Biotechnology Research Institute

We have identified a new protein fold--the alpha/beta hydrolase fold--that is common to several hydrolytic enzymes of widely differing phylogenetic origin and catalytic function. The core of each enzyme is similar: an alpha/beta sheet, not barrel, of eight beta-sheets connected by alpha-helices. These enzymes have diverged from a common ancestor so as to preserve the arrangement of the catalytic residues, not the binding site. They all have a catalytic triad, the elements of which are borne on loops which are the best-conserved structural features in the fold. Only the histidine in the nucleophile-histidine-acid catalytic triad is completely conserved, with the nucleophile and acid loops accommodating more than one type of amino acid. The unique topological and sequence arrangement of the triad residues produces a catalytic triad which is, in a sense, a mirror-image of the serine protease catalytic triad. There are now four groups of enzymes which contain catalytic triads and which are related by convergent evolution towards a stable, useful active site: the eukaryotic serine proteases, the cysteine proteases, subtilisins and the alpha/beta hydrolase fold enzymes.

BACKGROUND: Arginine vasopressin (AVP) is a key regulator of water balance, but its instability makes reliable measurement difficult and precludes routine use. We present a method for quantifying AVP release by use of copeptin, a glycopeptide comprising the C-terminal part of the AVP prohormone. METHODS: We measured copeptin in 50-microL serum and plasma samples from healthy individuals and from critically ill patients with sepsis. Our sandwich immunoluminometric assay used 2 polyclonal antibodies to amino acids 132-164 of pre-provasopressin. RESULTS: The assay yielded results within 3 h. The analytical detection limit was 1.7 pmol/L, and the interlaboratory CV was <20% for values >2.25 pmol/L. The assay was linear on dilution of the analyte. Ex vivo copeptin stability (<20% loss of analyte) for at least 7 days at room temperature and 14 days at 4 degrees C was shown for serum and EDTA-, heparin-, and citrate plasma. Copeptin (median, 4.2 pmol/L; range, 1-13.8 pmol/L) was detectable in 97.5% of 359 healthy individuals and was not associated with age. Median concentrations were considerably higher in men than women, increased significantly after exercise, and were influenced by fasting and water load. Copeptin was significantly (P <0.001) increased in 60 critically ill patients with sepsis (median, 79.5 pmol/L; range, 10.6-228.0 pmol/L). The correlation between copeptin and AVP for 110 samples was r = 0.78 (P <0.0001). CONCLUSIONS: Copeptin is stable for days after blood withdrawal and can be quickly and easily measured. The copeptin assay may be a useful alternative to direct measurement of AVP concentration.

Platinum nanoparticles with a diameter of 2-3 nm were prepared and used in combination with single-wall carbon nanotubes (SWCNTs) for fabricating electrochemical sensors with remarkably improved sensitivity toward hydrogen peroxide. Nafion, a perfluorosulfonated polymer, was used to solubilize SWCNTs and also displayed strong interactions with Pt nanoparticles to form a network that connected Pt nanoparticles to the electrode surface. TEM and AFM micrographs illustrated the deposition of Pt nanoparticles on carbon nanotubes whereas cyclic voltammetry confirmed an electrical contact through SWCNTs between Pt nanoparticles and the glassy carbon (GC) or carbon fiber backing. With glucose oxidase (GOx) as an enzyme model, we constructed a GC or carbon fiber microelectrode-based biosensor that responds even more sensitively to glucose than the GC/GOx electrode modified by Pt nanoparticles or CNTs alone. The response time and detection limit (S/N = 3) of this biosensor was determined to be 3 s and 0.5 microM, respectively.

