Calumenin-15 facilitates filopodia formation by promoting TGF-β superfamily cytokine GDF-15 transcription

Filopodia, which are actin-rich finger-like membrane protrusions, have an important role in cell migration and tumor metastasis. Here we identify 13 novel calumenin (Calu) isoforms (Calu 3-15) produced by alternative splicing, and find that Calu-15 promotes filopodia formation and cell migration. Calu-15 shuttles between the nucleus and cytoplasm through interacting with importin α, Ran GTPase, and Crm1. The phosphorylation of the threonine at position 73 (Thr-73) by casein kinase 2 (CK2) is essential for the nuclear import of Calu-15, and either Thr-73 mutation or inhibition of CK2 interrupts its nuclear localization. In the nucleus, Calu-15 increases the transcription of growth differentiation factor-15 (GDF-15), a member of the transforming growth factor-β (TGF-β) superfamily, via binding to its promoter region. Furthermore, Calu-15 induces filopodia formation mediated by GDF-15. Together, we identify that Calu-15, a novel isoform of Calu with phosphorylation-dependent nuclear localization, has a critical role in promoting filopodia formation and cell migration by upregulating the GDF-15 transcription.

Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers

BACKGROUND

Driven by high throughput next generation sequencing technologies and the pressing need to decipher cancer genomes, computational approaches for detecting somatic single nucleotide variants (sSNVs) have undergone dramatic improvements during the past 2 years. The recently developed tools typically compare a tumor sample directly with a matched normal sample at each variant locus in order to increase the accuracy of sSNV calling. These programs also address the detection of sSNVs at low allele frequencies, allowing for the study of tumor heterogeneity, cancer subclones, and mutation evolution in cancer development.

METHODS

We used whole genome sequencing (Illumina Genome Analyzer IIx platform) of a melanoma sample and matched blood, whole exome sequencing (Illumina HiSeq 2000 platform) of 18 lung tumor-normal pairs and seven lung cancer cell lines to evaluate six tools for sSNV detection: EBCall, JointSNVMix, MuTect, SomaticSniper, Strelka, and VarScan 2, with a focus on MuTect and VarScan 2, two widely used publicly available software tools. Default/suggested parameters were used to run these tools. The missense sSNVs detected in these samples were validated through PCR and direct sequencing of genomic DNA from the samples. We also simulated 10 tumor-normal pairs to explore the ability of these programs to detect low allelic-frequency sSNVs.

RESULTS

Out of the 237 sSNVs successfully validated in our cancer samples, VarScan 2 and MuTect detected the most of any tools (that is, 204 and 192, respectively). MuTect identified 11 more low-coverage validated sSNVs than VarScan 2, but missed 11 more sSNVs with alternate alleles in normal samples than VarScan 2. When examining the false calls of each tool using 169 invalidated sSNVs, we observed >63% false calls detected in the lung cancer cell lines had alternate alleles in normal samples. Additionally, from our simulation data, VarScan 2 identified more sSNVs than other tools, while MuTect characterized most low allelic-fraction sSNVs.

CONCLUSIONS

Our study explored the typical false-positive and false-negative detections that arise from the use of sSNV-calling tools. Our results suggest that despite recent progress, these tools have significant room for improvement, especially in the discrimination of low coverage/allelic-frequency sSNVs and sSNVs with alternate alleles in normal samples.

