bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multifunctionality and diversity of GDSL esterase/lipase gene family in rice (Oryza sativa L. japonica) genome: new insights from bioinformatics analysis
Authors: Chepyshko Hanna , Lai Chia-Ping , Huang Li-Ming , Liu Jyung-Hurng , Shaw Jei-Fu 
Published: July 2012

Abstract

Background
GDSL esterases/lipases are a newly discovered subclass of lipolytic enzymes that are very important and attractive research subjects because of their multifunctional properties, such as broad substrate specificity and regiospecificity. Compared with the current knowledge regarding these enzymes in bacteria, our understanding of the plant GDSL enzymes is very limited, although the GDSL gene family in plant species include numerous members in many fully sequenced plant genomes. Only two genes from a large rice GDSL esterase/lipase gene family were previously characterised, and the majority of the members remain unknown. In the present study, we describe the rice OsGELP (Oryza sativa GDSL esterase/lipase protein) gene family at the genomic and proteomic levels, and use this knowledge to provide insights into the multifunctionality of the rice OsGELP enzymes.

Results
In this study, an extensive bioinformatics analysis identified 114 genes in the rice OsGELP gene family. A complete overview of this family in rice is presented, including the chromosome locations, gene structures, phylogeny, and protein motifs. Among the OsGELPs and the plant GDSL esterase/lipase proteins of known functions, 41 motifs were found that represent the core secondary structure elements or appear specifically in different phylogenetic subclades. The specification and distribution of identified putative conserved clade-common and -specific peptide motifs, and their location on the predicted protein three dimensional structure may possibly signify their functional roles. Potentially important regions for substrate specificity are highlighted, in accordance with protein three-dimensional model and location of the phylogenetic specific conserved motifs. The differential expression of some representative genes were confirmed by quantitative real-time PCR. The phylogenetic analysis, together with protein motif architectures, and the expression profiling were analysed to predict the possible biological functions of the rice OsGELP genes.

Conclusions
Our current genomic analysis, for the first time, presents fundamental information on the organization of the rice OsGELP gene family. With combination of the genomic, phylogenetic, microarray expression, protein motif distribution, and protein structure analyses, we were able to create supported basis for the functional prediction of many members in the rice GDSL esterase/lipase family. The present study provides a platform for the selection of candidate genes for further detailed functional study.
REVIEWS
Authors: Davies Ian , Hasumi Jiro , Mead Nick 
Published: July 2012

VANISHED KINGDOMS, THE HISTORY OF HALF FORGOTTEN EUROPE, NORMAN DAVIES (2011) London: Allen Lane, 848 pp., ISBN: 978-1846143380, h/bk, £30.00
RETHINKING CITIZENSHIP EDUCATION: A CURRICULUM FOR PARTICIPATORY DEMOCRACY, TRISTAN McCOWAN (2012) London: Continuum Intl Pub Group,
232 pp., ISBN: 978-1441156310, p/bk, £24.99
CIVIC REPUBLICANISM AND CIVIC EDUCATION, ANDREW PETERSON (2011) Basingstoke: Palgrave Macmillan, 200 pp., ISBN: 978-0-230-25194-6, h/bk, £50
Estimating Population-Level Coancestry Coefficients by an Admixture F Model
Authors: Karhunen Markku , Ovaskainen Otso 
Published: July 2012

Abstract
In this article, we develop an admixture F model (AFM) for the estimation of population-level coancestry coefficients from neutral molecular markers. In contrast to the previously published F model, the AFM enables disentangling small population size and lack of migration as causes of genetic differentiation behind a given level of FST. We develop a Bayesian estimation scheme for fitting the AFM to multiallelic data acquired from a number of local populations. We demonstrate the performance of the AFM, using simulated data sets and real data on ninespine sticklebacks (Pungitius pungitius) and common shrews (Sorex araneus). The results show that the parameterization of the AFM conveys more information about the evolutionary history than a simple summary parameter such as FST. The methods are implemented in the R package RAFM.
Integrity and Function of theSaccharomyces cerevisiaeSpindle Pole Body Depends on Connections Between the Membrane Proteins Ndc1, Rtn1, and Yop1
Authors: Casey Amanda K , Dawson T Renee , Chen Jingjing , Friederichs Jennifer M , Jaspersen Sue L , Wente Susan R 
Published: July 2012

