bluuebunny/crossref_metadata_2025 huggingface dataset:
The Cloudy Universe
Authors: Walker Mark , Wardle Mark
Published: March 2011

Modelling of extreme scattering events suggests that the Galaxy's dark matter is an undetected population of cold, AU-sized, planetary-mass gas clouds. None of the direct observational constraints on this picture—thermal/non-thermal emission, extinction and lensing—are problematic. The theoretical situation is less comfortable, but still satisfactory. Galactic clouds can survive in their current condition for billions of years, but we do not have a firm description for either their origin or their evolution to the present epoch. We hypothesise that the proto-clouds formed during the quark–hadron phase transition, thereby introducing the inhomogeneity necessary for compatibility with light element nucleosynthesis in a purely baryonic universe. We outline the prospects for directly detecting the inferred cloud population. The most promising signatures are cosmic-ray-induced Hα emission from clouds in the solar neighbourhood, optical and X-ray flashes arising from cloud–cloud collisions, ultraviolet extinction, and three varieties of lensing phenomena.
Binding of ATP to the CBS domains in the C-terminal region of CLC-1
Authors: Tseng Pang-Yen , Yu Wei-Ping , Liu Hao-Yang , Zhang Xiao-Dong , Zou Xiaoqin , Chen Tsung-Yu
Published: March 2011

The common gating of CLC-1 has been shown to be inhibited by intracellular adenosine triphosphate (ATP) in acidic pH conditions. Such modulation is thought to be mediated by direct binding of ATP to the cystathionine β-synthase (CBS) domains at the C-terminal cytoplasmic region of CLC-1. Guided by the crystal structure of the C-terminal domain of CLC-5, we constructed a homology model of CLC-1’s C terminus and mutated critical amino acid residues lining the potential ATP-binding site. The CLC-1 mutations V634A and E865A completely abolished the ATP inhibition of CLC-1, consistent with the loss of ATP binding seen with the corresponding mutations in CLC-5. Mutating two other residues, V613 and V860, also disrupted the ATP modulation of CLC-1. However, placing aromatic amino acids at position 634 increases the apparent ATP affinity. Mutant cycle analyses showed that the modulation effects of ATP and cytidine triphosphate on wild-type CLC-1 and the V634F mutant were nonadditive, suggesting that the side chain of amino acid at position 634 interacts with the base moiety of the nucleotide. The mutation effects of V634F and V613A on the ATP modulation were also nonadditive, which is consistent with the assertion suggested from the homology model that these two residues may both interact with the bound nucleotide. These results provide evidence for a direct ATP binding for modulating the function of CLC-1 and suggest an overall conserved architecture of the ATP-binding sites in CLC-1 and CLC-5. This study also demonstrates that CLC-1 is a convenient experimental model for studying the interaction of nucleotides/nucleosides with the CBS domain.
On some constants for oscillation and stability of delay equations
Authors: Berezansky Leonid , Braverman Elena
Published: March 2011

We discuss the famous constants of1/e1/e, 1,3/23/2in necessary and/or sufficient oscillation and stability conditions for delay differential equations with one or more delays:\[<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="x prime left-parenthesis t right-parenthesis equals minus sigma-summation Underscript k equals 1 Overscript m Endscripts a Subscript k Baseline left-parenthesis t right-parenthesis x left-parenthesis t minus h Subscript k Baseline left-parenthesis t right-parenthesis right-parenthesis comma">x′(t)=−∑k=1mak(t)x(t−hk(t)),x^{\prime }(t)= - \sum _{k=1}^ma_k(t) x(t-h_k(t)),\]including equations with oscillatory coefficients. Some counterexamples (which refer to necessary oscillation and stability conditions) are presented and open problems are stated.
Genetic variation, predator–prey interactions and food web structure
Authors: Moya-Laraño Jordi
Published: March 2011

Food webs are networks of species that feed on each other. The role that within-population phenotypic and genetic variation plays in food web structure is largely unknown. Here, I show via simulation how variation in two key traits, growth rates and phenology, by influencing the variability of body sizes present through time, can potentially affect several structural parameters in the direction of enhancing food web persistence: increased connectance, decreased interaction strengths, increased variation among interaction strengths and increased degree of omnivory. I discuss other relevant traits whose variation could affect the structure of food webs, such as morphological and additional life-history traits, as well as animal personalities. Furthermore, trait variation could also contribute to the stability of food web modules through metacommunity dynamics. I propose future research to help establish a link between within-population variation and food web structure. If appropriately established, such a link could have important consequences for biological conservation, as it would imply that preserving (functional) genetic variation within populations could ensure the preservation of entire communities.
Genetic variation changes the interactions between the parasitic plant-ecosystem engineer
Rhinanthus
and its hosts
Authors: Rowntree Jennifer K. , Cameron Duncan D. , Preziosi Richard F.
Published: March 2011

