Polyethylene glycol-modified lipase catalyzes asymmetric alcoholysis of δ-decalactone in n-decanol

Summary Lipase from Pseudomonas cepacia was modified with 2,4-bis[O-methoxypoly(ethylene glycol)]-6-chloro-s-triazine(activated PEG₂) to form PEG-lipase. The PEG-lipase, soluble and active in organic solvents, catalyzes asymmetric alcoholysis of racemic -decalactone in alcohols to form (R)-5-hydroxydecanoic acid alkyl esters. The yield was 69% with 83% enantiomeric excess after 3 hr-reaction in n-decanol at 50°C. The advantage of this reaction is that the alcoholysis proceeds efficiently in straight hydrophobic substrates without any organic solvents.     

Effects on Interactions of Oppositely Charged Phospholipid Vesicles of Covalent Attachment of Polyethylene Glycol Oligomers to Their Surfaces: Adhesion, Hemifusion, Full Fusion and “Endocytosis”

Oppositely charged giant vesicles are known to adhere, hemifuse and fuse, all of which depend upon the nature of surface contacts. To further understand such interactions, vesicles were surface-modified with polyethylene glycol (PEG), a moiety that reduces surface-surface interactions. Positively charged vesicles were composed of O-ethyldioleoylphosphocholine (EDOPC), dioleoylphosphatidylcholine (DOPC) and a carbocyanine dye (DiO), with and without DPPE-PEG (dipalmitoylphosphatidylethanolamine-N-PEG MW of the PEG portion = 2000). Negatively charged vesicles were composed of dioleoylphosphatidylglycerol (DOPG), DOPC and a rhodamine B dye (Rh-PE), with as well as without DPPE-PEG (MW 2,000). A microscope-mounted electrophoresis chamber allowed selected pairs of vesicles to be brought into contact while color images were collected at video rates (30 frames/s). Data collection focused on effects of PEG on vesicle interactions as a function of the surface charge density. Relative to PEG-free preparations, vesicles containing DPPE-PEG (1) formed larger contact zones, (2) underwent adhesion and fusion processes more slowly (by two to four times) and (3) at high charge density were less susceptible to rupture upon contact. Unexpectedly, PEG-containing vesicles exhibited engulfment of a smaller by a larger vesicle, a process topologically similar to cellular endocytosis. These observations are interpreted to mean that, although initial surface-surface interactions are weakened by the intervening layer of PEG chains, eventual and strong bilayer-bilayer contact is still possible, evidently because the lipid anchors of these chains can diffuse away from the contact zone.     

Functional Changes of Polyethylene Glycol-modified Serine Proteinase from Aspergillus sojae and Interaction with α2-Macroglobulin

The covalent attachment of activated polyethylene glycol₂ (PEG₂) of 10,000 daltons to non- essential groups on a serine proteinase II (SepII) from Aspergillus sojae produced two modified preparations (PEG₂-SepII-S and PEG₂-SepII-L). The molecular weights of PEG₂-SepII-S and PEG₂-SepII-L were about 170,000 and 280,000, respectively. The PEG₂-SepII-S lost about 80 % of its antigenicity, while the PEG₂-SepU-L completely lost its antigenicity. In comparison of kinetic parameters with SepII there was less than 40 % variation in Km, but the values of k_cat towards succinyl-l-leucy 1-l-leucy 1-l-valy 1-l-tyrosine 4-methylcoumaryl-7-amide (Suc-LLVY-MCA) or succinyl-l- alanyl-l-alanyl-l-valyl-l-alanine β-nitroanilide (Suc-AAVA-/>NA) decreased to about 70% less than that of SepII. The modified preparations have about 20 % activity towards fibrin hydrolysis and a low affinity for a protein proteinase inhibitor, Streptomyces subtilisin inhibitor (SSI), with a molecular weight of 23,000, while the preparations have high affinity for a low molecular weight microbial inhibitor, chymostatin. The stoichiometry of the reaction of a₂-macroglobulin (α₂M) with PEG₂-SepII-S showed that PEG₂-SepII-L bound to α₂M in a molar ratio of 1:1. No appreciable differences were observed in the pH stabilities of the modified enzymes and the native one at pH 3.6, while the modified enzymes were more stable than that of the native one at pH 11.5. The two modified preparations were labile at 50°C, but the native enzyme was completely stable at 50°C.     

