Microbial degradation of nonylphenol and other alkylphenols—our evolving view

Because the endocrine disrupting effects of nonylphenol (NP) and octylphenol became evident, the degradation of long-chain alkylphenols (AP) by microorganisms was intensively studied. Most NP-degrading bacteria belong to the sphingomonads and closely related genera, while NP metabolism is not restricted to defined fungal taxa. Growth on NP and its mineralization was demonstrated for bacterial isolates, whereas ultimate degradation by fungi still remains unclear. While both bacterial and fungal degradation of short-chain AP, such as cresols, and the bacterial degradation of long-chain branched AP involves aromatic ring hydroxylation, alkyl chain oxidation and the formation of phenolic polymers seem to be preferential elimination pathways of long-chain branched AP in fungi, whereby both intracellular and extracellular oxidative enzymes may be involved. The degradation of NP by sphingomonads does not proceed via the common degradation mechanisms reported for short-chain AP, rather, via an unusual ipso-substitution mechanism. This fact underlies the peculiarity of long-chain AP such as NP isomers, which possess highly branched alkyl groups mostly containing a quaternary α-carbon. In addition to physicochemical parameters influencing degradation rates, this structural characteristic confers to branched isomers of NP a biodegradability different to that of the widely used linear isomer of NP. Potential biotechnological applications for the removal of AP from contaminated media and the difficulties of analysis and application inherent to the hydrophobic NP, in particular, are also discussed. The combination of bacteria and fungi, attacking NP at both the phenolic and alkylic moiety, represents a promising perspective.     

Neurodegeneration meets immunology – A chemical biology perspective

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Microbial pretreatment of coals: A tool for solubilization of lignite in organic solvent – quinoline

A method was developed for the conversion of low rank coals to products soluble in an organic solvent (quinoline). A selected group of polynuclear aromatic-compound-degrading and lignin-degrading facultative pure cultures and enriched anaerobic mixed microbial cultures developed for this purpose were used separately as well as together under co-culture conditions for stepwise treatment of Neyveli lignite (NL). This aerobic-anaerobic co-metabolic (co-culture) biodegradation (AACB) process resulted in the enhancement of quinoline extractability of the lignite, thereby yielding clean coal substance (the extract). The residual lignite obtained after quinoline extraction was subjected to a second step of AACB fermentation treatment. This resulted in further extraction of lignite in quinoline. The conditions were optimised for AACB fermentation treatment. The two-step AACB fermentation process under optimum conditions, resulted in an overall enhancement of yield of extract from 18% for the original lignite sample to 56% for the treated sample. The changes in the filtrate were evaluated using UV spectra, those in the residue were evaluated using FTIR spectroscopy and UV-reflectance and those in the extract using proton NMR spectra of the chloroform soluble fraction. The results indicated a decreased absorption in the carbonyl region in the AACB-treated residue and also a decrease in the overall mineral matter in the lignite samples. The mechanism of the AACB fermentation process is discussed. The process affords biosolubilization of lignite in organic solvent (quinoline) under milder conditions along with a simultaneous removal of a part of the mineral matter present in the coal. Uses for the clean coal extract obtained are suggested.     

Ethno-diversity within current ethno-pharmacology as part of Israeli traditional medicine – A review

Traditional human communities have a wide knowledge of their environment. Collection of animals in estuarine and coastal areas are directly influenced by tidal cycles. The aim of this study is to evaluate the understanding of the tides associated with the lunar cycle held by people who gather crustaceans and molluscs in the State of Paraiba. The empirical knowledge of 20 crab gatherers and 30 mollusc gatherers was recorded through open interviews and structured questionnaires. The results showed that the gatherers have an accurate comprehension of tidal phenomenon based on their exploitation of natural resources, which perpetuates through generations.     

The promise of e-Health – a Canadian perspective

Canadians value their health care system above any other social program. Canada's system of health care faces significant financial and population pressures, relating to cost, access, quality, accountability, and the integration of information and communication technologies (ICTs). The health-system also faces certain unique challenges that include care delivery within a highly decentralised system of financing and accountability, and care delivery to a significant portion of the population sparsely distributed across a landmass of 10 million square kilometres, in areas of extreme climatic conditions. All of these challenges are significant catalysts in the development of technologies that aim to significantly mitigate or eliminate these selfsame challenges.The system is undergoing widespread review, nationally, and within each province and territory, where the bulk of care provision is financed and managed. The challenges are being addressed by national, regional and provincial initiatives in the public, private and not-for-profit sectors.The promise of e-Health lies in the manner and degree to which it can mitigate or resolve these challenges to the health system and build on advancements in ICTs supporting the development of a health infostructure. Canada is actively developing and implementing technological solutions to deliver health information and health care services across the country. These solutions, while exciting and promising, also present new challenges, particularly in regard to acceptable standards, choice of technologies, overcoming traditional jurisdictional boundaries, up-front investment, and privacy and confidentially.Many organisations and governments are working to address these challenges. The Canadian Institute for Health Information (CIHI) will play an increasingly significant role in these initiatives, as the management of health information becomes a more crucial factor in the successful delivery of health care services in the new millennium.     

