bluuebunny/crossref_metadata_2025_split huggingface dataset:
Large herbivores promote habitat specialization and beta diversity of African savanna trees
Authors: Pringle Robert M. , Prior Kirsten M. , Palmer Todd M. , Young Truman P. , Goheen Jacob R. 
Published: July 2016

AbstractEdaphic variation in plant community composition is widespread, yet its underlying mechanisms are rarely understood and often assumed to be physiological. In East African savannas,Acaciatree species segregate sharply across soils of differing parent material: the ant‐defended whistling thorn,A. drepanolobium(ACDR), is monodominant on cracking clay vertisols that are nutrient rich but physically stressful, whereas poorly defended species such asA. brevispica(ACBR) dominate on nutrient‐poor but otherwise less‐stressful sandy loams. Using a series of field experiments, we show that large‐mammal herbivory interacts with soil properties to maintain this pattern. In the absence of large herbivores, transplanted saplings of both species established on both soil types. Browsers strongly suppressed survival and growth ofACDRsaplings on sandy soil, where resource limitation constrained defensive investment. On clay soil,ACBRsaplings established regardless of herbivory regime, but elephants prevented recruitment to maturity, apparently because trees could not tolerate the combination of biotic and abiotic stressors. Hence, each tree species was filtered out of one habitat by browsing in conjunction with different edaphic factors and at different ontogenetic stages. Browser abundance was greater on sandy soil, where trees were less defended, consistent with predicted feedbacks between plant community assembly and herbivore distributions. By exploring two inversely related axes of soil “quality” (abiotic stress and nutrient content), our study extends the range of mechanisms by which herbivores are known to promote edaphic specialization, illustrates how the high cost of a protection mutualism can constrain the realized niche of host trees, and shows that large‐scale properties of savanna ecosystems are shaped by species interactions in cryptic ways that mimic simple abiotic determinism. These results suggest that ongoing declines in large‐herbivore populations may relax spatial heterogeneity in plant assemblages and reduce the beta diversity of communities.
Tissue‐resident and memory properties of human T‐cell and NK‐cell subsets
Authors: Lugli Enrico , Hudspeth Kelly , Roberto Alessandra , Mavilio Domenico 
Published: July 2016

Efficient immune responses to invading pathogens are the result of the complex but coordinated synergy between a variety of cell types from both the innate and adaptive arms of the immune system. While adaptive and innate immune responses are highly complementary, some cells types within these two systems perform similar functions, underscoring the need for redundancy and increased flexibility. In this review, we will discuss the striking shared features of immunological memory and tissue residency recently discovered between T cells, a component of the adaptive immune system, and natural killer (NK) cells, members generally assigned to the innate compartment. Specifically, we will focus on the T‐cell and NK‐cell diversity at the single‐cell level, on the discrete function of specific subsets, and on their anatomical location. Finally, we will discuss the implication of such diversity in the generation of long‐term memory.
Localized Electrochemistry for Studying Functional Carbon Surfaces
Authors: Lagrost Corinne , Leroux Yann , Hapiot Philippe 
Published: July 2016

AbstractThe large amount of research about modified surfaces has inspired the concomitant development of analytical methods for investigating the properties of the modified interfaces. Local electrochemical methods offer new possibilities both for studying the properties of the functional interface and for following their preparation after each step. In this review, these different possibilities are illustrated with different examples of SECM analysis of modified surfaces with a special emphasis on carbon materials.
Voltammetric Detection of Oxidative DNA Damage Based on Interactions between Polymeric Dyes and DNA
Authors: Kuzin Yury , Ivanov Alexey , Evtugyn Gennady , Hianik Tibor 
Published: July 2016

AbstractOxidative damage of DNA was assessed with glassy carbon electrode (GCE) coated with electropolymerized Methylene Blue (MB). For this purpose, DNA solution was first mixed with an oxidant (Fenton reagent, H2O2 alone and in the presence of Cu(II) ions) and then placed on the polymeric film surface. After washing, the cyclic voltammogram was recorded in buffer solution and the anodic peak potential measured against that before the contact with DNA. Oxidative DNA damage resulted in remarkable decrease of the anodic peak potential which depended on the oxidant nature and incubation period. Specificity of the DNA – MB interactions was confirmed by surface plasmon resonance (SPR) measurements. Similar experiment performed with polymerized Methylene Green (MG) and Neutral Red (NR) showed lower selectivity of the response toward various sources of reactive oxygen species. The protocol of the DNA damage detection was tested on the estimation of antioxidant properties of green tea extract and red table wine.
Detection of Thiols by o‐Quinone Nanocomposite Modified Electrodes
Authors: Devasurendra Amila M. , Zhu Tianxia , Kirchhoff Jon R. 
Published: July 2016

