bluuebunny/crossref_metadata_2025 huggingface dataset:
Improving academic leadership and oversight in large industry-sponsored clinical trials: the ARO-CRO model
Authors: Goldenberg Neil A. , Spyropoulos Alex C. , Halperin Jonathan L. , Kessler Craig M. , Schulman Sam , Turpie Alexander G. G. , Skene Allan M. , Cutler Neal R. , Hiatt William R. ,   for the Antithrombotic Trials Leadership and Steering Group
Published: November 2010

Standards for clinical trial design, execution, and publication have increased in recent years. However, the current structure for interaction among the pharmaceutical sponsor funding a drug or device development program, the contract research organization (CRO) that typically assists in executing the trial, regulatory agencies, and academicians, provides inadequate leadership and oversight of the development process. Conventional academic steering committees are not provided with the independent infrastructure by which to verify statistical analyses and conclusions regarding safety and efficacy. We propose an alternative approach centered on partnerships between CROs and university-based academic research organizations (AROs). In this model, the ARO takes responsibility for processes that address journal requirements and regulatory expectations for independent academic oversight (including oversight of Steering Committee and Data and Safety Monitoring Board activities), whereas the CRO provides infrastructure for efficient trial execution, site monitoring, and data management. The ARO engages academic experts throughout the trial process and minimizes conflicts of interest in individual industry relationships via diversification of sponsors, agents, and therapeutic areas. Although numerous models can be entertained, the ARO-CRO model is uniquely structured to meet the demand for greater assurance of integrity in clinical trials and the needs of each stakeholder in the process.
PathEx: a novel multi factors based datasets selector web tool
Authors: Bareke Eric , Pierre Michael , Gaigneaux Anthoula , Meulder Bertrand De , Depiereux Sophie , Habra Naji , Depiereux Eric
Published: November 2010

Background

Microarray experiments have become very popular in life science research. However, if such experiments are only considered independently, the possibilities for analysis and interpretation of many life science phenomena are reduced. The accumulation of publicly available data provides biomedical researchers with a valuable opportunity to either discover new phenomena or improve the interpretation and validation of other phenomena that partially understood or well known. This can only be achieved by intelligently exploiting this rich mine of information.

Description

Considering that technologies like microarrays remain prohibitively expensive for researchers with limited means to order their own experimental chips, it would be beneficial to re-use previously published microarray data. For certain researchers interested in finding gene groups (requiring many replicates), there is a great need for tools to help them to select appropriate datasets for analysis. These tools may be effective, if and only if, they are able to re-use previously deposited experiments or to create new experiments not initially envisioned by the depositors. However, the generation of new experiments requires that all published microarray data be completely annotated, which is not currently the case. Thus, we propose the PathEx approach.

Conclusion

This paper presents PathEx, a human-focused web solution built around a two-component system: one database component, enriched with relevant biological information (expression array, omics data, literature) from different sources, and another component comprising sophisticated web interfaces that allow users to perform complex dataset building queries on the contents integrated into the PathEx database.
Spontaneously immortalised bovine mammary epithelial cells exhibit a distinct gene expression pattern from the breast cancer cells
Authors: Zhao Chenfu , Meng Lu , Hu Hongyu , Wang Xudong , Shi Fangyu , Wang Yajuan , Li Qianqian , Lin Aixing
Published: November 2010

Background

Spontaneous immortalisation of cultured mammary epithelial cells (MECs) is an extremely rare event, and the molecular mechanism behind spontaneous immortalisation of MECs is unclear. Here, we report the establishment of a spontaneously immortalised bovine mammary epithelial cell line (BME65Cs) and the changes in gene expression associated with BME65Cs cells.

Results

BME65Cs cells maintain the general characteristics of normal mammary epithelial cells in morphology, karyotype and immunohistochemistry, and are accompanied by the activation of endogenous bTERT (bovine Telomerase Reverse Transcriptase) and stabilisation of the telomere. Currently, BME65Cs cells have been passed for more than 220 generations, and these cells exhibit non-malignant transformation. The expression of multiple genes was investigated in BME65Cs cells, senescent BMECs (bovine MECs) cells, early passage BMECs cells and MCF-7 cells (a human breast cancer cell line). In comparison with early passage BMECs cells, the expression of senescence-relevant apoptosis-related gene were significantly changed in BME65Cs cells. P16INK4a was downregulated, p53 was low expressed and Bax/Bcl-2 ratio was reversed. Moreover, a slight upregulation of the oncogene c-Myc, along with an undetectable level of breast tumor-related gene Bag-1 and TRPS-1, was observed in BME65Cs cells while these genes are all highly expressed in MCF-7. In addition, DNMT1 is upregulated in BME65Cs. These results suggest that the inhibition of both senescence and mitochondrial apoptosis signalling pathways contribute to the immortality of BME65Cs cells. The expression of p53 and p16

INK4a
in BME65Cs was altered in the pattern of down-regulation but not "loss", suggesting that this spontaneous immortalization is possibly initiated by other mechanism rather than gene mutation of p53 or p16

INK4a
.

