Arrangement of type IV collagen on NH2 and COOH functionalized surfaces

Apart from the paradigm that cell–biomaterials interaction depends on the adsorption of soluble adhesive proteins we anticipate that upon distinct conditions also other, less soluble ECM proteins such as collagens, associate with the biomaterials interface with consequences for cellular response that might be of significant bioengineering interest. Using atomic force microscopy (AFM) we seek to follow the nanoscale behavior of adsorbed type IV collagen (Col IV)—a unique multifunctional matrix protein involved in the organization of basement membranes (BMs) including vascular ones. We have previously shown that substratum wettability significantly affects Col IV adsorption pattern, and in turn alters endothelial cells interaction. Here we introduce two new model surfaces based on self‐assembled monolayers (SAMs), a positively charged –NH₂, and negatively charged –COOH surface, to learn more about their particular effect on Col IV behavior. AFM studies revealed distinct pattern of Col IV assembly onto the two SAMs resembling different aspects of network‐like structure or aggregates (suggesting altered protein conformation). Moreover, the amount of adsorbed FITC‐labeled Col IV was quantified and showed about twice more protein on NH₂ substrata. Human umbilical vein endothelial cells attached less efficiently to Col IV adsorbed on negatively charged COOH surface judged by altered cell spreading, focal adhesions formation, and actin cytoskeleton development. Immunofluorescence studies also revealed better Col IV recognition by both α₁ and α₂ integrins on positively charged NH₂ substrata resulting in higher phosphorylated focal adhesion kinase recruitment in the focal adhesion complexes. On COOH surface, no integrin clustering was observed. Taken altogether these results, point to the possibility that combined NH₂ and Col IV functionalization may support endothelization of cardiovascular implants. Biotechnol. Bioeng. 2011;108: 3009–3018. © 2011 Wiley Periodicals, Inc.     

DNA-binding and Oxidative Properties of Cationic Phthalocyanines and Their Dimeric Complexes with Anionic Phthalocyanines Covalently Linked to Oligonucleotides

Abstract

Design of chemically modified oligonucleotides for regulation of gene expression has attracted considerable attention over the past decades. One actively pursued approach involves antisense or antigene oligonucleotide constructs carrying reactive groups, many of these based on transition metal complexes. The complexes of Fe(II) and Co(II) with phthalocyanines are extremely good catalysts of oxidation of organic compounds with molecular oxygen and hydrogen peroxide. The binding of positively charged Fe(II) and Co(II) phthalocyanines with single- and double-stranded DNA was investigated. It was shown that these phthalocyanines interact with nucleic acids through an outside binding mode. The site-directed modification of single-stranded DNA by O₂ and H₂O₂ in the presence of dimeric complexes of negatively and positively charged Fe(II) and Co(II) phthalocyanines was investigated. These complexes were formed directly on single-stranded DNA through interaction between negatively charged phthalocyanine in conjugate and positively charged phthalocyanine in solution. The resulting oppositely charged phthalocyanine complexes showed significant increase of catalytic activity compared with monomeric forms of phthalocyanines Fe(II) and Co(II). These complexes catalyzed the DNA oxidation with high efficacy and led to direct DNA strand cleavage. It was determined that oxidation of DNA by molecular oxygen catalyzed by complex of Fe(II)-phthalocyanines proceeds with higher rate than in the case of Co(II)-phthalocyanines but the latter led to a greater extent of target DNA modification.     

Packing scheme of α-helices in the histone core of the nucleosome

A nucleosome histone core model is presented which is compatible with experimental data. The model consists of 28 α-helices located as predicted by others^1–4. The histone wheel resembles the one proposed by Klug et al.⁵ Most of the helices are packed nearly parallel to the DNA superhelical axis, forming a bandoleer-like structure. About 10 to 20% of the nucleosomal phosphates may be neutralized by positively charged residues in the α-helices. Disregarding the charge of the NH₂-terminals, this is sifficient for the thermodynamic stability of the nucleosome under physiological conditions. The electrostatic charge on the protein surface is assumed to be relatively fixed due to the participation of the corresponding side chains to the hydrophobically packed helices. Thus, DNA wrapping appears to be determined by the core histones not by the histone NH₂-terminals.     

