bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional Genome Screening to Elucidate the Colistin Resistance Mechanism
Authors: Kumar Mohit , Gupta Ashutosh , Sahoo Rajesh Kumar , Jena Jayanti , Debata Nagen Kumar , Subudhi Enketeswara 
Published: March 2016

AbstractAntibiogram profile of 1590 clinical bacterial isolates based on thirteen different antimicrobial compounds showed that 1.6% of the bacterial isolates are multidrug resistant. Distribution pattern based on 16S rRNA sequence analysis showed that Pseudomonas aeruginosa constituted the largest group (83.6%) followed by Burkholderia pseudomallei sp. A191 (5.17%), Staphylococcus sp. A261 (3.45%). Among the various antibiotics used, colistin appeared to be the most effective against the Gram negative bacteria. Burkholderia pseudomallei sp. A191 and Pseudomonas aeruginosa sp. A111 showed resistance to 1500 μg/ml and 750 μg/ml of colistin respectively which constitutes 7.7% of the bacterial population. A functional genomics strategy was employed to discover the molecular support for colistin resistance in Burkholderia pseudomallei sp. A191. A pUC plasmid-based genomic expression library was constructed with an estimated library size of 2.1 × 107bp. Five colistin resistant clones were obtained after functional screening of the library. Analysis of DNA sequence of five colistin resistant clones showed homology to two component regularity systems (TCRS) encoding for a histidine kinase (mrgS) and its regulatory component (mrgR). Cross complementation assay showed that mutations in mrgS were sufficient enough to confer colistin resistant phenotype in a sensitive strain.
Proteome analysis of the macroscopically affected colonic mucosa of Crohn’s disease and intestinal tuberculosis
Authors: Rukmangadachar Lokesh A. , Makharia Govind K. , Mishra Asha , Das Prasenjit , Hariprasad Gururao , Srinivasan Alagiri , Gupta Siddhartha Datta , Ahuja Vineet , Acharya Subrat K. 
Published: March 2016

AbstractDifferentiation between intestinal tuberculosis (ITB) and Crohn’s disease (CD) is challenging in geographical regions where both these diseases are prevalent. There is a need of biomarkers for differentiation between these two disorders. Colonic biopsies from inflamed mucosa of treatment-naive patients with ITB, CD and controls were used for analysis. Protein extracted from biopsies was digested with trypsin and resulting peptides were labeled with iTRAQ reagents. The peptides were subsequently analyzed using LC-MS/MS for identification and quantification. Gene ontology annotation for proteins was analyzed in PANTHER. Validation experiments were done for six differentially expressed proteins using immunohistochemistry. 533 proteins were identified and 241 proteins were quantified from 5 sets of iTRAQ experiments. While 63 were differentially expressed in colonic mucosa of patients with CD and ITB in at least one set of iTRAQ experiment, 11 proteins were differentially expressed in more than one set of experiments. Six proteins used for validation using immunohistochemistry in a larger cohort of patients; none of them however was differentially expressed in patients with ITB and CD. There are differentially expressed proteins in tissue proteome of CD and ITB. Further experiments are required using a larger cohort of homogeneous tissue samples.
Spatiotemporal transcriptome provides insights into early fruit development of tomato (Solanum lycopersicum)
Authors: Zhang Shuaibin , Xu Meng , Qiu Zhengkun , Wang Ketao , Du Yongchen , Gu Lianfeng , Cui Xia 
Published: March 2016

AbstractEarly fruit development is crucial for crop production in tomato. After fertilization, the ovary undergoes cell division and cell expansion before maturation. Although the roles of regulatory signals such as hormone and carbohydrate during early fruit development have been studied, the spatial distribution and the sequential initiation of these regulatory signals still need to be explored. Using the tomato cultivar ‘Moneymaker’, we analyzed the transcriptome of the ovule and the ovary wall/pericarp dissected from four different stages of the early developing fruits by stereoscope. These datasets give us the whole picture about the spatial and temporal signal distribution in early development of ovule and pericarp. Our results indicate that the hormone signal was initiated in both ovule and pericarp after fertilization. After that, different signals were activated in ovule and pericarp due to their distinct developmental processes. Our study provides spatiotemporal regulatory landscape of gene expression with sequential information which was not studied by previous work and further strengthens the comprehension of the regulatory and metabolic events controlling early fruit development.
Spines slow down dendritic chloride diffusion and affect short-term ionic plasticity of GABAergic inhibition
Authors: Mohapatra Namrata , Tønnesen Jan , Vlachos Andreas , Kuner Thomas , Deller Thomas , Nägerl U. Valentin , Santamaria Fidel , Jedlicka Peter 
Published: March 2016