Colonization and Biodegradation of Photo-Oxidized Low-Density Polyethylene (LDPE) by New Strains of Aspergillus sp. and Lysinibacillus sp.

The primary objective of this study was the isolation of low-density polyethylene (LDPE)-degrading microorganisms. Soil samples were obtained from an aged municipal landfill in Tehran, Iran, and enrichment culture procedures were performed using LDPE films and powder. Screening steps were conducted using linear paraffin, liquid ethylene oligomer, and LDPE powder as the sole source of carbon. Two landfill-source isolates, identified as Lysinibacillus xylanilyticus XDB9 (T) strain S7-10F and Aspergillus niger strain F1-16S, were selected as super strains. Photo-oxidation (25 days under ultraviolet [UV] irradiation) was used as a pretreatment of the LDPE samples without pro-oxidant additives. The PE biodegradation process was performed for 56 days in a liquid mineral medium using UV-irradiated pure LDPE films without pro-oxidant additives in the presence of the bacterial isolate, the fungal isolate, and the mixture of the two isolates. The process was monitored by measuring the fungal biomass, the bacterial growth, and the pH of the medium. During the process, the fungal biomass and the bacterial growth increased, and the pH of the medium decreased, which suggests the utilization of the preoxidized PE by the selected isolates as the sole source of carbon. Carbonyl and double bond indices exhibited the highest amount of decrement and increment, respectively, in the presence of the fungal isolate, and the lowest indices were obtained from the treatment of a mixture of both fungal and bacterial isolates. Fourier transform infrared (FT-IR), x-ray diffraction (XRD), and scanning electron microscopy (SEM) analyses showed that the selected isolates modified and colonized preoxidized pure LDPE films without pro-oxidant additives.     

Polyethylene Glycol–Modified Papain Catalyzed Oligopeptide Synthesis from the Esters of l-Aspartic and l-Glutamic Acids in Benzene

Comparative studies were made of the polymerization of l-aspartic and l-glutamic acid dialkyl esters using polyethylene glycol–modified papain as a catalyst in phosphate buffer (pH 7.5) and in benzene. Changes in the substrate specificity of papain and in the composition of oligomerized products were observed. In the buffer, the diethyl and di-n-propyl esters of l-glutamic acid were sufficiently converted to high molecular weight oligomers with the accumulation of dimer and trimer, but l-aspartic acid esters were very poor substrates. In benzene, l-aspartic acid esters became more reactive than L-glutamic acid esters. In particular, from l-aspartic acid dimethyl ester the product, which was mainly composed of heptamer to decamer, was obtained in a 90% yield. The reaction in benzene required desalted substrates and a small amount of water to proceed extensively.     

Biofilm and Diatom Succession on Polyethylene (PE) and Biodegradable Plastic Bags in Two Marine Habitats: Early Signs of Degradation in the Pelagic and Benthic Zone?

The production of biodegradable plastic is increasing. Given the augmented littering of these products an increasing input into the sea is expected. Previous laboratory experiments have shown that degradation of plastic starts within days to weeks. Little is known about the early composition and activity of biofilms found on biodegradable and conventional plastic debris and its correlation to degradation in the marine environment. In this study we investigated the early formation of biofilms on plastic shopper bags and its consequences for the degradation of plastic. Samples of polyethylene and biodegradable plastic were tested in the Mediterranean Sea for 15 and 33 days. The samples were distributed equally to a shallow benthic (sedimentary seafloor at 6 m water depth) and a pelagic habitat (3 m water depth) to compare the impact of these different environments on fouling and degradation. The amount of biofilm increased on both plastic types and in both habitats. The diatom abundance and diversity differed significantly between the habitats and the plastic types. Diatoms were more abundant on samples from the pelagic zone. We anticipate that specific surface properties of the polymer types induced different biofilm communities on both plastic types. Additionally, different environmental conditions between the benthic and pelagic experimental site such as light intensity and shear forces may have influenced unequal colonisation between these habitats. The oxygen production rate was negative for all samples, indicating that the initial biofilm on marine plastic litter consumes oxygen, regardless of the plastic type or if exposed in the pelagic or the benthic zone. Mechanical tests did not reveal degradation within one month of exposure. However, scanning electron microscopy (SEM) analysis displayed potential signs of degradation on the plastic surface, which differed between both plastic types. This study indicates that the early biofilm formation and composition are affected by the plastic type and habitat. Further, it reveals that already within two weeks biodegradable plastic shows signs of degradation in the benthic and pelagic habitat.     

