bluuebunny/crossref_metadata_2025 huggingface dataset:
The dissipation of fipronil, chlorpyrifos, fosthiazate and ethoprophos in soils from potato monoculture areas: first evidence for the enhanced biodegradation of fosthiazate
Authors: Papadopoulou Evangelia S , Lagos Stathis , Spentza Flora , Vidiadakis Evangelos , Karas Panagiotis A , Klitsinaris Tassos , Karpouzas Dimitrios G
Published: August 2015

BACKGROUND

A limited number of pesticides are available for the control of soil pests in potato. This, together with the monoculture nature of potato cultivation, does not favour chemical rotation, increasing the risk of reduced biological efficacy due to microbial adaptation. The dissipation of three major organophosphates (chlorpyrifos, ethoprophos and fosthiazate) was studied in comparison with fipronil, an insecticide recently introduced in potato cultivation, in 17 soils from potato monoculture areas in Greece to explore the extent of enhanced biodegradation development.

RESULTS

The dissipation time of the four pesticides varied in the different soils, with DT50 values of 1.7–30.8 days, 2.7–56 days, 7.0–31.0 days and 24.5–116.5 days for fosthiazate, chlorpyrifos, ethoprophos and fipronil, respectively. A rapid dissipation of ethoprophos and fosthiazate in two soils with previous exposure to these nematicides provided first evidence for the development of enhanced biodegradation. Sterilisation of the given soils inhibited the dissipation of fosthiazate. Additionally, fosthiazate dissipation in the soils increased upon repeated applications.

CONCLUSION

The development of enhanced biodegradation of fosthiazate in soils from potato monoculture regions was verified. This is the first report of enhanced biodegradation for this chemical. Further studies will focus on the isolation of microorganisms responsible for the dissipation of fosthiazate. © 2015 Society of Chemical Industry
The Computerized Generation of Fractional‐replicate Designs Using Galois Fields and Hadamard Matrices
Authors: Zemroch Peter J.
Published: August 2015

Many statistical programs can now generate fractional‐replicate designs, but most depend on built‐in libraries of experimental plans. Relatively few have design generation algorithms that would give the user true flexibility in the numbers of tests, factors, and factor levels. Powerful search algorithms are now available for generating a wide range of blocked and fractional‐replicate designs using design keys, but these are mostly regular designs with pqunits and factors with p, p2, … levels, where p is prime.

Many useful classes of irregular design also exist with numbers of units and factor levels which are not powers of p, and the construction rules for most of these use Galois fields and Hadamard matrices in some way. However, the underlying mathematics can be difficult. The aim of this paper is to collate algorithms to expedite the implementation of these structures in software and to present these in an accessible form to a wider community. The use of Galois fields and Hadamard matrices in generating important design classes, such as the fractional 2kPlackett–Burman and skAddelman–Kempthorne designs, is then detailed.

Combining these algorithms with design key searches gives an arsenal of methods that can generate almost all existent balanced fractional‐replicate designs of sizes likely to be used in real‐world experimentation. These methods have all been implemented in the KEYFINDER program, which is available from the author, free of charge. Copyright © 2015 John Wiley & Sons, Ltd.
Relative quantification of human β‐defensins by a proteomics approach based on selected reaction monitoring
Authors: Kalló Gergő , Chatterjee Arunima , Tóth Márta , Rajnavölgyi Éva , Csutak Adrienne , Tőzsér József , Csősz Éva
Published: August 2015

Rationale

A targeted proteomics method based on selected reaction monitoring (SRM) is a relevant approach for the analysis of multiple analytes in biological samples. Defensins are phylogenetically conserved small antimicrobial peptides contributing to innate host defense and exhibiting low immunogenicity, resistance to proteolysis and a broad range of antimicrobial activities. The goal of the present study was to develop and optimize SRM‐based targeted proteomics methods for the detection of human β‐defensins 1–4 in various biological fluids.

Methods

An SRM‐based targeted proteomics method was developed and validated for the detection of human β‐defensins 1–4. The supernatants of resting and IL‐1β‐stimulated Caco2, HT‐29 and SW‐1116 colonic epithelial cells (CEC), cell lysates of CECs and tear samples of human healthy individuals were analyzed and the feasibility of the developed method was validated by ELISA and dot‐blot analysis complemented by RT‐qPCR.

Results

Our results demonstrate that the developed SRM method offers an alternative approach for the cost‐effective and rapid analysis of human β‐defensins in samples with biological relevance.

Conclusions

A semi‐quantitative targeted mass spectrometry method was developed and validated for the relative quantification of β‐defensins 1–4 in cell culture supernatants and body fluid analyses. Copyright © 2015 John Wiley & Sons, Ltd.
Topoisomerases interlink genetic network underlying autism
Authors: Vokálová Lenka , Durdiaková Jaroslava , Ostatníková Daniela
Published: August 2015

