bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of Clock Monitoring on Electroencephalographic Activity
Authors: Miller Jeff , Shepherdson Peter , Trevena Judy
Published: December 2010

Electroencephalographic (EEG) activity was recorded while participants waited to make spontaneous key-press movements (Experiment 1) or waited for tones in a pitch judgment task (Experiment 2). In one condition of each experiment, participants also had to report the position of a spot traveling on a clock at the crucial time point (i.e., when they decided to move or when the tone was presented), mimicking a procedure used to assess the time of conscious awareness of an event of interest. In a second condition, there was no clock or temporal judgment. Average EEG activity preceding key presses was substantially different when participants had to monitor the clock than when they did not. Smaller clock-related differences in average EEG activity were also present preceding tone onsets. The effects of clock monitoring on EEG activity could be responsible for previous reports that movement-related brain activity begins before participants have consciously decided to move (e.g., Libet, Gleason, Wright, & Pearl, 1983).
The Daughter–Mother Relationship in the Presence of Aphasia: How Daughters View Changes Over the First Year Poststroke
Authors: Hallé Marie-Christine , Duhamel Fabie , Le Dorze Guylaine
Published: December 2010

In this study we explored daughters’ perceptions of changes in their relationship with their mother who became aphasic as a result of stroke. Four daughters of aphasic women were each interviewed qualitatively at three different times over the course of a year, and their discourse was transcribed and analyzed. A conceptual model of dynamic relationship changes was drawn, showing how the daughters’ perceptions of maternal fragility, problems and/or abilities motivated protective and/or trusting behaviors that resulted in maternal reactions of satisfaction and/or dissatisfaction that, in turn, reinforced the daughters’ initial perceptions. Results also showed that daughter—mother relationship changes followed four distinct yet coexisting patterns. Aphasia and communication limitations explained many relationship changes. When communication was avoided or perceived to be too difficult, daughters were limited in the means they could use to adjust their relationship with their mother.
Are Older Adults Satisfied With the Implementation of Federal Programs to Serve Aging Populations? A Case Study Policy Implementation
Authors: Cruz Minerva
Published: December 2010

This study analyzes the findings of a fieldwork study conducted between two distinct cultural traditions: Puerto Rico, a U.S. territory with a predominantly Hispanic population, and Indiana, a predominantly Anglo Midwestern state. Specifically, the study compares the satisfaction of older adults with the implementation of the home health care policy sponsored by Medicare in both settings. The study focuses on older adults’ attitudes toward the qualities and performance of home health aides. Due to cultural differences in both settings, the thesis statement was that older adults in Indiana and Puerto Rico are likely to be satisfied with different qualities of home health aides. The results of the data, however, do not support this hypothesis, as older adults in both settings demonstrate satisfaction with similar qualities in their home health aides, although the Puerto Rican sample shows higher levels of satisfaction.
Predictors of Hospitalization Among Home Health Managed Care Patients
Authors: Enguidanos Susan , Hoang Tuyen , Hillary Kristine A. , Haynes Renee L.
Published: December 2010

Objectives: To identify variables associated with hospitalization among managed care patients enrolled in home health services. Design: Retrospective analysis using Home Health Outcome and Assessment Information Set (OASIS) and home health visit data. Setting: Three managed care agencies. Participants: Sixty-five and above, Medicare patients admitted between March 1, 2007 and February 29, 2008. Measurements: Home health care episodes were defined as the time from admission to hospitalization or discharge. Cox regression analyses were conducted to determine predictors of hospitalization. Results: The analysis included 6,805 episodes. Predictors of hospitalization included being male or African American, living in a board and care facility, and having therapies at home, among others. Nurse visits were associated with increased hospitalization whereas social worker visits were associated with decreased hospitalization. Conclusion: This study provides implications for improving clinical practice. Knowing factors associated with hospital admission, home health staff can identify potential risks and develop targeted care plans that may reduce avoidable hospital admission rates.
The Parent Experience
Authors: Miron Colleen
Published: December 2010

The purpose of this study was to explore the parent adaptation process for parents of children with childhood apraxia of speech (CAS). Professionals widely recognize the importance of parental involvement in achieving successful outcomes for children with disabilities, however, few studies have explored parents’ views and perspectives, in particular those of parents of children with speech and language disorders. The topic of how parents’ adapt to their child’s diagnosis is an exploratory topic among all disabilities and disorders, however, it is absent from the literature on CAS. Thus, this study sought to explore the parent adaptation experience when a child is diagnosed with CAS. If professionals understand what parents are thinking and feeling, it follows that they will be able to work more effectively in their treatment collaborations with parents of children with CAS.
The Ketogenic Diet
Authors: Plogsted Steven
Published: December 2010

The ketogenic diet is a specialized diet used primarily to control or reduce seizure activity in pediatric patients. The diet relies on altering the carbohydrate and fat content of food intake and is managed by a multidisciplinary team comprising physicians, dietitians, nurses, and pharmacists.
Nutrition Implications of Heart Failure and Heart Transplantation in Children With Dilated Cardiomyopathy
Authors: Bailer Judy , Kaufman Beth D.
Published: December 2010