Liposome-Encapsulated Polyethylenimine/Oligonucleotide Polyplexes Prepared by Reverse-Phase Evaporation Technique

Liposome-encapsulated polyplex system represents a promising delivery system for oligonucleotide-based therapeutics such as siRNA and asODN. Here, we report a novel method to prepare liposome-encapsulated cationic polymer/oligonucleotide polyplexes based on the reverse-phase evaporation following organic extraction of the polyplexes. The polyplexes of polyethylenimine and oligonucleotide were first formed in aqueous buffer at an N/P ratio of 6. The overall positively charged polyplexes were then mixed with the anionic phospholipids in overall organic media. The overall organic environment and electrostatic interaction between anionic phospholipids and positively charged polyplexes resulted in inverted micelle-like particles with the polyplexes in the core. After phase separation, the hydrophobic particles were recovered in organic phase. Reverse-phase evaporation of the organic solvent in the presence of hydrophilic polymer-grafted lipids resulted in a stable aqueous dispersion of hydrophilic lipid-coated particles with the polyplex in the core. Transmission electron microscopy visualization revealed spherical structures with heavily stained polyplex cores surrounded by lightly stained lipid coats. The lipid-coated polyplex particles showed colloidal stability, complete protection of the loaded oligonucleotide molecules from enzymatic degradation, and high loading efficiency of more than 80%. Thus, this technique represents an alternative method to prepare lipid-coated polyplex particles as a delivery system of oligonucleotide therapeutics.     

Selective gene delivery to cancer cells secreting matrix metalloproteinases using a gelatin/polyethylenimine/DNA complex

We developed a gene delivery strategy targeting metastatic tumors by exploiting the specific matrix metalloproteinases (MMPs) secreting properties of metastatic tumor cells. A ternary polyplex has been formed by coating polyethylenimine/DNA (PD) complex with an excessive amount of negatively charged gelatin B (GPDB). We show that GPD-B’s gene delivery activity could be targeted to cancer cells via the MMP-mediated proteolytic process, while GPD-A, made from positively charged gelatin A, was not successful in exhibiting such activity. The 1,10-Phenanthroline, an MMP2 inhibitor, abrogated the MMP-dependent transfection activity of GPD-B. GPD-B carried much less positive surface charges than PD, and thus exhibited significantly reduced interactions with erythrocytes. However, MMP2 elevated the positiveness in GPDB’s surface charge and, thus, its interaction with erythrocytes. These results suggest that the anionic gelatin coating may confer improved stabilities on GPD-B in the surrounding medium, while MMP2-mediated disintegration of the gelatin coat enhances the gene delivery to metastatic cancer cells via increasing the likelihood of local chargemediated interactions between the polyplex and cancer cell membrane.     

Free‐energy profiles for ions in the influenza M2‐TMD channel

M₂ transmembrane domain channel (M₂‐TMD) permeation properties are studied using molecular dynamics simulations of M₂‐TMD (1NYJ) embedded in a lipid bilayer (DMPC) with 1 mol/kg NaCl or KCl saline solution. This study allows examination of spontaneous cation and anion entry into the selectivity filter. Three titration states of the M₂‐TMD tetramer are modeled for which the four His³⁷ residues, forming the selectivity filter, are net uncharged, +2 charged, or +3 charged. M₂‐TMD structural properties from our simulations are compared with the properties of other models extracted from NMR and X‐ray studies. During 10 ns simulations, chloride ions occasionally occupy the positively‐charged selectivity filter region, and from umbrella sampling simulations, Cl^? has a lower free‐energy barrier in the selectivity‐filter region than either Na⁺ or NH, and NH has a lower free‐energy barrier than Na⁺. For Na⁺ and Cl^?, the free‐energy barriers are less than 5 kcal/mol, suggesting that the 1NYJ conformation would probably not be exquisitely proton selective. We also point out a rotameric configuration of Trp⁴¹ that could fully occlude the channel. Proteins 2009. © 2009 Wiley‐Liss, Inc.     

