Biological Degradation (biological + degradation)

Distribution by Scientific Domains

Selected Abstracts

ChemInform Abstract: Biological Degradation of Taxol by Action of Cultured Cells on 7-Acetyltaxol-2,,-yl Glucoside.

CHEMINFORM, Issue 29 2008
Kei Shimoda
Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source]

Pseudozyma jejuensis sp. nov., a novel cutinolytic ustilaginomycetous yeast species that is able to degrade plastic waste

Hyuk-Seong Seo
Abstract An ustilaginomycetous anamorphic yeast, isolated from orange leaves on Jeju island in South Korea, represents a novel Pseudozyma species according to morphologic and physiologic findings and molecular taxonomic analysis using the D1/D2 domains of the large subunit (26S) rRNA gene and the internally transcribed spacer (ITS) 1+2 regions. The name Pseudozyma jejuensis sp. nov. is proposed for this novel species, with OL71T (=KCTC 17482T=CBS 10454T) as type strain. In the present study, we have also demonstrated that Pseudozyma jejuensis OL71 is capable of producing cutinase and degrading polycaprolactone. These results suggest that Pseudozyma jejuensis or its cutinase may be useful for the biological degradation of plastic waste. [source]

Utilization of nanoscale zero-valent iron for source remediation,A case study

REMEDIATION, Issue 2 2006
Keith W. Henn
A pilot-scale study was performed using a palladium-catalyzed and polymer-coated nanoscale zero-valent iron (ZVI) particle suspension at the Naval Air Station in Jacksonville, Florida. A total of 300 pounds of nanoscale ZVI particle suspension was injected via a gravity feed and recirculated through a source area containing chlorinated volatile organic compounds (VOCs). The recirculation created favorable mixing and distribution of the iron suspension and enhanced the mass transfer of sorbed and nonaqueous constituents into the aqueous phase, where the contaminants could be reduced. Between 65 and 99 percent aqueous-phase VOC concentration reduction occurred, due to abiotic degradation, within five weeks of the injection. The rapid abiotic degradation processes then yielded to slower biological degradation as subsequent decreases in -elimination parameters were observed,yet favorable redox conditions were maintained as a result of the ZVI treatment. Post-treatment analyses revealed cumulative reduction of soil contaminant concentrations between 8 and 92 percent. Aqueous-phase VOC concentrations in wells side gradient and downgradient of the source were reduced up to 99 percent and were near or below applicable regulatory criteria. These reductions, coupled with the generation of innocuous by-products, indicate that nanoscale ZVI effectively degraded contamination and reduced the mass flux from the source, a critical metric identified for source treatment. A summary of this project was recently presented at the US EPA Workshop on Nanotechnology for Site Remediation in Washington, D.C., on October 21,22, 2005. This case study supplied evidence that nanoscale zero valent iron, an emerging remediation technology, has been implemented successfully in the field. More information about this workshop and this presentation can be found at © 2006 Wiley Periodicals, Inc. [source]

Review: Biodegradation of tributyltins (organotins) by marine bacteria

S. K. Dubey
Abstract Many marine bacterial strains have an inherent capability to degrade toxic organotin compounds, especially tributyltins (TBTs), that enter into the environment in the form of insecticides, fungicides and antifouling paints as a result of anthropogenic and industrial activities. Significant degradation of these compounds in the ambient environment may take several years, and it is necessary to consider methods or strategies that can accelerate the degradation process. There have been few demonstrations of biological degradation of these organotin biocides exclusively in laboratory-scale experiments. Compared with the few bench-scale degradation processes, there are no reports of field-scale processes for TBT bioremediation, in spite of its serious environmental threat to non-target organisms in the aquatic environment. Implementation of field-scale biodegradation of TBT requires inputs from biology, hydrology, geology, chemistry and civil engineering. A framework is emerging that can be adapted to develop new processes for bioremediation of toxic environmental wastes. In the case of TBT bioremediation, this framework incorporates screening and identification of natural bacterial strains, determination of optimal conditions for growth of isolates and TBT degradation, establishment of new metabolic pathways involved in TBT degradation, identification, localization and cloning of genes involved in degradation and in TBT resistance, development of suitable microbial strains using genetic manipulation techniques for practical applications and optimization of practical engineering processes for bioremediation of organotin-contaminated sites. The present review mainly addresses the aspect of TBT biodegradation with special reference to environmental sources of TBT, chemical structure and biological activity, resistant and degrading bacterial strains, possible mechanisms of resistance and degradation and the genetic and biochemical basis of TBT degradation and resistance. It also evaluates the feasibility and potential of natural and genetically modified TBT-degrading bacterial strains in field-scale experiments to bioremediate TBT-contaminated marine sites, and makes recommendations for more intensive and focused research in the area of TBT bioremediation mediated by marine bacterial strains. Copyright © 2002 John Wiley & Sons, Ltd. [source]

