bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of free‐flow IEF to identify protein candidates changing under microgravity conditions
Authors: Pietsch Jessica , Kussian Richard , Sickmann Albert , Bauer Johann , Weber Gerhard , Nissum Mikkel , Westphal Kriss , Egli Marcel , Grosse Jirka , Schönberger Johann , Wildgruber Robert , Infanger Manfred , Grimm Daniela 
Published: January 2010

AbstractUsing antibody‐related methods, we recently found that human thyroid cells express various proteins differently depending on whether they are cultured under normal gravity (1g) or simulated microgravity (s‐μg). In this study, we performed proteome analysis in order to identify more gravity‐sensitive thyroid proteins. Cells cultured under 1g or s‐μg conditions were sonicated. Proteins released into the supernatant and those remaining in the cell fragments were fractionated by free‐flow IEF. The fractions obtained were further separated by SDS‐gel electrophoresis. Selected gel pieces were excised and their proteins were determined by MS. A total of 235 different proteins were found. Out of 235 proteins, 37 appeared to be first identifications in human thyroid cells. Comparing SDS gel lanes of equally numbered free‐flow IEF fractions revealed similar patterns with a number of identical bands if proteins of a distinct cell line had been applied, irrespective of whether the cells had been cultured under 1g or s‐μg. Most of the identical band pairs contained identical proteins. However, the concentrations of some types of proteins were different within the two pieces of gel. Proteins that concentrated differently in such pieces of gel are considered as candidates for further investigations of gravitational sensitivity.
Unrestrictive identification of non‐phosphorylation PTMs in yeast kinases by MS and PTMap
Authors: Zhang Kai , Chen Yue , Zhang Zhihong , Tao Shengce , Zhu Heng , Zhao Yingming 
Published: January 2010

AbstractA few protein PTMs, such as phosphorylation and ubiquitination, are known to be critical in regulation of protein kinase activities. However, the roles of other PTMs have not been extensively studied in kinases. Development of a comprehensive description of all types of PTMs and discovering novel in vivo PTMs in low abundance represent major analytical challenges. Toward this goal, we have developed a strategy for systematic and accurate identification of the full‐spectrum of PTMs in yeast protein kinases. Our strategy involves isolation of GST‐fused kinase proteins, MS analysis, and unrestrictive PTM identification by PTMap algorithm. Among the 30 purified yeast kinases, we identified 27 different types of PTMs, and 53 PTM sites, among which are 13 novel mass shifts that have not been previously reported, likely representing novel PTMs. These results represent a significant expansion of our current understanding of PTMs in kinases and suggest highly complex regulation of kinase function.
Global phosphoproteomic effects of natural tyrosine kinase inhibitor, genistein, on signaling pathways
Authors: Yan Guang‐Rong , Xiao Chuan‐Le , He Gui‐Wei , Yin Xing‐Feng , Chen Nan‐Peng , Cao Ya , He Qing‐Yu 
Published: January 2010

AbstractGenistein is a natural protein tyrosine kinase inhibitor that exerts anti‐cancer effect by inducing G2/M arrest and apoptosis. However, the phosphotyrosine signaling pathways mediated by genistein are largely unknown. In this study, we combined tyrosine phosphoprotein enrichment with MS‐based quantitative proteomics technology to globally identify genistein‐regulated tyrosine phosphoproteins aiming to depict genistein‐inhibited phosphotyrosine cascades. Our experiments resulted in the identification of 213 phosphotyrosine sites on 181 genistein‐regulated proteins. Many identified phosphoproteins, including nine protein kinases, eight receptors, five protein phosphatases, seven transcriptical regulators and four signal adaptors, were novel inhibitory effectors with no previously known function in the anti‐cancer mechanism of genistein. Functional analysis suggested that genistein‐regulated protein tyrosine phosphorylation mainly by inhibiting the activity of tyrosine kinase EGFR, PDGFR, insulin receptor, Abl, Fgr, Itk, Fyn and Src. Core signaling molecules inhibited by genistein can be functionally categorized into the canonial Receptor‐MAPK or Receptor‐PI3K/AKT cascades. The method used here may be suitable for the identification of inhibitory effectors and tyrosine kinases regulated by anti‐cancer drugs.
Functionalized surfactant mediated reactions of carboxylate, phosphate and sulphonate esters
Authors: Tiwari Shuchi , Ghosh Kallol K. , Marek Jan , Kuca Kamil 
Published: January 2010

