bluuebunny/crossref_metadata_2025_split huggingface dataset:
A genomics approach to understanding the role of auxin in apple (Malus x domestica)fruit size control
Authors: Devoghalaere Fanny , Doucen Thomas , Guitton Baptiste , Keeling Jeannette , Payne Wendy , Ling Toby John , Ross John James , Hallett Ian Charles , Gunaseelan Kularajathevan , Dayatilake GA , Diak Robert , Breen Ken C , Tustin D Stuart , Costes Evelyne , Chagné David , Schaffer Robert James , David Karine Myriam 
Published: January 2012

Abstract

Background
Auxin is an important phytohormone for fleshy fruit development, having been shown to be involved in the initial signal for fertilisation, fruit size through the control of cell division and cell expansion, and ripening related events. There is considerable knowledge of auxin-related genes, mostly from work in model species. With the apple genome now available, it is possible to carry out genomics studies on auxin-related genes to identify genes that may play roles in specific stages of apple fruit development.

Results
High amounts of auxin in the seed compared with the fruit cortex were observed in 'Royal Gala' apples, with amounts increasing through fruit development. Injection of exogenous auxin into developing apples at the start of cell expansion caused an increase in cell size. An expression analysis screen of auxin-related genes involved in auxin reception, homeostasis, and transcriptional regulation showed complex patterns of expression in each class of gene. Two mapping populations were phenotyped for fruit size over multiple seasons, and multiple quantitative trait loci (QTLs) were observed. One QTL mapped to a region containing an Auxin Response Factor (ARF106). This gene is expressed during cell division and cell expansion stages, consistent with a potential role in the control of fruit size.

Conclusions
The application of exogenous auxin to apples increased cell expansion, suggesting that endogenous auxin concentrations are at least one of the limiting factors controlling fruit size. The expression analysis of ARF106 linked to a strong QTL for fruit weight suggests that the auxin signal regulating fruit size could partially be modulated through the function of this gene. One class of gene (GH3) removes free auxin by conjugation to amino acids. The lower expression of these GH3 genes during rapid fruit expansion is consistent with the apple maximising auxin concentrations at this point.
Growth independent rhamnolipid production from glucose using the non-pathogenic Pseudomonas putida KT2440
Authors: Wittgens Andreas , Tiso Till , Arndt Torsten T , Wenk Pamela , Hemmerich Johannes , Müller Carsten , Wichmann Rolf , Küpper Benjamin , Zwick Michaela , Wilhelm Susanne , Hausmann Rudolf , Syldatk Christoph , Rosenau Frank , Blank Lars M 
Published: January 2012

Abstract

Background
Rhamnolipids are potent biosurfactants with high potential for industrial applications. However, rhamnolipids are currently produced with the opportunistic pathogen Pseudomonas aeruginosa during growth on hydrophobic substrates such as plant oils. The heterologous production of rhamnolipids entails two essential advantages: Disconnecting the rhamnolipid biosynthesis from the complex quorum sensing regulation and the opportunity of avoiding pathogenic production strains, in particular P. aeruginosa. In addition, separation of rhamnolipids from fatty acids is difficult and hence costly.

Results
Here, the metabolic engineering of a rhamnolipid producing Pseudomonas putida KT2440, a strain certified as safety strain using glucose as carbon source to avoid cumbersome product purification, is reported. Notably, P. putida KT2440 features almost no changes in growth rate and lag-phase in the presence of high concentrations of rhamnolipids (> 90 g/L) in contrast to the industrially important bacteria Bacillus subtilis, Corynebacterium glutamicum, and Escherichia coli. P. putida KT2440 expressing the rhlAB-genes from P. aeruginosa PAO1 produces mono-rhamnolipids of P. aeruginosa PAO1 type (mainly C10:C10). The metabolic network was optimized in silico for rhamnolipid synthesis from glucose. In addition, a first genetic optimization, the removal of polyhydroxyalkanoate formation as competing pathway, was implemented. The final strain had production rates in the range of P. aeruginosa PAO1 at yields of about 0.15 g/gglucose corresponding to 32% of the theoretical optimum. What's more, rhamnolipid production was independent from biomass formation, a trait that can be exploited for high rhamnolipid production without high biomass formation.

