bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular characterization of Chikungunya virus isolates from clinical samples and adult Aedes albopictus mosquitoes emerged from larvae from Kerala, South India
Authors: Niyas Kudukkil P , Abraham Rachy , Unnikrishnan Ramakrishnan Nair , Mathew Thomas , Nair Sajith , Manakkadan Anoop , Issac Aneesh , Sreekumar Easwaran 
Published: August 2010

Abstract
Chikungunya virus (CHIKV), an arthritogenic alphavirus, is transmitted to humans by infected Aedes (Ae.) aegypti and Ae.albopictus mosquitoes. In the study, reverse-transcription PCR (RT PCR) and virus isolation detected CHIKV in patient samples and also in adult Ae.albopictus mosquitoes that was derived from larvae collected during a chikungunya (CHIK) outbreak in Kerala in 2009. The CHIKV strains involved in the outbreak were the East, Central and South African (ECSA) genotype that had the E1 A226V mutation. The viral strains from the mosquitoes and CHIK patients from the same area showed a close relationship based on phylogenetic analysis. Genetic characterization by partial sequencing of non-structural protein 2 (nsP2; 378 bp), envelope E1 (505 bp) and E2 (428 bp) identified one critical mutation in the E2 protein coding region of these CHIKV strains. This novel, non-conservative mutation, L210Q, consistently present in both human and mosquito-derived samples studied, was within the region of the E2 protein (amino acids E2 200-220) that determines mosquito cell infectivity in many alpha viruses. Our results show the involvement of Ae. albopictus in this outbreak in Kerala and appearance of CHIKV with novel genetic changes. Detection of virus in adult mosquitoes, emerged in the laboratory from larvae, also points to the possibility of transovarial transmission (TOT) of mutant CHIKV strains in mosquitoes.
Systems analysis of iron metabolism: the network of iron pools and fluxes
Authors: Lopes Tiago JS , Luganskaja Tatyana , Vujić Spasić Maja , Hentze Matthias W , Muckenthaler Martina U , Schümann Klaus , Reich Jens G 
Published: August 2010

Abstract

Background
Every cell of the mammalian organism needs iron as trace element in numerous oxido-reductive processes as well as for transport and storage of oxygen. The very versatility of ionic iron makes it a toxic entity which can catalyze the production of radicals that damage vital membranous and macromolecular assemblies in the cell. The mammalian organism maintains therefore a complex regulatory network of iron uptake, excretion and intra-body distribution. Intracellular regulation in different cell types is intertwined with a global hormonal signalling structure. Iron deficiency as well as excess of iron are frequent and serious human disorders. They can affect every cell, but also the organism as a whole.

Results
Here, we present a kinematic model of the dynamic system of iron pools and fluxes. It is based on ferrokinetic data and chemical measurements in C57BL6 wild-type mice maintained on iron-deficient, iron-adequate, or iron-loaded diet. The tracer iron levels in major tissues and organs (16 compartment) were followed for 28 days. The evaluation resulted in a whole-body model of fractional clearance rates. The analysis permits calculation of absolute flux rates in the steady-state, of iron distribution into different organs, of tracer-accessible pool sizes and of residence times of iron in the different compartments in response to three states of iron-repletion induced by the dietary regime.

Conclusions
This mathematical model presents a comprehensive physiological picture of mice under three different diets with varying iron contents. The quantitative results reflect systemic properties of iron metabolism: dynamic closedness, hierarchy of time scales, switch-over response and dynamics of iron storage in parenchymal organs.
Therefore, we could assess which parameters will change under dietary perturbations and study in quantitative terms when those changes take place.
The NRF2-mediated oxidative stress response pathway is associated with tumor cell resistance to arsenic trioxide across the NCI-60 panel
Authors: Liu Qian , Zhang Hao , Smeester Lisa , Zou Fei , Kesic Matt , Jaspers Ilona , Pi Jingbo , Fry Rebecca C 
Published: August 2010

