bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mondo complexes regulate TFEB via TOR inhibition to promote longevity in response to gonadal signals
Authors: Nakamura Shuhei , Karalay Özlem , Jäger Philipp S. , Horikawa Makoto , Klein Corinna , Nakamura Kayo , Latza Christian , Templer Sven E. , Dieterich Christoph , Antebi Adam 
Published: March 2016

AbstractGermline removal provokes longevity in several species and shifts resources towards survival and repair. Several Caenorhabditis elegans transcription factors regulate longevity arising from germline removal; yet, how they work together is unknown. Here we identify a Myc-like HLH transcription factor network comprised of Mondo/Max-like complex (MML-1/MXL-2) to be required for longevity induced by germline removal, as well as by reduced TOR, insulin/IGF signalling and mitochondrial function. Germline removal increases MML-1 nuclear accumulation and activity. Surprisingly, MML-1 regulates nuclear localization and activity of HLH-30/TFEB, a convergent regulator of autophagy, lysosome biogenesis and longevity, by downregulating TOR signalling via LARS-1/leucyl-transfer RNA synthase. HLH-30 also upregulates MML-1 upon germline removal. Mammalian MondoA/B and TFEB show similar mutual regulation. MML-1/MXL-2 and HLH-30 transcriptomes show both shared and preferential outputs including MDL-1/MAD-like HLH factor required for longevity. These studies reveal how an extensive interdependent HLH transcription factor network distributes responsibility and mutually enforces states geared towards reproduction or survival.
Function and evolution of local repeats in the Firre locus
Authors: Hacisuleyman Ezgi , Shukla Chinmay J. , Weiner Catherine L. , Rinn John L. 
Published: March 2016

AbstractMore than half the human and mouse genomes are comprised of repetitive sequences, such as transposable elements (TEs), which have been implicated in many biological processes. In contrast, much less is known about other repeats, such as local repeats that occur in multiple instances within a given locus in the genome but not elsewhere. Here, we systematically characterize local repeats in the genomic locus of the Firre long noncoding RNA (lncRNA). We find a conserved function for the RRD repeat as a ribonucleic nuclear retention signal that is sufficient to retain an otherwise cytoplasmic mRNA in the nucleus. We also identified a repeat, termed R0, that can function as a DNA enhancer element within the intronic sequences of Firre. Collectively, our data suggest that local repeats can have diverse functionalities and molecular modalities in the Firre locus and perhaps more globally in other lncRNAs.
Neuronal activity controls Bdnf expression via Polycomb de-repression and CREB/CBP/JMJD3 activation in mature neurons
Authors: Palomer Ernest , Carretero Javier , Benvegnù Stefano , Dotti Carlos G. , Martin Mauricio G. 
Published: March 2016

AbstractIt has been recently described that in embryonic stem cells, the expression of some important developmentally regulated genes is repressed, but poised for fast activation under the appropriate stimuli. In this work we show that Bdnf promoters are repressed by Polycomb Complex 2 in mature hippocampal neurons, and basal expression is guaranteed by the coexistence with activating histone marks. Neuronal stimulation triggered by N-methyl-D-aspartate application induces the transcription of these promoters by H3K27Me3 demethylation and H3K27Me3 phosphorylation at Serine 28 leading to displacement of EZH2, the catalytic subunit of Polycomb Repressor Complex 2. Our data show that the fast transient expression of Bdnf promoters II and VI after neuronal stimulation is dependent on acetylation of histone H3K27 by CREB-p/CBP. Thus, regulatory mechanisms established during development seem to remain after differentiation controlling genes induced by different stimuli, as would be the case of early memory genes in mature neurons.
Pairwise detection of site-specific receptor phosphorylations using single-molecule blotting
Authors: Kim Kyung Lock , Kim Daehyung , Lee Seongsil , Kim Su-Jeong , Noh Jung Eun , Kim Joung-Hun , Chae Young Chan , Lee Jong-Bong , Ryu Sung Ho 
Published: March 2016

