bluuebunny/crossref_metadata_2025 huggingface dataset:
Regulatory RNAs in Haloferax volcanii
Authors: Fischer Susan , Benz Juliane , Späth Bettina , Jellen-Ritter Angelika , Heyer Ruth , Dörr Marcella , Maier Lisa-Katharina , Menzel-Hobeck Clemens , Lehr Matthias , Jantzer Katharina , Babski Julia , Soppa Jörg , Marchfelder Anita
Published: January 2011

In organisms of all three domains of life, a plethora of sRNAs (small regulatory RNAs) exists in addition to the well-known RNAs such as rRNAs, tRNAs and mRNAs. Although sRNAs have been well studied in eukaryotes and in bacteria, the sRNA population in archaea has just recently been identified and only in a few archaeal species. In the present paper, we summarize our current knowledge about sRNAs and their function in the halophilic archaeon Haloferax volcanii. Using two different experimental approaches, 111 intergenic and 38 antisense sRNAs were identified, as well as 42 tRFs (tRNA-derived fragments). Observation of differential expression under various conditions suggests that these sRNAs might be active as regulators in gene expression like their bacterial and eukaryotic counterparts. The severe phenotypes observed upon deletion and overexpression of sRNA genes revealed that sRNAs are involved in, and important for, a variety of biological functions in H. volcanii and possibly other archaea. Investigation of the Haloferax Lsm protein suggests that this protein is involved in the archaeal sRNA pathway.
Protein–protein interactions in the archaeal core replisome
Authors: MacNeill Stuart A.
Published: January 2011

Most of the core components of the archaeal chromosomal DNA replication apparatus share significant protein sequence similarity with eukaryotic replication factors, making the Archaea an excellent model system for understanding the biology of chromosome replication in eukaryotes. The present review summarizes current knowledge of how the core components of the archaeal chromosome replication apparatus interact with one another to perform their essential functions.
Enzymology and ecology of the nitrogen cycle
Authors: Martínez-Espinosa Rosa María , Cole Jeffrey A. , Richardson David J. , Watmough Nicholas J.
Published: January 2011

The nitrogen cycle describes the processes through which nitrogen is converted between its various chemical forms. These transformations involve both biological and abiotic redox processes. The principal processes involved in the nitrogen cycle are nitrogen fixation, nitrification, nitrate assimilation, respiratory reduction of nitrate to ammonia, anaerobic ammonia oxidation (anammox) and denitrification. All of these are carried out by micro-organisms, including bacteria, archaea and some specialized fungi. In the present article, we provide a brief introduction to both the biochemical and ecological aspects of these processes and consider how human activity over the last 100 years has changed the historic balance of the global nitrogen cycle.
Oxygen control of nitrogen oxide respiration, focusing on α-proteobacteria
Authors: Shapleigh James P.
Published: January 2011

Denitrification is generally considered to occur under micro-oxic or anoxic conditions. With this in mind, the physiological function and regulation of several steps in the denitrification of model α-proteobacteria are compared in the present review. Expression of the periplasmic nitrate reductase is quite variable, with this enzyme being maximally expressed under oxic conditions in some bacteria, but under micro-oxic conditions in others. Expression of nitrite and NO reductases in most denitrifiers is more tightly controlled, with expression only occurring under micro-oxic conditions. A possible exception to this may be Roseobacter denitrificans, but the physiological role of these enzymes under oxic conditions is uncertain.
Nitric oxide detoxification in the rhizobia–legume symbiosis
Authors: Sánchez Cristina , Cabrera Juan J. , Gates Andrew J. , Bedmar Eulogio J. , Richardson David J. , Delgado María J.
Published: January 2011

NO (nitric oxide) is a signal molecule involved in diverse physiological processes in cells which can become very toxic under certain conditions determined by its rate of production and diffusion. Several studies have clearly shown the production of NO in early stages of rhizobia–legume symbiosis and in mature nodules. In functioning nodules, it has been demonstrated that NO, which has been reported as a potent inhibitor of nitrogenase activity, can bind Lb (leghaemoglobin) to form LbNOs (nitrosyl–leghaemoglobin complexes). These observations have led to the question of how nodules overcome the toxicity of NO. On the bacterial side, one candidate for NO detoxification in nodules is the respiratory Nor (NO reductase) that catalyses the reduction of NO to nitrous oxide. In addition, rhizobial fHbs (flavohaemoglobins) and single-domain Hbs which dioxygenate NO to form nitrate are candidates to detoxify NO under free-living and symbiotic conditions. On the plant side, sHbs (symbiotic Hbs) (Lb) and nsHbs (non-symbiotic Hbs) have been proposed to play important roles as modulators of NO levels in the rhizobia–legume symbiosis. In the present review, current knowledge of NO detoxification by legume-associated endosymbiotic bacteria is summarized.
The role of effector molecules in signal transduction by PII proteins
Authors: Radchenko Martha , Merrick Mike
Published: January 2011

