bluuebunny/crossref_metadata_2025 huggingface dataset:
Sesamin Manifests Chemopreventive Effects through the Suppression of NF-κB–Regulated Cell Survival, Proliferation, Invasion, and Angiogenic Gene Products
Authors: Harikumar Kuzhuvelil B. , Sung Bokyung , Tharakan Sheeja T. , Pandey Manoj K. , Joy Beena , Guha Sushovan , Krishnan Sunil , Aggarwal Bharat B.
Published: May 2010

Agents that are safe, affordable, and efficacious are urgently needed for the prevention of chronic diseases such as cancer. Sesamin, a lipid-soluble lignan, is one such agent that belongs to a class of phytoestrogens, isolated from sesame (Sesamum indicum), and has been linked with prevention of hyperlipidemia, hypertension, and carcinogenesis through an unknown mechanism. Because the transcription factor NF-κB has been associated with inflammation, carcinogenesis, tumor cell survival, proliferation, invasion, and angiogenesis of cancer, we postulated that sesamin might mediate its effect through the modulation of the NF-κB pathway. We found that sesamin inhibited the proliferation of a wide variety of tumor cells including leukemia, multiple myeloma, and cancers of the colon, prostate, breast, pancreas, and lung. Sesamin also potentiated tumor necrosis factor-α–induced apoptosis and this correlated with the suppression of gene products linked to cell survival (e.g., Bcl-2 and survivin), proliferation (e.g., cyclin D1), inflammation (e.g., cyclooxygenase-2), invasion (e.g., matrix metalloproteinase-9, intercellular adhesion molecule 1), and angiogenesis (e.g., vascular endothelial growth factor). Sesamin downregulated constitutive and inducible NF-κB activation induced by various inflammatory stimuli and carcinogens, and inhibited the degradation of IκBα, the inhibitor of NF-κB, through the suppression of phosphorylation of IκBα and inhibition of activation of IκBα protein kinase, thus resulting in the suppression of p65 phosphorylation and nuclear translocation, and NF-κB–mediated reporter gene transcription. The inhibition of IκBα protein kinase activation was found to be mediated through the inhibition of TAK1 kinase. Overall, our results showed that sesamin may have potential against cancer and other chronic diseases through the suppression of a pathway linked to the NF-κB signaling. Mol Cancer Res; 8(5); 751–61. ©2010 AACR.
First Report on Metastasizing Small Bowel Carcinoids in First-Degree Relatives in Three Generations
Authors: Järhult Johannes , Landerholm Kalle , Falkmer Sture , Nordenskjöld Magnus , Sundler Frank , Wierup Nils
Published: May 2010

Background/Aims: There is an established association between the multiple endocrine neoplasia type 1 (MEN 1) syndrome and foregut carcinoids. Some registry studies also indicate that offspring to carcinoid patients run an increased risk of developing a carcinoid tumor themselves. However, there are only scattered reports of gastrointestinal carcinoids in two generations. The aim of this study was to describe the clinical characteristics as well as the histopathological, immunohistochemical (IHC) and genetic data of metastasizing ileal carcinoids in three consecutive first-degree relatives. Methods: The histopathological and IHC analyses were performed on newly cut sections of the tumor specimens and included growth pattern, proliferation index (Ki-67) as well as expression of established neuroendocrine markers and recently introduced cocaine-amphetamine-regulated transcript (CART). The genetic analyses were focused on establishing whether a connection with the MEN 1 syndrome existed in this family, by means of mutation screening using polymerase chain reaction, multiple ligation-dependent probe amplification, and genotyping using fluorescent-labeled microsatellite markers. Results: Histopathology and IHC revealed that the tumors were virtually identical, with only minor differences in proliferation index and expression of CART. Genetic analyses indicated that the inheritance of the small bowel carcinoids in the family was not linked to the MEN1 gene. Conclusion: Metastasizing small bowel carcinoids have been found in first-degree relatives in three consecutive generations. All three tumors were very similar when characterized by histopathology and IHC. Based on clinical findings and genetic analyses, it seems unlikely, although not completely excluded, that inheritance was linked to the MEN 1 syndrome.
The Complexity of Social/Cultural Dimension in Communication Disorders
Authors: Threats Travis T.
Published: May 2010

There has been growing recognition in the field of communication disorders concerning the importance of multicultural and diversity issues. This discussion needs to move beyond the theoretical and descriptive stage to the clinical use of this knowledge to improve the communicative functioning of diverse populations. This paper argues that the tenets of evidence-based practice and the International Classification of Functioning, Disability and Health (ICF) by the World Health Organization can be used to advance the scholarship and service concerning diversity issues. Both evidence-based practice and the ICF are client-based approaches that can facilitate the achievement of culturally relevant rehabilitation outcomes. This article discusses the use of evidence-based practice and the ICF for providing assessment and intervention that address the social and cultural complexities of the persons we serve. In addition, the author states that work on diversity issues can also be used to discover crucial underlying knowledge regarding communication and communication disorders.
Developmental Approaches to Understanding and Treating Autism
Authors: Charman Tony
Published: May 2010