This article describes nutrition implications of pediatric dilated cardiomyopathy leading to heart transplantation with a focus on nutritional management of patients during the waiting time for a donor organ and the inpatient postoperative period. Optimization of nutritional status is essential during these periods as weight loss and malnutrition contribute to muscle atrophy, decreased functional capacity, reduced immune function, and prolonged hospital stay. Nutrition implications of heart failure vary with patient’s age and degree of symptoms. Infants may have increased caloric needs and poor feeding often due to tachypnea. Older children, 1-18 years, may have decreased appetite, abdominal pain, and vomiting. Ventricular assist devices or extracorporeal membrane oxygenation, necessary to sustain life in some cases, have additional nutrition implications related to wound healing from insertion of the device and device-related complications that can include pancreatitis and the need for total parenteral nutrition. Once symptomatic heart failure is relieved and heart transplant occurs, caloric needs often decrease while interest in eating can increase profoundly, changing the overall nutrition diagnosis and the need for nutrition support. A case series involving an infant, a young child, and an adolescent is presented to illustrate nutritional challenges and interventions for pediatric patients awaiting heart transplant and the inpatient postoperative period.
Allogeneic effector/memory Th-1 cells impair FoxP3+ regulatory T lymphocytes and synergize with chaperone-rich cell lysate vaccine to treat leukemia
Authors: Janikashvili Nona , LaCasse Collin J. , Larmonier Claire , Trad Malika , Herrell Amanda , Bustamante Sara , Bonnotte Bernard , Har-Noy Michael , Larmonier Nicolas , Katsanis Emmanuel
Published: December 2010

Therapeutic strategies combining the induction of effective antitumor immunity with the inhibition of the mechanisms of tumor-induced immunosuppression represent a key objective in cancer immunotherapy. Herein we demonstrate that effector/memory CD4+ T helper-1 (Th-1) lymphocytes, in addition to polarizing type-1 antitumor immune responses, impair tumor-induced CD4+CD25+FoxP3+ regulatory T lymphocyte (Treg) immunosuppressive function in vitro and in vivo. Th-1 cells also inhibit the generation of FoxP3+ Tregs from naive CD4+CD25−FoxP3− T cells by an interferon-γ–dependent mechanism. In addition, in an aggressive mouse leukemia model (12B1), Th-1 lymphocytes act synergistically with a chaperone-rich cell lysate (CRCL) vaccine, leading to improved survival and long-lasting protection against leukemia. The combination of CRCL as a source of tumor-specific antigens and Th-1 lymphocytes as an adjuvant has the potential to stimulate efficient specific antitumor immunity while restraining Treg-induced suppression.
A novel Ncr1-Cre mouse reveals the essential role of STAT5 for NK-cell survival and development
Authors: Eckelhart Eva , Warsch Wolfgang , Zebedin Eva , Simma Olivia , Stoiber Dagmar , Kolbe Thomas , Rülicke Thomas , Mueller Mathias , Casanova Emilio , Sexl Veronika
Published: December 2010

We generated a transgenic mouse line that expresses the Cre recombinase under the control of the Ncr1 (p46) promoter. Cre-mediated recombination was tightly restricted to natural killer (NK) cells, as revealed by crossing Ncr1-iCreTg mice to the eGFP-LSLTg reporter strain. Ncr1-iCreTg mice were further used to study NK cell–specific functions of Stat5 (signal transducers and activators of transcription 5) by generating Stat5f/fNcr1-iCreTg animals. Stat5f/fNcr1-iCreTg mice were largely devoid of NK cells in peripheral lymphoid organs. In the bone marrow, NK-cell maturation was abrogated at the NK cell–precursor stage. Moreover, we found that in vitro deletion of Stat5 in interleukin 2–expanded NK cells was incompatible with NK-cell viability. In vivo assays confirmed the complete abrogation of NK cell–mediated tumor control against B16F10-melanoma cells. In contrast, T cell–mediated tumor surveillance against MC38-adenocarcinoma cells was undisturbed. In summary, the results of our study show that STAT5 has a cell-intrinsic role in NK-cell development and that Ncr1-iCreTg mice are a powerful novel tool with which to study NK-cell development, biology, and function.
Pharmaceutical inhibition of glycogen synthetase kinase-3β reduces multiple myeloma–induced bone disease in a novel murine plasmacytoma xenograft model
Authors: Gunn W. Grady , Krause Ulf , Lee Narae , Gregory Carl A.
Published: December 2010

Multiple myeloma (MM) is a malignancy of plasma cells that accumulate in the bone marrow. MM is incurable with approximately 100 000 patients currently in the United States and 20 000 new cases diagnosed yearly. The malignancy causes displacement of hematopoiesis and formation of osteolytic bone lesions also known as myeloma bone disease (MBD). At diagnosis, 79% of patients suffer from MBD associated with severe pain and increased mortality. Wnt inhibitors secreted by MM cells inhibit osteogenesis and promote osteoclastogenesis, therefore rapid targeting of Wnt inhibitors is necessary to prevent potentially irreversible effects on the stroma, which could lead to incurable MBD. Inhibition of glycogen synthetase kinase-3β (GSK3β) causes accelerated Wnt signaling and enhanced osteogenesis in mesenchymal stem/progenitor cells, irrespective of the extracellular concentration of Wnt inhibitors. Our primary goal of this study was to evaluate a GSK3β inhibitor (6-bromoindirubin-3′-oxime BIO) for amelioration of bone destruction in a murine model of MBD. When measured using histomorphometry, peritumoral BIO administration improved bone quality at the bone-tumor interface and, surprisingly, increased histologically apparent tumor necrosis. Furthermore, in vitro assays demonstrated a proapoptotic effect on numerous MM cell lines. These preliminary data suggest that pharmaceutical GSK3β inhibition may improve bone quality in myeloma and other malignant bone diseases.
Engraftment of human central memory-derived effector CD8+ T cells in immunodeficient mice
Authors: Wang Xiuli , Berger Carolina , Wong ChingLam W. , Forman Stephen J. , Riddell Stanley R. , Jensen Michael C.
Published: December 2010