AbstractThe nuclear envelope in Saccharomyces cerevisiae harbors two essential macromolecular protein assemblies: the nuclear pore complexes (NPCs) that enable nucleocytoplasmic transport, and the spindle pole bodies (SPBs) that mediate chromosome segregation. Previously, based on metazoan and budding yeast studies, we reported that reticulons and Yop1/DP1 play a role in the early steps of de novo NPC assembly. Here, we examined if Rtn1 and Yop1 are required for SPB function in S. cerevisiae. Electron microscopy of rtn1Δ yop1Δ cells revealed lobular abnormalities in SPB structure. Using an assay that monitors lateral expansion of the SPB central layer, we found that rtn1Δ yop1Δ SPBs had decreased connections to the NE compared to wild type, suggesting that SPBs are less stable in the NE. Furthermore, large budded rtn1Δ yop1Δ cells exhibited a high incidence of short mitotic spindles, which were frequently misoriented with respect to the mother–daughter axis. This correlated with cytoplasmic microtubule defects. We found that overexpression of the SPB insertion factors NDC1, MPS2, or BBP1 rescued the SPB defects observed in rtn1Δ yop1Δ cells. However, only overexpression of NDC1, which is also required for NPC biogenesis, rescued both the SPB and NPC associated defects. Rtn1 and Yop1 also physically interacted with Ndc1 and other NPC membrane proteins. We propose that NPC and SPB biogenesis are altered in cells lacking Rtn1 and Yop1 due to competition between these complexes for Ndc1, an essential common component of both NPCs and SPBs.
Rapid Divergence of Prolamin Gene Promoters of Maize After Gene Amplification and Dispersal
Authors: Wu Yongrui , Messing Joachim 
Published: July 2012

Abstract
Seeds have evolved to accommodate complicated processes like senescence, dormancy, and germination. Central to these is the storage of carbohydrates and proteins derived from sugars and amino acids synthesized during photosynthesis. In the grasses, the bulk of amino acids is stored in the prolamin superfamily that specifically accumulates in seed endosperm during senescence. Their promoters contain a conserved cis-element, called prolamin-box (P-box), recognized by the trans-activator P-box binding factor (PBF). Because of the lack of null mutants in all grass species, its physiological role in storage–protein gene expression has been elusive. In contrast, a null mutant of another endosperm-specific trans-activator Opaque2 (O2) has been shown to be required for the transcriptional activation of subsets of this superfamily by binding to the O2 box. Here, we used RNAi to knockdown Pbf expression and found that only 27-kDa γ- and 22-kDa α-zein gene expression were affected, whereas the level of other zeins remained unchanged. Still, transgenic seeds had an opaque seed phenotype. Combination of PbfRNAi and o2 resulted in further reduction of α-zein expression. We also tested the interaction of promoters and constitutively expressed PBF and O2. Whereas transgenic promoters could be activated, endogenous promoters appeared to be not accessible to transcriptional activation, presumably due to differential chromatin states. Although analysis of the methylation of binding sites of PBF and O2 correlated with the expression of endogenous 22-kDa α-zein promoters, a different mechanism seems to apply to the 27-kDa γ-zein promoter, which does not undergo methylation changes.
Tissue-Specific Activation of a Single Gustatory Receptor Produces Opposing Behavioral Responses in Drosophila
Authors: Joseph Ryan M , Heberlein Ulrike 
Published: July 2012

