bluuebunny/crossref_metadata_2025_split huggingface dataset:
Placenta growth factor and vascular endothelial growth factor B expression in the hypoxic lung
Authors: Sands Michelle , Howell Katherine , Costello Christine M , McLoughlin Paul 
Published: February 2011

Abstract

Background
Chronic alveolar hypoxia, due to residence at high altitude or chronic obstructive lung diseases, leads to pulmonary hypertension, which may be further complicated by right heart failure, increasing morbidity and mortality. In the non-diseased lung, angiogenesis occurs in chronic hypoxia and may act in a protective, adaptive manner. To date, little is known about the behaviour of individual vascular endothelial growth factor (VEGF) family ligands in hypoxia-induced pulmonary angiogenesis. The aim of this study was to examine the expression of placenta growth factor (PlGF) and VEGFB during the development of hypoxic pulmonary angiogenesis and their functional effects on the pulmonary endothelium.

Methods
Male Sprague Dawley rats were exposed to conditions of normoxia (21% O2) or hypoxia (10% O2) for 1-21 days. Stereological analysis of vascular structure, real-time PCR analysis of vascular endothelial growth factor A (VEGFA), VEGFB, placenta growth factor (PlGF), VEGF receptor 1 (VEGFR1) and VEGFR2, immunohistochemistry and western blots were completed. The effects of VEGF ligands on human pulmonary microvascular endothelial cells were determined using a wound-healing assay.

Results
Typical vascular remodelling and angiogenesis were observed in the hypoxic lung. PlGF and VEGFB mRNA expression were significantly increased in the hypoxic lung. Immunohistochemical analysis showed reduced expression of VEGFB protein in hypoxia although PlGF protein was unchanged. The expression of VEGFA mRNA and protein was unchanged. In vitro PlGF at high concentration mimicked the wound-healing actions of VEGFA on pulmonary microvascular endothelial monolayers. Low concentrations of PlGF potentiated the wound-healing actions of VEGFA while higher concentrations of PlGF were without this effect. VEGFB inhibited the wound-healing actions of VEGFA while VEGFB and PlGF together were mutually antagonistic.

Conclusions
VEGFB and PlGF can either inhibit or potentiate the actions of VEGFA, depending on their relative concentrations, which change in the hypoxic lung. Thus their actions in vivo depend on their specific concentrations within the microenvironment of the alveolar wall during the course of adaptation to pulmonary hypoxia.
SUMO-1 regulates the conformational dynamics of Thymine-DNA Glycosylase regulatory domain and competes with its DNA binding activity
Authors: Smet-Nocca Caroline , Wieruszeski Jean-Michel , Léger Hélène , Eilebrecht Sebastian , Benecke Arndt 
Published: February 2011

Abstract

Background
The human thymine-DNA glycosylase (TDG) plays a dual role in base excision repair of G:U/T mismatches and in transcription. Regulation of TDG activity by SUMO-1 conjugation was shown to act on both functions. Furthermore, TDG can interact with SUMO-1 in a non-covalent manner.

Results
Using NMR spectroscopy we have determined distinct conformational changes in TDG upon either covalent sumoylation on lysine 330 or intermolecular SUMO-1 binding through a unique SUMO-binding motif (SBM) localized in the C-terminal region of TDG. The non-covalent SUMO-1 binding induces a conformational change of the TDG amino-terminal regulatory domain (RD). Such conformational dynamics do not exist with covalent SUMO-1 attachment and could potentially play a broader role in the regulation of TDG functions for instance during transcription. Both covalent and non-covalent processes activate TDG G:U repair similarly. Surprisingly, despite a dissociation of the SBM/SUMO-1 complex in presence of a DNA substrate, SUMO-1 preserves its ability to stimulate TDG activity indicating that the non-covalent interactions are not directly involved in the regulation of TDG activity. SUMO-1 instead acts, as demonstrated here, indirectly by competing with the regulatory domain of TDG for DNA binding.

