bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomes of the T4-related bacteriophages as windows on microbial genome evolution
Authors: Petrov Vasiliy M , Ratnayaka Swarnamala , Nolan James M , Miller Eric S , Karam Jim D 
Published: October 2010

AbstractThe T4-related bacteriophages are a group of bacterial viruses that share morphological similarities and genetic homologies with the well-studiedEscherichia coliphage T4, but that diverge from T4 and each other by a number of genetically determined characteristics including the bacterial hosts they infect, the sizes of their linear double-stranded (ds) DNA genomes and the predicted compositions of their proteomes. The genomes of about 40 of these phages have been sequenced and annotated over the last several years and are compared here in the context of the factors that have determined their diversity and the diversity of other microbial genomes in evolution. The genomes of the T4 relatives analyzed so far range in size between ~160,000 and ~250,000 base pairs (bp) and are mosaics of one another, consisting of clusters of homology between them that are interspersed with segments that vary considerably in genetic composition between the different phage lineages. Based on the known biological and biochemical properties of phage T4 and the proteins encoded by the T4 genome, the T4 relatives reviewed here are predicted to share a genetic core, or "Core Genome" that determines the structural design of their dsDNA chromosomes, their distinctive morphology and the process of their assembly into infectious agents (phage morphogenesis). The Core Genome appears to be the most ancient genetic component of this phage group and constitutes a mere 12-15% of the total protein encoding potential of the typical T4-related phage genome. The high degree of genetic heterogeneity that exists outside of this shared core suggests that horizontal DNA transfer involving many genetic sources has played a major role in diversification of the T4-related phages and their spread to a wide spectrum of bacterial species domains in evolution. We discuss some of the factors and pathways that might have shaped the evolution of these phages and point out several parallels between their diversity and the diversity generally observed within all groups of interrelated dsDNA microbial genomes in nature.
Dig1 protects against cell death provoked by glyphosate-based herbicides in human liver cell lines
Authors: Gasnier Céline , Benachour Nora , Clair Emilie , Travert Carine , Langlois Frédéric , Laurant Claire , Decroix-Laporte Cécile , Séralini Gilles-Eric 
Published: October 2010

AbstractBackgroundWorldwide used pesticides containing different adjuvants like Roundup formulations, which are glyphosate-based herbicides, can provoke some in vivo toxicity and in human cells. These pesticides are commonly found in the environment, surface waters and as food residues of Roundup tolerant genetically modified plants. In order to know their effects on cells from liver, a major detoxification organ, we have studied their mechanism of action and possible protection by precise medicinal plant extracts called Dig1.MethodsThe cytotoxicity pathways of four formulations of glyphosate-based herbicides were studied using human hepatic cell lines HepG2 and Hep3B, known models to study xenobiotic effects. We monitored mitochondrial succinate dehydrogenase activity and caspases 3/7 for cell mortality and protection by Dig1, as well as cytochromes P450 1A1, 1A2, 3A4 and 2C9 and glutathione-S-transferase to approach the mechanism of actions.ResultsAll the four Roundup formulations provoke liver cell death, with adjuvants having stronger effects than glyphosate alone. Hep3B are 3-5 times more sensitive over 48 h. Caspases 3/7 are greatly activated in HepG2 by Roundup at non-cytotoxic levels, and some apoptosis induction by Roundup is possible together with necrosis. CYP3A4 is specifically enhanced by Roundup at doses 400 times less than used in agriculture (2%). CYP1A2 is increased to a lesser extent together with glutathione-S-transferase (GST) down-regulation. Dig 1, non cytotoxic and not inducing caspases by itself, is able to prevent Roundup-induced cell death in a time-dependant manner with an important efficiency of up to 89%, within 48 h. In addition, we evidenced that it prevents Caspases 3/7 activation and CYP3A4 enhancement, and not GST reduction, but in turn it slightly inhibited CYP2C9 when added before Roundup.ConclusionRoundup is able to provoke intracellular disruption in hepatic cell lines at different levels, but a mixture of medicinal plant extracts Dig1 can protect to some extent human cell lines against this pollutants. All this system constitutes a tool for studying liver intoxication and detoxification.
Automated saccharification assay for determination of digestibility in plant materials
Authors: Gomez Leonardo D , Whitehead Caragh , Barakate Abdellah , Halpin Claire , McQueen-Mason Simon J 
Published: October 2010