AbstractBackgroundDrinking water contaminated with inorganic arsenic is associated with increased risk for different types of cancer. Paradoxically, arsenic trioxide can also be used to induce remission in patients with acute promyelocytic leukemia (APL) with a success rate of approximately 80%. A comprehensive study examining the mechanisms and potential signaling pathways contributing to the anti-tumor properties of arsenic trioxide has not been carried out.MethodsHere we applied a systems biology approach to identify gene biomarkers that underlie tumor cell responses to arsenic-induced cytotoxicity. The baseline gene expression levels of 14,500 well characterized human genes were associated with the GI50data of the NCI-60 tumor cell line panel from the developmental therapeutics program (DTP) database. Selected biomarkers were testedin vitrofor the ability to influence tumor susceptibility to arsenic trioxide.ResultsA significant association was found between the baseline expression levels of 209 human genes and the sensitivity of the tumor cell line panel upon exposure to arsenic trioxide. These genes were overlayed onto protein-protein network maps to identify transcriptional networks that modulate tumor cell responses to arsenic trioxide. The analysis revealed a significant enrichment for the oxidative stress response pathway mediated by nuclear factor erythroid 2-related factor 2 (NRF2) with high expression in arsenic resistant tumor cell lines. The role of the NRF2 pathway in protecting cells against arsenic-induced cell killing was validated in tumor cells using shRNA-mediated knock-down.ConclusionsIn this study, we show that the expression level of genes in the NRF2 pathway serve as potential gene biomarkers of tumor cell responses to arsenic trioxide. Importantly, we demonstrate that tumor cells that are deficient for NRF2 display increased sensitivity to arsenic trioxide. The results of our study will be useful in understanding the mechanism of arsenic-induced cytotoxicity in cells, as well as the increased applicability of arsenic trioxide as a chemotherapeutic agent in cancer treatment.
Nitric oxide in the control of luminescence from lantern shark (Etmopterus spinax) photophores
Authors: Claes Julien M. , Krönström Jenny , Holmgren Susanne , Mallefet Jérôme 
Published: August 2010

SUMMARY
Photophores (photogenic organs) of the lantern shark Etmopterus spinax are under hormonal control, with prolactin (PRL) and melatonin (MT) triggering the light emission. Differential sensitivity to these hormones in adult individuals suggests, however, that the luminescence of this shark is controlled by an additional mechanism. In this study, different techniques were used to investigate a potential modulator of E. spinax luminescence – nitric oxide (NO). NO synthase (NOS)-like immunoreactivity (IR) was found in the photocytes (photogenic cells) of the photophores. In addition, acetylated tubulin IR also supported the presence of nerves running through the photogenic tissue and innervating different structural elements of the photophores: photocytes, pigmented cells from the iris-like structure and lens cells. Pharmacological experiments confirmed a modulatory action of NO on the hormonally induced luminescence: NO donors sodium nitroprusside (SNP) and hydroxylamine decreased the time to reach the maximum amplitude (TLmax) of MT-induced luminescence while these substances decreased the maximum amplitude of PRL-induced luminescence (and also the TLmax in the case of SNP). The small impact of the NOS inhibitor l-NAME on hormonally induced luminescence suggests that NO is only produced on demand. The cGMP analogue 8BrcGMP mimicked the effects of NO donors suggesting that the effects of NO are mediated by cGMP.
Reliable detection of predator cues in afferent spike trains of a katydid under high background noise levels
Authors: Hartbauer Manfred , Radspieler Gerald , Römer Heiner 
Published: August 2010

SUMMARYKatydid receivers face the problem of detecting behaviourally relevant predatory cues from echolocating bats in the same frequency domain as their own conspecific mating signals. We therefore tested the hypothesis that katydids are able to detect the presence of insectivorous bats in spike discharges at early stages of nervous processing in the auditory pathway by using the temporal details characteristic for responses to echolocation sequences. Spike activity was recorded from an identified nerve cell (omega neuron) under both laboratory and field conditions. In the laboratory, the preparation was stimulated with sequences of bat calls at different repetition rates typical for the guild of insectivorous bats, in the presence of background noise. The omega cell fired brief high-frequency bursts of action potentials in response to each bat sound pulse. Repetition rates of 18 and 24 Hz of these pulses resulted in a suppression of activity resulting from background noise, thus facilitating the detection of bat calls. The spike activity typical for responses to bat echolocation contrasts to responses to background noise, producing different distributions of inter-spike intervals. This allowed development of a ‘neuronal bat detector’ algorithm, optimized to detect responses to bats in afferent spike trains. The algorithm was applied to more than 24 hours of outdoor omega-recordings performed either at a rainforest clearing with high bat activity or in rainforest understory, where bat activity was low. In 95% of cases, the algorithm detected a bat reliably, even under high background noise, and correctly rejected responses when an electronic bat detector showed no response.
Application of the two-sample doubly labelled water method alters behaviour and affects estimates of energy expenditure in black-legged kittiwakes
Authors: Schultner Jannik , Welcker Jorg , Speakman John R. , Nordøy Erling S. , Gabrielsen Geir W. 
Published: August 2010

