bluuebunny/crossref_metadata_2025_split huggingface dataset:
Partitioning the variation of woody plant β‐diversity in a landscape of secondary tropical dry forests across spatial scales
Authors: López‐Martínez J.O. , Hernández‐Stefanoni J.L. , Dupuy J.M. , Meave J.A. 
Published: July 2012

AbstractQuestionWhat is the relative importance of forest successional age, environmental heterogeneity, landscape structure and spatial structure of sampling sites on β‐diversity of tropical dry forests (TDF)? How do the magnitude of β‐diversity and the relative influence of factors, processes and mechanisms driving β‐diversity differ at different spatial grains? What are the effects of stand age on β‐diversity?LocationYucatán Peninsula, México.MethodsFloristic composition was obtained from a hierarchical survey performed in 276 sites distributed across 23 sampling landscapes (SL) (12 sites per SL). Land‐cover classes were derived from the classification of multi‐spectral SPOT 5 satellite imagery. We calculated landscape metrics of patch type for each SL, and characterized local soil conditions for each sampling site. A principal coordinates of neighbour matrices (PCNM) analysis was performed to estimate spatial variables, and partial redundancy analysis was used to decompose variation into spatial, stand age and landscape structure components.ResultsThe magnitude of β‐diversity varied with spatial scale (grain size), and was larger at the local than at the landscape grain. The magnitude of β‐diversity also decreased slightly but significantly with successional age. There were significant differences in species composition among vegetation classes. Environmental factors (local soil conditions, as well as landscape structure) and spatial structure both contributed to woody plant β‐diversity in our TDF landscape, but their relative importance was scale‐dependent. At the local grain size, both the environment (mainly soil conditions) and the spatial structure strongly affected β‐diversity, while at the landscape grain, environmental factors (variation in soil conditions, as well as landscape configuration) played a more prominent role.ConclusionsThe magnitude of β‐diversity decreased with increasing spatial grain and successional age, while the relative importance of mechanisms influencing β‐diversity was scale‐dependent: both niche partitioning and dispersal limitation affect β‐diversity at the local grain size, while niche partitioning prevails at the landscape grain.
The Incarnation and Jesus’ Apparent Limitation in Knowledge
Authors: Loke Andrew 
Published: July 2012

AbstractOne of the problems confronting the doctrine of the Incarnation concerns Jesus’ apparent limitation in knowledge. This paper assesses various constructive proposals by modern theologians and philosophers, focusing on three of the most widely discussed solutions, namely Ontological Kenoticism, Two Consciousnesses Model, and Divine Subconscious Model. I argue that despite recent work done on the first two, the difficulties of avoiding the implication that the Logos ceased to be divine (for the first) and the implication of Nestorianism (for the second) remain. I conclude that the most promising solution is to defend Functional Kenoticism and develop the Divine Subconscious Model.
SIRPα interacts with nephrin at the podocyte slit diaphragm
Authors: Kajiho Yuko , Harita Yutaka , Kurihara Hidetake , Horita Shigeru , Matsunaga Atsuko , Tsurumi Haruko , Kanda Shoichiro , Sugawara Noriko , Miura Kenichiro , Sekine Takashi , Hattori Seisuke , Hattori Motoshi , Igarashi Takashi 
Published: July 2012

The slit diaphragm (SD) is an intercellular junction between renal glomerular epithelial cells (podocytes) that is essential for permselectivity in glomerular ultrafiltration. The SD components, nephrin and Neph1, assemble a signaling complex in a tyrosine phosphorylation dependent manner, and regulate the unique actin cytoskeleton of podocytes. Mutations in the NPHS1 gene that encodes nephrin cause congenital nephrotic syndrome (CNS), which is characterized by the loss of the SD and massive proteinuria. Recently, we have identified the expression of the transmembrane glycoprotein signal regulatory protein α (SIRPα) at the SD. In the present study, we analyzed the expression of SIRPα in developing kidneys, in kidneys from CNS patients and in proteinuric rat models. The possibility that SIRPα interacts with known SD proteins was also investigated. SIRPα was concentrated at the SD junction during the maturation of intercellular junctions. In the glomeruli of CNS patients carrying mutations in NPHS1, where SD formation is disrupted, the expression of SIRPα as well as Neph1 and nephrin was significantly decreased, indicating that SIRPα is closely associated with the nephrin complex. Indeed, SIRPα formed hetero‐oligomers with nephrin in cultured cells and in glomeruli. Furthermore, the cytoplasmic domain of SIRPα was highly phosphorylated in normal glomeruli, and its phosphorylation was dramatically decreased upon podocyte injury in vivo. Thus, SIRPα interacts with nephrin at the SD, and its phosphorylation is dynamically regulated in proteinuric states. Our data provide new molecular insights into the phosphorylation events triggered by podocyte injury.Structured digital abstract
Sirp‐alpha physically interacts with Nephrin by anti bait coimmunoprecipitation (View interaction)
Sirp‐alpha physically interacts with Nephrin by anti tag coimmunoprecipitation (View interaction)
Lens epithelium‐derived growth factor deSumoylation by Sumo‐specific protease‐1 regulates its transcriptional activation of small heat shock protein and the cellular response
Authors: Ishihara Keiichi , Fatma Nigar , Bhargavan Biju , Chhunchha Bhavana , Kubo Eri , Dey Sanjib , Takamura Yoshihiro , Kumar Anil , Singh Dhirendra P. 
Published: July 2012

