bluuebunny/crossref_metadata_2025_split huggingface dataset:
The mitochondrial genomes of the ciliates Euplotes minuta and Euplotes crassus
Authors: de Graaf Rob M , van Alen Theo A , Dutilh Bas E , Kuiper Jan WP , van Zoggel Hanneke JAA , Huynh Minh Bao , Görtz Hans-Dieter , Huynen Martijn A , Hackstein Johannes HP 
Published: November 2009

Abstract

Background
There are thousands of very diverse ciliate species from which only a handful mitochondrial genomes have been studied so far. These genomes are rather similar because the ciliates analysed (Tetrahymena spp. and Paramecium aurelia) are closely related. Here we study the mitochondrial genomes of the hypotrichous ciliates Euplotes minuta and Euplotes crassus. These ciliates are only distantly related to Tetrahymena spp. and Paramecium aurelia, but more closely related to Nyctotherus ovalis, which possesses a hydrogenosomal (mitochondrial) genome.

Results
The linear mitochondrial genomes of the hypotrichous ciliates Euplotes minuta and Euplotes crassus were sequenced and compared with the mitochondrial genomes of several Tetrahymena species, Paramecium aurelia and the partially sequenced mitochondrial genome of the anaerobic ciliate Nyctotherus ovalis. This study reports new features such as long 5'gene extensions of several mitochondrial genes, extremely long cox1 and cox2 open reading frames and a large repeat in the middle of the linear mitochondrial genome. The repeat separates the open reading frames into two blocks, each having a single direction of transcription, from the repeat towards the ends of the chromosome. Although the Euplotes mitochondrial gene content is almost identical to that of Paramecium and Tetrahymena, the order of the genes is completely different. In contrast, the 33273 bp (excluding the repeat region) piece of the mitochondrial genome that has been sequenced in both Euplotes species exhibits no difference in gene order. Unexpectedly, many of the mitochondrial genes of E. minuta encoding ribosomal proteins possess N-terminal extensions that are similar to mitochondrial targeting signals.

Conclusion
The mitochondrial genomes of the hypotrichous ciliates Euplotes minuta and Euplotes crassus are rather different from the previously studied genomes. Many genes are extended in size compared to mitochondrial genes from other sources.
A Smac-mimetic sensitizes prostate cancer cells to TRAIL-induced apoptosis via modulating both IAPs and NF-kappaB
Authors: Dai Yao , Liu Meilan , Tang Wenhua , Li Yongming , Lian Jiqin , Lawrence Theodore S , Xu Liang 
Published: November 2009

AbstractBackgroundAlthough tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is a promising agent for human cancer therapy, prostate cancer still remains resistant to TRAIL. Both X-linked inhibitor of apoptosis (XIAP) and nuclear factor-kappaB function as key negative regulators of TRAIL signaling. In this study, we evaluated the effect of SH122, a small molecule mimetic of the second mitochondria-derived activator of caspases (Smac), on TRAIL-induced apoptosis in prostate cancer cells.MethodsThe potential of Smac-mimetics to bind XIAP or cIAP-1 was examined by pull-down assay. Cytotoxicity of TRAIL and/or Smac-mimetics was determined by a standard cell growth assay. Silencing of XIAP or cIAP-1 was achieved by transient transfection of short hairpin RNA. Apoptosis was detected by Annexin V-PI staining followed by flow cytometry and by Western Blot analysis of caspases, PARP and Bid. NF-kappaB activation was determined by subcellular fractionation, real time RT-PCR and reporter assay.ResultsSH122, but not its inactive analog, binds to XIAP and cIAP-1. SH122 significantly sensitized prostate cancer cells to TRAIL-mediated cell death. Moreover, SH122 enhanced TRAIL-induced apoptosis via both the death receptor and the mitochondrial pathway. Knockdown of both XIAP and cIAP-1 sensitized cellular response to TRAIL. XIAP-knockdown attenuated sensitivity of SH122 to TRAIL-induced cytotoxicity, confirming that XIAP is an important target for IAP-inhibitor-mediated TRAIL sensitization. SH122 also suppressed TRAIL-induced NF-kappaB activation by preventing cytosolic IkappaB-alpha degradation and RelA nuclear translocation, as well as by suppressing NF-kappaB target gene expression.ConclusionThese results demonstrate that SH122 sensitizes human prostate cancer cells to TRAIL-induced apoptosis by mimicking Smac and blocking both IAPs and NF-kappaB. Modulating IAPs may represent a promising approach to overcoming TRAIL-resistance in human prostate cancer with constitutively active NF-kappaB signaling.
Lack of association between mutations of gene-encoding mitochondrial D310 (displacement loop) mononucleotide repeat and oxidative stress in chronic dialysis patients in Taiwan
Authors: Chen Jin-Bor , Lin Tsu-Kung , Liao Shang-Chih , Lee Wen-Chin , Lee Lung-Chih , Liou Chia-Wei , Wang Pei-Wen , Tiao Mao-Meng 
Published: November 2009

