Overexpression of β1 integrin contributes to polarity reversal and a poor prognosis of breast invasive micropapillary carcinoma

© Liu et al. Invasive micropapillary carcinoma (IMPC) of the breast is a highly aggressive breast cancer. Polarity reversal exemplified by cluster growth is hypothesized to contribute to the invasiveness and metastasis of IMPC. In this study, we demonstrate that levels of β1 integrin and Rac1 expression were greater in breast IMPC than in invasive breast carcinoma of no specific type and paraneoplastic benign breast tissue. We show that silencing β1 integrin expression using the β1 integrin inhibitor AIIB2 partially restored polarity in IMPC primary cell clusters and downregulated Rac1. Thus, overexpression of β1 integrin upregulates Rac1. Univariate analysis showed that overexpression of β1 integrin and Rac1 was associated with breast cancer cell polarity reversal, lymph node metastasis, and poor disease-free survival in IMPC patients. Multivariate analysis revealed that polarity reversal was an independent predictor of poor disease-free survival. These findings indicate that overexpression of β1 integrin and the resultant upregulation of Rac1 contribute to polarity reversal and metastasis of breast IMPC, and that β1 integrin and Rac1 could be potential prognostic biomarkers and targets for treatment of breast IMPC

Transcriptomic analysis of Synechocystis sp PCC6803 under low-temperature stress

In this study, cDNA microarrays were developed from 3569 mRNA reads to analyze the expression profiles of the transcriptomes of Synechocystis sp. PCC6803 under low temperature (LT) stress. Among the genes on the cDNA microarrays, 899 LT-affected genes exhibited a 1.5-fold (or greater) difference in expression compared with the genes from normal unstressed Synechocystis sp. PCC6803. Of the differentially expressed genes, 353 were up-regulated and 246 were down-regulated. The results showed that genes involved in photosynthesis were activated at LT (10A degrees C), including genes for photosystem I, photosystem II, photosynthetic electron transport, and cytochrome b6/f complex. Moreover, desB, one of four genes that encode the fatty acid desaturases, was also induced by LT. However, the LT conditions to some degree enhanced the transcription of some genes. In addition, LT (10A degrees C) may reduce cellular motility by regulating the transcription of spkA (sll1575), a serine/threonine protein kinase. The results reported in this study may contribute to a better understanding of the responses of the Synechocystis cell to LT, including pathways involved in photosynthesis and repair.In this study, cDNA microarrays were developed from 3569 mRNA reads to analyze the expression profiles of the transcriptomes of Synechocystis sp. PCC6803 under low temperature (LT) stress. Among the genes on the cDNA microarrays, 899 LT-affected genes exhibited a 1.5-fold (or greater) difference in expression compared with the genes from normal unstressed Synechocystis sp. PCC6803. Of the differentially expressed genes, 353 were up-regulated and 246 were down-regulated. The results showed that genes involved in photosynthesis were activated at LT (10A degrees C), including genes for photosystem I, photosystem II, photosynthetic electron transport, and cytochrome b6/f complex. Moreover, desB, one of four genes that encode the fatty acid desaturases, was also induced by LT. However, the LT conditions to some degree enhanced the transcription of some genes. In addition, LT (10A degrees C) may reduce cellular motility by regulating the transcription of spkA (sll1575), a serine/threonine protein kinase. The results reported in this study may contribute to a better understanding of the responses of the Synechocystis cell to LT, including pathways involved in photosynthesis and repair

A flow cytometer based protocol for quantitative analysis of bloom-forming cyanobacteria (Microcystis) in lake sediments

