bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mitochondrial dysregulation and oxidative stress in patients with chronic kidney disease
Authors: Granata Simona , Zaza Gianluigi , Simone Simona , Villani Gaetano , Latorre Dominga , Pontrelli Paola , Carella Massimo , Schena Francesco Paolo , Grandaliano Giuseppe , Pertosa Giovanni 
Published: August 2009

AbstractBackgroundChronic renal disease (CKD) is characterized by complex changes in cell metabolism leading to an increased production of oxygen radicals, that, in turn has been suggested to play a key role in numerous clinical complications of this pathological condition. Several reports have focused on the identification of biological elements involved in the development of systemic biochemical alterations in CKD, but this abundant literature results fragmented and not exhaustive.ResultsTo better define the cellular machinery associated to this condition, we employed a high-throughput genomic approach based on a whole transcriptomic analysis associated with classical molecular methodologies. The genomic screening of peripheral blood mononuclear cells revealed that 44 genes were up-regulated in both CKD patients in conservative treatment (CKD, n = 9) and hemodialysis (HD, n = 17) compared to healthy subjects (HS, n = 8) (p < 0.001, FDR = 1%). Functional analysis demonstrated that 11/44 genes were involved in the oxidative phosphorylation system. Western blotting for COXI and COXIV, key constituents of the complex IV of oxidative phosphorylation system, performed on an independent testing-group (12 healthy subjects, 10 CKD and 14 HD) confirmed an higher synthesis of these subunits in CKD/HD patients compared to the control group. Only for COXI, the comparison between CKD and healthy subjects reached the statistical significance. However, complex IV activity was significantly reduced in CKD/HD patients compared to healthy subjects (p < 0.01). Finally, CKD/HD patients presented higher reactive oxygen species and 8-hydroxydeoxyguanosine levels compared to controls.ConclusionTaken together these results suggest, for the first time, that CKD/HD patients may have an impaired mitochondrial respiratory system and this condition may be both the consequence and the cause of an enhanced oxidative stress.
The Lactamase Engineering Database: a critical survey of TEM sequences in public databases
Authors: Thai Quan Ke , Bös Fabian , Pleiss Jürgen 
Published: August 2009

Abstract

Background
TEM β-lactamases are the main cause for resistance against β-lactam antibiotics. Sequence information about TEM β-lactamases is mainly found in the NCBI peptide database and TEM mutation table at http://www.lahey.org/Studies/temtable.asp. While the TEM mutation table is manually curated by experts in the lactamase field, who guarantee reliable and consistent information, the rapidly growing sequence and annotation information from the NCBI peptide database is sometimes inconsistent. Therefore, the Lactamase Engineering Database has been developed to collect the TEM β-lactamase sequences from the NCBI peptide database and the TEM mutation table, systematically compare sequence information and naming, identify inconsistencies, and thus provide a versatile tool for reconciliation of data and for an investigation of the sequence-function relationship.

Description
The LacED currently provides 2399 sequence entries and 37 structure entries. Sequence information on 150 different TEM β-lactamases was derived from the TEM mutation table which provides a unique number to each protein classified as TEM β-lactamase. 293 TEM-like proteins were found in the NCBI protein database, but only 113 TEM β-lactamase were common to both data sets. The 180 TEM β-lactamases from the NCBI protein database which have not yet been assigned to a TEM number fall in three classes: (1) 89 proteins from microbial organisms and 35 proteins from cloning or expression vectors had a new mutation profile; (2) 55 proteins had inconsistent annotation in terms of TEM assignment or reported mutation profile; (3) 39 proteins are fragments. The LacED is web accessible at http://www.LacED.uni-stuttgart.de and contains multisequence alignments, structure information and reconciled annotation of TEM β-lactamases. The LacED is weekly updated and supplies all data for download.

Conclusion
The Lactamase Engineering Database enables a systematic analysis of TEM β-lactamase sequence and annotation data from different data sources, and thus provides a valuable tool to identify inconsistencies in sequences from the NCBI peptide database, to detect TEM β-lactamases with a novel mutation profile, and to identify new amino acid positions at which mutations can occur.
CgOpt1, a putative oligopeptide transporter from Colletotrichum gloeosporioides that is involved in responses to auxin and pathogenicity
Authors: Chagué Véronique , Maor Rudy , Sharon Amir 
Published: August 2009

Abstract

Background
The fungus Colletotrichum gloeosporioides f. sp. aeschynomene produces high levels of indole-3-acetic acid (IAA) in axenic cultures and during plant infection. We generated a suppression subtractive hybridization library enriched for IAA-induced genes and identified a clone, which was highly expressed in IAA-containing medium.