Cardiotoxicity of breast cancer radiotherapy – overview of current results

Adjuvant radiotherapy after breast cancer surgery is an important part of breast cancer treatment improving local control and overall survival. However, a higher risk of cardiac mortality was observed when conventional radiotherapy techniques were used. Cardiac morbidity and mortality after radiation therapy have been studied in many meta-analyses. In those focused on modern radiotherapy techniques, cardiac morbidity and mortality were no longer presented. However, an extremely long follow-up period is required. Importantly, the cardiac morbidity rates vary depending not only on the dose delivered to the heart, but also on the systemic therapies administrated and the pre-existing cardiac disease. Systematic heart dose monitoring is of great importance, as are efforts to constantly decrease doses, using advanced radiotherapy techniques. Nowadays, it is essential to individualize treatment according to tumor characteristics and anatomical predispositions, and to consider the cost and benefits.     

A River's Liver – Microbial Processes within the Hyporheic Zone of a Large Lowland River

Little is known on microbial activities in the sediments of large lowland rivers despite of their potentially high influence on biogeochemical budgets. Based on field measurements in a variety of sedimentary habitats typical for a large lowland river (Elbe, Germany), we present results on the abundance and production of sedimentary bacteria, the potential activity of a set of extracellular enzymes, and potential nitrification and denitrification rates. A diving bell was used to access the sediments in the central river channel, enabling us to sample down to 1 m sediment depth. Depth gradients of all measures of microbial activity were controlled by sediment structure, hydraulic conditions, as well as by the supply with organic carbon and nitrogen. Microbial heterotrophic activity was tightly coupled with the availability of carbon and nitrogen, whereas chemolithotrophic activity (nitrification rate) was related to the available surface area of particles. In the central bed of the river, bacterial production and extracellular enzyme activity remained high down to the deepest sediment layers investigated. Due to the large inner surface area and their connectivity with the surface water, the shifting sediments in the central channel of the river were microbially highly active There, vertically integrated bacterial production amounted to 0.95 g C m⁻³ h⁻¹, which was 2.9 to 5.5 times higher than in the nearshore habitats. We conclude that carbon and nitrogen cycling in the river is controlled by the live sediments of the central river channel, which thus represent a “liver function” in the river's metabolism.     

Probing Oral Microbial Functionality – Expression of spxB in Plaque Samples

The Human Oral Microbiome Database (HOMD) provides an extensive collection of genome sequences from oral bacteria. The sequence information is a static snapshot of the microbial potential of the so far sequenced species. A major challenge is to connect the microbial potential encoded in the metagenome to an actual function in the in vivo oral biofilm. In the present study we took a reductionist approach and identified a considerably conserved metabolic gene, spxB to be encoded by a majority of oral streptococci using the HOMD metagenome information. spxB encodes the pyruvate oxidase responsible for the production of growth inhibiting amounts of hydrogen peroxide (H₂O₂) and has previously been shown as important in the interspecies competition in the oral biofilm. Here we demonstrate a strong correlation of H₂O₂ production and the presence of the spxB gene in dental plaque. Using Real-Time RT PCR we show that spxB is expressed in freshly isolated human plaque samples from several donors and that the expression is relative constant when followed over time in one individual. This is the first demonstration of an oral community encoded gene expressed in vivo suggesting a functional role of spxB in oral biofilm physiology. This also demonstrates a possible strategy to connect the microbial potential of the metagenome to its functionality in future studies by identifying similar highly conserved genes in the oral microbial community.     

Sea cucumbers of the Arabian Peninsula and Iran – A review of historical and current research trends