SUMMARYDespite the widespread use of the doubly labelled water (DLW) method in energetic studies of free-ranging animals, effects of the method on study animals are rarely assessed. We studied behavioural effects of two alternative DLW protocols. During two consecutive breeding seasons, 42 parent black-legged kittiwakes received either the commonly used two-sample (TS) or the less invasive single-sample (SS) DLW treatment. A third group served as a non-treated control. We evaluated the effect of treatment with respect to the time birds took to return to their nest after treatment and recaptures, and the nest attendance during DLW measurement periods. We found that TS kittiwakes took on average 20 times longer to return to their nest than SS kittiwakes after initial treatment, and nest attendance was reduced by about 40% relative to control birds. In contrast, nest attendance did not differ between control and SS kittiwakes. Estimates of energy expenditure of SS kittiwakes exceeded those of TS kittiwakes by 15%. This difference was probably caused by TS birds remaining inactive for extended time periods while at sea. Our results demonstrate that the common assumption that the TS DLW method has little impact on the behaviour of study subjects is in some circumstances fallacious. Estimates of energy expenditure derived by the SS approach may thus more accurately reflect unbiased rates of energy expenditure. However, the choice of protocol may be a trade-off between their impact on behaviour, and hence accuracy, and their differences in precision. Adopting procedures that minimize the impact of TS protocols may be useful.
Switching attraction to inhibition: mating-induced reversed role of sex pheromone in an insect
Authors: Barrozo Romina B. , Gadenne Christophe , Anton Sylvia 
Published: August 2010

SUMMARY
In the moth, Agrotis ipsilon, newly mated males cease to be attracted to the female-produced sex pheromone, preventing them from re-mating until the next night, by which time they would have refilled their reproductive glands for a potential new ejaculate. The behavioural plasticity is accompanied by a decrease in neuron sensitivity within the primary olfactory centre, the antennal lobe (AL). However, it was not clear whether the lack of the sexually guided behaviour results from the absence of sex pheromone detection in the ALs, or if they ignore it in spite of detection, or if the sex pheromone itself inhibits attraction behaviour after mating. To test these hypotheses, we performed behavioural tests and intracellular recordings of AL neurons to non-pheromonal odours (flower volatiles), different doses of sex pheromone and their mixtures in virgin and newly mated males. Our results show that, although the behavioural and AL neuron responses to flower volatiles alone were similar between virgin and mated males, the behavioural response of mated males to flower odours was inhibited by adding pheromone doses above the detection threshold of central neurons. Moreover, we show that the sex pheromone becomes inhibitory by differential central processing: below a specific threshold, it is not detected within the AL; above this threshold, it becomes inhibitory, preventing newly mated males from responding even to plant odours. Mated male moths have thus evolved a strategy based on transient odour-selective central processing, which allows them to avoid the risk-taking, energy-consuming search for females and delay re-mating until the next night for a potential new ejaculate.
On the role of copepod antennae in the production of hydrodynamic force during hopping
Authors: Borazjani Iman , Sotiropoulos Fotis , Malkiel Edwin , Katz Joseph 
Published: August 2010