Differential expression of L-FABP and L-BABP between fat and lean chickens

Liver fatty acid-binding protein (L-FABP) and liver bile acid-binding protein (L-BABP), in the liver intra-cytoplasm of chicken, are members of the fatty acid-binding protein subfamily. This study was designed to analyze and compare L-FABP and L-BABP expression levels between fat and lean lines in chicken liver tissue, and to determine the relationship between their expression and lipid metabolism. Real-time polymerase chain reaction (PCR) and Western blotting were used to detect the mRNA and protein expression in liver tissue between the lean and fat lines. Real-time PCR showed that L-FABP mRNA expression in fat male chickens was higher than that in lean male chickens at 2, 3, 4, 5, 6, and 10 weeks of age (P < 0.05), and L-BABP mRNA expression in fat male chickens was higher than that in lean male chickens at 1, 2, 3, 4, 8, and 10 weeks of age (P < 0.05). Western blotting showed that the L-FABP protein expression in fat male chickens was higher than that in lean male chickens at 3, 5, 6, and 7 weeks of age (P < 0.05), and L-BABP protein expression in fat male chickens was higher than that in lean male chickens at 3, 4, 5, and 6 weeks of age (P < 0.05). These results suggested that chicken L-FABP and L-BABP affect abdominal fat deposition through differences in their expression level, and the possible mechanism is that a high expression level of L-FABP and L-BABP leads to a high lipogenesis rate and, ultimately, to lipid deposition.

The central nervous system sites mediating the orexigenic actions of ghrelin

The peptide hormone ghrelin is important for both homeostatic and hedonic eating behaviors, and its orexigenic actions occur mainly via binding to the only known ghrelin receptor, the growth hormone secretagogue receptor (GHSR). GHSRs are located in several distinct regions of the central nervous system. This review discusses those central nervous system sites that have been found to play critical roles in the orexigenic actions of ghrelin, including hypothalamic nuclei, the hippocampus, the amygdala, the caudal brain stem, and midbrain dopaminergic neurons. Hopefully, this review can be used as a stepping stone for the reader wanting to gain a clearer understanding of the central nervous system sites of direct ghrelin action on feeding behavior, and as inspiration for future studies to provide an even-more-detailed map of the neurocircuitry controlling eating and body weight.

Fronto-parietal white matter microstructural deficits are linked to performance IQ in a first-episode schizophrenia Han Chinese sample

BACKGROUND

Evidence shows that cognitive deficits and white matter (WM) dysconnectivity can independently be associated with clinical manifestations in schizophrenia. It is important to explore this triadic relationship in order to investigate whether the triplet could serve as potential extended endophenotypes of schizophrenia.

METHOD

Diffusion tensor images and clinical performances were evaluated in 122 individuals with first-episode schizophrenia and 122 age- and gender-matched controls. In addition, 65 of 122 of the patient group and 40 of 122 controls were measured using intelligence quotient (IQ) testing.

RESULTS

The schizophrenia group showed lower fractional anisotropy (FA) values than controls in the right cerebral frontal lobar sub-gyral (RFSG) WM. The schizophrenia group also showed a significant positive correlation between FA in the RFSG and performance IQ (PIQ) ; in turn, their PIQ score showed a significant negative correlation with negative syndromes.

CONCLUSIONS

Overall, these findings support the hypothesis that WM deficits may be a core deficit that contributes to cognitive deficits as well as to negative symptoms.

Occurrence of Grapevine Leafroll-Associated Viruses in China

To characterize the prevalence of viruses associated with grapevine leafroll disease in China, 249 grapevine (Vitis spp.) samples (86 popular cultivars and a rootstock) from 19 provinces and regions were collected and tested for Grapevine leafroll-associated virus 1 (GLRaV-1), GLRaV-2, GLRaV-3, GLRaV-4, and GLRaV-4 strain 5 by SYBR Green real-time reverse-transcription polymerase chain reaction (RT-PCR), and RT-PCR and sequencing. GLRaV-3 was found in 100% of the samples while GLRaV-1, GLRaV-2, and GLRaV-4 were detected in 24.9% (62/249), 15.3% (38/249), and 0.80% (2/249) of the samples, respectively. Single infections with GLRaV-3 were found in 66.3% (165/249) of the samples, and the remaining samples were mixed infections of GLRaV-3 with one or two other GLRaVs, those with GLRaV-1 being the most common (18.5%, 46/249). The genetic variability of Chinese GLRaV-3 isolates was characterized based on the coat protein (CP) gene. In total, 153 full-length CP gene sequences (94 sequences newly generated) of Chinese GLRaV-3 isolates from different grapevine-growing regions showed 89.3 to 100.0% and 92.7 to 100.0% identity at the nucleotide and amino acid levels, respectively. The average nucleotide diversity for the population of Chinese GLRaV-3 isolates was estimated at 0.037 (standard error = 0.0032). GLRaV-3 isolates from China segregated into five distinct phylogenetic groups and two novel recombination events were found in the viral population. This is the first and most extensive report of the prevalent species of GLRaV in China, which also provides an assessment of genetic variability of GLRaV-3 Chinese isolates.