AbstractA chemically modified glassy carbon (GC) electrode was developed as an amperometric sensor for detection of biological thiols. The electrode was modified by inclusion of co‐enzyme pyrroloquinoline quinone (PQQ) and a co‐catalyst of oxidized single wall carbon nanotubes (Ox‐SWNT) into a gold polypyrrole (Au‐PPy) nanocomposite matrix. The electrode (PQQ/Ox‐SWNT/Au‐PPy/GC) was characterized using scanning electron microscopy and cyclic voltammetry. Optimal conditions for the PQQ/Ox‐SWNT/Au‐PPy/GC electrode were determined and then utilized for the amperometric detection of L‐cysteine, N‐acetyl‐L‐cysteine, L‐penicillamine and D, L‐glutathione. The electrochemical response for each thiol in pH 3.2 citrate phosphate buffer at +450 mV (vs. Ag/AgCl) was found to be linear with limit of detections (LOD, S/N=3) ranging from 0.50 µM for L‐penicillamine to 1.55 µM for D, L‐glutathione with sensitivities of 30.2 nA/µM and 3.6 nA/µM respectively. The electrode design is simple and easy to construct using a minimum amount of co‐enzyme and co‐catalyst, resulting in detection methods with very good stability and improved sensitivity for thiol detection.
CZE determination of submicromolar level of phenol in seawater using improved dynamic pH junction
Authors: Yasuno Koki , Fukushi Keiichi 
Published: July 2016

Using an improved dynamic pH junction as an on‐line concentration procedure, we developed CZE for determining submicromolar phenol in seawater for chloride to phenol concentration ratios of 1 000 000. To enhance the effect of conventional dynamic pH junction, a saturated fatty acid solution was injected into the capillary after sample injection. We named the procedure an improved dynamic pH junction. The method requires no sample pretreatment. The following optimum conditions were established: BGE, 40 mM sodium tetraborate decahydrate adjusted to pH 9.8 containing 0.001% m/v hexadimethrine bromide; 190 nm detection wavelength; 18 s (370 nL) vacuum injection period of sample; a saturated fatty acid solution, 30 mM sodium n‐hexanoate; 20 s (420 nL) vacuum injection period of the sodium n‐hexanoate; and 15 kV applied voltage with the sample inlet side as the cathode. The LOD for phenol was 5.9 μg/L at S/N of 3. The respective values of the RSD (intraday) of the peak area, peak height, and migration time for phenol were 1.9, 2.9, and 0.46%. The recoveries of phenol (25‒100 μg/L) spiked into the natural seawater sample obtained using the peak areas were 92‒110%. The proposed method was applied to simple biodegradation experiments using natural seawater samples containing phenol.
Online preconcentration by electrokinetic supercharging for separation of endocrine disrupting chemical and phenolic pollutants in water samples
Authors: Abdul Karim Nurul ’I. , Wan Ibrahim Wan A. , Sanagi Mohd M. , Abdul Keyon Aemi S. 
Published: July 2016

Online preconcentration using electrokinetic supercharging (EKS) was proposed to enhance the sensitivity of separation for endocrine disrupting chemical (methylparaben (MP)) and phenolic pollutants (2‐nitrophenol (NP) and 4‐chlorophenol (CP)) in water sample. Important EKS and separation conditions such as the concentration of BGE; the choice of terminating electrolyte (TE); and the injection time of leading electrolyte (LE), sample, and TE were optimized. The optimum EKS‐CE conditions were as follows: BGE comprising of 12 mM sodium tetraborate pH 10.1, 100 mM sodium chloride as LE hydrodynamically injected at 50 mbar for 30 s, electrokinetic injection (EKI) of sample at –3 kV for 200 s, and 100 mM CHES as TE hydrodynamically injected at 50 mbar for 40 s. The separation was conducted at negative polarity mode and UV detection at 214 nm. Under these conditions, the sensitivity of analytes was enhanced from 100‐ to 737‐fold as compared to normal CZE with hydrodynamic injection, giving LOD of 4.89, 5.29, and 53 μg/L for MP, NP and CP, respectively. The LODs were adequate for the analysis of NP and CP in environmental water sample having concentration at or lower than their maximum admissible concentration limit (240 and 2000 μg/L for NP and CP). The LOD of MP can be suitable for the analysis of MP exists at mid‐microgram per liter level, even though the LOD was slightly higher than the concentration usually found in water samples (from ng/L to 1 μg/L). The method repeatabilities (%RSD) were in the range of 1.07–2.39% (migration time) and 8.28–14.0% (peak area).
Increase of CIK cell efficacy by upregulating cell surface MICA and inhibition of NKG2D ligand shedding in multiple myeloma
Authors: Nwangwu Chidimma A. , Weiher Hans , Schmidt‐Wolf Ingo G. H. 
Published: July 2016