A scalable transfection procedure using polyethylenimine (PEI) is described for the human embryonic kidney 293 cell line grown in suspension. Green fluorescent protein (GFP) and human placental secreted alkaline phosphatase (SEAP) were used as reporter genes to monitor transfection efficiency and productivity. Up to 75% of GFP-positive cells were obtained using linear or branched 25 kDa PEI. The 293 cell line and two genetic variants, either expressing the SV40 large T-antigen (293T) or the Epstein-Barr virus (EBV) EBNA1 protein (293E), were tested for protein expression. The highest expression level was obtained with 293E cells using the EBV oriP-containing plasmid pCEP4. We designed the pTT vector, an oriP-based vector having an improved cytomegalovirus expression cassette. Using this vector, 10- and 3-fold increases in SEAP expression was obtained in 293E cells compared with pcDNA3.1 and pCEP4 vectors, respectively. The presence of serum had a positive effect on gene transfer and expression. Transfection of suspension-growing cells was more efficient with linear PEI and was not affected by the presence of medium conditioned for 24 h. Using the pTT vector, >20 mg/l of purified His-tagged SEAP was recovered from a 3.5 l bioreactor. Intracellular proteins were also produced at levels as high as 50 mg/l, representing up to 20% of total cell proteins.

Resistance to stress-induced apoptosis was examined in cells in which the expression of hsp70 was either constitutively elevated or inducible by a tetracycline-regulated transactivator. Heat-induced apoptosis was blocked in hsp70-expressing cells, and this was associated with reduced cleavage of the common death substrate protein poly(ADP-ribose) polymerase (PARP). Heat-induced cell death was correlated with the activation of the stress-activated protein kinase SAPK/JNK (c-Jun N-terminal kinase). Activation of SAPK/JNK was strongly inhibited in cells in which hsp70 was induced to a high level, indicating that hsp70 is able to block apoptosis by inhibiting signaling events upstream of SAPK/JNK activation. In contrast, SAPK/JNK activation was not inhibited by heat shock in cells with constitutively elevated levels of hsp70. Cells that constitutively overexpress hsp70 resist apoptosis induced by ceramide, a lipid signaling molecule that is generated by apoptosis-inducing treatments and is linked to SAPK/JNK activation. Similar to heat stress, resistance to ceramide-induced apoptosis occurs in spite of strong SAPK/JNK activation. Therefore, hsp70 is also able to inhibit apoptosis at some point downstream of SAPK/JNK activation. Since PARP cleavage is prevented in both cell lines, these results suggest that hsp70 is able to prevent the effector steps of apoptotic cell death. Processing of the CED-3-related protease caspase-3 (CPP32/Yama/apopain) is inhibited in hsp70-expressing cells; however, the activity of the mature enzyme is not affected by hsp70 in vitro. Caspase processing may represent a critical heat-sensitive target leading to cell death that is inhibited by the chaperoning function of hsp70. The inhibition of SAPK/JNK signaling and apoptotic protease effector steps by hsp70 likely contributes to the resistance to stress-induced apoptosis seen in transiently induced thermotolerance.

Cellular stress can trigger a process of self-destruction known as apoptosis. Cells can also respond to stress by adaptive changes that increase their ability to tolerate normally lethal conditions. Expression of the major heat-inducible protein hsp70 protects cells from heat-induced apoptosis. hsp70 has been reported to act in some situations upstream or downstream of caspase activation, and its protective effects have been said to be either dependent on or independent of its ability to inhibit JNK activation. Purified hsp70 has been shown to block procaspase processing in vitro but is unable to inhibit the activity of active caspase 3. Since some aspects of hsp70 function can occur in the absence of its chaperone activity, we examined whether hsp70 lacking its ATPase domain or the C-terminal EEVD sequence that is essential for peptide binding was required for the prevention of apoptosis. We generated stable cell lines with tetracycline-regulated expression of hsp70, hsc70, and chaperone-defective hsp70 mutants lacking the ATPase domain or the C-terminal EEVD sequence or containing AAAA in place of EEVD. Overexpression of hsp70 or hsc70 protected cells from heat shock-induced cell death by preventing the processing of procaspases 9 and 3. This required the chaperone function of hsp70 since hsp70 mutant proteins did not prevent procaspase processing or provide protection from apoptosis. JNK activation was inhibited by both hsp70 and hsc70 and by each of the hsp70 domain mutant proteins. The chaperoning activity of hsp70 is therefore not required for inhibition of JNK activation, and JNK inhibition was not sufficient for the prevention of apoptosis. Release of cytochrome c from mitochondria was inhibited in cells expressing full-length hsp70 but not in cells expressing the protein with ATPase deleted. Together with the recently identified ability of hsp70 to inhibit cytochrome c-mediated procaspase 9 processing in vitro, these data demonstrate that hsp70 can affect the apoptotic pathway at the levels of both cytochrome c release and initiator caspase activation and that the chaperone function of hsp70 is required for these effects.