In clinical trials of adoptive T-cell therapy, the persistence of transferred cells correlates with therapeutic efficacy. However, properties of human T cells that enable their persistence in vivo are poorly understood, and model systems that enable investigation of the fate of human effector T cells (TE) have not been described. Here, we analyzed the engraftment of adoptively transferred human cytomegalovirus pp65-specific CD8+ TE cells derived from purified CD45RO+CD62L+ central memory (TCM) or CD45RO+CD62L− effector memory (TEM) precursors in an immunodeficient mouse model. The engraftment of TCM-derived effector cells (TCM/E) was dependent on human interleukin-15, and superior in magnitude and duration to TEM-derived effector cells (TEM/E). T-cell receptor Vβ analysis of persisting cells demonstrated that CD8+ TCM/E engraftment was polyclonal, suggesting that the ability to engraft is a general feature of TCM/E. CD8+ TEM/E proliferated extensively after transfer but underwent rapid apoptosis. In contrast, TCM/E were less prone to apoptosis and established a persistent reservoir of functional T cells in vivo characterized by higher CD28 expression. These studies predict that human CD8+ effector T cells derived from TCM precursors may be preferred for adoptive therapy based on superior engraftment fitness.
Insights into the role of differential gene expression on the ecological adaptation of the snail Littorina saxatilis
Authors: Martínez-Fernández Mónica , Bernatchez Louis , Rolán-Alvarez Emilio , Quesada Humberto
Published: December 2010

Background

In the past 40 years, there has been increasing acceptance that variation in levels of gene expression represents a major source of evolutionary novelty. Gene expression divergence is therefore likely to be involved in the emergence of incipient species, namely, in a context of adaptive radiation. In this study, a genome-wide expression profiling approach (cDNA-AFLP), validated by quantitative real-time polymerase chain reaction (qPCR) were used to get insights into the role of differential gene expression on the ecological adaptation of the marine snail Littorina saxatilis. This gastropod displays two sympatric ecotypes (RB and SU) which are becoming one of the best studied systems for ecological speciation.

Results

Among the 99 transcripts shared between ecotypes, 12.12% showed significant differential expression. At least 4% of these transcripts still displayed significant differences after correction for multiple tests, highlighting that gene expression can differ considerably between subpopulations adapted to alternative habitats in the face of gene flow. One of the transcripts identified was Cytochrome c Oxidase subunit I (COI). In addition, 6 possible reference genes were validated to normalize and confirm this result using qPCR. α-Tubulin and histone H3.3 showed the more stable expression levels, being therefore chosen as the best option for normalization. The qPCR analysis confirmed a higher COI expression in SU individuals.

Conclusions

At least 4% of the transcriptome studied is being differentially expressed between ecotypes living in alternative habitats, even when gene flow is still substantial between ecotypes. We could identify a candidate transcript of such ecotype differentiation: Cytochrome c Oxidase Subunit I (COI), a mitochondrial gene involved in energy metabolism. Quantitative PCR was used to confirm the differences found in COI and its over-expression in the SU ecotype. Interestingly, COI is involved in the oxidative phosphorylation, suggesting an enhanced mitochondrial gene expression (or increased number of mitochondria) to improve energy supply in the ecotype subjected to the strongest wave action.
Analysis of transcript and protein overlap in a human osteosarcoma cell line
Authors: Klevebring Daniel , Fagerberg Linn , Lundberg Emma , Emanuelsson Olof , Uhlén Mathias , Lundeberg Joakim
Published: December 2010

Background

An interesting field of research in genomics and proteomics is to compare the overlap between the transcriptome and the proteome. Recently, the tools to analyse gene and protein expression on a whole-genome scale have been improved, including the availability of the new generation sequencing instruments and high-throughput antibody-based methods to analyze the presence and localization of proteins. In this study, we used massive transcriptome sequencing (RNA-seq) to investigate the transcriptome of a human osteosarcoma cell line and compared the expression levels with in situ protein data obtained in-situ from antibody-based immunohistochemistry (IHC) and immunofluorescence microscopy (IF).

Results

A large-scale analysis based on 2749 genes was performed, corresponding to approximately 13% of the protein coding genes in the human genome. We found the presence of both RNA and proteins to a large fraction of the analyzed genes with 60% of the analyzed human genes detected by all three methods. Only 34 genes (1.2%) were not detected on the transcriptional or protein level with any method. Our data suggest that the majority of the human genes are expressed at detectable transcript or protein levels in this cell line. Since the reliability of antibodies depends on possible cross-reactivity, we compared the RNA and protein data using antibodies with different reliability scores based on various criteria, including Western blot analysis. Gene products detected in all three platforms generally have good antibody validation scores, while those detected only by antibodies, but not by RNA sequencing, generally consist of more low-scoring antibodies.