Results
The corresponding gene showed similarity to oligopeptide transporters of the OPT family and was therefore named CgOPT1. Expression of CgOPT1 in mycelia was low, and was enhanced by external application of IAA. cgopt1-silenced mutants produced less spores, had reduced pigmentation, and were less pathogenic to plants than the wild-type strain. IAA enhanced spore formation and caused changes in colony morphology in the wild-type strain, but had no effect on spore formation or colony morphology of the cgopt1-silenced mutants.

Conclusion
Our results show that IAA induces developmental changes in C. gloeosporioides. These changes are blocked in cgopt1-silenced mutants, suggesting that this protein is involved in regulation of fungal response to IAA. CgOPT1 is also necessary for full virulence, but it is unclear whether this phenotype is related to auxin.
The mRNA expression of SETD2 in human breast cancer: correlation with clinico-pathological parameters
Authors: Al Sarakbi W , Sasi W , Jiang WG , Roberts T , Newbold RF , Mokbel K 
Published: August 2009

Abstract

Background
SET domain containing protein 2 (SETD2) is a histone methyltransferase that is involved in transcriptional elongation.
There is evidence that SETD2 interacts with p53 and selectively regulates its downstream genes. Therefore, it could be implicated in the process of carcinogenesis. Furthermore, this gene is located on the short arm of chromosome 3p and we previously demonstrated that the 3p21.31 region of chromosome 3 was associated with permanent growth arrest of breast cancer cells. This region includes closely related genes namely: MYL3, CCDC12, KIF9, KLHL18 and SETD2. Based on the biological function of these genes, SETD2 is the most likely gene to play a tumour suppressor role and explain our previous findings.
Our objective was to determine, using quantitative PCR, whether the mRNA expression levels of SETD2 were consistent with a tumour suppressive function in breast cancer. This is the first study in the literature to examine the direct relationship between SETD2 and breast cancer.

Methods
A total of 153 samples were analysed.
The levels of transcription of SETD2 were determined using quantitative PCR and normalized against (CK19).
Transcript levels within breast cancer specimens were compared to normal background tissues and analyzed against conventional pathological parameters and clinical outcome over a 10 year follow-up period.

Results
The levels of SETD2 mRNA were significantly lower in malignant samples (p = 0.0345) and decreased with increasing tumour stage.
SETD2 expression levels were significantly lower in samples from patients who developed metastasis, local recurrence, or died of breast cancer when compared to those who were disease free for > 10 years (p = 0.041).

Conclusion
This study demonstrates a compelling trend for SETD2 transcription levels to be lower in cancerous tissues and in patients who developed progressive disease. These findings are consistent with a possible tumour suppressor function of this gene in breast cancer.
Manipulating insulin signaling to enhance mosquito reproduction
Authors: Arik Anam J , Rasgon Jason L , Quicke Kendra M , Riehle Michael A 
Published: August 2009

Abstract

Backgrond
In the mosquito Aedes aegypti the insulin/insulin growth factor I signaling (IIS) cascade is a key regulator of many physiological processes, including reproduction. Two important reproductive events, steroidogenesis in the ovary and yolk synthesis in the fat body, are regulated by the IIS cascade in mosquitoes. The signaling molecule phosphatase and tensin homolog (PTEN) is a key inhibitor of the IIS cascade that helps modulate the activity of the IIS cascade. In Ae. aegypti, six unique splice variants of AaegPTEN were previously identified, but the role of these splice variants, particularly AaegPTEN3 and 6, were unknown.

Results
Knockdown of AaegPTEN or its specific splice variant AaegPTEN6 (the splice variant thought to regulate reproduction in the ovary and fat body) using RNAi led to a 15–63% increase in egg production with no adverse effects on egg viability during the first reproductive cycle. Knockdown of AaegPTEN3, expressed predominantly in the head, had no effect on reproduction. We also characterized the protein expression patterns of these two splice variants during development and in various tissues during a reproductive cycle.