A quantitative protocol for the rapid analysis of Microcystis cells and colonies in lake sediment was developed using a modified flow cytometer, the CytoSense. For cell enumeration, diluted sediment samples containing Microcystis were processed with sonication to disintegrate colonies into single cells. An optimized procedure suggested that 5 mg dw (dry weight)/mL dilution combined with 200 W x 2 min sonication yielded the highest counting efficiency. Under the optimized determination conditions, the quantification limit of this protocol was 3.3x10(4) cells/g dw. For colony analysis, Microcystis were isolated from the sediment by filtration. Colony lengths measured by flow cytometry were similar to those measured by microscopy for the size range of one single cell to almost 400 mu m in length. Moreover, the relationship between colony size and cell number was determined for three Microcystis species, including Microcystis flos-aquae, M. aeruginosa and M. wessenbergii. Regression formulas were used to calculate the cell numbers in different-sized colonies. The developed protocol was applied to field sediment samples from Lake Taihu. The results indicated the potential and applicability of flow cytometry as a tool for the rapid analysis of benthic Microcystis. This study provided a new capability for the high frequency monitoring of benthic overwintering and population dynamics of this bloom-forming cyanobacterium.A quantitative protocol for the rapid analysis of Microcystis cells and colonies in lake sediment was developed using a modified flow cytometer, the CytoSense. For cell enumeration, diluted sediment samples containing Microcystis were processed with sonication to disintegrate colonies into single cells. An optimized procedure suggested that 5 mg dw (dry weight)/mL dilution combined with 200 W x 2 min sonication yielded the highest counting efficiency. Under the optimized determination conditions, the quantification limit of this protocol was 3.3x10(4) cells/g dw. For colony analysis, Microcystis were isolated from the sediment by filtration. Colony lengths measured by flow cytometry were similar to those measured by microscopy for the size range of one single cell to almost 400 mu m in length. Moreover, the relationship between colony size and cell number was determined for three Microcystis species, including Microcystis flos-aquae, M. aeruginosa and M. wessenbergii. Regression formulas were used to calculate the cell numbers in different-sized colonies. The developed protocol was applied to field sediment samples from Lake Taihu. The results indicated the potential and applicability of flow cytometry as a tool for the rapid analysis of benthic Microcystis. This study provided a new capability for the high frequency monitoring of benthic overwintering and population dynamics of this bloom-forming cyanobacterium

Induction of oxidative stress and related transcriptional effects of perfluorononanoic acid using an in vivo assessment

Perfluorononanoic acid (PFNA) is an organic pollutant ubiquitous in the environment. However, the potential toxicity of PFNA remains largely unknown in teleost fish. This study defined the oxidative stress and related transcriptional effects of PFNA at various concentrations on zebrafish larvae. Activities of superoxide dismutase were induced in PFNA-treated groups but attenuated with exposure to higher concentration. Catalase activity and lipid peroxidation were significantly inhibited or increased at the highest concentration, respectively. To test the apoptotic pathway, several genes related to cell apoptosis were examined using real-time PCR. The expression of p53, apoptosis-inducing factor (AIF) and c-Jun NH (2)-terminal kinase (JNK) was partially increased, while Bcl-2, an anti-apoptotic gene, was reduced, with no significant effects on Bax and caspase-3 during the exposure period. The effect of PFNA on lipid beta-oxidation system was investigated by examining the activity of peroxisome fatty acyl-COA oxidase (ACOX) and the expression of peroxisome proliferating activating receptors (PPARs). ACOX activity was moderately elevated with marginal significance and was not a significant consequence of PPAR alpha and PPAR gamma expression. The overall results suggest that turbulence of oxidative stress and apoptotic pathway is involved in PFNA-induced toxicity in zebrafish larvae, and the gene expression patterns are able to reveal some potential mechanisms of developmental toxicity. Crown Copyright (C) 2013 Published by Elsevier Inc. All rights reserved.Perfluorononanoic acid (PFNA) is an organic pollutant ubiquitous in the environment. However, the potential toxicity of PFNA remains largely unknown in teleost fish. This study defined the oxidative stress and related transcriptional effects of PFNA at various concentrations on zebrafish larvae. Activities of superoxide dismutase were induced in PFNA-treated groups but attenuated with exposure to higher concentration. Catalase activity and lipid peroxidation were significantly inhibited or increased at the highest concentration, respectively. To test the apoptotic pathway, several genes related to cell apoptosis were examined using real-time PCR. The expression of p53, apoptosis-inducing factor (AIF) and c-Jun NH (2)-terminal kinase (JNK) was partially increased, while Bcl-2, an anti-apoptotic gene, was reduced, with no significant effects on Bax and caspase-3 during the exposure period. The effect of PFNA on lipid beta-oxidation system was investigated by examining the activity of peroxisome fatty acyl-COA oxidase (ACOX) and the expression of peroxisome proliferating activating receptors (PPARs). ACOX activity was moderately elevated with marginal significance and was not a significant consequence of PPAR alpha and PPAR gamma expression. The overall results suggest that turbulence of oxidative stress and apoptotic pathway is involved in PFNA-induced toxicity in zebrafish larvae, and the gene expression patterns are able to reveal some potential mechanisms of developmental toxicity. Crown Copyright (C) 2013 Published by Elsevier Inc. All rights reserved

Gene cloning and expression profile of a novel carotenoid hydroxylase (CYP97C) from the green alga Haematococcus pluvialis

