bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolution of anterior Hox regulatory elements among chordates
Authors: Natale Alfonso , Sims Carrie , Chiusano Maria L , Amoroso Alessandro , D'Aniello Enrico , Fucci Laura , Krumlauf Robb , Branno Margherita , Locascio Annamaria 
Published: November 2011

Abstract

Background
The Hox family of transcription factors has a fundamental role in segmentation pathways and axial patterning of embryonic development and their clustered organization is linked with the regulatory mechanisms governing their coordinated expression along embryonic axes. Among chordates, of particular interest are the Hox paralogous genes in groups 1-4 since their expression is coupled to the control of regional identity in the anterior nervous system, where the highest structural diversity is observed.

Results
To investigate the degree of conservation in cis-regulatory components that form the basis of Hox expression in the anterior nervous system, we have used assays for transcriptional activity in ascidians and vertebrates to compare and contrast regulatory potential. We identified four regulatory sequences located near the CiHox1, CiHox2 and CiHox4 genes of the ascidian Ciona intestinalis which direct neural specific domains of expression. Using functional assays in Ciona and vertebrate embryos in combination with sequence analyses of enhancer fragments located in similar positions adjacent to Hox paralogy group genes, we compared the activity of these four Ciona cis-elements with a series of neural specific enhancers from the amphioxus Hox1-3 genes and from mouse Hox paralogous groups 1-4.

Conclusions
This analysis revealed that Kreisler and Krox20 dependent enhancers critical in segmental regulation of the hindbrain appear to be specific for the vertebrate lineage. In contrast, neural enhancers that function as Hox response elements through the action of Hox/Pbx binding motifs have been conserved during chordate evolution. The functional assays reveal that these Hox response cis-elements are recognized by the regulatory components of different and extant species. Together, our results indicate that during chordate evolution, cis-elements dependent upon Hox/Pbx regulatory complexes, are responsible for key aspects of segmental Hox expression in neural tissue and appeared with urochordates after cephalochordate divergence.
Microsatellite distribution on sex chromosomes at different stages of heteromorphism and heterochromatinization in two lizard species (Squamata: Eublepharidae: Coleonyx elegans and Lacertidae: Eremias velox)
Authors: Pokorná Martina , Kratochvíl Lukáš , Kejnovský Eduard 
Published: November 2011

Abstract

Background
The accumulation of repetitive sequences such as microsatellites during the differentiation of sex chromosomes has not been studied in most squamate reptiles (lizards, amphisbaenians and snakes), a group which has a large diversity of sex determining systems. It is known that the Bkm repeats containing tandem arrays of GATA tetranucleotides are highly accumulated on the degenerated W chromosomes in advanced snakes. Similar, potentially homologous, repetitive sequences were found on sex chromosomes in other vertebrates. Using FISH with probes containing all possible mono-, di-, and tri-nucleotide sequences and GATA, we studied the genome distribution of microsatellite repeats on sex chromosomes in two lizard species (the gecko Coleonyx elegans and the lacertid Eremias velox) with independently evolved sex chromosomes. The gecko possesses heteromorphic euchromatic sex chromosomes, while sex chromosomes in the lacertid are homomorphic and the W chromosome is highly heterochromatic. Our aim was to test whether microsatellite distribution on sex chromosomes corresponds to the stage of their heteromorphism or heterochromatinization. Moreover, because the lizards lie phylogenetically between snakes and other vertebrates with the Bkm-related repeats on sex chromosomes, the knowledge of their repetitive sequence is informative for the determination of conserved versus convergently evolved repetitive sequences across vertebrate lineages.

Results
Heteromorphic sex chromosomes of C. elegans do not show any sign of microsatellite accumulation. On the other hand, in E. velox, certain microsatellite sequences are extensively accumulated over the whole length or parts of the W chromosome, while others, including GATA, are absent on this heterochromatinized sex chromosome.