AbstractCl−plays a crucial role in neuronal function and synaptic inhibition. However, the impact of neuronal morphology on the diffusion and redistribution of intracellular Cl−is not well understood. The role of spines in Cl−diffusion along dendritic trees has not been addressed so far. Because measuring fast and spatially restricted Cl−changes within dendrites is not yet technically possible, we used computational approaches to predict the effects of spines on Cl−dynamics in morphologically complex dendrites. In all morphologies tested, including dendrites imaged by super-resolution STED microscopy in live brain tissue, spines slowed down longitudinal Cl−diffusion along dendrites. This effect was robust and could be observed in both deterministic as well as stochastic simulations. Cl−extrusion altered Cl−diffusion to a much lesser extent than the presence of spines. The spine-dependent slowing of Cl−diffusion affected the amount and spatial spread of changes in the GABA reversal potential thereby altering homosynaptic as well as heterosynaptic short-term ionic plasticity at GABAergic synapses in dendrites. Altogether, our results suggest a fundamental role of dendritic spines in shaping Cl−diffusion, which could be of relevance in the context of pathological conditions where spine densities and neural excitability are perturbed.
Abnormal proplatelet formation and emperipolesis in cultured human megakaryocytes from gray platelet syndrome patients
Authors: Di Buduo Christian A. , Alberelli Maria Adele , Glembotsky Ana C. , Podda Gianmarco , Lev Paola R. , Cattaneo Marco , Landolfi Raffaele , Heller Paula G. , Balduini Alessandra , De Candia Erica 
Published: March 2016

AbstractThe Gray Platelet Syndrome (GPS) is a rare inherited bleeding disorder characterized by deficiency of platelet α-granules, macrothrombocytopenia and marrow fibrosis. The autosomal recessive form of GPS is linked to loss of function mutations in NBEAL2, which is predicted to regulate granule trafficking in megakaryocytes, the platelet progenitors. We report the first analysis of cultured megakaryocytes from GPS patients with NBEAL2 mutations. Megakaryocytes cultured from peripheral blood or bone marrow hematopoietic progenitor cells from four patients were used to investigate megakaryopoiesis, megakaryocyte morphology and platelet formation. In vitro differentiation of megakaryocytes was normal, whereas we observed deficiency of megakaryocyte α-granule proteins and emperipolesis. Importantly, we first demonstrated that platelet formation by GPS megakaryocytes was severely affected, a defect which might be the major cause of thrombocytopenia in patients. These results demonstrate that cultured megakaryocytes from GPS patients provide a valuable model to understand the pathogenesis of GPS in humans.
Glycoprotein nonmetastatic melanoma protein B extracellular fragment shows neuroprotective effects and activates the PI3K/Akt and MEK/ERK pathways via the Na+/K+-ATPase
Authors: Ono Yoko , Tsuruma Kazuhiro , Takata Masafumi , Shimazawa Masamitsu , Hara Hideaki 
Published: March 2016

AbstractGlycoprotein nonmetastatic melanoma protein B (GPNMB) plays important roles in various types of cancer and amyotrophic lateral sclerosis (ALS). The details of GPNMB function and its interacting protein have not been clarified. Therefore, to identify GPNMB binding partners on the cell membrane, we used membrane protein library/BLOTCHIP-MS technology, which enables us to analyze all cell membrane proteins as binding partners of the GPNMB extracellular fragment. As a result of a comprehensive search, we identified the alpha subunits of Na+/K+-ATPase (NKA) as a possible binding partner. We confirmed the interaction between the GPNMB extracellular fragment and NKA by immunoprecipitation and immunostaining in NSC-34 cells. Indeed, endogenous GPNMB extracellular fragment bound to and colocalized with NKA alpha subunits. Furthermore, exogenous GPNMB extracellular fragment, i.e., human recombinant GPNMB, also bound to and colocalized with NKA alpha subunits. Additionally, we found that the GPNMB extracellular fragment had neuroprotective effects and activated the phosphoinositide 3-kinase (PI3K)/Akt and mitogen-activated protein kinase (MAPK)-extracellular signal-regulated kinase (ERK) kinase (MEK)/ERK pathways via NKA. These findings indicated that NKA may act as a novel “receptor” for the GPNMB extracellular fragment, offering additional molecular targets for the treatment of GPNMB-related diseases, including various types of cancer and ALS.
Preferred Barefoot Step Frequency is Influenced by Factors Beyond Minimizing Metabolic Rate
Authors: Yandell Matthew B. , Zelik Karl E. 
Published: March 2016