Conclusions
A functional alternative to the pathogenic rhamnolipid producer P. aeruginosa was constructed and characterized. P. putida KT24C1 pVLT31_rhlAB featured the highest yield and titer reported from heterologous rhamnolipid producers with glucose as carbon source. Notably, rhamnolipid production was uncoupled from biomass formation, which allows optimal distribution of resources towards rhamnolipid synthesis. The results are discussed in the context of rational strain engineering by using the concepts of synthetic biology like chassis cells and orthogonality, thereby avoiding the complex regulatory programs of rhamnolipid production existing in the natural producer P. aeruginosa.
β-conglycinin combined with fenofibrate or rosuvastatin have exerted distinct hypocholesterolemic effects in rats
Authors: Ferreira Ederlan S , Silva Maraiza A , Demonte Aureluce , Neves Valdir A 
Published: January 2012

Abstract

Background
There is increasing interest in non-pharmacological control of cholesterol and triglyceride levels in the plasma and diet-drug association represent an important area of studies. The objective of this study was to observe the hypocholesterolemic effect of soybean β-conglycinin (7S protein) alone and combined with fenofibrate and rosuvastatin, two hypolipidemic drugs.

Methods
The protein and drugs were administered orally once a day to rats and the effects were evaluated after 28 days. Wistar rats were divided into six groups (n = 9): hypercholesterolemic diet (HC), HC+7S protein (300 mg.kg-1 day-1) (HC-7S), HC+fenofibrate (30 mg.kg-1 day-1)(HC-FF), HC+rosuvastatin (10 mg.kg-1 day-1)(HC-RO), HC+7S+fenofibrate (HC-7S-FF) and HC+7S+rosuvastatin (HC-7S-RO).

Results
Animals in HC-7S, HC-FF and HC-RO exhibited reductions of 22.9, 35.8 and 18.8% in total plasma cholesterol, respectively. In HC-7S-FF, animals did not show significant alteration of the level in HC+FF while the group HC-7S-RO showed a negative effect in comparison with groups taking only protein (HC-7S) or drug (HC-RO). The administration of the protein, fenofibrate and rosuvastatin alone caused increases in the plasma HDL-C of the animals, while the protein-drug combinations led to an increase compared to HC-FF and HC-RO. The plasma concentration of triacylgycerides was significantly reduced in the groups without association, while HC-7S-FF showed no alteration and HC-7S-RO a little reduction.

Conclusion
The results of our study indicate that conglycinin has effects comparable to fenofibrate and rosuvastatin on the control of plasma cholesterol, HDL-C and triacylglycerides, when given to hypercholesterolemic rats, and suggests that the association of this protein with rosuvastatin alters the action of drug in the homeostasis of cholesterol.
Metal work-function-dependent barrier height of Ni contacts with metal-embedded nanoparticles to 4H-SiC
Authors: Kang Min-Seok , Ahn Jung-Joon , Moon Kyoung-Sook , Koo Sang-Mo 
Published: January 2012

Abstract
Metal, typically gold [Au], nanoparticles [NPs] embedded in a capping metal contact layer onto silicon carbide [SiC] are considered to have practical applications in changing the barrier height of the original contacts. Here, we demonstrate the use of silver [Ag] NPs to effectively lower the barrier height of the electrical contacts to 4H-SiC. It has been shown that the barrier height of the fabricated SiC diode structures (Ni with embedded Ag-NPs) has significantly reduced by 0.11 eV and 0.18 eV with respect to the samples with Au-NPs and the reference samples, respectively. The experimental results have also been compared with both an analytic model based on Tung's theory and physics-based two-dimensional numerical simulations.
Near optimal bound of orthogonal matching pursuit using restricted isometric constant
Authors: Wang Jian , Kwon Seokbeop , Shim Byonghyo 
Published: January 2012

Abstract
As a paradigm for reconstructing sparse signals using a set of under sampled measurements, compressed sensing has received much attention in recent years. In identifying the sufficient condition under which the perfect recovery of sparse signals is ensured, a property of the sensing matrix referred to as the restricted isometry property (RIP) is popularly employed. In this article, we propose the RIP based bound of the orthogonal matching pursuit (OMP) algorithm guaranteeing the exact reconstruction of sparse signals. Our proof is built on an observation that the general step of the OMP process is in essence the same as the initial step in the sense that the residual is considered as a new measurement preserving the sparsity level of an input vector. Our main conclusion is that if the restricted isometry constant δ