Conclusions
SUMO-1 increases the enzymatic turnover of TDG by overcoming the product-inhibition of TDG on apurinic sites. The mechanism involves a competitive DNA binding activity of SUMO-1 towards the regulatory domain of TDG. This mechanism might be a general feature of SUMO-1 regulation of other DNA-bound factors such as transcription regulatory proteins.
Protein kinase A type I activates a CRE-element more efficiently than protein kinase A type II regardless of C subunit isoform
Authors: Stakkestad Øystein , Larsen Anja CV , Kvissel Anne-Katrine , Eikvar Sissel , Ørstavik Sigurd , Skålhegg Bjørn S 
Published: February 2011

Abstract

Background
Protein kinase A type I (PKAI) and PKAII are expressed in most of the eukaryotic cells examined. PKA is a major receptor for cAMP and specificity is achieved partly through tissue-dependent expression and subcellular localization of subunits with different biochemical properties. In addition posttranslational modifications help fine tune PKA activity, distribution and interaction in the cell. In spite of this the functional significance of two forms of PKA in one cell has not been fully determined. Here we have tested the ability of PKAI and PKAII formed by expression of the regulatory (R) subunits RIα or RIIα in conjunction with Cα1 or Cβ2 to activate a co-transfected luciferace reporter gene, controlled by the cyclic AMP responsive element-binding protein (CREB) in vivo.

Results
We show that PKAI when expressed at equal levels as PKAII was significantly (p < 0.01) more efficient in inducing Cre-luciferace activity at saturating concentrations of cAMP. This result was obtained regardless of catalytic subunit identity.

Conclusion
We suggest that differential effects of PKAI and PKAII in inducing Cre-luciferace activity depend on R and not C subunit identity.
DoBo: Protein domain boundary prediction by integrating evolutionary signals and machine learning
Authors: Eickholt Jesse , Deng Xin , Cheng Jianlin 
Published: February 2011

Abstract

Background
Accurate identification of protein domain boundaries is useful for protein structure determination and prediction. However, predicting protein domain boundaries from a sequence is still very challenging and largely unsolved.

Results
We developed a new method to integrate the classification power of machine learning with evolutionary signals embedded in protein families in order to improve protein domain boundary prediction. The method first extracts putative domain boundary signals from a multiple sequence alignment between a query sequence and its homologs. The putative sites are then classified and scored by support vector machines in conjunction with input features such as sequence profiles, secondary structures, solvent accessibilities around the sites and their positions. The method was evaluated on a domain benchmark by 10-fold cross-validation and 60% of true domain boundaries can be recalled at a precision of 60%. The trade-off between the precision and recall can be adjusted according to specific needs by using different decision thresholds on the domain boundary scores assigned by the support vector machines.

Conclusions
The good prediction accuracy and the flexibility of selecting domain boundary sites at different precision and recall values make our method a useful tool for protein structure determination and modelling. The method is available at http://sysbio.rnet.missouri.edu/dobo/.
The chromosomal association/dissociation of the chromatin insulator protein Cp190 of Drosophila melanogaster is mediated by the BTB/POZ domain and two acidic regions
Authors: Oliver Daniel , Sheehan Brian , South Heather , Akbari Omar , Pai Chi-Yun 
Published: February 2011

Abstract

Background
Chromatin insulators or boundary elements are a class of functional elements in the eukaryotic genome. They regulate gene transcription by interfering with promoter-enhancer communication. The Cp190 protein of Drosophila
melanogaster is essential to the function of at least three-types of chromatin insulator complexes organized by Su(Hw), CTCF and BEAF32.

Results
We mapped functional regions of Cp190 in vivo and identified three domains that are essential for the insulator function and for the viability of flies: the BTB/POZ domain, an aspartic acid-rich (D-rich) region and a C-terminal glutamic acid-rich (E-rich) region. Other domains including the centrosomal targeting domain and the zinc fingers are dispensable. The N-terminal CP190BTB-D fragment containing the BTB/POZ domain and the D-rich region is sufficient to mediate association with all three types of insulator complexes. The fragment however is not sufficient for insulator activity or viability. The Cp190 and CP190BTB-D are regulated differently in cells treated with heat-shock. The Cp190 dissociated from chromosomes during heat-shock, indicating that dissociation of Cp190 with chromosomes can be regulated. In contrast, the CP190BTB-D fragment didn't dissociate from chromosomes in the same heat-shocked condition, suggesting that the deleted C-terminal regions have a role in regulating the dissociation of Cp190 with chromosomes.