Abstract

Background
Cell wall resistance represents the main barrier for the production of second generation biofuels. The deconstruction of lignocellulose can provide sugars for the production of fuels or other industrial products through fermentation. Understanding the biochemical basis of the recalcitrance of cell walls to digestion will allow development of more effective and cost efficient ways to produce sugars from biomass. One approach is to identify plant genes that play a role in biomass recalcitrance, using association genetics. Such an approach requires a robust and reliable high throughput (HT) assay for biomass digestibility, which can be used to screen the large numbers of samples involved in such studies.

Results
We developed a HT saccharification assay based on a robotic platform that can carry out in a 96-well plate format the enzymatic digestion and quantification of the released sugars. The handling of the biomass powder for weighing and formatting into 96 wells is performed by a robotic station, where the plant material is ground, delivered to the desired well in the plates and weighed with a precision of 0.1 mg. Once the plates are loaded, an automated liquid handling platform delivers an optional mild pretreatment (< 100°C) followed by enzymatic hydrolysis of the biomass. Aliquots from the hydrolysis are then analyzed for the release of reducing sugar equivalents. The same platform can be used for the comparative evaluation of different enzymes and enzyme cocktails. The sensitivity and reliability of the platform was evaluated by measuring the saccharification of stems from lignin modified tobacco plants, and the results of automated and manual analyses compared.

Conclusions
The automated assay systems are sensitive, robust and reliable. The system can reliably detect differences in the saccharification of plant tissues, and is able to process large number of samples with a minimum amount of human intervention. The automated system uncovered significant increases in the digestibility of certain lignin modified lines in a manner compatible with known effects of lignin modification on cell wall properties. We conclude that this automated assay platform is of sufficient sensitivity and reliability to undertake the screening of the large populations of plants necessary for mutant identification and genetic association studies.
Analysis of the expression profile of Dickkopf-1 gene in human glioma and the association with tumor malignancy
Authors: Zhou Youxin , Liu Fang , Xu Qinian , Wang Xiuyun 
Published: October 2010

Abstract

Background
Gliomas represent the most common primary malignant brain tumors, yet little is known about the molecular pathogenesis of these tumors. The highly-regulated Wnt signal transduction pathway is essential for normal developmental processes, and defects in the pathway are closely linked to oncogenesis. Dickkopf-1 (DKK-1) is a secreted protein that acts as a potent inhibitor of the Wnt pathway. The aim of this study was to examine the expression profile of DKK-1 gene in human glioma and its association with tumor malignancy.

Methods
We determined the expression levels of DKK-1 transcript and protein in 12 glioblastoma cell lines, medulloblastoma cells, low-grade glioma cells, and human astrocyte cells by semiquantitative RT-PCR and ELISA. A total of 47 tumor biopsy specimens and 11 normal brain tissue samples from patients with cerebral trauma internal decompression were embedded in paraffin blocks and used for immunostaining. Twenty-six primary tumors and 7 corresponding brain samples were stored in liquid nitrogen and used for RT-PCR. We further examined serologic concentrations and cerebral fluid levels of DKK-1 in patients with tumors.

Results
DKK-1 could only be detected in 12 human glioblastoma cell lines, not in a panel of other tumor and normal cell lines. The difference between glioma patients and healthy individuals was significant. Kendall's tau-c association analysis also revealed the increased DKK-1 protein expression in tumor tissues of higher pathologic classification. The levels of cerebral fluid DKK-1 protein were significantly higher in glioma patients than in healthy donors or in neuronal benign tumor patients, suggesting that the DKK-1 molecule in cerebral fluids can be applicable to detect the presence of glioma and be developed as a novel prognostic treatment.