Conclusions

Spontaneously immortalised BME65Cs cells maintain many characteristics of normal BMEC cells and exhibit non-malignant transformation. Although this cell line displays altered patterns of gene expression, it is clearly distinct from malignant breast cancer cell line. It showed that co-inhibition of cellular senescence and mitochondrial apoptosis pathways coordinates BME65Cs cells immortalisation. Additionally, mechanisms other than gene mutation are likely to be involved in regulation of cellular functions. This study provides an insight into the relationship between cell senescence and immortalisation. BME65Cs cells will be useful in future studies of cellular senescence and tumorigenesis.
Maternal effects, flight versus fecundity trade-offs, and offspring immune defence in the Speckled Wood butterfly, Pararge aegeria
Authors: Gibbs Melanie , Breuker Casper J , Hesketh Helen , Hails Rosemary S , Van Dyck Hans
Published: November 2010

Background

Maternal condition can generate resource-related maternal effects through differential egg provisioning, and can greatly affect offspring performance. In the present study, the speckled wood butterflyPararge aegeria(L.) was used to investigate whether (after controlling for egg size) maternal age, and increased flight during the oviposition period, resulted in changes in egg provisioning and whether this contributed to variation in offspring performance, i) early in development (egg stage and early post-hatching development), and ii) later in larval development after being exposed to the model viral pathogen system; the baculovirusAutographa californicamultinucleocapsid nucleopolyhedrovirus (AcMNPV).

Results

Age-related changes in maternal egg provisioning were observed to influence egg stage development only. Flight-induced changes in maternal egg provisioning had direct consequences for offspring growth and survival across each life stage from egg to adulthood; offspring from forced flight mothers had lower larval masses and longer development times. Offspring with lower larval masses also had reduced survival after exposure to the viral pathogen.

Conclusion

The present study demonstrates that a change in maternal provisioning as a result of increased flight during the oviposition period has the potential to exert non-genetic cross-generational fitness effects inP. aegeria. This could have important consequences for population dynamics, particularly in fragmented anthropogenic landscapes.
Phospholipase D promotes Arcanobacterium haemolyticum adhesion via lipid raft remodeling and host cell death following bacterial invasion
Authors: Lucas Erynn A , Billington Stephen J , Carlson Petteri , McGee David J , Jost B Helen
Published: November 2010

Background

Arcanobacterium haemolyticumis an emerging bacterial pathogen, causing pharyngitis and more invasive infections. This organism expresses an unusual phospholipase D (PLD), which we propose promotes bacterial pathogenesis through its action on host cell membranes. Thepldgene is found on a genomic region of reduced %G + C, suggesting recent horizontal acquisition.

Results

Recombinant PLD rearranged HeLa cell lipid rafts in a dose-dependent manner and this was inhibited by cholesterol sequestration. PLD also promoted host cell adhesion, as apldmutant had a 60.3% reduction in its ability to adhere to HeLa cells as compared to the wild type. Conversely, thepldmutant appeared to invade HeLa cells approximately two-fold more efficiently as the wild type. This finding was attributable to a significant loss of host cell viability following secretion of PLD from intracellular bacteria. As determined by viability assay, only 15.6% and 82.3% of HeLa cells remained viable following invasion by the wild type orpldmutant, respectively, as compared to untreated HeLa cells. Transmission electron microscopy of HeLa cells inoculated withA. haemolyticumstrains revealed that thepldmutant was contained within intracellular vacuoles, as compared to the wild type, which escaped the vacuole. Wild type-infected HeLa cells also displayed the hallmarks of necrosis. Similarly inoculated HeLa cells displayed no signs of apoptosis, as measured by induction of caspase 3/7, 8 or 9 activities.

Conclusions

These data indicate that PLD enhances bacterial adhesion and promotes host cell necrosis following invasion, and therefore, may be important in the disease pathogenesis ofA. haemolyticuminfections.
Polymorphism of SERPINE2 gene is associated with pulmonary emphysema in consecutive autopsy cases
Authors: Fujimoto Koichi , Ikeda Shinobu , Arai Tomio , Tanaka Noriko , Kumasaka Toshio , Ishii Takeo , Kida Kozui , Muramatsu Masaaki , Sawabe Motoji
Published: November 2010

Background

The SERPINA1, SERPINA3, and SERPINE2 genes, which encode antiproteases, have been proposed to be susceptible genes for of chronic obstructive pulmonary disease (COPD) and related phenotypes. Whether they are associated with emphysema is not known.

Methods

Twelve previously reported single nucleotide polymorphisms (SNPs) in SERPINA1 (rs8004738, rs17751769, rs709932, rs11832, rs1303, rs28929474, and rs17580), SERPINA3 (rs4934, rs17473, and rs1800463), and SERPINE2 (rs840088 and rs975278) were genotyped in samples obtained from 1,335 consecutive autopsies of elderly Japanese people. The association between these SNPs and the severity of emphysema, as assessed using macroscopic scores, was determined.

Results

Emphysema of more than moderate degree was detected in 189 subjects (14.1%) and showed a significant gender difference (males, 20.5% and females, 7.0%; p < 0.0001). Among the 12 examined SNPs, only rs975278 in the SERPINE2 gene was positively associated with emphysema. Unlike the major alleles, homozygous minor alleles of rs975278 were associated with emphysema (odds ratio (OR) = 1.54; 95% confidence interval (CI) = 1.02-2.30; p = 0.037) and the association was very prominent in smokers (OR = 2.02; 95% CI = 1.29-3.15; p = 0.002).