Conclusions
The N-terminal fragment of Cp190 containing the BTB/POZ domain and the D-rich region mediates association of Cp190 with all three types of insulator complexes and that the E-rich region of Cp190 is required for dissociation of Cp190 from chromosomes during heat-shock. The heat-shock-induced dissociation is strong evidence indicating that dissociation of the essential insulator protein Cp190 from chromosomes is regulated. Our results provide a mechanism through which activities of an insulator can be modulated by internal and external cues.
Interaction of annexin A6 with alpha actinin in cardiomyocytes
Authors: Mishra Sumita , Chander Vivek , Banerjee Priyam , Oh Jae G , Lifirsu Ekaterina , Park Woo J , Kim Do H , Bandyopadhyay Arun 
Published: February 2011

Abstract

Background
Annexins are calcium dependent phospholipid binding proteins that are expressed in a wide variety of tissues and implicated in various extra- and intracellular processes. In myocardial tissue, annexins A2, A5 and A6 are particularly abundant, of which the expression levels of annexin A6 has been found to be maximal. Conflicting reports from transgenic mice overexpressing annexin A6 or null mice lacking annexin A6 showed imbalances in intracellular calcium turnover and disturbed cardiac contractility. However, few studies have focussed on the signalling module of annexin A6 in the heart either in normal or in pathological state.

Results
To identify the putative binding partners of annexin A6 in the heart, ventricular extracts were subjected to glutathione S-transferase (GST)- annexin A6 pull down assay and the GST- annexin A6 bound proteins were identified by mass spectrometry. The pull down fractions of ventricular extracts with GST-full length annexin A6 as well as GST-C terminus deleted annexin A6 when immunoblotted with anti sarcomeric alpha (α)-actinin antibody showed the presence of α-actinin in the immunoblot which was absent when GST-N terminus deleted annexin A6 was used for pull down. Overexpression of green fluorescent protein (GFP) tagged full length annexin A6 showed z-line like appearance in cardiomyocytes whereas GFP-N termimus deleted annexin A6 was mostly localized to the nucleus. Overexpression of GFP-C terminus deleted annexin A6 in cardiomyocytes showed aggregate like appearance in the cytoplasm. Double immunofluorescent staining of cardiomyocytes with anti annexin A6 and anti sarcomeric α-actinin antibodies showed perfect co-localization of these two proteins with annexin A6 appearing like a component of sarcomere. Transient knockdown of annexin A6 in cardiomyocytes by shRNA significantly enhances the contractile functions but does not affect the z-band architecture, as revealed by α-actinin immunostaining in shRNA treated cells.

Conclusions
In overall, the present study demonstrated for the first time that annexin A6 physically interacts with sarcomeric α-actinin and alters contractility of cardiomyocytes suggesting that it might play important role in excitation and contraction process.
Back to the sea twice: identifying candidate plant genes for molecular evolution to marine life
Authors: Wissler Lothar , Codoñer Francisco M , Gu Jenny , Reusch Thorsten BH , Olsen Jeanine L , Procaccini Gabriele , Bornberg-Bauer Erich 
Published: February 2011