PII proteins are one of the most widely distributed signal transduction proteins in Nature, being ubiquitous in bacteria, archaea and plants. They act by protein–protein interaction to control the activities of a wide range of enzymes, transcription factors and transport proteins, the great majority of which are involved in cellular nitrogen metabolism. The regulatory activities of PII proteins are mediated through their ability to bind the key effector metabolites 2-OG (2-oxoglutarate), ATP and ADP. However, the molecular basis of these regulatory effects remains unclear. Recent advances in the solution of the crystal structures of PII proteins complexed with some of their target proteins, as well as the identification of the ATP/ADP- and 2-OG-binding sites, have improved our understanding of their mode of action. In all of the complex structures solved to date, the flexible T-loops of PII facilitate interaction with the target protein. The effector molecules appear to play a key role in modulating the conformation of the T-loops and thereby regulating the interactions between PII and its targets.
The catalytic mechanism of Pseudomonas aeruginosa cd1 nitrite reductase
Authors: Rinaldo Serena , Giardina Giorgio , Castiglione Nicoletta , Stelitano Valentina , Cutruzzolà Francesca
Published: January 2011

The cd1 NiRs (nitrite reductases) are enzymes catalysing the reduction of nitrite to NO (nitric oxide) in the bacterial energy conversion denitrification process. These enzymes contain two distinct redox centres: one covalently bound c-haem, which is reduced by external electron donors, and another peculiar porphyrin, the d1-haem (3,8-dioxo-17-acrylate-porphyrindione), where nitrite is reduced to NO. In the present paper, we summarize the most recent results on the mechanism of nitrite reduction by the cd1 NiR from Pseudomonas aeruginosa. We discuss the essential catalytic features of this enzyme, with special attention to the allosteric regulation of the enzyme's activity and to the mechanism employed to avoid product inhibition, i.e. trapping of the active-site reduced haem by the product NO. These results shed light on the reactivity of cd1 NiRs and assign a central role to the unique d1-haem, present only in this class of enzymes.
Electron transfer and half-reactivity in nitrogenase
Authors: Clarke Thomas A. , Fairhurst Shirley , Lowe David J. , Watmough Nicholas J. , Eady Robert R.
Published: January 2011

Nitrogenase is a globally important enzyme that catalyses the reduction of atmospheric dinitrogen into ammonia and is thus an important part of the nitrogen cycle. The nitrogenase enzyme is composed of a catalytic molybdenum–iron protein (MoFe protein) and a protein containing an [Fe4–S4] cluster (Fe protein) that functions as a dedicated ATP-dependent reductase. The current understanding of electron transfer between these two proteins is based on stopped-flow spectrophotometry, which has allowed the rates of complex formation and electron transfer to be accurately determined. Surprisingly, a total of four Fe protein molecules are required to saturate one MoFe protein molecule, despite there being only two well-characterized Fe-protein-binding sites. This has led to the conclusion that the purified Fe protein is only half-active with respect to electron transfer to the MoFe protein. Studies on the electron transfer between both proteins using rapid-quench EPR confirmed that, during pre-steady-state electron transfer, the Fe protein only becomes half-oxidized. However, stopped-flow spectrophotometry on MoFe protein that had only one active site occupied was saturated by approximately three Fe protein equivalents. These results imply that the Fe protein has a second interaction during the initial stages of mixing that is not involved in electron transfer.
A new intra-aerobic metabolism in the nitrite-dependent anaerobic methane-oxidizing bacterium Candidatus ‘Methylomirabilis oxyfera’
Authors: Wu Ming L. , Ettwig Katharina F. , Jetten Mike S.M. , Strous Marc , Keltjens Jan T. , Niftrik Laura van
Published: January 2011

Biological methane oxidation proceeds either through aerobic or anaerobic pathways. The newly discovered bacterium Candidatus ‘Methylomirabilis oxyfera’ challenges this dichotomy. This bacterium performs anaerobic methane oxidation coupled to denitrification, but does so in a peculiar way. Instead of scavenging oxygen from the environment, like the aerobic methanotrophs, or driving methane oxidation by reverse methanogenesis, like the methanogenic archaea in sulfate-reducing systems, it produces its own supply of oxygen by metabolizing nitrite via nitric oxide into oxygen and dinitrogen gas. The intracellularly produced oxygen is then used for the oxidation of methane by the classical aerobic methane oxidation pathway involving methane mono-oxygenase. The present mini-review summarizes the current knowledge about this process and the micro-organism responsible for it.
Partial and complete denitrification in Thermus thermophilus: lessons from genome drafts
Authors: Bricio Carlos , Alvarez Laura , Gómez Manuel J. , Berenguer José
Published: January 2011

We have obtained draft genomic sequences of PD (partial denitrificant) and CD (complete denitrificant) strains of Thermus thermophilus. Their genomes are similar in size to that of the aerobic strains sequenced to date and probably contain a similar megaplasmid. In the CD strain, the genes encoding a putative cytochrome cd1 Nir (nitrite reductase) and ancillary proteins were clustered with a cytochrome c-dependent Nor (nitric oxide reductase), and with genes that are probably implicated in their regulation. The Nar (nitrate reductase) and associated genes were also clustered and located 7 kb downstream of the genes coding for the Nir. The whole nar–nir–nor denitrification supercluster was identified as part of a variable region of a megaplasmid. No homologues of NosZ were found despite nitrogen balance supports the idea that such activity actually exists.
Denitrification in Gram-positive bacteria: an underexplored trait
Authors: Verbaendert Ines , De Vos Paul , Boon Nico , Heylen Kim
Published: January 2011