A full-length complementary DNA (cDNA) sequence of epsilon-ring CHY (designated Haecyp97c) was cloned from the green alga Haematococcus pluvialis by reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends methods. The Haecyp97c cDNA sequence was 1,995 base pairs (bp) in length, which contained a 1,620-bp open reading frame, a 46-bp 5'-untranslated region (UTR), and a 329-bp 3'-UTR with the characteristic of the poly (A) tail. The deduced protein had a calculated molecular mass of 58.71 kDa with an estimated isoelectric point of 7.94. Multiple alignment analysis revealed that the deduced amino acid sequence of HaeCYP97C shared high identity of 72-85 % with corresponding CYP97Cs from other eukaryotes. The catalytic motifs of cytochrome P450s were detected in the amino acid sequence of HaeCYP97C. The transcriptional levels of Haecyp97c and xanthophylls accumulation under high light (HL) stress have been examined. The results revealed that Haecyp97c transcript was strongly increased after 13-28 h under HL stress. Meanwhile, the concentrations of chlorophylls, carotenes, and lutein were decreased, and zeaxanthin and astaxanthin concentrations were increased rapidly, respectively. These facts indicated that HaeCYP97C was perhaps involved in xanthophyll biosynthesis, which plays an important role in adaption to HL for H. pluvialis.A full-length complementary DNA (cDNA) sequence of epsilon-ring CHY (designated Haecyp97c) was cloned from the green alga Haematococcus pluvialis by reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends methods. The Haecyp97c cDNA sequence was 1,995 base pairs (bp) in length, which contained a 1,620-bp open reading frame, a 46-bp 5'-untranslated region (UTR), and a 329-bp 3'-UTR with the characteristic of the poly (A) tail. The deduced protein had a calculated molecular mass of 58.71 kDa with an estimated isoelectric point of 7.94. Multiple alignment analysis revealed that the deduced amino acid sequence of HaeCYP97C shared high identity of 72-85 % with corresponding CYP97Cs from other eukaryotes. The catalytic motifs of cytochrome P450s were detected in the amino acid sequence of HaeCYP97C. The transcriptional levels of Haecyp97c and xanthophylls accumulation under high light (HL) stress have been examined. The results revealed that Haecyp97c transcript was strongly increased after 13-28 h under HL stress. Meanwhile, the concentrations of chlorophylls, carotenes, and lutein were decreased, and zeaxanthin and astaxanthin concentrations were increased rapidly, respectively. These facts indicated that HaeCYP97C was perhaps involved in xanthophyll biosynthesis, which plays an important role in adaption to HL for H. pluvialis

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Erratum to: 36th International Symposium on Intensive Care and Emergency Medicine

[This corrects the article DOI: 10.1186/s13054-016-1208-6.]

Design challenges of direct-drive permanent magnet superconducting wind turbine generators

In recent years, permanent magnet superconducting (PMSC) generators have become a candidate for applying superconducting (SC) generators in large direct-drive wind turbines. This configuration keeps the SC armature winding and its cooling system stationary and eliminates rotational cooling couplings. However, the low excitation by permanent magnets may lead to poor power factors if the armature current is high. Furthermore, the permanent magnets are prone to demagnetization when the armature reaction is strong. This paper investigates the design challenges regarding the power factor, demagnetization and short circuit characteristics by analyzing two PMSC generator designs. The results show that the power factor cannot be as high as 0.9 and a low power factor such as 0.6 can take advantage of the high current carrying capability of the SC armature winding. However, this low power factor will cause demagnetization. The armature current may cause quenching of the SC wires during a three-phase short circuit. Demagnetization of the permanent magnets during the short circuit is strong and could be an intrinsic weakness of a PMSC generator.Accepted Author ManuscriptTransport Engineering and Logistic

Performance of Multi-Layer and Stator-Shifting Fractional-Slot Concentrated Windings for Superconducting Wind Turbine Generators under Normal and Short-Circuit Operation Conditions

High temperature superconducting (HTS) generators are being considered for large offshore direct-drive (DD) wind turbines as they are expected to be lightweight and compact. However, short circuit torques of an HTS generator with integral-slot distributed windings (ISDWs) are too high for wind turbine constructions, mainly due to the large magnetic air gap. Fractional-slot concentrated windings (FSCWs) can be considered to address this issue since their high leakage inductance can limit short circuit currents and torques. Unlike ISDWs, FSCWs produce great contents of space harmonics that induce excessive losses in rotor components. Multi-layer and stator-shifting windings have been proposed to effectively reduce such losses. Based on a conventional 12-slot 10-pole configuration, this paper evaluates the effects of multi-layer and stator-shifting FSCWs on torque production and loss reduction in a 10 MW DD HTS generator. The examined losses include eddy current losses in the rotor shields and AC losses in the HTS field winding. This paper also checks if these FSCW schemes maintain the advantage of achieving a low short circuit torque. The results show that a 6-phase stator-shifting winding is the best choice for applying FSCWs to HTS generators.Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.DC systems, Energy conversion & Storag