bluuebunny/crossref_metadata_2025 huggingface dataset:
The identification of novel targets of miR-16 and characterization of their biological functions in cancer cells
Authors: Yan Xin , Liang Hongwei , Deng Ting , Zhu Kegan , Zhang Suyang , Wang Nan , Jiang Xueyuan , Wang Xueliang , Liu Rui , Zen Ke , Zhang Chen-Yu , Ba Yi , Chen Xi
Published: August 2013

Background

In eukaryotes, miR-16 is an important microRNA (miRNA) that is involved in numerous biological processes. However, it is not fully understood how miR-16 executes its physiological functions. In the present study, we aimed to identify novel miR-16 targets and study their biological functions.

Methods

Candidate target genes of miR-16 were screened by microarray analysis of mRNA levels in several cancer cell lines with enhanced miR-16. Three bioinformatics algorithms, including TargetScan, PicTar, and miRanda, were used in combination to calculate the miR-16 targets. The expression levels of miR-16 and target mRNA were examined by relative quantification RT-PCR, and the expression levels of target protein were detected by Western blot. Luciferase reporter plasmids were constructed to confirm direct targeting. The effect of miR-16 and target gene on cell viability was evaluated using MTT assays. The effects of miR-16 and target gene on apoptosis and cell cycle distribution were evaluated by flow cytometry analysis.

Results

By overexpressing miR-16 in several cancer cell lines and measuring global mRNA levels using microarray analysis, we identified 27 genes that may be regulated by miR-16. After the bioinformatics filtering process, 18 genes were selected as candidate miR-16 targets. Furthermore, we experimentally validated three of these candidates, MAP7 (microtubule-associated protein 7), PRDM4 (PR domain containing 4) and CDS2 (CDP-diacylglycerol synthase 2), as direct targets of miR-16. Finally, we demonstrated that miR-16 targeting MAP7 played a critical role in regulating proliferation but not apoptosis and cell cycle progression in cancer cells.

Conclusion

In summary, the present study identifies several novel miR-16 targets and illustrates a novel function of miR-16 targeting MAP7 in modulating proliferation in cancer cells.
Utilization of TREC and KREC quantification for the monitoring of early T- and B-cell neogenesis in adult patients after allogeneic hematopoietic stem cell transplantation
Authors: Mensen Angela , Ochs Christoph , Stroux Andrea , Wittenbecher Friedrich , Szyska Martin , Imberti Luisa , Fillatreau Simon , Uharek Lutz , Arnold Renate , Dörken Bernd , Thiel Andreas , Scheibenbogen Carmen , Na Il-Kang
Published: August 2013

Background

After hematopoietic stem cell transplantation (HSCT) T- and B-cell reconstitution from primary lymphoid organs are a prerequisite for an effective early lymphocyte reconstitution and a long-term survival for adult patients suffering from acute leukemia. Here, we asked whether quantification of T cell receptor excision circle, (TREC) and kappa-deleting recombination excision circle (KREC) before and within six month after allogeneic HSCT could be used to measure the thymic and bone marrow outputs in such patients.

Methods

We used a duplex real time PCR assay to quantify the absolute copy counts of TREC and KREC, and correlated the data with absolute cell counts of CD3+CD4+T-cell and CD19+B-cell subsets determined by flow cytometry, respectively.

Results

By comparing two recently proposed naïve T cell subsets, CD31+naive and CD31-naive T cells, we found a better correlation for the CD31+subset with TREC level post alloHSCT, in line with the assumption that it contained T cells recently derived from the thymus, indicating that TREC levels reflected real thymicde novoproduction. Transitional as well as naïve B cells highly correlated with KREC levels, which suggested an association of KREC levels with ongoing bone marrow B cell output. CD45RO+memory T cells and CD27+memory B cells were significantly less correlated with TREC and KREC recovery, respectively.

Conclusion

We conclude that simultaneous TREC/ KREC quantification is as a suitable and practicable method to monitor thymic and bone marrow output post alloHSCT in adult patients diagnosed with acute leukemia.
Flotillin-2 is associated with breast cancer progression and poor survival outcomes
Authors: Wang Xi , Yang Qi , Guo Ling , Li Xing-Hua , Zhao Xiao-Hui , Song Li-Bing , Lin Huan-Xin
Published: August 2013

Background

Flotillin-2 (FLOT2) has been implicated in several signaling pathways in tumor cells. Our study aimed to investigate the expression pattern and clinicopathological significance of FLOT2 in patients with breast cancer.

Methods

The expression level of FLOT2 in normal breast epithelial cells, breast cancer cell lines, and four breast cancer biopsies paired with adjacent noncancerous tissues were quantified using real-time RT-PCR and Western blotting. FLOT2 protein expression was analyzed in 171 archived paraffin-embedded breast cancer samples using immunohistochemistry (IHC). Statistical analyses were performed to evaluate the clinicopathological significance of FLOT2 expression.

Results

FLOT2 was significantly upregulated in breast cancer cell lines and tissue samples compared with normal cells and adjacent noncancerous breast tissues, respectively. IHC analysis revealed high expression levels of FLOT2 in 82 of 171 (48.0%) breast cancer specimens. Statistical analysis revealed that FLOT2 expression was significantly correlated with clinical stage (P < 0.001), T classification (P < 0.001), M classification (P < 0.001), histological differentiation (P = 0.005) and ErbB2 expression (P = 0.003). Patients with higher levels of FLOT2 expression had a shorter overall survival duration than patients with lower FLOT2 expression levels. Multivariate analysis suggested that FLOT2 expression was an independent prognostic marker for survival in patients with breast cancer.