AbstractPost-translational modifications (PTMs) of receptor tyrosine kinases (RTKs) at the plasma membrane (PM) determine the signal transduction efficacy alone and in combination. However, current approaches to identify PTMs provide ensemble results, inherently overlooking combinatorial PTMs in a single polypeptide molecule. Here, we describe a single-molecule blotting (SiMBlot) assay that combines biotinylation of cell surface receptors with single-molecule fluorescence microscopy. This method enables quantitative measurement of the phosphorylation status of individual membrane receptor molecules and colocalization analysis of multiple immunofluorescence signals to directly visualize pairwise site-specific phosphorylation patterns at the single-molecule level. Strikingly, application of SiMBlot to study ligand-dependent epidermal growth factor receptor (EGFR) phosphorylation, which is widely thought to be multi-phosphorylated, reveals that EGFR on cell membranes is hardly multi-phosphorylated, unlike in vitro autophosphorylated EGFR. Therefore, we expect SiMBlot to aid understanding of vast combinatorial PTM patterns, which are concealed in ensemble methods, and to broaden knowledge of RTK signaling.
Amyloid-like ribbons of amelogenins in enamel mineralization
Authors: Carneiro Karina M. M. , Zhai Halei , Zhu Li , Horst Jeremy A. , Sitlin Melody , Nguyen Mychi , Wagner Martin , Simpliciano Cheryl , Milder Melissa , Chen Chun-Long , Ashby Paul , Bonde Johan , Li Wu , Habelitz Stefan 
Published: March 2016

AbstractEnamel, the outermost layer of teeth, is an acellular mineralized tissue that cannot regenerate; the mature tissue is composed of high aspect ratio apatite nanocrystals organized into rods and inter-rod regions. Amelogenin constitutes 90% of the protein matrix in developing enamel and plays a central role in guiding the hierarchical organization of apatite crystals observed in mature enamel. To date, a convincing link between amelogenin supramolecular structures and mature enamel has yet to be described, in part because the protein matrix is degraded during tissue maturation. Here we show compelling evidence that amelogenin self-assembles into an amyloid-like structure in vitro and in vivo. We show that enamel matrices stain positive for amyloids and we identify a specific region within amelogenin that self-assembles into β-sheets. We propose that amelogenin nanoribbons template the growth of apatite mineral in human enamel. This is a paradigm shift from the current model of enamel development.
Regulation of Multi-drug Resistance in hepatocellular carcinoma cells is TRPC6/Calcium Dependent
Authors: Wen Liang , Liang Chao , Chen Enjiang , Chen Wei , Liang Feng , Zhi Xiao , Wei Tao , Xue Fei , Li Guogang , Yang Qi , Gong Weihua , Feng Xinhua , Bai Xueli , Liang Tingbo 
Published: March 2016

AbstractHepatocellular carcinoma (HCC) is notoriously refractory to chemotherapy because of its tendency to develop multi-drug resistance (MDR), whose various underlying mechanisms make it difficult to target. The calcium signalling pathway is associated with many cellular biological activities, and is also a critical player in cancer. However, its role in modulating tumour MDR remains unclear. In this study, stimulation by doxorubicin, hypoxia and ionizing radiation was used to induce MDR in HCC cells. A sustained aggregation of intracellular calcium was observed upon these stimuli, while inhibition of calcium signalling enhanced the cells’ sensitivity to various drugs by attenuating epithelial-mesenchymal transition (EMT), Hif1-α signalling and DNA damage repair. The effect of calcium signalling is mediated via transient receptor potential canonical 6 (TRPC6), a subtype of calcium-permeable channel. An in vivo xenograft model of HCC further confirmed that inhibiting TRPC6 enhanced the efficacy of doxorubicin. In addition, we deduced that STAT3 activation is a downstream signalling pathway in MDR. Collectively, this study demonstrated that the various mechanisms regulating MDR in HCC cells are calcium dependent through the TRPC6/calcium/STAT3 pathway. We propose that targeting TRPC6 in HCC may be a novel antineoplastic strategy, especially combined with chemotherapy.
Factors associated with doctors’ knowledge on antibiotic use in China
Authors: Bai Yu , Wang Sijie , Yin Xiaoxv , Bai Jigeng , Gong Yanhong , Lu Zuxun 
Published: March 2016