Abstract

Background
Mitochondria (mt) are highly susceptible to reactive oxygen species (ROS). In this study, we investigated the association between a region within the displacement loop (D-loop) in mtDNA that is highly susceptible to ROS and oxidative stress markers in chronic dialysis patients. We enrolled 184 chronic dialysis patients and 213 age-matched healthy subjects for comparison. Blood levels of oxidative stress markers, such as thiobarbituric acid reactive substances (TBARS) and free thiol, and the mtDNA copy number were determined. A mononucleotide repeat sequence (CCCC...CCCTCCCCCC) between nucleotides 303 and 316-318 (D310) was identified in mtDNA.

Results
Depending on alterations in the D310 mononucleotide repeat, subjects were categorized into 4 subgroups: 7-C, 8-C, 9 or 10-C, and T-to-C transition. Oxidative stress was higher in chronic dialysis patients, evidenced by higher levels of TBARS and mtDNA copy number, and a lower level of free thiol. The distribution of 7-C, 8-C, and 9-10C in dialysis and control subjects was as follows: 7-C (38% vs. 31.5%), 8-C (35.3% vs. 43.2%), and 9-10C (24.5% vs. 22.1%). Although there were significant differences in levels of TBARS, free thiol, and the mtDNA copy number in the D310 repeat subgroups (except T-to-C transition) between dialysis patients and control subjects, post hoc analyses within the same study cohort revealed no significant differences.

Conclusion
Although oxidative stress was elevated in chronic dialysis patients and resulted in a compensatory increase in the mtDNA copy number, homopolymeric C repeats in the mtDNA region (D310), susceptible to ROS, were not associated with oxidative stress markers in these patients.
Enrichment and proteomic analysis of plasma membrane from rat dorsal root ganglions
Authors: Xiong Xia , Huang Sha , Zhang Hai , Li Jianjun , Shen Jianying , Xiong Jixian , Lin Yong , Jiang Liping , Wang Xianchun , Liang Sonping 
Published: November 2009

Abstract

Background
Dorsal root ganglion (DRG) neurons are primary sensory neurons that conduct neuronal impulses related to pain, touch and temperature senses. Plasma membrane (PM) of DRG cells plays important roles in their functions. PM proteins are main performers of the functions. However, mainly due to the very low amount of DRG that leads to the difficulties in PM sample collection, few proteomic analyses on the PM have been reported and it is a subject that demands further investigation.

Results
By using aqueous polymer two-phase partition in combination with high salt and high pH washing, PMs were efficiently enriched, demonstrated by western blot analysis. A total of 954 non-redundant proteins were identified from the plasma membrane-enriched preparation with CapLC-MS/MS analysis subsequent to protein separation by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) or shotgun digestion. 205 (21.5%) of the identified proteins were unambiguously assigned as PM proteins, including a large number of signal proteins, receptors, ion channel and transporters.

Conclusion
The aqueous polymer two-phase partition is a simple, rapid and relatively inexpensive method. It is well suitable for the purification of PMs from small amount of tissues. Therefore, it is reasonable for the DRG PM to be enriched by using aqueous two-phase partition as a preferred method. Proteomic analysis showed that DRG PM was rich in proteins involved in the fundamental biological processes including material exchange, energy transformation and information transmission, etc. These data would help to our further understanding of the fundamental DRG functions.
Large-scale insertional mutagenesis of a coleopteran stored grain pest, the red flour beetle Tribolium castaneum, identifies embryonic lethal mutations and enhancer traps
Authors: Trauner Jochen , Schinko Johannes , Lorenzen Marcé D , Shippy Teresa D , Wimmer Ernst A , Beeman Richard W , Klingler Martin , Bucher Gregor , Brown Susan J 
Published: November 2009

Abstract

Background

Given its sequenced genome and efficient systemic RNA interference response, the red flour beetle Tribolium castaneum is a model organism well suited for reverse genetics. Even so, there is a pressing need for forward genetic analysis to escape the bias inherent in candidate gene approaches.