Conclusions

The current results demonstrated that high FLOT2 protein expression was associated with poor outcomes in patients with breast cancer. FLOT2 could be used as a prognostic biomarker for breast cancer progression.
Joint-specific changes in locomotor complexity in the absence of muscle atrophy following incomplete spinal cord injury
Authors: Hillen Brian K , Yamaguchi Gary T , Abbas James J , Jung Ranu
Published: August 2013

Background

Following incomplete spinal cord injury (iSCI), descending drive is impaired, possibly leading to a decrease in the complexity of gait. To test the hypothesis that iSCI impairs gait coordination and decreases locomotor complexity, we collected 3D joint angle kinematics and muscle parameters of rats with a sham or an incomplete spinal cord injury.

Methods

12 adult, female, Long-Evans rats, 6 sham and 6 mild-moderate T8 iSCI, were tested 4 weeks following injury. The Basso Beattie Bresnahan locomotor score was used to verify injury severity. Animals had reflective markers placed on the bony prominences of their limb joints and were filmed in 3D while walking on a treadmill. Joint angles and segment motion were analyzed quantitatively, and complexity of joint angle trajectory and overall gait were calculated using permutation entropy and principal component analysis, respectively. Following treadmill testing, the animals were euthanized and hindlimb muscles removed. Excised muscles were tested for mass, density, fiber length, pennation angle, and relaxed sarcomere length.

Results

Muscle parameters were similar between groups with no evidence of muscle atrophy. The animals showed overextension of the ankle, which was compensated for by a decreased range of motion at the knee. Left-right coordination was altered, leading to left and right knee movements that are entirely out of phase, with one joint moving while the other is stationary. Movement patterns remained symmetric. Permutation entropy measures indicated changes in complexity on a joint specific basis, with the largest changes at the ankle. No significant difference was seen using principal component analysis. Rats were able to achieve stable weight bearing locomotion at reasonable speeds on the treadmill despite these deficiencies.

Conclusions

Decrease in supraspinal control following iSCI causes a loss of complexity of ankle kinematics. This loss can be entirely due to loss of supraspinal control in the absence of muscle atrophy and may be quantified using permutation entropy. Joint-specific differences in kinematic complexity may be attributed to different sources of motor control. This work indicates the importance of the ankle for rehabilitation interventions following spinal cord injury.
SETX mutations are a frequent genetic cause of juvenile and adult onset cerebellar ataxia with neuropathy and elevated serum alpha-fetoprotein
Authors: Nanetti Lorenzo , Cavalieri Simona , Pensato Viviana , Erbetta Alessandra , Pareyson Davide , Panzeri Marta , Zorzi Giovanna , Antozzi Carlo , Moroni Isabella , Gellera Cinzia , Brusco Alfredo , Mariotti Caterina
Published: August 2013

Objectives/background

Ataxia with oculomotor apraxia defines a group of genetically distinct recessive ataxias including ataxia-telangectasia (A-T,ATMgene), ataxia with oculomotor apraxia type 1 (AOA1,APTXgene) and type 2 (AOA2,SETXgene). Although, a few unique clinical features differentiate each of these forms, the patients also share common clinical signs, such as the presence of cerebellar atrophy, sensorimotor axonal neuropathy, and elevated alpha-fetoprotein (AFP) serum level.

Materials and methods

We selected 22 Italian patients from 21 families, presenting progressive cerebellar ataxia, axonal neuropathy, and elevated serum AFP. We screened the coding regions ofATM,APTXandSETXgenes for point mutations by direct sequencing or DHPLC, and searched genomic rearrangements inSETXby MLPA analysis. In selected cases, quantification of ATM and senataxin proteins was performed by Western blot. Clinical, neurophysiological, and neuroimaging data were collected.

Results

Thirteen patients (12 families) carriedSETXmutations (AOA2, 57%), two were mutated inATM(A-T), and three inAPTX(AOA1). In three remaining patients, we could not find pathogenic mutations, and in one case we found, in homozygosis, theSETXp.K992R polymorphism (population frequency 1-2%). In AOA2 cases, we identified 14 novel and three reportedSETXmutations. Signs at onset were gait ataxia and facial dyskinesia, and the age ranged between 11 and 18 years. None had obvious oculomotor apraxia at the latest examination (age 14–45 years). The patient carrying the p.K992RSETXpolymorphism had a phenotype similar to that of the diagnosed AOA2 patients, while the other three undiagnosed subjects had a very late onset and a few distinguishing clinical features.