Conclusions

SERPINE2 may be a risk factor for the development of emphysema and its association with emphysema may be stronger in smokers.
Current practices in treatment of female genital fistula: a cross sectional study
Authors: Arrowsmith Steven D , Ruminjo Joseph , Landry Evelyn G
Published: November 2010

Background

Maternal outcomes in most countries of the developed world are good. However, in many developing/resource-poor countries, maternal outcomes are bleaker: Every year, more than 500,000 women die in childbirth, mostly in resource-poor countries. Those who survive often suffer from severe and long-term morbidities. One of the most devastating injuries is obstetric fistula, occurring most often in south Asia and sub-Saharan Africa. Fistula treatment and care are available in many countries across Africa and Asia, but there is a lack of reliable data around clinical factors associated with the success of fistula repair surgery. Most published research has been retrospective. While these studies have provided useful information about the care and treatment of fistula, they are limited by the design. This study was designed to identify practices in care that could lead to the design of prospective and randomized controlled trials.

Methods

Self-administered questionnaires were completed by 40 surgeons known to provide fistula treatment services in Africa and Asia at private and government hospitals. The questionnaire was divided into three parts to address the following issues: prophylactic use of antibiotics before, during, and after fistula surgery; urethral catheter management; and management practices for patients with urinary incontinence following fistula repair.

Results

The results provide a glimpse into current practices in fistula treatment and care across a wide swath of geographic, economic, and organizational considerations. There is consensus in treatment in some areas (routine use of prophylactic antibiotics, limited bed rest until the catheter is removed, nonsurgical treatment for postsurgical incontinence), while there are wide variations in practice in other areas (duration of catheter use, surgical treatments for postsurgical incontinence). These findings are based on a small sample and do not allow for recommending changes in clinical care, but they point to issues for possible clinical trial research that would contribute to more efficient and effective fistula care.

Conclusions

The findings from the survey allowed us to consider clinical practices most influential in the cost, efficacy, and safety of fistula treatment. These considerations led us to formulate recommendations for eight randomized controlled trials on the following subjects: 1) Efficacy/safety of short-term catheterization; 2) efficacy of surgical and nonsurgical therapies for urinary incontinence; 3) technical measures during fistula repair to reduce the incidence of post-surgery incontinence; 4) identification of predictive factors for "incurable fistula"; 5) usefulness of urodynamic studies in the management of urinary incontinence; 6) incidence and significance of multi-drug resistant bacteria in the fistula population; 7) primary management of small, new fistulas by catheter drainage; and 8) antibiotic prophylaxis in fistula repair.
Epigenetic inactivation of the NORE1gene correlates with malignant progression of colorectal tumors
Authors: Lee Chang Kyun , Lee Jin-Hee , Lee Min-Goo , Jeong Seong-In , Ha Tae-Kyu , Kang Min-Ju , Ryu Byung-Kyu , Hwangbo Young , Shim Jae-Jun , Jang Jae Young , Lee Kil Yeon , Kim Hyo Jong , Chi Sung-Gil
Published: November 2010

Background

NORE1 (RASSF5) is a newly described member of the RASSF family with Ras effector function. NORE1 expression is frequently inactivated by aberrant promoter hypermethylation in many human cancers, suggesting that NORE1 might be a putative tumor suppressor. However, expression and mutation status of NORE1 and its implication in colorectal tumorigenesis has not been evaluated.

Methods

Expression, mutation, and methylation status of NORE1A and NORE1B in 10 cancer cell lines and 80 primary tumors were characterized by quantitative PCR, SSCP, and bisulfite DNA sequencing analyses. Effect of NORE1A and NORE1B expression on tumor cell growth was evaluated using cell number counting, flow cytometry, and colony formation assays.

Results

Expression of NORE1A and NORE1B transcript was easily detectable in all normal colonic epithelial tissues, but substantially decreased in 7 (70%) and 4 (40%) of 10 cancer cell lines and 31 (38.8%) and 25 (31.3%) of 80 primary carcinoma tissues, respectively. Moreover, 46 (57.6%) and 38 (47.5%) of 80 matched tissue sets exhibited tumor-specific reduction of NORE1A and NORE1B, respectively. Abnormal reduction of NORE1 was more commonly observed in advanced stage and high grade tumors compared to early and low grade tumors. While somatic mutations of the gene were not identified, its expression was re-activated in all low expressor cells after treatment with the demethylating agent 5-aza-dC. Bisulfite DNA sequencing analysis of 31 CpG sites within the promoter region demonstrated that abnormal reduction of NORE1A is tightly associated with promoter CpG sites hypermethylation. Moreover, transient expression and siRNA-mediated knockdown assays revealed that both NORE1A and NORE1B decrease cellular growth and colony forming ability of tumor cells and enhance tumor cell response to apoptotic stress.