Denitrifying organisms are essential in removing fixed nitrogen pollutants from ecosystems (e.g. sewage sludge). They can be detrimental (e.g. for agricultural soil) and can also produce the greenhouse gas N2O (nitrous oxide). Therefore a more comprehensive understanding of this process has become increasingly important regarding its global environmental impact. Even though bacterial genome sequencing projects may reveal new data, to date the denitrification abilities and features in Gram-positive bacteria are still poorly studied and understood. The present review evaluates current knowledge on the denitrification trait in Gram-positive bacteria and addresses the likely existence of unknown denitrification genes. In addition, current molecular tools to study denitrification gene diversity in pure cultures and environmental samples seem to be highly biased, and additional novel approaches for the detection of denitrifying (Gram-positive) bacteria appear to be crucial in re-assessing the real diversity of denitrifiers.
In vitroproof of direct regulation of glutamine synthetase by GlnK proteins in the extreme halophilic archaeonHaloferax mediterranei
Authors: Pedro-Roig Laia , Camacho Mónica , Bonete María José
Published: January 2011

Haloferax mediterranei is an extreme halophilic micro-organism belonging to the Archaea domain that was isolated from the Santa Pola solar salterns (Alicante, Spain) in 1983. The biochemistry of the proteins involved in nitrogen metabolism is being studied, but the knowledge of their regulation is very scarce at present. The PII superfamily is constituted by major regulators of nitrogen metabolism, which are widespread in prokaryotic and eukaryotic organisms. These trimeric proteins (12 kDa per subunit) have in Escherichia coli long been known to regulate GS (glutamine synthetase) activity via its adenylyltransferase/adenylyl-removing enzyme and, more recently, to be able to interact directly with this enzyme in methanogenic archaea. We have tested the possible role of PII proteins in the regulation of ammonium assimilation in our model organism and the results clearly indicate that the direct influence of GS by PII proteins can also take place in halophilic archaea, starting with the comprehension of nitrogen regulation in those organisms.
Bacterial cyanide degradation is under review: Pseudomonas pseudoalcaligenes CECT5344, a case of an alkaliphilic cyanotroph
Authors: Luque-Almagro Victor M. , Blasco Rafael , Martínez-Luque Manuel , Moreno-Vivián Conrado , Castillo Francisco , Roldán M. Dolores
Published: January 2011

There are thousands of areas in the U.S.A. and Europe contaminated with cyanide-containing wastes as a consequence of a large number of industrial activities such as gold mining, steel and aluminium manufacturing, electroplating and nitrile pesticides used in agriculture. Chemical treatments to remove cyanide are expensive and generate other toxic products. By contrast, cyanide biodegradation constitutes an appropriate alternative treatment. In the present review we provide an overview of how cells deal in the presence of the poison cyanide that irreversible binds to metals causing, among other things, iron-deprivation conditions outside the cell and metalloenzymes inhibition inside the cell. In this sense, several systems must be present in a cyanotrophic organism, including a siderophore-based acquisition mechanism, a cyanide-insensitive respiratory system and a cyanide degradation/assimilation pathway. The alkaliphilic autochthonous bacterium Pseudomonas pseudocaligenes CECT5344 presents all these requirements with the production of siderophores, a cyanide-insensitive bd-related cytochrome [Cio (cyanide-insensitive oxidase)] and a cyanide assimilation pathway that generates ammonium, which is further incorporated into organic nitrogen.
Emerging complexity in the denitrification regulatory network ofBradyrhizobium japonicum
Authors: Torres María J. , Bueno Emilio , Mesa Socorro , Bedmar Eulogio J. , Delgado María J.
Published: January 2011

Bradyrhizobium japonicum is a Gram-negative soil bacterium symbiotically associated with soya bean plants, which is also able to denitrify under free-living and symbiotic conditions. In B. japonicum, the napEDABC, nirK, norCBQD and nosRZDYFLX genes which encode reductases for nitrate, nitrite, nitric oxide and nitrous oxide respectively are required for denitrification. Similar to many other denitrifiers, expression of denitrification genes in B. japonicum requires both oxygen limitation and the presence of nitrate or a derived nitrogen oxide. In B. japonicum, a sophisticated regulatory network consisting of two linked regulatory cascades co-ordinates the expression of genes required for microaerobic respiration (the FixLJ/FixK2 cascade) and for nitrogen fixation (the RegSR/NifA cascade). The involvement of the FixLJ/FixK2 regulatory cascade in the microaerobic induction of the denitrification genes is well established. In addition, the FNR (fumarase and nitrate reduction regulator)/CRP(cAMP receptor protein)-type regulator NnrR expands the FixLJ/FixK2 regulatory cascade by an additional control level. A role for NifA is suggested in this process by recent experiments which have shown that it is required for full expression of denitrification genes in B. japonicum. The present review summarizes the current understanding of the regulatory network of denitrification in B. japonicum.
Transcriptional regulation by the dedicated nitric oxide sensor, NorR: a route towards NO detoxification
Authors: Bush Matthew , Ghosh Tamaswati , Tucker Nicholas , Zhang Xiaodong , Dixon Ray
Published: January 2011