The femtosecond laser ablation of a gold target in aqueous solutions has been used to produce colloidal Au nanoparticles with controlled surface chemistry. A detailed chemical analysis showed that the nanoparticles formed were partially oxidized by the oxygen present in solution. The hydroxylation of these Au−O compounds, followed by a proton loss to give surface Au−O-, resulted in the negative charging of the nanoparticles. The partial oxidation of the gold nanoparticle surface enhances its chemical reactivity and consequently has a strong impact on its growth. In particular, the oxidized surface reacted efficiently with Cl- and OH- to augment its net surface charge. This limited the coalescence of the particles, due to electrostatic repulsion, and led to a significant reduction of their size. Taking advantage of the repulsion effect, efficient size control was achieved using different salts (7 ± 5 nm for 10 mM KCl, 5.5 ± 4 nm for 10 mM NaCl, 8 ± 5 nm for NaOH, pH 9.4), a considerable improvement comparatively to particles prepared in deionized water, using identical ablation conditions, where particles of 1−250 nm were produced. The partially oxidized gold surface was also suitable for surface modification through both covalent and electrostatic interactions during particle formation. Using solutions of N-propylamine, we showed an efficient control of nanoparticle size (5−8 ± 4−7 nm) by the involvement of these interactions. The results obtained help to develop methodologies for the control of laser-ablation-based nanoparticle growth and the functionalization of nanoparticle surfaces by specific interactions.

The rapid yet transient transcriptional activation of heat shock genes is mediated by the reversible conversion of HSF1 from an inert negatively regulated monomer to a transcriptionally active DNA-binding trimer. During attenuation of the heat shock response, transcription of heat shock genes returns to basal levels and HSF1 reverts to an inert monomer. These events coincide with elevated levels of Hsp70 and other heat shock proteins (molecular chaperones). Here, we show that the molecular chaperone Hsp70 and the cochaperone Hdj1 interact directly with the transactivation domain of HSF1 and repress heat shock gene transcription. Overexpression of either chaperone represses the transcriptional activity of a transfected GAL4-HSF1 activation domain fusion protein and endogenous HSF1. As neither the activation of HSF1 DNA binding nor inducible phosphorylation of HSF1 was affected, the primary autoregulatory role of Hsp70 is to negatively regulate HSF1 transcriptional activity. These results reveal that the repression of heat shock gene transcription, which occurs during attenuation, is due to the association of Hsp70 with the HSF1 transactivation domain, thus providing a plausible explanation for the role of molecular chaperones in at least one key step in the autoregulation of the heat shock response.

Elevated expression of members of the BCL-2 pro-survival family of proteins can confer resistance to apoptosis in cancer cells. Small molecule obatoclax (GX15-070), which is predicted to occupy a hydrophobic pocket within the BH3 binding groove of BCL-2, antagonizes these members and induces apoptosis, dependent on BAX and BAK. Reconstitution in yeast confirmed that obatoclax acts on the pathway and overcomes BCL-2-, BCL-XL-, BCL-w-, and MCL-1-mediated resistance to BAX or BAK. The compound potently interfered with the direct interaction between MCL-1 and BAK in intact mitochondrial outer membrane and inhibited the association between MCL-1 and BAK in intact cells. MCL-1 has been shown to confer resistance to the BCL-2/BCL-XL/BCL-w-selective antagonist ABT-737 and to the proteasome inhibitor bortezomib. In both cases, this resistance was overcome by obatoclax. These findings support a rational clinical development opportunity for the compound in cancer indications or treatments where MCL-1 contributes to resistance to cell killing.