AbstractMisuse of antibiotics by the medical profession is a global concern. Examining doctors’ knowledge about antimicrobials will be important in developing strategies to improve antibiotic use. The aim of the study was to survey Chinese doctors’ knowledge on antibiotics and reveal the factors associated with their level of knowledge. A cross-sectional survey was conducted in Shanxi in central China. A total of 761 physicians were surveyed using a structured self-administered questionnaire. A generalized linear regression model was used to identify the factors associated with doctors’ knowledge on antibiotic. Based on a full score of 10, the average score for doctors’ knowledge on antibiotics was 6.29 (SD = 1.79). Generalized linear regression analysis indicated that doctors who either worked in the internal medicine department, who were chief doctors or who received continuing education on antibiotic, had better knowledge of antibiotics. Compared with doctors working in tertiary hospitals, doctors working in secondary hospitals or primary healthcare facilities had poorer knowledge about antibiotics. Chinese doctors have suboptimal knowledge about antimicrobials. Ongoing education is effective to enhance doctors’ knowledge, but the effect remains to be further improved. More targeted interventions and education programs should improve knowledge about antimicrobials, especially for doctors working in primary healthcare institutions.
HBx-upregulated lncRNA UCA1 promotes cell growth and tumorigenesis by recruiting EZH2 and repressing p27Kip1/CDK2 signaling
Authors: Hu Jiao-Jiao , Song Wei , Zhang Shao-Dan , Shen Xiao-Hui , Qiu Xue-Mei , Wu Hua-Zhang , Gong Pi-Hai , Lu Sen , Zhao Zhu-Jiang , He Ming-Liang , Fan Hong 
Published: March 2016

AbstractIt is well accepted that HBx plays the major role in hepatocarcinogenesis associated with hepatitis B virus (HBV) infections. However, little was known about its role in regulating long noncoding RNAs (lncRNAs), a large group of transcripts regulating a variety of biological processes including carcinogenesis in mammalian cells. Here we report that HBx upregulates UCA1 genes and downregulates p27 genes in hepatic LO2 cells. Further studies show that the upregulated UCA1 promotes cell growth by facilitating G1/S transition through CDK2 in both hepatic and hepatoma cells. Knock down of UCA1 in HBx-expressing hepatic and hepatoma cells resulted in markedly increased apoptotic cells by elevating the cleaved caspase-3 and caspase-8. More importantly, UCA1 is found to be physically associated with enhancer of zeste homolog 2 (EZH2), which suppresses p27Kip1 through histone methylation (H3K27me3) on p27Kip1 promoter. We also show that knockdown of UCA1 in hepatoma cells inhibits tumorigenesis in nude mice. In a clinic study, UCA1 is found to be frequently up-regulated in HBx positive group tissues in comparison with the HBx negative group, and exhibits an inverse correlation between UCA1 and p27Kip1 levels. Our findings demonstrate an important mechanism of hepatocarcinogenesis through the signaling of HBx-UCA1/EZH2-p27Kip1 axis, and a potential target of HCC.
Dosimetric evaluation of a simple planning method for improving intensity-modulated radiotherapy for stage III lung cancer
Authors: Lu Jia-Yang , Lin Zhu , Zheng Jing , Lin Pei-Xian , Cheung Michael Lok-Man , Huang Bao-Tian 
Published: March 2016

AbstractThis study aimed to evaluate the dosimetric outcomes of a base-dose-plan-compensation (BDPC) planning method for improving intensity-modulated radiotherapy (IMRT) for stage III lung cancer. For each of the thirteen included patients, three types of planning methods were applied to obtain clinically acceptable plans: (1) the conventional optimization method (CO); (2) a split-target optimization method (STO), in which the optimization objectives were set higher dose for the target with lung density; (3) the BDPC method, which compensated for the optimization-convergence error by further optimization based on the CO plan. The CO, STO and BDPC methods were then compared regarding conformity index (CI), homogeneity index (HI) of the target, organs at risk (OARs) sparing and monitor units (MUs). The BDPC method provided better HI/CI by 54%/7% on average compared to the CO method and by 38%/3% compared to the STO method. The BDPC method also spared most of the OARs by up to 9%. The average MUs of the CO, STO and BDPC plans were 890, 937 and 1023, respectively. Our results indicated that the BDPC method can effectively improve the dose distribution in IMRT for stage III lung cancer, at the expense of more MUs.
Receptor activator of NF-κB ligand induces cell adhesion and integrin α2 expression via NF-κB in head and neck cancers
Authors: Yamada Tamaki , Tsuda Masumi , Wagatsuma Takanori , Fujioka Yoichiro , Fujioka Mari , Satoh Aya O. , Horiuchi Kosui , Nishide Shinya , Nanbo Asuka , Totsuka Yasunori , Haga Hisashi , Tanaka Shinya , Shindoh Masanobu , Ohba Yusuke 
Published: March 2016