A flavorubredoxin and its associated oxidoreductase (encoded by norV and norW respectively) detoxify NO (nitric oxide) to form N2O (nitrous oxide) under anaerobic conditions in Escherichia coli. Transcription of the norVW genes is activated in response to NO by the σ54-dependent regulator and dedicated NO sensor, NorR, a member of the bacterial enhancer-binding protein family. In the absence of NO, the catalytic activity of the central ATPase domain of NorR is repressed by the N-terminal regulatory domain that contains a non-haem iron centre. Binding of NO to this centre results in the formation of a mononitrosyl iron species, enabling the activation of ATPase activity. Our studies suggest that the highly conserved GAFTGA loop in the ATPase domain, which engages with the alternative σ factor σ54 to activate transcription, is a target for intramolecular repression by the regulatory domain. Binding of NorR to three conserved enhancer sites upstream of the norVW promoter is essential for transcriptional activation and promotes the formation of a stable higher-order NorR nucleoprotein complex. We propose that enhancer-driven assembly of this oligomeric complex, in which NorR apparently forms a DNA-bound hexamer in the absence of NO, provides a ‘poised’ system for transcriptional activation that can respond rapidly to nitrosative stress.
The Pseudomonas aeruginosa DNR transcription factor: light and shade of nitric oxide-sensing mechanisms
Authors: Giardina Giorgio , Castiglione Nicoletta , Caruso Manuela , Cutruzzolà Francesca , Rinaldo Serena
Published: January 2011

In response to environmental conditions, NO (nitric oxide) induces global changes in the cellular metabolism of Pseudomonas aeruginosa, which are strictly related to pathogenesis. In particular, at low oxygen tensions and in the presence of NO the denitrification alternative respiration is activated by a key regulator: DNR (dissimilative nitrate respiration regulator). DNR belongs to the CRP (cAMP receptor protein)–FNR (fumarate and nitrate reductase regulatory protein) superfamily of bacterial transcription factors. These regulators are involved in many different pathways and distinct activation mechanism seems to be operative in several cases. Recent results indicate that DNR is a haem protein capable of discriminating between NO and CO (carbon monoxide). On the basis of the available structural data, a suggested activation mechanism is discussed.
Enzymology under global change: organic nitrogen turnover in alpine and sub-Arctic soils
Authors: Weedon James T. , Aerts Rien , Kowalchuk George A. , van Bodegom Peter M.
Published: January 2011

Understanding global change impacts on the globally important carbon storage in alpine, Arctic and sub-Arctic soils requires knowledge of the mechanisms underlying the balance between plant primary productivity and decomposition. Given that nitrogen availability limits both processes, understanding the response of the soil nitrogen cycle to shifts in temperature and other global change factors is crucial for predicting the fate of cold biome carbon stores. Measurements of soil enzyme activities at different positions of the nitrogen cycling network are an important tool for this purpose. We review a selection of studies that provide data on potential enzyme activities across natural, seasonal and experimental gradients in cold biomes. Responses of enzyme activities to increased nitrogen availability and temperature are diverse and seasonal dynamics are often larger than differences due to experimental treatments, suggesting that enzyme expression is regulated by a combination of interacting factors reflecting both nutrient supply and demand. The extrapolation from potential enzyme activities to prediction of elemental nitrogen fluxes under field conditions remains challenging. Progress in molecular ‘-omics’ approaches may eventually facilitate deeper understanding of the links between soil microbial community structure and biogeochemical fluxes. In the meantime, accounting for effects of the soil spatial structure and in situ variations in pH and temperature, better mapping of the network of enzymatic processes and the identification of rate-limiting steps under different conditions should advance our ability to predict nitrogen fluxes.
Bioturbation: impact on the marine nitrogen cycle
Authors: Laverock Bonnie , Gilbert Jack A. , Tait Karen , Osborn A. Mark , Widdicombe Steve
Published: January 2011

Sediments play a key role in the marine nitrogen cycle and can act either as a source or a sink of biologically available (fixed) nitrogen. This cycling is driven by a number of microbial remineralization reactions, many of which occur across the oxic/anoxic interface near the sediment surface. The presence and activity of large burrowing macrofauna (bioturbators) in the sediment can significantly affect these microbial processes by altering the physicochemical properties of the sediment. For example, the building and irrigation of burrows by bioturbators introduces fresh oxygenated water into deeper sediment layers and allows the exchange of solutes between the sediment and water column. Burrows can effectively extend the oxic/anoxic interface into deeper sediment layers, thus providing a unique environment for nitrogen-cycling microbial communities. Recent studies have shown that the abundance and diversity of micro-organisms can be far greater in burrow wall sediment than in the surrounding surface or subsurface sediment; meanwhile, bioturbated sediment supports higher rates of coupled nitrification–denitrification reactions and increased fluxes of ammonium to the water column. In the present paper we discuss the potential for bioturbation to significantly affect marine nitrogen cycling, as well as the molecular techniques used to study microbial nitrogen cycling communities and directions for future study.
Four PCR primers necessary for the detection of periplasmic nitrate reductase genes in all groups of Proteobacteria and in environmental DNA
Authors: Klatte Tobias , Evans Laura , Whitehead Rebekah N. , Cole Jeffrey A.
Published: January 2011