Conclusion
The accumulation of microsatellite repeats corresponds to the stage of heterochromatinization of sex chromosomes rather than to their heteromorphism. The lack of GATA repeats on the sex chromosomes of both lizards suggests that the Bkm-related repeats on sex chromosomes in snakes and other vertebrates evolved convergently. The comparison of microsatellite sequences accumulated on sex chromosomes in E. velox and in other eukaryotic organisms suggests that historical contingency, not characteristics of particular sequences, plays a major role in the determination of which microsatellite sequence is accumulated on the sex chromosomes in a particular lineage.
QTL detection for Aeromonas salmonicida resistance related traits in turbot (Scophthalmus maximus)
Authors: Rodríguez-Ramilo Silvia T , Toro Miguel A , Bouza Carmen , Hermida Miguel , Pardo Belén G , Cabaleiro Santiago , Martínez Paulino , Fernández Jesús 
Published: November 2011

Abstract

Background
Interactions between fish and pathogens, that may be harmless under natural conditions, often result in serious diseases in aquaculture systems. This is especially important due to the fact that the strains used in aquaculture are derived from wild strains that may not have had enough time to adapt to new disease pressures. The turbot is one of the most promising European aquaculture species. Furunculosis, caused by the bacterium Aeromonas salmonicida, produces important losses to turbot industry. An appealing solution is to achieve more robust broodstock, which can prevent or diminish the devastating effects of epizooties. Genomics strategies have been developed in turbot to look for candidate genes for resistance to furunculosis and a genetic map with appropriate density to screen for genomic associations has been also constructed. In the present study, a genome scan for QTL affecting resistance and survival to A. salmonicida in four turbot families was carried out. The objectives were to identify consistent QTL using different statistical approaches (linear regression and maximum likelihood) and to locate the tightest associated markers for their application in genetic breeding strategies.

Results
Significant QTL for resistance were identified by the linear regression method in three linkage groups (LGs 4, 6 and 9) and for survival in two LGs (6 and 9). The maximum likelihood methodology identified QTL in three LGs (5, 6 and 9) for both traits. Significant association between disease traits and genotypes was detected for several markers, some of them explaining up to 17% of the phenotypic variance. We also identified candidate genes located in the detected QTL using data from previously mapped markers.

Conclusions
Several regions controlling resistance to A. salmonicida in turbot have been detected. The observed concordance between different statistical methods at particular linkage groups gives consistency to our results. The detected associated markers could be useful for genetic breeding strategies. A finer mapping will be necessary at the detected QTL intervals to narrow associations and around the closely associated markers to look for candidate genes through comparative genomics or positional cloning strategies. The identification of associated variants at specific genes will be essential, together with the QTL associations detected in this study, for future marker assisted selection programs.
Identification of novel maize miRNAs by measuring the precision of precursor processing
Authors: Jiao Yinping , Song Weibin , Zhang Mei , Lai Jinsheng 
Published: November 2011

Abstract

Background
miRNAs are known to play important regulatory roles throughout plant development. Until recently, nearly all the miRNAs in maize were identified by comparative analysis to miRNAs sequences of other plant species, such as rice and Arabidopsis.

Results
To find new miRNA in this important crop, small RNAs from mixed tissues were sequenced, resulting in over 15 million unique sequences. Our sequencing effort validated 23 of the 28 known maize miRNA families, including 49 unique miRNAs. Using a newly established criterion, based on the precision of miRNA processing from precursors, we identified 66 novel miRNAs in maize. These miRNAs can be grouped into 58 families, 54 of which have not been identified in any other species. Five new miRNAs were validated by northern blot. Moreover, we found targets for 23 of the 66 new miRNAs. The targets of two of these newly identified miRNAs were confirmed by 5'RACE.

Conclusion
We have implemented a novel method of identifying miRNA by measuring the precision of miRNA processing from precursors. Using this method, 66 novel miRNAs and 50 potential miRNAs have been identified in maize.
Characterization of heterogeneous vancomycin-intermediate resistance, MIC and accessory gene regulator (agr) dysfunction among clinical bloodstream isolates of staphyloccocus aureus
Authors: Harigaya Yoriko , Ngo Dung , Lesse Alan J , Huang Vanthida , Tsuji Brian T 
Published: November 2011

Abstract

Background
The development of hVISA has been associated with vancomycin clinical failures and is commonly misidentified in clinical microbiology laboratories. Therefore, the objectives of this present study was to improve the reliability of methodologies and criteria for identifying hVISA, evaluate the prevalence of hVISA among clinical bloodstream isolates of S. aureus and determine if there exists a relationship between accessory gene regulator (agr) dysfunction and the hVISA phenotype.