Over the past decade our understanding of early social communication development in young children with autism has undergone a remarkable change. We now know something about how young children with autism process the social world in a very different way from typical children. This has led to truly developmental models of autism. In turn, these have had profound impacts on research and practice. Several screening instruments to prospectively identify autism have been developed. In some cases autism can be diagnosed in children as young as 2 years of age. The study of ‘high-risk’ siblings has allowed prospective study of infants from as young as 6 months of age. There is increasing evidence that intervention approaches that focus on social and communication development can ameliorate symptoms and change the developmental course of the disorder. This article will highlight some of the key theoretical and clinical lessons learned from this decade of research.
Functional Histology of the Macula Flava in the Human Vocal Fold – Part 1: Its Role in the Adult Vocal Fold
Authors: Sato Kiminori , Umeno Hirohito , Nakashima Tadashi
Published: May 2010

Objective: This study aims to clarify the role of the maculae flavae (MFe) in the human adult vocal fold mucosa (VFM). Methods: Our current results concerning MFe in the human adult VFM are summarized. Results: MFe were found to be composed of dense masses of vocal fold stellate cells (VFSCs) and extracellular matrices (EM), such as fibrous proteins and glycosaminoglycans, which are essential for the EM in the human VFM. VFSCs in the MFe demonstrated marked morphologic differences from conventional fibroblasts. They were irregular and stellate in shape and possessed slender cytoplasmic processes. They had well-developed intracellular organelles. A number of vesicles were present at the periphery of the cytoplasm. They constantly synthesized EM. The VFSCs possessed lipid droplets and stored vitamin A. VFSCs formed an independent cell category of cells in the human VFM. The VFSCs in aged adult MFe decreased their activity, and had abnormal metabolism. Conclusion: Human MFe including VFSCs seem to be involved in the metabolism of EM which are essential for the viscoelasticity of the lamina propria of the VFM, and to be responsible for maintaining the characteristic layered structure of the human VFM. Age-related changes in VFSCs were found to influence the metabolism of EM in the VFM.
Coordination between Posture and Phonation in Vocal Effort Behavior
Authors: Lagier Aude , Vaugoyeau Marianne , Ghio Alain , Legou Thierry , Giovanni Antoine , Assaiante Christine
Published: May 2010

Background: Postural correlates of vocal effort are rarely described in the literature, while they are extensively dealt with in speech therapy. Objectives: This study aims at determining whether body movement is a side effect of vocal effort or an integral part of communication effort behavior. The answer to this question is mainly based on correlations between posture and phonation. Method: Twenty healthy subjects participated in this study. They had to communicate with a listener under 3 conditions requiring different levels of vocal effort. Results: The vocal parameters increased and confirmed that the subjects had made a vocal effort. The kinematic parameters (amplitude and duration of body movement) increased with vocal effort. Lastly, vocal and kinematic characteristics were significantly correlated. Conclusion: The close correlation of posture with vocal production shows that movement is not a mere consequence of vocal effort. Posture and voice are coordinated in communication behavior, and each body segment plays its specific role in the vocal effort behavior.
Using Monte-Carlo-Simulated Radiation Transport to Calculate Dose Distribution in Rats before Irradiation with Leksell Gamma Knife® 4C: Technical Note
Authors: Marcelin Béatrice , Kjäll Per , Johansson Jonas , Lundin Anders , Nordström Håkan , Eriksson Markus , Bernard Christophe , Régis Jean
Published: May 2010

Background: Gamma knife surgery (GKS) is used at subnecrotic doses for temporal lobe epilepsy (TLE) treatment. Rat models of TLE have been used to probe the mechanisms underlying GKS. Previous GKS studies on rats have used the Leksell GammaPlan® (LGP) treatment planning system to determine the irradiation time to achieve the dose to deliver. Since LGP is not designed for such small structures, it is important to calibrate the system for the rat brain. Methods: We have used a Monte Carlo simulation (MCS) radiation transport scheme, with CT data as anatomical and tissue-specific information, to simulate the dose distribution in a rat brain when using a Leksell Gamma Knife®. Results: We show how dose distributions obtained by MCS quantitatively compare to those predicted by LGP, and discuss whether LGP should be used for studies involving rats. The energy deposited when using the 4-mm collimators was calculated for targets on both sides of the rat brain in the dorsal hippocampus, which allowed us to determine the exact time to irradiate rats with a given dose. Conclusion: The MCS method used in this study can easily be used for future GKS studies on small animals when accurate dose distributions are required.
The mTOR Pathway Is Activated in Human Autosomal-Recessive Polycystic Kidney Disease
Authors: Becker Jan Ulrich , Opazo Saez Anabelle , Zerres Klaus , Witzke Oliver , Hoyer Peter Friedrich , Schmid Kurt Werner , Kribben Andreas , Bergmann Carsten , Nürnberger Jens
Published: May 2010

Background: An inappropriate activation of the mTOR pathway was demonstrated in the autosomal dominant (AD) form of polycystic kidney disease (PKD). To date it is unclear whether the mTOR pathway is activated in autosomal-recessive (AR) PKD, a cystic disease which occurs in childhood. The purpose of the present study was to evaluate the mTOR pathway in AR PKD. Methods: We evaluated the expression of mTOR pathway molecules in paraffin-embedded liver and kidney samples from patients with AR PKD and control specimens from animals as well as humans. Monoclonal antibodies, the phosphorylated proteins pmTOR, pS6-ribosomal-protein (pS6K), p4E-BP1, peIF4G, and phospho-tuberin/TSC2 were used. Results: mTOR was strongly expressed in renal cyst-lining cells and bile ducts from AR PKD specimen. S6K immunostaining was strong in smaller tubules and weak both in larger renal cysts and in the bile duct epithelium. In controls, mTOR and S6K were expressed in distal tubule segments. 4E-BP1-immunostaining was restricted to noncystic tubules in AR PKD. eIFG4-immunostaining was observed in bile duct epithelium in AR PKD, but not in control tissue. Tuberin/TSC2 immunostaining was negative in all specimens. Conclusion: Our data suggest that the mTOR pathway may be activated in AR PKD, and mTOR molecules may represent a potential target to slow down cyst development in this disease.
Changes in the Sodium and Potassium Transporters in the Course of Chronic Renal Failure
Authors: Kim Sejoong , Heo Nam Ju , Jung Ji Yong , Son Min-Jeong , Jang Hye Ryoun , Lee Jay Wook , Oh Yun Kyu , Na Ki Young , Joo Kwon Wook , Han Jin Suk
Published: May 2010