AbstractNucleophilic reactivity of some functionalized surfactants, i.e. quaternary pyridinium aldoximes towards the hydrolysis of p‐nitrophenyl acetate (PNPA), p‐nitrophenyl benzoate (PNPB), p‐nitrophenyldiphenyl phosphate (PNPDPP) and p‐nitrophenyl p‐toluene sulphonate (PNPTS) has been studied at pH 7.1 and 27 °C. Addition of functionalized surfactant to reaction medium causes progressive increase in the rate of hydrolysis and reaches a maximum and then decreases due to further addition of surfactant. An increase in the alkyl chain length of functionalized surfactants resulted in an increase in the first‐order rate constant. The apparent pKa and CMC of functionalized surfactants have also been determined by spectrophotometric and conductometric methods, respectively. Copyright © 2009 John Wiley & Sons, Ltd.
How to observe the oxidation of magnesia‐supported Pd clusters by scanning tunnelling microscopy
Authors: Walter Michael , Moseler Michael 
Published: January 2010

AbstractThe structure of adsorbed bare and oxidised Pd9 clusters on a MgO(001) bilayer supported by an Ag(001) surface are studied by density functional theory (DFT). Results for the bare cluster are compared with corresponding calculations of Pd9 on a free‐standing MgO(001) trilayer – a system that already reproduces the adsorption properties of thick MgO films. A 3D double trigonal antiprism is compared to a 2D fragment of a Pd(111) plane. In contrast to the findings for gold clusters, the Pd9 3D ground state on a thick MgO film is still energetically favourable on a thin metal supported MgO film – despite the substantial charge transfer from the metal support to the 2D cluster. Simulated scanning tunnelling microscopy images predict that the oxide formation should be easily detectable for negative bias voltages, since the highest occupied molecular orbitals of both the pristine as well as the oxidised clusters possess a strong Pd(d) contribution localised on the Pd atoms. At positive bias, the nodal structure of delocalised unoccupied orbitals sometimes masks the nuclear positions.magnified image
Simulated STM images for (a,d) Pd9@MgO(001)@Ag(001), (b,e) Pd9O2@MgO(001)@Ag(001) and (c,f) Pd9O4@MgO (001)@Ag(001).
Fragmentation of plumeran indole alkaloids from Aspidosperma spruceanum by electrospray ionization tandem mass spectrometry
Authors: Aguiar Gabriela P. , Wakabayashi Kamila A. L. , Luz Guilherme F. , Oliveira Vilma B. , Mathias Leda , Vieira Ivo J. C. , Braz‐Filho Raimundo , Crotti Antonio E. M. 
Published: January 2010

AbstractThe fragmentation of six plumeran indole alkaloids (PIAs) previously isolated from Aspidosperma spruceanum has been investigated by electrospray ionization tandem mass spectrometry (ESI‐MS/MS) in the positive ion mode. The fragmentation pathways have been established on the basis of MS/MS experiments using fragment ions generated in‐source and deuterium‐labeled alkaloids as precursor ions and on the basis of accurate mass measurements. Our results demonstrated that the fragmentation routes observed for the protonated PIAs are essentially derived from a pericyclic reaction and from the opening of rings D and E, followed by 1,4‐hydrogen rearrangements. Product ions resulting from radical eliminations were also observed, contrary to the ‘even‐electron rule’. Our data reveals that some product ions from protonated PIAs provide crucial information for the characterization of the acyl substituent at N‐1, the methoxyl and hydroxyl groups at the aromatic moiety, and give evidence of an ether bridge between C‐18 and C‐21. The data reported here were used for the dereplication of these compounds in a stem bark methanolic extract of Aspidosperma spruceanum. Copyright © 2010 John Wiley & Sons, Ltd.
A microfluidic reactor for rapid, low‐pressure proteolysis with on‐chip electrospray ionization
Authors: Liuni Peter , Rob Tamanna , Wilson Derek J. 
Published: January 2010