Cryoenzymology of β-galactosidase: Effects of cryosolvents

Experimental support for the use of fluid aqueous organic solvent systems and subzero temperatures in mechanistic studies of β-galactosidase is presented. The enzyme was stable and retained catalytic activity and structural integrity in 50% aqueous dimethyl sulfoxide and 60% aqueous methanol at 0°C; at lower temperatures higher concentrations of cosolvent may be successfully used. The effects of dimethyl sulfoxide on the catalytic and structural properties of the enzyme were investigated in detail. For the β-galactoside-catalyzed h ydrolysis ofo-nitrophenyl-β-D-galactoside the value ofk _cat decreased in a linear manner with increasing cosolvent concentration, whereasK _m increased exponentially. The decrease ink _cat paralleled the decrease in water concentration, consistent with rate-limiting hydrolysis of a galactosylenzyme intermediate. The increase inK _m is attributed to less favorable partitioning of the substrate to the active site in the cryosolvent compared to aqueous solution. ThepH*-rate profile for this reaction at 0°C in 50% dimethyl sulfoxide was similar to that in aqueous solution, withpK*₁=5.8 andpK*₂=8.0. Linear Arrhenius plots, with energies of activation of 13.9 and 16.0 kcal mol^?1, respectively, were obtained for the β-galactosidase-catalyzed hydrolysis ofo-nitrophenyl- andp-nitrophenyl-β-D-galactosides in 50% dimethyl sulfoxide at temperatures to ?57°C. Examination of the intrinsic fluorescence and ultraviolet spectra of the enzyme as a function of increasing cosolvent concentration showed no evidence for structural perturbation up to and including 50% dimethyl sulfoxide at 0°C. We conclude that these cryosolvent systems are suitable for mechanistic investigations of β-galactosidase, in particular for trapping intermediates at subzero temperatures.     

Catabolism of carotenoids: Involvement of peroxidase?

In primary leaves of barley allowed to senesce under natural conditions, carotenoids, like chlorophylls, disappear gradually. Commercial horse-radish peroxidase catalizes the oxidation of lutein to unknown colorless products. This reaction depends on the presence of 2,4 dichlorophenol. It is independent of peroxide but is nullified in the presence of catalase. Preparations of thylakoids from barley chloroplasts show an activity with features comparable to those of horse-radish peroxidase.Abbreviation DCP 2,4 Dichlorophenol     

Gibberellin: inhibitor of an inhibitor of...?

Gibberellin is an endogenous plant growth regulator. Here, we describe our present understanding of how gibberellin regulates plant growth, using recent results gained from studies of gibberellin-signalling mutants of Arabidopsis. These results show that a signalling pathway represses plant growth and that gibberellin releases this repression. In consequence, the well-known growth-promoting properties of gibberellin are due to its activity as an "inhibitor of an inhibitor" [Brian Pw. Sym Soc. Exp Bio 1957; 11:166-182 (Ref. 1)] of plant growth.     

Islands of Fertility: A Byproduct of Grazing?