Methods
The presence of hVISA in 220 clinical S. aureus isolates (121 MSSA, 99 MRSA) from bloodstream infections was examined by CLSI broth microdilution, Macro & Standard Etest. Isolates which were classified as hVISA by Macro Etest, were additionally evaluated using a modified PAP-AUC method using a modified starting inoculum of 1010 CFU/mL, and growth on brain heart infusion agar with 4 mg/L vancomycin (BHIV4) at 108 and 1010 CFU/mL, and agr function was assessed by delta-hemolysin production.

Results
Broth microdilution MIC50/90 of S.aureus and hVISA was 1.0/2.0 and 1.5/2.0 mg/L (p= 0.02), respectively. Macro Etest identified 12 (5.5%) hVISA isolates; higher among MRSA (9.1%) versus MSSA (2.5%) (p = 0.03). The mean modified PAP-AUC ratios (> 0.8) of 7 MRSA strains and 3 MSSA strains were significantly different (p = 0.001). 58% of hVISA strains were found to be agr dysfunctional when 21% of MRSA strains were agr dysfunctional. hVISA was detected among S. aureus bloodstream isolates, which were classified as susceptible among clinical microbiology laboratories.

Conclusions
Evaluating the correlation between Etest MICs and modified PAP-AUC ratio values will add further improvement of discriminating hVISA, and agr dysfunction may be predictive of strains which display a greater predilection to display the hVISA phenotype.
Validation of metabolic syndrome using medical records in the SUN cohort
Authors: Barrio-Lopez Maria Teresa , Bes-Rastrollo Maira , Beunza Juan Jose , Fernandez-Montero Alejandro , Garcia-Lopez Martin , Martinez-Gonzalez Miguel Angel 
Published: November 2011

Abstract

Background
The objective of this study was to evaluate the validity of self reported criteria of Metabolic Syndrome (MS) in the SUN (Seguimiento Universidad de Navarra) cohort using their medical records as the gold standard.

Methods
We selected 336 participants and we obtained MS related data according to Adult Treatment Panel III (ATP III) and International Diabetes Federation (IDF). Then we compared information on the self reported diagnosis of MS and MS diagnosed in their medical records. We calculated the proportion of confirmed MS, the proportion of confirmed non-MS and the intraclass correlation coefficients for each component of the MS.

Results
From those 336 selected participants, we obtained sufficient data in 172 participants to confirm or reject MS using ATP III criteria. The proportion of confirmed MS was 91.2% (95% CI: 80.7- 97.1) and the proportion of confirmed non-MS was 92.2% (95% CI: 85.7-96.4) using ATP III criteria. The proportion of confirmed MS using IDF criteria was 100% (95% CI: 87.2-100) and the proportion of confirmed non-MS was 97.1% (95% CI: 85.1-99.9). Kappa Index was 0.82 in the group diagnosed by ATP III criteria and 0.97 in the group diagnosed by IDF criteria. Intraclass correlation coefficients for the different component of MS were: 0.93 (IC 95%:0.91- 0.95) for BMI; 0.96 (IC 95%: 0.93-0.98) for waist circumference; 0.75 (IC 95%: 0.66-0.82) for fasting glucose; 0.50 (IC 95%:0.35-0.639) for HDL cholesterol; 0.78 (IC 95%: 0.70-0.84) for triglycerides; 0.49 (IC 95%:0.34-0.61) for systolic blood pressure and 0.55 (IC 95%: 0.41-0.65) for diastolic blood pressure.