AbstractBackgroundSeagrasses are a polyphyletic group of monocotyledonous angiosperms that have adapted to a completely submerged lifestyle in marine waters. Here, we exploit two collections of expressed sequence tags (ESTs) of two wide-spread and ecologically important seagrass species, the Mediterranean seagrassPosidonia oceanica(L.) Delile and the eelgrassZostera marinaL., which have independently evolved from aquatic ancestors. This replicated, yet independent evolutionary history facilitates the identification of traits that may have evolved in parallel and are possible instrumental candidates for adaptation to a marine habitat.ResultsIn our study, we provide the first quantitative perspective on molecular adaptations in two seagrass species. By constructing orthologous gene clusters shared between two seagrasses (Z. marinaandP. oceanica) and eight distantly related terrestrial angiosperm species, 51 genes could be identified with detection of positive selection along the seagrass branches of the phylogenetic tree. Characterization of these positively selected genes using KEGG pathways and the Gene Ontology uncovered that these genes are mostly involved in translation, metabolism, and photosynthesis.ConclusionsThese results provide first insights into which seagrass genes have diverged from their terrestrial counterparts via an initial aquatic stage characteristic of the order and to the derived fully-marine stage characteristic of seagrasses. We discuss how adaptive changes in these processes may have contributed to the evolution towards an aquatic and marine existence.
A new mapping method for quantitative trait loci of silkworm
Authors: Xu Hai-Ming , Wei Chang-Shuai , Tang Yun-Ting , Zhu Zhi-Hong , Sima Yang-Fu , Lou Xiang-Yang 
Published: February 2011

Abstract

Background
Silkworm is the basis of sericultural industry and the model organism in insect genetics study. Mapping quantitative trait loci (QTLs) underlying economically important traits of silkworm is of high significance for promoting the silkworm molecular breeding and advancing our knowledge on genetic architecture of the Lepidoptera. Yet, the currently used mapping methods are not well suitable for silkworm, because of ignoring the recombination difference in meiosis between two sexes.

Results
A mixed linear model including QTL main effects, epistatic effects, and QTL × sex interaction effects was proposed for mapping QTLs in an F2 population of silkworm. The number and positions of QTLs were determined by F-test and model selection. The Markov chain Monte Carlo (MCMC) algorithm was employed to estimate and test genetic effects of QTLs and QTL × sex interaction effects. The effectiveness of the model and statistical method was validated by a series of simulations. The results indicate that when markers are distributed sparsely on chromosomes, our method will substantially improve estimation accuracy as compared to the normal chiasmate F2 model. We also found that a sample size of hundreds was sufficiently large to unbiasedly estimate all the four types of epistases (i.e., additive-additive, additive-dominance, dominance-additive, and dominance-dominance) when the paired QTLs reside on different chromosomes in silkworm.

Conclusion
The proposed method could accurately estimate not only the additive, dominance and digenic epistatic effects but also their interaction effects with sex, correcting the potential bias and precision loss in the current QTL mapping practice of silkworm and thus representing an important addition to the arsenal of QTL mapping tools.
Coexistence of diploid, triploid and tetraploid crucian carp (Carassius auratus) in natural waters
Authors: Xiao Jun , Zou Tuomi , Chen Yubao , Chen Lin , Liu Shaojun , Tao Min , Zhang Chun , Zhao Rurong , Zhou Yi , Long Yu , You Cuiping , Yan Jinpeng , Liu Yun 
Published: February 2011

AbstractBackgroundCrucian carp (abbreviated CC) belongs to the genus ofCarassiuswithin the family ofCyprinidae. It has been one of the most important freshwater species for Chinese aquaculture and is especially abundant in the Dongting water system of Hunan province. CC used to be considered as all diploid forms. However, coexistence of diploid (abbreviated 2nCC), triploid (abbreviated 3nCC) and tetraploid crucian carp (abbreviated 4nCC) population of the Dongting water system was first found by our recently researches.ResultsWe examined the ploidy level and compared biological characteristics in different ploidy CC. In reproductive mode, 2nCC was bisexual generative and 4nCC generated all-female offspring by gynogenesis. However, 3nCC generated progenies in two different ways. 3nCC produced bisexual triploid offspring fertilized with 3nCC spermatozoa, while it produced all-female triploid offspring by gynogenesis when its ova were activated by heterogenous spermatozoa. The complete mitochondrial DNA of three different ploidy fishes was sequenced and analyzed, suggesting no significant differences. Interestingly, microchromosomes were found only in 3nCC, which were concluded to be the result of hybridization. Allogenetic DNA fragments of Sox genes were obtained in 3nCC and 4nCC, which were absent in 2nCC. Phylogenetics analysis based on Sox4 gene indicated 3nCC and 4nCC formed a separate group from 2nCC.ConclusionsIn summary, this is the first report of the co-existence of three types of different ploidy crucian carps in natural waters in China. It was proved that the coexistence of different ploidy CC was reproductively maintained. We further hypothesized that 3nCC and 4nCC were allopolyploids that resulted from hybridization. The different ploidy CC population we obtained in this study possesses great significance for the study of polyploidization and the evolution of vertebrates.
Comparative population genetics of mimetic Heliconius butterflies in an endangered habitat; Brazil's Atlantic Forest
Authors: Albuquerque de Moura Priscila , Quek Swee-Peck , Cardoso Márcio Z , Kronforst Marcus R 
Published: February 2011