AbstractHumans tend to increase their step frequency in barefoot walking, as compared to shod walking at the same speed. Based on prior studies and the energy minimization hypothesis we predicted that people make this adjustment to minimize metabolic cost. We performed an experiment quantifying barefoot walking metabolic rate at different step frequencies, specifically comparing preferred barefoot to preferred shod step frequency. We found that subjects increased their preferred frequency when walking barefoot at 1.4 m/s (~123 vs. ~117 steps/min shod, P = 2e-5). However, average barefoot walking metabolic rates at the preferred barefoot and shod step frequencies were not significantly different (P = 0.40). Instead, we observed subject-specific trends: five subjects consistently reduced (−8% average) and three subjects consistently increased (+10% average) their metabolic rate at preferred barefoot vs. preferred shod frequency. Thus, it does not appear that people ubiquitously select a barefoot step frequency that minimizes metabolic rate. We concluded that preferred barefoot step frequency is influenced by factors beyond minimizing metabolic rate, such as shoe properties and/or perceived comfort. Our results highlight the subject-specific nature of locomotor adaptations and how averaging data across subjects may obscure meaningful trends. Alternative experimental designs may be needed to better understand individual adaptations.
Predicting protein thermal stability changes upon point mutations using statistical potentials: Introducing HoTMuSiC
Authors: Pucci Fabrizio , Bourgeas Raphaël , Rooman Marianne 
Published: March 2016

AbstractThe accurate prediction of the impact of an amino acid substitution on the thermal stability of a protein is a central issue in protein science, and is of key relevance for the rational optimization of various bioprocesses that use enzymes in unusual conditions. Here we present one of the first computational tools to predict the change in melting temperature ΔTm upon point mutations, given the protein structure and, when available, the melting temperature Tm of the wild-type protein. The key ingredients of our model structure are standard and temperature-dependent statistical potentials, which are combined with the help of an artificial neural network. The model structure was chosen on the basis of a detailed thermodynamic analysis of the system. The parameters of the model were identified on a set of more than 1,600 mutations with experimentally measured ΔTm. The performance of our method was tested using a strict 5-fold cross-validation procedure, and was found to be significantly superior to that of competing methods. We obtained a root mean square deviation between predicted and experimental ΔTm values of 4.2 °C that reduces to 2.9 °C when ten percent outliers are removed. A webserver-based tool is freely available for non-commercial use at soft.dezyme.com.
Nighttime warming enhances drought resistance of plant communities in a temperate steppe
Authors: Yang Zhongling , Jiang Lin , Su Fanglong , Zhang Qian , Xia Jianyang , Wan Shiqiang 
Published: March 2016

AbstractDrought events could have profound influence on plant community structure and ecosystem function, and have subsequent impacts on community stability, but we know little about how different climate warming scenarios affect community resistance and resilience to drought. Combining a daytime and nighttime warming experiment in the temperate steppe of north China with a natural drought event during the study period, we tested how daytime and nighttime warming influences drought resistance and resilience. Our results showed that the semi-arid steppe in north China was resistant to both daytime and nighttime warming, but vulnerable to drought. Nighttime warming, but not daytime warming, enhanced community resistance to drought via stimulating carbon sequestration, whereas neither daytime nor nighttime warming affected community resilience to drought. Large decline in plant community cover, primarily caused by the reduction in the cover of dominant and rare species rather than subordinate species during drought, did not preclude rapid ecosystem recovery. These findings suggest that nighttime warming may facilitate ecosystem sustainability and highlight the need to assess the effects of climate extremes on ecosystem functions at finer temporal resolutions than based on diurnal mean temperature.
Sox2 in the differentiation of cochlear progenitor cells
Authors: Kempfle Judith S. , Turban Jack L. , Edge Albert S. B. 
Published: March 2016

