New materials from proteins and peptides

In this review we highlight recent accomplishments in the design of materials from proteins and peptides. Examples include hydrogels made from aggregating designed β-hairpin peptides, whose physical properties respond to small changes in the amino acid composition of the peptide; materials that combine different segments of natural elastomeric proteins - such as elastin, resilin, silk fibroin whose bulk properties are dictated in unanticipated ways by their composition; and hydrogels formed by strings or arrays of protein modules, which are cross-linked by multivalent versions of their peptide ligands, and which may exhibit exquisite stimuli-responsive behavior. The suitability of the unique properties of such new materials for practical applications is also considered.     

A direct interaction between the Utp6 half-a-tetratricopeptide repeat domain and a specific peptide in Utp21 is essential for efficient pre-rRNA processing

The small subunit (SSU) processome is a ribosome biogenesis intermediate that assembles from its subcomplexes onto the pre-18S rRNA with yet unknown order and structure. Here, we investigate the architecture of the UtpB subcomplex of the SSU processome, focusing on the interaction between the half-a-tetratricopeptide repeat (HAT) domain of Utp6 and a specific peptide in Utp21. We present a comprehensive map of the interactions within the UtpB subcomplex and further show that the N-terminal domain of Utp6 interacts with Utp18 while the HAT domain interacts with Utp21. Using a panel of point and deletion mutants of Utp6, we show that an intact HAT domain is essential for efficient pre-rRNA processing and cell growth. Further investigation of the Utp6-Utp21 interaction using both genetic and biophysical methods shows that the HAT domain binds a specific peptide ligand in Utp21, the first example of a HAT domain peptide ligand, with a dissociation constant of 10 μM.     

Isolation of the exoelectrogenic bacterium Ochrobactrum anthropi YZ-1 by using a U-tube microbial fuel cell

Exoelectrogenic bacteria have potential for many different biotechnology applications due to their ability to transfer electrons outside the cell to insoluble electron acceptors, such as metal oxides or the anodes of microbial fuel cells (MFCs). Very few exoelectrogens have been directly isolated from MFCs, and all of these organisms have been obtained by techniques that potentially restrict the diversity of exoelectrogenic bacteria. A special U-tube-shaped MFC was therefore developed to enrich exoelectrogenic bacteria with isolation based on dilution-to-extinction methods. Using this device, we obtained a pure culture identified as Ochrobactrum anthropi YZ-1 based on 16S rRNA gene sequencing and physiological and biochemical characterization. Strain YZ-1 was unable to respire using hydrous Fe(III) oxide but produced 89 mW/m(2) using acetate as the electron donor in the U-tube MFC. Strain YZ-1 produced current using a wide range of substrates, including acetate, lactate, propionate, butyrate, glucose, sucrose, cellobiose, glycerol, and ethanol. Like another exoelectrogenic bacterium (Pseudomonas aeruginosa), O. anthropi is an opportunistic pathogen, suggesting that electrogenesis should be explored as a characteristic that confers advantages to these types of pathogenic bacteria. Further applications of this new U-tube MFC system should provide a method for obtaining additional exoelectrogenic microorganisms that do not necessarily require metal oxides for cell respiration.     

Analysis of ammonia loss mechanisms in microbial fuel cells treating animal wastewater

Ammonia losses during swine wastewater treatment were examined using single- and two-chambered microbial fuel cells (MFCs). Ammonia removal was 60% over 5 days for a single-chamber MFC with the cathode exposed to air (air-cathode), versus 69% over 13 days from the anode chamber in a two-chamber MFC with a ferricyanide catholyte. In both types of systems, ammonia losses were accelerated with electricity generation. For the air-cathode system, our results suggest that nitrogen losses during electricity generation were increased due to ammonia volatilization with conversion of ammonium ion to the more volatile ammonia species as a result of an elevated pH near the cathode (where protons are consumed). This loss mechanism was supported by abiotic tests (applied voltage of 1.1 V). In a two-chamber MFC, nitrogen losses were primarily due to ammonium ion diffusion through the membrane connecting the anode and cathode chambers. This loss was higher with electricity generation as the rate of ammonium transport was increased by charge transfer across the membrane. Ammonia was not found to be used as a substrate for electricity generation, as intermittent ammonia injections did not produce power. The ammonia-oxidizing bacterium Nitrosomonas europaea was found on the cathode electrode of the single-chamber system, supporting evidence of biological nitrification, but anaerobic ammonia-oxidizing bacteria were not detected by molecular analyses. It is concluded that ammonia losses from the anode chamber were driven primarily by physical-chemical factors that are increased with electricity generation, although some losses may occur through biological nitrification and denitrification.     