Conclusion

This suggests that some antibodies are staining the cells in an unspecific manner, and that assessment of transcript presence by RNA-seq can provide guidance for validation of the corresponding antibodies.
Refining orthologue groups at the transcript level
Authors: Jia Yizhen , Wong Thomas KF , Song You-Qiang , Yiu Siu-Ming , Smith David K
Published: December 2010

Background

Orthologues are genes in different species that are related through divergent evolution from a common ancestor and are expected to have similar functions. Many databases have been created to describe orthologous genes based on existing sequence data. However, alternative splicing (in eukaryotes) is usually disregarded in the determination of orthologue groups and the functional consequences of alternative splicing have not been considered. Most multi-exon genes can encode multiple protein isoforms which often have different functions and can be disease-related. Extending the definition of orthologue groups to take account of alternate splicing and the functional differences it causes requires further examination.

Results

A subset of the orthologous gene groups between human and mouse was selected from the InParanoid database for this study. Each orthologue group was divided into sub-clusters, at the transcript level, using a method based on the sequence similarity of the isoforms. Transcript based sub-clusters were verified by functional signatures of the cluster members in the InterPro database. Functional similarity was higher within than between transcript-based sub-clusters of a defined orthologous group. In certain cases, cancer-related isoforms of a gene could be distinguished from other isoforms of the gene. Predictions of intrinsic disorder in protein regions were also correlated with the isoform sub-clusters within an orthologue group.

Conclusions

Sub-clustering of orthologue groups at the transcript level is an important step to more accurately define functionally equivalent orthologue groups. This work appears to be the first effort to refine orthologous groupings of genes based on the consequences of alternative splicing on function. Further investigation and refinement of the methodology to classify and verify isoform sub-clusters is needed, particularly to extend the technique to more distantly related species.
RNA editing of nuclear transcripts in Arabidopsis thaliana
Authors: Meng Yijun , Chen Dijun , Jin YongFeng , Mao Chuanzao , Wu Ping , Chen Ming
Published: December 2010

Background

RNA editing is a transcript-based layer of gene regulation. To date, no systemic study on RNA editing of plant nuclear genes has been reported. Here, a transcriptome-wide search for editing sites in nuclear transcripts of Arabidopsis (Arabidopsis thaliana) was performed.

Results

MPSS (massively parallel signature sequencing) and PARE (parallel analysis of RNA ends) data retrieved from public databases were utilized, focusing on one-base-conversion editing. Besides cytidine (C)-to-uridine (U) editing in mitochondrial transcripts, many nuclear transcripts were found to be diversely edited. Interestingly, a sizable portion of these nuclear genes are involved in chloroplast- or mitochondrion-related functions, and many editing events are tissue-specific. Some editing sites, such as adenosine (A)-to-U editing loci, were found to be surrounded by peculiar elements. The editing events of some nuclear transcripts are highly enriched surrounding the borders between coding sequences (CDSs) and 3′ untranslated regions (UTRs), suggesting site-specific editing. Furthermore, RNA editing is potentially implicated in new start or stop codon generation, and may affect alternative splicing of certain protein-coding transcripts. RNA editing in the precursor microRNAs (pre-miRNAs) of ath-miR854 family, resulting in secondary structure transformation, implies its potential role in microRNA (miRNA) maturation.

Conclusions

To our knowledge, the results provide the first global view of RNA editing in plant nuclear transcripts.
Qualitative reasoning of dynamic gene regulatory interactions from gene expression data
Authors: Chen Yu , Park Byungkyu , Han Kyungsook
Published: December 2010

Background

A gene regulatory relation often changes over time rather than being constant. But many gene regulatory networks available in databases or literatures are static in the sense that they are either snapshots of gene regulatory relations at a time point or union of successive gene regulations over time. Such static networks cannot represent temporal aspects of gene regulatory interactions such as the order of gene regulations or the pace of gene regulations.

Results

We developed a new qualitative method for representing dynamic gene regulatory relations and algorithms for identifying dynamic gene regulations from the time-series gene expression data using two types of scores. The identified gene regulatory interactions and their temporal properties are visualized as a gene regulatory network. All the algorithms have been implemented in a program called GeneNetFinder (http://wilab.inha.ac.kr/genenetfinder/) and tested on several gene expression data.

Conclusions

The dynamic nature of dynamic gene regulatory interactions can be inferred and represented qualitatively without deriving a set of differential equations describing the interactions. The approach and the program developed in our study would be useful for identifying dynamic gene regulatory interactions from the large amount of gene expression data available and for analyzing the interactions.
Construction of a genetic AND gate under a new standard for assembly of genetic parts
Authors: Ayukawa Shotaro , Kobayashi Akio , Nakashima Yusaku , Takagi Hidemasa , Hamada Shogo , Uchiyama Masahiko , Yugi Katsuyuki , Murata Satoshi , Sakakibara Yasubumi , Hagiya Masami , Yamamura Masayuki , Kiga Daisuke
Published: December 2010

Background

Appropriate regulation of respective gene expressions is a bottleneck for the realization of artificial biological systems inside living cells. The modification of several promoter sequences is required to achieve appropriate regulation of the systems. However, a time-consuming process is required for the insertion of an operator, a binding site of a protein for gene expression, to the gene regulatory region of a plasmid. Thus, a standardized method for integrating operator sequences to the regulatory region of a plasmid is required.