AbstractA microfluidic reactor that enables rapid digestion of proteins prior to on‐line analysis by electrospray ionization mass spectrometry (ESI‐MS) is introduced. The device incorporates a wide (1.5 cm), shallow (10 µm) reactor ‘well’ that is functionalized with pepsin‐agarose, a design that facilitates low‐pressure operation and high clogging resistance. Electrospray ionization is carried out directly from a short metal capillary integrated into the chip outlet. Fabrication, involving laser ablation of polymethyl methacrylate (PMMA), is exceedingly straightforward and inexpensive. High sequence coverage spectra of myoglobin (Mb), ubiquitin (Ub) and bovine serum albumin (BSA) digests were obtained after <4 s of residence time in the reactor. Stress testing showed little loss of performance over ∼2 h continuous use at high flow rates (30 µL/min). The device provides a convenient platform for a range of applications in proteomics and structural biology, i.e. to enable high‐throughput workflows or to limit back‐exchange in spatially resolved hydrogen/deuterium exchange (HDX) experiments. Copyright © 2010 John Wiley & Sons, Ltd.
Investigation of collision‐induced dissociations involving odd‐electron ion formation under positive electrospray ionization conditions using accurate mass
Authors: Xu Guifen , Huang Tom , Zhang Jennifer , Huang Jennifer K. , Carlson Timothy , Miao Shichang 
Published: January 2010

AbstractCollision induced dissociation (CID) has been extensively used for structure elucidation. CID in the electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI) modes has been found to generate mostly even‐electron fragment ions while it has been occasionally reported to form odd‐electron free radical ions. However, the structural requirements and the fragmentation mechanisms for free‐radical CIDs have not been well characterized in the literature. For this purpose, we studied a series of aromatic and non‐aromatic compounds such as sulfonamides, N‐aryl amides, tert‐butyl‐substituted aromatic compounds, aryl alkyl ethers, and O‐alkyl aryl oximes using the LTQ™ and LTQ Orbitrap™ linear ion trap mass spectrometers. The accurate measurement of the fragment ion masses established the unambiguous assignment of the fragment structures resulting from the test compounds. Our results showed that free radical fragmentation is structure dependent and is to a large extent correlated with the neighboring groups in the structures that stabilize the newly formed free radical ions. Copyright © 2010 John Wiley & Sons, Ltd.
Determination and imaging of metabolites from Vitis vinifera leaves by laser desorption/ionisation time‐of‐flight mass spectrometry
Authors: Hamm Gregory , Carré Vincent , Poutaraud Anne , Maunit Benoît , Frache Gilles , Merdinoglu Didier , Muller Jean‐François 
Published: January 2010

AbstractAnalysis of grapevine phytoalexins at the surface of Vitis vinifera leaves has been achieved by laser desorption/ionisation time‐of‐flight mass spectrometry (LDI‐ToFMS) without matrix deposition. This simple and rapid sampling method was successfully applied to map small organic compounds at the surface of grapevine leaves. It was also demonstrated that the laser wavelength is a highly critical parameter. Both 266 and 337 nm laser wavelengths were used but the 266 nm wavelength gave increased spatial resolution and better sensitivity for the detection of the targeted metabolites (resveratrol and linked stilbene compounds). Mass spectrometry imaging of grapevine Cabernet Sauvignon leaves revealed specific locations with respect to Plasmopara viticola pathogen infection or light illumination. Copyright © 2010 John Wiley & Sons, Ltd.
Evaporation of solvent molecules by ultrafast heating: effect on conformation of solvated protein
Authors: Thirumuruganandham Saravana Prakash , Urbassek Herbert M. 
Published: January 2010

AbstractUsing molecular dynamics simulation, we compare two cases of ultrafast heating of a small water droplet containing a solvated protein (echistatin). If the water temperature after irradiation is above the critical temperature, explosive boiling liberates the protein within some 10 ps of its hydration shell, while its temperature remains relatively low. By comparing with the case where the water shell is heated to the same final temperature, but without complete evaporation, we demonstrate that the protein conformation is governed by the hydration shell rather than by the protein temperature. Copyright © 2010 John Wiley & Sons, Ltd.
Matrix vapor deposition/recrystallization and dedicated spray preparation for high‐resolution scanning microprobe matrix‐assisted laser desorption/ionization imaging mass spectrometry (SMALDI‐MS) of tissue and single cells
Authors: Bouschen Werner , Schulz Oliver , Eikel Daniel , Spengler Bernhard 
Published: January 2010