Conclusion

Our data indicate that epigenetic inactivation of NORE1 due to aberrant promoter hypermethylation is a frequent event in colorectal tumorigenesis and might be implicated in the malignant progression of colorectal tumors.
mTOR signaling is activated by FLT3 kinase and promotes survival of FLT3- mutated acute myeloid leukemia cells
Authors: Chen Weina , Drakos Elias , Grammatikakis Ioannis , Schlette Ellen J , Li Jiang , Leventaki Vasiliki , Staikou-Drakopoulou Efi , Patsouris Efstratios , Panayiotidis Panayiotis , Medeiros L Jeffrey , Rassidakis George Z
Published: November 2010

Activating mutations of the FLT3 gene mediate leukemogenesis, at least in part, through activation of PI3K/AKT. The mammalian target of rapamycin (mTOR)-Raptor signaling pathway is known to act downstream of AKT. Here we show that the mTOR effectors, 4EBP1, p70S6K and rpS6, are highly activated in cultured and primary FLT3-mutated acute myeloid leukemia (AML) cells. Introduction of FLT3-ITD expressing constitutively activated FLT3 kinase further activates mTOR and its downstream effectors in BaF3 cells. We also found that mTOR signaling contributes to tumor cell survival, as demonstrated by pharmacologic inhibition of PI3K/AKT/mTOR, or total silencing of the mTOR gene. Furthermore, inhibition of FLT3 kinase results in downregulation of mTOR signaling associated with decreased survival of FLT3-mutated AML cells. These findings suggest that mTOR signaling operates downstream of activated FLT3 kinase thus contributing to tumor cell survival, and may represent a promising therapeutic target for AML patients with mutated-FLT3.
Interleukin-13 receptor α2 DNA prime boost vaccine induces tumor immunity in murine tumor models
Authors: Nakashima Hideyuki , Fujisawa Toshio , Husain Syed R , Puri Raj K
Published: November 2010

Background

DNA vaccines represent an attractive approach for cancer treatment by inducing active T cell and B cell immune responses to tumor antigens. Previous studies have shown that interleukin-13 receptor α2 chain (IL-13Rα2), a tumor-associated antigen is a promising target for cancer immunotherapy as high levels of IL-13Rα2 are expressed on a variety of human tumors. To enhance the effectiveness of DNA vaccine, we used extracellular domain of IL-13Rα2 (ECDα2) as a protein-boost against murine tumor models.

Methods

We have developed murine models of tumors naturally expressing IL-13Rα2 (MCA304 sarcoma, 4T1 breast carcinoma) and D5 melanoma tumors transfected with human IL-13Rα2 in syngeneic mice and examined the antitumor activity of DNA vaccine expressing IL-13Rα2 gene with or without ECDα2 protein mixed with CpG and IFA adjuvants as a boost vaccine.

Results

Mice receiving IL-13Rα2 DNA vaccine boosted with ECDα2 protein were superior in exhibiting inhibition of tumor growth, compared to mice receiving DNA vaccine alone, in both prophylactic and therapeutic vaccine settings. In addition, prime-boost vaccination significantly prolonged the survival of mice compared to DNA vaccine alone. Furthermore, ECDα2 booster vaccination increased IFN-γ production and CTL activity against tumor expressing IL-13Rα2. The immunohistochemical analysis showed the infiltration of CD4 and CD8 positive T cells and IFN-γ-induced chemokines (CXCL9 and CXCL10) in regressing tumors of immunized mice. Finally, the prime boost strategy was able to reduce immunosuppressive CD4+CD25+Foxp3+regulatory T cells (Tregs) in the spleen and tumor of vaccinated mice.

Conclusion

These results suggest that immunization with IL-13Rα2 DNA vaccine followed by ECDα2 boost mixed with CpG and IFA adjuvants inhibits tumor growth in T cell dependent manner. Thus our results show an enhancement of efficacy of IL-13Rα2 DNA vaccine with ECDα2 protein boost and offers an exciting approach in the development of new DNA vaccine targeting IL-13Rα2 for cancer immunotherapy.
Distinctive Response of CNS Glial Cells in Orofacial Pain Associated with Injury, Infection and Inflammation
Authors: Lee SeungHwan , Zhao Yuan Qing , Ribeiro-da-Silva Alfredo , Zhang Ji
Published: November 2010

Oro-facial pain following injury and infection is frequently observed in dental clinics. While neuropathic pain evoked by injury associated with nerve lesion has an involvement of glia/immune cells, inflammatory hyperalgesia has an exaggerated sensitization mediated by local and circulating immune mediators. To better understand the contribution of central nervous system (CNS) glial cells in these different pathological conditions, in this study we sought to characterize functional phenotypes of glial cells in response to trigeminal nerve injury (loose ligation of the mental branch), infection (subcutaneous injection of lipopolysaccharide-LPS) and to sterile inflammation (subcutaneous injection of complete Freund's adjuvant-CFA) on the lower lip. Each of the three insults triggered a specific pattern of mechanical allodynia. In parallel with changes in sensory response, CNS glial cells reacted distinctively to the challenges. Following ligation of the mental nerve, both microglia and astrocytes in the trigeminal nuclear complex were highly activated, more prominent in the principal sensory nucleus (Pr5) and subnucleus caudalis (Sp5C) area. Microglial response was initiated early (days 3–14), followed by delayed astrocytes activation (days 7–28). Although the temporal profile of microglial and astrocyte reaction corresponded respectively to the initiation and chronic stage of neuropathic pain, these activated glial cells exhibited a low profile of cytokine expression. Local injection of LPS in the lower lip skin also triggered a microglial reaction in the brain, which started in the circumventricular organs (CVOs) at 5 hours post-injection and diffused progressively into the brain parenchyma at 48 hours. This LPS-induced microglial reaction was accompanied by a robust induction of IκB-α mRNA and pro-inflammatory cytokines within the CVOs. However, LPS induced microglial activation did not specifically occur along the pain signaling pathway. In contrast, CFA injection led to minor microglial morphological changes and an induction of IκB-α mRNA in the CVO regions; a significant increase in IL-1β and IL-6 mRNA started only at 48 hours post-injection, when the induced pain-related behavior started to resolve. Our detailed analysis of CNS glial response clearly revealed that both nerve injury and oro-facial infection/inflammation induced CNS glial activation, but in a completely different pattern, which suggests a remarkable plasticity of glial cells in response to dynamic changes in their microenvironment and different potential involvement of this non-neuronal cell population in pathological pain development.
Concomitant heterochromatinisation and down-regulation of gene expression unveils epigenetic silencing of RELBin an aggressive subset of chronic lymphocytic leukemia in males
Authors: Marteau Jean-Brice , Rigaud Odile , Brugat Thibaut , Gault Nathalie , Vallat Laurent , Kruhoffer Mogens , Orntoft Torben F , Nguyen-Khac Florence , Chevillard Sylvie , Merle-Beral Hélène , Delic Jozo
Published: November 2010