AbstractCellular interactions with the extracellular matrix play critical roles in tumor progression. We previously reported that receptor activator of NF-κB ligand (RANKL) specifically facilitates head and neck squamous cell carcinoma (HNSCC) progression in vivo. Here, we report a novel role for RANKL in the regulation of cell adhesion. Among the major type I collagen receptors, integrin α2 was significantly upregulated in RANKL-expressing cells and its knockdown suppressed cell adhesion. The mRNA abundance of integrin α2 positively correlated with that of RANKL in human HNSCC tissues. We also revealed that RANK-NF-κB signaling mediated integrin α2 expression in an autocrine/paracrine manner. Interestingly, the amount of active integrin β1 on the cell surface was increased in RANKL-expressing cells through the upregulation of integrin α2 and endocytosis. Moreover, the RANK-integrin α2 pathway contributed to RANKL-dependent enhanced survival in a collagen gel and inhibited apoptosis in a xenograft model, demonstrating an important role for RANKL-mediated cell adhesion in three-dimensional environments.
An essential role for the intra-oocyte MAPK activity in the NSN-to-SN transition of germinal vesicle chromatin configuration in porcine oocytes
Authors: Sun Ming-Ju , Zhu Shuai , Li You-Wei , Lin Juan , Gong Shuai , Jiao Guang-Zhong , Chen Fei , Tan Jing-He 
Published: March 2016

AbstractThe mechanisms for the transition from non-surrounded nucleolus (NSN) to surrounded nucleolus (SN) chromatin configuration during oocyte growth/maturation are unclear. By manipulating enzyme activities and measuring important molecules using small-follicle pig oocytes with a high proportion of NSN configuration and an extended germinal vesicle stage in vitro, this study has the first time up-to-date established the essential role for intra-oocyte mitogen-activated protein kinase (MAPK) in the NSN-to-SN transition. Within the oocyte in 1–2 mm follicles, a cAMP decline activates MAPK, which prevents the NSN-to-SN transition by activating nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) while inhibiting histone deacetylase (HDAC). In cumulus cells of 1–2 mm follicles, a lower level of estradiol and oocyte-derived paracrine factor (ODPF) reduces natriuretic peptide receptor 2 (NPR2) while enhancing FSH and cAMP actions. FSH elevates cAMP levels, which decreases NPR2 while activating MAPK. MAPK closes the gap junctions, which, together with the NPR2 decrease, reduces cyclic guanosine monophosphate (cGMP) delivery leading to the cAMP decline within oocytes. In 3–6 mm follicles, a higher level of estradiol and ODPF and a FSH shortage initiate a reversion of the above events leading to MAPK inactivation and NSN-to-SN transition within oocytes.
Erbium-doped fiber laser passively mode locked with few-layer WSe2/MoSe2 nanosheets
Authors: Mao Dong , She Xiaoyang , Du Bobo , Yang Dexing , Zhang Wending , Song Kun , Cui Xiaoqi , Jiang Biqiang , Peng Tao , Zhao Jianlin 
Published: March 2016

AbstractFew-layer transition-metal dichalcogenide WSe2/MoSe2 nanosheets are fabricated by a liquid exfoliation technique using sodium deoxycholate bile salt as surfactant and their nonlinear optical properties are investigated based on a balanced twin-detector measurement scheme. It is demonstrated that both types of nanosheets exhibit nonlinear saturable absorption properties at the wavelength of 1.55 μm. By depositing the nanosheets on side polished fiber (SPF) or mixing the nanosheets with polyvinyl alcohol (PVA) solution, SPF-WSe2 saturable absorber (SA), SPF-MoSe2 SA, PVA-WSe2 SA and PVA-MoSe2 SA are successfully fabricated and further tested in erbium-doped fiber lasers. The SPF-based SA is capable of operating at the high pump regime without damage and a train of 3252.65 MHz harmonically mode-locked pulses are obtained based on the SPF-WSe2 SA. Soliton mode locking operations are also achieved in the fiber laser separately with other three types of SAs, confirming that the WSe2 and MoSe2 nanosheets could act as cost-effective high-power SAs for ultrafast optics.
Metformin stimulates IGFBP-2 gene expression through PPARalpha in diabetic states
Authors: Kang Hye Suk , Cho Ho-Chan , Lee Jae-Ho , Oh Goo Taeg , Koo Seung-Hoi , Park Byung-Hyun , Lee In-Kyu , Choi Hueng-Sik , Song Dae-Kyu , Im Seung-Soon 
Published: March 2016