The structure of the Candida rugosa lipase determined at 2.06-A resolution reveals a conformation with a solvent-accessible active site. Comparison with the crystal structure of the homologous lipase from Geotrichum candidum, in which the active site is covered by surface loops and is inaccessible from the solvent, shows that the largest structural differences occur in the vicinity of the active site. Three loops in this region differ significantly in conformation, and the interfacial activation of these lipases is likely to be associated with conformational rearrangements of these loops. The "open" structure provides a new image of the substrate binding region and active site access, which is different from that inferred from the structure of the "closed" form of the G. candidum lipase.

Abstract Based on the recently determined X‐ray structures of Torpedo californica acetylcholinesterase and Geotrichum candidum lipase and on their three‐dimensional superposition, an improved alignment of a collection of 32 related amino acid sequences of other esterases, lipases, and related proteins was obtained. On the basis of this alignment, 24 residues are found to be invariant in 29 sequences of hydrolytic enzymes, and an additional 49 are well conserved. The conservation in the three remaining sequences is somewhat lower. The conserved residues include the active site, disulfide bridges, salt bridges, and residues in the core of the proteins. Most invariant residues are located at the edges of secondary structural elements. A clear structural basis for the preservation of many of these residues can be determined from comparison of the two X‐ray structures.

Abstract BACKGROUND: This paper describes results obtained for different participating research groups in an interlaboratory study related to biochemical methane potential (BMP). In this research work, all experimental conditions influencing the test such as inoculum, substrate characteristics and experimental conditions were investigated. The study was performed using four substrates: three positive control substrates (starch, cellulose and gelatine), and one raw biomass material (mung bean) at two different inoculum to substrate ratios (ISR). RESULTS: The average methane yields for starch, cellulose, gelatine and mung bean at ISR of 2 and 1 were 350 ± 33, 350 ± 29, 380 ± 42, 370 ± 36 and 370 ± 35 mL CH 4 g −1 VS added , respectively. The percentages of biotransformation of these substrates into methane were 85 ± 8, 85 ± 7, 88 ± 9, 85 ± 8 and 85 ± 8%, respectively. On the other hand, the first‐order rate constants obtained from the experimental data were 0.24 ± 0.14, 0.23 ± 0.15, 0.27 ± 0.13, 0.31 ± 0.17 and 0.23 ± 0.13 d −1 , respectively. CONCLUSION: The influence of inocula and experimental factors was nearly insignificant with respect to the extents of the anaerobic biodegradation, while the rates differed significantly according to the experimental approaches. Copyright © 2011 Society of Chemical Industry

Harmful conditions including heat shock, oxidative stress, UV, and so forth cause programmed cell death, whose triggering requires activation of the Jun N-terminal kinase, JNK. High levels of Hsp72, a heat-inducible member of Hsp70 family, protect cells against a variety of stresses by a mechanism that is unclear at present. Here we report that elevated levels of Hsp72 inhibit a signal transduction pathway leading to programmed cell death by preventing stress-induced activation of JNK. Stress-induced activation of another stress-kinase, p38 (HOG1), is also blocked when the level of Hsp72 is increased. Similarly, addition of a purified recombinant Hsp72 to a crude cell lysate reduced p38 kinase activation, while depletion of the whole family of Hsp70 proteins with a monoclonal antibody enhanced such activation. In addition, we have found that accumulation of abnormal proteins in cells upon incubation with amino acid analogs causes activation of JNK and p38 kinases, which can be prevented by overproduction of Hsp72. Taken together, these data suggest that, in regulation of JNK and p38 kinases, Hsp70 serves as a "sensor" of the build-up of abnormal proteins after heat shock and other stresses. The inhibitory effect of an increased level of Hsp70 on JNK appears to be a major contributor to acquired thermotolerance in mammalian cells.

High quality cellulose nanocrystals are synthesized using a simple one-step procedure with ammonium persulfate. This versatile method processes a variety of cellulosic biomass without the need for pretreatments to remove non- cellulosic plant contents.