Enhanced Biodegradation of Diesel Oil in Seawater Supplemented with Nutrients

The imbalance of C, N, and P caused by the spilled oil could be regulated by the addition of nitrogen and phosphorous. Moreover, different kinds of N and P sources were used in order to stimulate oil biodegradation under laboratory and field conditions, but the results were conflicting. To evaluate the effectiveness of nutrient supplementation, N sources (NO₃‐N and NH₄‐N) and P sources (PO₄‐P) were applied to the simulated diesel‐polluted seawater in the N/P ratio of 10:1 and 20:1, respectively. The results showed that the addition of nutrients increased the oil biodegradation rate and the counts of petroleum degrading bacteria (PDB) and heterotrophic bacteria (HB). A strongly positive correlation existed (the interrelated coefficient was nearly 0.9) between the percentage ratio of PDB/HB and the oil biodegradation rates, and therefore the percentage ratio of PDB/HB could be used as a good indicator to predict oil biodegradation. Among the four samples treated with nutrients, the biodegradation efficiency of the group amended with NO₃‐N and PO₄‐P in the ratio of 10:1 (10NO₃‐P group) was as much as 75.8 %, while in the 10NH₄‐P, 20NO₃‐P and 20NH₄‐P groups this value was 61.3 %, 52.4 % and 40.5, respectively. It would take natural degradation without nutrient supplementation about 78 days to achieve the result obtained within 14 days with 10NO₃‐P amendment . Chemical and microbiological analyses confirmed that the addition of nutrients in the same N/P ratio remarkably enhanced the biodegradation rate and the counts of microorganisms in the NO₃‐N treated groups, indicating that the microorganisms tend to utilize NO₃‐N rather than NH₄‐N as their growth N source. When the same kind of N source was added to the system, the promoted efficiency in the 10:1 (N/P ratio) groups was notable compared to the 20:1 groups, i.e., adding nutrients in the ratio of 10:1 is superior in the stimulation of oil biodegradation to the ratio of 20:1.     

Structure–activity relationship of a novel pentapeptide with cancer cell growth‐inhibitory activity

We previously reported that yamamarin, a pentapeptide with an amidated C‐terminus (DILRG‐NH₂) isolated from larvae of the silkmoth, and its palmitoylated analog (C16‐DILRG‐NH₂) suppressed proliferation of rat hepatoma (liver cancer) cells. In this study, we investigated the structure–activity relationship of yamamarin by in vitro assay and spectroscopic methods (CD and NMR) for various analogs. The in vitro assay results demonstrated that the chemical structure of the C‐terminal part (‐RG‐NH₂) of yamamarin is essential for its activity. The CD and NMR results indicated that yamamarin and its analog adopt predominantly a random coil conformation. Moreover, a comparison of NMR spectra of DILRG‐NH₂ and C16‐DILRG‐NH₂ revealed that the N‐terminal palmitoyl group of C16‐DILRG‐NH₂ did not affect the conformation of the C‐terminal part, which is essential for activity. Together, these results should assist in the design of more sophisticated anticancer drugs. Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd.     