Background

The sensitivity of chronic lymphocytic leukemia (CLL) cells to current treatments, both in vitro and in vivo, relies on their ability to activate apoptotic death. CLL cells resistant to DNA damage-induced apoptosis display deregulation of a specific set of genes.

Methods

Microarray hybridization (Human GeneChip, Affymetrix), immunofluorescent in situ labeling coupled with video-microscopy recording/analyses, chromatin-immunoprecipitation (ChIP), polymerase chain reactions (PCR), real-time quantitative PCR (RT-QPCR) and bisulfite genome sequencing were the main methods applied. Statistical analyses were performed by applying GCRMA and SAM analysis (microarray data) and Student's t-test or Mann & Whitney's U-test.

Results

Herein we show that, remarkably, in a resistant male CLL cells the vast majority of genes were down-regulated compared with sensitive cells, whereas this was not the case in cells derived from females. This gene down-regulation was found to be associated with an overall gain of heterochromatin as evidenced by immunofluorescent labeling of heterochromatin protein 1α (HP-1), trimethylated histone 3 lysine 9 (3metH3K9), and 5-methylcytidine (5metC). Notably, 17 genes were found to be commonly deregulated in resistant male and female cell samples. Among these, RELB was identified as a discriminatory candidate gene repressed in the male and upregulated in the female resistant cells.

Conclusion

The molecular defects in the silencing of RELB involve an increase in H3K9- but not CpG-island methylation in the promoter regions. Increase in acetyl-H3 in resistant female but not male CLL samples as well as a decrease of total cellular level of RelB after an inhibition of histone deacetylase (HDAC) by trichostatin A (TSA), further emphasize the role of epigenetic modifications which could discriminate two CLL subsets. Together, these results highlighted the epigenetic RELB silencing as a new marker of the progressive disease in males.
MT1-MMP regulates VEGF-A expression through a complex with VEGFR-2 and Src
Authors: Eisenach Patricia A. , Roghi Christian , Fogarasi Marton , Murphy Gillian , English William R.
Published: November 2010

Membrane-type-1 matrix metalloproteinase (MT1-MMP) is a zinc-dependent type-I transmembrane metalloproteinase involved in pericellular proteolysis, migration and invasion, with elevated levels correlating with a poor prognosis in cancer. MT1-MMP-mediated transcriptional regulation of genes in cancer cells can contribute to tumour growth, although this is poorly understood at a mechanistic level. In this study, we investigated the mechanism by which MT1-MMP regulates the expression of VEGF-A in breast cancer cells. We discovered that MT1-MMP regulates VEGFR-2 cell surface localisation and forms a complex with VEGFR-2 and Src that is dependent on the MT1-MMP hemopexin domain and independent of its catalytic activity. Although the localisation of VEGFR-2 was independent of the catalytic and intracellular domain of MT1-MMP, intracellular signalling dependent on VEGFR-2 activity leading to VEGF-A transcription still required the MT1-MMP catalytic and intracellular domain, including residues Y573, C574 and DKV582. However, there was redundancy in the function of the catalytic activity of MT1-MMP, as this could be substituted with MMP-2 or MMP-7 in cells expressing inactive MT1-MMP. The signalling cascade dependent on the MT1-MMP–VEGFR-2–Src complex activated Akt and mTOR, ultimately leading to increased VEGF-A transcription.
Structural model of the p14/SF3b155·branch duplex complex
Authors: Schellenberg Matthew J. , Dul Erin L. , MacMillan Andrew M.
Published: November 2010

Human p14 (SF3b14), a component of the spliceosomal U2 snRNP, interacts directly with the pre-mRNA branch adenosine within the context of the bulged duplex formed between the pre-mRNA branch region and U2 snRNA. This association occurs early in spliceosome assembly and persists within the fully assembled spliceosome. Analysis of the crystal structure of a complex containing p14 and a peptide derived from p14-associated SF3b155 combined with the results of cross-linking studies has suggested that the branch nucleotide interacts with a pocket on a non-canonical RNA binding surface formed by the complex. Here we report a structural model of the p14•bulged duplex interaction based on a combination of X-ray crystallography of an adenine p14/SF3b155 peptide complex, biochemical comparison of a panel of disulfide cross-linked protein–RNA complexes, and small-angle X-ray scattering (SAXS). These studies reveal specific recognition of the branch adenosine within the p14 pocket and establish the orientation of the bulged duplex RNA bound on the protein surface. The intimate association of one surface of the bulged duplex with the p14/SF3b155 peptide complex described by this model buries the branch nucleotide at the interface and suggests that p14•duplex interaction must be disrupted before the first step of splicing.
Remembrance of Things Future: Prospective Memory in Laboratory, Workplace, and Everyday Settings
Authors: Dismukes R. Key
Published: November 2010