Abstract
Understanding sensory systems that perceive environmental inputs and neural circuits that select appropriate motor outputs is essential for studying how organisms modulate behavior and make decisions necessary for survival. Drosophila melanogaster oviposition is one such important behavior, in which females evaluate their environment and choose to lay eggs on substrates they may find aversive in other contexts. We employed neurogenetic techniques to characterize neurons that influence the choice between repulsive positional and attractive egg-laying responses toward the bitter-tasting compound lobeline. Surprisingly, we found that neurons expressing Gr66a, a gustatory receptor normally involved in avoidance behaviors, receive input for both attractive and aversive preferences. We hypothesized that these opposing responses may result from activation of distinct Gr66a-expressing neurons. Using tissue-specific rescue experiments, we found that Gr66a-expressing neurons on the legs mediate positional aversion. In contrast, pharyngeal taste cells mediate the egg-laying attraction to lobeline, as determined by analysis of mosaic flies in which subsets of Gr66a neurons were silenced. Finally, inactivating mushroom body neurons disrupted both aversive and attractive responses, suggesting that this brain structure is a candidate integration center for decision-making during Drosophila oviposition. We thus define sensory and central neurons critical to the process by which flies decide where to lay an egg. Furthermore, our findings provide insights into the complex nature of gustatory perception in Drosophila. We show that tissue-specific activation of bitter-sensing Gr66a neurons provides one mechanism by which the gustatory system differentially encodes aversive and attractive responses, allowing the female fly to modulate her behavior in a context-dependent manner.
Genetic Annotation of Gain-Of-Function Screens Using RNA Interference and in Situ Hybridization of Candidate Genes in the Drosophila Wing
Authors: Molnar Cristina , Casado Mar , López-Varea Ana , Cruz Cristina , de Celis Jose F 
Published: July 2012

Abstract
Gain-of-function screens in Drosophila are an effective method with which to identify genes that affect the development of particular structures or cell types. It has been found that a fraction of 2–10% of the genes tested, depending on the particularities of the screen, results in a discernible phenotype when overexpressed. However, it is not clear to what extent a gain-of-function phenotype generated by overexpression is informative about the normal function of the gene. Thus, very few reports attempt to correlate the loss- and overexpression phenotype for collections of genes identified in gain-of-function screens. In this work we use RNA interference and in situ hybridization to annotate a collection of 123 P-GS insertions that in combination with different Gal4 drivers affect the size and/or patterning of the wing. We identify the gene causing the overexpression phenotype by expressing, in a background of overexpression, RNA interference for the genes affected by each P-GS insertion. Then, we compare the loss and gain-of-function phenotypes obtained for each gene and relate them to its expression pattern in the wing disc. We find that 52% of genes identified by their overexpression phenotype are required during normal development. However, only in 9% of the cases analyzed was there some complementarity between the gain- and loss-of-function phenotype, suggesting that, in general, the overexpression phenotypes would not be indicative of the normal requirements of the gene.
Energy-Dependent Modulation of Glucagon-Like Signaling inDrosophilavia the AMP-Activated Protein Kinase
Authors: Braco Jason T , Gillespie Emily L , Alberto Gregory E , Brenman Jay E , Johnson Erik C 
Published: July 2012

AbstractAdipokinetic hormone (AKH) is the equivalent of mammalian glucagon, as it is the primary insect hormone that causes energy mobilization. In Drosophila, current knowledge of the mechanisms regulating AKH signaling is limited. Here, we report that AMP-activated protein kinase (AMPK) is critical for normal AKH secretion during periods of metabolic challenges. Reduction of AMPK in AKH cells causes a suite of behavioral and physiological phenotypes resembling AKH cell ablations. Specifically, reduced AMPK function increases life span during starvation and delays starvation-induced hyperactivity. Neither AKH cell survival nor gene expression is significantly impacted by reduced AMPK function. AKH immunolabeling was significantly higher in animals with reduced AMPK function; this result is paralleled by genetic inhibition of synaptic release, suggesting that AMPK promotes AKH secretion. We observed reduced secretion in AKH cells bearing AMPK mutations employing a specific secretion reporter, confirming that AMPK functions in AKH secretion. Live-cell imaging of wild-type AKH neuroendocrine cells shows heightened excitability under reduced sugar levels, and this response was delayed and reduced in AMPK-deficient backgrounds. Furthermore, AMPK activation in AKH cells increases intracellular calcium levels in constant high sugar levels, suggesting that the underlying mechanism of AMPK action is modification of ionic currents. These results demonstrate that AMPK signaling is a critical feature that regulates AKH secretion, and, ultimately, metabolic homeostasis. The significance of these findings is that AMPK is important in the regulation of glucagon signaling, suggesting that the organization of metabolic networks is highly conserved and that AMPK plays a prominent role in these networks.
Unresectable Metastatic Colorectal Cancer Treatment and Survival – Pauls Stradins Clinical University Hospital Experience
Authors: Skuja Elīna , Purkalne Gunta , Miklasevics Edvins 
Published: July 2012