Discussion and conclusions

We describe a large series of 13 AOA2 Italian patients. The phenotype was consistent with previous descriptions of AOA2, except for a higher frequency of strabism, and for the absence of oculomotor apraxia. In our survey ~60% of juvenile-to-adult cases with cerebellar ataxia, sensorimotor neuropathy and increased AFP are due to mutations in theSETXgene, and a smaller percentage toAPTXandATMgene mutations.
Successful pregnancy in each half uterus cavity of the septate uterus after transferring three embryos in one half-cavity: a case report
Authors: Guo Xiaoqiao , Sun Xiaofang , Xu Haiyan , Si Shasha , Yu Bolan , Liu Jianqiao
Published: August 2013

The incidence of Müllerian duct anomalies in women is rare, associating with urinary tract anomalies such as horseshoe or pelvic kidney, renal agenesis, duplication of the collecting system, or ectopic uterus. Septate uterus is one type of congenital uterine anomalies, in which there is a septum from the fundus to the cervix. Currently, it is believed that hysteroscopic metroplasty is a leading choice for patients if their recurrent spontaneous abortion is resulted from septate uterus. But, some people refuse to have a surgery, and successfully delivery. In this case report, we report a successful pregnancy with two gestational sacs, one in each half-cavity, in a woman with septate uterus after transfer of three embryos into one half–cavity. Finally, the women gave birth to two healthy babies in our hospital.
Compassion fatigue, burnout and compassion satisfaction among family physicians in the Negev area - a cross-sectional study
Authors: El-bar Nurit , Levy Amalia , Wald Hedy S , Biderman Aya
Published: August 2013

Background

Compassion fatigue among health care professionals has gained interest over the past decade. Compassion fatigue, as well as burnout, has been associated with depersonalization and suboptimal patient care. Professional caregivers in general are exposed to the risk of compassion fatigue (CF), burnout (BO) and low levels of compassion satisfaction (CS). While CF has been studied in health care professionals, few publications address its incidence among family physicians, specifically. The objectives of this study were to assess the prevalence and severity of CF among family practitioners (FPs) in the Negev (Israel’s southern region), evaluating the correlations between CF, BO and CS and their relations with socio-demographic variables and work related characteristics.

Methods

Self-report anonymous Compassion Satisfaction and Fatigue Test questionnaires (CSFT) measuring CF, BO, and CS were distributed among 194 family physicians at Clalit Health Services clinics in the Negev between July 2007 and April 2008. Correlations between CF, BO and CS were assessed. Multivariable logistic regression models with backward elimination were constructed.

Results

128 (66%) physicians responded. 46.1% of respondents scored extremely high and high for CF, 21.1% scored low for CS and 9.4% scored high for BO. Strong correlations were found between BO and CF (r = 0.769, p < 0.001), and between BO and CS (r = −0.241, p = 0.006), but no correlation was found between CS and CF. The logistic regression model showed that the only factor associated with a significantly increased risk for CF was former immigration to Israel. Increased risk for BO was associated with female gender, history of personal trauma and lack of academic affiliation. Higher CS was associated with holding management positions and teaching residents.

Conclusions and policy recommendations

Family physicians in the Negev are at high risk for CF, with the potential for CF- associated patient dissatisfaction, compromised patient safety and increased medical error. We propose creation of a CF educational and early intervention treatment program for family physicians and other health care professionals. Such programs would train facilitators of physician well-being and resiliency building. We also recommend analyzing contributing variables and organizational factors related to higher CF. Policy recommendations include integrating such programs within required risk management continuing medical education.
mPUMA: a computational approach to microbiota analysis by de novo assembly of operational taxonomic units based on protein-coding barcode sequences
Authors: Links Matthew G , Chaban Bonnie , Hemmingsen Sean M , Muirhead Kevin , Hill Janet E
Published: August 2013

Background

Formation of operational taxonomic units (OTU) is a common approach to data aggregation in microbial ecology studies based on amplification and sequencing of individual gene targets. The de novo assembly of OTU sequences has been recently demonstrated as an alternative to widely used clustering methods, providing robust information from experimental data alone, without any reliance on an external reference database.

Results

Here we introduce mPUMA (microbial Profiling Using Metagenomic Assembly, http://mpuma.sourceforge.net), a software package for identification and analysis of protein-coding barcode sequence data. It was developed originally for Cpn 60 universal target sequences (also known as Gro EL or Hsp 60). Using an unattended process that is independent of external reference sequences, mPUMA forms OTUs by DNA sequence assembly and is capable of tracking OTU abundance. mPUMA processes microbial profiles both in terms of the direct DNA sequence as well as in the translated amino acid sequence for protein coding barcodes. By forming OTUs and calculating abundance through an assembly approach, mPUMA is capable of generating inputs for several popular microbiota analysis tools. Using SFF data from sequencing of a synthetic community of Cpn 60 sequences derived from the human vaginal microbiome, we demonstrate that mPUMA can faithfully reconstruct all expected OTU sequences and produce compositional profiles consistent with actual community structure.

Conclusions

mPUMA enables analysis of microbial communities while empowering the discovery of novel organisms through OTU assembly.
Novel xylanases from Simplicillium obclavatum MTCC 9604: comparative analysis of production, purification and characterization of enzyme from submerged and solid state fermentation
Authors: Roy Saugata , Dutta Tanmay , Sarkar Tuhin Subhra , Ghosh Sanjay
Published: August 2013

The production of extracellular xylanase by a newly isolated fungus Simplicillium obclavatum MTCC 9604 was studied in solid-state and submerged fermentation. Multiple xylanases and endoglucanases were produced by the strain during growth on wheat bran in solid state fermentation (SSF). A single xylanase isoform was found to be produced by the same fungus under submerged fermentation (SF) using wheat bran as sole carbon source. Enzyme activity, stability and the protein yield were much higher in SSF than SF. The two dimensional zymogram of the crude enzyme indicated the presence of six isoforms with different pI values starting from pH 3–10. The optimum temperature and pH for the partially purified xylanase activity were 50°C and pH 5.0 respectively; xylanase enzymes exhibited remarkable stability over a broad pH range and the temperature range of 30-60°C which has great potential to be used in biofuels, animal feed and food industry applications.
Oxygen doping of HTSC and resistive switching in HTSC-based heterostructures
Authors: Tulina Natalia A , Borisenko Ivan Yu , Ivanov Andrey A , Ionov Andrey M , Shmytko Ivan M
Published: August 2013