First look at RNA in l -configuration

RNA in l -configuration
Nucleic acid molecules in the mirror image or l -configuration are unknown in nature and are extraordinarily resistant to biological degradation. The identification of functional l -­oligonucleotides called Spiegelmers offers a novel approach for drug discovery based on RNA. The sequence r(CUGGGCGG)·r(CCGCCUGG) was chosen as a model system for structural analysis of helices in the l -configuration as the structure of the d -form of this sequence has previously been determined in structural studies of 5S RNA domains, in particular domain E of the Thermus flavus 5S rRNA [Perbandt et al. (2001), Acta Cryst. D57, 219,224]. Unexpectedly, the results of crystallization trials showed little similarity between the d - and the l -forms of the duplex in either the crystallization hits or the diffraction performance. The crystal structure of this l -RNA duplex has been determined at 1.9,Ć resolution with Rwork and Rfree of 23.8 and 28.6%, respectively. The crystals belong to space group R32, with unit-cell parameters a = 45.7, c = 264.6,Ć. Although there are two molecules in the asymmetric unit rather than one, the structure of the l -form arranges helical pairs in a head-to-tail fashion to form pseudo-continuous infinite helices in the crystal as in the d -form. On the other hand, the wobble-like G·C+ base pair seen in the D-RNA analogue does not appear in the l -RNA duplex, which forms a regular double-helical structure with typical Watson,Crick base pairing. [source]

Adsorption, absorption, and biological degradation of ammonia in different biofilter organic media

Estela Pagans
Abstract A tailor-made apparatus called ammoniometer, which is a batch mode respirometer applied to the study of ammonia biodegradation in biofilter media, has been used to evaluate adsorption, absorption, and biodegradation in five different organic materials (compost, coconut fibre, bark, pruning wastes, and peat) obtained from full-scale biofilters in operation in several waste treatment plants. The results showed that absorption could be represented by a Henry's law linear equation, with values of the Henry coefficient significantly higher (from 1,866 to 15,320) than that of pure water (1,498). Adsorption data were successfully fitted to Langmuir and Freundlich isotherms and maximum adsorption capacity varies from 1.06 to 1.81 mg NH3/g dry media. Ammonia biodegradation rates for each organic material were also calculated. Biodegradation rates varied from 0.67 to 7.82 mg NH3/kg media/d depending on the material tested. The data obtained showed important differences in the behaviour of the biofilter organic media, which has important implications in the design and modelling of these systems. Biotechnol. Bioeng. 2007;97: 515,525. © 2006 Wiley Periodicals, Inc. [source]

4237: New biomaterials for keratoprostheses

Purpose Although a wide range of keratoprostheses have been developed from various materials over the last 30 years there has been limited optimisation of material properties to enhance clinical performance and minimise tissue incompatibility within the ocular environment. The development of our understanding of the biological interactions between materials and corneal tissues, the failure of existing keratoprostheses, the advances in the design and synthesis of materials of controlled molecular architectures and the advancements in composite biomaterials in recent years provides an opportunity to design enhanced biomaterials for the fabrication of the next generation of keratoprosthetic with improved clinical performance. Methods This paper will review studies undertaken by our group which have enhanced our understanding of the biological interactions of existing keratoprosthetic materials in the ocular environment and the development of novel approaches to new materials for the fabrication of keratoprosthetic based on the utilisation of biomimetic and composite systems and recent advances in the polymeric biomaterials. Results The paper will review data relating to the biological degradation of biomimetic materials and approaches to optimising these processes to provide materials with enhanced tissue integration and reduced inflammatory response. The in vitro biological evaluation of some of these materials indicates that material engineering may improve the clinical performance of biomaterials in the corneal environment. Conclusion The development of novel materials for the fabrication of keratoprostheses relies on improving our understanding of the mechanisms of failure of existing devices and how biomaterials can be engineered to overcome these challenges [source]