AbstractHMG domain transcription factor, Sox2, is a critical gene for the development of cochlear hair cells, the receptor cells for hearing, but this has been ascribed to expansion of the progenitors that become hair cells. Here, we show that Sox2 activated Atoh1, a transcription factor important for hair cell differentiation, through an interaction with the 3′ enhancer of Atoh1. Binding to consensus sequences in the Atoh1 enhancer was dependent on the level of Sox2 and the extent of enhancer binding correlated to the extent of activation. Atoh1 activation by Sox2 was required for embryonic hair cell development: deletion of Sox2 in an inducible mutant, even after progenitor cells were fully established, halted development of hair cells and silencing also inhibited postnatal differentiation of hair cells induced by inhibition of γ-secretase. Sox2 is thus required in the cochlea to both expand the progenitor cells and initiate their differentiation to hair cells.
Demonstration of single crystal growth via solid-solid transformation of a glass
Authors: Savytskii Dmytro , Knorr Brian , Dierolf Volkmar , Jain Himanshu 
Published: March 2016

AbstractMany advanced technologies have relied on the availability of single crystals of appropriate material such as silicon for microelectronics or superalloys for turbine blades. Similarly, many promising materials could unleash their full potential if they were available in a single crystal form. However, the current methods are unsuitable for growing single crystals of these oftentimes incongruently melting, unstable or metastable materials. Here we demonstrate a strategy to overcome this hurdle by avoiding the gaseous or liquid phase and directly converting glass into a single crystal. Specifically, Sb2S3 single crystals are grown in Sb-S-I glasses as an example of this approach. In this first unambiguous demonstration of an all-solid-state glass → crystal transformation, extraneous nucleation is avoided relative to crystal growth via spatially localized laser heating and inclusion of a suitable glass former in the composition. The ability to fabricate patterned single-crystal architecture on a glass surface is demonstrated, providing a new class of micro-structured substrate for low cost epitaxial growth, active planar devices, etc.
More for less: Improving the biomass yield of a pear cell suspension culture by design of experiments
Authors: Rasche Stefan , Herwartz Denise , Schuster Flora , Jablonka Natalia , Weber Andrea , Fischer Rainer , Schillberg Stefan 
Published: March 2016

AbstractPlant cell suspension cultures are widely used for the production of recombinant proteins and secondary metabolites. One of the most important steps during process development is the optimization of yields by testing different cultivation parameters, including the components of the growth medium. However, we have shown that the biomass yield of a cell suspension culture derived from the pear cultivar Pyrus communis cv. Champagner Bratbirne can be significantly improved solely by varying the temperature, inoculum density, illumination and incubation time. In contrast to medium optimization, these simple physical factors are easily controlled and varied, thereby reducing the effort required. Using an experimental design approach, we improved the biomass yield from 146 g fresh weight (FW)/L to 407 g FW/L in only 5 weeks, simultaneously reducing the costs of goods sold per kg biomass from €125 to €45. Our simple approach therefore offers a rapid, efficient and economical process for the optimization of plant cell suspension cultures.
NMR Observation of Mobile Protons in Proton-Implanted ZnO Nanorods
Authors: Park Jun Kue , Kwon Hyeok-Jung , Lee Cheol Eui 
Published: March 2016

AbstractThe diffusion properties of H+ in ZnO nanorods are investigated before and after 20 MeV proton beam irradiation by using 1H nuclear magnetic resonance (NMR) spectroscopy. Herein, we unambiguously observe that the implanted protons occupy thermally unstable site of ZnO, giving rise to a narrow NMR line at 4.1 ppm. The activation barrier of the implanted protons was found to be 0.46 eV by means of the rotating-frame spin-lattice relaxation measurements, apparently being interstitial hydrogens. High-energy beam irradiation also leads to correlated jump diffusion of the surface hydroxyl group of multiple lines at ~1 ppm, implying the presence of structural disorder at the ZnO surface.
Pathobiological Characterization of a Novel Reassortant Highly Pathogenic H5N1 Virus Isolated in British Columbia, Canada, 2015
Authors: Berhane Yohannes , Kobasa Darwyn , Embury-Hyatt Carissa , Pickering Brad , Babiuk Shawn , Joseph Tomy , Bowes Victoria , Suderman Mathew , Leung Anders , Cottam-Birt Colleen , Hisanaga Tamiko , Pasick John 
Published: March 2016