Results

To produce easy-to-maintain insertional mutations and to obtain fluorescent marker lines to aid phenotypic analysis, we undertook a large-scale transposon mutagenesis screen. In this screen, we produced more than 6,500 new piggyBac insertions. Of these, 421 proved to be recessive lethal, 75 were semi-lethal, and eight indicated recessive sterility, while 505 showed new enhancer-trap patterns. Insertion junctions were determined for 403 lines and often appeared to be located within transcription units. Insertion sites appeared to be randomly distributed throughout the genome, with the exception of a preference for reinsertion near the donor site.

Conclusion

A large collection of enhancer-trap and embryonic lethal beetle lines has been made available to the research community and will foster investigations into diverse fields of insect biology, pest control, and evolution. Because the genetic elements used in this screen are species-nonspecific, and because the crossing scheme does not depend on balancer chromosomes, the methods presented herein should be broadly applicable for many insect species.
Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness
Authors: Marques Ana C , Ponting Chris P 
Published: November 2009

Abstract
Background
Despite increasing interest in the noncoding fraction of transcriptomes, the number, species-conservation and functions, if any, of many non-protein-coding transcripts remain to be discovered. Two extensive long intergenic noncoding RNA (ncRNA) transcript catalogues are now available for mouse: over 3,000 macroRNAs identified by cDNA sequencing, and 1,600 long intergenic noncoding RNA (lincRNA) intervals that are predicted from chromatin-state maps. Previously we showed that macroRNAs tend to be more highly conserved than putatively neutral sequence, although only 5% of bases are predicted as constrained. By contrast, over a thousand lincRNAs were reported as being highly conserved. This apparent difference may account for the surprisingly small fraction (11%) of transcripts that are represented in both catalogues. Here we sought to resolve the reported discrepancy between the evolutionary rates for these two sets.

Results
Our analyses reveal lincRNA and macroRNA exon sequences to be subject to the same relatively low degree of sequence constraint. Nonetheless, our observations are consistent with the functionality of a fraction of ncRNA in these sets, with up to a quarter of ncRNA exons having evolved significantly slower than neighboring neutral sequence. The more tissue-specific macroRNAs are enriched in predicted RNA secondary structures and thus may often act in trans, whereas the more highly and broadly expressed lincRNAs appear more likely to act in the cis-regulation of adjacent transcription factor genes.

Conclusions
Taken together, our results indicate that each of the two ncRNA catalogues unevenly and lightly samples the true, much larger, ncRNA repertoire of the mouse.
Opposite effects of simvastatin on the bactericidal and inflammatory response of macrophages to opsonized S. aureus
Authors: Benati Daniela , Ferro Micol , Savino Maria Teresa , Ulivieri Cristina , Schiavo Ebe , Nuccitelli Annalisa , Pasini Franco Laghi , Baldari Cosima T 
Published: November 2009

Abstract
By impairing prenylation of Ras-related GTPases, simvastatin blocks phagocytosis and oxidative burst while enhancing production of proinflammatory mediators in human macrophages challenged with IgG-coated bacteria.
Besides lowering circulating cholesterol, statins act as immunomodulators. Although the effects of statins on lymphocyte activation and differentiation have been clearly defined, there is no consensus as to effects of these drugs on phagocytes. We have addressed the outcome of simvastatin treatment on the activation and effector function of human macrophages in the pathophysiologically relevant context of challenge with an opportunistic pathogen. We provide evidence that: simvastatin blocks the biological effects rapidly triggered by IgG-opsonized bacteria (phagocytosis and oxidative burst) while enhancing the delayed effects elicited by FcγR stimulation (production of proinflammatory mediators); these opposite effects of simvastatin result from enhancement of the JNK pathway and concomitant impairment of other signaling modules activated by FcγR engagement; and these activities are dependent on the capacity of simvastatin to block protein prenylation. The results provide novel mechanistic insight into the activities of statins on phagocytes and are of relevance to the assessment of potential side-effects in patients undergoing long-term hypocholesterolemic therapy.
Effects of a Mixed Meal on Hemodynamics and Autonomic Control of the Heart in Patients with Type 1 Diabetes
Authors: Cozzolino Domenico , Furlan Raffaello , Gruosso Domenico , Di Maggio Cristiana , Miraglia del Giudice Emanuele , Torella Roberto , Giugliano Dario 
Published: November 2009