SummaryIntroduction.Despite recent advances in the medical treatment of metastatic colorectal cancer (mCRC), which include oxaliplatinand irinotecan-based first-line regimens and the increasing use of targeted monoclonal antibodies, survival rates for patients with mCRC remain unacceptably low.Aim of the Study.Is to analyze survival in patients with unresectable metastatic colorectal cancer.Materials and Methods.Retrospective study of unresectable metastatic colorectal cancer patients who underwent palliative chemotherapy in Clinic of Oncology of PaulsStradins Clinical University Hospital from 2004 to 2011was done.Results.102 patients had a median PFS of 8 months and median OS of 16 months. Subgroup analysis revealed median PFS of 9 months in the synchronous metastatic disease group and 7 months in the metachronous metastatic disease group (p=0.0089) and median OS of 16 months and 12 months, respectively (p=0.0168).Median OS was 11 months in patients received only one line palliative chemotherapy compared to 19 months in patients received more than one line therapy (p<0.0001).Conclusions.The parameter of synchronous and metachronous metastases is of prognostic value in mCRC patients.Second line palliative chemotherapy prolongs overall survival in patient with mCRC.
The Value of Magnetic Resonance in Differentiation between Brain Glioma and Treatment Induced Injury
Authors: Bieza Anvita , Krumina Gaida 
Published: July 2012

SummaryIntroduction.The further therapeutic management decisions in glioma patients after the radiation/chemotherapy may be difficult because the treatment induced brain injury can mimic tumor recurrence clinically and on neuroimaging.Aim of the Studywas to assess the usefulness of magnetic resonance spectroscopy (MRS) and diffusion tensor imaging (DTI) in differentiation between glial tumor recurrence and radiation/chemotherapy-induced changes in the brain.Material and methods.73 patients with primary brain gliomas and 77 gliomas patients after combined therapy with possibly treatment induced changes underwent MRS and DTI. Fractional anisotropy (FA) and metabolite ratios were measured in the tumor and pathological signal intensity area adjacent to post-surgical cavity.Results.Mean choline/creatine (Cho/Cr), myoinositol/creatine (MI/Cr), lactate-lipid/creatine (LL/Cr) ratios of brain gliomas was statistically significant higher and FA values lower than those in the pathological signal intensity area adjacent to post-surgical cavity. No differences were found in mean N-acetyl aspartate/creatine (NAA/Cr) ratios among two groups.Conclusions.Our study suggests that Cho/Cr, MI/Cr, LL/Cr and FA measures should be recommended as additional highly informative tool to conventional structural magnetic resonance imaging (MRI) when monitoring gliomas patients after combined therapy.
Pathology of Breast Cancer: from Classic Concepts to Molecular Pathology and Pathogenesis
Authors: Strumfa Ilze , Vanags Andrejs , Abolins Arnis , Gardovskis Janis 
Published: July 2012

SummaryBreast cancer has high incidence and still significant mortality. Due to the widespread application and efficacy of surgery in breast cancer treatment, the surgeon has a crucial role in the treatment planning. Taking into account the tendency to personalized cancer care and the heterogeneity of breast cancer, the surgeon has to be aware about the prognostic and predictive characteristics of breast cancer. We discuss here the classaic pathology of breast cancer along with molecular subtypes, novel prognostic markers and molecular pathogenesis.
Primary Adenocarcinoma of the Appendix
Authors: Vanags Andrejs , Strumfa Ilze , Abolins Arnis , Brikuns Andrejs , Simtniece Zane , Gardovskis Janis 
Published: July 2012

Primary Adenocarcinoma of the AppendixPrimary adenocarcinoma of the appendix is exceedingly rare type of malignancy with the incidence of 0.4 cases per 100,000. It composes less than 0.5% of gastrointestinal malignant neoplasms. Frequently, the diagnosis is reached only after histological examination of surgically excised appendix due to suspected inflammation. Despite the low survival rate in case of primary appendix tumours aggressive therapy is necessary to obtain long-term survival. We present a well-documented case of instant neoplasm evaluated at our institution. To the best of our knowledge, no such detailed studies have been carried out before in Latvia.
Human Dirofilariasis in Latvia - the First Case in Surgical Practice
Authors: Melbarde-Gorkusa Inga , Abolins Arnis , Strumfa Ilze , Martinsons Aigars , Gardovskis Janis 
Published: July 2012