A Comparison of the Efficacy of Pond-Net and Box Sampling Methods in Turloughs - Irish Ephemeral Aquatic Systems

Two methods were used to sample aquatic macroinvertebrates in three turloughs. Turloughs are systems that flood periodically from groundwater, in response to local rainfall patterns and contain rare aquatic species and assemblages. The first method used a standard pond net that was swept through the water column, while the second involved fixing a rectangular, open-bottomed box to the substrata and removing all organisms with a net. Similar overall sampling effort was applied to each method and individual box samples were found to take longer to gather than pond net samples. The box method, however, gave the maximum yield for a given sampling effort. Significantly more beetle species and individuals were recorded per unit area of bottom at all three turloughs using the box method. Multivariate analysis segregated samples, firstly according to site and secondly, with respect to method. The box method is a viable alternative to sampling with a pond net. It is more quantitative, objective, specific and reliable. This is particularly important in habitats distinguished by rare species and assemblages, and for which monitoring is driven by legislative needs.     

Activation of extracellular signal-regulated kinases potentiates hemin toxicity in astrocyte cultures

Hemin is present in intracranial hematomas in high micromolar concentrations and is a potent, lipophilic oxidant. Growing evidence suggests that heme-mediated injury may contribute to the pathogenesis of CNS hemorrhage. Extracellular signal-regulated kinases (ERKs) are activated by oxidants in some cell types, and may alter cellular vulnerability to oxidative stress. In this study, the effect of hemin on ERK activation was investigated in cultured murine cortical astrocytes, and the consequence of this activation on cell viability was quantified. Hemin was rapidly taken up by astrocytes, and generated reactive oxygen species (ROS) within 30 min. Increased immunoreactivity of dually phosphorylated ERK1/2 was observed in hemin-treated cultures at 30-120 min, without change in total ERK. Surprisingly, ERK activation was not attenuated by concomitant treatment with antioxidants (U74500A or 1,10-phenanthroline) at concentrations that blocked ROS generation. Cell death commenced after 2 h of hemin exposure and was reduced by antioxidants and by the caspase inhibitor Z-VAD-FMK. Cytotoxicity was also attenuated by MEK inhibition with PD98059 or U0126 at concentrations that were sufficient to prevent ERK activation. Whereas the effect of Z-VAD-FMK on cell survival was transient, the effect of MEK inhibitors was long-lasting. MEK inhibitors had no effect on cellular hemin uptake or subsequent ROS generation. The present results suggest that hemin activates ERK in astrocytes via a mechanism that is independent of ROS generation. This activation sensitizes astrocytes to hemin-mediated oxidative injury.     

Defective repair of gamma-ray induced DNA damage in xeroderma pigmentosum cells.

We used the bromouracil-photolysis technique to estimate the sizes of the repaired regions in normal human and xeroderma pigmentosum (XP) cells irradiated by gamma-rays aerobically or anoxically. After 1 1/2 hours of incubation, single-strand breaks were repaired and the repaired regions were small--one to two BrUra residues--for cells irradiated aerobically or anoxically. After a 20-hour incubation, the repaired region in normal cells showed a component mimicking U.V.-repair. There were large patches (approximately 30 BrUra residues) in the approximate ratios of one per six chain breaks for aerobic irradiation and one per three chain breaks for anoxic irradiation. XP cells, however, only showed large patches at 20 hours if they had been irradiated aerobically. We could not detect such regions in XP cells irradiated anoxically. These results indicate (1) that some part of ionizing damage mimics excision of U.V. damage in that the repair patches are large and the repair takes an appreciable time; (2) the types of such damage depend on whether the irradiation is done aerobically or anoxically; and (3) XP cells are defective in repairing a component of anoxic damage.     

Increased amounts of hybrid (heavy/heavy) DNA in Bloom's syndrome fibroblasts

The nuclear DNA of fibroblasts from patients suffering with Bloom's syndrome, density labeled for less than one round of DNA replication to give heavy/light molecules, was examined for spontaneous amounts of heavy/heavy DNA (hybrid DNA). When compared to normal fibroblasts the Bloom's syndrome cells exhibited a sixfold increase in such DNA.