DNA topoisomerases belong to the group of proteins that play an important role in the organizational dynamics of the human genome. Their enzymatic activity solves topological strain rising from DNA supercoiling occurring during transcription. DNA topoisomerases are especially important for transcription of genes involved in neurodevelopment. Disruption of topoisomerase activity in animal models resulted in impaired neurodevelopment and changed brain architecture. Recent research revealed that topoisomerases induced expression of the same group of genes as those associated with autism. Transcriptional inhibition of neuronal genes during critical stages of brain development may be responsible for pathology of neurodevelopmental disorders such as autism. In this review we aim to outline the role of topoisomerase in neurodevelopment and its possible linkage to neuropathology of autism.
Understanding pelagic stingray (Pteroplatytrygon violacea) by-catch by Spanish longliners in the Mediterranean Sea
Authors: Báez José C. , Crespo Guillermo Ortuño , García-Barcelona Salvador , Ortiz De Urbina José M. , Macías David
Published: August 2015

The pelagic stingray Pteroplatytrygon violacea is known to be a frequent by-catch in longline fisheries worldwide. This study analysed the eco-geographic, technical and temporal parameters that affect pelagic stingray by-catch by the Spanish surface drifting longline fleet that operates in the Mediterranean Sea. Between 2000 and 2013, 3007 longline fishing operations were monitored. Over this period, we recorded 57 574 pelagic stingray by-catches by this fleet. Two gear types were involved in 96.05% of the pelagic stingray by-catch observed: traditional surface longliners targeting swordfish (LLHB) and surface drifting longliners targeting albacore (LLALB). We obtained two statistically significant explanatory models for the two types of gear. In both cases, two of the most important variables were fisheries being sited over the continental shelf and fishing during the summer season. The LLHB explanatory model included the following variables: number of hooks, latitude where setting started, distance between the ends of the longline, and the spring season. Regarding the LLHB, we found an association between the Capture per Unit Effort of pelagic stingray from favourable sets per year and the North Atlantic Oscillation in the previous year.
Single-neuron activity and eye movements during human REM sleep and awake vision
Authors: Andrillon Thomas , Nir Yuval , Cirelli Chiara , Tononi Giulio , Fried Itzhak
Published: August 2015

Are rapid eye movements (REMs) in sleep associated with visual-like activity, as during wakefulness? Here we examine single-unit activities (n=2,057) and intracranial electroencephalography across the human medial temporal lobe (MTL) and neocortex during sleep and wakefulness, and during visual stimulation with fixation. During sleep and wakefulness, REM onsets are associated with distinct intracranial potentials, reminiscent of ponto-geniculate-occipital waves. Individual neurons, especially in the MTL, exhibit reduced firing rates before REMs as well as transient increases in firing rate immediately after, similar to activity patterns observed upon image presentation during fixation without eye movements. Moreover, the selectivity of individual units is correlated with their response latency, such that units activated after a small number of images or REMs exhibit delayed increases in firing rates. Finally, the phase of theta oscillations is similarly reset following REMs in sleep and wakefulness, and after controlled visual stimulation. Our results suggest that REMs during sleep rearrange discrete epochs of visual-like processing as during wakefulness.
Human GPR42 is a transcribed multisite variant that exhibits copy number polymorphism and is functional when heterologously expressed
Authors: Puhl III Henry L. , Won Yu-Jin , Lu Van B. , Ikeda Stephen R.
Published: August 2015

FFAR3 (GPR41) is a G-protein coupled receptor for which short-chain fatty acids serve as endogenous ligands. The receptor is found on gut enteroendocrine L-cells, pancreatic β-cells and sympathetic neurons and is implicated in obesity, diabetes, allergic airway disease and altered immune function. In primates, FFAR3 is segmentally duplicated resulting in GPR42, a gene currently classified as a suspected pseudogene. In this study, we sequenced FFAR3 and GPR42 open reading frames from 56 individuals and found an unexpectedly high frequency of polymorphisms contributing to several complex haplotypes. We also identified a frequent (18.8%) structural variation that results in GPR42 copy number polymorphism. Finally, sequencing revealed that 50.6% of GPR42 haplotypes differed from FFAR3 by only a single non-synonymous substitution and that the GPR42 reference sequence matched only 4.4% of the alleles. Sequencing of cDNA from human sympathetic ganglia and colon revealed processed transcripts matching the GPR42 genotype. Expression of several GPR42 haplotypes in rat sympathetic neurons revealed diverse pharmacological phenotypes that differed in potency and efficacy. Our data suggest that GPR42 be reclassified as a functioning gene and that recognition of sequence and copy number polymorphism of the FFAR3/GPR42 complex be considered during genetic and pharmacological investigation of these receptors.
Atypical spatiotemporal signatures of working memory brain processes in autism
Authors: Urbain C M , Pang E W , Taylor M J
Published: August 2015

Working memory (WM) impairments may contribute to the profound behavioural manifestations in children with autism spectrum disorder (ASD). However, previous behavioural results are discrepant as are the few functional magnetic resonance imaging (fMRI) results collected in adults and adolescents with ASD. Here we investigate the precise temporal dynamics of WM-related brain activity using magnetoencephalography (MEG) in 20 children with ASD and matched controls during an n-back WM task across different load levels (1-back vs 2-back). Although behavioural results were similar between ASD and typically developing (TD) children, the between-group comparison performed on functional brain activity showed atypical WM-related brain processes in children with ASD compared with TD children. These atypical responses were observed in the ASD group from 200 to 600 ms post stimulus in both the low- (1-back) and high- (2-back) memory load conditions. During the 1-back condition, children with ASD showed reduced WM-related activations in the right hippocampus and the cingulate gyrus compared with TD children who showed more activation in the left dorso-lateral prefrontal cortex and the insulae. In the 2-back condition, children with ASD showed less activity in the left insula and midcingulate gyrus and more activity in the left precuneus than TD children. In addition, reduced activity in the anterior cingulate cortex was correlated with symptom severity in children with ASD. Thus, this MEG study identified the precise timing and sources of atypical WM-related activity in frontal, temporal and parietal regions in children with ASD. The potential impacts of such atypicalities on social deficits of autism are discussed.
Concave or convex π-dimers: the role of the pancake bond in substituted phenalenyl radical dimers
Authors: Cui Zhong-hua , Gupta Abhinav , Lischka Hans , Kertesz Miklos
Published: August 2015