Results

We developed a standardized method for integrating operator sequences to the regulatory region of a plasmid and constructed a synthetic promoter that functions as a genetic AND gate. By standardizing the regulatory region of a plasmid and the operator parts, we established a platform for modular assembly of the operator parts. Moreover, by assembling two different operator parts on the regulatory region, we constructed a regulatory device with an AND gate function.

Conclusions

We implemented a new standard to assemble operator parts for construction of functional genetic logic gates. The logic gates at the molecular scale have important implications for reprogramming cellular behavior.
Gerontome: a web-based database server for aging-related genes and analysis pipelines
Authors: Kwon Jekeun , Lee Byungwook , Chung Haeyoung
Published: December 2010

Background

Aging is a complex and challenging phenomenon that requires interdisciplinary efforts to unravel its mystery. Insight into genes relevant to the aging process would offer the chance to delay and avoid some of deteriorative aspects of aging through the use of preventive methods. To assist basic research on aging, a comprehensive database and analysis platform for aging-related genes is required.

Results

We developed a web-based database server, called Gerontome that contains aging-related gene information and user-friendly analysis pipelines. To construct the Gerontome database, we integrated aging-related genes and their annotation data. The aging-related genes were categorized by a set of structural terms from Gene Ontology (GO). Analysis pipelines for promoter analysis and protein-ligand docking were developed. The promoter analysis pipeline allows users to investigate the age-dependent regulation of gene expression. The protein-ligand docking pipeline provides information on the position and orientation of a ligand in an age-related protein surface.

Conclusion

Gerontome can be accessed through web interfaces for querying and browsing. The server provides comprehensive age-related gene information and analysis pipelines. Gerontome is available free at http://gerontome.kobic.re.kr.
Essential role for ALCAM gene silencing in megakaryocytic differentiation of K562 cells
Authors: Tan Fang , Ghosh Samit , Mbeunkui Flaubert , Thomas Robert , Weiner Joshua A , Ofori-Acquah Solomon F
Published: December 2010

Background

Activated leukocyte cell adhesion molecule (ALCAM/CD166) is expressed by hematopoietic stem cells. However, its role in hematopoietic differentiation has not previously been defined.

Results

In this study, we show that ALCAM expression is silenced in erythromegakaryocytic progenitor cell lines. In agreement with this finding, the ALCAM promoter is occupied by GATA-1 in vivo, and a cognate motif at -850 inhibited promoter activity in K562 and MEG-01 cells. Gain-of-function studies showed that ALCAM clusters K562 cells in a process that requires PKC. Induction of megakaryocytic differentiation in K562 clones expressing ALCAM activated PKC-δ and triggered apoptosis.

Conclusions

There is a lineage-specific silencing of ALCAM in bi-potential erythromegakaryocytic progenitor cell lines. Marked apoptosis of ALCAM-expressing K562 clones treated with PMA suggests that aberrant ALCAM expression in erythromegakaryocytic progenitors may contribute to megakaryocytopenia.
Two distinct regions in the model protein Peb1 are critical for its heterologous transport out of Escherichia coli
Authors: Anton Lena , Majander Katariina , Savilahti Harri , Laakkonen Liisa , Westerlund-Wikström Benita
Published: December 2010

Background

Escherichia coli is frequently the first-choice host organism in expression of heterologous recombinant proteins in basic research as well as in production of commercial, therapeutic polypeptides. Especially the secretion of proteins into the culture medium of E. coli is advantageous compared to intracellular production due to the ease in recovery of the recombinant protein. Since E. coli naturally is a poor secretor of proteins, a few strategies for optimization of extracellular secretion have been described. We have previously reported efficient secretion of the diagnostically interesting model protein Peb1 of Campylobacter jejuni into the growth medium of Escherichia coli strain MKS12 (ΔfliCfliD). To generate a more detailed understanding of the molecular mechanisms behind this interesting heterologous secretion system with biotechnological implications, we here analyzed further the transport of Peb1 in the E. coli host.

Results

When mature Peb1 was expressed without its SecA-YEG -dependent signal sequence and without the putative signal peptidase II recognition sequence in E. coli MKS111ΔHBB lacking the flagellar secretion complex, the protein was found in the periplasm and growth medium which indicated a flagellum-independent translocation. We assessed the Peb1 secretion proficiency by an exhaustive search for transport-affecting regions using a transposition-based scanning mutagenesis strategy. Strikingly, insertion mutagenesis of only two segments, called TAR1 (residues 42 and 43) and TAR2 (residues 173 to 180), prevented Peb1 secretion individually. We confirmed the importance of TAR regions by subsequent site-specific mutagenesis and verified that the secretion deficiency of Peb1 mutants was not due to insolubility or aggregation of the proteins in the cytoplasm. We found by cell fractionation that the mutant proteins were present in the periplasm as well as in the cytoplasm of MKS12. Hence, mutagenesis of TAR regions did not affect export of Peb1 across the cytoplasmic membrane, whereas its export over the outer membrane was markedly impaired.