Composites of peptide nucleic acids with ttitanium dioxide nanoparticles. I. Construction of nanocomposites containing DNA/PNA duplexes and their delivery into HeLa cells

In order to study the possibility of using titanium dioxide (TiO₂) nanoparticles to deliver peptide nucleic acids (PNA) in eukaryotic cells, a PNA oligomer was synthesized, and a method of PNA immobilization in the form of hybrid DNA/PNA duplexes on the surface of TiO₂ nanoparticles covered with polylysine (PL) was developed. The attachment of a DNA/PNA duplex to TiO₂ · PL nanoparticles occurs due to electrostatic interactions between the negatively charged DNA chain and the positively charged amino groups of PL. The binding of the PNA to the nanocomposite is achieved through noncovalent Watson-Crick interactions between PNA and complementary DNA. The capacity of the obtained TiO₂ · PL · DNA/PNA nano-composites depending on immobilization conditions was 10?C30 nmol PNA per 1 mg of TiO₂ particles, which corresponds to ??1?C3 PNA molecules per one TiO₂ particle with a size of 4?C6 nm. It was shown by confocal laser scanning microscopy that fluorescently-labeled PNA molecules in the TiO₂ · PL · DNA/^FluPNA nano-composites effectively penetrate into HeLa cells without transfection agents, electroporation, or other auxiliary procedures.     

Synthesis of a Precursor Dipeptide of Thymopentin in Organic Solvents by an Enzymatic Method

Abstract

The protease‐catalyzed, kinetically controlled synthesis of a precursor dipeptide of thymopentin(TP‐5), Z‐Arg‐Lys‐NH₂ in organic solvents was studied. Z‐Arg‐OMe was used as the acyl donor and Lys‐NH₂ was used as the nucleophile. An industrial alkaline protease alcalase and trypsin were used to catalyze the synthesis of the target dipeptide in water‐organic cosolvent systems. The conditions of the synthesis reaction were optimized by examining the effects of several factors, including organic solvents, water content, temperature, pH, and reaction time on the yield of Z‐Arg‐Lys‐NH₂. The optimum conditions using alcalase as the catalyst are pH 10.0, 35°C, in acetonitrile/DMF/Na₂CO₃‐NaHCO₃ buffer system (80∶10∶10, V/V), 6 h, with the dipeptide yield of 71.1%. Compared with alcalase, the optimum conditions for trypsin are pH 8.0, 35°C, in ethanol/Tris‐HCl buffer system (80∶20, V/V), 4 h, with the dipeptide yield of 76.1%.     

Adsorption of Adenine, Cytosine, Thymine, and Uracil on Sulfide-Modified Montmorillonite: FT-IR, M?ssbauer and EPR Spectroscopy and X-Ray Diffractometry Studies

In the present work the interactions of nucleic acid bases with and adsorption on clays were studied at two pHs (2.00, 7.00) using different techniques. As shown by Mössbauer and EPR spectroscopies and X-ray diffractometry, the most important finding of this work is that nucleic acid bases penetrate into the interlayer of the clays and oxidize Fe²⁺ to Fe³⁺, thus, this interaction cannot be regarded as a simple physical adsorption. For the two pHs the order of the adsorption of nucleic acid bases on the clays was: adenine????cytosine?>?thymine?>?uracil. The adsorption of adenine and cytosine on clays increased with decreasing of the pH. For unaltered montmorillonite this result could be explained by electrostatic forces between adenine/cytosine positively charged and clay negatively charged. However for montmorillonite modified with Na₂S, probably van der Waals forces also play an important role since both adenine/cytosine and clay were positively charged. FT-IR spectra showed that the interaction between nucleic acid bases and clays was through NH⁺ or NH ₂ ⁺ groups. X-ray diffractograms showed that nucleic acid bases adsorbed on clays were distributed into the interlayer surface, edge sites and external surface functional groups (aluminol, silanol) EPR spectra showed that the intensity of the line g????2 increased probably because the oxidation of Fe²⁺ to Fe³⁺ by nucleic acid bases and intensity of the line g?=?4.1 increased due to the interaction of Fe³⁺ with nucleic acid bases. Mössbauer spectra showed a large decreased on the Fe²⁺ doublet area of the clays due to the reaction of nucleic acid bases with Fe²⁺.     