A survey of China's plant biotechnologists shows that China is developing the largest plant biotechnology capacity outside of North America. The list of genetically modified plant technologies in trials, including rice, wheat, potatoes, and peanuts, is impressive and differs from those being worked on in other countries. Poor farmers in China are cultivating more area of genetically modified plants than are small farmers in any other developing country. A survey of agricultural producers in China demonstrates that Bacillus thuringiensis cotton adoption increases production efficiency and improves farmer health.

Biodegradation of petroleum hydrocarbons in cold environments, including Alpine soils, is a result of indigenous cold-adapted microorganisms able to degrade these contaminants. In the present study, the prevalence of seven genotypes involved in the degradation of n-alkanes (Pseudomonas putida GPo1 alkB; Acinetobacter spp. alkM; Rhodococcus spp. alkB1, and Rhodococcus spp. alkB2), aromatic hydrocarbons (P. putida xylE), and polycyclic aromatic hydrocarbons (P. putida ndoB and Mycobacterium sp. strain PYR-1 nidA) was determined in 12 oil-contaminated (428 to 30,644 mg of total petroleum hydrocarbons [TPH]/kg of soil) and 8 pristine Alpine soils from Tyrol (Austria) by PCR hybridization analyses of total soil community DNA, using oligonucleotide primers and DNA probes specific for each genotype. The soils investigated were also analyzed for various physical, chemical, and microbiological parameters, and statistical correlations between all parameters were determined. Genotypes containing genes from gram-negative bacteria (P. putida alkB, xylE, and ndoB and Acinetobacter alkM) were detected to a significantly higher percentage in the contaminated (50 to 75%) than in the pristine (0 to 12.5%) soils, indicating that these organisms had been enriched in soils following contamination. There was a highly significant positive correlation (P < 0.001) between the level of contamination and the number of genotypes containing genes from P. putida and Acinetobacter sp. but no significant correlation between the TPH content and the number of genotypes containing genes from gram-positive bacteria (Rhodococcus alkB1 and alkB2 and Mycobacterium nidA). These genotypes were detected at a high frequency in both contaminated (41.7 to 75%) and pristine (37.5 to 50%) soils, indicating that they are already present in substantial numbers before a contamination event. No correlation was found between the prevalence of hydrocarbon-degradative genotypes and biological activities (respiration, fluorescein diacetate hydrolysis, lipase activity) or numbers of culturable hydrocarbon-degrading soil microorganisms; there also was no correlation between the numbers of hydrocarbon degraders and the contamination level. The measured biological activities showed significant positive correlation with each other, with the organic matter content, and partially with the TPH content and a significant negative correlation with the soil dry-mass content (P < 0.05 to 0.001).

In recent years, conductive diamond electrodes for electrochemical applications have been a major focus of research and development. The impetus behind such endeavors could be attributed to their wide potential window, low background current, chemical inertness, and mechanical durability. Several analytes can be oxidized by conducting diamond compared to other carbon-based materials before the breakdown of water in aqueous electrolytes. This is important for detecting and/or identifying species in solution since oxygen and hydrogen evolution do not interfere with the analysis. Thus, conductive diamond electrodes take electrochemical detection into new areas and extend their usefulness to analytes which are not feasible with conventional electrode materials. Different types of diamond electrodes, polycrystalline, microcrystalline, nanocrystalline and ultrananocrystalline, have been synthesized and characterized. Of particular interest is the synthesis of boron-doped diamond (BDD) films by chemical vapor deposition on various substrates. In the tetrahedral diamond lattice, each carbon atom is covalently bonded to its neighbors forming an extremely robust crystalline structure. Some carbon atoms in the lattice are substituted with boron to provide electrical conductivity. Modification strategies of doped diamond electrodes with metallic nanoparticles and/or electropolymerized films are of importance to impart novel characteristics or to improve the performance of diamond electrodes. Biofunctionalization of diamond films is also feasible to foster several useful bioanalytical applications. A plethora of opportunities for nanoscale analytical devices based on conducting diamond is anticipated in the very near future.