The studies of the bipolar resistive switching effect in thin film heterojunctions (YBa2Cu3O7−δ
/Ag) and (Nd 2−x
Ce
x
CuO4−y
/Ag) have exhibited the role of oxygen as a doping element in hole- and electron-doped HTSC compounds.
Agent-based modeling and simulation of emergent behavior in air transportation
Authors: Bouarfa Soufiane , Blom Henk AP , Curran Richard , Everdij Mariken HC
Published: August 2013

Purpose

Commercial aviation is feasible thanks to the complex socio-technical air transportation system, which involves interactions between human operators, technical systems, and procedures. In view of the expected growth in commercial aviation, significant changes in this socio-technical system are in development both in the USA and Europe. Such a complex socio-technical system may generate various types of emergent behavior, which may range from simple emergence, through weak emergence, up to strong emergence. The purpose of this paper is to demonstrate that agent-based modeling and simulation allows identifying changed and novel rare emergent behavior in this complex socio-technical system.

Methods

An agent based model of a specific operation at an airport has been developed. The specific operation considered is the controlled crossing by a taxiing aircraft of a runway that is in use for controlled departures. The agent-based model includes all relevant human and technical agents, such as the aircraft, the pilots, the controllers and the decision support systems involved. This agent-based model is used to conduct rare event Monte Carlo (MC) simulations.

Results

The MC simulation results obtained confirm that agent based modeling and simulation of a socio-technical air transportation system allows to identify rare emergent behavior that was not identified through earlier, non-agent-based simulations, including human-in-the-loop simulations of the same operation. A typical example of such emergent behavior is the finding that alerting systems do not really reduce the safety risk.

Conclusions

Agent based MC simulations of commercial aviation operations has been demonstrated as a viable way to be evaluated regarding rare emergent behaviour. This rare emergent behaviour could not have been found through the more traditional simulation approaches.
Degradation of neutrophil extracellular traps co-varies with disease activity in patients with systemic lupus erythematosus
Authors: Leffler Jonatan , Gullstrand Birgitta , Jönsen Andreas , Nilsson Jan-Åke , Martin Myriam , Blom Anna M , Bengtsson Anders A
Published: August 2013

Introduction

The ability to degrade neutrophil extracellular traps (NETs) is reduced in a subset of patients with systemic lupus erythematosus (SLE). NETs consist of chromatin covered with antimicrobial enzymes and are normally degraded by DNase-I, an enzyme which is known to have reduced activity in SLE. Decreased ability to degrade NETs is associated with disease activity. In the current study we investigated how the ability of serum from SLE patients to degrade NETs varies during the course of SLE as well as what impact this may have for the clinical phenotype of SLE.

Methods

Serum from 69 patients with SLE, included in a prospective study, was taken every 60 days for a median of 784 days. The ability of serum to degrade NETs was determined and associated with clinical parameters occurring before and at the time of sampling, as well as after sampling by using conditional logistic regression.

Results

As many as 41% of all patients in the study showed decreased ability to degrade NETs at least once, but with a median of 20% of all time points. Decreased degradation was associated with manifestations of glomerulonephritis as well as low complement levels and elevated levels of antibodies directed against histones and DNA. Furthermore, the odds ratio for the patient to develop alopecia and fever after an episode of decreased NETs degradation was increased by four to five times compared to normal.

Conclusions

Decreased degradation of NETs is associated with clinical manifestations in SLE and may contribute to disease pathogenesis. Potential therapeutics restoring the ability to degrade NETs could be beneficial for certain patients with SLE.
HIF-1α/GPER signaling mediates the expression of VEGF induced by hypoxia in breast cancer associated fibroblasts (CAFs)
Authors: De Francesco Ernestina Marianna , Lappano Rosamaria , Santolla Maria Francesca , Marsico Stefania , Caruso Arnaldo , Maggiolini Marcello
Published: August 2013

Introduction

Carcinoma-associated fibroblasts (CAFs) play a pivotal role in cancer progression by contributing to invasion, metastasis and angiogenesis. Solid tumors possess a unique microenvironment characterized by local hypoxia, which induces gene expression changes and biological features leading to poor outcomes. Hypoxia Inducible Factor 1 (HIF-1) is the main transcription factor that mediates the cell response to hypoxia through different mechanisms that include the regulation of genes strongly associated with cancer aggressiveness. Among the HIF-1 target genes, the G-protein estrogen receptor (GPER) exerts a stimulatory role in diverse types of cancer cells and in CAFs.

Methods

We evaluated the regulation and function of the key angiogenic mediator vascular endothelial growth factor (VEGF) in CAFs exposed to hypoxia. Gene expression studies, Western blotting analysis and immunofluorescence experiments were performed in CAFs and breast cancer cells in the presence of cobalt chloride (CoCl2) or cultured under low oxygen tension (2% O2), in order to analyze the involvement of the HIF-1α/GPER signaling in the biological responses to hypoxia. We also explored the role of the HIF-1α/GPER transduction pathway in functional assays like tube formation in human umbilical vein endothelial cells (HUVECs) and cell migration in CAFs.