Within-species genetic variation is a potent factor influencing between-species interactions and community-level structure. Species of the hemi-parasitic plant genus
Rhinanthus
act as ecosystem engineers, significantly altering above- and below-ground community structure in grasslands. Here, we show the importance of genotypic variation within a single host species (barley—
Hordeum vulgare
), and population-level variation among two species of parasite (
Rhinanthus minor
and
Rhinanthus angustifolius
) on the outcome of parasite infection for both partners. We measured host fitness (number of seeds) and calculated parasite virulence as the difference in seed set between infected and uninfected hosts (the inverse of host tolerance). Virulence was determined by genetic variation within the host species and among the parasite species, but
R. angustifolius
was consistently more virulent than
R. minor
. The most tolerant host had the lowest inherent fitness and did not gain a fitness advantage over other infected hosts. We measured parasite size as a proxy for transmission ability (ability to infect further hosts) and host resistance. Parasite size depended on the specific combination of host genotype, parasite species and parasite population, and no species was consistently larger. We demonstrate that the outcome of infection by
Rhinanthus
depends not only on the host species, but also on the underlying genetics of both host and parasite. Thus, genetic variations within host and parasite are probably essential components of the ecosystem-altering effects of
Rhinanthus
.
Fine-scale community and genetic structure are tightly linked in species-rich grasslands
Authors: Whitlock Raj , Bilton Mark C. , Grime J. Phil , Burke Terry
Published: March 2011

Recent evidence indicates that grassland community structure and species diversity are influenced by genetic variation within species. We review what is known regarding the impact of intraspecific diversity on grassland community structure, using an ancient limestone pasture as a focal example. Two genotype-dependent effects appear to modify community structure in this system. First, the abundance of individual constituent species can depend upon the combined influence of direct genetic effects stemming from individuals within the population. Second, the outcome of localized interspecific interactions occurring within the community can depend on the genotypes of participating individuals (indicating indirect genetic effects). Only genotypic interactions are thought to be capable of allowing the long-term coexistence of both genotypes and species. We discuss the implications of these effects for the maintenance of diversity in grasslands. Next, we present new observations indicating that losses of genotypic diversity from each of two species can be predicted by the abundance of other coexisting species within experimental grassland communities. These results suggest genotype-specific responses to abundance in other coexisting species. We conclude that both direct and indirect genetic effects are likely to shape community structure and species coexistence in grasslands, implying tight linkage between fine-scale genetic and community structure.
Community genetics: what have we accomplished and where should we be going?
Authors: Hersch-Green Erika I. , Turley Nash E. , Johnson Marc T. J.
Published: March 2011

Research in community genetics seeks to understand how the dynamic interplay between ecology and evolution shapes simple and complex communities and ecosystems. A community genetics perspective, however, may not be necessary or informative for all studies and systems. To better understand when and how intraspecific genetic variation and microevolution are important in community and ecosystem ecology, we suggest future research should focus on three areas: (i) determining the relative importance of intraspecific genetic variation compared with other ecological factors in mediating community and ecosystem properties; (ii) understanding the importance of microevolution in shaping ecological dynamics in multi-trophic communities; and (iii) deciphering the phenotypic and associated genetic mechanisms that drive community and ecosystem processes. Here, we identify key areas of research that will increase our understanding of the ecology and evolution of complex communities but that are currently missing in community genetics. We then suggest experiments designed to meet these current gaps.
Berberine induces cell death in human hepatoma cells in vitro by downregulating CD147
Authors: Hou Qian , Tang Xu , Liu Hanqiang , Tang Junqi , Yang Ying , Jing Xiaohong , Xiao Qian , Wang Wen , Gou Xingchun , Wang Zongren
Published: March 2011

The isoquinoline plant alkaloid berberine has anti‐tumor effects on a variety of carcinoma cells, mainly through inhibition of cell proliferation, apoptosis induction and cell cycle arrest. However, the mechanisms underlying its role in tumor progression are unknown. In the present study, we investigated the molecular mechanisms involved in berberine‐induced cell death in human hepatoma carcinoma cell (HCC) lines HepG2 and SMMC7721. Our results showed that berberine inhibited tumor cell viability in a dose‐ and time‐dependent manner, and induced cell death via apoptosis and autophagy. Moreover, berberine treatment significantly inhibited CD147 expression by HCC cells in a dose‐dependent manner. Overexpression of CD147 protein markedly reduced berberine‐induced cell death. Our data provide the first experimental evidence that berberine induces cell death in HCC cells via downregulation of CD147 and suggest a new mechanism to explain its anti‐tumor effects. (Cancer Sci 2011; 102: 1287–1292)
Aberrant expression of chemokine receptor CCR4 in human gastric cancer contributes to tumor‐induced immunosuppression
Authors: Yang Yong‐Mei , Feng A‐Lei , Zhou Cheng‐Jun , Liang Xiao‐Hong , Mao Hai‐Ting , Deng Bi‐Ping , Yan Shi , Sun Jin‐Tang , Du Lu‐Tao , Liu Jia , Wang Qing‐Jie , Neckenig Markus R. , Yang Qi‐Feng , Qu Xun
Published: March 2011