K
of the sensing matrix satisfies

δ

K

<

K
-
1

K
-
1
+
K

then the OMP algorithm can perfectly recover K(> 1)-sparse signals from measurements. We show that our bound is sharp and indeed close to the limit conjectured by Dai and Milenkovic.
Dual-task motor performance with a tongue-operated assistive technology compared with hand operations
Authors: Johnson Ashley N , Huo Xueliang , Ghovanloo Maysam , Shinohara Minoru 
Published: January 2012

Abstract

Background
To provide an alternative motor modality for control, navigation, and communication in individuals suffering from impairment or disability in hand functions, a Tongue Drive System (TDS) has been developed that allows for real time tracking of tongue motion in an unobtrusive, wireless, and wearable device that utilizes the magnetic field generated by a miniature disk shaped magnetic tracer attached to the tip of the tongue. The purpose of the study was to compare the influence of a concurrent motor or cognitive task on various aspects of simple movement control between hand and tongue using the TDS technology.

Methods
Thirteen young able-bodied adults performed rapid and slow goal-directed movements of hand and tongue (with TDS) with and without a concurrent motor (hand or tongue) or cognitive (arithmetic and memory) task. Changes in reaction time, completion time, speed, correctness, accuracy, variability of displacement, and variability of time due to the addition of a concurrent task were compared between hand and tongue.

Results
The influence of an additional concurrent task on motor performance was similar between the hand and tongue for slow movement in controlling their displacement. In rapid movement with a concurrent motor task, most aspects of motor performance were degraded in hand, while tongue speed during rapid continuous task was maintained. With a concurrent cognitive task, most aspects of motor performance were degraded in tongue, while hand accuracy during the rapid discrete task and hand speed during the rapid continuous task were maintained.

Conclusion
Rapid goal-directed hand and tongue movements were more consistently susceptible to interference from concurrent motor and cognitive tasks, respectively, compared with the other movement.
A novel study on amyloid β peptide 40, 42 and 40/42 ratio in Saudi autistics
Authors: Al-Ayadhi Laila Y , Ben Bacha Abir G , Kotb Malak , El-Ansary Afaf K 
Published: January 2012

Abstract

Objectives
We examined whether plasma concentrations of amyloid beta (Aβ) as protein derivatives play a central role in the etiology of autistic features.

Design and Methods
Concentrations of human Aβ (1-42), Aβ (1-40), and Aβ (40/42) in the plasma of 52 autistic children (aged 3-16 years) and 36 age-matched control subjects were determined by using the ELISA technique and were compared.

Results
Compared to control subjects, autistic children exhibited significantly lower concentrations of both Aβ (1-40) and Aβ (1-42) and lower Aβ (40/42) concentration ratio. Receiver operating characteristics curve (ROC) analysis showed that these measurements of Aβ peptides showed high specificity and sensitivity in distinguishing autistic children from control subjects.

Conclusions
Lower concentrations of Aβ (1-42) and Aβ (1-40) were attributed to loss of Aβ equilibrium between the brain and blood, an imbalance that may lead to failure to draw Aβ from the brain and/or impairment of β- and γ- secretase's concentration or kinetics as enzymes involving in Aβ production.
Precursor uptake assays and metabolic analyses in isolated tomato fruit chromoplasts
Authors: Angaman Djédoux Maxime , Petrizzo Rocco , Hernández-Gras Francesc , Romero-Segura Carmen , Pateraki Irene , Busquets Montserrat , Boronat Albert 
Published: January 2012

Abstract

Background
Carotenoids are the most widespread group of pigments found in nature. In addition to their role in the physiology of the plant, carotenoids also have nutritional relevance as their incorporation in the human diet provides health benefits. In non-photosynthetic tissues, carotenoids are synthesized and stored in specialized plastids called chromoplasts. At present very little is known about the origin of the metabolic precursors and cofactors required to sustain the high rate of carotenoid biosynthesis in these plastids. Recent proteomic data have revealed a number of biochemical and metabolic processes potentially operating in fruit chromoplasts. However, considering that chloroplast to chromoplast differentiation is a very rapid process during fruit ripening, there is the possibility that some of the proteins identified in the proteomic analysis could represent remnants no longer having a functional role in chromoplasts. Therefore, experimental validation is necessary to prove whether these predicted processes are actually operative in chromoplasts.