AbstractMultiple myeloma, which is a monoclonal plasma cell malignancy, still remains incurable despite recent progress in our understanding of this disorder. Adoptive immunotherapy of multiple myeloma using cytokine‐induced killer cells is yielding promising results in clinical trials; however, some myeloma cells still evade immune surveillance by various unknown molecular mechanisms. This study aims at increasing the efficacy of cytokine‐induced killer cells in targeting this tumor, using selective small‐molecule inhibitors which increase and stabilize surface expression of the natural killer group 2, member D ligand, major histocompatibility complex class I polypeptide‐related sequence A (MICA) on myeloma cells. We treated 2 multiple myeloma cell lines—U266 and KMS‐12‐PE—with 3 drugs. One of these drugs (sodium butyrate) is a histone deacetylase inhibitor. Another drug which was used (matrix metalloproteinase inhibitor III) blocks ligand shedding while the third drug (phenylarsine oxide) obstructs surface ligand internalization. The effect of these drugs on cell viability was determined using the 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide assay, surface ligand expression was examined using flow cytometry, and ligand shedding was assessed using enzyme‐linked immunosorbent assay. We demonstrated that cytokine‐induced killer cells have increased cytotoxicity against multiple myeloma cells after combined drug treatment than without drug pretreatment. We also established that this increased cytotoxicity was due to potent upregulation and stabilization of surface MICA on the surface of these tumor cell lines. Our study thus highlights further therapeutic options which could be used for the treatment of multiple myeloma patients.
High‐Valent Iron‐Oxo and ‐Nitrido Complexes: Bonding and Reactivity
Authors: Mondal Bhaskar , Roy Lisa , Neese Frank , Ye Shengfa 
Published: July 2016

AbstractMultiple‐bonded iron‐oxo and ‐nitrido species have been identified or proposed as key intermediates in a range of important chemical transformations. The reported model complexes feature various coordination geometries and distinct electronic structures, and therefore exhibit diverse reactivity. The present contribution highlights the synergy from both experimental and theoretical standpoints to elucidate their different bonding situations and delineate their common mechanistic features in hydrogen‐atom abstraction processes. Our analysis reveals that a radical centered on the abstracting atom E (E=O, N), which is generated via homolysis of covalent Fe−E bonds upon approaching the transition state, is an intrinsic C−H cleaving agent. The iron‐oxo species is predicted to be more reactive than its nitride congener, in general, because the O−H bond formed in the H‐atom transfer process is often stronger than the corresponding N−H bond.
Intravital multiphoton photoconversion with a cell membrane dye
Authors: Turcotte Raphaël , Wu Juwell W. , Lin Charles P. 
Published: July 2016

Photoconversion, an irreversible shift in a fluorophore emission spectrum after light exposure, is a powerful tool for marking cellular and subcellular compartments and tracking their dynamics in vivo. This paper reports on the photoconversion properties of Di‐8‐ANEPPS, a commercially available membrane dye. When illuminated with near‐infrared femtosecond laser pulses, Di‐8‐ANEPPS undergoes multiphoton photoconversion as indicated by the supralinear dependence of the conversion rate ρpc on the incident power (), and by the ability to photoconvert a thin optical section in a three‐dimensional matrix. The characteristic emission spectrum changed from red to blue, and ratiometric analysis on single cells in vitro revealed a 65‐fold increase in the blue to red wavelength ratio after photoconversion. The spectral shift is preserved in vivo for hours, making Di‐8‐ANEPPS a useful dye for intravital cell marking and tracking applications.
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Effect of postharvest ethylene treatment on sugar content, glycosidase activity and its gene expression in mango fruit
Authors: Chidley Hemangi G , Deshpande Ashish B , Oak Pranjali S , Pujari Keshav H , Giri Ashok P , Gupta Vidya S 
Published: July 2016