Generic primers are available for detecting bacterial genes required for almost every reaction of the biological nitrogen cycle, the one notable exception being napA (gene for the molybdoprotein of the periplasmic nitrate reductase) encoding periplasmic nitrate reductases. Using an iterative approach, we report the first successful design of three forward oligonucleotide primers and one reverse primer that, in three separate PCRs, can amplify napA DNA from all five groups of Proteobacteria. All 140 napA sequences currently listed in the NCBI (National Center for Biotechnology Information) database are predicted to be amplified by one or more of these primer pairs. We demonstrate that two pairs of these primers also amplify PCR products of the predicted sizes from DNA isolated from human faeces, confirming their ability to direct the amplification of napA fragments from mixed populations. Analysis of the resulting amplicons by high-throughput sequencing will enable a good estimate to be made of both the range and relative abundance of nitrate-reducing bacteria in any community, subject only to any unavoidable bias inherent in a PCR approach to molecular characterization of a highly diverse target.
Discovering new clinical markers in the field of glycomics
Authors: Telford Jayne E. , Doherty Margaret A. , Tharmalingam Tharmala , Rudd Pauline M.
Published: January 2011

Glycosylation modifications have been reported in a number of disease states and, as a result, there is significant focus on the discovery and development of glycan-based biomarkers. Glyco-biomarkers have the potential to enhance the efficacy and efficiency of the diagnostic procedures for these diseases.
Glycoconjugate markers of joint diseases
Authors: Popko Janusz , Olszewski Sławomir , Guszczyn Tomasz , Zwierz Krzysztof , Pancewicz Sławomir
Published: January 2011

A number of different types of glycoconjugate are found associated with joint tissue and fluids, comprising glycoproteins, glycolipids and glycosaminoglycans. Oligosaccharide chains of glycoconjugates are degraded by exoglycosidases, and the dominant exoglycosidase found in human blood, synovial fluid, the synovial membrane and chondrocytes of articular cartilage is HEX (N-acetyl-β-hexosaminidase). HEX is localized mostly intracellularly in synovial cells. Serum activity of HEX may be used to monitor the course and efficiency of treatment of Lyme arthritis, and activity of HEX, above 10 μkat/kg of protein in the synovial fluid, suggests rheumatoid disease. There is a shortage of HEX inhibitors able to penetrate synoviocytes, so the development of drugs which inhibit synthesis and/or the activity of HEX will be a promising field for future investigations.
Glycomarkers for muscular dystrophy
Authors: Hewitt Jane E.
Published: January 2011

During the last 10 years it has become apparent that a significant subset of inherited muscular dystrophy is caused by errors in the glycosylation of α-dystroglycan. Many of these dystrophies are also associated with abnormalities of the central nervous system. Dystroglycan has to be fully glycosylated in order bind to its ligands. To date, six genes have been shown to be essential for functional dystroglycan glycosylation and most, if not all, of these genes act in the formation of O-mannosyl glycans. Genetic heterogeneity indicates that other genes are involved in this pathway. Identification of these additional genes would increase our understanding of this specific and essential glycosylation pathway.
Carbohydrate markers of pancreatic cancer
Authors: Szajda Sławomir Dariusz , Waszkiewicz Napoleon , Chojnowska Sylwia , Zwierz Krzysztof
Published: January 2011

Pancreatic cancer is the fourth most common cause of death from cancer in the world and the sixth in Europe. Pancreatic cancer is more frequent in males than females. Worldwide, following diagnosis of pancreatic cancer, <2% of patients survive for 5 years, 8% survive for 2 years and <50% survive for only approx. 3 months. The biggest risk factor in pancreatic cancer is age, with a peak of morbidity at 65 years. Difficulty in the diagnosis of pancreatic cancer causes a delay in its detection. It is one of the most difficult cancers to diagnose and therefore to treat successfully. Additional detection of carbohydrate markers may offer a better diagnosis of pancreatic cancer. Carbohydrate markers of cancer may be produced by the cancer itself or by the body in response to cancer, whose presence in body fluids suggests the presence and growth of the cancer. The most widely used, and best-recognized, carbohydrate marker of pancreatic cancer is CA 19–9 [CA (carbohydrate antigen) 19–9]. However, the relatively non-specific nature of CA 19–9 limits its routine use in the early diagnosis of pancreatic cancer, but it may be useful in monitoring treatment of pancreatic cancer (e.g. the effectiveness of chemotherapy), as a complement to other diagnostic methods. Some other carbohydrate markers of pancreatic cancer may be considered, such as CEA (carcinoembryonic antigen), CA 50 and CA 242, and the mucins MUC1, MUC2 and MUC5AC, but enzymes involved in the processing of glycoconjugates could also be involved. Our preliminary research shows that the activity of lysosomal exoglycosidases, including HEX (N-acetyl-β-D-hexosaminidase), GAL (β-D-galactosidase), FUC (α-L-fucosidase) and MAN (α-D-mannosidase), in serum and urine may be used in the diagnosis of pancreatic cancer.
Terminal monosaccharide expression on amniotic glycoproteins as biomarkers of fetus maturity
Authors: Orczyk-Pawiłowicz Magdalena , Kątnik-Prastowska Iwona
Published: January 2011

Glycotypes, particularly those that terminate with sialic acid and fucose are known to play a fundamental role in human development, during implantation, growth and differentiation of fetal tissues. The present review describes changes in the exposition of terminal sialic acid and fucose isoforms in the amniotic fluid glycoconjugates, α1-acid glycoprotein and fibronectin during critical stages of pregnancy, i.e. second and third trimester, perinatal period, delivery and post-date pregnancy. The distinct amniotic glycoforms are suggested to be implicated in regulatory processes to ensure homoeostasis during pregnancy and to protect the fetus. These may have the potential of becoming additional laboratory makers in obstetrics to monitor pregnancy.
Glycosylation changes as important factors for the susceptibility to urinary tract infection
Authors: Taganna Joemar , de Boer Arjen R. , Wuhrer Manfred , Bouckaert Julie
Published: January 2011