Results
A method has been established for high-yield purification of tomato fruit chromoplasts suitable for metabolic studies. Radiolabeled precursors were efficiently incorporated and further metabolized in isolated chromoplast. Analysis of labeled lipophilic compounds has revealed that lipid biosynthesis is a very efficient process in chromoplasts, while the relatively low incorporation levels found in carotenoids suggest that lipid production may represent a competing pathway for carotenoid biosynthesis. Malate and pyruvate are efficiently converted into acetyl-CoA, in agreement with the active operation of the malic enzyme and the pyruvate dehydrogenase complex in the chromoplast. Our results have also shown that isolated chromoplasts can actively sustain anabolic processes without the exogenous supply of ATP, thus suggesting that these organelles may generate this energetic cofactor in an autonomous way.

Conclusions
We have set up a method for high yield purification of intact tomato fruit chromoplasts suitable for precursor uptake assays and metabolic analyses. Using targeted radiolabeled precursors we have been able to unravel novel biochemical and metabolic aspects related with carotenoid and lipid biosynthesis in tomato fruit chromoplasts. The reported chromoplast system could represent a valuable platform to address the validation and characterization of functional processes predicted from recent transcriptomic and proteomic data.
Engineering better biomass-degrading ability into a GH11 xylanase using a directed evolution strategy
Authors: Song Letian , Siguier Béatrice , Dumon Claire , Bozonnet Sophie , O'Donohue Michael J 
Published: January 2012

AbstractBackgroundImproving the hydrolytic performance of hemicellulases on lignocellulosic biomass is of considerable importance for second-generation biorefining. To address this problem, and also to gain greater understanding of structure-function relationships, especially related to xylanase action on complex biomass, we have implemented a combinatorial strategy to engineer the GH11 xylanase fromThermobacillus xylanilyticus(Tx-Xyn).ResultsFollowingin vitroenzyme evolution and screening on wheat straw, nine best-performing clones were identified, which display mutations at positions 3, 6, 27 and 111. All of these mutants showed increased hydrolytic activity on wheat straw, and solubilized arabinoxylans that were not modified by the parental enzyme. The most active mutants, S27T and Y111T, increased the solubilization of arabinoxylans from depleted wheat straw 2.3-fold and 2.1-fold, respectively, in comparison to the wild-type enzyme. In addition, five mutants, S27T, Y111H, Y111S, Y111T and S27T-Y111H increased total hemicellulose conversion of intact wheat straw from 16.7%tot. xyl(wild-type Tx-Xyn) to 18.6% to 20.4%tot. xyl. Also, all five mutant enzymes exhibited a better ability to act in synergy with a cellulase cocktail (Accellerase 1500), thus procuring increases in overall wheat straw hydrolysis.ConclusionsAnalysis of the results allows us to hypothesize that the increased hydrolytic ability of the mutants is linked to (i) improved ligand binding in a putative secondary binding site, (ii) the diminution of surface hydrophobicity, and/or (iii) the modification of thumb flexibility, induced by mutations at position 111. Nevertheless, the relatively modest improvements that were observed also underline the fact that enzyme engineering alone cannot overcome the limits imposed by the complex organization of the plant cell wall and the lignin barrier.
Molecular prediction for atherogenic risks across different cell types of leukocytes
Authors: Cheng Feng , Keeley Ellen C , Lee Jae K 
Published: January 2012

Abstract

Background
Diagnosing subclinical atherosclerosis is often difficult since patients are asymptomatic. In order to alleviate this limitation, we have developed a molecular prediction technique for predicting patients with atherogenic risks using multi-gene expression biomarkers on leukocytes.

Methods
We first discovered 356 expression biomarkers which showed significant differential expression between genome-wide microarray data of monocytes from patients with familial hyperlipidemia and increased risk of atherosclerosis compared to normal controls. These biomarkers were further triaged with 56 biomarkers known to be directly related to atherogenic risks. We also applied a COXEN algorithm to identify concordantly expressed biomarkers between monocytes and each of three different cell types of leukocytes. We then developed a multi-gene predictor using all or three subsets of these 56 biomarkers on the monocyte patient data. These predictors were then applied to multiple independent patient sets from three cell types of leukocytes (macrophages, circulating T cells, or whole white blood cells) to predict patients with atherogenic risks.

Results
When the 56 predictor was applied to the three patient sets from different cell types of leukocytes, all significantly stratified patients with atherogenic risks from healthy people in these independent cohorts. Concordantly expressed biomarkers identified by the COXEN algorithm provided slightly better prediction results.