The chemokine receptor CCR4 is preferentially expressed on certain immune cells and some hematological tumor cells, which play pivotal roles in suppression of host immune response. However, the reasons for the upmodulation of CCR4 and its immune functions in solid tumors remain unclear. Herein, we aimed to determine the expression profiles of CCR4 in gastric cancer cells and its role in regulating antitumor immunity. CCR4 expression was assessed in 63 cases of gastric carcinomas by immunohistochemistry. We found cancer cells in lymphocyte‐rich carcinomas more frequently showed moderate to strong positive staining for CCR4 than those in conventional carcinomas (P = 0.041), and also found a positive relationship between expression of CCR4 and tumor necrosis factor‐α (P = 0.012). Stimulation of gastric cell lines with various cytokines showed that tumor necrosis factor‐α uniquely upmodulated CCR4 expression through activation of nuclear factor‐κB. Additional coculture experiments showed the forced expression of CCR4 in SGC‐7901 cells caused a significant reduction of γ‐interferon and elevation of interleukin‐10 secretion in the supernatants from cocultured SGC‐7901 cells and PBMCs. In addition, granzyme A production in cancer cell‐cocultured CD56+ natural killer cells was significantly downregulated. Inhibition of the overexpressed CCR4 in cancer cells by an inhibitor of CCR4, compound 39, proved to partly restore the antitumor immunity in respect of the inverse changes in those factors. Our studies suggest that the aberrant expression of CCR4 in human gastric cancer could contribute to tumor‐induced immunosuppression. Conceivably, downmodulation of CCR4 expression could be a promising immunotherapy for human gastric cancer. (Cancer Sci 2011; 102: 1264–1271)
Nucleostemin affects the proliferation but not differentiation of oral squamous cell carcinoma cells
Authors: Yoshida Ryoji , Fujimoto Tetsuhiro , Kudoh Shinji , Nagata Masashi , Nakayama Hideki , Shinohara Masanori , Ito Takaaki
Published: March 2011

Nucleostemin (NS) has been reported as essential for stem and cancer cell proliferation. To investigate the significance of NS in oral squamous cell carcinomas (OSCCs), we examined NS expression in neoplastic tissue of the tongue and in OSCC cell lines. Nucleostemin expression in the histological samples showed positive correlation with Ki‐67 expression. Furthermore, NS expression was associated with cellular proliferation in OSCC cell lines using siRNA, which upregulated p27, a cyclin‐dependent kinase inhibitor. Regarding OSCC differentiation, NS expression did not influence cornification or oral epithelial differentiation markers such as involucrin and cytokeratin19. Thus, NS is widely expressed in normal and neoplastic oral epithelial tissues, and is likely a marker of proliferation. (Cancer Sci 2011; 102: 1418–1423)
Insig2 is overexpressed in pancreatic cancer and its expression is induced by hypoxia
Authors: Kayashima Tadashi , Nakata Kohei , Ohuchida Kenoki , Ueda Junji , Shirahane Kengo , Fujita Hayato , Cui Lin , Mizumoto Kazuhiro , Tanaka Masao
Published: March 2011

A hypoxic microenvironment is a characteristic feature of pancreatic cancer, and induces the expressions of various genes involved in malignant behaviors. Insulin‐induced gene 2 (Insig2) has recently been shown to be correlated with cellular invasion in colon cancer. However, there have been no reports regarding its expression in pancreatic cancer. In this study, we evaluated Insig2 mRNA expression and the biological function of Insig2 in pancreatic cancer. We measured Insig2 mRNA expression in cultured pancreatic cancer cell lines and invasive ductal carcinoma (IDC) cells, normal pancreatic epithelial cells, and pancreatic intraepithelial neoplasia cells obtained by laser‐capture microdissection. We also investigated the effects of Insig2‐targeting siRNAs on the cell proliferation and cell invasion of pancreatic cancer cell lines. All pancreatic cancer cell lines expressed Insig2 mRNA. The PANC‐1 and MIA PaCa‐2 pancreatic cancer cell lines showed >2‐fold higher Insig2 mRNA expression levels under hypoxic conditions (1% O2) than under normoxic conditions (21% O2). Cell proliferation was significantly decreased in SUIT‐2 cells and cell invasion was significantly decreased in SUIT‐2, Capan‐2, and CFPAC‐1 cells after transfection of the Insig2‐targeting siRNAs. In analyses of microdissected cells, cells from IDC tissues expressed significantly higher levels of Insig2 mRNA than normal pancreatic cells (P < 0.001) and pancreatic intraepithelial neoplasia cells (P = 0.082). In analyses of IDC cells, the levels of Insig2 mRNA expression were significantly higher in late‐stage patients than in early‐stage patients. The present data suggest that Insig2 is associated with the malignant potential of pancreatic cancer under hypoxic conditions. (Cancer Sci 2011; 102: 1137–1143)
Remifentanil as single agent to facilitate awake fibreoptic intubation in the absence of premedication*
Authors: Vennila R. , Hall A. , Ali M. , Bhuiyan N. , Pirotta D. , Raw D. A.
Published: March 2011

Remifentanil is increasingly being used as the primary agent to provide sedation during awake fibreoptic nasal intubation. In this observational study, we aimed to determine the optimal effect site concentration of remifentanil, using a target controlled infusion based on the Minto pharmacological model, to provide optimal safe intubation conditions without the use of other sedatives/premedication and/or spray‐as‐you‐go local anaesthesia. Twenty patients with anticipated difficult airway participated in the study. Good intubating conditions were achieved in all patients with mean (SD) effect site concentration of 6.3 (3.87) ng.ml−1 of remifentanil recorded at nasal endoscopy and 8.06 (3.52) ng.ml−1 during tracheal intubation. No serious adverse event occurred during any of these procedures. These preliminary findings suggest that this is a feasible and safe technique for awake fibreoptic nasal intubation.
An exploration of parents' and young people's perspectives of hospice support
Authors: Kirk S. , Pritchard E.
Published: March 2011

Background  Hospices are an important component of children's palliative care provision and increasing numbers of children/young people with life‐limiting conditions mean that the demand placed on them for support is likely to increase. However, there has been a lack of published research examining how families experience the support provided by children's hospices.