Prospective memory involves remembering—and sometimes forgetting—to perform tasks that must be deferred. This chapter summarizes and provides a perspective on research and theory in this new and rapidly growing field. I explore the limits of existing experimental paradigms, which fail to capture some critical aspects of performance outside of laboratory settings, and review the relatively few studies in workplace and everyday settings. I suggest countermeasures to reduce vulnerability to forgetting to perform deferred tasks, identify roles for human factors practitioners, and propose a research agenda that would extend the current understanding of prospective memory performance.
Neural Correlates of Associative Face Memory in the Anterior Inferior Temporal Cortex of Monkeys
Authors: Eifuku Satoshi , Nakata Ryuzaburo , Sugimori Michiya , Ono Taketoshi , Tamura Ryoi
Published: November 2010

To investigate the neural basis of the associative aspects of facial identification, we recorded neuronal activity from the ventral, anterior inferior temporal cortex (AITv) of macaque monkeys during the performance of an asymmetrical paired-association (APA) task that required associative pairing between an abstract pattern and five different facial views of a single person. In the APA task, after one element of a pair (either an abstract pattern or a face) was presented as a sample cue, the reward-seeking monkey correctly identified the other element of the pair among various repeatedly presented test stimuli (faces or patterns) that were temporally separated by interstimulus delays. The results revealed that a substantial number of AITv neurons responded both to faces and abstract patterns, and the majority of these neurons responded selectively to a particular associative pair. It was demonstrated that in addition to the view-invariant identity of faces used in the APA task, the population of AITv neurons was also able to represent the associative pairing between faces and abstract patterns, which was acquired by training in the APA task. It also appeared that the effect of associative pairing was not so strong that the abstract pattern could be treated in a manner similar to a series of faces belonging to a unique identity. Together, these findings indicate that the AITv plays a crucial role in both facial identification and semantic associations with facial identities.
Matrix-Binding Vascular Endothelial Growth Factor (VEGF) Isoforms Guide Granule Cell Migration in the Cerebellum via VEGF Receptor Flk1
Authors: Ruiz de Almodovar Carmen , Coulon Cathy , Salin Paul Antoine , Knevels Ellen , Chounlamountri Naura , Poesen Koen , Hermans Karlien , Lambrechts Diether , Van Geyte Katie , Dhondt Joke , Dresselaers Tom , Renaud Julie , Aragones Julian , Zacchigna Serena , Geudens Ilse , Gall David , Stroobants Stijn , Mutin Mireille , Dassonville Karel , Storkebaum Erik , Jordan Bénédicte F. , Eriksson Ulf , Moons Lieve , D'Hooge Rudi , Haigh Jody J. , Belin Marie-Françoise , Schiffmann Serge , Van Hecke Paul , Gallez Bernard , Vinckier Stefan , Chédotal Alain , Honnorat Jérôme , Thomasset Nicole , Carmeliet Peter , Meissirel Claire
Published: November 2010

Vascular endothelial growth factor (VEGF) regulates angiogenesis, but also has important, yet poorly characterized roles in neuronal wiring. Using several genetic andin vitroapproaches, we discovered a novel role for VEGF in the control of cerebellar granule cell (GC) migration from the external granule cell layer (EGL) toward the Purkinje cell layer (PCL). GCs express the VEGF receptor Flk1, and are chemoattracted by VEGF, whose levels are higher in the PCL than EGL. Lowering VEGF levels in micein vivoor ectopic VEGF expression in the EGLex vivoperturbs GC migration. Using GC-specificFlk1knock-out mice, we provide for the first timein vivoevidence for a direct chemoattractive effect of VEGF on neurons via Flk1 signaling. Finally, using knock-in mice expressing single VEGF isoforms, we show that pericellular deposition of matrix-bound VEGF isoforms around PC dendrites is necessary for proper GC migrationin vivo. These findings identify a previously unknown role for VEGF in neuronal migration.
Ablation of Glutamate Receptor GluRδ2 in Adult Purkinje Cells Causes Multiple Innervation of Climbing Fibers by Inducing Aberrant Invasion to Parallel Fiber Innervation Territory
Authors: Miyazaki Taisuke , Yamasaki Miwako , Takeuchi Tomonori , Sakimura Kenji , Mishina Masayoshi , Watanabe Masahiko
Published: November 2010