Conclusion
The Wnt antagonist DKK-1 gene may have important roles in glioma tumorigenesis and act as a novel biomarker in human malignant glioblastoma.
Gum Guar fiber associated with fructose reduces serum triacylglycerol but did not improve the glucose tolerance in rats
Authors: Motoyama Caio SM , Pinto Mônica JS , Lira Fabio S , Ribeiro Eliane B , do Nascimento Claudia MO , Oyama Lila M 
Published: October 2010

Abstract

Introduction
The increased intake of dietary fructose can be associated with alterations on energy homeostasis and lipid/carbohydrate metabolism, such as insulin resistance and dislipidemia. On the other hand, the ingestion of soluble fiber gum guar could improve benefic mechanism on glucose tolerance and lipids profile.

Objective
The aim of the present study were to investigate the effects of the supplemental feeding partially hydrolyzed gum guar on glucose and lipid homeostasis, in rats fed with fructose solution.

Methods
The study was performed on thirty day-old male Wistar rats randomly assigned into four groups: control(C) or treated with fructose (F-20%), fiber (FB-5%), or fructose plus fiber (F-20% + FB-5% = FF) solution for 30 days on glucose tolerance (OGTT), triacylglycerol concentration in the liver by chloroform/methanol method, glucose, triacylglycerol and total cholesterol serum concentration by assayed by enzymatic colorimetric method, insulin receptor (IR) concentration in the liver by Western Blotting.

Results
The total body weight gain was not different between groups; in regards of total caloric intake, in the F group was significantly higher and in the FB group was lower than other groups. The triacylglycerol concentration in the liver of FF group was significantly higher than F group, the triacylglycerol concentration in the serum was higher the F group compared with other groups. The OGTT reveal impaired on glucose tolerance in the F, FB, FF compared with C. The IR concentration in the liver was lower in the F, FB, FF compared with C, no significant difference was observed between groups for IR concentration in the gastrocnemius muscle. No significant difference was observed between groups for carcass fat content and serum total cholesterol.

Conclusion
Fructose induced important alterations on glucose tolerance and lipid metabolism, despite of fiber showed reversion of part this alterations. The association fructose plus fiber to seem decrease insulin receptor concentration in the liver, with consequent impair on glucose tolerance.
MicroR159 regulation of most conserved targets in Arabidopsis has negligible phenotypic effects
Authors: Allen Robert S , Li Junyan , Alonso-Peral Maria M , White Rosemary G , Gubler Frank , Millar Anthony A 
Published: October 2010

Abstract

Background
A current challenge of microRNA (miRNA) research is the identification of biologically relevant miRNA:target gene relationships. In plants, high miRNA:target gene complementarity has enabled accurate target predictions, and slicing of target mRNAs has facilitated target validation through rapid amplification of 5' cDNA ends (5'-RACE) analysis. Together, these approaches have identified more than 20 targets potentially regulated by the deeply conserved miR159 family in Arabidopsis, including eight MYB genes with highly conserved miR159 target sites. However, genetic analysis has revealed the functional specificity of the major family members, miR159a and miR159b is limited to only two targets, MYB33 and MYB65. Here, we examine the functional role of miR159 regulation for the other potential MYB target genes.

Results
For these target genes, functional analysis failed to identify miR159 regulation that resulted in any major phenotypic impact, either at the morphological or molecular level. This appears to be mainly due to the quiescent nature of the remaining family member, MIR159c. Although its expression overlaps in a temporal and spatial cell-specific manner with a subset of these targets in anthers, the abundance of miR159c is extremely low and concomitantly a mir159c mutant displays no anther defects. Examination of potential miR159c targets with conserved miR159 binding sites found neither their spatial or temporal expression domains appeared miR159 regulated, despite the detection of miR159-guided cleavage products by 5'-RACE. Moreover, expression of a miR159-resistant target (mMYB101) resulted predominantly in plants that are indistinguishable from wild type. Plants that displayed altered morphological phenotypes were found to be ectopically expressing the mMYB101 transgene, and hence were misrepresentative of the in vivo functional role of miR159.