Conclusion
Previous studies in a range of organisms, including Drosophila melanogaster and Caenorhabditis elegans, have demonstrated that disruption of the IIS cascade leads to decreased reproduction or sterility. In this study we demonstrate that knockdown of the IIS inhibitor PTEN can actually increase reproduction in the mosquito, at least during the first reproductive cycle.
The human placenta releases substances that drive lung cancer into apoptosis
Authors: Marwitz Sebastian , Zeiser Tobias , Schultz Holger , Kähler Daniel , Abdullah Mahdi , Hauber Hans-Peter , Zabel Peter , Vollmer Ekkehard , Goldmann Torsten 
Published: August 2009

Abstract

Background
As there is no optimal treatment of non small cell lung cancer due to its resistance to common chemotherapeutics, we investigated the effect of human placenta-conditioned medium on tumor tissue. The human placenta constitutes a mixture of maternal and fetal origin and displays a variety of immunomodulatory aspects.

Methods
Freshly resected non small cell lung cancer tissues were incubated with placenta-conditioned medium in a short-term tissue culture model and A549 cells were challenged, respectively. Term placenta was used for producing conditioned medium and HOPE-fixed stimulated tumor tissue was analyzed for expression of caspase-3 and Ki67 via immunohistochemistry. The effects of conditioned medium on squamous cell carcinoma were further compared to physiological concentrations of Carboplat/Gemzar.

Results
Conditioned medium caused in 2 of 3 cases elevated expression of caspase-3 and reduced expression of Ki67 in 3 out of 3 cases, while the chemotherapeutic agents caused no comparable expression of caspase-3 or reduction of Ki67. In cell culture up to 50% of karyopyknosis was investigated and even sterile-filtrated medium caused widespread reduction of Ki67 on protein level.

Conclusion
Human placenta releases substances that mediate apoptosis and reduce proliferation in tumor tissue and cell culture. As even sterile-filtrated medium caused the mentioned effects we hypothesize one or more soluble mediators. The detailed way of promoting apoptosis and nature of these mediators need to be elucidated in further studies.
Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes
Authors: Dong Xianjun , Fredman David , Lenhard Boris 
Published: August 2009

AbstractGenomic regulatory blocks are chromosomal regions spanned by long clusters of highly conserved noncoding elements devoted to long-range regulation of developmental genes, often immobilizing other, unrelated genes into long-lasting syntenic arrangements. Synorth http://synorth.genereg.net/ is a web resource for exploring and categorizing the syntenic relationships in genomic regulatory blocks across multiple genomes, tracing their evolutionary fate after teleost whole genome duplication at the level of genomic regulatory block loci, individual genes, and their phylogenetic context.
Pivotal Advance: Kaposi’s sarcoma-associated herpesvirus (KSHV)-encoded microRNA specifically induce IL-6 and IL-10 secretion by macrophages and monocytes
Authors: Qin Zhiqiang , Kearney Patricia , Plaisance Karlie , Parsons Chris H 
Published: August 2009

Abstract
MicroRNA encoded by KSHV, a common tumor virus, induces macrophage secretion of tumor-promoting cytokines by down-regulating the transcription factor C/EBPβ p20 isoform (LIP).
Macrophages are an important source of inflammatory cytokines generated during the innate immune response, but in the microenvironment of certain tumors, macrophages promote tumor progression through their preferential secretion of cytokines that support tumor cell growth and suppress antitumoral immune responses. KSHV is the causative agent of KS and lymphomas preferentially arising in immunocompromised patients, and specific cytokines, including IL-6 and IL-10, have been implicated in KSHV-associated cancer pathogenesis. However, the contribution of KSHV-infected macrophages to the cytokine milieu within KSHV-related tumors is unclear. We found that individual KSHV-encoded miRNA induce IL-6 and IL-10 secretion independently and additively by murine macrophages and human myelomonocytic cells. Bioinformatics analysis identified KSHV miRNA binding sites for miR-K12-3 and miR-K12-7 within the 3′UTR of the basic region/leucine zipper motif transcription factor C/EBPβ, a known regulator of IL-6 and IL-10 transcriptional activation. Subsequent immunoblot analyses revealed that miR-K12-3 and miR-K12-7 preferentially reduce expression of C/EBPβ p20 (LIP), an isoform of C/EBPβ known to function as a negative transcription regulator. In addition, RNA interference specifically targeting LIP induced basal secretion of IL-6 and IL-10 by macrophages. Taken together, these data support a role for KSHV miRNA in the programming of macrophage cytokine responses in favor of KSHV-related tumor progression.
Peripheral blood CD4+ T lymphocytes from multiple sclerosis patients are characterized by higher PSGL-1 expression and transmigration capacity across a human blood-brain barrier-derived endothelial cell line
Authors: Bahbouhi Bouchaib , Berthelot Laureline , Pettré Ségolène , Michel Laure , Wiertlewski Sandrine , Weksler Babette , Romero Ignacio-Andres , Miller Florence , Couraud Pierre-Olivier , Brouard Sophie , Laplaud David-Axel , Soulillou Jean-Paul 
Published: August 2009