Conclusions

We propose that the localization of the model protein Peb1 in the growth medium of E. coli is due to active secretion by a still unknown pathway of E. coli. The secretion apparently is a two-step process involving a periplasmic step and the TAR regions.
Targeting the oncogenic protein beta-catenin to enhance chemotherapy outcome against solid human cancers
Authors: Saifo Maher S , Rempinski Donald R , Rustum Youcef M , Azrak Rami G
Published: December 2010

Background

Beta-catenin is a multifunctional oncogenic protein that contributes fundamentally to cell development and biology. Elevation in expression and activity of β-catenin has been implicated in many cancers and associated with poor prognosis. Beta-catenin is degraded in the cytoplasm by glycogen synthase kinase 3 beta (GSK-3β) through phosphorylation. Cell growth and proliferation is associated with β-catenin translocation from the cytoplasm into the nucleus.

This laboratory was the first to demonstrate that selenium-containing compounds can enhance the efficacy and cytotoxicity of anticancer drugs in several preclinical xenograft models. These data provided the basis to identify mechanism of selenium action focusing on β-catenin as a target. This study was designed to: (1) determine whether pharmacological doses of methylseleninic acid (MSeA) have inhibitory effects on the level and the oncogenic activity of β-catenin, (2) investigate the kinetics and the mechanism of β-catenin inhibition, and (3) confirm that inhibition of β-catenin would lead to enhanced cytotoxicity of standard chemotherapeutic drugs.

Results

In six human cancer cell lines, the inhibition of total and nuclear expression of β-catenin by MSeA was dose and time dependent. The involvement of GSK-3β in the degradation of β-catenin was cell type dependent (GSK-3β-dependent in HT-29, whereas GSK-3β-independent in HCT-8). However, the pronounced inhibition of β-catenin by MSeA was independent of various drug treatments and was not reversed after combination therapy.

Knockout of β-catenin by ShRNA and its inhibition by MSeA yielded similar enhancement of cytotoxicity of anticancer drugs.

Collectively, the generated data demonstrate that β-catenin is a target of MSeA and its inhibition resulted in enhanced cytotoxicity of chemotherapeutic drugs.

Conclusions

This study demonstrates that β-catenin, a molecule associated with drug resistance, is a target of selenium and its inhibition is associated with increased multiple drugs cytotoxicity in various human cancers. Further, degradation of β-catenin by GSK-3β is not a general mechanism but is cell type dependent.
Prevalence of the GJB2 IVS1+1G >A mutation in Chinese hearing loss patients with monoallelic pathogenic mutation in the coding region of GJB2
Authors: Yuan Yongyi , Yu Fei , Wang Guojian , Huang Shasha , Yu Ruili , Zhang Xin , Huang Deliang , Han Dongyi , Dai Pu
Published: December 2010

Background

Mutations in the GJB2 gene are the most common cause of nonsyndromic recessive hearing loss in China. In about 6% of Chinese patients with severe to profound sensorineural hearing impairment, only monoallelic GJB2 mutations known to be either recessive or of unclear pathogenicity have been identified. This paper reports the prevalence of the GJB2 IVS1+1G>A mutation in a population of Chinese hearing loss patients with monoallelic pathogenic mutation in the coding region of GJB2.

Methods

Two hundred and twelve patients, screened from 7133 cases of nonsyndromic hearing loss in China, with monoallelic mutation (mainly frameshift and nonsense mutation) in the coding region of GJB2 were examined for the GJB2 IVS1+1G>A mutation and mutations in the promoter region of this gene. Two hundred and sixty-two nonsyndromic hearing loss patients without GJB2 mutation and 105 controls with normal hearing were also tested for the GJB2 IVS1+1G>A mutation by sequencing.

Results

Four patients with monoallelic mutation in the coding region of GJB2 were found carrying the GJB2 IVS1+1G>A mutation on the opposite allele. One patient with the GJB2 c.235delC mutation carried one variant, -3175 C>T, in exon 1 of GJB2. Neither GJB2 IVS1+1G>A mutation nor any variant in exon 1 of GJB2 was found in the 262 nonsyndromic hearing loss patients without GJB2 mutation or in the 105 normal hearing controls.

Conclusion

Testing for the GJB2 IVS 1+1 G to A mutation explained deafness in 1.89% of Chinese GJB2 monoallelic patients, and it should be included in routine testing of patients with GJB2 monoallelic pathogenic mutation.
CCL2/CCR2 and CX3CL1/CX3CR1 chemokine axes and their possible involvement in age-related macular degeneration
Authors: Raoul William , Auvynet Constance , Camelo Serge , Guillonneau Xavier , Feumi Charles , Combadière Christophe , Sennlaub Florian
Published: December 2010

The causes of age-related macular degeneration (AMD) are not well understood. Due to demographic shifts in the industrialized world a growing number of people will develop AMD in the coming decades. To develop treatments it is essential to characterize the disease's pathogenic process. Over the past few years, numerous studies have focused on the role of chemotactic cytokines, also known as chemokines. Certain chemokines, such as CCL2 and CX3CL1, appear to be crucial in subretinal microglia and macrophage accumulation observed in AMD, and participate in the development of retinal degeneration as well as in choroidal neovascularization. This paper reviews the possible implications of CCL2 and CX3CL1 signaling in AMD. Expression patterns, single nucleotide polymorphisms (SNPs) association studies, chemokine and chemokine receptor knockout models are discussed. Future AMD treatments could target chemokines and/or their receptors.
Lignin monomer composition affects Arabidopsis cell-wall degradability after liquid hot water pretreatment
Authors: Li Xu , Ximenes Eduardo , Kim Youngmi , Slininger Mary , Meilan Richard , Ladisch Michael , Chapple Clint
Published: December 2010

Background

Lignin is embedded in the plant cell wall matrix, and impedes the enzymatic saccharification of lignocellulosic feedstocks. To investigate whether enzymatic digestibility of cell wall materials can be improved by altering the relative abundance of the two major lignin monomers, guaiacyl (G) and syringyl (S) subunits, we compared the degradability of cell wall material from wild-type Arabidopsis thaliana with a mutant line and a genetically modified line, the lignins of which are enriched in G and S subunits, respectively.