Conclusions
This study presents a novel explanation for a paradox common to plant and animal miRNA systems, where among many potential miRNA-target relationships usually only a few appear physiologically relevant. The identification of a quiescent miR159c:target gene regulatory module in anthers provides a likely rationale for the presence of conserved miR159 binding sites in many targets for which miR159 regulation has no obvious functional role. Remnants from the demise of such modules may lead to an overestimation of miRNA regulatory complexity when investigated using bioinformatic, 5'-RACE or transgenic approaches.
Cancer-related ectopic expression of the bone-related transcription factor RUNX2 in non-osseous metastatic tumor cells is linked to cell proliferation and motility
Authors: Leong David T , Lim Joleen , Goh Xuewei , Pratap Jitesh , Pereira Barry P , Kwok Hui Si , Nathan Saminathan Suresh , Dobson Jason R , Lian Jane B , Ito Yoshiaki , Voorhoeve P Mathijs , Stein Gary S , Salto-Tellez Manuel , Cool Simon M , van Wijnen Andre J 
Published: October 2010

Abstract
Introduction
Metastatic breast cancer cells frequently and ectopically express the transcription factor RUNX2, which normally attenuates proliferation and promotes maturation of osteoblasts. RUNX2 expression is inversely regulated with respect to cell growth in osteoblasts and deregulated in osteosarcoma cells.

Methods
Here, we addressed whether the functional relationship between cell growth and RUNX2 gene expression is maintained in breast cancer cells. We also investigated whether the aberrant expression of RUNX2 is linked to phenotypic parameters that could provide a selective advantage to cells during breast cancer progression.

Results
We find that, similar to its regulation in osteoblasts, RUNX2 expression in MDA-MB-231 breast adenocarcinoma cells is enhanced upon growth factor deprivation, as well as upon deactivation of the mitogen-dependent MEK-Erk pathway or EGFR signaling. Reduction of RUNX2 levels by RNAi has only marginal effects on cell growth and expression of proliferation markers in MDA-MB-231 breast cancer cells. Thus, RUNX2 is not a critical regulator of cell proliferation in this cell type. However, siRNA depletion of RUNX2 in MDA-MB-231 cells reduces cell motility, while forced exogenous expression of RUNX2 in MCF7 cells increases cell motility.

Conclusions
Our results support the emerging concept that the osteogenic transcription factor RUNX2 functions as a metastasis-related oncoprotein in non-osseous cancer cells.
Circulating retinol binding protein 4 in critically ill patients before specific treatment: prognostic impact and correlation with organ function, metabolism and inflammation
Authors: Koch Alexander , Weiskirchen Ralf , Sanson Edouard , Zimmermann Henning W , Voigt Sebastian , Dückers Hanna , Trautwein Christian , Tacke Frank 
Published: October 2010

Abstract
Introduction
Hyperglycemia and insulin resistance are well-known features of critical illness and impact the mortality rate, especially in sepsis. Retinol binding protein 4 (RBP4) promotes insulin resistance in mice and is systemically elevated in patients with obesity and type 2 diabetes. We investigated the potential role of RBP4 in critically ill patients.

Methods
We conducted a prospective single-center study of serum RBP4 concentrations in critically ill patients. One hundred twenty-three patients (85 with sepsis, 38 without sepsis) were studied at admission to a medical intensive care unit (ICU) before initiation of specific intensive care treatment measures and compared to 42 healthy nondiabetic controls. Clinical data, various laboratory parameters and metabolic and endocrine functions were assessed. Patients were followed for approximately 3 years.

Results
Serum RBP4 was significantly reduced in ICU patients, independently of sepsis, as compared to healthy controls (P < 0.001). Patients with liver cirrhosis as the primary underlying diagnosis for ICU admission had significantly lower RBP4 levels as compared with other ICU patients. Accordingly, in all ICU patients, serum RBP4 closely correlated with liver function and increased with renal failure. No significant differences of serum RBP4 concentrations in septic patients with pulmonary or other origins of sepsis or nonseptic patients could be revealed. Acute phase proteins were inversely correlated with RBP4 in sepsis patients. RBP4 did not differ between patients with or without obesity or preexisting diabetes. However, serum RBP4 levels correlated with endogenous insulin secretion (C-peptide) and insulin resistance (HOMA index). Low serum RBP4 upon admission was an adverse predictor of short-term survival in the ICU, but was not associated with overall survival during long-term follow-up.