Methods  The aim of the study was to investigate parents' and young people's perceptions of hospice support and identify how support could be improved. A mixed‐method approach was used involving a postal survey of families and in‐depth qualitative interviews with a purposively sampled subsample of parents and young people.

Results  A total of 108 (49.8% response rate) questionnaires were returned and interviews were conducted with 12 parents and seven young people. Families were highly satisfied with the support provided in terms of quality of care; interpersonal qualities of the staff; the individualized, family‐focused approach; accessibility of support and involvement in decision making. Young people valued the opportunity to meet with other young people and take part in different activities. For parents the provision of a break from caring was the main way in which they were supported although they felt they wanted more of this form of support. A consistent theme in relation to support for young people and siblings was the need to develop facilities, activities and bereavement support specifically for teenagers/young people.

Conclusions  Parents value a model of care that provides holistic, family‐focused support that is responsive to individual needs and which promotes control and active involvement in decision making. The key challenge now is to respond to increasing need and a changing population of users.
Comparison of the prevalence and impact of health problems of pre‐school children with and without cerebral palsy
Authors: Wong C. , Bartlett D. J. , Chiarello L. A. , Chang H‐J. , Stoskopf B.
Published: March 2011

Background  The range of health problems associated with children with cerebral palsy (CP) is well documented in the literature; however, the existing data are often either reported for samples of children with all types of CP, or stratified by typology of motor disorder, rather than using the Gross Motor Function Classification System (GMFCS), which has been shown to be the most reliable way of classifying children with CP. Furthermore, availability of research on pre‐school‐aged children (under 5 years) is sparse. The aim of this study is to compare the prevalence and impact of health problems in pre‐school children with and without CP, stratified by the GMFCS.

Methods  Parents of 430 pre‐school‐aged children with CP (243 boys, 187 girls; mean age = 3 years 2 months, SD = 11 months) and 107 typically developing (TD) children (56 boys, 51 girls; mean age = 3 years 4 months, SD = 11 months) participated. Using the consensus definition of CP and the World Health Organization's International Classification of Functioning, Disability and Health, a parent survey was developed to assess the prevalence and impact of 16 health problems. The measure demonstrates good test–retest reliability (ICC > 0.80) and discriminant validity across GMFCS levels (P < 0.001).

Results  Both the prevalence and impact of health problems is greater in children with CP compared with TD children (P < 0.001). The number and impact of health problems increase with ascending GMFCS level (P≤ 0.01), except for the impact of health problems between groups GMFCS I and GMFCS II/III (P= 0.19). Children with CP have an average of between 3.4 and 6.7 health problems, compared with fewer than one in TD children.

Conclusions  Service providers working with pre‐school‐aged children with CP need to consider health problems and their impact when planning care.
Improvement of palm oil and sunflower oil blends by enzymatic interestrification
Authors: Yazdi Zahra Kouchak , Alemzadeh Iran
Published: March 2011

Palm oil (PO) and sunflower oil (SFO) blends with varying proportions were subjected to enzymatic interesterification (EIE) using a 1,3‐specific immobilised lipase. The interesterified blends were evaluated for their slip melting point (SMP), solid fat content (SFC) at 10–40 °C, p‐anisidine value, peroxide value, free fatty acids (FFA), induction period of oxidation at 110 °C (IP110) and composition of fatty acids by gas chromatography. Under EIE treatment, the blends of PO and SFO in different proportions (20:80, 40:60, 50:50, 60:40 and 80:20) had saturated and unsaturated fatty acid content in the range of 37.6–52.0% and 48.0–62.4%, respectively. The blends showed a considerable reduction in their SFC, SMP, peroxide value and oxidative stability at 110 °C, but presented increase in FFA and p‐anisidine value. The optimum condition for minimising the fatty acid in oil was obtained, at 64 °C, using 8.9% enzyme and 3 h reaction time.
Evaluation of volatile compounds and antioxidant capacity of some commercial rums from Dominican republic
Authors: Da Porto Carla , Decorti Deborha , Tubaro Franco
Published: March 2011

Some Dominican ‘heavy’ rums, of a single brand, available commercially and labelled as 8, 15, 18, 21 and 25 year‐old have been evaluated and compared. Headspace solid‐phase microextraction (HS‐SPME) coupled to gas chromatography–mass spectrometry (GC–MS) was used to analyse volatile compounds and crocin kinetic competition test to evaluate their antioxidant capacity. The alcohols and esters profiles of rums labelled as 21‐ and 25 year‐old were similar. The alcohols and fatty acids profiles of rums labelled as 15 and 18 year‐old were similar. The esters profile of rums labelled as 8 and 15 year‐old was similar. Significant differences were found for aldehydes and volatile phenols between all the rum samples. The antioxidant capacity resulted significantly higher in the older rums (21 and 25 year‐old) than in the younger ones (8, 15 and 18 year‐old).
Formulation optimisation of gluten‐free functional spaghetti based on quinoa, maize and soy flours
Authors: Mastromatteo Marcella , Chillo Stefania , Iannetti Mariapia , Civica Valentina , Del Nobile Matteo Alessandro
Published: March 2011