Conclusions
Self-reported MS based on self reported components of the SM in a Spanish cohort of university graduates was sufficiently valid as to be used in epidemiological studies.
Efficient production of chimeric Human papillomavirus 16 L1 protein bearing the M2e influenza epitope in Nicotiana benthamiana plants
Authors: Matić Slavica , Rinaldi Riccardo , Masenga Vera , Noris Emanuela 
Published: November 2011

Abstract

Background

Human papillomavirus 16 (HPV-16) L1 protein has the capacity to self-assemble into capsomers or virus-like particles (VLPs) that are highly immunogenic, allowing their use in vaccine production. Successful expression of HPV-16 L1 protein has been reported in plants, and plant-produced VLPs have been shown to be immunogenic after administration to animals.

Results
We investigated the potential of HPV-16 L1 to act as a carrier of two foreign epitopes from Influenza A virus: (i) M2e2-24, ectodomain of the M2 protein (M2e), that is highly conserved among all influenza A isolates, or (ii) M2e2-9, a shorter version of M2e containing the N-terminal highly conserved epitope, that is common for both M1 and M2 influenza proteins. A synthetic HPV-16 L1 gene optimized with human codon usage was used as a backbone gene to design four chimeric sequences containing either the M2e2-24 or the M2e2-9 epitope in two predicted surface-exposed L1 positions. All chimeric constructs were transiently expressed in plants using the Cowpea mosaic virus-derived expression vector, pEAQ-HT. Chimeras were recognized by a panel of linear and conformation-specific anti HPV-16 L1 MAbs, and two of them also reacted with the anti-influenza MAb. Electron microscopy showed that chimeric proteins made in plants spontaneously assembled in higher order structures, such as VLPs of T = 1 or T = 7 symmetry, or capsomers.

Conclusions
In this study, we report for the first time the transient expression and the self-assembly of a chimeric HPV-16 L1 bearing the M2e influenza epitope in plants, representing also the first record of a successful expression of chimeric HPV-16 L1 carrying an epitope of a heterologous virus in plants. This study further confirms the usefulness of human papillomavirus particles as carriers of exogenous epitopes and their potential relevance for the production in plants of monovalent or multivalent vaccines.
Leaf extracts from Nitraria retusa promote cell population growth of human cancer cells by inducing apoptosis
Authors: Boubaker Jihed , Bhouri Wissem , Sghaier Mohamed Ben , Bouhlel Ines , Skandrani Ines , Ghedira Kamel , Chekir-Ghedira Leila 
Published: November 2011

Abstract

Background
In this report the phytochemical profile of Nitraria. Retusa (N. Retusa) leaf extracts were identified and their ability to induce apoptosis in human chronic myelogenous erythroleukaemia (K562) was evaluated.

Methods
Apoptosis of the human chronic myelogenous erythroleukaemia (K562) was evidenced by investigating DNA fragmentation, PARP cleavage and caspases 3 and 8 inducing activities, in the presence of N. retusa extracts.

Results
Our study revealed that the tested extracts from N. Retusa contain many useful bioactive compounds. They induced in a time-dependent manner the apoptosis the tested cancerous our cell line. This result was confirmed by ladder DNA fragmentation profile and PARP cleavage, as well as a release in caspase-3 and caspase-8 level.

Conclusion
Our results indicate that the tested compounds have a significant antiproliferative effect which may be due to their involvement in the induction of the extrinsic apoptosic pathway.
The effect of short-term canola oil ingestion on oxidative stress in the vasculature of stroke-prone spontaneously hypertensive rats
Authors: Papazzo Annateresa , Conlan Xavier , Lexis Louise , Lewandowski Paul 
Published: November 2011

Abstract

Background
This study aimed to determine if 25 days of canola oil intake in the absence of excess dietary salt or together with salt loading affects antioxidant and oxidative stress markers in the circulation. A further aim was to determine the mRNA expression of NADPH oxidase subunits and superoxide dismutase (SOD) isoforms in the aorta of stroke-prone spontaneously hypertensive (SHRSP) rats.

Methods
Male SHRSP rats, were fed a defatted control diet containing 10% wt/wt soybean oil or a defatted treatment diet containing 10% wt/wt canola oil, and given tap water or water containing 1% NaCl. Blood was collected at the end of study for analysis of red blood cell (RBC) antioxidant enzymes, RBC and plasma malondialdehyde (MDA), plasma 8-isoprostane and plasma lipids. The aorta was removed and the mRNA expression of NOX2, p22
phox
, CuZn-SOD, Mn-SOD and EC-SOD were determined.