Abstract
Significant alterations in the transmigration capacity of peripheral blood T-lymphocytes found as a feature in multiple sclerosis.
Mechanisms of T lymphocyte trafficking in the brain remain unclear in MS. We hypothesized that MS is associated with increased CD4+ and CD8+ T lymphocyte trafficking across the BBB. To test this hypothesis, we calculated the frequency of PSGL-1+/CD4+ and PSGL-1+CD8+ or LFA-1+/CD4+/CD8+ T cells in the PBMC of 27 patients with a RR-MS (21 untreated and six IFN-β-treated) and 18 HI. Next, we measured their ex vivo TR across resting and TNF-α-activated human BBB-derived hCMEC/D3 endothelial layers under static conditions. The frequency of PSGL-1+CD4+ T lymphocytes was significantly higher in treated or untreated MS patients than HI. Furthermore, resting hCMEC/D3 TR of CD4+ lymphocytes (purified or in PBMC) from treated or untreated MS patients were significantly higher than those of HI and associated with significant enrichments of CD4+PSGL+ or CD4+PSGL-1+CD45RO+ T cells in their transmigrating fractions. The TR of CD4+ and CD8+ from MS patients across TNF-α-activated hCMEC/D3 were also significantly higher than that observed in HI. Resting hCMEC/D3 transmigration was blocked significantly by anti-PSGL-1/anti-LFA-1 in all groups, and anti-VLA-4 inhibited transmigration of MS T cells specifically. Purified PSGL-1-negative CD4+ lymphocytes transmigrated resting hCMEC/D3 with &lt;10% of transmigrating cells re-expressing PSGL-1, suggesting PSGL-1-independent transmigration mechanisms. The frequency of PSGL-1 was unchanged in CD8+ cells from MS patients, whereas CD8+LFA-1high were reduced significantly in IFN-β-treated patients specifically. Collectively, MS is associated with an expanding pool of PSGL-1+CD4+ T lymphocytes able to transmigrate the BBB endothelium in vitro and possibly contributing to brain pathology.
Effect of grouped-hole nozzle geometry on the improvement of biodiesel fuel atomization characteristics in a compression ignition engine
Authors: Suh H K , Park S W , Lee C S 
Published: August 2009

This paper describes the influence of grouped-hole nozzle geometry on the atomization characteristics of a biodiesel fuel. The effects of injection rate profile, spray evolution, droplet mean diameter, and mean velocity of the droplets are investigated in a high-pressure injection system. A grouped-hole nozzle with 16 holes driven by piezo stack was used in the experiments and the obtained results are compared with those obtained using a single-hole nozzle with the same overall nozzle area. The effect of using a split fuel injection strategy on the spray atomization was analysed using a grouped-hole nozzle with 12 holes. The time-based injection rate profiles for a biodiesel fuel, i.e. the mass flowrate of the fuel injector nozzle were obtained from the pressure variation generated when the fuel was injected into a tube filled with fuel. The spray and atomization performance for biodiesel fuel injected through a grouped-hole nozzle were visualized and measured by a visualization system and droplet analyser system, respectively. It was revealed that the biodiesel injection rate profile from a single-hole nozzle with the same overall nozzle area shows a similar injection rate profile to that of the grouped-hole nozzle. The injection rate profiles for a split injection strategy are lower than for a single injection and the peak value of the second injection is lower than for the first injection. The Sauter mean diameter distributions of biodiesel from the grouped-hole nozzle have a larger diameter because the small droplets injected through the grouped-hole nozzle collide and coalesce with each other, which leads to an increase in droplet diameter. From these results, it can be concluded that the use of a grouped-hole nozzle and split injection strategy does not improve on the fuel atomization performance for biodiesel fuel for a single-hole nozzle.
Karanja oil utilization in a direct-injection engine by preheating. Part 1: experimental investigations of engine performance, emissions, and combustion characteristics
Authors: Agarwal A K , Dhar A 
Published: August 2009