Results

We first determined that hypoxia induces the expression of HIF-1α and GPER in CAFs, then we ascertained that the HIF-1α/GPER signaling is involved in the regulation of VEGF expression in breast cancer cells and in CAFs exposed to hypoxia. We also assessed by ChIP assay that HIF-1α and GPER are both recruited to the VEGF promoter sequence and required for VEGF promoter stimulation upon hypoxic condition. As a biological counterpart of these findings, conditioned medium from hypoxic CAFs promoted tube formation in HUVECs in a HIF-1α/GPER dependent manner. The functional cooperation between HIF-1α and GPER in CAFs was also evidenced in the hypoxia-induced cell migration, which involved a further target of the HIF-1α/GPER signaling like connective tissue growth factor (CTGF).

Conclusions

The present results provide novel insight into the role elicited by the HIF-1α/GPER transduction pathway in CAFs towards the hypoxia-dependent tumor angiogenesis. Our findings further extend the molecular mechanisms through which the tumor microenvironment may contribute to cancer progression.
Joe-Answers
Authors: Straus Nina Pelikan
Published: August 2013

This interview with Joseph Frank — best known as the author of a five-volume biography of Dostoevsky (published 1976 – 2002) and of Spatial Form in Modern Literature (1945) — was conducted in 2012 at Stanford and is published here, shortly after his death at age ninety-four, as a memorial to him. The conversation highlights Frank's representation of Dostoevsky as a critic and a satirist of the nihilist intelligentsia of nineteenth-century Russia — a portrayal that runs counter to the understanding and use of his writings and his characters by Marxists, Nietzscheans, Freudians, Surrealists, crisis theologians, and Existentialists. Frank tells the story of how his friendship in the 1950s with Ralph Ellison, author of Invisible Man, led to Frank's teaching himself Russian in order to read Notes from Underground and write an article on the novella that changed the face of Dostoevsky scholarship. The conversation also provides hints as to how — as director of the Christian Gauss Seminars at Princeton and as a contributor to debates about Spatial Form in Critical Inquiry — he negotiated the intellectual trends and distractions of Grand Theory, which came to dominate literary criticism in the 1970s and confirmed Frank in his counterfocus on the importance of historical context, not only in criticism but also in literary creation. Above all, the interview shows how a scholar can overcome institutional pressures and the temptations of careerism by shrugging them off and concentrating attention on scholarship alone.
Fuzziness and Perceptions of Language in the Middle Ages
Authors: Butterfield Ardis
Published: August 2013

This is the final part of a three-part essay on fuzziness in medieval literary language. Each part corresponds broadly to Clifford Geertz's trifold instances of blur as involving “face-to-face interaction” (“life as game”), “collective intensities” (“life as stage”), and “imaginative forms” (“life as text”). Part 3 considers what Geertz might mean by describing text as a “dangerously unfocused term,” through discussing how bilingualism is negotiated in poetry. Three areas of vagueness are explored: the linguistic boundaries in a bilingual poem, the definition of a poem in the trilingual culture of insular medieval writing, and the relationship between literary and ordinary language. Examples are taken from a fifteenth-century bilingual carol, an early fourteenth-century trilingual poem, a bilingual sermon, a passage of love-writing discovered in the midst of a fifteenth-century legal roll, and finally a pair of French poems about the death of the English commander, Thomas Montagu, fourth earl of Salisbury, at the English siege of Orléans in 1428, contrasted with some English translations of poems by Charles d'Orléans. The essay argues that blurriness in medieval bilingualism gives us a fresh way of approaching primary questions about poetry and the literary.
FGF signaling regulates Wnt ligand expression to control vulval cell lineage polarity in C. elegans
Authors: Minor Paul J. , He Ting-Fang , Sohn Chang Ho , Asthagiri Anand R. , Sternberg Paul W.
Published: August 2013

The interpretation of extracellular cues leading to the polarization of intracellular components and asymmetric cell divisions is a fundamental part of metazoan organogenesis. The Caenorhabditis elegans vulva, with its invariant cell lineage and interaction of multiple cell signaling pathways, provides an excellent model for the study of cell polarity within an organized epithelial tissue. Here, we show that the fibroblast growth factor (FGF) pathway acts in concert with the Frizzled homolog LIN-17 to influence the localization of SYS-1, a component of the Wnt/β-catenin asymmetry pathway, indirectly through the regulation of cwn-1. The source of the FGF ligand is the primary vulval precursor cell (VPC) P6.p, which controls the orientation of the neighboring secondary VPC P7.p by signaling through the sex myoblasts (SMs), activating the FGF pathway. The Wnt CWN-1 is expressed in the posterior body wall muscle of the worm as well as in the SMs, making it the only Wnt expressed on the posterior and anterior sides of P7.p at the time of the polarity decision. Both sources of cwn-1 act instructively to influence P7.p polarity in the direction of the highest Wnt signal. Using single molecule fluorescence in situ hybridization, we show that the FGF pathway regulates the expression of cwn-1 in the SMs. These results demonstrate an interaction between FGF and Wnt in C. elegans development and vulval cell lineage polarity, and highlight the promiscuous nature of Wnts and the importance of Wnt gradient directionality within C. elegans.
Dual role of delta-like 1 homolog (DLK1) in skeletal muscle development and adult muscle regeneration
Authors: Andersen Ditte Caroline , Laborda Jorge , Baladron Victoriano , Kassem Moustapha , Sheikh Søren Paludan , Jensen Charlotte Harken
Published: August 2013