A risk score for predicting post-traumatic stress disorder in adults in a Chinese earthquake area

OBJECTIVES

This study aimed to identify risk factors for post-traumatic stress disorder (PTSD) and develop a risk score model for predicting PTSD in adults in a Chinese earthquake area.

METHODS

Questionnaires covering demographic information, earthquake experience and social support were administered to subjects experiencing a major earthquake. The PTSD Checklist-Civilian Version questionnaire was used for PTSD diagnosis. Subjects were randomly assigned to training (70%) or validation (30%) subsets. A risk score model for predicting PTSD risk was established, based on logistic regression of PTSD risk factors that were significant on univariate analysis of the training data.

RESULTS

In total, 9556 subjects completed questionnaires; PTSD prevalence was 4.5%. Divorced or widowed status, various adverse earthquake events and low levels of social support were identified as risk factors for PTSD. When tested in the validation dataset, the risk score model had good discriminative power and a good fit between predicted and observed values.

CONCLUSIONS

The risk score shows an acceptable predictive value and may be useful for early prediction of PTSD, in Chinese earthquake areas.

Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives

Copy number variation (CNV) is a prevalent form of critical genetic variation that leads to an abnormal number of copies of large genomic regions in a cell. Microarray-based comparative genome hybridization (arrayCGH) or genotyping arrays have been standard technologies to detect large regions subject to copy number changes in genomes until most recently high-resolution sequence data can be analyzed by next-generation sequencing (NGS). During the last several years, NGS-based analysis has been widely applied to identify CNVs in both healthy and diseased individuals. Correspondingly, the strong demand for NGS-based CNV analyses has fuelled development of numerous computational methods and tools for CNV detection. In this article, we review the recent advances in computational methods pertaining to CNV detection using whole genome and whole exome sequencing data. Additionally, we discuss their strengths and weaknesses and suggest directions for future development.

Histone demethylase retinoblastoma binding protein 2 regulates the expression of α-smooth muscle actin and vimentin in cirrhotic livers

Liver cirrhosis is one of the most common diseases of Chinese patients. Herein, we report the high expression of a newly identified histone 3 lysine 4 demethylase, retinoblastoma binding protein 2 (RBP2), and its role in liver cirrhosis in humans. The siRNA knockdown of RBP2 expression in hepatic stellate cells (HSCs) reduced levels of α-smooth muscle actin (α-SMA) and vimentin and decreased the proliferation of HSCs; and overexpression of RBP2 increased α-SMA and vimentin levels. Treatment with transforming growth factor β (TGF-β) upregulated the expression of RBP2, α-SMA, and vimentin, and the siRNA knockdown of RBP2 expression attenuated TGF-β-mediated upregulation of α-SMA and vimentin expression and HSC proliferation. Furthermore, RBP2 was highly expressed in cirrhotic rat livers. Therefore, RBP2 may participate in the pathogenesis of liver cirrhosis by regulating the expression of α-SMA and vimentin. RBP2 may be a useful marker for the diagnosis and treatment of liver cirrhosis.