Conclusions
Serum RBP4 concentrations are significantly reduced in critically ill patients. The strong associations with hepatic and renal function, insulin resistance and acute mortality collectively suggest a role of RBP4 in the pathogenesis of critical illness, possibly as a negative acute phase reactant, and allow a proposition as a potential novel biomarker for ICU patients.
Global DNA methylation: comparison of enzymatic- and non-enzymatic-based methods
Authors: Rocha Monica S. , Castro Rita , Rivera Isabel , Kok Robert M. , Smulders Yvo M. , Jakobs Cornelis , de Almeida Isabel Tavares , Blom Henk J. 
Published: October 2010

Abstract

Background: The most frequently used methods for meas-uring global DNA methylation are based on two different principles: the use of methylation-sensitive restriction endonucleases followed by analysis of the obtained fragments, or the hydrolysis of genomic DNA followed by specific detection and quantification of the 5-methylcytosine content. We aimed to compare two different methods for evaluation of global DNA methylation: the cytosine extension assay after enzymatic digestion of DNA (Cyt-Ext), and a recently described method using liquid chromatography-electrospray ionization-tandem mass spectrometry after DNA hydrolysis (LC-MS/MS).

Methods: Both approaches were applied to evaluate global DNA methylation in leukocyte DNA from 96 healthy subjects. Calf thymus and pBR322 DNAs were used as hyper- and hypo-methylated references, respectively.

Results: Using the Cyt-Ext method, the DNA from healthy individuals showed radiolabel incorporation of 11,312± 1600 Dpm/μg DNA, while the LC-MS/MS method showed 4.55±0.1% methylation. Results are shown as mean±SD. The analysis of hypo- and hyper-methylated references showed that both methods are practical for discriminating different levels of methylation.

Conclusions: Cyt-Ext and LC-MS/MS are viable methods in evaluating global DNA methylation status. However, the LC-MS/MS assay allows absolute quantification and displays far superior intra-day precision. Therefore, we consider the later approach to be better for use in global DNA methylation studies.
Clin Chem Lab Med 2010;48:1793–8.
Abstraction-based Efficiency in the Lexicon
Authors: Cutler Anne 
Published: November 2010

AbstractListeners learn from their past experience of listening to spoken words, and use this learning to maximise the efficiency of future word recognition. This paper summarises evidence that the facilitatory effects of drawing on past experience are mediated by abstraction, enabling learning to be generalised across new words and new listening situations. Phoneme category retuning, which allows adaptation to speaker-specific articulatory characteristics, is generalised on the basis of relatively brief experience to words previously unheard from that speaker. Abstract knowledge of prosodic regularities is applied to recognition even of novel words for which these regularities were violated. Prosodic word-boundary regularities drive segmentation of speech into words independently of the membership of the lexical candidate set resulting from the segmentation operation. Each of these different cases illustrates how abstraction from past listening experience has contributed to the efficiency of lexical recognition.
Zur Übersetzung der skandinavischen Pseudokoordination
Authors: Hesse Andrea 
Published: November 2010

Abstract
Pseudocoordination is a specific grammatical construction in Scandinavian (i. e. Danish, Norwegian, Swedish and Faroese), combining local (and several other) verbs as auxiliaries with another finite verbal phrase as in Swedish Emil sitter och täljer ‘(lit.) Emil sit-PRS and carve-PRS → Emil is carving’. The construction is partially grammaticalized: on the one hand it is an aspectual marker, referring to an ongoing action or process; on the other hand it still contains some lexical background information about the subject referent's sitting or standing or the like. This paper investigates how German and Icelandic translators deal with pseudocoordination, since neither language has equivalents with this special set of semantics. In addition, both target languages differ in their possibilities to indicate aspectual meanings. Based on four Scandinavian novels and their translations, the article discusses translation strategies in isolated cases and their effect on text cohesion. It will be shown that the translators often do not focus on the construction's aspectuality, but on its lexical contents. As a result, Icelandic translations repeatedly adapt the pseudocoordination as an interference, while German translations prefer a more complex local construction.