In this work, the formulation of non‐conventional gluten‐free fresh and dry pasta based on quinoa, maize and defatted soy was optimised. Results showed that the dough samples with high content of maize had the higher value of elongation and shear viscosity and then increased dough firmness. The pre‐gelatinised maize content also affected the rheological properties by increasing the dough firmness. Regarding the dry spaghetti sensorial properties, the surface response plot showed that the overall acceptability of both non‐cooked and cooked spaghetti increases with the increase of the pre‐gelatinised maize content and the decrease of the quinoa flour, whereas the soy flour did not affect the overall quality. In particular, the pre‐gelatinised maize improved the resistance to break and the taste of non‐cooked and cooked spaghetti, respectively. Regarding the fresh spaghetti, results showed that the overall acceptability for fresh non‐cooked spaghetti increases with the increase of the pre‐gelatinised maize content and with the decrease of the quinoa flour; whereas, only the pre‐gelatinised maize content affected the overall acceptability of fresh cooked spaghetti.
Drying of plums (Prunus sp, c.v Gulfblaze) treated with KCl in the field and subjected to pulsed vacuum osmotic dehydration
Authors: Fante Camila , Corrêa Jefferson , Natividade Mariana , Lima Juliana , Lima Luiz
Published: March 2011

The pulsed vacuum osmotic dehydration (PVOD) promotes more homogeneous concentration profiles in the product and quality improvement of several fruits. The objective of this work was to study the drying of plums submitted to treatments of plants manure with KCl and PVOD (5” c.a., 10 min). Experimental planning was done with the following independent variables: doses of KCl (400, 700 and 1000 g/plant), concentration of sucrose solution (40; 50 and 60 ºBrix) and drying temperature (50, 60 and 70C). The tested variables were: color, shrinkage, visual quality and rehydration. Temperature leads to a skin browning at fruit pulps and lower visual quality. The treatment with KCl leads to final products with lower moisture content. The higher the values of all the independent variables, the lower the shrinkage and the rehydration capacity. Plums submitted to convective drying with previous PVOD promote a new product with good visual quality and satisfactory shrinkage.
The unfolding story of anthrax toxin translocation
Authors: Thoren Katie L. , Krantz Bryan A.
Published: March 2011

The essential cellular functions of secretion and protein degradation require a molecular machine to unfold and translocate proteins either across a membrane or into a proteolytic complex. Protein translocation is also critical for microbial pathogenesis, namely bacteria can use translocase channels to deliver toxic proteins into a target cell. Anthrax toxin (Atx), a key virulence factor secreted by Bacillus anthracis, provides a robust biophysical model to characterize transmembrane protein translocation. Atx is comprised of three proteins: the translocase component, protective antigen (PA) and two enzyme components, lethal factor (LF) and oedema factor (OF). Atx forms an active holotoxin complex containing a ring‐shaped PA oligomer bound to multiple copies of LF and OF. These complexes are endocytosed into mammalian host cells, where PA forms a protein‐conducting translocase channel. The proton motive force unfolds and translocates LF and OF through the channel. Recent structure and function studies have shown that LF unfolds during translocation in a force‐dependent manner via a series of metastable intermediates. Polypeptide‐binding clamps located throughout the PA channel catalyse substrate unfolding and translocation by stabilizing unfolding intermediates through the formation of a series of interactions with various chemical groups and α‐helical structure presented by the unfolding polypeptide during translocation.
From hormones to secondary metabolism: the emergence of metabolic gene clusters in plants
Authors: Chu Hoi Yee , Wegel Eva , Osbourn Anne
Published: March 2011

Gene clusters for the synthesis of secondary metabolites are a common feature of microbial genomes. Well‐known examples include clusters for the synthesis of antibiotics in actinomycetes, and also for the synthesis of antibiotics and toxins in filamentous fungi. Until recently it was thought that genes for plant metabolic pathways were not clustered, and this is certainly true in many cases; however, five plant secondary metabolic gene clusters have now been discovered, all of them implicated in synthesis of defence compounds. An obvious assumption might be that these eukaryotic gene clusters have arisen by horizontal gene transfer from microbes, but there is compelling evidence to indicate that this is not the case. This raises intriguing questions about how widespread such clusters are, what the significance of clustering is, why genes for some metabolic pathways are clustered and those for others are not, and how these clusters form. In answering these questions we may hope to learn more about mechanisms of genome plasticity and adaptive evolution in plants. It is noteworthy that for the five plant secondary metabolic gene clusters reported so far, the enzymes for the first committed steps all appear to have been recruited directly or indirectly from primary metabolic pathways involved in hormone synthesis. This may or may not turn out to be a common feature of plant secondary metabolic gene clusters as new clusters emerge.
Genome‐level and biochemical diversity of the acyl‐activating enzyme superfamily in plants
Authors: Shockey Jay , Browse John
Published: March 2011