The World of , - and , -Peptides Comprised of Homologated Proteinogenic Amino Acids and Other Components

Dieter Seebach
The origins of our nearly ten-year research program of chemical and biological investigations into peptides based on homologated proteinogenic amino acids are described. The road from the biopolymer poly[ethyl (R)-3-hydroxybutanoate] to the , -peptides was primarily a step from organic synthesis methodology (the preparation of enantiomerically pure compounds (EPCs)) to supramolecular chemistry (higher-order structures maintained through non-covalent interactions). The performing of biochemical and biological tests on the , - and , -peptides, which differ from natural peptides/proteins by a single or two additional CH2 groups per amino acid, then led into bioorganic chemistry and medicinal chemistry. The individual chapters of this review article begin with descriptions of work on , -amino acids, , -peptides, and polymers (Nylon-3) that dates back to the 1960s, even to the times of Emil Fischer, but did not yield insights into structures or biological properties. The numerous, often highly physiologically active, or even toxic, natural products containing ,- and ,-amino acid moieties are then presented. Chapters on the preparation of homologated amino acids with proteinogenic side chains, their coupling to provide the corresponding peptides, both in solution (including thioligation) and on the solid phase, their isolation by preparative HPLC, and their characterization by mass spectrometry (HR-MS and MS sequencing) follow. After that, their structures, predominantly determined by NMR spectroscopy in methanolic solution, are described: helices, pleated sheets, and turns, together with stack-, crankshaft-, paddlewheel-, and staircase-like patterns. The presence of the additional CC bonds in the backbones of the new peptides did not give rise to a chaotic increase in their secondary structures as many protein specialists might have expected: while there are indeed more structure types than are observed in the , -peptide realm , three different helices (10/12 -, 12 -, and 14 -helix) if we include oligomers of trans -2-aminocyclopentanecarboxylic acid, for example , the structures are already observable with chains made up of only four components, and, having now undergone a learning process, we are able to construct them by design. The structures of the shorter , -peptides can also be reliably determined by molecular-dynamics calculations (in solution; GROMOS program package). Unlike in the case of the natural helices, these compounds' folding into secondary structures is not cooperative. In , - and , -peptides, it is possible to introduce heteroatom substituents (such as halogen or OH) onto the backbones or to incorporate heteroatoms (NH, O) directly into the chain, and, thanks to this, it has been possible to study effects unobservable in the world of the , -peptides. Tests with proteolytic enzymes of all types (from mammals, microorganisms, yeasts) and in vivo examination (mice, rats, insects, plants) showed , - and , -peptides to be completely stable towards proteolysis and, as demonstrated for two , -peptides, extraordinarily stable towards metabolism, even when bearing functionalized side chains (such as those of Thr, Tyr, Trp, Lys, or Arg). The , -peptides so far examined also normally display no or only very weak cytotoxic, antiproliferative, antimicrobial, hemolytic, immunogenic, or inflammatory properties either in cell cultures or in vivo. Even biological degradation by microbial colonies of the types found in sewage-treatment plants or in soil is very slow. That there are indeed interactions of ,- and ,-peptides with biological systems, however, can be seen in the following findings: i) organ-specific distribution takes place after intravenous (i.v.) administration in rats, ii) transport through the intestines of rodents has been observed, iii) , -peptides with positively charged side chains (Arg and Lys) settle on cell surfaces, are able to enter into mammalian cells (fibroplasts, keratinocytes, HeLa cells), and migrate into their cell nuclei (and nucleoli), and iv) in one case, it has already been established that a , -peptide derivative can up- and down-regulate gene expression rates. Besides these less sharply definable interactions, it has also been possible to construct , - and , -peptide agonists of naturally occurring peptide hormones, MHC-binding , -peptides, or amphipathic , -peptide inhibitors of membrane-bound proteins in a controlled fashion. Examples include somatostatin mimics and the suppression of cholesterol transport through the intestinal brush-border membrane (by the SR-BI-protein). The results so far obtained from investigations into peptides made up of homologues of the proteinogenic amino acids also represent a contribution to deepening of our knowledge of the natural peptides/proteins, while potential for biomedicinal application of this new class of substances has also been suggested. [source]