Enhancement of long-term depression by soluble amyloid β protein in rat hippocampus is mediated by metabotropic glutamate receptor and involves activation of p38MAPK, STEP and caspase-3

It is reported that the amyloid-β protein (Aβ)-induced impairments in synaptic plasticity coincide with memory decline and dementia. Although Aβ-induced inhibition of hippocampal long-term potentiation has been intensively investigated, the underlying mechanism of Aβ-enhanced long-term depression (LTD) is not clear. Here, we report that acute exposure of rat hippocampal slices to soluble Aβ-enhanced LTD induced by weak low-frequency stimulation (wLFS; 1Hz for 3 min, 180 pulses) in granule cells of the dentate gyrus. Application of LY341495 (a non-selective Group I/II metrabotropic glumate receptor (mGluR) antagonist) completely blocked Aβ-enhanced LTD, whereas D-AP5 (a not selective N-methyl-d-aspartate receptor (NMDAR) antagonist) had no effect on Aβ-enhanced LTD compared with controls. In addition, Aβ-enhanced LTD was occluded by pre-application of 3,5-dihydroxyphenylglycine, a Group1 mGluR (mGluR1/5) agonist, suggesting Aβ-enhanced LTD depends on mGluR1/5 but not NMDAR. We also report here that p38 mitogen-activated protein kinase (p38MAPK) inhibitor SB203580 and postsynaptic protein tyrosine phosphatase inhibitors phenylarsine oxide and sodium orthovanadate prevented the facilitatory effect of Aβ on LTD. Application of striatal-enriched protein tyrosine phosphatase (STEP) activator MG132 facilitated induction of LTD by wLFS, but did not block following Aβ-enhanced LTD induced by another wLFS. On the other hand, Aβ-enhanced LTD blocked following MG132-LTD by wLFS, suggesting Aβ-enhanced hippocampal LTD involves STEP activation. Application of either non-selective caspase inhibitor Z-VAD-FMK or caspase-3 selective inhibitor Z-DEVD-FMK prevented Aβ-enhanced LTD. However, neither the tumor necrosis factor-α converting enzyme inhibitor TAPI-2 nor the mammalian target of rapamycin inhibitor rapamycin prevented the enhancement of Aβ on LTD. Therefore, we conclude that soluble Aβ enhances LTD in the hippocampal dentate gyrus region, and the facilitatory effect of Aβ on LTD involves mGluR1/5, p38MAPK, STEP and caspase-3 activation.

Reversing endogenous alloreactive B cell GC responses with anti-CD154 or CTLA-4Ig

Alloantibodies mediate acute antibody-mediated rejection as well as chronic allograft rejection in clinical transplantation. To better understand the cellular dynamics driving antibody production, we focused on the activation and differentiation of alloreactive B cells in the draining lymph nodes and spleen following sensitization to allogeneic cells or hearts. We used a modified staining approach with a single MHC Class I tetramer (K(d)) bound to two different fluorochromes to discriminate between the Class I-binding and fluorochrome-streptavidin-binding B cells with a high degree of specificity and binding efficiency. By Day 7-8 postsensitization, there was a 1.5- to 3.2-fold increase in the total numbers of K(d) -binding B cells. Within this K(d) -binding B cell population, approximately half were IgD(low) , MHC Class II(high) and CD86(+), 30-45% expressed a germinal center (Fas(+) GL7(+)) phenotype and 3-12% were IRF4(hi) plasma cells. Remarkably, blockade with anti-CD40 or CTLA-4Ig, starting on Day 7 postimmunization for 1 or 4 weeks, completely dissolved established GCs and halted further development of the alloantibody response. Thus MHC Class I tetramers can specifically track the in vivo fate of endogenous, Class I-specific B cells and was used to demonstrate the ability of delayed treatment with anti-CD154 or CTLA-4Ig to halt established allo-B cell responses.