In higher plants, the superfamily of carboxyl‐CoA ligases and related proteins, collectively called acyl activating enzymes (AAEs), has evolved to provide enzymes for many pathways of primary and secondary metabolism and for the conjugation of hormones to amino acids. Across the superfamily there is only limited sequence similarity, but a series of highly conserved motifs, including the AMP‐binding domain, make it easy to identify members. These conserved motifs are best understood in terms of the unique domain‐rotation architecture that allows AAE enzymes to catalyze the two distinct steps of the CoA ligase reaction. Arabidopsis AAE sequences were used to identify the AAE gene families in the sequenced genomes of green algae, mosses, and trees; the size of the respective families increased with increasing degree of organismal cellular complexity, size, and generation time. Large‐scale genome duplications and small‐scale tandem gene duplications have contributed to AAE gene family complexity to differing extents in each of the multicellular species analyzed. Gene duplication and evolution of novel functions in Arabidopsis appears to have occurred rapidly, because acquisition of new substrate specificity is relatively easy in this class of proteins. Convergent evolution has also occurred between members of distantly related clades. These features of the AAE superfamily make it difficult to use homology searches and other genomics tools to predict enzyme function.
The RLK/Pelle family of kinases
Authors: Gish Lindsey A. , Clark Steven E.
Published: March 2011

The RLK/Pelle class of proteins kinases is composed of over 600 members in Arabidopsis. Many of the proteins in this family are receptor‐like kinases (RLK), while others have lost their extracellular domains and are found as cytoplasmic kinases. Proteins in this family that are RLKs have a variety of extracellular domains that drive function in a large number of processes, from cell wall interactions to disease resistance to developmental control. This review will briefly cover the major subclasses of RLK/Pelle proteins and their roles. In addition, two specific groups on RLKs will be discussed in detail, relating recent findings in Arabidopsis and how well these conclusions have been able to be translated to agronomically important species. Finally, some details on kinase activity and signal transduction will be addressed, along with the mystery of RLK/Pelle members lacking kinase enzymatic activity.
From nucleosome to chromosome: a dynamic organization of genetic information
Authors: Fransz Paul , de Jong Hans
Published: March 2011

Gene activity is controlled at different levels of chromatin organization, which involve genomic sequences, nucleosome structure, chromatin folding and chromosome arrangement. These levels are interconnected and influence each other. At the basic level nucleosomes generally occlude the DNA sequence from interacting with DNA‐binding proteins. Evidently, nucleosome positioning is a major factor in gene control and chromatin organization. Understanding the biological rules that govern the deposition and removal of the nucleosomes to and from the chromatin fiber is the key to understanding gene regulation and chromatin organization. In this review we describe and discuss the relationship between the different levels of chromatin organization in plants and animals.
Organisation of the plant genome in chromosomes
Authors: Heslop‐Harrison J. S. (Pat) , Schwarzacher Trude
Published: March 2011

The plant genome is organized into chromosomes that provide the structure for the genetic linkage groups and allow faithful replication, transcription and transmission of the hereditary information. Genome sizes in plants are remarkably diverse, with a 2350‐fold range from 63 to 149 000 Mb, divided into n = 2 to n = approximately 600 chromosomes. Despite this huge range, structural features of chromosomes like centromeres, telomeres and chromatin packaging are well‐conserved. The smallest genomes consist of mostly coding and regulatory DNA sequences present in low copy, along with highly repeated rDNA (rRNA genes and intergenic spacers), centromeric and telomeric repetitive DNA and some transposable elements. The larger genomes have similar numbers of genes, with abundant tandemly repeated sequence motifs, and transposable elements alone represent more than half the DNA present. Chromosomes evolve by fission, fusion, duplication and insertion events, allowing evolution of chromosome size and chromosome number. A combination of sequence analysis, genetic mapping and molecular cytogenetic methods with comparative analysis, all only becoming widely available in the 21st century, is elucidating the exact nature of the chromosome evolution events at all timescales, from the base of the plant kingdom, to intraspecific or hybridization events associated with recent plant breeding. As well as being of fundamental interest, understanding and exploiting evolutionary mechanisms in plant genomes is likely to be a key to crop development for food production.
Two amino acid changes located in the alpha 1 domain specify the novel HLA‐B*27:67 allele affecting the peptide‐binding‐site characteristics
Authors: Becker P. S. , Richter R. , Schulz M. , Seifried E. , Seidl C.
Published: March 2011

The novel HLA‐B*27:67 contains three nucleotide substitutions in exon 2 leading to two amino acid changes.
Sequence‐based typing confirmed a new HLA‐A allele, A*68:71
Authors: Witter K. , Kutsch M. , Zahn R. , Volgger A. , Dick A.
Published: March 2011

In this report, we present the full length coding sequence of A*68:71, a novel allele with a single nucleotide difference to A*68:45.
The new HLA‐C allele C*07:170 shows a new polymorphism at amino acid position 147
Authors: Balas A. , Planelles D. , Rodríguez‐Cebriá M. , García‐Sánchez F. , Vicario J. L.
Published: March 2011

The new HLA‐C allele C*07:170 differs from C*07:01:01 by two nucleotides at exon 3.
Diagnosis of undifferentiated type early gastric cancers by magnification endoscopy with narrow‐band imaging
Authors: Okada Kazuhisa , Fujisaki Junko , Kasuga Akiyoshi , Omae Masami , Hirasawa Toshiaki , Ishiyama Akiyoshi , Inamori Masahiko , Chino Akiko , Yamamoto Yorimasa , Tsuchida Tomohiro , Nakajima Atsushi , Hoshino Etsuo , Igarashi Masahiro
Published: March 2011

Background and Aims:  The diagnostic use of magnification endoscopy with narrow‐band imaging (ME‐NBI) to assess histopathologically undifferentiated‐type early gastric cancers (UD‐type EGCs) is not well elucidated. The purpose of this study was to examine the comparative relationship between ME‐NBI images and histopathological findings in UD‐type EGCs.