π-stacking phenalenyl radical dimers are overwhelmingly convex (a) and not concave (b) due to electron sharing at the SOMO centers.
ICP-MS/MS as a tool to study abiotic methylation of inorganic mercury reacting with VOCs
Authors: He Qian , Xing Zhi , Zhang Sichun , Zhang Xinrong
Published: August 2015

In this work, ICP-MS/MS was chosen as a tool for the first time to study abiotic methylation of inorganic mercury reacting with VOCs in a gas environment.
Three dimensional nitrogen-doped graphene hydrogels with in situ deposited cobalt phosphate nanoclusters for efficient oxygen evolution in a neutral electrolyte
Authors: Vasileff Anthony , Chen Sheng , Qiao Shi Zhang
Published: August 2015

Nitrogen doped graphene hydrogel electrocatalysts with in situ deposited cobalt phosphate demonstrated excellent catalytic performance toward oxygen evolution in a neutral electrolyte.
Highly facile and efficient assembly of palladium nanoparticles on polystyrene microspheres and their application in catalysis
Authors: Li Yunxing , Wu Zhengfeng , Ye Sunjie
Published: August 2015

Herein we develop a facile and effective strategy for the synthesis of composite particles composed of polystyrene microspheres decorated with palladium nanoparticles, which exhibited excellent catalytic activity and stability towards the reduction of p-nitrophenol by NaBH4.
Probing resistivity and doping concentration of semiconductors at the nanoscale using scanning microwave microscopy
Authors: Brinciotti Enrico , Gramse Georg , Hommel Soeren , Schweinboeck Thomas , Altes Andreas , Fenner Matthias A. , Smoliner Juergen , Kasper Manuel , Badino Giorgio , Tuca Silviu-Sorin , Kienberger Ferry
Published: August 2015

A new method to probe the resistivity and dopant concentration of semiconductors with nanoscale resolution using SMM is presented.
Overview on in vitro and in vivo investigations of nanocomposite based cancer diagnosis and therapeutics
Authors: Subramanian A. P. , Jaganathan S. K. , Supriyanto Eko
Published: August 2015

The nanodevices are synthesized using nanocomposites by the researchers around the globe. Most of their applications are related to in vivo visualization and therapy with anticancer drugs in the field of oncology.
Review on the extraction, characterization and application of soybean polysaccharide
Authors: Jia Xuejing , Chen Meiwan , Wan Jian-Bo , Su Huanxing , He Chengwei
Published: August 2015

In this review, we critically appraise the latest literature on the extraction and the structural features of SPS, and provide a perspective on the biological applications of SPS.
Three-dimensional NiCo2O4 nanowire arrays: preparation and storage behavior for flexible lithium-ion and sodium-ion batteries with improved electrochemical performance
Authors: Mo Yudi , Ru Qiang , Chen Junfen , Song Xiong , Guo Lingyun , Hu Shejun , Peng Shaomin
Published: August 2015

The as-prepared 3D NCO@CFC nanowire arrays show high reversible capacity, excellent cycling stability, and good rate capability when used as an anode material for LIBs and SIBs.
The role of natural selection in circadian behaviour: a molecular-genetic approach
Authors: Rosato Ezio , Kyriacou Charalambos P
Published: August 2015

Circadian rhythms (~24 h) in biochemistry, physiology and behaviour are found in almost all eukaryotes and some bacteria. The elucidation of the molecular components of the 24 h circadian clock in a number of model organisms in recent years has provided an opportunity to assess the adaptive value of variation in clock genes. Laboratory experiments using artificially generated mutants reveal that the circadian period is adaptive in a 24 h world. Natural genetic variation can also be studied, and there are a number of ways in which the signature of natural selection can be detected. These include the study of geographical patterns of genetic variation, which provide a first indication that selection may be at work, and the use of sophisticated statistical neutrality tests, which examine whether the pattern of variation observed is consistent with a selective rather than a neutral (or drift) scenario. Finally, examining the probable selective agents and their differential effects on the circadian phenotype of the natural variants provides the final compelling evidence for selection. We present some examples of how these types of analyses have not only enlightened the evolutionary study of clocks, but have also contributed to a more pragmatic molecular understanding of the function of clock proteins.
Gene expression regulation in trypanosomatids
Authors: De Gaudenzi Javier G. , Noé Griselda , Campo Vanina A. , Frasch Alberto C. , Cassola Alejandro
Published: August 2015