Background: In chronic renal failure (CRF), residual nephrons can increase their excretion of sodium (Na) and potassium (K). However, the mechanisms of renal Na and K regulation in late-stage CRF have not been clearly investigated. Methods: We examined altered expression of major renal Na and K transporters in Sprague-Dawley rats at 4 and 12 weeks after a 5/6 nephrectomy. Results: CRF rats were azotemic and had gradually increased levels of urinary Na and K excretion over time. At 4 weeks, the abundance of Na-K-2Cl cotransporter (NKCC2), and Na-Cl cotransporter (NCC) in CRF rats increased significantly (477 and 222% of the control, respectively). In contrast, expression of NKCC2 and NCC decreased markedly at 12 weeks (55.4 and 30.8%, respectively). Expression of epithelial Na channel-α increased throughout the whole period. The abundance of renal outer medullary K-channel (ROMK) and Na-K-ATPase did not decrease at 4 weeks, but it was reduced at 12 weeks. Conclusion: We suggest that increased urinary Na excretion in late-stage CRF may be associated with decreased expression of renal Na transporters except ENaC compared to early-stage CRF, and that increased urinary K excretion in the late stage of CRF may not be related to expression of ROMK.
Shattered Vision: Disenchantment of Couplehood Among Female Survivors of Violence in the Shadow of Their Family-of-Origin Experiences
Authors: Buchbinder Eli , Goldblatt Hadass
Published: May 2010

This article describes and analyzes the relationship disenchantment of couplehood among female survivors of violence and their family-of-origin experiences of abuse. Twenty Israeli women who were survivors of violence participated in this qualitative research. Each woman underwent three in-depth interviews, two for data collection and one for validating the themes emerging from content analysis. Data analysis revealed that female survivors of violence aim to overcome the distress and pain of emotional and physical violence experienced in their family of origin, by constructing a couplehood vision imbued with a feeling of power, meaning, hope, and freedom. Partner violence shattered the women’s vision of couplehood, leading to crisis, disillusionment, and disenchantment in their marital relationships.
Explaining Difficult States
Authors: Subotić Jelena
Published: May 2010

Why has Serbia’s path toward European integration been fraught with so much difficulty? This article explains Serbia’s reluctance to Europeanize by exploring why Serbian elites persistently refused to fulfill the European Union’s principal requirement—full cooperation with the Hague war crimes tribunal—even when it meant getting off the road to Brussels. The article offers a theoretical framework that incorporates domestic political identity, power of veto players, and competing elite strategies to explain how Serbian political actors used European Union norms and institutions to advance local political agendas. The article concludes that, instead of being a successful change agent that brought about policy shift in the areas of democratization and human rights, the European Union was used on many occasions by Serbian political elites to pursue strategies far removed from EU norms and standards.
Extracellular Purine Metabolism in Blood Vessels (Part II): Activity of Ecto-Enzymes in Blood Vessels of Patients With Abdominal Aortic Aneurysm
Authors: Lecka Joanna , Bloch-Boguslawska Elzbieta , Molski Stanislaw , Komoszynski Michal
Published: May 2010

Both platelet aggregation and high blood pressure are associated with development of atherosclerosis. Among other factors that modulate platelet aggregation and blood pressure, extracellular purines (e-purines) influence these processes via purinoceptors P1 and P2 for which they are natural ligands. We hypothesized that ecto-enzymes such as nucleoside triphosphate diphosphohydrolases (NTPDases), adenylate kinase, 5′-nucleotidase, and adenosine deaminase that regulate the level of e-purines may be involved in the development of atherosclerosis. The enzymatic assays were performed either on the fragments of human abdominal aortas obtained after death or on abdominal aneurysm samples collected during surgery. The substrates and products such as adenine nucleosides and nucleotides were analyzed using reverse phase high-performance liquid chromatography (HPLC) method. Here, we estimated and demonstrated the activities of these ecto-enzymes in the patients with atherosclerosis or atherosclerosis-like diseases such as abdominal aneurysm, myocardial infarction, or Leriche syndrome (LS) with worse thrombosis of extremities. In particular, we noticed reduction in activity of NTPDase1app, NTPDase2app, ecto-adenylate kinaseapp, and ecto-adenosine deaminaseapp; however, ecto-5′-nucleotidaseappthat hydrolyzed e-adenosine monophosphate (e-AMP) into e-adenosine did not show any significant changes. This led us to suggest that alteration of the activity of examined ecto-enzymes is responsible for the development of atherosclerosis or atherosclerosis-like diseases.
Ex Vivo Thrombin Generation in Patients With Venous Thromboembolic Disease or Atrial Fibrillation on Long-Term Oral Anticoagulation
Authors: Musiał Jacek , Brzezińska-Kolarz B. , Żółciński M. , Lelakowski J. , Szczeklik A.
Published: May 2010