Muscle development and regeneration is tightly orchestrated by a specific set of myogenic transcription factors. However, factors that regulate these essential myogenic inducers remain poorly described. Here, we show that delta-like 1 homolog (Dlk1), an imprinted gene best known for its ability to inhibit adipogenesis, is a crucial regulator of the myogenic program in skeletal muscle. Dlk1-/- mice were developmentally retarded in their muscle mass and function owing to inhibition of the myogenic program during embryogenesis. Surprisingly however, Dlk1 depletion improves in vitro and in vivo adult skeletal muscle regeneration by substantial enhancement of the myogenic program and muscle function, possibly by means of an increased number of available myogenic precursor cells. By contrast, Dlk1 fails to alter the adipogenic commitment of muscle-derived progenitors in vitro, as well as intramuscular fat deposition during in vivo regeneration. Collectively, our results suggest a novel and surprising dual biological function of DLK1 as an enhancer of muscle development, but as an inhibitor of adult muscle regeneration.
Differential roles for 3-OSTs in the regulation of cilia length and motility
Authors: Neugebauer Judith M. , Cadwallader Adam B. , Amack Jeffrey D. , Bisgrove Brent W. , Yost H. Joseph
Published: August 2013

As cells integrate molecular signals from their environment, cell surface receptors require modified proteoglycans for the robust activation of signaling pathways. Heparan sulfate proteoglycans (HSPGs) have long unbranched chains of repetitive disaccharide units that can be sulfated at specific positions by heparan sulfate O-sulfotransferase (OST) families. Here, we show that two members of the 3-OST family are required in distinct signaling pathways to control left-right (LR) patterning through control of Kupffer’s vesicle (KV) cilia length and motility. 3-OST-5 functions in the fibroblast growth factor pathway to control cilia length via the ciliogenic transcription factors FoxJ1a and Rfx2. By contrast, a second 3-OST family member, 3-OST-6, does not regulate cilia length, but regulates cilia motility via kinesin motor molecule (Kif3b) expression and cilia arm dynein assembly. Thus, two 3-OST family members cell-autonomously control LR patterning through distinct pathways that regulate KV fluid flow. We propose that individual 3-OST isozymes create distinct modified domains or ‘glycocodes’ on cell surface proteoglycans, which in turn regulate the response to diverse cell signaling pathways.
Foxp1 maintains hair follicle stem cell quiescence through regulation of Fgf18
Authors: Leishman Erin , Howard Jeffrey M. , Garcia Gloria E. , Miao Qi , Ku Amy T. , Dekker Joseph D. , Tucker Haley , Nguyen Hoang
Published: August 2013

Hair follicles cyclically degenerate and regenerate throughout adult life and require regular stem cell activation to drive the cycle. In the resting phase of the hair cycle, hair follicle stem cells are maintained in a quiescent state until they receive signals to proliferate. We found that the forkhead transcription factor Foxp1 is crucial for maintaining the quiescence of hair follicle stem cells. Loss of Foxp1 in skin epithelial cells leads to precocious stem cell activation, resulting in drastic shortening of the quiescent phase of the hair cycle. Conversely, overexpression of Foxp1 in keratinocytes prevents cell proliferation by promoting cell cycle arrest. Finally, through both gain- and loss-of-function studies, we identify fibroblast growth factor 18 (Fgf18) as the key downstream target of Foxp1. We show that exogenously supplied FGF18 can prevent the hair follicle stem cells of Foxp1 null mice from being prematurely activated. As Fgf18 controls the length of the quiescent phase and is a key downstream target of Foxp1, our data strongly suggest that Foxp1 regulates the quiescent stem cell state in the hair follicle stem cell niche by controlling Fgf18 expression.
Developmental stage-dependent transcriptional regulatory pathways control neuroblast lineage progression
Authors: Feng Guoxin , Yi Peishan , Yang Yihong , Chai Yongping , Tian Dong , Zhu Zhiwen , Liu Jianhong , Zhou Fanli , Cheng Ze , Wang Xiangming , Li Wei , Ou Guangshuo
Published: August 2013

Neuroblasts generate neurons with different functions by asymmetric cell division, cell cycle exit and differentiation. The underlying transcriptional regulatory pathways remain elusive. Here, we performed genetic screens in C. elegans and identified three evolutionarily conserved transcription factors (TFs) essential for Q neuroblast lineage progression. Through live cell imaging and genetic analysis, we showed that the storkhead TF HAM-1 regulates spindle positioning and myosin polarization during asymmetric cell division and that the PAR-1-like kinase PIG-1 is a transcriptional regulatory target of HAM-1. The TEAD TF EGL-44, in a physical association with the zinc-finger TF EGL-46, instructs cell cycle exit after the terminal division. Finally, the Sox domain TF EGL-13 is necessary and sufficient to establish the correct neuronal fate. Genetic analysis further demonstrated that HAM-1, EGL-44/EGL-46 and EGL-13 form three transcriptional regulatory pathways. We have thus identified TFs that function at distinct developmental stages to ensure appropriate neuroblast lineage progression and suggest that their vertebrate homologs might similarly regulate neural development.
Probing cellular processes by long-term live imaging – historic problems and current solutions
Authors: Coutu Daniel L. , Schroeder Timm
Published: August 2013