Pyruvate kinase M2 is highly correlated with the differentiation and the prognosis of esophageal squamous cell cancer

It's frequently stated that the pyruvate kinase M2 (PKM2) and Warburg effect are important for cancer development by accumulating more raw materials for macromolecule biosynthesis. However, the correlation between PKM2 and cancer is poorly reported. Here, we investigated the PKM2 expression in esophageal squamous cell cancer (ESCC). We observed that the expression of PKM2 was much higher in ESCC than in control normal tissue, and it is highly associated with many clinical features and prognosis. Specially, we found that the expression of PKM2 was closely related to the differentiation state of ESCC, and we further confirmed this discovery in vitro. As a result, out data indicated that PKM2 might be a useful indicator for determining the survival of patients with ESCC. Considering previous researches on the link among PKM2, Warburg effect, and differentiation, our study inferred the direct roles of PKM2 and Warburg effect in the differentiation of cancer cells rather than only providing synthetic intermediates for the promotion of cancer's progression.

Variation in the stress response between high- and low-neuroticism female undergraduates across the menstrual cycle

This study was undertaken to elucidate possible relationships between menstrual cycle stage, neuroticism and behavioral and physiological responses to a cognitive challenge. The study investigated the differences between high neuroticism and low neuroticism groups across the menstrual cycle (luteal, menstrual and ovulatory stages). The Stroop color-naming task was used as a stressor. During the task, the galvanic skin response (GSR), heart rate (HR) and HR variability (HRV) were simultaneously recorded by a polygraph. The results showed a significant difference in reaction times (RT) on the Stroop task between the high- and low-neuroticism groups during menstruation. However, there were no significant RT differences between groups during the luteal or ovulatory cycle stages. The GSR of the high-neuroticism group during menstruation was significantly lower than it was in the luteal and ovulatory stages. Moreover, during menstruation, the cardiovascular responses (high-frequency HRV (HF) and low-frequency HRV (LF)) and accuracy on the Stroop task were positively correlated, while the correlations between HF, LF and the RT were negative. The results demonstrate that during menstruation, there were consistent variations in female behavior and physiology when facing a cognitive stressor. Specifically, the high-neuroticism group was more sensitive to the stressor than the low neuroticism group, with decreased reaction time on the Stroop task, and increased GSR and HRV.

Ultrasonic morphology of uterus and ovaries in girls with pituitary hyperplasia secondary to primary hypothyroidism

We aimed to study uterine and ovarian morphology, hormonal levels, and pituitary height in prepubertal girls with pituitary hyperplasia secondary to primary hypothyroidism (PH) before and after thyroid hormone replacement therapy. We investigated 24 prepubertal girls with severe PH who were divided into 2 groups: secondary pituitary hyperplasia (group A, n=18), without pituitary hyperplasia (group B, n=6). Serum levels of free triiodothyronine (FT3), free thyroxine (FT4), thyrotropin (TSH), follicle stimulating hormone (FSH), luteinizing hormone (LH), estradiol (E2), testosterone (T) and prolactin (PRL), pituitary height, uterine volume (UV), ovarian volume (OV), follicular diameter (FD), and follicular number (FN) in group A were measured before and 3-month after levothyroxine therapy. Age-matched healthy prepubertal girls (control group, n=30) were also enrolled in the study. The levels of FT3 and FT4 were significantly lower and the values of TSH, FSH, E2, PRL, pituitary height, UV, OV, and FD were significantly higher in group A than in the control group (all p<0.05). In group B, FT4 levels were significantly lower and TSH levels were significantly higher than in the control group (both p<0.05); the values of FSH, E2, PRL, UV, OV, and FD tended to be higher than those in the control group; there were no statistically significant differences (all p>0.05). After 3-month of therapy, hormonal levels regressed and imaging abnormalities decreased. Our results indicate that PH patients with pituitary hyperplasia have enlarged uterus, ovaries and follicles, as well as high values of FSH, E2, PRL, and pituitary height, which are improved after levothyroxine therapy.