Glutamate receptor GluRδ2 is exclusively expressed in Purkinje cells (PCs) from early development and plays key roles in parallel fiber (PF) synapse formation, elimination of surplus climbing fibers (CFs), long-term depression, motor coordination, and motor learning. To address its role in adulthood, we previously developed a mouse model of drug-induced GluRδ2 ablation in adult PCs (Takeuchi et al., 2005). In that study, we demonstrated an essential role to maintain the connectivity of PF–PC synapses, based on the observation that both mismatching of presynaptic and postsynaptic specializations and disconnection of PF–PC synapses are progressively increased after GluRδ2 ablation. Here, we pursued its role for CF wiring in adult cerebellum. In parallel with the disconnection of PF–PC synapses, ascending CF branches exhibited distal extension to innervate distal dendrites of the target and neighboring PCs. Furthermore, transverse CF branches, a short motile collateral rarely forming synapses in wild-type animals, displayed aberrant mediolateral extension to innervate distal dendrites of neighboring and remote PCs. Consequently, many PCs were wired by single main CF and other surplus CFs innervating a small part of distal dendrites. Electrophysiological recording further revealed that surplus CF-EPSCs characterized with slow rise time and small amplitude emerged after GluRδ2 ablation, and increased progressively both in number and amplitude. Therefore, GluRδ2 is essential for maintaining CF monoinnervation in adult cerebellum by suppressing aberrant invasion of CF branches to the territory of PF innervation. Thus, GluRδ2 fuels heterosynaptic competition and gives PFs the competitive advantages over CFs throughout the animal's life.
Lgi4 Promotes the Proliferation and Differentiation of Glial Lineage Cells throughout the Developing Peripheral Nervous System
Authors: Nishino Jinsuke , Saunders Thomas L. , Sagane Koji , Morrison Sean J.
Published: November 2010

The mechanisms that regulate peripheral nervous system (PNS) gliogenesis are incompletely understood. For example, gut neural crest stem cells (NCSCs) do not respond to known gliogenic factors, suggesting that yet-unidentified factors regulate gut gliogenesis. To identify new mechanisms, we performed gene expression profiling to identify factors secreted by gut NCSCs during the gliogenic phase of development. These cells highly expressed leucine-rich glioma inactivated 4 (Lgi4) despite the fact that Lgi4 has never been implicated in stem cell function or enteric nervous system development. Lgi4 is known to regulate peripheral nerve myelination (having been identified as the mutated gene in spontaneously arisingclaw pawmutant mice), but Lgi4 is not known to play any role in PNS development outside of peripheral nerves. To systematically analyze Lgi4 function, we generated gene-targeted mice.Lgi4-deficient mice exhibited a more severe phenotype thanclaw pawmice and had gliogenic defects in sensory, sympathetic, and enteric ganglia. We found thatLgi4is required for the proliferation and differentiation of glial-restricted progenitors throughout the PNS. Analysis of compound-mutant mice revealed that the mechanism by which Lgi4 promotes enteric gliogenesis involves binding the ADAM22 receptor. Our results identify a new mechanism regulating enteric gliogenesis as well as novel functions for Lgi4 regulating the proliferation and maturation of glial lineage cells throughout the PNS.
Context-Specific Grasp Movement Representation in Macaque Ventral Premotor Cortex
Authors: Fluet Marie-Christine , Baumann Markus A. , Scherberger Hansjörg
Published: November 2010

Hand grasping requires the transformation of sensory signals to hand movements. Neurons in area F5 (ventral premotor cortex) represent specific grasp movements (e.g., precision grip) as well as object features like orientation, and are involved in movement preparation and execution. Here, we examined how F5 neurons represent context-dependent grasping actions in macaques. We used a delayed grasping task in which animals grasped a handle either with a power or a precision grip depending on context information. Additionally, object orientation was varied to investigate how visual object features are integrated with context information. In 420 neurons from two animals, object orientation and grip type were equally encoded during the instruction epoch (27% and 26% of all cells, respectively). While orientation representation dropped during movement execution, grip type representation increased (20% vs 43%). According to tuning onset and offset, we classified neurons as sensory, sensorimotor, or motor. Grip type tuning was predominantly sensorimotor (28%) or motor (25%), whereas orientation-tuned cells were mainly sensory (11%) or sensorimotor (15%) and often also represented grip type (86%). Conversely, only 44% of grip-type tuned cells were also orientation-tuned. Furthermore, we found marked differences in the incidence of preferred conditions (power vs precision grips and middle vs extreme orientations) and in the anatomical distribution of the various cell classes. These results reveal important differences in how grip type and object orientation is processed in F5 and suggest that anatomically and functionally separable cell classes collaborate to generate hand grasping commands.
BDNF Signaling during Learning Is Regionally Differentiated within Hippocampus
Authors: Chen Lulu Y. , Rex Christopher S. , Pham Danielle T. , Lynch Gary , Gall Christine M.
Published: November 2010

Learning-induced neurotrophic signaling at synapses is widely held to be critical for neuronal viability in adult brain. A previous study provided evidence that unsupervised learning of a novel environment is accompanied by activation of the TrkB receptor for brain-derived neurotrophic factor (BDNF) in hippocampal field CA1b of adult rats. Here we report that this effect is regionally differentiated, in accord with “engram” type memory encoding. A 30 min exposure to a novel, complex environment caused a marked, NMDA receptor-dependent increase in postsynaptic densities associated with activated (phosphorylated) Trk receptors in rostral hippocampus. Increases were pronounced in field CA3a, moderate in the dentate gyrus, and absent in field CA1a. Synapses with Trk activation were significantly larger than their neighbors. Surprisingly, unsupervised learning had no effect on Trk phosphorylation in more temporal sections of hippocampus. It thus appears that commonplace forms of learning interact with regional predispositions to produce spatially differentiated effects on BDNF signaling.
Toward the Second Generation of Optogenetic Tools
Authors: Knöpfel Thomas , Lin Michael Z. , Levskaya Anselm , Tian Lin , Lin John Y. , Boyden Edward S.
Published: November 2010