Abstract
Context: Food intake induces relevant cardiovascular changes together with parallel increases in cardiac sympathetic activity and insulin plasma levels in man.
Objective: We evaluated hemodynamics, neurohormones, and cardiac autonomic control after eating in patients with type 1 diabetes, a disease characterized by the absence of basal and stimulated insulin production.
Design and Setting: Fifteen type 1 diabetic patients and 15 healthy controls underwent blood sampling, electrocardiogram, blood pressure and respiration recordings, and heart rate variability analysis while recumbent, during the 70° head-up tilt, and 20 min after a mixed meal; on another occasion, diabetic patients were also studied 20 min after a mixed meal preceded by their scheduled bolus of exogenous insulin. Spectrum analysis of RR interval provided the indices of sympathetic (LFRR) and vagal (HFRR) modulation of the sinoatrial node.
Results: At baseline, no significant differences were found between groups, except for metabolic parameters. Compared with baseline, heart rate, plasma catecholamines, and LFRR significantly (P &lt; 0.005) increased, whereas HFRR significantly (P &lt; 0.0001) decreased during the tilt in all subjects. Compared with baseline, plasma norepinephrine, heart rate, and LFRR significantly (P &lt; 0.05) increased, whereas HFRR significantly (P &lt; 0.02) decreased after eating in controls but not in diabetic patients (with and without insulin administered before eating). In both controls and diabetic patients, no relationship between postprandial changes of insulin and LFRR and HFRR was found.
Conclusions: Hemodynamic, neurohormonal, and cardiac neural responses to eating are abnormal in type 1 diabetic patients, independently of insulin.
The Democratic Insect: Productive Swarms
Authors: Dubois Page 
Published: November 2009

How does the insect swarm serve as a figure for humanity? In recent formulations by Michael Hardt and Antonio Negri, the swarm buzzes for the anonymous multitude, achieving creative solutions to humankind's problems “through collective and distributed techniques of problem solving without centralized control or the provision of a global model.” Such a vision constructs a benign and beneficent swarm that, although it lacks differentiation and specificity, accomplishes democracy without sovereignty. Achille Mbembe points out, nonetheless, that the swarm can have a more sinister and deadly aspect.The ancient Greeks used the figure of the swarm to connote an anonymous and undifferentiated mass of human beings. Achilles' army of Myrmidons in the Iliad are at least antlike, perhaps even metamorphosed ants, ants become warriors. In the classical period, the comic poet Aristophanes uses the insect swarm of wasps to embody his crowd, his chorus of furious, cantankerous, militant, and class-conscious jurors. Such a swarm is depicted with affection even as Aristophanes seems to deplore their manipulation by demagogues. Their “becoming-animal” offers a riotous, exhilarating line of flight from the decorum of nouveau riche Athenian society, a form of politics as the demos, the people, demand their part. But the philosopher Plato removes the sting from the wasps and represents docile and obedient bees, model citizen-workers, and even cicadas, transformed from human beings who once loved the muses into tattletales for the gods; the swarm becomes an instrument of antidemocratic, philosophical espionage.
Design and manufacture of the DEMON unmanned air vehicle demonstrator vehicle
Authors: Fielding J P , Mills A , Smith H 
Published: November 2009

This article will describe the design process, final design, and manufacture of the DEMON unmanned air vehicle (UAV) flying demonstrator aircraft. This is one of the main activities of the multi-University FLAVIIR programme. FLAVIIR's aim is to develop technologies that will allow development of future UAVs. It is vital that these technologies be integrated and demonstrated at higher technology readiness levels than are usual in the University sector. One means of achieving this is to use a number of technology demonstrators, culminating in the DEMON demonstrator. A particularly challenging requirement is that the vehicle must demonstrate an entire flight cycle, without the use of conventional flying control surfaces. This article will describe some of the technologies developed by partner Universities, and their integration into DEMON. The vehicle has a novel configuration and uses advanced composite construction in a vehicle some 3 m long and weighing 80 kg. It is powered by a small gas turbine and utilizes sophisticated thrust-vectoring devices. A novel feature is the use of an auxiliary gas turbine that provides compressed air for some of the fluidic control devices. This article gives details of the innovative manufacturing and assembly methods used for the DEMON. The vehicle is expected to fly shortly.
Adoption, White Women, and the Keeping of Culture
Authors: Brienza Casey 
Published: November 2009