Trypanosomatids are protozoan micro-organisms that cause serious health problems in humans and domestic animals. In addition to their medical relevance, these pathogens have novel biological structures and processes. From nuclear DNA transcription to mRNA translation, trypanosomes use unusual mechanisms to control gene expression. For example, transcription by RNAPII (RNA polymerase II) is polycistronic, and only a few transcription initiation sites have been identified so far. The sequences present in the polycistronic units code for proteins having unrelated functions, that is, not involved in a similar metabolic pathway. Owing to these biological constraints, these micro-organisms regulate gene expression mostly by post-transcriptional events. Consequently, the function of proteins that recognize RNA elements preferentially at the 3′ UTR (untranslated region) of transcripts is central. It was recently shown that mRNP (messenger ribonucleoprotein) complexes are organized within post-transcriptional operons to co-ordinately regulate gene expression of functionally linked transcripts. In the present chapter we will focus on particular characteristics of gene expression in the so-called TriTryp parasites: Trypanosoma cruzi, Trypanosoma brucei and Leishmania major.
Cytochrome P450s and chemoprevention
Authors: Henderson C.J. , Sahraouei A. , Wolf C. R.
Published: August 2015

The cytochrome P450 mono-oxygenase system represents a major defence against chemical challenge from the environment, constituting part of an adaptive response mounted by an organism following exposure to harmful agents. Cytochrome P450s are also able to catalyse the activation of compounds to toxic products, and participate in a variety of essential ‘housekeeping’ functions, such as biosynthesis of steroid hormones and fatty acid oxidation. It is clear that the modulation of expression of these enzymes can have a significant effect on chemical toxicity, carcinogenicity and mutagenicity. The concept of cancer chemoprevention, i.e. the administration of a (non-toxic) chemical or dietary component in order to prevent neoplastic disease or to inhibit its progression, is an attractive one. Despite this, relatively little work has been done to characterize the ability of putative chemopreventive agents to modulate P450 expression, or to understand the interaction between P450s and chemopreventive agents. Before chemopreventive treatment can become a reality, it is essential that this complex issue is addressed; for instance, it is likely that any single chemopreventive agent will induce more than one P450 isoenzyme, and while altered expression of a particular P450 may attenuate the effects of one toxic agent, the effects of others might well be potentiated. Our laboratory has created a transgenic mouse line in which the rat CYP1A1 promoter drives expression of the β-galactosidase gene. These mice can be used to define which compounds act via the Ah receptor, in which tissues, and at which stage of development. We are currently developing another mouse line in which β-galactosidase expression is controlled by the mouse GstA1 promoter, allowing us to define the role of the antioxidant responsive element in the action of chemopreventive agents. Finally, using cre-1oxP transgenic technology, we have generated a mouse line in which P450 reductase can be deleted in a conditional, i.e. tissue-specific, manner, permitting us to investigate the role of P450s in chemoprevention in a more defined manner.
Two-photon fluorescence excitation in detection of biomolecules
Authors: Soini E. , Meltola N. J. , Soini A. E. , Soukka J. , Soini J. T. , Hänninen P. E.
Published: August 2015

Two-photon fluorescence excitation has been found to be a very powerful method for enhancing the sensitivity and resolution in far-field light microscopy. Two-photon fluorescence excitation also provides a substantially background-free detection on the single-molecule level. It allows direct monitoring of formation of labelled bio-molecule complexes in solution. Two-photon excitation is created when, by focusing an intensive light source, the density of photons per unit volume and per unit time becomes high enough for two photons to be absorbed into the same chromophore. In this case, the absorbed energy is the sum of the energies of the two photons. In two-photon excitation, dye molecules are excited only when both photons are absorbed simultaneously. The probability of absorption of two photons is equal to the product of probability distributions of absorption of the single photons. The emission of two photons is thus a quadratic process with respect to illumination intensity. Thus in two-photon excitation, only the fluorescence that is formed in the clearly restricted three-dimensional vicinity of the focal point is excited. We have developed an assay concept that is able to distinguish optically between the signal emitted from a microparticle in the focal point of the laser beam, and the signal emitted from the surrounding free labelled reagent. Moreover, the free labels outside the focal volume do not contribute any significant signal. This means that the assay is separation-free. The method based on two-photon fluorescence excitation makes possible fast single-step and separation-free immunoassays, for example, for whole blood samples. Since the method allows a separation-free assay in very small volumes, the method is very useful for high-throughput screening assays. Consequently we believe that two-photon fluorescence excitation will make a remarkable impact as a research tool and a routine method in many fields of analysis.
Function of the mitochondrial outer membrane as a diffusion barrier in health and diseases
Authors: Gellerich F. N. , Trumbeckaite S. , Opalka J. R. , Seppet E. , Rasmussen H. N. , Neuhoff C. , Zierz S.
Published: August 2015

The mitochondrial outer membrane separates the intermembrane space from the cytosol. The whole exchange of metabolites, cations and information between mitochondria and the cell occurs through the outer membrane. Experimental evidence is reviewed supporting the hypothesis of dynamic ADP compartmentation within the intermembrane space. The outer membrane creates a diffusion barrier for small molecules (adenine nucleotides, creatine phosphate, creatine etc.) causing rate-dependent concentration gradients as a prerequisite for the action of ADP shuttles via creatine kinases or adenylate kinases. If the outer membrane becomes leaky, cytochrome c and apoptosis-inducing factor can be released, leading to apoptosis, and as a bioenergetic consequence the cytosolic phosphorylation potential decreases. Leaky outer membranes can be detected in saponin-skinned fibres with spectrophotometric and oxygraphic methods. This is of special interest in respect to acute impairment of mitochondria during ischaemia/reperfusion.
Reaction mechanism and phospholipid structures of bovine heart cytochrome c oxidase
Authors: Yoshikawa S.
Published: August 2015