This mini-symposium aims to provide an integrated perspective on recent developments in optogenetics. Research in this emerging field combines optical methods with targeted expression of genetically encoded, protein-based probes to achieve experimental manipulation and measurement of neural systems with superior temporal and spatial resolution. The essential components of the optogenetic toolbox consist of two kinds of molecular devices: actuators and reporters, which respectively enable light-mediated control or monitoring of molecular processes. The first generation of genetically encoded calcium reporters, fluorescent proteins, and neural activators has already had a great impact on neuroscience. Now, a second generation of voltage reporters, neural silencers, and functionally extended fluorescent proteins hold great promise for continuing this revolution. In this review, we will evaluate and highlight the limitations of presently available optogenic tools and discuss where these technologies and their applications are headed in the future.
MicroRNA Regulation of Neural Stem Cells and Neurogenesis: Figure 1.
Authors: Shi Yanhong , Zhao Xinyu , Hsieh Jenny , Wichterle Hynek , Impey Soren , Banerjee Sourav , Neveu Pierre , Kosik Kenneth S.
Published: November 2010

MicroRNAs are a class of small RNA regulators that are involved in numerous cellular processes, including development, proliferation, differentiation, and plasticity. The emerging concept is that microRNAs play a central role in controlling the balance between stem cell self-renewal and fate determination by regulating the expression of stem cell regulators. This review will highlight recent advances in the regulation of neural stem cell self-renewal and neurogenesis by microRNAs. It will cover microRNA functions during the entire process of neurogenesis, from neural stem cell self-renewal and fate determination to neuronal maturation, synaptic formation, and plasticity. The interplay between microRNAs and both cell-intrinsic and -extrinsic stem cell players, including transcription factors, epigenetic regulators, and extrinsic signaling molecules will be discussed. This is a summary of the topics covered in the mini-symposium on microRNA regulation of neural stem cells and neurogenesis in SFN 2010 and is not meant to be a comprehensive review of the subject.
A Link between Visual Disambiguation and Visual Memory
Authors: Hegdé Jay , Kersten Daniel
Published: November 2010

Sensory information in the retinal image is typically too ambiguous to support visual object recognition by itself. Theories of visual disambiguation posit that to disambiguate, and thus interpret, the incoming images, the visual system must integrate the sensory information with previous knowledge of the visual world. However, the underlying neural mechanisms remain unclear. Using functional magnetic resonance imaging (fMRI) of human subjects, we have found evidence for functional specialization for storing disambiguating information in memory versus interpreting incoming ambiguous images. Subjects viewed two-tone, “Mooney” images, which are typically ambiguous when seen for the first time but are quickly disambiguated after viewing the corresponding unambiguous color images. Activity in one set of regions, including a region in the medial parietal cortex previously reported to play a key role in Mooney image disambiguation, closely reflected memory for previously seen color images but not the subsequent disambiguation of Mooney images. A second set of regions, including the superior temporal sulcus, showed the opposite pattern, in that their responses closely reflected the subjects' percepts of the disambiguated Mooney images on a stimulus-to-stimulus basis but not the memory of the corresponding color images. Functional connectivity between the two sets of regions was stronger during those trials in which the disambiguated percept was stronger. This functional interaction between brain regions that specialize in storing disambiguating information in memory versus interpreting incoming ambiguous images may represent a general mechanism by which previous knowledge disambiguates visual sensory information.
Cognition Enhancement Strategies: Figure 1.
Authors: Bibb James A. , Mayford Mark R. , Tsien Joe Z. , Alberini Cristina M.
Published: November 2010

Many mental disorders and neurodegenerative and neurodevelopmental diseases involve cognitive deficits. Remarkable advances and new technologies are providing a clearer picture of the molecular basis of cognition. In conjunction with an SFN2010 symposium, we provided here a brief overview of the molecular mechanisms of cognition, with emphasis on the development of treatments for cognitive disorders. Activity-dependent changes in gene expression and protein synthesis integrate with synapse selection to form memory circuits. A neuronal activity-dependent molecular tagging system that uses the gene expression program to record memory circuit formation represents one new tool to study cognition. Regulation of protein translation, protein degradation, cytoskeletal dynamics, extracellular matrix interactions, second messenger signaling, and neurotransmitter receptor trafficking and function are all components of synaptic remodeling essential for cognition. Selective targeting of specific effectors in these processes, such as NMDA receptors, may serve as an effective strategy to treat cognitive deficits.
Perceptual Learning Increases the Strength of the Earliest Signals in Visual Cortex
Authors: Bao Min , Yang Lin , Rios Cristina , He Bin , Engel Stephen A.
Published: November 2010

Training improves performance on most visual tasks. Such perceptual learning can modify how information is read out from, and represented in, later visual areas, but effects on early visual cortex are controversial. In particular, it remains unknown whether learning can reshape neural response properties in early visual areas independent from feedback arising in later cortical areas. Here, we tested whether learning can modify feedforward signals in early visual cortex as measured by the human electroencephalogram. Fourteen subjects were trained for >24 d to detect a diagonal grating pattern in one quadrant of the visual field. Training improved performance, reducing the contrast needed for reliable detection, and also reliably increased the amplitude of the earliest component of the visual evoked potential, the C1. Control orientations and locations showed smaller effects of training. Because the C1 arises rapidly and has a source in early visual cortex, our results suggest that learning can increase early visual area response through local receptive field changes without feedback from later areas.