6dEB production. Our results indicate that the deletion and over‐expression of sbm did not influence 6dEB production; ygfG over‐expression reduced 6dEB production by fourfold while ygfH deletion increased 6dEB titers from 65 to 129 mg/L in shake flask experiments. It was also found that native E. coli metabolism could support 6dEB biosynthesis in the absence of exogenous propionate and the substrate provision pcc genes. Lastly, the effect of the ygfH deletion was tested in batch bioreactor cultures in which 6dEB titers improved from 206 to 527 mg/L. Biotechnol. Bioeng. 2010; 105: 567–573. © 2009 Wiley Periodicals, Inc.     

Sperm plasma membrane breakdown during Drosophila fertilization requires sneaky, an acrosomal membrane protein

Fertilization typically involves membrane fusion between sperm and eggs. In Drosophila, however, sperm enter eggs with membranes intact. Consequently, sperm plasma membrane breakdown (PMBD) and subsequent events of sperm activation occur in the egg cytoplasm. We previously proposed that mutations in the sneaky (snky) gene result in male sterility due to failure in PMBD. Here we support this proposal by demonstrating persistence of a plasma membrane protein around the head of snky sperm after entry into the egg. We further show that snky is expressed in testes and encodes a predicted integral membrane protein with multiple transmembrane domains, a DC-STAMP-like domain, and a variant RING finger. Using a transgene that expresses an active Snky-Green fluorescent protein fusion (Snky-GFP), we show that the protein is localized to the acrosome, a membrane-bound vesicle located at the apical tip of sperm. Snky-GFP also allowed us to follow the fate of the protein and the acrosome during fertilization. In many animals, the acrosome is a secretory vesicle with exocytosis essential for sperm penetration through the egg coats. Surprisingly, we find that the Drosophila acrosome is a paternally inherited structure. We provide evidence that the acrosome induces changes in sperm plasma membrane, exclusive of exocytosis and through the action of the acrosomal membrane protein Snky. Existence of testis-expressed Snky-like genes in many animals, including humans, suggests conserved protein function. We relate the characteristics of Drosophila Snky, acrosome function and sperm PMBD to membrane fusion events that occur in other systems.     

Modulation of eukaryotic cell apoptosis by members of the bacterial order Actinomycetales

Apoptosis, or programmed cell death, is normally responsible for the orderly elimination of aged or damaged cells, and is a necessary part of the homeostasis and development of multicellular organisms. Some pathogenic bacteria can disrupt this process by triggering excess apoptosis or by preventing it when appropriate. Either event can lead to disease. There has been extensive research into the modulation of host cell death by microorganisms, and several reviews have been published on the phenomenon. Rather than covering the entire field, this review focuses on the dysregulation of host cell apoptosis by members of the order Actinomycetales, containing the genera Corynebacterium, Mycobacterium, Rhodococcus, and Nocardia.     

Regulation of ISW2 by concerted action of histone H4 tail and extranucleosomal DNA

The stable contact of ISW2 with nucleosomal DNA approximately 20 bp from the dyad was shown by DNA footprinting and photoaffinity labeling using recombinant histone octamers to require the histone H4 N-terminal tail. Efficient ISW2 remodeling also required the H4 N-terminal tail, although the lack of the H4 tail can be mostly compensated for by increasing the incubation time or concentration of ISW2. Similarly, the length of extranucleosomal DNA affected the stable contact of ISW2 with this same internal nucleosomal site, with the optimal length being 70 to 85 bp. These data indicate the histone H4 tail, in concert with a favorable length of extranucleosomal DNA, recruits and properly orients ISW2 onto the nucleosome for efficient nucleosome remodeling. One consequence of this property of ISW2 is likely its previously observed nucleosome spacing activity.     

Detecting emergent effects of multiple predator species

When foraging together, multiple predator species that share a single prey often cause prey mortality that cannot be predicted based on knowledge of predation by each species separately. Modeling and managing the effects of multiple predator species depend on accurately assessing these combined effects. Two methods are currently used to experimentally examine combined predation by multiple predator species: the additive and substitutive experimental designs. I simultaneously employed both experimental designs to examine predation by two crab species on shared mussel prey. I show that the two methods yield results that disagree both quantitatively and qualitatively, leading to very different conclusions about the way that predator species combine to affect prey mortality. This discrepancy occurred because the two methods examine complimentary, but not interchangeable questions. I advocate using an experimental design that incorporates both additive and substitutive designs to achieve a more complete understanding of the combined effects of multiple predator species.     

Genome sequence of the human- and animal-pathogenic strain Nocardia cyriacigeorgica GUH-2

The pathogenic strain Nocardia cyriacigeorgica GUH-2 was isolated from a fatal human nocardiosis case, and its genome was sequenced. The complete genomic sequence of this strain contains 6,194,645 bp, an average G+C content of 68.37%, and no plasmids. We also identified several protein-coding genes to which N. cyriacigeorgica's virulence can potentially be attributed.     

A Blessing and a Curse? Political Institutions in the Growth and Decay of Generalized Trust: A Cross-National Panel Analysis, 1980–2009

Despite decades of research on social capital, studies that explore the relationship between political institutions and generalized trust-a key element of social capital-across time are sparse. To address this issue, we use various cross-national public-opinion data sets including the World Values Survey and employ pooled time-series OLS regression and fixed- and random-effects estimation techniques on an unbalanced panel of 74 countries and 248 observations spread over a 29-year time period. With these data and methods, we investigate the impact of five political-institutional factors-legal property rights, market regulations, labor market regulations, universality of socioeconomic provisions, and power-sharing capacity-on generalized trust. We find that generalized trust increases monotonically with the quality of property rights institutions, that labor market regulations increase generalized trust, and that power-sharing capacity of the state decreases generalized trust. While generalized trust increases as the government regulation of credit, business, and economic markets decreases and as the universality of socioeconomic provisions increases, both effects appear to be more sensitive to the countries included and the modeling techniques employed than the other political-institutional factors. In short, we find that political institutions simultaneously promote and undermine generalized trust.