SUMMARYWe integrate high-resolution experimental observations of a freely hopping copepod with three-dimensional numerical simulations to investigate the role of the copepod antennae in production of hydrodynamic force during hopping. The experimental observations revealed a distinctive asymmetrical deformation of the antennae during the power and return strokes, which lead us to the hypothesis that the antennae are active contributors to the production of propulsive force with kinematics selected in nature in order to maximize net thrust. To examine the validity of this hypothesis we carried out numerical experiments using an anatomically realistic, tethered, virtual copepod, by prescribing two sets of antenna kinematics. In the first set, each antenna moves as a rigid, oar-like structure in a reversible manner, whereas in the second set, the antenna is made to move asymmetrically as a deformable structure as revealed by the experiments. The computed results show that for both cases the antennae are major contributors to the net thrust force during hopping, and the results also clearly demonstrate the significant hydrodynamic benefit in terms of thrust enhancement and drag reduction derived from the biologically realistic, asymmetric antenna motion. This finding is not surprising given the low local Reynolds number environment within which the antenna operates, and points to striking similarities between the copepod antenna motion and ciliary propulsion. Finally, the simulations provide the first glimpse into the complex, highly 3-D structure of copepod wakes.
Goal seeking in honeybees: matching of optic flow snapshots?
Authors: Dittmar Laura , Stürzl Wolfgang , Baird Emily , Boeddeker Norbert , Egelhaaf Martin 
Published: August 2010

SUMMARYVisual landmarks guide humans and animals including insects to a goal location. Insects, with their miniature brains, have evolved a simple strategy to find their nests or profitable food sources; they approach a goal by finding a close match between the current view and a memorised retinotopic representation of the landmark constellation around the goal. Recent implementations of such a matching scheme use raw panoramic images (‘image matching’) and show that it is well suited to work on robots and even in natural environments. However, this matching scheme works only if relevant landmarks can be detected by their contrast and texture. Therefore, we tested how honeybees perform in localising a goal if the landmarks can hardly be distinguished from the background by such cues. We recorded the honeybees' flight behaviour with high-speed cameras and compared the search behaviour with computer simulations. We show that honeybees are able to use landmarks that have the same contrast and texture as the background and suggest that the bees use relative motion cues between the landmark and the background. These cues are generated on the eyes when the bee moves in a characteristic way in the vicinity of the landmarks. This extraordinary navigation performance can be explained by a matching scheme that includes snapshots based on optic flow amplitudes (‘optic flow matching’). This new matching scheme provides a robust strategy for navigation, as it depends primarily on the depth structure of the environment.
Zonation of heme synthesis enzymes in mouse liver and their regulation by β-catenin and Ha-ras
Authors: Braeuning Albert , Schwarz Michael 
Published: August 2010

AbstractCytochrome P450 (CYP) hemoproteins play an important role in hepatic biotransformation. Recently, β-catenin and Ha-ras signaling have been identified as players controlling transcription of various CYP genes in mouse liver. The aim of the present study was to analyze the role of β-catenin and Ha-ras in the regulation of heme synthesis. Heme synthesis-related gene expression was analyzed in normal liver, in transgenic mice expressing activated β-catenin or Ha-ras, and in hepatomas. Regulation of the aminolevulinate dehydratase promoter was studiedin vitro. Elevated expression of mRNAs and proteins involved in heme biosynthesis was linked to β-catenin activation in perivenous hepatocytes, in transgenic hepatocytes, and in hepatocellular tumors. Stimulation of the aminolevulinate dehydratase promoter by β-catenin was independent of the β-catenin/T-cell-specific transcription factor dimer. By contrast, activation of Ha-ras repressed heme synthesis-related gene expression. The present data suggest that β-catenin enhances the expression of both CYPs and heme synthesis-related genes, thus coordinating the availability of CYP apoprotein and its prosthetic group heme. The reciprocal regulation of heme synthesis by β-catenin and Ha-ras-dependent signaling supports our previous hypothesis that antagonistic action of these pathways plays a major role in the control of zonal gene expression in healthy mouse liver and aberrant expression patterns in hepatocellular tumors.
Amino acid residues modulating the activities of staphylococcal glutamyl endopeptidases
Authors: Ono Toshio , Ohara-Nemoto Yuko , Shimoyama Yu , Okawara Hisami , Kobayakawa Takeshi , Baba Tomomi T. , Kimura Shigenobu , Nemoto Takayuki K. 
Published: August 2010