AbstractMatrix preparation techniques such as air spraying or vapor deposition were investigated with respect to lateral migration, integration of analyte into matrix crystals and achievable lateral resolution for the purpose of high‐resolution biological imaging. The accessible mass range was found to be beyond 5000 u with sufficient analytical sensitivity. Gas‐assisted spraying methods (using oxygen‐free gases) provide a good compromise between crystal integration of analyte and analyte migration within the sample. Controlling preparational parameters with this method, however, is difficult. Separation of the preparation procedure into two steps, instead, leads to an improved control of migration and incorporation. The first step is a dry vapor deposition of matrix onto the investigated sample. In a second step, incorporation of analyte into the matrix crystal is enhanced by a controlled recrystallization of matrix in a saturated water atmosphere. With this latter method an effective analytical resolution of 2 µm in the x and y direction was achieved for scanning microprobe matrix‐assisted laser desorption/ionization imaging mass spectrometry (SMALDI‐MS). Cultured A‐498 cells of human renal carcinoma were successfully investigated by high‐resolution MALDI imaging using the new preparation techniques. Copyright © 2010 John Wiley & Sons, Ltd.
Set‐up and docking of the da Vinci® surgical system: prospective analysis of initial experience
Authors: Iranmanesh Pouya , Morel Philippe , Wagner Oliver J. , Inan Ihsan , Pugin François , Hagen Monika E. 
Published: January 2010

AbstractBackgroundSet‐up and docking of the da Vinci® surgical system are assumed to extend overall operating times. We hypothesized that these tasks could be achieved in adequate times. Therefore, a prospective analysis of set‐up and docking times of the da Vinci® Surgical System was conducted.MethodsWe prospectively analysed set‐up and docking times with the da Vinci surgical system in our division.ResultsNinety‐six patients were operated on over 30 months in our institution. Median set‐up time was 22 (range 9–50) min and median docking time was 10 (range 2–70) min. Surgeons with previous docking experience were significantly faster than inexperienced surgeons: 8 (range 2–50) vs. 17.5 (range 10–70) min. Both set‐up and docking showed a fast learning curve.ConclusionThe data support the conclusion that both set‐up and docking of the robot can be achieved in adequate times and have a low impact on overall operating time. Copyright © 2010 John Wiley & Sons, Ltd.
Robotic port‐site and pelvic recurrences after robot‐assisted laparoscopic radical hysterectomy for a stage IB1 adenocarcinoma of the cervix with negative lymph nodes
Authors: Sert Bilal 
Published: January 2010

AbstractBackgroundPort‐site metastasis (PSM) following minimally invasive surgery for gynaecological cancer has been recognized as a potential problem over the last two decades.MethodsA 60 year‐old woman with stage Ib1 adenocarcinoma of the cervix was treated with radical hysterectomy, bilateral salpingo‐oophorectomy and bilateral pelvic lymph node dissection, using robot‐assisted laparoscopy.ResultsEighteen months after primary surgery, the patient developed a pelvic recurrence invading both the bladder mucosa and the parametrium. During the routine recurrence work‐up, we found an 8 mm robotic port‐site metastasis (PSM) on the abdominal computed tomography (CT) scan.ConclusionThis is the first case report emphasizing the risk of PSM and early pelvic recurrences in robot‐assisted laparoscopic radical hysterectomy and bilateral pelvic lymph node dissection for an early‐stage cervical adenocarcinoma patient with negative lymph nodes, histologically examined by immunohistochemical ultrastaging. Copyright © 2010 John Wiley & Sons, Ltd.
Enteroviruses, type 1 diabetes and hygiene: a complex relationship
Authors: Tracy S. , Drescher K. M. , Jackson J. D. , Kim K. , Kono K. 
Published: January 2010

AbstractType 1 diabetes (T1D) is an autoimmune disease in which the immune system mounts an attack on the host's insulin‐producing β cells. Because most cases of T1D cannot be attributed only to individual genetics, it is strongly inferred that there is a significant environmental contribution, such as infection, impacting disease development. The human enteroviruses (HEV) are common picornaviruses often implicated as triggers of human T1D, although precisely which of the numerous HEV may be involved in human T1D development is unknown. Experiments using non‐obese diabetic (NOD) mice, commonly used to model T1D, show that induction of T1D by HEV infection in NOD mice is a multifactorial process involving both the virus and the host. Interestingly, results demonstrate that HEV infection of NOD mice can also induce long‐term protection from T1D under certain conditions, suggesting that a similar mechanism may occur in humans. Based upon both experimental animal and observational human studies, we postulate that HEV have a dual role in T1D development and can either cause or prevent autoimmune disease. Whichever outcome occurs depends upon multiple variables in the host‐virus equation, many of which can be deduced from results obtained from NOD mouse studies. We propose that the background to the sharply rising T1D incidences observed in the 20th century correlates with increased levels of hygiene in human societies. Viewing T1D in this perspective suggests that potential preventative options could be developed. Copyright © 2009 John Wiley & Sons, Ltd.
Coordinated aerobiological sampling of a plant pathogen in the lower atmosphere using two autonomous unmanned aerial vehicles
Authors: Techy Laszlo , Schmale David G. , Woolsey Craig A. 
Published: January 2010