Empirical work in arid shrubland systems has documented a distinct spatial pattern of soil nutrient distribution, with higher concentrations of nutrients under shrub canopies compared to bare ground interspaces between shrubs. This “fertile island” pattern is considered characteristic of arid ecosystems. However, recent work at a desertified shrubland site reported no island of fertility pattern for nitrogen inside a long-term grazing exclosure despite a strong fertile island pattern outside the exclosure, leading to a hypothesis that the pattern may be associated with grazing. In this paper we examine this hypothesis in two ways. First, we collected soil nitrogen data inside and outside two long-term livestock exclosures. Second, we examined published work on the fertile island pattern for nitrogen, phosphorus and carbon, and its association with livestock grazing. At the field sites, there was a strong fertile island pattern for soil nitrogen in the grazed area outside each exclosure but no fertile island pattern in the ungrazed area inside the fence. From the literature, we identified 49 studies, which represent 99 cases that examine differences in soil nutrients under and between shrubs (that is, tests of the fertile island pattern). In 92 cases, fertile islands were present for at least one of the nutrients. All cases where livestock grazing was present exhibited fertile island patterns for nitrogen and most did so for carbon and phosphorus. In contrast, fertile islands were less consistent where livestock grazing was absent; all nine cases that had been ungrazed for more than 30 years did not exhibit fertile islands for nitrogen. Our empirical data and literature review suggest that the fertile island pattern may be an artifact of grazing rather than an inherent property of arid shrublands. Further, we suggest that the grazing history of a site needs to be explicitly considered when documenting spatial patterns of soil nutrients in arid systems. This has significant implications for our understanding of soil nutrient dynamics in arid systems, the management of rangelands, and the potential for reversal of desertification.     

First steps of otolith formation of the zebrafish: role of glycogen?

The first steps of otolith formation were studied by electron microscopy in zebrafish embryos at different postfertilization (PF) time intervals. Between 19 and 22 h PF, the otic cavity contains glycogen particles derived by an apocrine process from the apical portions of the epithelial cells of the inner ear. The particles are arranged in parallel arrays, then in pseudocrystalloid structures, and finally in concentric arrays to form dense clusters referred to as "spherules". At 23 h PF, a group of "globules", consisting of modified aggregated "spherules" surrounded by several free "spherules", forms the nascent otolith. At 30 h PF, fused globules form a roughly spherical otolith. Spherules undergoing their process of modification and aggregation, are located in its central part, and constitute the so-called "nucleus". At 50 h PF, the otolith is a flattened hemisphere. It is made up of fused globules surrounded by two concentric layers whose organization is similar to that observed in the otolith of the adult fish. At this stage, calcium may be detected in the otolith except in its nucleus. We suggest that glycogen molecules found in the nascent otolith might allow the insertion of molecules such as glycoproteins (collagens) which are known to fix calcium. As a result, glycogen might play a key role in initiating the formation of otoliths and possibly that of other calcified tissues.     

Nematicidal Activity of α -Chaconine: Effect of Hydrogen-ion Concentration

α-Chaconine, a steroid-glycoalkaloid from Solanum tuberosum L., was increasingly more toxic to a free-living nematode, Panagrellus redivivus, with decreasing acidity from about pH 5 to 7. A study of the toxicity to adult nematodes at three concentrations of α-chaconine in buffer from pH 4 to 7.5 indicated that the free base is the nematicidal form of the compound. The median effective doses (ED₅₀) of α-chaconine to inhibit the motility of P. redivivus were estimated as 85 μg/ml at pH 6.7, 170 μg/ml at pH 6.5, and 340 μg/ml at pH 6.2.     

A Review of: “Handbook of Material Culture”

The examination of a well‐documented petroglyph site, located near the northeastern shoreline of now‐dry Owens Lake, California, is used as a springboard for a review of explanatory models for the interpretation of rock art sites in California and the Great Basin. Interpretive models and methods of analysis used by Julian Steward, Robert Heizer, and others who have visited or reported on this site are reviewed. The persistence of Heizer's “hunting‐magic” explanation for the creation of the rock art is used as one of several examples of how preconceived notions can affect interpretations of ancient art.     

A molecular phylogeny of ichthyophiid caecilians (Amphibia: Gymnophiona: Ichthyophiidae): out of India or out of South East Asia?