Lens epithelium‐derived growth factor (LEDGF), a ubiquitously expressed nuclear protein, acts by interacting with DNA and protein and is involved in widely varying cellular functions. Despite its importance, the mechanism(s) that regulate naturally occurring LEDGF activity are unidentified. In the present study, we report that LEDGF is constitutively Sumoylated, and that the dynamical regulatory mechanism(s) (i.e. Sumoylation and deSumoylation) act as a molecular switch in modulating the DNA‐binding and transcriptional activity of LEDGF with the functional consequences. Using bioinformatics analysis coupled with in vitro and in vivo Sumoylation assays, we found that lysine (K) 364 of LEDGF was Sumoylated, repressing its transcriptional activity. Conversely, mutation of K364 to arginine (R) or deSumoylation by small ubiquitin‐like modifier (Sumo)‐specific protease‐1, a nuclear deSumoylase, enhanced the transactivation capacity of LEDGF and its cellular abundance. The enhancements were directly correlated with an increase in the DNA‐binding activity and small heat shock protein transcription of LEDGF, whereas the process was reversed in cells overexpressing Sumo1. Interestingly, cells expressing Sumoylation‐deficient pEGFP‐K364R protein showed increased cellular survival compared to wild‐type LEDGF protein. The findings provide insights into the regulation and regulatory functions of LEDGF in Sumoylation‐dependent transcriptional control that may be essential for modifying the physiology of cells to maintain cellular homeostasis. These studies also provide new evidence of the important role of post‐translational modification in controlling LEDGF function.Structured digital abstract
LEDGF and SUMO1 colocalize by fluorescence microscopy (View interaction)
LEDGFphysically interacts with SUMO1 by anti bait coimmunoprecipitation (View Interaction: 1, 2, 3)
Structure and stability of a thermostable carboxylesterase from the thermoacidophilic archaeon Sulfolobus tokodaii
Authors: Angkawidjaja Clement , Koga Yuichi , Takano Kazufumi , Kanaya Shigenori 
Published: July 2012

The hormone‐sensitive lipase (HSL) family is comprised of carboxylesterases and lipases with similarity to mammalian HSL. Thermophilic enzymes of this family have a high potential for use in biocatalysis. We prepared and crystallized a carboxylesterase of the HSL family from Sulfolobus tokodaii (Sto‐Est), and determined its structures in the presence and absence of an inhibitor. Sto‐Est forms a dimer in solution and the crystal structure suggests the presence of a stable biological dimer. We identified a residue close to the dimer interface, R267, which is conserved in archaeal enzymes of HSL family and is in close proximity to the same residue from the other monomer. Mutations of R267 to Glu, Gly and Lys were conducted and the resultant R267 mutants were characterized and crystallized. The structures of R267E, R267G and R267K are highly similar to that of Sto‐Est with only slight differences in atomic coordinates. The dimerized states of R267E and R267G are unstable under denaturing conditions or at high temperature, as shown by a urea‐induced dimer dissociation experiment and molecular dynamics simulation. R267E is the most unstable mutant protein, followed by R267G and R267K, as shown by the thermal denaturation curve and optimum temperature for activity. From the data, we discuss the importance of R267 in maintaining the dimer integrity of Sto‐Est.DatabaseThe atomic coordinates and structural factors have been deposited in the Protein Data Bank with accession numbers of PDB: 3AIK for noninhibited Sto‐Est, PDB: 3AIL for DEP‐bound, PDB: 3AIM for R267E, PDB: 3AIN for R267G, and PDB: 3AIO for R267KStructured digital abstract
Sto‐Es and Sto‐Es bind by comigration in gel electrophoresis (View Interaction: 1, 2)
Sto‐Es and Sto‐Es bind by x‐ray crystallography (View interaction)
SUSCEPTIBILITY OF MONOSPECIES AND DUAL‐SPECIES BIOFILMS OF STAPHYLOCOCCUS AUREUS AND ESCHERICHIA COLI TO ESSENTIAL OILS
Authors: MILLEZI F.M. , PEREIRA M.O. , BATISTA N.N. , CAMARGOS N. , AUAD I. , CARDOSO M.D.G. , PICCOLI R.H. 
Published: July 2012