Methods:  We analyzed 78 consecutive cases of UD‐type EGCs ≤ 20 mm in diameter that underwent ME‐NBI ≤ 2 weeks prior to resection. The ME‐NBI images were compared with histopathological findings following either endoscopic submucosal dissection (ESD) or surgery. Applying the comparative results, we prospectively evaluated the success of identifying the lateral extent of UD‐type EGCs resected by ESD in additional consecutive cases.

Results:  Lesions with preserved but irregular surface microstructures (S‐type based on ME‐NBI) showed mucosal atrophy and corresponded histologically to the non‐whole‐layer type of intramucosal cancer (24/24, 100%). Lesions with an irregular microvasculature type (V‐type, for example, corkscrew pattern) or mixed type upon ME‐NBI corresponded histopathologically to the non‐whole‐layer type of intramucosal cancer (15/54, 27.8%), the whole‐layer type of intramucosal cancer (27/54, 50.0%) or submucosal (sm) invasion cancer (12/54, 22.2%). Applying these comparative results, we used ME‐NBI to successfully predict the lateral extent of cancer, which corresponded to the histopathological lateral extent in all 18 additional consecutive UD‐type EGCs resected by ESD.

Conclusions:  ME‐NBI images of UD‐type EGCs were very closely related to the histopathological findings. Thus, ME‐NBI can be useful in the pretreatment assessment of the histopathological patterns of cancer development and the lateral extent of such lesions.
Increased Golgi protein 73 expression in hepatocellular carcinoma tissue correlates with tumor aggression but not survival
Authors: Sun Yongliang , Yang Huayu , Mao Yilei , Xu Haifeng , Zhang Jinchun , Li Guangbing , Lu Xin , Sang Xinting , Zhao Haitao , Zhong Shouxian , Huang Jiefu , Zhang Hongbing
Published: March 2011

Background and Aim:  Serum Golgi protein 73 (sGP73) is a novel and promising biomarker for hepatocellular carcinoma (HCC). However, there are few reports on the pattern of GP73 expression in HCC and the relationship of this expression to clinicopathologic features of patients. This study aimed to investigate the expression of GP73 and it correlation with clinical parameters.

Methods:  We examined GP73 expression in HCC and adjacent paracarcinomatous liver (PCL) tissue in 36 HCC patients, and took 14 normal liver (NL) samples from hepatic hemangioma patients. Western blot analysis and quantitative real‐time reverse transcriptase‐polymerase chain reaction (qRT‐PCR) were used for analyses.

Results:  GP73 expression in HCC was significantly higher than in the corresponding PCL and NL samples at both protein and mRNA levels (P < 0.001). The elevated level of GP73 protein was strongly associated with tumor size, vein invasion, and tumor differentiation, suggesting augmented tumor invasion and metastasis. However, there was no association between GP73 expression and patient survival.

Conclusion:  Significant overexpression of GP73 at both protein and mRNA levels along with overexpression of GP73 protein is associated with aggressive behavior of HCC, but not overall patient survival. Further research is needed to determine the potential of GP73 as a therapeutic target.
Hospitalizations and testing in gastroparesis
Authors: Dudekula Anwar , O'Connell Michael , Bielefeldt Klaus
Published: March 2011

Background and Aim:  Gastroparesis significantly impairs the quality of life in affected individuals and may lead to repeat hospitalizations due to refractory symptoms. We hypothesized that pain is a key reason for emergency encounters and diagnostic testing.

Methods:  Using the ICD9 code 536.3, electronic medical records were analyzed retrospectively. Multivariate regression was used to determine predictors of hospital stays and use of diagnostic testing.

Results:  In total, 326 patients (80% women, age: 44.1 ± 0.8 years) were identified. During 504 patient‐years of follow up, patients were hospitalized on average slightly more than once annually for about 8 days and underwent 320 endoscopies, 366 computed tomography scans, 390 abdominal X‐rays, 90 upper gastrointestinal contrast studies and 163 gastric emptying studies; 37 patients exceeded an annual radiation exposure of 20 mSv at least once. The majority of tests were confirmatory, with results not altering treatment. Vomiting and pain were the most common cause for emergency encounters and diagnostic testing. Age and comorbidity, but not opioid use (present in 25%) or the presence of chronic pain disorders (present in 32%) correlated with increased hospital days.