AbstractBACKGROUNDRipening‐associated softening is one of the important attributes that largely determines the shelf‐life of mango (Mangifera indica Linn.) fruits. To reveal the effect of pre‐climacteric ethylene treatment on ripening‐related softening of Alphonso mango, ethylene treatment was given to mature, raw Alphonso fruits. Changes in the pool of reducing and non‐reducing sugars, enzymatic activity of three glycosidases: β‐d‐galactosidase, α‐d‐mannosidase and β‐d‐glucosidase and their relative transcript abundance were analysed for control and ethylene treated fruits during ripening.RESULTSEarly activity of all the three glycosidases and accelerated accumulation of reducing and non‐reducing sugars on ethylene treatment was evident. β‐d‐Galactosidase showed the highest activity among three glycosidases in control fruits and marked increase in activity upon ethylene treatment. This was confirmed by the histochemical assay of its activity in control and ethylene treated ripe fruits. Relative transcript abundance revealed high transcript levels of β‐d‐galactosidase in control fruits. Ethylene‐treated fruits showed early and remarkable increase in the β‐d‐galactosidase transcripts while α‐d‐mannosidase transcript variants displayed early accumulation.CONCLUSIONThe findings suggest reduction in the shelf‐life of Alphonso mango upon pre‐climacteric ethylene treatment, a significant role of β‐d‐galactosidase and α‐d‐mannosidase in the ripening related softening of Alphonso fruits and transcriptional regulation of their expression by ethylene. © 2016 Society of Chemical Industry
A highly sensitive method for analyzing marker phytoplankton pigments: Ultra‐high‐performance liquid chromatography‐tandem triple quadrupole mass spectrometry
Authors: Zhang Jingjing , Liu Dongyan , Cao Peng , Wang Yujue , Keesing John K. , Li Jinhua , Chen Lingxin 
Published: July 2016

AbstractA sensitive and specific ultra‐high‐performance liquid chromatography‐tandem triple quadrupole mass spectrometry (UHPLC–MS/MS) method was developed for the purpose of decreasing the detection limit of quantification (LOQ) and reducing sample analysis time. In total, 14 marker pigments were determined and validated using an internal standard (IS) method with trans‐8′‐Apo‐beta‐carotenal as the IS. Electrospray ionization in positive mode was applied for the detection of pigments. The 14 types of pigments were separated in less than 15 min and presented good linearity, with the coefficients ranging from 0.9915 to 0.9991 using a UHPLC C8 column. The LOQ attained for 14 pigments were from 0.005 ng mL−1 to 0.500 ng mL−1, which enabled quantification of the pigments in seawater at ppt level. Both intra‐day and inter‐day precisions were less than 15%. The method was validated using seawater samples and the recovery of the analytes ranged from 62.8% to 120.2% at two spiked concentrations. Compared with previous methods, UHPLC–MS/MS method improved the efficiency of qualitative analysis and significantly decreased the detection LOQ for analyzing marker phytoplankton pigments at trace/ultra‐trace levels in complex matrices.
Changes in Verbal Fluency in Parkinson's Disease
Authors: Rosenthal Liana S. , Salnikova Yekaterina A. , Pontone Gregory M. , Pantelyat Alexander , Mills Kelly A. , Dorsey E. Ray , Wang Jiangxia , Wu Samuel S. , Mari Zoltan 
Published: July 2016