FimH is the type 1 fimbrial tip adhesin and invasin of Escherichia coli. Its ligands are the glycans on specific proteins enriched in membrane microdomains. FimH binding shows high-affinity recognition of paucimannosidic glycans, which are shortened high-mannose glycans such as oligomannose-3 and -5. FimH can recognize equally the (single) high-mannose glycan on uroplakin Ia, on the urinary defence protein uromodulin or Tamm–Horsfall glycoprotein and on the intestinal GP2 glycoprotein present in Peyer's patches. E. coli bacteria may attach to epithelial cells via hundreds of fimbriae in a multivalent fashion. This binding is considered to provoke conformational changes in the glycoprotein receptor that translate into signalling in the cytoplasm of the infected epithelial cell. Bladder cell invasion by the uropathogenic bacterium is the prelude to recurrent and persistent urinary tract infections in humans. Patients suffering from diabetes mellitus are more prone to contract urinary tract infections. In a study of women, despite longer treatments with a more potent antibiotic, these patients also have more often recurrences of urinary tract infections compared with women without diabetes. Type 1 fimbriae are the most important virulence factors used not only for adhesion of E. coli in the urinary tract, but also for the colonization by E. coli in patients with Crohn's disease or ulcerative colitis. It appears that the increased prevalence of urinary tract infections in diabetic women is not the result of a difference in the bacteria, but is due to changes in the uroepithelial cells leading to an increased adherence of E. coli expressing type 1 fimbriae. Hypothetically, these changes are in the glycosylation of the infected cells. The present article focuses on possible underlying mechanisms for glycosylation changes in the uroepithelial cell receptors for FimH. Like diabetes, bacterial adhesion induces apoptosis that may bring the endoplasmic reticulum membrane with immature mannosylated glycoproteins to the surface. Indicatively, clathrin-mediated vesicle trafficking of glucose transporters is disturbed in diabetics, which would interfere further with the biosynthesis and localization of complex N-linked glycans.
Expression and potential biological role of α(1,2)fucosylated glycotopes on amniotic and seminal fibronectins
Authors: Kątnik-Prastowska Iwona , Orczyk-Pawiłowicz Magdalena
Published: January 2011

The present paper describes concisely the expression and role of α(1,2)-linked fucose on some glycoconjugates as well as the detection, distribution and potential role of that glycotope on human soluble plasma and cellular fibronectins in addition to the expression on both normal and pathological amniotic fluid and seminal plasma fibronectins. The determination of α(1,2)fucosylated glycans is considered with respect to its usefulness as a potential clinically applicable biomarker in obstetrics to monitor pregnancy and in andrology to evaluate the ejaculate of infertile men and in vitro fertilization.
Glycomarkers in parasitic infections and allergy
Authors: Hoffmann-Sommergruber Karin , Paschinger Katharina , Wilson Iain B.H.
Published: January 2011

Both helminth infections and contact with allergens result in development of a Th2 type of immune response in the affected individual. In this context, the hygiene hypothesis suggests that reduced prevalence of parasitic infections and successful vaccination strategies are causative for an increase of allergies in industrialized countries. It is therefore of interest to study glycans and their role as immunogenic structures in both parasitic infections and allergies. In the present paper we review information on the different types of glycan structure present in proteins from plant and animal food, insect venom and helminth parasites, and their role as diagnostic markers. In addition, the application of these glycan structures as immunomodulators in novel immunotherapeutic strategies is discussed.
Glycans in melanoma screening. Part 1. The role of β1,6-branched N-linked oligosaccharides in melanoma
Authors: Przybyło Małgorzata , Lityńska Anna
Published: January 2011

Melanoma, which is one of the most aggressive human tumours, originates from melanin-producing melanocytes. As no effective systemic therapy exists for advanced-stage melanoma, the best chance of recovery remains surgical removal of thin early-stage melanoma. Aberrant glycosylation is a hallmark of malignancy and a well-studied class of β1,6-branched oligosaccharides is associated with malignant transformation of rodent and human cells, and poor prognosis in cancer patients. It is evident that increased β1,6 branching significantly contributes to the phenotype of melanoma cells, influencing the adhesion to extracellular matrix components and motility as well as invasive and metastatic potential. Despite the considerable success in establishing the role of β1,6-branched N-linked oligosaccharides in melanoma biology, there is virtually no progress in using these glycans as a screening tool for the early diagnosis of the disease, or a target-specific therapeutic agent.
Highly glycosylated tumour antigens: interactions with the immune system
Authors: Saeland Eirikur , van Kooyk Yvette
Published: January 2011

A common phenotypic change in cancer is a dramatic transformation of cellular glycosylation. Functional studies of particular tumour-associated oligosaccharides are difficult to interpret conclusively, but carbohydrate-binding proteins are likely to contribute to progression of the tumour. This review discusses the potential role of CLRs (C-type lectin receptors), expressed by antigen-presenting cells of the immune system, in tumour recognition and immune modulation. Studies in recent years have provided significant insight into the immunomodulatory function of CLR during infections, but their role in cancer remains elusive; some strongly bind tumour cells and antigens, indicating participation in malignancy. The potential to use recombinant CLR as diagnostic tools will also be discussed.
Exoglycosidase markers of diseases
Authors: Chojnowska Sylwia , Kępka Alina , Szajda Sławomir Dariusz , Waszkiewicz Napoleon , Bierć Marcin , Zwierz Krzysztof
Published: January 2011

