Cloning and Characterization of Cold-Adapted α-Amylase from Antarctic <Emphasis Type="Italic">Arthrobacter agilis</Emphasis>

In this study, the gene encoding an α-amylase from a psychrophilic Arthrobacter agilis PAMC 27388 strain was cloned into a pET-28a(+) vector and heterologously expressed in Escherichia coli BL21(DE3). The recombinant α-amylase with a molecular mass of about 80 kDa was purified by using Ni²⁺-NTA affinity chromatography. This recombinant α-amylase exhibited optimal activity at pH 3.0 and 30 °C and was highly stable at varying temperatures (30–60 °C) and within the pH range of 4.0–8.0. Furthermore, α-amylase activity was enhanced in the presence of FeCl₃ (1 mM) and β-mercaptoethanol (5 mM), while CoCl₂ (1 mM), ammonium persulfate (5 mM), SDS (10 %), Triton X-100 (10 %), and urea (1 %) inhibited the enzymatic activity. Importantly, the presence of Ca²⁺ ions and phenylmethylsulfonyl fluoride (PMSF) did not affect enzymatic activity. Thin layer chromatography (TLC) analysis showed that recombinant A. agilis α-amylase hydrolyzed starch, maltotetraose, and maltotriose, producing maltose as the major end product. These results make recombinant A. agilis α-amylase an attractive potential candidate for industrial applications in the textile, paper, detergent, and pharmaceutical industries.     

Developing Novel Antimicrobial and Antiviral Textile Products

In conjunction with an increasing public awareness of infectious diseases, the textile industry and scientists are developing hygienic fabrics by the addition of various antimicrobial and antiviral compounds. In the current study, sodium pentaborate pentahydrate and triclosan are applied to cotton fabrics in order to gain antimicrobial and antiviral properties for the first time. The antimicrobial activity of textiles treated with 3 % sodium pentaborate pentahydrate, 0.03 % triclosan, and 7 % Glucapon has been investigated against a broad range of microorganisms including bacteria, yeast, and fungi. Moreover, modified cotton fabrics were tested against adenovirus type 5 and poliovirus type 1. According to the test results, the modified textile goods attained very good antimicrobial and antiviral properties. Thus, the results of the present study clearly suggest that sodium pentaborate pentahydrate and triclosan solution-treated textiles can be considered in the development of antimicrobial and antiviral textile finishes.     

High-Performance Biogas Upgrading Using a Biotrickling Filter and Hydrogenotrophic Methanogens

This research reports the development of a biotrickling filter (BTF) to upgrade biogas, which is achieved by adding H₂ to reduce CO₂. H₂ and CO₂ (80:20% vol.) were fed to a bench-scale BTF packed with polyurethane foam (PUF) and inoculated with hydrogenotrophic methanogens. Maximum CH₄ production rates recorded were as high as 38 m³ _CH4 m^?3 _reactor day^?1, which is 5–30 times faster than earlier reports with other kinds of bioreactors. The high rates were attributed to the efficient mass transfer and high density of methanogens in the BTF. The removal efficiencies for H₂ and CO₂ were 83 and 96%, respectively. 5-Cyano-2,3-ditolyl tetrazolium chloride/DAPI staining revealed that 67% of cells were alive near the gas entrance port, while only 8.3% were alive at the exit. Furthermore, DNA sequencing showed that only 27% of the biomass was composed of Euryarchaeota, the phylum which includes methanogens. These two observations suggest that optimizing the methanogen density and activity could possibly reach even higher biogas upgrading rates.     

Expression and Enzyme Activity Detection of a Sepiapterin Reductase Gene from <Emphasis Type="Italic">Musca domestica</Emphasis> Larva

Tetrahydrobiopterin (BH4) is an essential cofactor for aromatic acid hydroxylases and nitric oxide synthase. Sepiapterin reductase (SPR) catalyzes the final steps of BH4 biosynthesis. Studies on SPR from several insects and other organisms have been reported. However, thus far, enzyme activity of SPR in Musca domestica is kept unknown. In this study, 186 differentially expressed genes including SPR gene from Musca domestica (MDSPR) were screened in subtractive cDNA library. The MDSPR gene was cloned, and the recombinant MDSPI16 protein was expressed as a 51-kDa protein in soluble form. The MDSPR exhibited strong activity to the substrate sepiapterin (SP). The values of V_max and K_m of the MDSPR for SP were 6.83 μM/min and 23.48 μM, and the optimum temperature and pH of MDSPR were 50 °C and 4.0, respectively. This study provides new hypotheses and methods for the production of BH4 using insect-derived SPR.     

Decomposition and Debromination of Monobromoacetic Acid by Radio Frequency Discharge in an Aqueous Solution

In this study, efficient decomposition and debromination of monobromoacetic acid (MBAA) induced by radio frequency discharge in an aqueous solution in the concentration range from 0.1 to 8.0 mM were investigated. The decomposition and debromination intermediate byproducts were analyzed by ion chromatography. The experimental results showed that the decay of MBAA followed first-order kinetics. Increasing pH and adding organic additives to the solution enhanced MBAA removal and debromination. Acetic acid, bromate ion, oxalic acid and formic acid were determined as the major intermediate byproducts. Final products were bromide ion and carbon dioxide. Hydrated electrons are the primary species for the debromination and reactive oxygen species are the ones for the decomposition. A probable reaction pathway was proposed. The present study may provide a promising alternative for the complete mineralization of MBAA.     