Sea cucumbers are benthic marine invertebrates with immense ecological and commercial value. Processed sea cucumbers known as “Beche-de-mer” are a delicacy in southeast Asian countries with an ever-increasing demand depleting wild stocks on a global scale. Aquaculture techniques are well developed for commercially important species (e.g. Holothuria scabra) to aid in conservation and trade. In the Arabian Peninsula and Iran, where the major land mass is surrounded by marginal seas (Arabian Gulf, Gulf of Oman, Arabian Sea, Gulf of Aden, and Red Sea), studies on sea cucumbers are rather limited and its economic value is underestimated. Historical and current research trends indicate impoverished diversity (82 species) due to environmental extremes. Artisanal fisheries exist for the sea cucumbers of Iran, Oman, and Saudi Arabia, with Yemen and United Arab Emirates (UAE) playing a key role in collection and export to Asian countries. Stock assessment and data on export indicates depletion of natural stocks in Saudi Arabia and Oman. Aquaculture trials of high value species (H. scabra) were successful in Saudi Arabia, Oman and Iran with prospects for further expansion. Research on ecotoxicological properties and bioactive substances conducted in Iran demonstrates an immense research potential. Molecular phylogeny, biology, use in bioremediation, and characterisation of bioactive compounds were identified as potential gaps in research. Expanding aquaculture operations could revive exports and recuperate damaged stocks through sea ranching. Furthermore, regional cooperation, networking, training, and capacity building could help fill the gaps in sea cucumber research, which will aid in its effective conservation and management.     

Microbial hydantoinases – industrial enzymes from the origin of life?

Hydantoinases are valuable enzymes for the production of optically pure d- and l-amino acids. They catalyse the reversible hydrolytic ring cleavage of hydantoin or 5′-monosubstituted hydantoins and are therefore classified in the EC nomenclature as cyclic amidases (EC 3.5.2.). In the EC nomenclature, four different hydantoin-cleaving enzymes are described: dihydropyrimidinase (3.5.2.2), allantoinase (EC 3.5.2.5), carboxymethylhydantoinase (EC 3.5.2.4), and N-methylhydantoinase (EC 3.5.2.14). Beside these, other hydantoinases with known metabolic functions, such as imidase and carboxyethylhydantoinase and enzymes with unknown metabolic function, are described in the literature and have not yet been classified. An important question is whether the distinct hydantoinases, which are frequently classified as l-, d-, and non-selective hydantoinases depending on their substrate specificity and stereoselectivity, are related to each other. In order to investigate the evolutionary relationship, amino acid sequence data can be used for a phylogenetic analysis. Although most of these enzymes only share limited sequence homology (identity<15%) and therefore are only distantly related, it can be shown (i) that most of them are members of a broad set of amidases with similarities to ureases and build a protein superfamily, whereas ATP-dependent hydantoinases are not related, (ii) that the urease-related amidases have evolved divergently from a common ancestor and (iii) that they share a metal-binding motif consisting of conserved histidine residues. The difference in enantioselectivity used for the classification of hydantoinases on the basis of their biotechnological value does not reflect their evolutionary relationship, which is to a more diverse group of enzymes than was assumed earlier. This protein superfamily probably has its origin in the prebiotic conditions of the primitive earth. Received: 24 August 1998 / Received revision: 9 November 1998 / Accepted: 21 November 1998     

Photoinhibition – a historical perspective

Photoinhibition is a state of physiological stress that occurs in all oxygen evolving photosynthetic organisms exposed to light. The primary damage occurs within the reaction center of Photosystem II (PS II). While irreversible photoinduced damage to PS II occurs at all light intensities, the efficiency of photosynthetic electron transfer decreases markedly only when the rate of damage exceeds the rate of its repair, which requires de novo PS II protein synthesis. Photoinhibition has been studied for over a century using a large variety of biochemical, biophysical and genetic methodologies. The discovery of the light induced turnover of a protein, encoded by the plastid psbA gene (the D1 protein), later identified as one of the photochemical reaction center II proteins, has led to the elucidation of the underlying mechanism of photoinhibition and to a deeper understanding of the PS II `life cycle.' This revised version was published online in August 2006 with corrections to the Cover Date.     

Patents – a practical perspective

Patent Update is a regular column dedicated to the complex issues that affect patents in the genomics and proteomics field. In each issue, there are two sections compiled by patent attorneys. The first section, Patents – a Practical Perspective, is a commentary on current issues, landmark patents, useful patent resources and how to search them, and legislative changes that impact the pharma and biotech industries. The second section, Patent News, provides brief synopses of recently issued patents and other patent events, and their significance to drug discovery R&D.     

Microbial and fungal protease inhibitors—current and potential applications

Proteolytic enzymes play essential metabolic and regulatory functions in many biological processes and also offer a wide range of biotechnological applications. Because of their essential roles, their proteolytic activity needs to be tightly regulated. Therefore, small molecules and proteins that inhibit proteases can be versatile tools in the fields of medicine, agriculture and biotechnology. In medicine, protease inhibitors can be used as diagnostic or therapeutic agents for viral, bacterial, fungal and parasitic diseases as well as for treating cancer and immunological, neurodegenerative and cardiovascular diseases. They can be involved in crop protection against plant pathogens and herbivorous pests as well as against abiotic stress such as drought. Furthermore, protease inhibitors are indispensable in protein purification procedures to prevent undesired proteolysis during heterologous expression or protein extraction. They are also valuable tools for simple and effective purification of proteases, using affinity chromatography. Because there are such a large number and diversity of proteases in prokaryotes, yeasts, filamentous fungi and mushrooms, we can expect them to be a rich source of protease inhibitors as well.     

