bluuebunny/crossref_metadata_2025 huggingface dataset:
Non-compliance, renegotiation and justice in international adjudication: A WTO perspective
Authors: SHLOMO AGON SIVAN
Published: June 2016

Focusing on the expanding realm of international adjudication, this article approaches justice from the domain of the empirical and shows – through a careful, interview-based case study analysis in the WTO context – that justice in the international context is not only a contested concept, but also a multifaceted one, deeply embedded in notions such as the rule of law, fairness, equality, transformation, and cooperation. Whereas in the past, the primary, if not the sole role of international courts was that of settling disputes, in their modern legalised reincarnation these empowered international institutions have come to be seen primarily as enforcement mechanisms. Mechanisms that have been put in place by states in order to give effect to their originally negotiated commitments, and to hold states (or other entities) accountable for the international rules agreed-upon. Within this common enforcement-centred discourse of international courts, in turn, the natural tendency has so far been to think of ‘justice’ mainly through its ‘legal’ or ‘rule of law’ dimension. This article challenges this enforcement-centred discourse. Focusing on the vibrant WTO dispute settlement system (DSS) and its operation throughout the perennial EC–Bananas dispute, the article argues that the current enforcement-oriented debate of international courts, and the WTO DSS in particular, is lacking in several aspects. First, it brushes aside other important roles served by the DSS, and consequently overshadows the manifold social outcomes – beyond rule-compliance – produced by this system. Second, the prevalent rule-enforcement discourse further works in turn as to mask the multiple challenges of justice encapsulated in international disputes reaching the DSS docket, and obstructs the need to explore other conceptions of justice – beyond its legal-procedural meaning – such as global distributive, corrective, or transformative justice, through which the diverse roles and outcomes of the DSS may (and should) be evaluated. Against this backdrop, the article puts forwards a broad multifunctional account of the WTO DSS, which goes beyond the prevalent view of the system as primarily an enforcement mechanism, portraying it instead as a system of multiple, competing, and shifting roles. Among them, providing an orderly mechanism of renegotiation, redistribution, and settlement. Roles that essentially allow WTO Members to readjust their original WTO commitments and reallocate their burdens and benefits of international cooperation, and thereby to arrive at new – at times not fully legally-compliant – but not necessarily ‘unjust’ cooperative and sustainable social outcomes.
Investigating the Relationship Between Self-Esteem and Stigma Among Young Adults With History of Suicide Attempts
Authors: Lehmann Meshan , Hilimire Matthew R. , Yang Lawrence H. , Link Bruce G. , DeVylder Jordan E.
Published: June 2016

Abstract. Background: Self-esteem is a major contributor to risk for repeated suicide attempts. Prior research has shown that awareness of stigma is associated with reduced self-esteem among people with mental illness. No prior studies have examined the association between self-esteem and stereotype awareness among individuals with past suicide attempts. Aims: To understand the relationship between stereotype awareness and self-esteem among young adults who have and have not attempted suicide. Method: Computerized surveys were administered to college students (N = 637). Linear regression analyses were used to test associations between self-esteem and stereotype awareness, attempt history, and their interaction. Results: There was a significant stereotype awareness by attempt interaction (β = –.74, p = .006) in the regression analysis. The interaction was explained by a stronger negative association between stereotype awareness and self-esteem among individuals with past suicide attempts (β = –.50, p = .013) compared with those without attempts (β = –.09, p = .037). Conclusion: Stigma is associated with lower self-esteem within this high-functioning sample of young adults with histories of suicide attempts. Alleviating the impact of stigma at the individual (clinical) or community (public health) levels may improve self-esteem among this high-risk population, which could potentially influence subsequent suicide risk.
Characteristics and Proximal Outcomes of Calls Made to Suicide Crisis Hotlines in California
Authors: Ramchand Rajeev , Jaycox Lisa , Ebener Pat , Gilbert Mary Lou , Barnes-Proby Dionne , Goutam Prodyumna
Published: June 2016