Bovine heart cytochrome c oxidase is a large multi-component membrane protein containing several phospholipids. X-ray structures of this enzyme at high resolution, determined recently, show a trigonal planar structure of CuB site in the O2 reduction site, which could contribute critically to the four-electron reduction of O2 bound at haem a3, and a hydrogen bond network, through which the proton pump is driven by haem a. The possible roles of phospholipids in the enzyme functions are discussed.
Organ specificity in the circadian control of plant gene expression
Authors: Sullivan S. , Shenton M. , Nimmo H.G.
Published: August 2015

Of the many plant genes whose expressions are controlled by the circadian clock, one of the phosphoenolpyruvate carboxylase kinase genes in soya bean (Glycine max) exhibits the unusual property that its control is organ-specific – it is under circadian control in leaves but not in roots. Preliminary experiments suggest that the same is true for at least one gene in Arabidopsis thaliana. It will be important to define the extent and function of this phenomenon and the underlying mechanism.
Zebrafish circadian clocks: cells that see light
Authors: Tamai T.K. , Carr A.J. , Whitmore D.
Published: August 2015

In the classical view of circadian clock organization, the daily rhythms of most organisms were thought to be regulated by a central, ‘master’ pacemaker, usually located within neural structures of the animal. However, with the results of experiments performed in zebrafish, mammalian cell lines and, more recently, mammalian tissues, this view has changed to one where clock organization is now seen as being highly decentralized. It is clear that clocks exist in the peripheral tissues of animals as diverse as Drosophila, zebrafish and mammals. In the case of Drosophila and zebrafish, these tissues are also directly light-responsive. This light sensitivity and direct clock entrainability is also true for zebrafish cell lines and early-stage embryos. Using luminescent reporter cell lines containing clock gene promoters driving the expression of luciferase and single-cell imaging techniques, we have been able to show how each cell responds rapidly to a single light pulse by being shifted to a common phase, equivalent to the early day. This direct light sensitivity might be related to the requirement for light in these cells to activate the transcription of genes involved in DNA repair. It is also clear that the circadian clock in zebrafish regulates the timing of the cell cycle, demonstrating the wide impact that this light sensitivity and daily rhythmicity has on the biology of zebrafish.
Protein import into mitochondria
Authors: Mokranjac D. , Neupert W.
Published: August 2015

Mitochondria comprise approx. 1000–3000 different proteins, almost all of which must be imported from the cytosol into the organelle. So far, six complex molecular machines, protein translocases, were identified that mediate this process. The TIM23 complex is a major translocase in the inner mitochondrial membrane. It uses two energy sources, namely membrane potential and ATP, to facilitate preprotein translocation across the inner membrane and insertion into the inner membrane. Recent research has led to the discovery of a number of new constituents of the TIM23 complex and to the unravelling of the mechanisms of preprotein translocation.
The complexity of pathways for protein import into thylakoids: it's not easy being green
Authors: Di Cola A. , Klostermann E. , Robinson C.
Published: August 2015

Numerous proteins are transported into or across the chloroplast thylakoid membrane. To date, two major pathways have been identified for the transport of luminal proteins (the Sec- and Tat-dependent pathways) and it is now clear that these protein translocases use fundamentally different transport mechanisms. Integral membrane proteins are inserted by means of at least two further pathways. One involves the input of numerous targeting factors, including SRP (signal recognition particle), FtsY and Albino3. Surprisingly, the other pathway does not involve any of the known chloroplastic targeting factors, and insertion is energy-independent, raising the possibility of an unusual ‘spontaneous’ insertion mechanism.
Adipose tissue function in the insulin-resistance syndrome
Authors: Karpe F. , Tan G.D.
Published: August 2015

Insulin resistance is often seen as a consequence of obesity and there are several possible links between adipose tissue function and insulin resistance determined in other organs such as skeletal muscle or liver. One such link is the regulation of NEFA (non-esterified fatty acid) delivery to the rest of the body. Simplistically, an expanded adipose tissue mass delivers more NEFA to the systemic circulation and these fatty acids compete for substrate utilization in skeletal muscle, which in turn reduces glucose utilization. This increases blood glucose concentration and provides the stimulus for increased insulin secretion and hyperinsulinaemia is a key feature of the insulin-resistance syndrome. However, there is abundant evidence that adipose tissue is exquisitely insulin sensitive and hyperinsulinaemia may therefore lead to a constant lipolytic inhibition in adipose tissue. Consequently, the main function of adipose tissue, to rapidly switch between fat uptake and fat release, will be hampered. Adipose tissue blood flow is the conveyor of signals and substrates to and from the adipose tissue. In healthy people adipose tissue blood flow is much enhanced by food intake, whereas in insulin-resistant subjects this response is blunted. This is another facet of unresponsiveness of adipose tissue in the insulin-resistance syndrome.
Protein lipidation of BACE
Authors: Parsons R.B. , Austen B.M.
Published: August 2015