Recent molecular phylogenetic studies indicate that the rafting Indian plate harboured several isolated vertebrate lineages between ca. 130 and 56 Myr ago that dispersed and diversified 'out of India' following accretion with Eurasia. A single family of the amphibian order Gymnophiona, the Ichthyophiidae, presently occurs on the Indian plate and across much of South East Asia. Ichthyophiid phylogeny is investigated in order to test competing out of India and out of South East Asia hypotheses for their distribution. Partial sequences of mitochondrial 12S and 16S rRNA and cytochrome b genes for 20 ichthyophiids and proximate outgroups were assembled. Parsimony, maximum-likelihood and distance analyses all recover optimum trees in which uraeotyphlids plus Ichthyophis cf. malabarensis are the sister taxa to all other Ichthyophis, among which the South East Asian taxa are monophyletic. Tree topology and branch lengths indicate that the Indian lineages are more basal and older, and thus are more consistent with the hypothesis that ichthyophiids dispersed from the Indian subcontinent into South East Asia. The estimated relationships also support monophyly of Sri Lankan Ichthyophis, and non-monophyly of striped and unstriped Ichthyophis species groups. Mitochondrial DNA sequences provide evidence that should assist current problematic areas of caecilian taxonomy.     

Survival of the fittest: Law of evolution or law of probability?

In a recent issue of Biology and Philosophy, Kenneth Waters argues that the principle of survival of the fittest should be eliminated from the theory of natural selection, because it is an untestable law of probability, and as such, has no place in evolutionary theory. His argument is impressive, but it does not do justice to the practice of biology. The principle of survival of the fittest should not be eliminated from the theory of natural selection because it is important to biological practice: it plays an essential role in explanation and discovery, and in unffying the theory of natural selection.I am grateful to John Beatty, Robert Brandon, Susan Mills (Susan Finsen), William Lycan, Michael Resnik, Mary Williams, and Brad Wilson, and an anonymous reviewer for Biology and Philosophy for their helpful comments snd criticism.     

Hospital sources of Aspergillus: New routes of transmission?

With the continuing increase in the number of severely immunocompromised patients, hospitals are faced with the growing problem of invasive aspergillosis and other opportunistic fungal infections. Since treatment of these infections are difficult and outcome is often fatal, preventive measures are of major importance in the control of invasive filamentous fungal infections. Until recently, inhalation of airborne conidia was believed to be the primary route of acquiring Aspergillus infection. Despite the fact, that efforts to filter the hospital air has led to a reduction of airborne conidia paralleled by a decrease in the frequency of invasive infections, the correlation between the concentration of Aspergillus conidia in hospital air and the risk of invasive infections remains unclear. Furthermore, alternative modes of transmission may exist and should be recognized and investigated. The discovery of hospital water as a potential source of Aspergillus fumigatus and other filamentous fungi may suggest a new route for the transmission of invasive filamentous fungal infections. Epidemiological studies, based on molecular characterization and comparisons of fungal isolates recovered from patients and environment, are needed to expand our understanding of these alternative routes of transmission.     

Origin of glutaminyl-tRNA synthetase: An example of palimpsest?

Sequence data and evolutionary arguments suggest that a similarity may exist between the C-terminal end of glutaminyl-tRNA synthetase (GlnRS) and the catalytic domain of glutamine amidotransferases (GATs). If true, this would seem to imply that the amidation reaction of the Glu-tRNA^GIn complex was the evolutionary precursor of the direct tRNA^GIn aminoacylation pathway. Since the C-terminal end of GlnRS does not now have an important functional role, it can be concluded that this sequence contains vestiges that lead us to believe that it represents a palimpsest. This sequence still conserves the remains of the evolutionary transition: amidation reaction aminoacylation reaction. This may be important in deciding which mechanism gave origin to the genetic code organization. These observations, together with results obtained by Gatti and Tzagoloff [J. Mol. Biol. (1991) 218: 557–568], lead to the hypothesis that the class I aminoacyl-tRNA synthetases (ARSs) may be homologous to the GATs of the trpG subfamily, while the class Il ARSs may be homologous to the GATs of the purF subfamily. Overall, this seems to point to the existence of an intimate evolutionary link between the proteins involved in the primitive metabolism and aminoacyl-tRNA synthetases.