International normalized ratio (INR) is used to monitor chronic oral anticoagulant (OA) treatment; however, it is poorly understood how this simple test reflects in vivo hemostatic reactions, culminating in thrombin generation and clot formation. We studied the process of thrombin generation using an ex vivo model, where thrombin—antithrombin (TAT) complexes are measured in blood emerging from standardized skin incisions in 55 patients (35 with venous thromboembolism [VTE] and 20 with sustained atrial fibrillation [AF]) treated with acenocoumarol (INR 2.0-3.0). In addition, in venous blood, we measured the activity of factor VIII (FVIII) and vitamin K-dependent coagulation proteins. Chronic anticoagulation led to significant reductions in maximum TAT concentrations as compared to 35 healthy controls, in maximum TAT generation rates, and in mean amount of thrombin generated. Parameters of thrombin generation did not correlate with INR or any coagulation factor measured. International normalized ratio was significantly and independently affected by the decrease in the activity of all vitamin K-dependent coagulation proteins. The strongest influence was shown for FVII. Factor VIII activity was increased in all patients studied independently of the duration of anticoagulation and did not change over time. In conclusion, in patients with VTE and AF on OA, there is no correlation between INR values and parameters of ex vivo thrombin generation. This may indicate an important role of protein C (PC) system and possibly other endothelium-dependent mechanisms in controlling hemostasis. Increased FVIII activity in patients with VTE and AF does not change significantly during anticoagulation and is probably related to the pretreatment prothrombotic state.
Indigenous MediaSpace and the Production of (Trans)locality on Nicaragua’s Mosquito Coast
Authors: Glynn Kevin , Cupples Julie
Published: May 2010

This article draws on notions of networked and multiscalar globalities to explore recent developments around indigenous and Afro-Caribbean media in Nicaragua’s Atlantic Coast region, whose inhabitants are reasserting their collective autonomy by reinvigorating and reformulating a centuries-old ideal of cosmopolitanism forged through a long history of intercultural exchange and the indigenization of foreign elements. The authors argue that their activities are advancing the development of convergent cultures associated with counterinscriptions of a grassroots globalization and the expansion of contexts in which new forms of indigenous and Afro-Caribbean cultural citizenship can emerge and become effective. Hence, mediated practices of cultural persistence on Nicaragua’s Mosquito Coast intensify and broaden the revivification and circulation of relational, nonmodern ontologies whose epistemic force contributes to wider Latin American movements for social transformation and illustrates in new ways the importance and the potential of indigenous media operations and the intercultural global networks within which they are implicated.
Victim Strategies to Stop Bullying
Authors: Black Sally , Weinles Dan , Washington Ericka
Published: May 2010

One of the most commonly recommended strategies for youth to stop bullying is to report incidents to an adult. Although reporting is preferred, ultimately, victims will use strategies that they perceive to be most effective. This study investigated victims’ strategies to stop bullying, as well as their perceptions of each strategy’s effectiveness. In all, 50% of participating school students (n = 2,615) reported at least one form of victimization. The most common strategies used against bullying were fighting back (63%), ignoring the bullying (52%), telling an adult at home (44%), and reporting the abuse to a peer (42%). The most successful strategies reported were counter-aggression (75%), making a safety plan (74%), and telling a peer (71%) or an adult at home (71%). Implications for practice are for school staff to deconstruct the idea of counter-aggression as an effective strategy against violence and to improve perceptions of staff responses to victimization.
In search of the original leukemic clone in chronic myeloid leukemia patients in complete molecular remission after stem cell transplantation or imatinib
Authors: Sobrinho-Simões Manuel , Wilczek Vicki , Score Joannah , Cross Nicholas C. P. , Apperley Jane F. , Melo Junia V.
Published: May 2010

It is not clear if absence of BCR-ABL transcripts—complete molecular response (CMR)—is synonymous with, or required for, cure of chronic myeloid leukemia (CML). Some patients achieve CMR with imatinib (IM), but most relapse shortly after treatment discontinuation. Furthermore, most patients in long-term remission (LTR) post–stem cell transplantation (SCT) are considered functionally cured, although some remain occasionally positive for low-level BCR-ABL mRNA. Interpretation of the latter is complicated because it has been observed in healthy subjects. We designed a patient-specific, highly sensitive, DNA quantitative polymerase chain reaction to test follow-up samples for the original leukemic clone, identified by its unique genomic BCR-ABL fusion (gBCR-ABL). In 5 IM-treated patients in CMR, gBCR-ABL was detected in transcript-negative samples; 4 patients became gBCR-ABL-negative with continuing IM therapy. In contrast, of 9 patients in LTR (13-27 years) post-SCT, gBCR-ABL was detected in only 1, despite occasional transcript-positive samples in 8 of them. In conclusion, in IM-treated patients, absence of transcripts should not be interpreted as absence of the leukemic clone, although continuing IM after achievement of CMR may lead to further reduction of residual disease. Post-SCT, we found little evidence that the transcripts occasionally detected originate from the leukemic clone.
The PD-1/PD-L1 axis modulates the natural killer cell versus multiple myeloma effect: a therapeutic target for CT-011, a novel monoclonal anti–PD-1 antibody
Authors: Benson Don M. , Bakan Courtney E. , Mishra Anjali , Hofmeister Craig C. , Efebera Yvonne , Becknell Brian , Baiocchi Robert A. , Zhang Jianying , Yu Jianhua , Smith Megan K. , Greenfield Carli N. , Porcu Pierluigi , Devine Steven M. , Rotem-Yehudar Rinat , Lozanski Gerard , Byrd John C. , Caligiuri Michael A.
Published: May 2010