ABSTRACTThe aim of this study was to investigate the susceptibility of Staphylococcus aureus and Escherichia coli biofilms formed on the polypropylene surface. The cultures were developed for 240 h, planktonic growth was characterized by colony‐forming unit (cfu)/mL and biofilms was characterized by quantifying biomass and cfu/cm2. Essential oils (EOs) of citronella and lemon were extracted by hydrodistillation and characterized by gas chromatography. Biofilm formation occured after 3 h of contact. In dual‐species biofilms, there was competition; S. aureus was the number of viable cells damaged by E. coli (P < 0.05). The EOs disinfectant action was similar in biofilms monospecies, viable cells and biomass decreased significantly. Dual‐species biofilms were more resistant to EOs. The action EOs on biofilm suggest promising alternatives to sanitize industrial polypropylene surfaces.PRACTICAL APPLICATIONSHistorically, the majority of new drugs has been generated from natural products (secondary metabolites) and from compounds derived from natural products. The extracts of higher plants have been and still are widely used to obtain substances with antimicrobial action. However, their low concentration in the extract often makes the purification processes or the synergistic action of the different compounds unfeasible, causing major problems for industries. Seeking to reduce the parameters involved in the isolation and purification of compounds, these essential oils (EOs) have been studied. They present high antimicrobial efficiency, and in appropriate concentrations they are considered safe. The antimicrobial activity of EOs was showed that such substances can be used with sanitizing agents in industrial surfaces against bacterial biofilms. However, this line of research is still very new, so it is important to continue research for the development of industrial sanitizing with EOs.
Effect of Small Change in Oil Phase Composition on Rheological and Textural Properties of w/o Emulsion
Authors: Lukic Milica , Jaksic Ivana , Krstonosic Veljko , Dokic Ljubica , Savic Snezana 
Published: July 2012

AbstractIn this work, we have modified oil phase composition in one component (mineral oil, isocetyl palmitate, special Olive butter and dimethicone 200/350) and the aim of our work was to establish the influence of that alteration on emulsion rheological and textural properties. Additionally, continuous and oscillatory rheological measurements along with texture analysis were assessed in order to predict emulsion application behavior. Based on the obtained results, the change of oil phase has induced a change in the observed rheological and textural parameters and investigated samples can be divided into two distinct groups: the first group – samples with special Olive butter and dimethicone 200/350 and the second group – samples with isocetyl palmitate and mineral oil. Results confirmed that instrumental measurements, as sensitive tools, can be used in order to differentiate emulsions regarding textural properties and especially regarding their actual usage and sensory properties.Practical ApplicationsIt is a known fact that the structure of semisolid systems can be characterized by various rheological and textural parameters that are also apt to define certain sensory attributes. Sensory attributes dependent on structure characteristics and flow properties, used for the description of the product in pickup and rub‐out phase, could be predicted by instrumental, i.e., rheological and textural measurements. Expensive and time‐consuming studies performed with human panelists could be, at least to some extent, replaced with simple rheological and textural measurements. These findings could also contribute to the faster and easier introduction of new raw materials, regarding their characterization and prediction of their influence on the final product characteristics. A combined approach like this could be helpful as both time and money‐saving tool for full characterization of a novel consumer‐acceptable emulsion product.
Differences in Chewing Behavior during Mastication of Foods with Different Textures
Authors: Shiozawa Megumi , Taniguchi Hiroshige , Hayashi Hirokazu , Hori Kazuhiro , Tsujimura Takanori , Nakamura Yuki , Ito Kayoko , Inoue Makoto 
Published: July 2012