Targeting of NH2-terminal–processed Microsomal Protein to Mitochondria: A Novel Pathway for the Biogenesis of Hepatic Mitochondrial P450MT2

Cytochrome P4501A1 is a hepatic, microsomal membrane–bound enzyme that is highly induced by various xenobiotic agents. Two NH₂-terminal truncated forms of this P450, termed P450MT2a and MT2b, are also found localized in mitochondria from β-naphthoflavone–induced livers. In this paper, we demonstrate that P4501A1 has a chimeric NH₂-terminal signal that facilitates the targeting of the protein to both the ER and mitochondria. The NH₂-terminal 30–amino acid stretch of P4501A1 is thought to provide signals for ER membrane insertion and also stop transfer. The present study provides evidence that a sequence motif immediately COOH-terminal (residues 33–44) to the transmembrane domain functions as a mitochondrial targeting signal under both in vivo and in vitro conditions, and that the positively charged residues at positions 34 and 39 are critical for mitochondrial targeting. Results suggest that 25% of P4501A1 nascent chains, which escape ER membrane insertion, are processed by a liver cytosolic endoprotease. We postulate that the NH₂-terminal proteolytic cleavage activates a cryptic mitochondrial targeting signal. Immunofluorescence microscopy showed that a portion of transiently expressed P4501A1 is colocalized with the mitochondrial-specific marker protein cytochrome oxidase subunit I. The mitochondrial-associated MT2a and MT2b are localized within the inner membrane compartment, as tested by resistance to limited proteolysis in both intact mitochondria and mitoplasts. Our results therefore describe a novel mechanism whereby proteins with chimeric signal sequence are targeted to the ER as well as to the mitochondria.     

A new approach to ammonium sulphate feeding for fed‐batch Arthrospira (Spirulina) platensis cultivation in tubular photobioreactor

Arthrospira platensis was cultivated in tubular photobioreactor using different photosynthetic photon flux densities (PPFD) and protocols of (NH₄)₂SO₄ fed‐batch supply. Results were evaluated by variance analysis selecting maximum cell concentration (X_m), cell productivity (P_x), nitrogen‐to‐cell conversion factor (Y_X/N) and biomass, protein and lipid contents as responses. At PPFD of 120 and 240 μmol‐photons/m² s, a parabolic profile of (NH₄)₂SO₄ addition aiming at producing biomass with 7% nitrogen content ensured X_m values (14.1 and 12.2 g/L, respectively) comparable to those obtained with NaNO₃. At PPFD of 240 μmol‐photons/m² s, P_x (1.69 g/Ld) was 36% higher, although the photosynthetic efficiency (3.0%) was less than one‐half that at PPFD of 120 μmol‐photons/m² s. Biomass was shown to be constituted by about 35% proteins and 10% lipids, without any dependence on PPFD or kind of nitrogen source. These results highlight the possible use of (NH₄)₂SO₄ as alternative, cheap nitrogen source for A. platensis cultivation in tubular photobioreactors. © 2010 American Institute of Chemical Engineers Biotechnol. Prog., 2010     

Biotic and abiotic controls on the ecosystem significance of consumer excretion in two contrasting tropical streams