T-cell expression of programmed death receptor-1 (PD-1) down-regulates the immune response against malignancy by interacting with cognate ligands (eg, PD-L1) on tumor cells; however, little is known regarding PD-1 and natural killer (NK) cells. NK cells exert cytotoxicity against multiple myeloma (MM), an effect enhanced through novel therapies. We show that NK cells from MM patients express PD-1 whereas normal NK cells do not and confirm PD-L1 on primary MM cells. Engagement of PD-1 with PD-L1 should down-modulate the NK-cell versus MM effect. We demonstrate that CT-011, a novel anti–PD-1 antibody, enhances human NK-cell function against autologous, primary MM cells, seemingly through effects on NK-cell trafficking, immune complex formation with MM cells, and cytotoxicity specifically toward PD-L1+ MM tumor cells but not normal cells. We show that lenalidomide down-regulates PD-L1 on primary MM cells and may augment CT-011's enhancement of NK-cell function against MM. We demonstrate a role for the PD-1/PD-L1 signaling axis in the NK-cell immune response against MM and a role for CT-011 in enhancing the NK-cell versus MM effect. A phase 2 clinical trial of CT-011 in combination with lenalidomide for patients with MM should be considered.
Rapid detection of epidermal growth factor receptor mutations with multiplex PCR and primer extension in lung cancer
Authors: Lin Ching-Hsiung , Yeh Kun-Tu , Chang Ya-Sian , Hsu Nicholas C , Chang Jan-Gowth
Published: May 2010

Epidermal growth factor receptor(EGFR) kinase domain mutations hyperactivate the kinase and confer kinase addiction of the non-small-cell lung cancer (NSCLC) tumor cells. Almost all of these mutations are located within exons 18-21. The -216 single nucleotide polymorphism in the promoter region is associated with increased EGFR production. We present a method for detecting these common mutations in 81 cases of NSCLC. The protocol is based on the multiplex amplification of promoter region and exons 18-21 of theEGFRgenes in a single tube, followed by primer extension of the PCR products using various sizes of primers to detect base changes at -216 promoter region and codons 719, 746-750, 790, 858 of theEGFRgene. We compared the results with that from direct sequencing for detectingEGFRmutations in 81 cases of NSCLC. The two methods identified the same 26 mutations, but our method is superior to direct sequencing in terms of the amount of work and time required. We presented a simple and fast method to detect mutations ofEGFRgenes in NSCLC.
Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction
Authors: Bryant Drew H , Moll Mark , Chen Brian Y , Fofanov Viacheslav Y , Kavraki Lydia E
Published: May 2010

Background

Structural variations caused by a wide range of physico-chemical and biological sources directly influence the function of a protein. For enzymatic proteins, the structure and chemistry of the catalytic binding site residues can be loosely defined as asubstructureof the protein. Comparative analysis of drug-receptor substructures across and within species has been used for lead evaluation. Substructure-level similarity between the binding sites of functionally similar proteins has also been used to identify instances of convergent evolution among proteins. In functionally homologous protein families, shared chemistry and geometry at catalytic sites provide a common, local point of comparison among proteins that may differ significantly at the sequence, fold, or domain topology levels.

Results

This paper describes two key results that can be used separately or in combination for protein function analysis. The Family-wise Analysis of SubStructural Templates (FASST) method uses all-against-all substructure comparison to determine Substructural Clusters (SCs). SCs characterize the binding site substructural variation within a protein family. In this paper we focus on examples of automatically determined SCs that can be linked to phylogenetic distance between family members, segregation by conformation, and organization by homology among convergent protein lineages. The Motif Ensemble Statistical Hypothesis (MESH) framework constructs a representative motif for each protein cluster among the SCs determined by FASST to buildmotif ensemblesthat are shown through a series of function prediction experiments to improve the function prediction power of existing motifs.

Conclusions

FASST contributes a critical feedback and assessment step to existing binding site substructure identification methods and can be used for the thorough investigation of structure-function relationships. The application of MESH allows for an automated, statistically rigorous procedure for incorporating structural variation data into protein function prediction pipelines. Our work provides an unbiased, automated assessment of the structural variability of identified binding site substructures among protein structure families and a technique for exploring the relation of substructural variation to protein function. As available proteomic data continues to expand, the techniques proposed will be indispensable for the large-scale analysis and interpretation of structural data.
Rescue of placental phenotype in a mechanistic model of Beckwith-Wiedemann syndrome
Authors: Oh-McGinnis Rosemary , Bogutz Aaron B , Lee Kang Yun , Higgins Michael J , Lefebvre Louis
Published: May 2010

Background

Several imprinted genes have been implicated in the process of placentation. The distal region of mouse chromosome 7 (Chr 7) contains at least ten imprinted genes, several of which are expressed from the maternal homologue in the placenta. The corresponding paternal alleles of these genes are silenced in cis by an incompletely understood mechanism involving the formation of a repressive nuclear compartment mediated by the long non-coding RNA Kcnq1ot1 initiated from imprinting centre 2 (IC2). However, it is unknown whether some maternally expressed genes are silenced on the paternal homologue via a Kcnq1ot1-independent mechanism. We have previously reported that maternal inheritance of a large truncation of Chr7 encompassing the entire IC2-regulated domain (DelTel7 allele) leads to embryonic lethality at mid-gestation accompanied by severe placental abnormalities. Kcnq1ot1 expression can be abolished on the paternal chromosome by deleting IC2 (IC2KO allele). When the IC2KO mutation is paternally inherited, epigenetic silencing is lost in the region and the DelTel7 lethality is rescued in compound heterozygotes, leading to viable DelTel7/IC2KO mice.