Exoglycosidases are hydrolases involved in lysosomal degradation of oligosaccharide chains of glycoconjugates (glycoproteins, glycolipids and proteoglycans). In tissues and body fluids, a higher exoglycosidase specific activity is found in N-acetyl-β-hexosaminidase, than β-glucuronidase, α-L-fucosidase, β-galactosidase, α-mannosidase and α-glucosidase. Determination of exoglycosidases (especially N-acetyl-β-hexosaminidase and β-glucuronidase) in body fluids could be an inexpensive, easy to perform and sensitive test for pathological evaluation, as well as in screening and monitoring many diseases, including alcohol abuse, risk of arteriosclerosis, bacterial infections (e.g. Lyme borreliosis), chronic inflammatory processes, such as rheumatoid arthritis and juvenile idiopathic arthritis, asthma, autoimmune hepatitis and primary biliary cirrhosis, as well as cancers.
Faster proton transfer dynamics of water on SnO2 compared to TiO2
Authors: Kumar Nitin , Kent Paul R. C. , Bandura Andrei V. , Kubicki James D. , Wesolowski David J. , Cole David R. , Sofo Jorge O.
Published: January 2011

Proton jump processes in the hydration layer on the iso-structural TiO2 rutile (110) and SnO2 cassiterite (110) surfaces were studied with density functional theory molecular dynamics. We find that the proton jump rate is more than three times faster on cassiterite compared with rutile. A local analysis based on the correlation between the stretching band of the O–H vibrations and the strength of H-bonds indicates that the faster proton jump activity on cassiterite is produced by a stronger H-bond formation between the surface and the hydration layer above the surface. The origin of the increased H-bond strength on cassiterite is a combined effect of stronger covalent bonding and stronger electrostatic interactions due to differences of its electronic structure. The bridging oxygens form the strongest H-bonds between the surface and the hydration layer. This higher proton jump rate is likely to affect reactivity and catalytic activity on the surface. A better understanding of its origins will enable methods to control these rates.
Visualizing the very-large-scale motions in turbulent pipe flow
Authors: Hellström Leo H. O. , Sinha Aman , Smits Alexander J.
Published: January 2011

Time-resolved stereoscopic particle image velocimetry is used to investigate the structure of the very-large-scale motions (VLSMs) in fully developed turbulent pipe flow. The motions are visualized using snapshot proper orthogonal decomposition. It is shown that the structures can be reconstructed using a small number of the most energetic modes. The results strongly suggest a possible connection between the origin of the VLSM and linear stability analysis. The structures are seen to be highly three-dimensional, meandering azimuthally and radially. At this Reynolds number (ReD=12 500), they occasionally extend from the near-wall region to the wake region of the pipe.
Structure and dynamics of water in mixed solutions including laponite and PEO
Authors: Morikubo Satoshi , Sekine Yurina , Ikeda-Fukazawa Tomoko
Published: January 2011

To investigate the structure and dynamics of water in mixed solutions including laponite clay particles and poly(ethylene oxide) (PEO), we measured the Raman spectra of the mixed solutions in the temperature range 283−313 K. The results show that the vibrational energies of the O−H stretching modes in the mixed solutions depend on the water content and temperature. The energy shifts of the O−H stretching modes are attributed to changes in the water structure. By applying a structural model of bulk water to the spectra in the O−H stretching region, the local structures of water in the solutions were analyzed. The result shows that the formation probability of hydrogen bonds in the solutions decreases as the water content decreases. Laponite and PEO have effects to disrupt the network structure of hydrogen bonds between water molecules. Further, it was found that laponite and PEO cause increase in the strength of hydrogen bonds of surrounding water,although the strength of the hydrogen bonds increases with the order water–laponite < water–water < water–PEO. It is concluded that water in laponite–PEO mixed solutions has a less-networked structure with strong hydrogen bonds compared with bulk water.
The possibility of regime changing in chain reactions with degenerate branching under the influence of external magnetic field
Authors: Kipriyanov A. A. , Purtov P. A.
Published: January 2011

A reaction of hydrocarbons oxidation in the liquid phase is treated theoretically. The reaction system under discussion is a flow reactor, to the inlet of which the hydrocarbon is constantly delivered in the mixture with an inhibitor under oxygen saturation conditions; the reaction mixture constantly flows from the chamber at the same rate. The reaction gives rise to radicals that can subsequently recombine. It is shown that under certain conditions in this reaction system, three steady states may arise, two of which are stable and the third state is unstable. By varying rate constants of radical reactions by means of an external magnetic field, one can disturb the steady state stability and transfer the system to another steady state, which will be accompanied by an abrupt change in the concentration of reacting substances.
Structure, scaling, and synthesis of proper orthogonal decomposition modes of inhomogeneous turbulence
Authors: Baltzer Jon R. , Adrian Ronald J.
Published: January 2011