AbstractThe present study was designed to evaluate how typical Japanese staple foods – rice and rice cake – with different physical properties influence the patterns of muscle activity during chewing. Six normal adults were asked to eat rice and rice cake freely in a natural manner. Surface electromyographic recordings of the masseter and suprahyoid muscles were performed. There were large differences between the foods in terms of masticatory duration. The masseter activity per cycle was significantly greater for rice cake than for rice. The masseter activity gradually decreased as chewing progressed, although the suprahyoid activity did not change throughout the sequence of rice cake chewing. The results suggest that the process of bolus formation with rice cake is very different from that with rice in terms of jaw‐closing and jaw‐opening muscle activities.Practical ApplicationsThis study aimed to examine how the masticatory sequence adapts to variations in the initial properties of foods. This research may enhance our understanding of the oral physiology of bolus formation and changes in the physical properties of foods during chewing.
Hypolipidemic Activity in Sprague–Dawley Rats and Constituents of a Novel Natural Vegetable Oil from Cornus Wilsoniana Fruits
Authors: Fu Jie , Zhang Xue‐Wei , Liu Kai , Li Qing‐Shan , Zhang Li‐Rong , Yang Xian‐Hui , Zhang Zhi‐Ming , Li Chang‐Zhu , Luo Yin , He Zhen‐Xiang , Zhu Hai‐Liang 
Published: July 2012

Abstract:  Cornus wilsoniana Wanger is a woody oil plant distributed in the south region of the Yellow River, China. Its oil has been taken as edible oil for over 100 y, and consumption of such oil is believed to prevent hyperlipidemia in Chinese folk recipe. This study has investigated the hypolipidemic effect of Cornus wilsoniana oil (CWO) in Sprague–Dawley rats. The results demonstrated that CWO could significantly decrease total cholesterol (TC), total triacylglycerol (TG), and low‐density lipoprotein cholesterol (HDL‐C) in serum, liver weight, hepatic TC, and TG. After analyzing the chemical constituents of CWO, we found that the content of unsaturated fatty acids (UFA) was very high (69.12%). Specially, the n‐6 polyunsaturated fatty acids (PUFA), including linoleic acid, γ‐linolenic acid, and 11,14‐eicosadienoic acid, accounted very great proportion (38.86%). The high hypolipidemic activity of CWO might be attributed to the lipid‐lowering functions of these polyunsaturated fatty acids. Molecular docking was further performed to study the binding model of fatty acids (FA) from CWO to a possible hypolipidemic target, peroxisome proliferator‐activated receptor δ (PPARδ). The results showed that linoleic acid and γ‐linolenic acid could bind PPARδ very well.Practical Application:  Cornus wilsoniana oil could be used as equilibrated dietary oil, not only having hypolipidemic function, but also helping to overcome essential fatty acids deficiency.
Top Food Sources Contributing to Vitamin D Intake and the Association of Ready‐to‐Eat Cereal and Breakfast Consumption Habits to Vitamin D Intake in Canadians and United States Americans
Authors: Hill Kathleen M. , Jonnalagadda Satya S. , Albertson Ann M. , Joshi Nandan A. , Weaver Connie M. 
Published: July 2012

Abstract:  This study aimed to determine dietary vitamin D intake of U.S. Americans and Canadians and contributions of food sources to total vitamin D intake. Total of  7‐ or 14‐d food intake data were analyzed for vitamin D by a proprietary nutrient assessment methodology that utilized food intake data from the Natl. Eating Trends® service, portion size data from NHANES 1999–2004, and nutrient values using the Univ. of Minnesota's Nutrition Data System for Research software. Study participants were 7837 U.S. Americans and 4025 Canadians, ≥2‐y‐old males and females. The main outcome measures were total dietary vitamin D intake, percent contribution of foods to total vitamin D intake, and vitamin D intake by cereal and breakfast consumption habits. ANOVA was used to determine differences in means or proportions by age and gender and according to breakfast consumption habits. Mean vitamin D intake ranged from 152 to 220 IU/d. Less than 2% of participants in all age groups from the United States and Canada met the 2011 Recommended Daily Allowance (RDA) for vitamin D from foods. Milk, meat, and fish were the top food sources for vitamin D for both Americans and Canadians. Ready‐to‐eat (RTE) cereal was a top 10 source of vitamin D for Americans but not Canadians. Vitamin D intake was higher with more frequent RTE cereal and breakfast consumption in both countries, largely attributable to greater milk intake.Practical Application:  Most U.S. Americans and Canadians do not meet the 2011 Inst. of Medicine recommended daily allowance (RDA) for vitamin D for their age groups from foods. Increasing breakfast and cereal consumption may be a useful strategy to increase dietary vitamin D intake to help individuals meet the RDA for vitamin D, particularly by increasing milk intake. However, it is likely that additional food fortification or vitamin D supplementation is required to achieve the RDA.
Expression of DnaJ Gene in Alicyclobacillus acidoterrestris under Stress Conditions by Quantitative Real‐Time PCR
Authors: Jiao Lingxia , Fan Mingtao , Hua Chengwei , Wang Shulin , Wei Xinyuan 
Published: July 2012