AbstractThe glutamyl endopeptidase family of enzymes from staphylococci has been shown to be important virulence determinants of pathogenic family members, such asStaphylococcus aureus. Previous studies have identified the N-terminus and residues from positions 185–195 as potentially important regions that determine the activity of three members of the family. Cloning and sequencing of the new family members fromStaphylococcus caprae(GluScpr) andStaphylococcus cohnii(GluScoh) revealed that the N-terminal Val residue is maintained in all family members. Mutants of the GluV8 enzyme fromS. aureuswith altered N-terminal residues, including amino acids with similar properties, were inactive, indicating that the Val residue is specifically required at the N-terminus of this enzyme family in order for them to function correctly. Recombinant GluScpr was found to have peptidase activity intermediate between GluV8 and GluSE fromStaphylococcus epidermisand to be somewhat less specific in its substrate requirements than other family members. The 185–195 region was found to contribute to the activity of GluScpr, although other regions of the enzyme must also play a role in defining the activity. Our results strongly indicate the importance of the N-terminal and the 185–195 region in the activity of the glutamyl endopeptidases of staphylococci.
Multiplex analysis of mitochondrial DNA pathogenic and polymorphic sequence variants
Authors: Poole Jason C. , Procaccio Vincent , Brandon Martin C. , Merrick Greg , Wallace Douglas C. 
Published: August 2010

Abstract
The mitochondrial DNA (mtDNA) encompasses two classes of functionally important sequence variants: recent pathogenic mutations and ancient adaptive polymorphisms. To rapidly and cheaply evaluate both classes of single nucleotide variants (SNVs), we have developed an integrated system in which mtDNA SNVs are analyzed by multiplex primer extension using the SNaPshot system. A multiplex PCR amplification strategy was used to amplify the entire mtDNA, a computer program identifies optimal extension primers, and a complete global haplotyping system is also proposed. This system genotypes SNVs on multiplexed mtDNA PCR products or directly from enriched mtDNA samples and can quantify heteroplasmic variants down to 0.8% using a standard curve. With this system, we have developed assays for testing the common pathogenic mutations in four multiplex panels: two genotype the 13 most common pathogenic mtDNA mutations and two genotype the 10 most common Leber Hereditary Optic Neuropathy mutations along with haplogroups J and T. We use a hierarchal system of 140 SNVs to delineate the major global mtDNA haplogroups based on a global phylogenetic tree of coding region polymorphisms. This system should permit rapid and inexpensive genotyping of pathogenic and lineage-specific mtDNA SNVs by clinical and research laboratories.
Real-time polymerase chain reaction quantification of free DNA in serum of patients with polyps and colorectal cancers
Authors: Danese Elisa , Montagnana Martina , Minicozzi Anna Maria , De Matteis Giovanna , Scudo Giovanni , Salvagno Gian Luca , Cordiano Claudio , Lippi Giuseppe , Guidi Gian Cesare 
Published: August 2010

Abstract

Background: Colorectal cancer (CRC) is one of the most frequent causes of cancer related deaths worldwide. Recently, the use of cell-free DNA as diagnostic tools to identify cancer has been investigated. The aim of this work was to assess whether circulating DNA could be considered a useful marker for detection of early stage CRC and polyps.

Methods: A total of 118 patients with CRC were included in the study along with 49 patients with colorectal polyps and 26 control subjects. Cell-free DNA was quantified using a real-time TaqMan-polymerase chain reaction assay. Non-parametric tests (Mann-Whitney test and Spearman correlation) were utilized for statistical analysis.

Results: Serum DNA concentrations were significantly higher in CRC patients and patients with polyps (median value 105.0 ng/mL and 40.0 ng/mL) compared with controls (median value 14.0 ng/mL; p<0.05). Although carcinoembryonic antigen was above the cut-off in only 13/66 (19.7%) patients with early stage CRC, serum free DNA showed values above the threshold identified using receiver operator characteristic (ROC) curve analysis in 53/66 (80.3%) patients.

Conclusions: Our data confirm that serum DNA concentrations are significantly increased in CRC patients with early stage disease and in patients with polyps. This marker might be useful for identifying high-risk individuals.
Clin Chem Lab Med 2010;48:1665–8.