1. Excretion of nitrogen (N) and phosphorus (P) is a direct and potentially important role for aquatic consumers in nutrient cycling that has recently garnered increased attention. The ecosystem‐level significance of excreted nutrients depends on a suite of abiotic and biotic factors, however, and few studies have coupled measurements of excretion with consideration of its likely importance for whole‐system nutrient fluxes. 2. We measured rates and ratios of N and P excretion by shrimps (Xiphocaris elongata and Atya spp.) in two tropical streams that differed strongly in shrimp biomass because a waterfall excluded predatory fish from one site. We also made measurements of shrimp and basal resource carbon (C), N and P content and estimated shrimp densities and ecosystem‐level N and P excretion and uptake. Finally, we used a 3‐year record of discharge and NH₄‐N concentration in the high‐biomass stream to estimate temporal variation in the distance required for excretion to turn over the ambient NH₄‐N pool. 3. Per cent C, N, and P body content of Xiphocaris was significantly higher than that of Atya. Only per cent P body content showed significant negative relationships with body mass. C:N of Atya increased significantly with body mass and was higher than that of Xiphocaris. N : P of Xiphocaris was significantly higher than that of Atya. 4. Excretion rates ranged from 0.16–3.80 μmol NH₄‐N shrimp^?1 h^?1, 0.23–5.76 μmol total dissolved nitrogen (TDN) shrimp^?1 h^?1 and 0.002–0.186 μmol total dissolved phosphorus (TDP) shrimp^?1 h^?1. Body size was generally a strong predictor of excretion rates in both taxa, differing between Xiphocaris and Atya for TDP but not NH₄‐N and TDN. Excretion rates showed statistically significant but weak relationships with body content stoichiometry. 5. Large between‐stream differences in shrimp biomass drove differences in total excretion by the two shrimp communities (22.3 versus 0.20 μmol NH₄‐N m^?2 h^?1, 37.5 versus 0.26 μmol TDN m^?2 h^?1 and 1.1 versus 0.015 μmol TDP m^?2 h^?1), equivalent to 21% and 0.5% of NH₄‐N uptake and 5% and <0.1% of P uptake measured in the high‐ and low‐biomass stream, respectively. Distances required for excretion to turn over the ambient NH₄‐N pool varied more than a hundredfold over the 3‐year record in the high‐shrimp stream, driven by variability in discharge and NH₄‐N concentration. 6. Our results underscore the importance of both biotic and abiotic factors in controlling consumer excretion and its significance for nutrient cycling in aquatic ecosystems. Differences in community‐level excretion rates were related to spatial patterns in shrimp biomass dictated by geomorphology and the presence of predators. Abiotic factors also had important effects through temporal patterns in discharge and nutrient concentrations. Future excretion studies that focus on nutrient cycling should consider both biotic and abiotic factors in assessing the significance of consumer excretion in aquatic ecosystems.     

Global ammonia emissions from synthetic nitrogen fertilizer applications in agricultural systems: Empirical and process‐based estimates and uncertainty

Excessive ammonia (NH₃) emitted from nitrogen (N) fertilizer applications in global croplands plays an important role in atmospheric aerosol production, resulting in visibility reduction and regional haze. However, large uncertainty exists in the estimates of NH₃ emissions from global and regional croplands, which utilize different data and methods. In this study, we have coupled a process‐based Dynamic Land Ecosystem Model (DLEM) with the bidirectional NH₃ exchange module in the Community Multiscale Air‐Quality (CMAQ) model (DLEM‐Bi‐NH₃) to quantify NH₃ emissions at the global and regional scale, and crop‐specific NH₃ emissions globally at a spatial resolution of 0.5° × 0.5° during 1961–2010. Results indicate that global NH₃ emissions from N fertilizer use have increased from 1.9 ± 0.03 to 16.7 ± 0.5 Tg N/year between 1961 and 2010. The annual increase of NH₃ emissions shows large spatial variations across the global land surface. Southern Asia, including China and India, has accounted for more than 50% of total global NH₃ emissions since the 1980s, followed by North America and Europe. Rice cultivation has been the largest contributor to total global NH₃ emissions since the 1990s, followed by corn and wheat. In addition, results show that empirical methods without considering environmental factors (constant emission factor in the IPCC Tier 1 guideline) could underestimate NH₃ emissions in context of climate change, with the highest difference (i.e., 6.9 Tg N/year) occurring in 2010. This study provides a robust estimate on global and regional NH₃ emissions over the past 50 years, which offers a reference for assessing air quality consequences of future nitrogen enrichment as well as nitrogen use efficiency improvement.     