Results

Considering the important functions of several IC2-regulated genes in placentation, we set out to determine whether these DelTel7/IC2KO rescued conceptuses develop normal placentae. We report no abnormalities with respect to the architecture and vasculature of the DelTel7/IC2KO rescued placentae. Imprinted expression of several of the IC2-regulated genes critical to placentation is also faithfully recapitulated in DelTel7/IC2KO placentae.

Conclusion

Taken together, our results demonstrate that all the distal chromosome 7 imprinted genes implicated in placental function are silenced by IC2 and Kcnq1ot1 on the paternal allele. Furthermore, our results demonstrate that the methylated maternal IC2 is not required for the regulation of nearby genes. The results show the potential for fully rescuing trans placental abnormalities that are caused by imprinting defects.
Multiplex Amplicon Quantification (MAQ), a fast and efficient method for the simultaneous detection of copy number alterations in neuroblastoma
Authors: Kumps Candy , Van Roy Nadine , Heyrman Lien , Goossens Dirk , Del-Favero Jurgen , Noguera Rosa , Vandesompele Jo , Speleman Frank , De Preter Katleen
Published: May 2010

Background

Cancer genomes display characteristic patterns of chromosomal imbalances, often with diagnostic and prognostic relevance. Therefore assays for genome-wide copy number screening and simultaneous detection of copy number alterations in specific chromosomal regions are of increasing importance in the diagnostic work-up of tumors.

Results

We tested the performance of Multiplex Amplicon Quantification, a newly developed low-cost, closed-tube and high-throughput PCR-based technique for detection of copy number alterations in regions with prognostic relevance for neuroblastoma. Comparison with array CGH and the established Multiplex Ligation-dependent Probe Amplification method on 52 neuroblastoma tumors showed that Multiplex Amplicon Quantification can reliably detect the important genomic aberrations.

Conclusion

Multiplex Amplicon Quantification is a low-cost and high-throughput PCR-based technique that can reliably detect copy number alterations in regions with prognostic relevance for neuroblastoma.
Proteomics-based confirmation of protein expression and correction of annotation errors in the Brucella abortus genome
Authors: Lamontagne Julie , Béland Maxime , Forest Anik , Côté-Martin Alexandra , Nassif Najib , Tomaki Fadi , Moriyón Ignacio , Moreno Edgardo , Paramithiotis Eustache
Published: May 2010

Background

Brucellosis is a major bacterial zoonosis affecting domestic livestock and wild mammals, as well as humans around the globe. While conducting proteomics studies to better understand Brucella abortus virulence, we consolidated the proteomic data collected and compared it to publically available genomic data.

Results

The proteomic data was compiled from several independent comparative studies of Brucella abortus that used either outer membrane blebs, cytosols, or whole bacteria grown in media, as well as intracellular bacteria recovered at different times following macrophage infection. We identified a total of 621 bacterial proteins that were differentially expressed in a condition-specific manner. For 305 of these proteins we provide the first experimental evidence of their expression. Using a custom-built protein sequence database, we uncovered 7 annotation errors. We provide experimental evidence of expression of 5 genes that were originally annotated as non-expressed pseudogenes, as well as start site annotation errors for 2 other genes.

Conclusions

An essential element for ensuring correct functional studies is the correspondence between reported genome sequences and subsequent proteomics studies. In this study, we have used proteomics evidence to confirm expression of multiple proteins previously considered to be putative, as well as correct annotation errors in the genome of Brucella abortus strain 2308.
A simple, high throughput method to locate single copy sequences from Bacterial Artificial Chromosome (BAC) libraries using High Resolution Melt analysis
Authors: Vu Giang TH , Caligari Peter DS , Wilkinson Mike J
Published: May 2010

Background

The high-throughput anchoring of genetic markers into contigs is required for many ongoing physical mapping projects. Multidimentional BAC pooling strategies for PCR-based screening of large insert libraries is a widely used alternative to high density filter hybridisation of bacterial colonies. To date, concerns over reliability have led most if not all groups engaged in high throughput physical mapping projects to favour BAC DNA isolation prior to amplification by conventional PCR.

Results

Here, we report the first combined use of Multiplex Tandem PCR (MT-PCR) and High Resolution Melt (HRM) analysis on bacterial stocks of BAC library superpools as a means of rapidly anchoring markers to BAC colonies and thereby to integrate genetic and physical maps. We exemplify the approach using a BAC library of the model plant Arabidopsis thaliana. Super pools of twenty five 384-well plates and two-dimension matrix pools of the BAC library were prepared for marker screening. The entire procedure only requires around 3 h to anchor one marker.