Abstract:  This article describes the cloning, sequence analysis and expression of the DnaJ gene from Alicyclobacillus acidoterrestris. The genome walking technique was used to clone the full‐length sequence of DnaJ and quantitative real‐time PCR was used to analyze DnaJ expression under stress conditions. AadnaJ (GenBank accession nr: HQ893544) containing an open reading frame of 1137 bp encoding 378 amino acid residues was cloned from A. acidoterrestris DSM 3922T. The nucleotide sequence of AadnaJ shows 77% homology with the DnaJ of A. acidocaldarius LAA1. The DnaJ expression level was upgraded rapidly under heat or acid stress. Its mRNA expression level reached a peak value at 25 min after the onset of heat stress (70 °C) and at 1 h after the onset of acid stress (pH = 1). Acid stress at pH 1 for 25 and 60 min led to the DnaJ expression levels 2.1 times and 35.7 times above that of the control, respectively. In response to cold stress at 0 °C, the DnaJ expression level decreased drastically to 0.04 times that of the control level after 1 h. The expression patterns of DnaJ in response to the stress conditions shown here explained the heat and acidity endurance of A. acidoterrestris.Practical Application:  This study directly addresses the role of the DnaJ gene in temperature and acid endurance in A. acidoterrestris. This provides a basis for the development of genetic and molecular techniques that may minimize the adverse effects of A. acidoterrestris in fruit juice production. This study also sheds light on the design of heat‐ and acid‐tolerant recombinases and the understanding of the molecular mechanisms underlying heat and acid resistance in A. acidoterrestris.
Inactivation Kinetics of Listeria monocytogenes by High‐Pressure Processing: Pressure and Temperature Variation
Authors: Doona Christopher J. , Feeherry Florence E. , Ross Edward W. , Kustin Kenneth 
Published: July 2012

Abstract:  The enhanced quasi‐chemical kinetics (EQCK) model is presented as a methodology to evaluate the nonlinear inactivation kinetics of baro‐resistant Listeria monocytogenes in a surrogate protein food system by high‐pressure processing (HPP) for various combinations of pressure (P= 207 to 414 MPa) and temperature (T= 20 to 50 °C). The EQCK model is based on ordinary differential equations derived from 6 “quasi‐chemical reaction” steps. The EQCK model continuously fits the conventional stages of the microbial lifecycle: lag, growth, stationary phase, and death; and tailing. Depending on the conditions, the inactivation kinetics of L. monocytogenes by HPP show a lag, inactivation, and tailing. Accordingly, we developed a customized, 4‐step subset version of the EQCK model sufficient to evaluate the HPP inactivation kinetics of L. monocytogenes and obtain values for the model parameters of lag (λ), inactivation rate (μ), rate constants (k), and “processing time” (tp). This latter parameter was developed uniquely to evaluate kinetics data showing tailing. Secondary models are developed by interrelating the fitting parameters with experimental parameters, and Monte Carlo simulations are used to evaluate parameter reproducibility. This 4‐step model is also compared with the empirical Weibull and Polylog models. The success of the EQCK model (as its 4‐step subset) for the HPP inactivation kinetics of baro‐resistant L. monocytogenes showing tailing establishes several advantages of the EQCK modeling approach for investigating nonlinear microbial inactivation kinetics, and it has implications for determining mechanisms of bacterial spore inactivation by HPP.Practical Application:  Results of this study will be useful to the many segments of the food processing industry (ready‐to‐eat meats, fresh produce, seafood, dairy) concerned with ensuring the safety of consumers from the health hazards of Listeria monocytogenes, particularly through the use of emerging food preservation technologies such as high‐pressure processing.