DNA/PEI/Alginate polyplex as an efficient<Emphasis Type="Italic">in vivo</Emphasis> gene delivery system

A novel non-viral gene delivery system comprised of a DNA/PEI/Alginate (DPA) polyplex was prepared and assessedin vitro andin vivo. Coating the positively charged DNA/PEI (DP) complex with a polyanion resulted in a high level ofin vitro reporter gene transfection in the presence of 50 vol% serum due to the minimized cytotoxicity of PEI and the reduced nonspecific interactions with serum components. Among the tested anionic polymers, which included sodium alginate, poly(methacrylic acid) and poly(acrylic acid), the sodium alginate showed the highest gene transfection efficiency. The DPA polyplex also showed a reduced level of erythrocyte aggregation in target cells when compared with the DP complex. According toin vivo studies in which reporter genes encoding green fluorescent protein (GFP) and luciferase were used, injection of the DPA polyplex into tumor cells in six week old female C57/BL6 mice resulted in a much higher level of GFP expression and approximately 7 fold higher luciferase expression than treatment with the DP complex. Taken together, these results demonstrated that the anionic alginate coating of the DP complex contributed to efficient gene deliveryin vitro andin vivo.     

Interspecies variation in nitrogen uptake kinetic responses of temperate forest species to elevated CO2: potential causes and consequences

Despite the recognition that the capacity to acquire N is critical in plant response to CO₂ enrichment, there is little information on how elevated CO₂ affects root N uptake kinetics. The few available data indicate a highly variable pattern of response to elevated CO₂, but it is presently unclear if the observed inconsistencies are caused by differences in experimental protocols or by true species differences. Furthermore, if there are interspecific variations in N uptake responses to elevated CO₂, it is not clear whether these are associated with different functional groups. Accordingly, we examined intact root‐system NH₄⁺ and NO₃^– uptake kinetic responses to elevated CO₂ in seedlings of six temperate forest tree species, representing (i) fast‐ vs. slow‐growers and (ii) broad‐leaves vs. conifers, that were cultured and assayed in otherwise similar conditions. In general, the species tested had a higher uptake capacity (V_max) for NH₄⁺ than for NO₃^–. Species substantially differed in their NO₃^– and NH₄⁺ uptake capacities, but the interspecific differences were markedly greater for NO₃^– than NH₄⁺ uptake. Elevated CO₂ had a species‐dependent effect on root uptake capacity for NH₄⁺ ranging from an increase of 215% in Acer negundo L. to a decrease of about 40% in Quercus macrocarpa Michx. In contrast, NO₃^– uptake capacity responded little to CO₂ in all the species except A. negundo in which it was significantly down‐regulated at elevated CO₂. Across species, the capacity for NH₄⁺ uptake was positively correlated with the relative growth rate (RGR) of species; however, the CO₂ effect on NH₄⁺ uptake capacity could not be explained by changes in RGR. The observed variation in NH₄⁺ uptake response to elevated CO₂ was also inconsistent with life‐form differences. Other possible mechanisms that may explain why elevated CO₂ elicits a species‐specific response in root N uptake kinetics are discussed. Despite the fact that the exact mechanism(s) for such interspecific variation remains unresolved, these differences may have a significant implication for competitive interactions and community responses to elevated CO₂ environment. We suggest that differential species responses in nutrient uptake capacity could be one potential mechanism for the CO₂‐induced shifts in net primary productivity and species composition that have been observed in experimental communities exposed to elevated levels of CO₂.     

The ASPP interaction network: electrostatic differentiation between pro‐ and anti‐apoptotic proteins