Conclusions

A pre-amplification step during MT-PCR allows high multiplexing and increases the sensitivity and reliability of subsequent HRM discrimination. This simple gel-free protocol is more reliable, faster and far less costly than conventional PCR screening. The option to screen in parallel 3 genetic markers in one MT-PCR-HRM reaction using templates from directly pooled bacterial stocks of BAC-containing bacteria further reduces time for anchoring markers in physical maps of species with large genomes.
Photorhabdus adhesion modification protein (Pam) binds extracellular polysaccharide and alters bacterial attachment
Authors: Jones Robert T , Sanchez-Contreras Maria , Vlisidou Isabella , Amos Matthew R , Yang Guowei , Muñoz-Berbel Xavier , Upadhyay Abhishek , Potter Ursula J , Joyce Susan A , Ciche Todd A , Jenkins A Toby A , Bagby Stefan , ffrench-Constant Richard H , Waterfield Nicholas R
Published: May 2010

Background

Photorhabdus are Gram-negative nematode-symbiotic and insect-pathogenic bacteria. The species Photorhabdus asymbiotica is able to infect humans as well as insects. We investigated the secreted proteome of a clinical isolate of P. asymbiotica at different temperatures in order to identify proteins relevant to the infection of the two different hosts.

Results

A comparison of the proteins secreted by a clinical isolate of P. asymbiotica at simulated insect (28°C) and human (37°C) temperatures led to the identification of a small and highly abundant protein, designated Pam, that is only secreted at the lower temperature. The pam gene is present in all Photorhabdus strains tested and shows a high level of conservation across the whole genus, suggesting it is both ancestral to the genus and probably important to the biology of the bacterium. The Pam protein shows limited sequence similarity to the 13.6 kDa component of a binary toxin of Bacillus thuringiensis. Nevertheless, injection or feeding of heterologously produced Pam showed no insecticidal activity to either Galleria mellonella or Manduca sexta larvae. In bacterial colonies, Pam is associated with an extracellular polysaccharide (EPS)-like matrix, and modifies the ability of wild-type cells to attach to an artificial surface. Interestingly, Surface Plasmon Resonance (SPR) binding studies revealed that the Pam protein itself has adhesive properties. Although Pam is produced throughout insect infection, genetic knockout does not affect either insect virulence or the ability of P. luminescens to form a symbiotic association with its host nematode, Heterorhabditis bacteriophora.

Conclusions

We studied a highly abundant protein, Pam, which is secreted in a temperature-dependent manner in P. asymbiotica. Our findings indicate that Pam plays an important role in enhancing surface attachment in insect blood. Its association with exopolysaccharide suggests it may exert its effect through mediation of EPS properties. Despite its abundance and conservation in the genus, we find no evidence for a role of Pam in either virulence or symbiosis.
Development and characterization of an oat TILLING-population and identification of mutations in lignin and β-glucan biosynthesis genes
Authors: Chawade Aakash , Sikora Per , Bräutigam Marcus , Larsson Mikael , Vivekanand Vivekanand , Nakash Montedar All , Chen Tingsu , Olsson Olof
Published: May 2010

Background

Oat, Avena sativa is the sixth most important cereal in the world. Presently oat is mostly used as feed for animals. However, oat also has special properties that make it beneficial for human consumption and has seen a growing importance as a food crop in recent decades. Increased demand for novel oat products has also put pressure on oat breeders to produce new oat varieties with specific properties such as increased or improved β-glucan-, antioxidant- and omega-3 fatty acid levels, as well as modified starch and protein content. To facilitate this development we have produced a TILLING (Targeting Induced Local Lesions IN Genomes) population of the spring oat cultivar SW Belinda.

Results

Here a population of 2600 mutagenised M2 lines, producing 2550 M3 seed lots were obtained. The M2 population was initially evaluated by visual inspection and a number of different phenotypes were seen ranging from dwarfs to giants, early flowering to late flowering, leaf morphology and chlorosis. Phloroglucinol/HCl staining of M3 seeds, obtained from 1824 different M2 lines, revealed a number of potential lignin mutants. These were later confirmed by quantitative analysis. Genomic DNA was prepared from the M2 population and the mutation frequency was determined. The estimated mutation frequency was one mutation per 20 kb by RAPD-PCR fingerprinting, one mutation per 38 kb by MALDI-TOF analysis and one mutation per 22.4 kb by DNA sequencing. Thus, the overall mutation frequency in the population is estimated to be one mutation per 20-40 kb, depending on if the method used addressed the whole genome or specific genes. During the investigation, 6 different mutations in the phenylalanine ammonia-lyase (AsPAL1) gene and 10 different mutations in the cellulose synthase-like (AsCslF6) β-glucan biosynthesis gene were identified.

Conclusion

The oat TILLING population produced in this work carries, on average, hundreds of mutations in every individual gene in the genome. It will therefore be an important resource in the development of oat with specific characters. The population (M5) will be available for academic research via Nordgen http://www.nordgen.org as soon as enough seeds are obtained.

[Genbank accession number for the cloned AsPAL1 is GQ373155 and GQ379900 for AsCslF6]
In vitro and in vivo anti-malarial activity of Boerhavia elegans and Solanum surattense
Authors: Ramazani Ali , Zakeri Sedigheh , Sardari Soroush , Khodakarim Nastaran , Djadidt Navid Dinparas
Published: May 2010

Background

There is an urgent need to identify new anti-malarial drug targets for both prophylaxis and chemotherapy, due to the increasing problem of drug resistance to malaria parasites. In the present study, the aim was to discover novel, effective plant-based extracts for the activity against malaria.