Living organisms, tissues, cells and molecules are highly dynamic. The importance of their continuous and long-term observation has been recognized for over a century but has been limited by technological hurdles. Improvements in imaging technologies, genetics, protein engineering and data analysis have more recently allowed us to answer long-standing questions in biology using quantitative continuous long-term imaging. This requires a multidisciplinary collaboration between scientists of various backgrounds: biologists asking relevant questions, imaging specialists and engineers developing hardware, and informaticians and mathematicians developing software for data acquisition, analysis and computational modeling. Despite recent improvements, there are still obstacles to be addressed before this technology can achieve its full potential. This Commentary aims at providing an overview of currently available technologies for quantitative continuous long-term single-cell imaging, their limitations and what is required to bring this field to the next level. We provide an historical perspective on the development of this technology and discuss key issues in time-lapse imaging: keeping cells alive, using labels, reporters and biosensors, and hardware and software requirements. We highlight crucial and often non-obvious problems for researchers venturing into the field and hope to inspire experts in the field and from related disciplines to contribute to future solutions.
Protein 4.1R binds to CLASP2 and regulates dynamics, organization and attachment of microtubules to the cell cortex
Authors: Ruiz-Saenz Ana , van Haren Jeffrey , Sayas Laura , Rangel Laura , Demmers Jeroen , Millán Jaime , Alonso Miguel A. , Galjart Niels , Correas Isabel
Published: August 2013

The microtubule (MT) cytoskeleton is essential for many cellular processes, including cell polarity and migration. Cortical platforms, formed by a subset of MT plus-end-tracking proteins, such as CLASP2, and non-MT binding proteins such as LL5β, attach distal ends of MTs to the cell cortex. However, the mechanisms involved in organizing these platforms have not yet been described in detail. Here we show that 4.1R, a FERM domain-containing protein, interacts and colocalizes with cortical CLASP2 and is required for the correct number and dynamics of CLASP2 in cortical platforms. Protein 4.1R also controls binding of CLASP2 to MTs at the cell edge by locally altering GSK3 activity. Furthermore, in 4.1R-knock down cells MT plus-ends were maintained for longer in the vicinity of cell edges, but instead of being tethered to the cell cortex, MTs continued to grow, bending at cell margins and losing their radial distribution. Our results suggest a novel role for the scaffolding protein 4.1R that, by locally controlling CLASP2 behavior, CLASP2 cortical platform turnover, and GSK3 activity, enables correct MT organization and dynamics essential for cell polarity.
Epidermal keratinocyte polarity and motility require Ca2+ influx through TRPV1
Authors: Graham David M. , Huang Ling , Robinson Kenneth R. , Messerli Mark A.
Published: August 2013

Ca2+ has long been known to play an important role in cellular polarity and guidance. We studied the role of Ca2+ signaling during random and directed cell migration to better understand whether Ca2+ directs cell motility from the leading edge and which ion channels are involved in this function using primary zebrafish keratinocytes. Rapid linescan and time lapse imaging of Ca2+i during migration and automated image alignment enabled us to characterize and map the spatiotemporal changes in Ca2+i. We show that asymmetric distributions of lamellipodial Ca2+ sparks are encoded in frequency, not amplitude, and correlate with cellular rotation during migration. Directed migration during galvanotaxis increases the frequency of Ca2+ sparks over the entire lamellipod; however, these events do not give rise to asymmetric Ca2+i signals that correlate with turning. We demonstrate that Ca2+ permeable channels within these cells are mechanically activated and include several transient receptor potential family members, including TRPV1. Lastly, we demonstrate that cell motility and Ca2+i activity are affected by TRPV1 pharmacological agents, indicating a novel role for this channel during cell migration.
Effect of Dopants Pr and La on the Catalytic Activity of Cerium Oxide for Soot Oxidation
Authors: Harada Koichiro , Oishi Tetsuya , Hamamoto Seiji , Ishihara Tatsumi
Published: August 2013

Effects of rare earth or transition metal doping on the activity of CeO2 to particulate matter oxidation were investigated, and it was found that a Ce–Pr–La–O mixed oxide demonstrates the lowest ignition temperature of carbon, as low as 550 K. Oxygen-temperature-programmed desorption measurements suggested that the amount of O2 desorbed from CeO2 increases with the substitution of Pr, and furthermore, La doping reduces the desorption temperature of the lattice oxygen. Even in the absence of oxygen, carbon oxidation occurs on Ce–Pr–La–O, and the ignition temperature of carbon is almost the same as the desorption temperature of the lattice oxygen. Doping of La and Pr into CeO2 has a positive impact on carbon oxidation because of this decreased desorption temperature of the lattice oxygen.
Reusable Cobalt(III) Complex Catalysts for Enantioselective Borohydride Reduction of Ketones
Authors: Tsubo Tatsuyuki , Chen Hsiu-Hui , Yokomori Minako , Kikuchi Satoshi , Yamada Tohru
Published: August 2013

A reusable catalytic system was developed for the catalytic enantioselective borohydride reduction of ketones. The optically active 1-chlorovinylketoiminatocobalt(III) complexes were recovered after the reaction by silica gel column chromatography, and then efficiently catalyzed the enantioselective reduction several times without any loss of reactivity as well as enantioselectivity.
Supramolecular Helical Columnar Structures Formed by Hydrogen-Bonded Disk-Like (Phenylethynyl)benzene Derivatives with l-Alanine Pendant Groups: Helix Stability and Supramolecular Helical Sense Inversion
Authors: Sakajiri Koichi , Hirama Takahiro , Yasuda Keiichi , Kutsumizu Shoichi , Watanabe Junji
Published: August 2013