Vegetable oils have an energy content suitable for use as a fuel in diesel engines. Some of these oils have already been evaluated as substitutes for diesel fuels. However, several operational and durability problems of using straight vegetable oils in diesel engines have been reported in the literature, caused by their relatively higher viscosity and low volatility compared to mineral diesel. This viscosity can be brought into the acceptable range by transesterification, by blending of vegetable oil with diesel, or by preheating the vegetable oil using the waste heat of exhaust gases. The reduction in the viscosity by blending or exhaust gas preheating saves the processing cost incurred in the transesterification process involving expensive chemicals. Experimental investigations were carried out for the combustion, performance, and emission characteristics of heated Karanja oil in a direct-injection compression ignition engine at different loads at a constant engine speed of 1500r/min. Analysis of the cylinder pressure rise, instantaneous heat release, and cumulative heat release was carried out. Combustion phasing of preheated Karanja oil was found to be identical with that of mineral diesel. Heating the vegetable oil substantially reduces the combustion duration. The brake specific fuel consumption and exhaust gas temperatures for heated Karanja oil were found to be higher than mineral diesel. The thermal efficiency was slightly lower for heated Karanja oil than for diesel. The carbon dioxide, carbon monoxide, hydrocarbon, and nitric oxide emissions were lower for heated Karanja oil than for diesel.
Effect of Carbon Source on the Textural and Electrochemical Properties of Novel Cage-type Mesoporous Carbon as a Replica of KIT-5 Mesoporous Silica
Authors: Inagaki Satoshi , Oikawa Koji , Kubota Yoshihiro 
Published: August 2009

Abstract
Novel cage-type mesoporous carbon “carbon nanocage (CNC),” which is prepared as a carbon replica of KIT-5 mesoporous silica, showed a high electrochemical performance as an electrode material, due to the high specific surface area and mesopore volume as well as the sparse carbon network.
Biochemical and nutritional indices as cardiovascular risk factors among Iranian firefighters
Authors: Azabdaftari Nazli , Amani Reza , Taha Jalali Mohammad 
Published: August 2009

Aim Limited cardiovascular disease (CVD) risk data are available for firefighters worldwide. This comparative study was aimed at investigating the biochemical and nutritional indices of firefighters in Iran. Materials and methods Individuals’ anthropometric measurements, including weight, height, and waist and hip circumferences, were measured and the percent of body fat (BF%) was also obtained. Blood sampling was done in order to determine lipid profile, including total cholesterol (TC), triglycerides (TG), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), lipoprotein a (Lp(a)) and fasting blood sugar (FBS) concentrations. Systolic and diastolic blood pressures (SBP and DBP) were also measured. Results The mean ages of firefighters and administrative staff were 42.45 ± 6.75 and 44.64 ± 5.83 y, respectively. The prevalence of overweight and obesity was 45% and 24% in firefighters and 54% and 23% in administrative staff, respectively. High waist-to-hip and waist-to-stature ratios were detected in 26.4% and 81.3% of firefighters versus 33.3% and 89.7% of the control group, respectively. No significant differences were observed between the mean of TC, TG, HDL-C, LDL-C and FBS concentrations. The mean of Lp(a) was significantly higher among firefighters ( P<0.05). About half of the subjects in both groups had TC >5.17, TG >1.69, HDL-C <1.03 nmol/L and Lp(a) >25 mg/dL. There were no significant differences between the SBP and DBP of subjects. There was no significant difference in smoking habits between the two groups. Conclusions Considering the high prevalence of overweight and obesity, high TC, TG and Lp(a) and low HDL-C concentrations among all firefighters, it seems necessary to provide fitness-promotion and nutritional education programs for the prevention of obesity-related chronic diseases such as CVD.