Our research has concentrated upon the protein lipid modification of BACE [β-site amyloid precursor protein cleaving enzyme (β-secretase)], of which very little is currently known. Lipidation influences the production of Aβ (amyloid β-protein) by promoting the dimerization of BACE.
Protein and lipid motifs regulate phosphatidylserine traffic in yeast
Authors: Voelker D.R.
Published: August 2015

Phosphatidylserine (PtdSer) is synthesized in the endoplasmic reticulum and its subdomains associated with the mitochondria [MAM (mitochondria-associated membrane)] and subsequently transported to the loci of the PtdSer decarboxylases, Pds1p (phosphatidylserine decarboxylase 1 encoded by the PSD1 gene that complements psd1 mutations) in the mitochondria, and Psd2p (PtdSer decarboxylase 2 encoded by the PSD2 gene that complements psd2 mutations) in the Golgi. Decarboxylation of PtdSer to PtdEtn (phosphatidylethanolamine) can be used as a biochemical indicator of transport to these organelles, which is regulated by specific lipid and protein motifs. PtdSer transport to mitochondria is controlled by ubiquitination via the action of the ubiquitin ligase subunit Met30p (a ubiquitin ligase subunit encoded by the MET30 gene that complements the met30 mutation affecting methionine biosynthesis). Mutant strains with lesions in the MET30 gene are defective in PtdSer transport and show altered ubiquitination of specific target proteins, such as the transcription factor Met4p (a transcription factor encoded by the MET4 gene that complements the met4 mutation affecting methionine biosynthesis). Mutations to MET30 cause defects in both the MAM as a donor of PtdSer, and the mitochondria as an acceptor of PtdSer in the transport reaction. PtdSer transport to the locus of Psd2p is controlled by specific protein and lipid motifs. The C2 (Ca2+ and phospholipid-binding sequence) domain of Psd2p, and the lipid-binding protein PstB2p (PtdSer transport B pathway protein encoded by the PSTB2 gene that complements the pstB2 mutation affecting PtdSer transport), must be present on acceptor membranes for PtdSer transport to occur. In addition, the action of the PtdIns 4-kinase, Stt4p (PtdIns 4-kinase encoded by the STT4 gene that complements the stt4 mutation causing staurosporine and temperature-sensitive growth) is also required for PtdSer transport to the locus of Psd2p. Reconstitution of PtdSer transport to Psd2p using liposomes demonstrates that PtdSer-rich domains present in vesicles are preferred substrates for transport. In addition, the incorporation of phosphatidic acid into donor membranes enhances the rate of PtdSer transport. Collectively, these data support a model for PtdSer transport in which specific proteins and lipids are required on donor and acceptor membranes.
Azole susceptibility and resistance in Candida dubliniensis
Authors: Pinjon E. , Moran G.P. , Coleman D.C. , Sullivan D.J.
Published: August 2015

Candida dubliniensis is a recently described species of pathogenic yeast that shares many phenotypic features with Candida albicans. It is primarily associated with oral colonization and infection in HIV-infected individuals. Isolates of C. dubliniensis are generally susceptible to commonly used azole antifungal agents; however, resistance has been observed in clinical isolates and can be induced by in vitro exposure. Molecular mechanisms of azole resistance in C. dubliniensis include increased drug efflux, modifications of the target enzyme and alterations in the ergosterol biosynthetic pathway.
Phosphoinositide regulation of clathrin-mediated endocytosis
Authors: Haucke V.
Published: August 2015

Endocytosis of transmembrane receptors largely occurs via clathrin-coated vesicles that bud from the plasma membrane and deliver their cargo to the endosomal system for recycling or degradation. PIs (phosphoinositides) control the timing and localization of endocytic membrane trafficking by recruiting adaptors and other components of the transport machinery, thereby being part of a coincidence detection system in adaptor-mediated vesicle transport. Activation of organelle- and substrate-specific PI kinases by small GTPases such as Arf (ADP-ribosylation factor) and other factors may result in local changes of PI content, thereby regulating activity-dependent endocytic events including the recycling of synaptic vesicle membranes at nerve terminals. One such example is the PtdIns(4)P 5-kinase-mediated formation of PI(4,5)P2 [PtdIns(4,5)P2], which is required for the exo- and endo-cytic cycling of presynaptic vesicles and secretory granules. Over the last few years, protein X-ray crystallography in combination with biochemical and cell biological assays has been used to investigate the structure and function of many PI-binding proteins, including protein components of the endocytic machinery. These studies have provided molecular insights into the mechanisms by which PI(4,5)P2 recruits and activates adaptor proteins and their binding partners. In this mini-review, I will discuss the pathways of PI(4,5)P2 formation and its interactions with endocytic trafficking adaptors.
Microtubule-associated proteins (MAPs) regulate cAMP signalling through exchange protein directly activated by cAMP (EPAC)
Authors: Yarwood S.J.
Published: August 2015

cAMP is an essential signalling molecule whose concentration in cells is regulated by a wide range of hormones. A large number of diseases, including cancer and asthma, are linked to improper regulation of the cAMP signalling system, and manipulation of cAMP levels by pharmaceutical agents has proven therapeutic benefit. The action of cAMP in cells is mediated through the signalling enzymes PKA (protein kinase A) and EPAC (exchange protein directly activated by cAMP). The study of the function of these proteins is essential to understand the role of cAMP in controlling disease. We have found that EPAC interacts with an ancillary protein, called LC2 (light chain 2), and this interaction enhances EPAC's ability to activate its substrate protein, Rap1 GTPase. This is an important finding because Rap1 is involved in the control of cell migration and cell shape, functions that are disrupted in diseases like cancer. LC2 appears to enhance EPAC activity towards Rap1 by increasing the ability of EPAC to interact with cAMP, so that EPAC activation occurs at lower concentrations of cAMP. The design of inhibitors that disrupt or enhance EPAC1–LC2 interaction may therefore form the basis of future therapeutics for diseases where cAMP signalling through Rap1 is improperly regulated.
Regulation of exocytosis by protein kinase C
Authors: Morgan A. , Burgoyne R.D. , Barclay J.W. , Craig T.J. , Prescott G.R. , Ciufo L.F. , Evans G.J.O. , Graham M.E.
Published: August 2015