To investigate the influence of the number of substituents on supramolecular assemblies of hydrogen-bonded disk-like (phenylethynyl)benzene derivatives with chiral l-alanine dodecyl groups, a tris(phenylethynyl)benzene derivative 3 and a tetrakis(phenylethynyl)benzene derivative 4 were synthesized. The behavior of these supramolecular assemblies was compared with that of the previously reported hexakis(phenylethynyl)benzene derivative 6. It is clearly shown that the stability of the supramolecular helical columnar structure is enhanced by increasing the number of substituents, namely the number of amide groups contributing to the hydrogen bonding. In addition, along with 6, 4 also exhibits a solvent-induced supramolecular helical sense inversion. Furthermore, 4 exhibits a thermally reversible supramolecular helical sense inversion at a critical solvent composition.
Variação na infestação de mosca-das-frutas (Diptera: Tephritidae) e parasitismo em diferentes fases de frutificação em mirtaceas nativas no Rio Grande do Sul
Authors: Pereira Rêgo Diogo Ricardo Goulart , Jahnke Simone Mundstock , Redaelli Luiza Rodrigues , Schaffer Naihana
Published: August 2013

A mosca-das-frutas sul-americana Anastrepha fraterculus (Wiedemann) (Diptera: Tephritidae) é uma importante praga da fruticultura no Rio Grande do Sul. Assim como outras espécies tropicais, apresenta sucessão de hospedeiros nativos e exóticos, de acordo com a época de frutificação. O objetivo deste trabalho foi comparar índices de infestação, intensidade de infestação da mosca-das-frutas e o parasitismo em diferentes fases de frutificação de quatro mirtáceas nativas.  Os frutos coletados foram armazenados em condições ambientais até a emergência das moscas ou dos parasitoides. Foram avaliadas a infestação, a intensidade de infestação e o parasitismo entre as espécies frutíferas, entre frutos coletados na copa e no solo e entre os estágios de maturação dos frutos da copa. O maior índice de infestação de mosca-das-frutas ocorreu na goiaba (89,5%) e o menor na goiaba–serrana (67%). A maior intensidade de infestação por fruto foi registrada na goiaba (17,33) e a menor no araçá-vermelho (1,62), a maior média de pupários por grama de fruto foi obtida na goiaba-serrana (0,50) e a menor, na goiaba (0,22). A goiaba-serrana apresentou o maior índice de parasitismo (21,40%) e o araçá-amarelo, o menor (2,81%). Existe maior ocorrência da mosca nas goiabas e goiabas-serranas revelando maior atratividade da praga por estes hospedeiros. A goiaba–serrana demonstrou ser um repositório para espécies de parasitoides nativos.

Variation on Infestation on Fruit Flies (Diptera: Tephritidae) and Parasitism in Native Myrtaceae in Rio Grande do Sul

Abstract. The fruit fly Anastrepha fraterculus (Wiedemann) (Diptera: Tephritidae) is an important pest of fruit production in Rio Grande do Sul. A. fraterculus presents native and exotic hosts, according to fruiting time. The objective of this study was compare infestation rate, the intensity of infestation of fruit fly and parasitism in four native Myrtaceae. The fruits were stored under ambient conditions until flies or parasitoids emergence. These evaluation were made in fruits collected from the canopy and soil, and between stages of ripening of the canopy. The largest infestation rate of fruit fly occurred in guava (89.5%) and the lowest in feijoa (67%). The intensity of infestation per fruit was highest in guava (17.33) and lowest in red strawberry guava (1.62).  The highest rate of puparia per gram of fruit was obtained in the feijoa (0.50) and the lowest in guava (0.22). The highest parasitism rate was in feijoa (21.40%) and the lowest in yellow strawberry guava (2.81%). A greater occurrence of this pest in guava and feijoa revealing highest attractiveness in these hosts. Feijoa is a repository for native parasitodes species.
Hybrid Algorithm for Route Design on Bus Rapid Transit Systems
Authors: Walteros Jose L. , Medaglia Andrés L. , Riaño Germán
Published: August 2013

In recent years, well-designed bus rapid transit (BRT) systems have become a real alternative to more expensive rail-based public transportation systems around the world. However, once the BRT system is operational, its success often depends on the routes offered to passengers. Thus, the bus rapid transit route design problem (BRTRDP) is the problem of finding a set of routes and frequencies that minimizes the operational and passenger costs (travel time) while simultaneously satisfying the system’s technical constraints, such as meeting the demands for trips, bus frequencies, and lane capacities. To address this problem, we propose a mathematical formulation of the BRTRDP as a mixed-integer program (MIP) with an underlying network structure. However, because of the vast number of routes, solving the MIP via branch and bound is out of reach for most practical instances. Hence, we propose a decomposition strategy that, given a certain set of routes, decouples the route selection decisions from the BRT system performance evaluation. The latter evaluation is done by solving a linear optimization problem using a column generation scheme. We embedded this decomposition strategy in a hybrid genetic algorithm (HGA) and tested it in 14 instances ranging from 5 to 40 stations with different BRT system topologies. The results show that in 8 of 14 problems, the HGA was able to obtain a solution that is provably optimal within 0.20%. Additionally, in 4 of 14 instances, HGA obtained the optimal solution.