Conclusions:  While surrogate markers of pain do not predict repeat hospitalizations, pain was the primary reason for emergency encounters and frequent diagnostic testing. Repeated testing had a limited impact on treatment and outcome, but certainly contributes to the cost and even risk of care. Concerted efforts are needed to not only improve the care and quality of life of patients with gastroparesis, but also to reduce the number of potentially unnecessary or even harmful interventions.
Kinetics of glucose stimulatory effect on silica deposition and growth of natural populations of Fragilaria crotonensis
Authors: Znachor Petr , Nedoma Jičí , Rychtecký Pavel
Published: March 2011

Diatoms are known to exploit organic substrates for growth; however, convincing evidence that they can utilize dissolved organic carbon under natural conditions is not available. In 2008–2009, we performed in situ experiments examining the effect of glucose addition on silica deposition kinetics and growth rates of Fragilaria crotonensis in the eutrophic Římov Reservoir (Czech Republic). Silica deposition kinetics was measured at 4‐h intervals over a 24‐h incubation with PDMPO [2‐(4‐pyridyl)‐5{[4‐dimethylaminoethyl‐aminocarbamyl)‐methoxy] phenyl}oxazole] fluorescence probe. A significant stimulatory effect of glucose supplemented at the concentration of 10−4 M on Fragilaria silification was observed at 20 and 24 h. Fragilaria growth rates almost doubled upon glucose enrichment compared with the untreated control at 24 h. In addition, we conducted a dose‐response experiment testing the glucose additions from 10−8 to 10−3 M in a 24‐h incubation. Glucose stimulated both Fragilaria silification and growth at concentrations >10–7 M, which might occasionally occur in a reservoir as a result of accidental contamination of water by organic pollution.
Semen quality after extracorporeal shockwave lithotripsy for the management of lower ureteric stones: a review of the literature
Authors: Gulur Dev Mohan , Philip Joe
Published: March 2011

What’s known on the subject? and What does the study add?

ESWL is effective in treating distal ureteric stones. However, the effect of lithotripsy on semen parameters and the testis has not been reviewed.

This review reports that lithotripsy to distal ureteric stones causes a transient oligoasthenozoospermia for up to three months after lithotripsy. We have highlighted this important after‐effect to be discussed while counselling men with a procreative intent before lithotripsy.

Extracorporeal Shockwave Lithotripsy has long been an important tool in the urologists’ armamentarium for the treatment of distal ureteric stones. Several studies have been conducted on the morbidity and adverse effects of ESWL on human tissues but the effect of lithotripsy on semen and testes remains inconclusive. Impact on semen analysis and testes is important because the seminal vesicles and testes are exposed to the shock waves due to their anatomical proximity to the distal ureter. This article has reviewed all the published literature in English language on semen analysis after lithotripsy.
Multiphoton microscopy for structure identification in human prostate and periprostatic tissue: implications in prostate cancer surgery
Authors: Tewari Ashutosh K. , Shevchuk Maria M. , Sterling Joshua , Grover Sonal , Herman Michael , Yadav Rajiv , Mudalair Kumaran , Srivastava Abhishek , Rubin Mark A. , Zipfel Warren R. , Maxfield Frederick R. , Xu Chris , Webb Watt W. , Mukherjee Sushmita
Published: March 2011

Study Type – Diagnostic (exploratory cohort)

Level of Evidence 2b

What’s known on the subject? and What does the study add?

Prostate cancer surgery outcomes depend on an optimal balance of three aspects: complete removal of cancerous glands, preservation of nerves for sexual function and of sphincteric structures for urinary control. Current surgical techniques, even with the magnification provided by the robotic stereoscope, are insufficient to identify these structures in the surgical field. Multiphoton microscopy has been shown to produce high contrast images with subcellular resolution in fresh (unprocessed and unstained tissue) utilizing intrinsic tissue emission signals.

We provide evidence that Multiphoton microscopy of freshly excised tissue from human radical prostatectomy specimens, without any processing or use of exogenous contrast, can identify all relevant prostatic and periprostatic structures. These include the prostatic acini, the stroma and the capsule, as well as periprostatic fascial structures such as loose connective tissue, nerves, blood vessels and fat, as well as areas of local inflammation. We also show that multiphoton microscopy is able to distinguish between normal prostate gland, those with benign hyperplasia, and those harboring cancer.

OBJECTIVE

• To test whether multiphoton microscopy (MPM) might allow identification of prostatic and periprostatic structures with magnification and resolution similar to gold standard histopathology.

MATERIAL AND METHODS

• The present study included 95 robotic radical prostatectomy patients who consented to participate in an Institutional Review Board‐approved study starting in 2007.

• The types of specimens used for imaging were excised surgical margins and biopsies, and sections obtained from the excised prostate.

• The specimens were imaged with a custom‐built MPM system.

• All images were compared with haematoxylin/eosin histopathology of the same specimen.

RESULTS

• MPM of freshly excised, unprocessed and unstained tissue can identify all relevant prostatic and periprostatic structures, such as nerves, blood vessels, capsule, underlying acini and also pathological changes, including prostate cancer.

•  Histological confirmation and correlation of these structures and pathologies have validated the findings of MPM.

CONCLUSIONS

• MPM shows great promise as a tool for real‐time intra‐surgical histopathology without needing excision or administration of contrast agents.

• The results will, however, need to be confirmed in true surgical settings using a miniaturized MPM microendoscope.
THE PROPERTY VALUE PREMIUM OF A PLACE OF WORSHIP
Authors: THOMPSON ERIC , BUTTERS ROGER B. , SCHMITZ BENJAMIN T.
Published: March 2011

Using a unique data set of residential housing values, we improve on previous hedonic pricing and event studies literature to estimate the amenity effects of a new religious structure on local property values. We improve on previous research by extending our analysis with a pre‐ and post‐treatment model. Using a pre‐ and post‐treatment model, we do not find that the religious structure that we examined influenced the value of surrounding properties in the period after its completion. The results suggest that previous research using only post‐completion data may mischaracterize the amenity effects of religious structures. (JEL R3)