AbstractThe anti-diabetic drug, metformin, exerts its action through AMP-activated protein kinase (AMPK), and Sirtuin (Sirt1) signaling. Insulin-like growth factor (IGF)-binding protein 2 (IGFBP-2) prevents IGF-1 binding to its receptors, thereby contributing to modulate insulin sensitivity. In this study, we demonstrate that metformin upregulates Igfbp-2 expression through the AMPK-Sirt1-PPARα cascade pathway. In the liver of high fat diet, ob/ob, and db/db mice, Igfbp-2 expression was significantly decreased compared to the expression levels in the wild-type mice (p < 0.05). Upregulation of Igfbp-2 expression by metformin administration was disrupted by gene silencing of Ampk and Sirt1, and this phenomenon was not observed in Pparα-null mice. Notably, activation of IGF-1 receptor (IGF-1R)-dependent signaling by IGF-1 was inhibited by metformin. Finally, when compared to untreated type 2 diabetes patients, the metformin-treated diabetic patients showed increased IGFBP-2 levels with diminished serum IGF-1 levels. Taken together, these findings indicate that IGFBP-2 might be a new target of metformin action in diabetes and the metformin-AMPK-Sirt1-PPARα-IGFBP-2 network may provide a novel pathway that could be applied to ameliorate metabolic syndromes by controlling IGF-1 bioavailability.
Conserved differences in protein sequence determine the human pathogenicity of Ebolaviruses
Authors: Pappalardo Morena , Juliá Miguel , Howard Mark J. , Rossman Jeremy S. , Michaelis Martin , Wass Mark N. 
Published: March 2016

AbstractReston viruses are the only Ebolaviruses that are not pathogenic in humans. We analyzed 196 Ebolavirus genomes and identified specificity determining positions (SDPs) in all nine Ebolavirus proteins that distinguish Reston viruses from the four human pathogenic Ebolaviruses. A subset of these SDPs will explain the differences in human pathogenicity between Reston and the other four ebolavirus species. Structural analysis was performed to identify those SDPs that are likely to have a functional effect. This analysis revealed novel functional insights in particular for Ebolavirus proteins VP40 and VP24. The VP40 SDP P85T interferes with VP40 function by altering octamer formation. The VP40 SDP Q245P affects the structure and hydrophobic core of the protein and consequently protein function. Three VP24 SDPs (T131S, M136L, Q139R) are likely to impair VP24 binding to human karyopherin alpha5 (KPNA5) and therefore inhibition of interferon signaling. Since VP24 is critical for Ebolavirus adaptation to novel hosts and only a few SDPs distinguish Reston virus VP24 from VP24 of other Ebolaviruses, human pathogenic Reston viruses may emerge. This is of concern since Reston viruses circulate in domestic pigs and can infect humans, possibly via airborne transmission.
Identification of a dTDP-rhamnose biosynthetic pathway that oscillates with the molting cycle in Caenorhabditis elegans
Authors: Feng Likui , Shou Qingyao , Butcher Rebecca A. 
Published: March 2016

L-Rhamnose is a common component of cell-wall polysaccharides, glycoproteins and some natural products in bacteria and plants, but is rare in fungi and animals. In the present study, we identify and characterize a biosynthetic pathway for dTDP-rhamnose in Caenorhabditis elegans that is highly conserved across nematode species. We show that RML-1 activates glucose 1-phosphate (Glc-1-P) in the presence of either dTTP or UTP to yield dTDP-glucose or UDP-glucose, respectively. RML-2 is a dTDP-glucose 4,6-dehydratase, converting dTDP-glucose into dTDP-4-keto-6-deoxyglucose. Using mass spectrometry and NMR spectroscopy, we demonstrate that coincubation of dTDP-4-keto-6-deoxyglucose with RML-3 (3,5-epimerase) and RML-4 (4-keto-reductase) produces dTDP-rhamnose. RML-4 could only be expressed and purified in an active form through co-expression with a co-regulated protein, RML-5, which forms a complex with RML-4. Analysis of the sugar nucleotide pool in C. elegans established the presence of dTDP-rhamnose in vivo. Targeting the expression of the rhamnose biosynthetic genes by RNAi resulted in significant reductions in dTDP-rhamnose, but had no effect on the biosynthesis of a closely related sugar, ascarylose, found in the ascaroside pheromones. Therefore, the rhamnose and ascarylose biosynthetic pathways are distinct. We also show that transcriptional reporters for the rhamnose biosynthetic genes are expressed highly in the embryo, in the hypodermis during molting cycles and in the hypodermal seam cells specifically before the molt to the stress-resistant dauer larval stage. These expression patterns suggest that rhamnose biosynthesis may play an important role in hypodermal development or the production of the cuticle or surface coat during molting.