AbstractUnmanned aerial vehicles (UAVs) are an important tool to track the long‐distance movement of plant pathogens above crop fields. Here, we describe the use of a control strategy (coordination via speed modulation) to synchronize two autonomous UAVs during aerobiological sampling of the potato late blight pathogen, Phytophthora infestans. The UAVs shared position coordinates via a wireless mesh network and modulated their speeds so that they were properly phased within their sampling orbits. Three coordinated control experiments were performed August 14–15, 2008. In the first two experiments, two UAVs were vertically aligned at two different altitudes [25 and 45 m above ground level (AGL)] with identical sampling orbits (radii of 150 m). In the third experiment, two UAVs shared the same altitude (35 m AGL) with different sampling orbits (radii of 130 and 160 m). Orbit times did not vary significantly between the two UAVs across all three aerobiological sampling missions, and the phase error during sampling converged to zero within 2 min following the start of the coordinated control algorithm. Viable sporangia of P. infestans were recovered following two of the coordinated flights. This is the first detailed report of autonomous UAV coordination during the aerobiological sampling of a plant pathogen in the lower atmosphere. UAVs operating independently of one another may experience significant sampling variations during the course of a flight. Coordinating the flight of two or more UAVs ensures that the vehicles enter, sample, and exit a spore plume at consistent times. © 2010 Wiley Periodicals, Inc.
River science—What has it contributed to general ecological theory?
Authors: Milner Alexander M. , Tockner Klement 
Published: January 2010

AbstractA special session of the 56th Annual Meeting of the North American Benthological Society in Utah in 2008 explored the contribution riverine benthic science has made to general concepts of ecological theory. Advances in general ecological theory have been made by riverine science in many areas, including metabolic theory, decomposition, reciprocal subsidies between ecosystems, ecotonal patterns and processes, secondary production and biodiversity‐ecosystem functioning (B‐EF). However in many cases these advances have not been taken up by other ecologists in their publications. In this special issue, we explore these contributions and examine reasons for the lack of uptake and suggest possible ways forward so that riverine benthic science can make a greater overall contribution to general ecological theory. Copyright © 2009 John Wiley & Sons, Ltd.
The influence of initial surface conditions on field crystallization of anodic aluminum oxide films determined by synchrotron X‐ray diffraction
Authors: Sakairi M. , Kikuchi T. , Suda T. , Nagasawa D. , Sato M. 
Published: January 2010

AbstractX‐ray diffraction measurements were performed using synchrotron radiation at the SPring‐8 facility and electrochemical techniques to investigate the effect of polishing methods and storage conditions on the crystal structure of air‐formed oxide films and anodic oxide films formed on highly pure aluminum. Storage in an N2 environment hinders local film breakdown during anodizing, and it was established that the X‐ray diffraction measurements showed the presence of a γ‐Al2O3 in the anodic oxide film formed on mechanically polished (MP) specimens. Formation of γ‐Al2O3 during anodizing was inhibited by electropolishing because of the removal of the work‐hardened layer that was formed on the MP by electro‐polishing. The X‐ray diffraction results do not show clear differences in the influence of the polishing method on the crystal structure of air formed oxide film. This is due to the very fast oxidation rate of the air‐formed oxide film and very long storage times for the X‐ray measurements. The anodic oxide film formed on aluminum, which has a very flat surface, shows color and the color depended on grain orientation. The electrochemical impedance of the MP specimen is slightly lower than that of the mechanically and then electrochemically polished specimen at the middle frequency range. This impedance difference may be due to formation of γ‐Al2O3 in the amorphous anodic oxide film and the thickness of the film. Copyright © 2010 John Wiley & Sons, Ltd.