Methods

Ten plants found in Iran were selected by ethnobotanical survey of medicinal plants. The crude ethanolic extracts were tested for in vitro anti-plasmodial activity against two strains of Plasmodium falciparum: K1 (chloroquine-resistant strain) and CY27 (chloroquine-sensitive strain), using the parasite lactate dehydrogenase (pLDH) assay. The anti-plasmodial activity of the extracts was also assessed in the 4-day suppressive anti-malarial assay in mice inoculated with Plasmodium berghei (ANKA strain). Crude ethanolic extracts showed good anti-plasmodial activity were further fractionated by partitioning in water and dichloromethane.

Results

Of 10 plant species assayed, three species: Boerhavia elegans (Choisy), Solanum surattense (Burm.f.) and Prosopis juliflora (Sw.) showed promising anti-plasmodial activity in vitro (IC50 ≤ 50 μg/ml) and in vivo with no toxicity. The dichloromethane fraction of three extracts revealed stronger anti-plasmodial activity than the total extracts.

Conclusion

Anti-plasmodial activities of extracts of B. elegans and S. surattense are reported for the first time.
Gene-based outcome prediction in multiple cohorts of pediatric T-cell acute lymphoblastic leukemia: a Children's Oncology Group study
Authors: Cleaver Amanda L , Beesley Alex H , Firth Martin J , Sturges Nina C , O'Leary Rebecca A , Hunger Stephen P , Baker David L , Kees Ursula R
Published: May 2010

Background

Continuous complete clinical remission in T-cell acute lymphoblastic leukemia (T-ALL) is now approaching 80% due to the implementation of aggressive chemotherapy protocols but patients that relapse continue to have a poor prognosis. Such patients could benefit from augmented therapy if their clinical outcome could be more accurately predicted at the time of diagnosis. Gene expression profiling offers the potential to identify additional prognostic markers but has had limited success in generating robust signatures that predict outcome across multiple patient cohorts. This study aimed to identify robust gene classifiers that could be used for the accurate prediction of relapse in independent cohorts and across different experimental platforms.

Results

Using HG-U133Plus2 microarrays we modeled a five-gene classifier (5-GC) that accurately predicted clinical outcome in a cohort of 50 T-ALL patients. The 5-GC was further tested against three independent cohorts of T-ALL patients, using either qRT-PCR or microarray gene expression, and could predict patients with significantly adverse clinical outcome in each. The 5-GC featured the interleukin-7 receptor (IL-7R), low-expression of which was independently predictive of relapse in T-ALL patients. In T-ALL cell lines, low IL-7R expression was correlated with diminished growth response to IL-7 and enhanced glucocorticoid resistance. Analysis of biological pathways identified the NF-κB and Wnt pathways, and the cell adhesion receptor family (particularly integrins) as being predictive of relapse. Outcome modeling using genes from these pathways identified patients with significantly worse relapse-free survival in each T-ALL cohort.

Conclusions

We have used two different approaches to identify, for the first time, robust gene signatures that can successfully discriminate relapse and CCR patients at the time of diagnosis across multiple patient cohorts and platforms. Such genes and pathways represent markers for improved patient risk stratification and potential targets for novel T-ALL therapies.
Captopril reduces cardiac inflammatory markers in spontaneously hypertensive rats by inactivation of NF-kB
Authors: Miguel-Carrasco José L , Zambrano Sonia , Blanca Antonio J , Mate Alfonso , Vázquez Carmen M
Published: May 2010

Background

Captopril is an angiotensin-converting enzyme (ACE) inhibitor widely used in the treatment of arterial hypertension and cardiovascular diseases. Our objective was to study whether captopril is able to attenuate the cardiac inflammatory process associated with arterial hypertension.

Methods

Left ventricle mRNA expression and plasma levels of pro-inflammatory (interleukin-1β (IL-1β) and IL-6) and anti-inflammatory (IL-10) cytokines, were measured in spontaneously hypertensive rats (SHR) and their control normotensive, Wistar-Kyoto (WKY) rats, with or without a 12-week treatment with captopril (80 mg/Kg/day; n = six animals per group). To understand the mechanisms involved in the effect of captopril, mRNA expression of ACE, angiotensin II type I receptor (AT1R) and p22phox (a subunit of NADPH oxidase), as well as NF-κB activation and expression, were measured in the left ventricle of these animals.

Results

In SHR, the observed increases in blood pressures, heart rate, left ventricle relative weight, plasma levels and cardiac mRNA expression of IL-1β and IL-6, as well as the reductions in the plasma levels and in the cardiac mRNA expression of IL-10, were reversed after the treatment with captopril. Moreover, the mRNA expressions of ACE, AT1R and p22phox, which were enhanced in the left ventricle of SHR, were reduced to normal values after captopril treatment. Finally, SHR presented an elevated cardiac mRNA expression and activation of the transcription nuclear factor, NF-κB, accompanied by a reduced expression of its inhibitor, IκB; captopril administration corrected the observed changes in all these parameters.

Conclusion

These findings show that captopril decreases the inflammation process in the left ventricle of hypertensive rats and suggest that NF-κB-driven inflammatory reactivity might be responsible for this effect through an inactivation of NF-κB-dependent pro-inflammatory factors.