AbstractBackgroundThe test for semantic verbal fluency is quick and easy to administer. Decreases in semantic verbal fluency would suggest executive dysfunction among individuals with Parkinson's disease (PD).MethodsThe National Parkinson Foundation's Outcomes Project is a multicenter study that seeks to determine best practices in PD management. We analyzed data from the baseline and two annual follow‐up visits to determine the annual rate of verbal fluency change and determinants of that change. Linear mixed modeling was used to assess relationships between verbal fluency, clinical characteristics, quality of life, and caregiver burden.ResultsThere were 1,322 participants with an average age of 67.3 years, of whom 37% were women. Mean baseline verbal fluency scores at baseline were 18.81 (standard deviation = 6.25). Verbal fluency scores did not change among patients who were at our cohort's average age and average PD duration (8.4 years) and who had no other associated conditions (beta = −0.02; P = 0.80). Verbal fluency, however, did decrease for individuals with PD duration greater than the average (beta = −0.25; P = 0.03), age greater than the average (beta = −0.022; P < 0.01), a Hoehn and Yahr >=3 (beta = −0.31; P = 0.04), and in those with cardiovascular disease (beta = −0.32; P = 0.01) or psychiatric symptomatology (beta = −0.34; P = 0.01). Individuals with higher verbal fluency scores had better quality of life (P < 0.01) and decreased caregiver burden (P < 0.01).ConclusionsClinicians should monitor verbal fluency scores to evaluate cognitive decline among individuals with PD. Modifiable risk factors for verbal fluency changes include psychiatric symptomatology and cardiovascular disease. Clinicians may use verbal fluency testing to identify individuals at risk for decreased quality of life and increased caregiver burden, allowing for focused interventions.
New Trends in Inspecting GPCR‐ligand Recognition Process: the Contribution of the Molecular Modeling Section (MMS) at the University of Padova
Authors: Ciancetta Antonella , Cuzzolin Alberto , Deganutti Giuseppe , Sturlese Mattia , Salmaso Veronica , Cristiani Andrea , Sabbadin Davide , Moro Stefano 
Published: July 2016

AbstractIn this review, we present a survey of the recent advances carried out by our research groups in the field of ligand‐GPCRs recognition process simulations recently implemented at the Molecular Modeling Section (MMS) of the University of Padova. We briefly describe a platform of tools we have tuned to aid the identification of novel GPCRs binders and the better understanding of their binding mechanisms, based on two extensively used computational techniques such as molecular docking and MD simulations. The developed methodologies encompass: (i) the selection of suitable protocols for docking studies, (ii) the exploration of the dynamical evolution of ligand‐protein interaction networks, (iii) the detailed investigation of the role of water molecules upon ligand binding, and (iv) a glance at the way the ligand might go through prior reaching the binding site.
Docking Studies and Molecular Dynamic Simulations Reveal Different Features of IDO1 Structure
Authors: Greco Francesco Antonio , Bournique Answald , Coletti Alice , Custodi Chiara , Dolciami Daniela , Carotti Andrea , Macchiarulo Antonio 
Published: July 2016

AbstractIn the last decade, indoleamine 2,3‐dioxygenase 1 (IDO1) has attracted a great deal of attention being recognized as key regulator of immunosuppressive pathways in the tumor immuno‐editing process. Several classes of inhibitors have been developed as potential anticancer agents, but only few of them have advanced in clinical trials. Hence, the quest of novel potent and selective inhibitors of the enzyme is still active and mostly pursued by structure‐based drug design strategies based on early and more recent crystal structures of IDO1. Combining docking studies and molecular dynamic simulations, in this work we have comparatively investigated the structural features of each crystal structure of IDO1. The results pinpoint different features in specific crystal structures of the enzyme that may benefit the medicinal chemistry arena aiding the design of novel potent and selective inhibitors of IDO1.
Molecular Simulations Bring New Insights into Protoporphyrinogen IX Oxidase/Protoporphyrinogen IX Interaction Modes
Authors: Wang Baifan , Wen Xin , Xi Zhen 
Published: July 2016

AbstractProtoporphyrinogen IX oxidase (PPO, EC 1.3.3.4) catalyzes the oxidation of protoporphyrinogen IX (protogen IX) to protoporphyrin IX (proto IX) in the haem/chlorophyll biosynthetic pathway. Although extensive studies of PPO have already afforded many insights into its biological function and its significance to agriculture and medicine, details of the enzymatic mechanism as well as the nature of the specific amino acids involved in substrate binding still remain largely unknown due to the lack of structural information about protogen IX binding to PPO. In this study, we carried out a detailed and systematic investigation on the binding mode of protogen IX in the Nicotiana tabacum PPO (mtPPO) by performing a computational docking followed by molecular simulations, quantum mechanics calculations, and an integrated analysis. The proposed binding mode was consistent with experimental studies, and several potential key residues that have not been investigated in previous studies, such as Thr70, Arg233, Ser235, Ser474 and Lys477, were identified. In addition, we compared the binding modes of protogen IX in mtPPO and Homo sapiens PPO, and found their differences. Considering the low sequence identity and the differences of biochemical properties among the PPOs from various species, the investigation could provide a valuable basis for the design of PPO inhibitors with high potency and species‐selectivity.