AbstractIn the current study, we describe the pathobiologic characteristics of a novel reassortant virus - A/chicken/BC/FAV-002/2015 (H5N1) belonging to clade 2.3.4.4 that was isolated from backyard chickens in British Columbia, Canada. Sequence analyses demonstrate PB1, PA, NA and NS gene segments were of North American lineage while PB2, HA, NP and M were derived from a Eurasian lineage H5N8 virus. This novel virus had a 19 amino acid deletion in the neuraminidase stalk. We evaluated the pathogenic potential of this isolate in various animal models. The virus was highly pathogenic to mice with a LD50 of 10 plaque forming units (PFU), but had limited tissue tropism. It caused only subclinical infection in pigs which did result in seroconversion. This virus was highly pathogenic to chickens, turkeys, juvenile Muscovy ducks (Cairnia moschata foma domestica) and adult Chinese geese (Anser cynoides domesticus) causing a systemic infection in all species. The virus was also efficiently transmitted and resulted in mortality in naïve contact ducks, geese and chickens. Our findings indicate that this novel H5N1 virus has a wide host range and enhanced surveillance of migratory waterfowl may be necessary in order to determine its potential to establish itself in the wild bird reservoir.
The effect of positioning cations on acidity and stability of the framework structure of Y zeolite
Authors: Deng Changshun , Zhang Junji , Dong Lihui , Huang Meina , Bin Li  , Jin Guangzhou , Gao Junbin , Zhang Feiyue , Fan Minguang , Zhang Luoming , Gong Yanjun 
Published: March 2016

AbstractThe investigation on the modification of NaY zeolite on LaHY and AEHY (AE refers Ca and Sr and the molar ratio of Ca and Sr is 1:1) zeolites was proformed by XRD, N2-physisorption (BET), XRF, XPS, NH3-TPD, Py-IR, hydrothermal stability, and catalytic cracking test. These results indicate that HY zeolite with ultra low content Na can be obtained from NaY zeolite through four exchange four calcination method. The positioning capability of La3+ in sodalite cage is much better than that of AE2+ and about 12 La3+ can be well coordinated in sodalite cages of one unit cell of Y zeolite. Appropriate acid amount and strength favor the formation of propylene and La3+ is more suitable for the catalytic cracking of cyclohexane than that of AE2+. Our results not only elaborate the variation of the strong and weak acid sites as well as the Brönsted and Lewis acid sites with the change of exchanged ion content but also explore the influence of hydrothermal aging of LaHY and AEHY zeolites and find the optimum ion exchange content for the most reserved acid sites. At last, the coordination state and stabilization of ion exchanged Y zeolites were discussed in detail.
A rapid method to authenticate vegetable oils through surface-enhanced Raman scattering
Authors: Lv Ming Yang , Zhang Xin , Ren Hai Rui , Liu Luo , Zhao Yong Mei , Wang Zheng , Wu Zheng Long , Liu Li Min , Xu Hai Jun 
Published: March 2016

AbstractVegetable oils are essential in our daily diet. Among various vegetable oils, the major difference lies in the composition of fatty acids, including unsaturated fatty acids (USFA) and saturated fatty acids (SFA). USFA include oleic acid (OA), linoleic acid (LA), and α-linolenic acid (ALA), while SFA are mainly palmitic acid (PA). In this study, the most typical and abundant USFA present with PA in vegetable oils were quantified. More importantly, certain proportional relationships between the integrated intensities of peaks centered at 1656 cm−1 (S1656) in the surface-enhanced Raman scattering spectra of different USFA were confirmed. Therefore, the LA or ALA content could be converted into an equivalent virtual OA content enabling the characterization of the USFA content in vegetable oils using the equivalent total OA content. In combination with the S1656 of pure OA and using peanut, sesame, and soybean oils as examples, the ranges of S1656 corresponding to the National Standards of China were established to allow the rapid authentication of vegetable oils. Gas chromatograph-mass spectrometer analyses verified the accuracy of the method, with relative errors of less than 5%. Moreover, this method can be extended to other detection fields, such as diseases.