Conclusion
These results demonstrated the potential of molecular prediction of atherogenic risks across different cell types of leukocytes.
Nasopharyngeal carriage rate of Streptococcus pneumoniae in Ugandan children with sickle cell disease
Authors: Kateete David P , Kajumbula Henry , Kaddu-Mulindwa Deogratias H , Ssevviri Augustine K 
Published: January 2012

AbstractBackgroundNasopharyngeal carriage ofStreptococcus pneumoniaeis a determinant for invasive pneumococcal disease, which often complicates homozygous sickle cell disease. Here, we determined the nasopharyngeal carriage rate ofS. pneumoniaein Ugandan children with homozygous sickle cell disease, who attended the outpatient Sickle Cell Clinic at Mulago National Referral hospital in Kampala, Uganda.ResultsS. pneumoniaeoccurred in 27 of the 81 children with homozygous sickle cell disease (giving a carriage rate of 33%, 27/81). Twenty three children were previously hospitalized of whomS. pneumoniaeoccurred in only two (9%, 2/23), while among the 58 who were not previously hospitalized it occurred in 25 (43%, 25/58, χ2= 8.8,p= 0.003), meaning there is an association between high carriage rate and no hospitalization. Two children previously immunized with the pneumococcal conjugate vaccine did not carry the organism. Prior antimicrobial usage was reported in 53 children (65%, 53/81). There was high resistance of pneumococci to penicillin (100%, 27/27) and trimethoprime-sulfamethoxazole (97%, 26/27), but low resistance to other antimicrobials. Of the 70 children without sickle cell disease,S. pneumoniaeoccurred in 38 (54%, 38/70) of whom 43 were males and 27 females (53% males, 23/43, and 56% females, 15/27).ConclusionNasopharyngeal carriage of penicillin resistant pneumococci in Ugandan children with homozygous sickle cell disease is high. While nasopharyngeal carriage ofS. pneumoniaeis a determinant for invasive pneumococcal disease, pneumococcal bacteremia is reportedly low in Ugandan children with sickle cell disease. Studies on the contribution of high carriage rates to invasive pneumococcal disease in these children will be helpful. This is the first report on pneumococcal carriage rate in Ugandan children with sickle cell disease.
Sialoglycoproteins adsorbed byPseudomonas aeruginosafacilitate their survival by impeding neutrophil extracellular trap through siglec-9
Authors: Khatua Biswajit , Bhattacharya Kaushik , Mandal Chitra 
Published: January 2012

ABSTRACTPA is an opportunistic pathogen that is commonly associated with severe infection in immunocompromised hosts. Siglec-9 binds with Sias by cis interaction on the neutrophil surface, thereby reducing immunological activity. However, neutrophils bind with pathogens through trans interactions of siglec-9 with Sias. Neutrophils kill invading pathogens by NETs, along with extracellular phagocytosis. Here, we report the mode of the adsorption of Sias by PA from host serum, the interaction of PA+Sias with human neutrophils, and the resulting neutrophil immunological activity. The α2–3-linked sialoglycoproteins adsorbed by PA exhibited potent binding with the soluble siglec-9-Fc chimeras, CHO-siglec-9 and siglec-9 on neutrophils. The binding between PA+Sias and neutrophils was blocked by the synthetic sialoglycan Neu5Acα2–3Galβ1–4GlcNAc, confirming the linkage-specific, Sias–siglec-9 interaction. The PA+Sias and siglec-9 interaction on neutrophils reduced the level of ROS and the release of elastase, resulting in a reduction of NETs formation, demonstrating the role of the sialoglycoproteins adsorbed by PA in the weakening of neutrophil activity. The resistance of PA+Sias to NETs was made evident by the increased survival of PA+Sias. Moreover, the decrease in PA−Sias survival demonstrated the involvement of NETs formation in the absence of the Sias–siglec-9 interaction. N-actylcysteine or sivelestat-pretreated neutrophils enhanced the survival of PA−Sias. DNAse-pretreated neutrophils did not exhibit any NETs formation, resulting in the enhanced escape of PA−Sias. Taken together, one of the survival mechanisms of PA+Sias is the diminution of innate immunity via its adsorption of sialoglycoproteins by its engagement of the inhibitory molecule siglec-9. This is possibly a general mechanism for pathogens that cannot synthesize Sias to subvert immunity.