Results
In the absence of salt, canola oil reduced RBC SOD and glutathione peroxidase, and increased total cholesterol and LDL cholesterol compared with soybean oil. RBC glutathione peroxidase activity was significantly lower in both the salt loaded groups compared to the soybean oil only group. In addition, RBC MDA and plasma HDL cholesterol were significantly higher in both the salt loaded groups compared to the no salt groups. Plasma MDA concentration was higher and LDL cholesterol concentration lower in the canola oil group loaded with salt compared to the canola oil group without salt. The mRNA expression of NADPH oxidase subunits and SOD isoforms were significantly reduced in the canola oil group with salt compared to canola oil group without salt.

Conclusion
In conclusion, these results indicate that canola oil reduces antioxidant status and increases plasma lipids, which are risk factors for cardiovascular disease. However, canola oil in combination with salt intake increased MDA, a marker of lipid peroxidation and decreased NAPDH oxidase subunits and aortic SOD gene expression.
Autonomic nervous system and lipid metabolism: findings in anxious-depressive spectrum and eating disorders
Authors: Pistorio Elisabetta , Luca Maria , Luca Antonina , Messina Vincenzo , Calandra Carmela 
Published: November 2011

Abstract

Objective
To correlate lipid metabolism and autonomic dysfunction with anxious-depressive spectrum and eating disorders. To propose the lipid index (LI) as a new possible biomarker.

Methods
95 patients and 60 controls were enrolled from the University Psychiatry Unit of Catania and from general practitioners (GPs). The patients were divided into four pathological groups: Anxiety, Depression, Anxious-Depressive Disorder and Eating Disorders [Diagnostic and Statistical Manual of Mental Disorders Fourth Edition Text Revision (DSM-IV-TR) official/appendix criteria]. The levels of the cholesterol, triglycerides and apolipoproteins A and B were determined. The LI, for each subject, was obtained through a mathematical operation on the values of the cholesterol and triglycerides levels compared with the maximum cut-off of the general population. The autonomic functioning was tested with Ewing battery tests. Particularly, the correlation between heart rate variability (HRV) and lipid metabolism has been investigated.

Results
Pathological and control groups, compared among each other, presented some peculiarities in the lipid metabolism and the autonomic dysfunction scores. In addition, a statistically significant correlation has been found between HRV and lipid metabolism.

Conclusions
Lipid metabolism and autonomic functioning seem to be related to the discussed psychiatric disorders. LI, in addition, could represent a new possible biomarker to be considered.
Orthogonal Stability of an Additive-Quadratic Functional Equation
Authors: Park Choonkil 
Published: November 2011

AbstractUsing the fixed point method and using the direct method, we prove the Hyers-Ulam stability of an orthogonally additive-quadratic functional equation in orthogonality spaces.(2010) Mathematics Subject Classification: Primary 39B55; 47H10; 39B52; 46H25.
Robust video super resolution algorithm using measurement validation method and scene change detection
Authors: Kim Minjae , Ku Bonhwa , Chung Daesung , Shin Hyunhak , Han David K , Ko Hanseok 
Published: November 2011

Abstract
Explicit motion estimation is considered a major factor in the performance of classical motion-based super resolution (SR) algorithms. To reconstruct video frames sequentially, we applied a dynamic SR algorithm based on the Kalman recursive estimator. Our approach includes a novel measurement validation process to attain robust image reconstruction results under inexplicit motion estimation. In our method, the suitability for high-resolution pixel estimation is determined by the accuracy of motion estimation. We measured the accuracy of the image registration result using the Mahalanobis distance between the input low-resolution frame and the motion compensated high-resolution estimation. We also incorporate an effective scene change detection method dedicated to the proposed SR approach for minimizing erroneous results when abrupt scene changes occur in the video frames. According to the ratio of well-aligned pixels (i.e., motion is compensated accurately) to the total number of pixels, we are able to detect sudden changes of scene and context in the input video. Representative experiments on synthetic and real video data show robust performance of the proposed algorithm in terms of its reconstruction quality even with errors in the estimated motion.