Results

Arabidopsis tissue containing G- and S-rich lignins had the same saccharification performance as the wild type when subjected to enzyme hydrolysis without pretreatment. After a 24-hour incubation period, less than 30% of the total glucan was hydrolyzed. By contrast, when liquid hot water (LHW) pretreatment was included before enzyme hydrolysis, the S-lignin-rich tissue gave a much higher glucose yield than either the wild-type or G-lignin-rich tissue. Applying a hot-water washing step after the pretreatment did not lead to a further increase in final glucose yield, but the initial hydrolytic rate was doubled.

Conclusions

Our analyses using the model plant A. thaliana revealed that lignin composition affects the enzymatic digestibility of LHW pretreated plant material. Pretreatment is more effective in enhancing the saccharification of A. thaliana cell walls that contain S-rich lignin. Increasing lignin S monomer content through genetic engineering may be a promising approach to increase the efficiency and reduce the cost of biomass to biofuel conversion.
Decay rate of fluid-induced seismicity after termination of reservoir stimulations
Authors: Langenbruch Cornelius , Shapiro Serge A.
Published: December 2010

We present a model describing the seismicity rate of fluid injection-induced seismicity. We put the focus on seismicity induced after termination of fluid injections. Here, our primary objective is the identification of parameters controlling the decay rate of seismicity. The particular importance of a theoretical model for postinjection seismicity is underlined by observations after stimulations of geothermal reservoirs at different locations. For instance, the postinjection phase is relevant for a seismic risk, which up to now has been difficult to control, because processes leading to postinjection events are not well understood. Based on the assumption of pore pressure diffusion as the governing mechanism leading to the triggering of seismic events, we develop a method to calculate the seismicity rate during and after fluid injections. We find that the decay rate of seismicity after termination of injection is very similar to the Omori law, which describes the decay rate of aftershock activity after tectonically driven earthquakes. We propose a modified Omori law for fluid-induced seismicity to estimate the decay rate in dependence on parameters of injection, reservoir rock, and the strength of preexisting fractures in a reservoir. We analyze two models of fracture-strength distribution, which represent stable and unstable preexisting fracture systems. We find that the decay rate of induced seismicity depends on the fracture strength. We present a possible application of this dependency to reservoir characterization. Furthermore, we find that the existence of unstable fractures results in a critical temporal trend of seismicity, which can enhance the occurrence probability of events with large magnitudes shortly after injection has been terminated. We verify our model by finite-element modeling and application to real data collected in case studies performed at Fenton Hill in the United States and Soultz-sous-Forêts in France.
One-way wave-equation migration of compressional and converted waves in a VTI medium
Authors: Pedersen Ørjan , Ursin Bjørn , Helgesen Hans-Kristian
Published: December 2010

In seismic reflection surveying, by recording both pressure and shear-wave reflections, one can increase the amount of information obtained about the subsurface rather than by recording pressure waves alone. Geologic structures that are not visible by using conventional pressure-data may possibly be imaged using shear waves, thus mitigating the risk in oil and gas exploration and production. Horizontally layered sedimentary rocks exhibit anisotropy that can be approximated by an effective transverse isotropic medium with a vertical axis of symmetry. Taking into account a vertically transverse isotropic earth, we derive phase-slowness expressions for quasi-P and quasi-SV waves that are used in a one-way wave-equation migration scheme. We derive simplified slowness-expressions that are useful for processing of conventional pressure data. Numerical examples demonstrate that the slowness approximations are valid for wide-angle propagation, and the resulting one-way propagators are validated on a series of synthetic tests and applied on a field ocean-bottom seismic data set. The results show that the method accurately images both compressional and converted waves in OBS data over a vertically transverse isotropic medium.
Nonoxidative Free Fatty Acid Disposal Is Greater in Young Women than Men
Authors: Koutsari Christina , Basu Rita , Rizza Robert A. , Nair K. Sreekumaran , Khosla Sundeep , Jensen Michael D.
Published: December 2010

abstract

Context:

Large increases in systemic free fatty acid (FFA) availability in the absence of a corresponding increase in fatty acid oxidation can create a host of metabolic abnormalities. These adverse responses are thought to be the result of fatty acids being shunted into hepatic very low-density lipoprotein-triglyceride production and/or intracellular lipid storage and signaling pathways because tissues are forced to increase nonoxidative FFA disposal.

Objective:

The objective of the study was to examine whether variations in postabsorptive nonoxidative FFA disposal within the usual range predict insulin resistance and hypertriglyceridemia.

Design:

We measured: systemic FFA turnover using a continuous iv infusion of [9–10, 3H]palmitate; substrate oxidation with indirect calorimetry combined with urinary nitrogen excretion; whole-body and peripheral insulin sensitivity with the labeled iv glucose tolerance test minimal model.