PKC (protein kinase C) has been known for many years to modulate regulated exocytosis in a wide variety of cell types. In neurons and neuroendocrine cells, PKC regulates several different stages of the exocytotic process, suggesting that these multiple actions of PKC are mediated by phosphorylation of distinct protein targets. In recent years, a variety of exocytotic proteins have been identified as PKC substrates, the best characterized of which are SNAP-25 (25 kDa synaptosome-associated protein) and Munc18. In the present study, we review recent evidence suggesting that site-specific phosphorylation of SNAP-25 and Munc18 by PKC regulates distinct stages of exocytosis.
RIM function in short- and long-term synaptic plasticity
Authors: Kaeser P.S. , Südhof T.C.
Published: August 2015

RIM1α (Rab3-interacting molecule 1α) is a large multidomain protein that is localized to presynaptic active zones [Wang, Okamoto, Schmitz, Hofmann and Südhof (1997) Nature (London) 388, 593–598] and is the founding member of the RIM protein family that also includes RIM2α, 2β, 2γ, 3γ and 4γ [Wang and Südhof (2003) Genomics 81, 126–137]. In presynaptic nerve termini, RIM1α interacts with a series of presynaptic proteins, including the synaptic vesicle GTPase Rab3 and the active zone proteins Munc13, liprins and ELKS (a protein rich in glutamate, leucine, lysine and serine). Mouse KOs (knockouts) revealed that, in different types of synapses, RIM1α is essential for different forms of synaptic plasticity. In CA1-region Schaffer-collateral excitatory synapses and in GABAergic synapses (where GABA is γ-aminobutyric acid), RIM1α is required for maintaining normal neurotransmitter release and short-term synaptic plasticity. In contrast, in excitatory CA3-region mossy fibre synapses and cerebellar parallel fibre synapses, RIM1α is necessary for presynaptic long-term, but not short-term, synaptic plasticity. In these synapses, the function of RIM1α in presynaptic long-term plasticity depends, at least in part, on phosphorylation of RIM1α at a single site, suggesting that RIM1α constitutes a ‘phosphoswitch’ that determines synaptic strength. However, in spite of the progress in understanding RIM1α function, the mechanisms by which RIM1α acts remain unknown. For example, how does phosphorylation regulate RIM1α, what is the relationship of the function of RIM1α in basic release to synaptic plasticity and what is the physiological significance of different forms of RIM-dependent plasticity? Moreover, the roles of other RIM isoforms are unclear. Addressing these important questions will contribute to our view of how neurotransmitter release is regulated at the presynaptic active zone.
Thiol redox control via thioredoxin and glutaredoxin systems
Authors: Holmgren A. , Johansson C. , Berndt C. , Lönn M.E. , Hudemann C. , Lillig C.H.
Published: August 2015

The Trx (thioredoxin) and Grx (glutaredoxin) systems control cellular redox potential, keeping a reducing thiol-rich intracellular state, which on generation of reactive oxygen species signals through thiol redox control mechanisms. Here, we give a brief overview of the human Trx and Grx systems. The main part focuses on our current knowledge about mitochondrial Grx2, which facilitates mitochondrial redox homoeostasis during oxidative stress-induced apoptosis.
Transcriptional control by chromosome-associated protein phosphatase-1
Authors: Bennett D.
Published: August 2015

Tight regulation of gene expression is critical for cells to respond normally to physiological and environmental cues and to allow cell specialization. Reversible phosphorylation of key structural and regulatory proteins, from histones to the transcriptional machinery, is acknowledged to be an important mechanism of regulating spatial and temporal patterns of gene expression. PP1 (protein phosphatase-1), a major class of serine/threonine protein phosphatase, is found at many sites on Drosophila polytene chromosomes where it is involved in controlling gene expression and chromatin structure. PP1 is targeted to different chromosomal loci through interaction with a variety of different regulatory subunits, which modify PP1's activity towards specific substrates. This mini-review gives an overview of known chromosome-associated PP1 complexes, their role in transcriptional control and the prospects for future analysis.
Helicase-catalysed translocation and strand separation
Authors: Eoff R.L. , Raney K.D.
Published: August 2015