Highly efficient, spectrally pure 340 nm ultraviolet emission from AlxGa₁-xN nanowire based light emitting diodes

High crystal quality, vertically aligned AlxGa1-xN nanowire based double heterojunction light emitting diodes (LEDs) are grown on Si substrate by molecular beam epitaxy. Such AlxGa1-xN nanowires exhibit unique core-shell structures, which can significantly suppress surface nonradiative recombination. We successfully demonstrate highly efficient AlxGa1-xN nanowire array based LEDs operating at ∼340 nm. Such nanowire devices exhibit superior electrical and optical performance, including an internal quantum efficiency of ∼59% at room temperature, a relatively small series resistance, highly stable emission characteristics, and the absence of efficiency droop under pulsed biasing conditions.

Immune tolerance of skin allograft transplantation induced by immature dendritic cells of a third party carrying donor antigens in mice

BACKGROUND

Dendritic cells (DCs) are the most powerful antigen-presenting cells in the body. Immature DCs (imDCs) can induce transplantation tolerance. In this study, using a mouse model of skin transplantation. We explored the antigen uptake by imDCs, changes in phenotype and function after antigen loading, as well as survival of skin grafts.

METHODS

Mononuclear cells from C57BL/6 mice mixed with a tritiated leucine ([(3)H]Leu) antigen supernate were incubated with Kunming mice imDC and mature DCs. We recorded the expressions of surface molecules that were detected using flow cytometry, mixed lymphocyte reactions, mean survival times, and postoperative morphological changes in skin grafts.

RESULTS

After the addition of allogeneic antigen supernate, the counts per minute of imDCs were significantly higher than those of mature DCs. The expression rates of I(A)/I(E) and CD80 significantly increased on the cell surface of imDCs. The counts per minute of imDCs in mixed lymphocyte reactions in the presence of allogeneic antigens was significantly higher than those of controls. Comparing mean survival times with controls, skin grafts were significantly longer in the imDCs groups from donors or from a third party carrying donor antigens.

CONCLUSIONS

ImDCs display a strong antigen uptake, gradually maturing in terms of phenotype and function after loading. Complementary application of cytotoxic T-lymphocyte-associated antigen 4 immunoglobulin blocks the immune response of imDCs. Both imDCs from the third party carrying donor antigens and those from the donor strain can establish antigen-specific immune tolerance to allogeneic skin grafts.

Impact of liver fibrosis on prognosis following liver resection for hepatitis B-associated hepatocellular carcinoma

BACKGROUND

This study aims to evaluate the impact of liver fibrosis severity on prognosis following liver resection among HBV-HCC patients.

METHODS

Data were extracted from a prospective database of 189 HBV-HCC patients treated at Mount Sinai between 1995 and 2008. Fibrosis staging of each surgical resection specimen using the modified Ishak method was performed by a single liver pathologist.

RESULTS

A wide range of Ishak fibrosis stage was observed among this patient population, with 29% having established cirrhosis (Ishak stage 6). Ishak stage 6 was independently associated with poor overall and recurrence-free survival. In patients with Ishak stage 1-5, Ishak stage did not affect survival; rather, tumour size was associated with poor overall survival, and tumour size, histologic activity index and serum AFP>20 ng ml(-1) were associated with poor recurrence-free survival. In patients with Ishak stage 6, poorly differentiated histology and tumour size were associated with poor overall survival, and tumour size was associated with poor recurrence-free survival.

CONCLUSION

HBV-HCC develops with varying degrees of underlying liver fibrosis; however, progressive liver fibrosis does not affect the outcomes following resection until cirrhosis is reached. Established cirrhosis, as defined histologically by Ishak stage 6, is an independent predictor of poor overall and recurrence-free survival among these patients.

Measurement of J/ψ azimuthal anisotropy in Au+Au collisions at sqrt[s(NN)]=200 GeV

The measurement of J/ψ azimuthal anisotropy is presented as a function of transverse momentum for different centralities in Au+Au collisions at sqrt[s(NN)]=200 GeV. The measured J/ψ elliptic flow is consistent with zero within errors for transverse momentum between 2 and 10 GeV/c. Our measurement suggests that J/ψ particles with relatively large transverse momenta are not dominantly produced by coalescence from thermalized charm quarks, when comparing to model calculations.