AbstractBackgroundBrazil's Atlantic Forest is a biodiversity hotspot endangered by severe habitat degradation and fragmentation. Habitat fragmentation is expected to reduce dispersal among habitat patches resulting in increased genetic differentiation among populations. Here we examined genetic diversity and differentiation among populations of twoHeliconiusbutterfly species in the northern portion of Brazil's Atlantic Forest to estimate the potential impact of habitat fragmentation on population connectivity in butterflies with home-range behavior.ResultsWe generated microsatellite, AFLP and mtDNA sequence data for 136Heliconius eratospecimens from eight collecting locations and 146H. melpomenespecimens from seven locations. Population genetic analyses of the data revealed high levels of genetic diversity inH. eratorelative toH. melpomene, widespread genetic differentiation among populations of both species, and no evidence for isolation-by-distance.ConclusionsThese results are consistent with the hypothesis that the extensive habitat fragmentation along Brazil's Atlantic Forest has reduced dispersal ofHeliconiusbutterflies among neighboring habitat patches. The results also lend support to the observation that fine-scale population genetic structure may be common inHeliconius. If such population structure also exists independent of human activity, and has been common over the evolutionary history ofHeliconiusbutterflies, it may have contributed to the evolution of wing pattern diversity in the genus.
Smed454 dataset: unravelling the transcriptome of Schmidtea mediterranea
Authors: Abril Josep F , Cebrià Francesc , Rodríguez-Esteban Gustavo , Horn Thomas , Fraguas Susanna , Calvo Beatriz , Bartscherer Kerstin , Saló Emili 
Published: February 2011

Abstract

Background
Freshwater planarians are an attractive model for regeneration and stem cell research and have become a promising tool in the field of regenerative medicine. With the availability of a sequenced planarian genome, the recent application of modern genetic and high-throughput tools has resulted in revitalized interest in these animals, long known for their amazing regenerative capabilities, which enable them to regrow even a new head after decapitation. However, a detailed description of the planarian transcriptome is essential for future investigation into regenerative processes using planarians as a model system.

Results
In order to complement and improve existing gene annotations, we used a 454 pyrosequencing approach to analyze the transcriptome of the planarian species Schmidtea mediterranea Altogether, 598,435 454-sequencing reads, with an average length of 327 bp, were assembled together with the ~10,000 sequences of the S. mediterranea UniGene set using different similarity cutoffs. The assembly was then mapped onto the current genome data. Remarkably, our Smed454 dataset contains more than 3 million novel transcribed nucleotides sequenced for the first time. A descriptive analysis of planarian splice sites was conducted on those Smed454 contigs that mapped univocally to the current genome assembly. Sequence analysis allowed us to identify genes encoding putative proteins with defined structural properties, such as transmembrane domains. Moreover, we annotated the Smed454 dataset using Gene Ontology, and identified putative homologues of several gene families that may play a key role during regeneration, such as neurotransmitter and hormone receptors, homeobox-containing genes, and genes related to eye function.

Conclusions
We report the first planarian transcript dataset, Smed454, as an open resource tool that can be accessed via a web interface. Smed454 contains significant novel sequence information about most expressed genes of S. mediterranea. Analysis of the annotated data promises to contribute to identification of gene families poorly characterized at a functional level. The Smed454 transcriptome data will assist in the molecular characterization of S. mediterranea as a model organism, which will be useful to a broad scientific community.