Human Dirofilariasis in Latvia - the First Case in Surgical PracticeThough dirofilariasis in humans occurs rarely, the number of cases due toDirofilaria repenshas been increasing worldwide over the last decade. Climatic changes and animal migration extend geographic area of human dirofilariasis, now including Latvia. The diagnosis is based on histopathological features. Surgical excision is the only curative treatment. Practitioners should bear in mind the possibility of human dirofilariasis in residents of Latvia.
Recurrent Pericarditis in a Pediatric Patient
Authors: Ligere Elina , Leznina Marija , Lacis Aris , Bergmane Inta , Ozolins Valts , Smits Lauris 
Published: July 2012

Recurrent Pericarditis in a Pediatric PatientRecurrent pericarditis is a chronic condition with the recurrence of pericardial effusion within 3 months after the documented acute pericarditis. The knowledge about this disease is based on observations in adults (6). The common identifiable causes of pericardial effusion in children are a prior cardiac surgery, bacterial pericarditis, malignancy or connective tissue disorders. In a significant number of children, however, despite extensive investigation, it is not possible to identify a clear aetiology. A viral cause is often suspected, though rarely confirmed. There are only few reports on the clinical course of idiopathic pericardial effusions in children. We demonstrate a case of recurrent idiopathic pericarditis with 3 episodes of recurrence within a period of 6 months with no autoimmune disease present, not related to prior surgery or malignancy.
Spinal Cord Stimulation for Chronic Pain Relief: First Experience in Baltics
Authors: Golubovska Iveta , Miscuks Aleksejs , Jurkevics Vitolds , Skaida Sarmite 
Published: July 2012

Spinal Cord Stimulation for Chronic Pain Relief: First Experience in BalticsWe report the first case of spinal cord stimulator implantation in Baltics to patient with massive posttraumatic plexus lumbosacralis dxtr lesion, severe neuropathic pain syndrome and drug addiction problems. Follow-up time is 6 month since December 2011 and we have observed an obvious clinical and social improvement in patient status. Besides significant pain relief she has got employed and is tax payer instead of low-income person.
Monitoring of Oral and Nasal Exhaled Nitric Oxide in Eosinophilic Chronic Rhinosinusitis: A Prospective Study
Authors: Noda Noriaki , Takeno Sachio , Fukuiri Takashi , Hirakawa Katsuhiro 
Published: July 2012

Background We aimed to examine the effect of different therapeutic modalities on levels of fractional concentrations of exhaled nitric oxide (FeNO) in patients with eosinophilic chronic rhinosinusitis (ECRS). Methods Thirty-six ECRS patients with nasal polyps were treated either medically or surgically. Oral and nasal FeNO levels were measured using an electrochemical NO analyzer initially and at 1 and 6 months. The mRNA expression and localization of nitric oxide synthase (NOS) isoforms in sinus mucosa and nasal polyps were analyzed by real-time polymerase chain reaction (PCR) and immunohistochemistry. Results The mean oral FeNO levels in the surgical group had decreased significantly from 50.9 to 36.8 ppb 6 months after endoscopic sinus surgery. All patients in this group showed significantly higher nasal FeNO levels after treatment. The mean nasal FeNO levels were 62.3 ppb at 1 month and 93.6 ppb at 6 months. Mean oral and nasal FeNO levels in the medical group after treatment remained unchanged when compared with the baseline levels. Positive immunoreactivity of inducible NOS (iNOS) was observed in both epithelial cells and submucosal inflammatory cells. Real-time PCR analysis showed significant up-regulation of iNOS and IL-5 mRNA expression. Conclusion A combination of oral and nasal FeNO measurements is useful to monitor the extent of inflammation in CRS patients. The increase in nasal FeNO in the surgical group indicates prompt recovery of NO release from healed sinus mucosa through the opened sinus ostia. Reduction of oral FeNO levels may reflect a cessation of the underlying lower airway inflammation that is characteristic of ECRS.