By examining the proper orthogonal decomposition (POD) of turbulent channel flow and turbulent thermal convection in the inhomogeneous direction of each flow, it is found that the POD eigenfunctions separate into two types of modes having different structure and scaling. For these flows, the modes can be represented in the form of amplitude-modulated and phase-modulated oscillations in the wall-normal direction. The phase functions can be extracted by several means and they contain much of the physics embedded in the two-point spatial correlation function. The phase and envelope functions are analyzed to interpret POD mode behavior. The first several most energetic modes are large-scale and their structure is idiosyncratic relative to the rest of the modes and characteristic of the type of the flow. Outside this group of idiosyncratic modes, the remaining modes are less energetic, smaller scale, and asymptotically self-similar in the sense that the phases scaled using sequency correlate well and approach a single limiting curve with increasing order (mode number). This asymptotic phase function is characteristic of the type of turbulence, i.e., it differs between channel flow and thermal convection, despite it being small-scale and, therefore, presumably insensitive to the form of the boundary conditions. The work of Moser [“Kolmogorov inertial range spectra for inhomogeneous turbulence,” Phys. Fluids 6, 794 (1994)] provides an approximate relationship for the asymptotic phase function in terms of the distribution of viscous dissipation ϵ(y). A more general framework for this relationship is presented in which the idiosyncratic modes determine the energy distribution and the asymptotically self-similar modes determine the distribution of viscous dissipation. The foregoing results are exploited to develop a complete set of orthonormal basis functions that approximate the POD modes and possess convergence properties that are comparable to the optimal convergence of the exact POD and significantly better than those of conventional orthogonal polynomials. This procedure, called “synthetic POD,” uses only knowledge of the distribution of mean dissipation (or equivalently, the asymptotic phase function) without a priori computation of the more complicated two-point correlation functions.
Air trapped nanocavity induced superhydrophobicity on GaN microbelt
Authors: Sahoo Prasana , Dhara S. , Dash S. , Raj Baldev , Manna I. , Tyagi A. K.
Published: January 2011

In the present study, nanotextured surface protrusion induced superhydrophobicity in GaN microbelt is reported. The results show that along with nanometer-scale topographic features, the special air trapped nanocavities formed beneath the liquid droplet are solely responsible for the transition of superhydrophobicity having hydrophilic origin in GaN. The built-in nanocavities, (∼80 nm in diameter) provide an ideal model for producing stable air trapped region. A calculation of shape of the meniscus at the interface of air and water in an isolated cavity correlates well with the macroscopic surface wetting behavior.
Epitaxial growth of lanthanide oxides La2O3 and Sc2O3 on GaN
Authors: Jur Jesse S. , Wheeler Virginia D. , Lichtenwalner Daniel J. , Maria Jon-Paul , Johnson Mark A. L.
Published: January 2011

Deposition of lanthanide oxides on GaN is investigated as a means to produce stable dielectric with good interface quality. Epitaxial growth of cubic ⟨111⟩-oriented Sc2O3 is observed on GaN [0001] with a lattice mismatch of 7.2%, whereas La2O3 growth, with a lattice mismatch of ∼21%, results in a mixed phase epitaxial film comprised of the bixbyite and hexagonal allotropes. Substantial roughening accompanies this mixed phase film. By inserting a thin Sc2O3 interfacial layer between La2O3 and GaN and a Sc2O3 capping layer, the crystal quality of the predominantly La2O3 layer is improved and the stack is stabilized against hydroxide formation under ambient conditions.
Molecular dynamics at ambient and elevated pressure of the amorphous pharmaceutical: Nonivamide (pelargonic acid vanillylamide)
Authors: Wojnarowska Z. , Hawelek L. , Paluch M. , Sawicki W. , Ngai K. L.
Published: January 2011

Broadband dielectric spectroscopy was employed to investigate the relaxation dynamics of supercooled and glassy nonivamide—the synthetic form of capsaicin being the most spicy-hot substance known to man. The material is of great importance in the pharmaceutical industry because it has wide usage in the medical field for relief of pain, and more recently it has been shown to be effective in fighting cancers. Dielectric measurements carried out at various isobaric and isothermal conditions (pressure up to 400 MPa) revealed very narrow α-loss peak and unresolved secondary relaxations appearing in the form of an excess wing on the high frequency flank. Moreover, our studies have shown the shape of dielectric loss spectrum at any fixed loss peak frequency is invariant to different combinations of temperature and pressure, i.e., validity of the time–temperature–pressure superpositioning. We also found the fragility index is nearly constant on varying pressure. This property is likely due to the unusual structure of nonivamide, which has a part characteristic of van der Waals glass-former and another part characteristic of hydrogen-bonded glass-former.
Continuously voltage-tunable electroluminescence from a monolayer of ZnS quantum dots
Authors: Xuan Rong-Wei , Xu Jian-Ping , Zhang Xiao-Song , Li Ping , Luo Cheng-Yuan , Wu Yan-Yu , Li Lan
Published: January 2011

A monolayer electroluminescence (EL) device with ZnS quantum dots (QDs) as emitting layer was fabricated by spin-coating technique. Continuously tunable EL spectra from ZnS QDs are observed at room temperature. By increasing excitation voltage, the EL spectra can be tuned from yellow green (560 nm) to blue (470 nm), corresponding to chromaticity coordinates from (0.45, 0.52) to (0.22, 0.26). In order to understand the mechanism of the device, the dependences of the photoluminescence of the ZnS QDs on temperature, excitation energy, and particle size have been studied, respectively, which indicates that the possible mechanisms of tunable EL spectra are related to selective excitation of QDs with different particle sizes.