The work reported here describes interactions between nanoscale Au colloids and two main types of organic functional groups, viz., alkanethiols and amino acids. The surface chemistry of particulate Au is dominated by electrodynamic factors related to its (negative) surface charge. Generalized multiparticle Mie calculations were used to model the optical absorption characteristics of Au particles, existing either singly or in varying degrees of aggregation. Experiments with standard (monodisperse) Au colloids confirm the theoretical prediction of a new peak appearing at longer wavelength that intensifies and shifts further from the original peak with increasing particle size, increasing aggregate size, or shorter interparticle spacing. Control of aggregation degree in alkanethiols is achieved by judicious selection of terminal group composition (single- or double-ended), alkyl chain length, and the presence of pH sensitive groups such as carboxylates. In amino acids, the reactivity of the α-amine (adjacent to −COOH) is found to be pH-dependent. Linking via the α-amine is activated at low pH but suppressed at intermediate and high pH due to electrostatic repulsive forces between the Au surface and the charged carboxylate group or even the (formally neutral) polar carbonyl group in amides. However, dibasic amino acids can still be used to cross-link Au colloids at high pH. The pH insensitive (remote) amine binds amino acids to each particle, leaving protruding pairs of α-amines that can be bridged by a symmetrical linker molecule like glutaraldehyde (via its electrophilic centers). This offers a new way to organize Au nanoparticles into extended architectures and functional materials over a wide range of pH. The potential of Au colloids to recognize and determine dibasic amino acids based on optical absorption changes is briefly assessed. A higher detection limit for cysteine (1.2 μg/mL) was found for larger (40 nm) Au particles.

To gain insight into the factors driving the structure of bacterial communities in soil, we applied real-time PCR, PCR-denaturing gradient gel electrophoreses, and phylogenetic microarray approaches targeting the 16S rRNA gene across a range of different land usages in the Netherlands. We observed that the main differences in the bacterial communities were not related to land-use type, but rather to soil factors. An exception was the bacterial community of pine forest soils (PFS), which was clearly different from all other sites. PFS had lowest bacterial abundance, lowest numbers of operational taxonomic units (OTUs), lowest soil pH, and highest C : N ratios. C : N ratio strongly influenced bacterial community structure and was the main factor separating PFS from other fields. For the sites other than PFS, phosphate was the most important factor explaining the differences in bacterial communities across fields. Firmicutes were the most dominant group in almost all fields, except in PFS and deciduous forest soils (DFS). In PFS, Alphaproteobacteria was most represented, while in DFS, Firmicutes and Gammaproteobacteria were both highly represented. Interestingly, Bacillii and Clostridium OTUs correlated with pH and phosphate, which might explain their high abundance across many of the Dutch soils. Numerous bacterial groups were highly correlated with specific soil factors, suggesting that they might be useful as indicators of soil status.

What is life without oxygen is a rhetorical question. On the other hand, unraveling the intricacies and understanding the various mechanisms underpinning the biological processes beg many answers. The activation of hydrocarbon C-H bonds by oxygenases exemplifies an important biological process and prerequisite to the eventual transformation of these raw materials into value-added chemicals or bioproducts. Oxygenases come in two forms: those that introduce one atom of molecular oxygen into an organic substrate, called monooxygenases (also referred to as mixed function oxygenases) and those that insert both oxygen atoms into a substrate, namely, dioxygenases. For a historical account on the discovery of oxygenases see a review by Hayaishi.(1) In monooxygenase-catalyzed reactions, the other oxygen atom undergoes reduction to water. Hence, in a biotransformation or biocatalysis setting, having water as a byproduct cannot be greener. This review focuses on the monooxygenase-catalyzed Baeyer-Villiger oxidation of linear or cyclic ketones as a green chemistry tool to address environmental sustainability, a system to study its molecular diversity and catalytic mechanism, industrial-scale bioprocess development, and a challenging model for protein engineering to evolve new biotechnological applications.Biocatalysis at large is poised to play an ever increasingly important role in meeting the needs of industrial and environmental sustainability as manufacturers and industries are striving to improve efficiency and implement cleaner processes.(2) In the context of the three pillars of sustainable development, the use of biocatalysts, as opposed to strictly harsh chemical methods, is meeting the needs of environmental care and social responsibility, although rapid economic progress requires serious financial investment.