Development of new antileishmanial drugs – current knowledge and future prospects

Leishmaniasis is a protozoan vector borne disease prevalent throughout the world and present in at least 88 countries. The parasite is transmitted by infected phlebotomine sandfly bites. While conventional therapies i.e. pentavalent antimonials, amphotericin B and pentamidine continue to play a major role, it is evident that new drugs or strategies must circumvent the limitations, such as a long-term parenteral administration, toxicity, the high cost in endemic countries and the emergence of resistance, that prevail. One of the most promising drugs is miltefosine, a new oral, approved alkylphospholipid for visceral leishmaniasis with only slight adverse effects. Although we have now this recent and encouraging advance, there is still a need to develop safe, efficient and affordable new treatments for the different clinical forms that exist. This review summarises conventional therapy and the current efforts in the discovery of drugs to treat leishmaniasis with the emphasis on drug combinations to enhance efficiency and prevent the emergence of resistance, the investigation of natural products with the objective of offering new bioactive chemical structures and the development of novel antileishmanial targets.     

Histone deacetylases – a new target for suppression of cartilage degradation?

Increased expression of metalloproteinases is a fundamental aspect of arthritispathology and its control is a major therapeutic objective. In cartilage cultured in the presence of the cytokines interleukin-1 and oncostatin M, chondrocytes produce enhanced levels of metalloproteinases of the ADAMTS (a disintegrin and metalloproteinase with thrombospondin motifs) and MMP (matrix metalloproteinase) families, resulting in the degradation of aggrecan and collagen. The histone deacetylase inhibitors trichostatin A and butyrate were shown to drastically reduce expression of these enzymes relatively selectively, with concomitant inhibition of breakdown of matrix components. This family of enzymes is therefore a promising target for therapeutic intervention.     

Microbial transformation of α-pinene

Summary A bacterium capable of utilizing -pinene as a sole carbon and energy source was isolated from soil. This strain, named strain S201-1, which was identified as Pseudomonas maltophilia on the basis of its taxonomical properties, accumulated limonene, borneol, camphor, perillic acid, and 2-(4-methyl-3-cyclohexenylidene) propionic acid from -pinene in the culture broth. It was demonstrated that -pinene, -pinene, borneol, camphor, and a number of p-menthane derivatives were oxidized by this strain. Relations between the protonation of -pinene and the formation of the products by the microbe are discussed.     

Polychaete phylogeny based on morphological data – a comparison of current attempts

Annelid phylogeny is one of the largest unresolved problems within the Metazoa. This is due to the enormous age of this taxon and also strongly influenced by the current discussion on the position of the Arthropoda, which traditionally is hypothesized to be the annelid sister taxon. Within the framework of recent discussions on the position of the Annelida, the ground pattern of this taxon is either a clitellate-like, parapodia-less dwelling organism or an organisms that resembles errant polychaetes in having parapodia and gills and probably being a predator. To solve this problem different attempts have been made in the past, cladistic analysis, scenario based plausibility considerations and a successive search for sister taxa base on isolated characters. These attempts are presented and critically discussed. There is at least strong support for the Annelida as wells as for several of its taxa above the level of traditional families; the monophyly of the Polychaeta, however, remains questionable. The term taxon is used here in the sense of group of things that share certain characteristics. Biological taxa are not necessarily monophyletic, although many of them turned out to be. In terms of phylogenetic systematics taxa should be monophyletic.     

Hyperthermia in cervical cancer – current status

BackgroundThis article reviews the salient features of recent results of clinical studies. It puts a special emphasis on technical aspects, mechanisms of action together with radiotherapy and chemotherapy and points out areas for additional investigation.AimTo present the current state of knowledge on hyperthermia (HT) and to highlight its role in the treatment of cervical cancer.Materials and methodsThe literature on the clinical use of combined hyperthermia for cervical cancer was analyzed. Clinical outcomes together with the technical aspects and the role of HT were also evaluated.ResultsClinically randomized trials have demonstrated benefit including survival with the addition of hyperthermia to radiation or chemotherapy in the treatment of cervical cancer without significant acute or late morbidities. The technological advances have led to an effective and safer treatment delivery, thermal treatment planning, thermal dose monitoring and online adaptive temperature modulation.ConclusionsDue to rapid development over the last decade of hyperthermia systems and new studies at the basic science and clinical level, the perception of hyperthermia as a part of multimodality treatment in cervical cancer has been changed. However, there is still a need for multicentre randomized clinical trials.