Setting:

the study was conducted at the Mayo Clinic General Clinical Research Center.

Participants:

Participants included healthy, postabsorptive, nonobese adults (21 women and 21 men).

Interventions:

There were no interventions.

Main Outcome Measures:

Nonoxidative FFA disposal (micromoles per minute), defined as the FFA disappearance rate minus fatty acid oxidation.

Results:

Women had 64% greater nonoxidative FFA disposal rate than men but a better lipid profile and similar insulin sensitivity. There was no significant correlation between nonoxidative FFA disposal and whole-body sensitivity, peripheral insulin sensitivity, or fasting serum triglyceride concentrations in men or women.

Conclusions:

Healthy nonobese women have greater rates of nonoxidative FFA disposal than men, but this does not appear to relate to adverse health consequences. Understanding the sex-specific interaction between adipose tissue lipolysis and peripheral FFA removal will help to discover new approaches to treat FFA-induced abnormalities.
A New Small-Molecule Antagonist Inhibits Graves' Disease Antibody Activation of the TSH Receptor
Authors: Neumann Susanne , Eliseeva Elena , McCoy Joshua G. , Napolitano Giorgio , Giuliani Cesidio , Monaco Fabrizio , Huang Wenwei , Gershengorn Marvin C.
Published: December 2010

abstract

Context:

Graves' disease (GD) is caused by persistent, unregulated stimulation of thyrocytes by thyroid-stimulating antibodies (TSAbs) that activate the TSH receptor (TSHR). We previously reported the first small-molecule antagonist of human TSHR and showed that it inhibited receptor signaling stimulated by sera from four patients with GD.

Objective:

Our objective was to develop a better TSHR antagonist and use it to determine whether inhibition of TSAb activation of TSHR is a general phenomenon.

Design:

We aimed to chemically modify a previously reported small-molecule TSHR ligand to develop a better antagonist and determine whether it inhibits TSHR signaling by 30 GD sera. TSHR signaling was measured in two in vitro systems: model HEK-EM293 cells stably overexpressing human TSHRs and primary cultures of human thyrocytes. TSHR signaling was measured as cAMP production and by effects on thyroid peroxidase mRNA.

Results:

We tested analogs of a previously reported small-molecule TSHR inverse agonist and selected the best NCGC00229600 for further study. In the model system, NCGC00229600 inhibited basal and TSH-stimulated cAMP production. NCGC00229600 inhibition of TSH signaling was competitive even though it did not compete for TSH binding; that is, NCGC00229600 is an allosteric inverse agonist. NCGC00229600 inhibited cAMP production by 39 ± 2.6% by all 30 GD sera tested. In primary cultures of human thyrocytes, NCGC00229600 inhibited TSHR-mediated basal and GD sera up-regulation of thyroperoxidase mRNA levels by 65 ± 2.0%.

Conclusion:

NCGC00229600, a small-molecule allosteric inverse agonist of TSHR, is a general antagonist of TSH receptor activation by TSAbs in GD patient sera.
Concentration Determination of Individual Components in Methanol–Raffinose Mixtures Using Diffusion through Agar Membrane Attached to a Surface Plasmon Resonance Sensor
Authors: Montecillo Menchie E , Yoshidome Toshifumi , Yamagata Toshiyuki , Yamasaki Tatsuya , Mitsushio Masaru , Sarno Brian John , Higo Morihide
Published: December 2010

A surface plasmon resonance (SPR) sensor with agar membrane was developed and applied to aqueous solutions containing methanol and raffinose. The concentrations of the components in the mixture were determined by fitting diffusion-based equations to the SPR time chart. Good agreement between the measured and expected concentrations was observed.
Stationary Behavior in Effective Magnetic Moment and Magnetization of 2,3,6-Trifluorophenyl Nitronyl Nitroxide Radical Crystals
Authors: Kanzawa Tsuneki , Nishihara Sadafumi , Nojiri Hiroyuki , Hosokoshi Yuko
Published: December 2010

A new stable organic radical, 2,3,6-trifluorophenyl nitronyl nitroxide (=2-(2,3,6-trifluorophenyl)-4,4,5,5-tetramethyl-4,5-dihydro-1H-imidazol-1-oxyl 3-oxide) was synthesized, and its crystal structure and magnetic properties were examined. The magnetization curve measured at 0.4 K in magnetic field up to 30 T revealed two-step saturation. A magnetization plateau was observed when the magnetization was one half the value of the saturation magnetization. The temperature dependence of the product of paramagnetic susceptibility (χp) and temperature (T), χpT (χpT ∝ μeff2, square of the effective magnetic moment) showed stationary behavior in the range 2–4 K at two-thirds the value at room temperature. The magnetic structure of this material could be elucidated on the basis of magnetization (M) measurements. Complementary analysis of χpT and M revealed the formation of magnetic clusters comprising triplet (S = 1) and singlet (S = 0) species in the ground state. The intradimer interactions were attributed to the special molecular overlaps, as reported previously. Interdimer interactions were also investigated: the difference in the molecular overlap between the trifluorophenyl groups was responsible for the difference in the sign of the magnetic coupling. This is the first experimental evidence for the molecular overlap between the phenyl groups being responsible for the strong magnetic interactions.