Helicases are molecular-motor enzymes that manipulate DNA or RNA during replication, repair, recombination, transcription, translation and processing of nucleic acids. The mechanisms for helicase activity have been studied intensely over the past decade. Recent advances in our understanding of the helicase mode of action have led to a general convergence of models that describe this diverse class of enzymes. One mechanism has been proposed that appears to have withstood the test of time, namely the inchworm mechanism. As the name implies, this mechanism involves a process whereby a helicase maintains at least two sites of contact with the nucleic acid. These binding sites can move relative to one another in a sequential fashion, resulting in net movement of the enzyme along the nucleic acid. The inchworm mechanism appears to be applicable to oligomeric states beyond the simple monomeric molecular motor. Although there are certainly many pertinent questions that remain unanswered, striking similarities in both form and function of seemingly disparate enzymes are becoming evident.
Post-transcriptional regulation in Xenopus embryos: role and targets of EDEN-BP
Authors: Osborne H.B. , Gautier-Courteille C. , Graindorge A. , Barreau C. , Audic Y. , Thuret R. , Pollet N. , Paillard L.
Published: August 2015

EDEN (embryo deadenylation element)-dependent deadenylation is a regulatory process that was initially identified in Xenopus laevis early embryos and was subsequently shown to exist in Drosophila oocytes. Recent data showed that this regulatory process is required for somitic segmentation in Xenopus. Inactivation of EDEN-BP (EDEN-binding protein) causes severe segmentation defects, and the expression of segmentation markers in the Notch signalling pathway is disrupted. We showed that the mRNA encoding XSu(H) (Xenopus suppressor of hairless), a protein central to the Notch pathway, is regulated by EDEN-BP. Our data also indicate that other segmentation RNAs are targets for EDEN-BP. To identify new EDEN-BP targets, a microarray analysis has been undertaken.
Paneth cell defensins: key effector molecules of innate immunity
Authors: Bevins C.L.
Published: August 2015

Antimicrobial peptides are fundamental effector molecules of innate immunity, utilized in host defence by virtually all organisms studied. These gene-encoded peptides have direct antibiotic activity against a wide range of bacteria and other microbes. In humans and other mammals, defensins are a predominant class of such peptides. In the mammalian small intestine, Paneth cells, specialized secretory epithelial cells located at the base of the crypt invaginations lining the intestinal wall, produce defensins and other antibiotic proteins. Recent investigations in murine models provide compelling support for the hypothesis that enteric defensins play a pivotal role in defence from food- and water-borne pathogens in the intestinal lumen. Investigations by others indicate that intestinal commensal bacteria are key factors in the pathogenesis of IBD (inflammatory bowel disease) in genetically susceptible humans. Recent studies provide evidence that reduced expression of Paneth cell defensins may be a key factor in the pathogenesis of ileal Crohn's disease, a subgroup of IBD. Future studies to further define the function and regulation of Paneth cell defensins will enhance our understanding of normal small bowel physiology, and probably contribute to a better understanding of the pathogenesis of inflammatory and infectious diseases of the bowel. Such knowledge may provide new therapeutic targets and strategies.
Biocatalytic approaches for the quantitative production of single stereoisomers from racemates
Authors: Gadler P. , Glueck S.M. , Kroutil W. , Nestl B.M. , Larissegger-Schnell B. , Ueberbacher B.T. , Wallner S.R. , Faber K.
Published: August 2015

Strategies for the chemoenzymatic transformation of a racemate into a single stereoisomeric product in quantitative yield have been developed. A range of industrially relevant α-hydroxycarboxylic acids was deracemized in a stepwise fashion via lipase-catalysed enantioselective O-acylation, followed by mandelate racemase-catalysed racemization of the remaining non-reacted substrate enantiomer. Alternatively, aliphatic α-hydroxycarboxylic acids were enzymatically isomerized using whole resting cells of Lactobacillus spp. Enantioselective hydrolysis of rac-sec-alkyl sulphate esters was accomplished using novel alkyl sulphatases of microbial origin. The stereochemical path of catalysis could be controlled by choice of the biocatalyst. Whereas Rhodococcus ruber DSM 44541 and Sulfolobus acidocaldarius DSM 639 act through inversion of configuration, stereo-complementary retaining sulphatase activity was detected in the marine planctomycete Rhodopirellula baltica DSM 10527.
DNA mimicry by proteins
Authors: Dryden D.T.F. , Tock M.R.
Published: August 2015

It has been discovered recently, via structural and biophysical analyses, that proteins can mimic DNA structures in order to inhibit proteins that would normally bind to DNA. Mimicry of the phosphate backbone of DNA, the hydrogen-bonding properties of the nucleotide bases and the bending and twisting of the DNA double helix are all present in the mimics discovered to date. These mimics target a range of proteins and enzymes such as DNA restriction enzymes, DNA repair enzymes, DNA gyrase and nucleosomal and nucleoid-associated proteins. The unusual properties of these protein DNA mimics may provide a foundation for the design of targeted inhibitors of DNA-binding proteins.
Tn5 transposition: a molecular tool for studying protein structure–function
Authors: Reznikoff W.S.
Published: August 2015

Transposon-based technologies are important genetic tools for global genome analysis and, as discussed in the present paper, in detailed studies of protein structure–function. Various different transposition systems can be used in these studies but this paper uses Tn5-related systems as a model. In particular, the following four different technologies are described in this paper: (i) using transposition to generate nested deletion families, (ii) using transposons to generate functional protein fusions to reporter functions, (iii) mapping protein secondary structures through the generation and analysis of in-frame linker insertions and (iv) using sequential transposition events to generate random gene fusions. The success of these forward genetic technologies requires that the transposition system be efficient and manifest near-random target sequence selection.