The ASPP proteins are apoptosis regulators: ASPP1 and ASPP2 promote, while iASPP inhibits, apoptosis. The mechanism by which these different outcomes are achieved is still unknown. The C‐terminal ankyrin repeats and SH3 domain (ANK‐SH3) mediate the interactions of the ASPP proteins with major apoptosis regulators such as p53, Bcl‐2, and NFκB. The structure of the complex between ASPP2_ANK‐SH3 and the core domain of p53 (p53CD) was previously determined. We have recently characterized the individual interactions of ASPP2_ANK‐SH3 with Bcl‐2 and NFκB, as well as a regulatory intramolecular interaction with the proline rich domain of ASPP2. Here we compared the ASPP interactions at two levels: ASPP2_ANK‐SH3 with different proteins, and different ASPP family members with each protein partner. We found that the binding sites of ASPP2 to p53CD, Bcl‐2, and NFκB are different, yet lie on the same face of ASPP2_ANK‐SH3. The intramolecular binding site to the proline rich domain overlaps the three intermolecular binding sites. To reveal the basis of functional diversity in the ASPP family, we compared their protein‐binding domains. A subset of surface‐exposed residues differentiates ASPP1 and ASPP2 from iASPP: ASPP1/2 are more negatively charged in specific residues that contact positively charged residues of p53CD, Bcl‐2, and NFκB. We also found a gain of positive charge at the non‐protein binding face of ASPP1/2, suggesting a role in electrostatic direction towards the negatively charged protein binding face. The electrostatic differences in binding interfaces between the ASPP proteins may be one of the causes for their different function. Copyright © 2010 John Wiley & Sons, Ltd.     

Bactrocerin‐1: A novel inducible antimicrobial peptide from pupae of oriental fruit fly Bactrocera dorsalis Hendel

A novel antimicrobial peptide, Bactrocerin‐1, was purified and characterized from an immunized dipteran insect, Bactrocera dorsalis. Bactrocerin‐1 has 20 amino acid residues with a mass of 2,325.95 Da. The amino acid sequence of Bactrocerin‐1 showed very high similarity to the active fragment (46V‐65S‐NH₂) of Coleoptericin A. The composition of amino acid residues revealed that Bactrocerin‐1 is a hydrophobic, positively charged, and Lys/Ile/Gly‐rich peptide. Minimal growth inhibition concentration (MIC) measurements for synthesized Bactrocerin‐1 showed a very broad spectrum of anti‐microbial activity against Gram‐positive bacteria, Gram‐negative bacteria, and fungi. Bactrocerin‐1 did not show hemolytic activity toward mouse red blood cells even at a concentration of 50 µM. Analysis of the Helical‐wheel projection and the CD spectrum suggested that Bactrocerin‐1 contains the amphipathic α‐helix. © 2009 Wiley Periodicals, Inc.     

Anaerobic mixed‐culture fermentation of aqueous ammonia‐treated sugarcane bagasse in consolidated bioprocessing

The MixAlco process is an example of consolidated bioprocessing (CBP) in which anaerobic mixed‐culture fermentation biochemically converts any biodegradable feedstock into carboxylate salts. Downstream processing thermochemically transforms the resulting salts into mixed alcohol fuels or gasoline. To enhance digestibility, sugarcane bagasse was treated under mild conditions (55°C, 24 h, and 30% aqueous ammonia solution with a loading of 10 mL/g dry biomass). Using NH₄HCO₃ buffer, the feedstock (80% ammonia‐treated sugarcane bagasse/20% chicken manure) was anaerobically fermented by a mixed culture of marine microorganisms at 55°C. Four‐stage countercurrent fermentations were performed at various volatile solids loading rates (VSLRs) and liquid residence times (LRTs). The highest acid productivity (1.14 g/(L day)) occurred at a total acid concentration of 29.8 g/L. The highest conversion (65%) occurred at a total acid concentration of 27.6 g/L. The continuum particle distribution model (CPDM) predicted the experimental total acid concentrations and conversions within 4.98% and 10.41%, respectively. When using NH₄HCO₃ buffer, ammonia pretreatment is an attractive option. The CPDM “map” shows that both high volatile solid conversions (78.8%) and high acid concentrations (32.6 g/L) are possible with 300 g/(L liquid) substrate concentration, 30 days LRT, 2 g/(L day) solid loading rate and NH₄HCO₃ buffer. Biotechnol. Bioeng. 2010;106: 216–227. © 2010 Wiley Periodicals, Inc.