Addition of Surfactants and Non-Hydrolytic Proteins and Their Influence on Enzymatic Hydrolysis of Pretreated Sugarcane Bagasse

Poly(ethylene glycol) (PEG 4000) and bovine serum albumin (BSA) were investigated with the purpose of evaluating their influence on enzymatic hydrolysis of sugarcane bagasse. Effects of these supplements were assayed for different enzymatic cocktails (Trichoderma harzianum and Penicillium funiculosum) that acted on lignocellulosic material submitted to different pretreatment methods with varying solid (25 and 100 g/L) and protein (7.5 and 20 mg/g cellulose) loadings. The highest levels of glucose release were achieved using partially delignified cellulignin as substrate, along with the T. harzianum cocktail: increases of 14 and 18 % for 25 g/L solid loadings and of 33 and 43 % for 100 g/L solid loadings were reached for BSA and PEG supplementation, respectively. Addition of these supplements could maintain hydrolysis yield even for higher solid loadings, but for higher enzymatic cocktail protein loadings, increases in glucose release were not observed. Results indicate that synergism might occur among these additives and cellulase and xylanases. The use of these supplements, besides depending on factors such as pretreatment method of sugarcane bagasse, enzymatic cocktails composition, and solid and protein loadings, may not always lead to positive effects on the hydrolysis of lignocellulosic material, making it necessary further statistical studies, according to process conditions.     

TMDIM: an improved algorithm for the structure prediction of transmembrane domains of bitopic dimers

\(\alpha\)-Helical transmembrane proteins are the most important drug targets in rational drug development. However, solving the experimental structures of these proteins remains difficult, therefore computational methods to accurately and efficiently predict the structures are in great demand. We present an improved structure prediction method TMDIM based on Park et al. (Proteins 57:577–585, 2004) for predicting bitopic transmembrane protein dimers. Three major algorithmic improvements are introduction of the packing type classification, the multiple-condition decoy filtering, and the cluster-based candidate selection. In a test of predicting nine known bitopic dimers, approximately 78% of our predictions achieved a successful fit (RMSD <2.0 Å) and 78% of the cases are better predicted than the two other methods compared. Our method provides an alternative for modeling TM bitopic dimers of unknown structures for further computational studies. TMDIM is freely available on the web at https://cbbio.cis.umac.mo/TMDIM. Website is implemented in PHP, MySQL and Apache, with all major browsers supported.     

Comparing pharmacophore models derived from crystallography and NMR ensembles

NMR and X-ray crystallography are the two most widely used methods for determining protein structures. Our previous study examining NMR versus X-Ray sources of protein conformations showed improved performance with NMR structures when used in our Multiple Protein Structures (MPS) method for receptor-based pharmacophores (Damm, Carlson, J Am Chem Soc 129:8225–8235, 2007). However, that work was based on a single test case, HIV-1 protease, because of the rich data available for that system. New data for more systems are available now, which calls for further examination of the effect of different sources of protein conformations. The MPS technique was applied to Growth factor receptor bound protein 2 (Grb2), Src SH2 homology domain (Src-SH2), FK506-binding protein 1A (FKBP12), and Peroxisome proliferator-activated receptor-γ (PPAR-γ). Pharmacophore models from both crystal and NMR ensembles were able to discriminate between high-affinity, low-affinity, and decoy molecules. As we found in our original study, NMR models showed optimal performance when all elements were used. The crystal models had more pharmacophore elements compared to their NMR counterparts. The crystal-based models exhibited optimum performance only when pharmacophore elements were dropped. This supports our assertion that the higher flexibility in NMR ensembles helps focus the models on the most essential interactions with the protein. Our studies suggest that the “extra” pharmacophore elements seen at the periphery in X-ray models arise as a result of decreased protein flexibility and make very little contribution to model performance.     

Temperature effect on the optical properties of two different triphenylamine-based organic dyes

In this paper, we present the absorption and photoluminescence (PL) spectra of conjugated, metal-free organic dyes, triphenylamine derivatives 3-(4-(bis(4-(5-(4-(hexyloxy)phenyl)thiophenyl)phenyl)amino)phenyl)-2-cyanoacrylic acid (OD3) and (E)-3-(5′-(4-(bis(4-(5-(4-hexyloxy)phenyl)thiophen-2-yl)phenyl)amino)phenyl)-2,2′-bithiophen-5-yl)-2-cyanoacrylic acid (OD3DT), with and without a π-conjugated bridge, respectively, in film at a temperature range from 13 to 400 K. We find that the intensities of absorption and PL of OD3 decrease gradually beyond 200 K, as well as the ratios of integral areas of absorption to PL spectra. However, the other compound, OD3DT, shows a very different behavior. An increase is discovered in the ratio of the absorption to PL integral area when the temperature is higher than 200 K. A π-conjugated bridge gives this compound a higher degree of symmetry, and therefore, a better alignment of the molecules in the film, which causes a stacking aggregation such that the temperature effect on this compound is different than OD3.