Culture Keeping: White Mothers, International Adoption, and the Negotiation of Family Difference By Heather Jacobson Vanderbilt University Press, 2008 216 pages Call Me Okaasan: Adventures in Multicultural Mothering Edited by Suzanne Kamata Wyatt-MacKenzie Publishing, 2009 224 pages Kimchi & Calamari By Rose Kent Har perCollins, 2007 240 pages
The Role of EGFR Inhibition in the Treatment of Non-Small Cell Lung Cancer
Authors: Ray Mandira , Salgia Ravi , Vokes Everett E. 
Published: November 2009

AbstractThe identification of certain molecular mechanisms underlying lung carcinogenesis and progression has led to the development of targeted agents against different families of growth factors and receptors. The epidermal growth factor receptor (EGFR) is one such target for therapeutic exploitation. Inhibition of EGFR downstream signaling can be accomplished through two primary mechanisms: (a) the direct blocking of intracellular kinase activity with small-molecule tyrosine kinase inhibitors (TKIs) (e.g., gefitinib, erlotinib) and (b) the blocking of EGFR ligand binding using antibodies directed against the extracellular domain of the receptor (e.g., cetuximab). Resistance to available EGFR-targeted treatments has emerged as a substantial clinical issue in non-small cell lung cancer (NSCLC). Several novel agents with the potential to overcome such resistance are currently in clinical development, including irreversible EGFR TKIs, monoclonal antibodies, and TKIs directed against multiple signaling pathways. Here we discuss the clinical application of the currently available EGFR-targeted agents in NSCLC, the underlying mechanisms of resistance, and the novel agents in clinical development that may overcome resistance.
Effects of Aging and Cyclosporin A on Collagen Turnover in Human Gingiva
Authors: Gagliano N , Costa F , Tartaglia G.M , Pettinari L , Grizzi F , Sforza C , Portinaro N , Gioia M , Annoni G 
Published: November 2009

Background:
We aimed at characterizing the aging gingiva analyzing: i) collagen content and turnover in human gingival tissues and fibroblasts obtained from healthy young and aging subjects. ii) the effect of cyclosporin A administration in human cultured gingival fibroblasts obtained from aging compared to young subjects.

Methods:
Morphological analysis was performed on haematoxylin-eosin and Sirius red stained paraffin-embedded gingival biopsies from young and aging healthy subjects. The expression of the main genes and proteins involved in collagen turnover were determined by real time PCR, dot blot and SDS-zymography on cultured young and aging gingival fibroblasts, and after cyclosporin A administration.

Results:
Our results suggest that in healthy aged people, gingival connective tissue is characterized by a similar collagen content and turnover. Collagen turnover pathways are similarly affected by cyclosporin A treatment in young and aging gingival fibroblasts.

Conclusions:
Cyclosporin A administration affects gingival collagen turnover pathways in young and aging fibroblasts at the same extent, suggesting that during aging cyclosporin A administration is not related to relevant collagen turnover modifications.
Intracranial plasmacytoma as an initial presentation of multiple myeloma
Authors: Erikci Alev , Sayan Ozkan , Karagoz Bulent , Kucukodaci Zafer , Velioglu Murat 
Published: November 2009

Abstract
Intra-cranial involvement is an uncommon complication of multiple myeloma. We report a 68-year-old woman hospitalized for acute renal failure, vertigo and headache. Magnetic Resonance Imaging (MRI) revealed two and a half and 3cm length cranial lesion, which proved to be plasmacytoma. After complete staging, we retained the diagnosis of immunoglobulin G lambda-type multiple myeloma with intracranial involvement. Cytogenetic analysis of plasma cells detected no change. Currently, she is a regular hemodialysis patient. She is planned to have both systemic therapy with 40mg dexamethasone and cranial radiotherapy. Involvement of the CNS in multiple myeloma is very rare. Diagnosis of multiple myeloma subsequent to initial intrcranial involvement is confined to exceptional cases. Despite aggressive systemic treatments, including autologous stem cell transplantation and local treatments such as cerebral radiotherapy, the prognosis for patients with CNS myeloma is extremely poor. Our unique case implies that physicians should be alert in case of vertigo or headache in cases with acute renal failure.