Abstract. Background: Suicide hotlines are commonly used to prevent suicides, although centers vary with respect to their management and operations. Aims: To describe variability across suicide prevention hotlines. Method: Live monitoring of 241 calls was conducted at 10 suicide prevention hotlines in California. Results: Call centers are similar with respect to caller characteristics and the concerns callers raise during their calls. The proportion of callers at risk for suicide varied from 3 to 57%. Compliance with asking about current suicide risk, past ideation, and past attempts also ranged considerably. Callers to centers that were part of the National Suicide Prevention Lifeline (NSPL) were more likely to experience reduced distress than callers to centers that were not part of the NSPL. Conclusion: Because callers do not generally choose the center or responder that will take their call, it is critical to promote quality across call centers and minimize the variability that currently exists. Accrediting bodies, funders, and crisis centers should require that centers continuously monitor calls to ensure and improve call quality.
A data-driven network model of primary myelofibrosis: transcriptional and post-transcriptional alterations in CD34+ cells
Authors: Calura E , Pizzini S , Bisognin A , Coppe A , Sales G , Gaffo E , Fanelli T , Mannarelli C , Zini R , Norfo R , Pennucci V , Manfredini R , Romualdi C , Guglielmelli P , Vannucchi A M , Bortoluzzi S ,   on behalf of the Associazione Italiana per la Ricerca sul Cancro Gruppo Italiano Malattie Mieloproliferative (AGIMM) Investigators
Published: June 2016

microRNAs (miRNAs) are relevant in the pathogenesis of primary myelofibrosis (PMF) but our understanding is limited to specific target genes and the overall systemic scenario islacking. By both knowledge-based and ab initio approaches for comparative analysis of CD34+ cells of PMF patients and healthy controls, we identified the deregulated pathways involving miRNAs and genes and new transcriptional and post-transcriptional regulatory circuits in PMF cells. These converge in a unique and integrated cellular process, in which the role of specific miRNAs is to wire, co-regulate and allow a fine crosstalk between the involved processes. The PMF pathway includes Akt signaling, linked to Rho GTPases, CDC42, PLD2, PTEN crosstalk with the hypoxia response and Calcium-linked cellular processes connected to cyclic AMP signaling. Nested on the depicted transcriptional scenario, predicted circuits are reported, opening new hypotheses. Links between miRNAs (miR-106a-5p, miR-20b-5p, miR-20a-5p, miR-17-5p, miR-19b-3p and let-7d-5p) and key transcription factors (MYCN, ATF, CEBPA, REL, IRF and FOXJ2) and their common target genes tantalizingly suggest new path to approach the disease. The study provides a global overview of transcriptional and post-transcriptional deregulations in PMF, and, unifying consolidated and predicted data, could be helpful to identify new combinatorial therapeutic strategy. Interactive PMF network model: http://compgen.bio.unipd.it/pmf-net/.
STAT3 modulates β-cell cycling in injured mouse pancreas and protects against DNA damage
Authors: De Groef S , Renmans D , Cai Y , Leuckx G , Roels S , Staels W , Gradwohl G , Baeyens L , Heremans Y , Martens G A , De Leu N , Sojoodi M , Van de Casteele M , Heimberg H
Published: June 2016

Partial pancreatic duct ligation (PDL) of mouse pancreas induces a doubling of the β-cell mass mainly through proliferation of pre-existing and newly formed β-cells. The molecular mechanism governing this process is still largely unknown. Given the inflammatory nature of PDL and inflammation-induced signaling via the signal transducer and activator of transcription 3 (STAT3), the activation and the role of STAT3 in PDL-induced β-cell proliferation were investigated. Duct ligation stimulates the expression of several cytokines that can act as ligands inducing STAT3 signaling and phosphorylation in β-cells. β-Cell cycling increased by conditional β-cell-specific Stat3 knockout and decreased by STAT3 activation through administration of interleukin-6. In addition, the level of DNA damage in β-cells of PDL pancreas increased after deletion of Stat3. These data indicate a role for STAT3 in maintaining a steady state in the β-cell, by modulating its cell cycle and protection from DNA damage.
NUPR1, a new target in liver cancer: implication in controlling cell growth, migration, invasion and sorafenib resistance
Authors: Emma M R , Iovanna J L , Bachvarov D , Puleio R , Loria G R , Augello G , Candido S , Libra M , Gulino A , Cancila V , McCubrey J A , Montalto G , Cervello M
Published: June 2016

Sorafenib, an oral multikinase inhibitor, is the only approved agent for the treatment of advanced hepatocellular carcinoma (HCC). However, its benefits are modest, and as its mechanisms of action remain elusive, a better understanding of its anticancer effects is needed. Based on our previous study results, we investigated here the implication of the nuclear protein 1 (NUPR1) in HCC and its role in sorafenib treatment. NUPR1 is a stress-inducible protein that is overexpressed in various malignancies, but its role in HCC is not yet fully understood. We found that NUPR1 expression was significantly higher in primary human HCC samples than in the normal liver. Knockdown of NUPR1 significantly increased cell sensitivity to sorafenib and inhibited the cell growth, migration and invasion of HCC cells, both in vitro and in vivo. Moreover, NUPR1 silencing influenced the expression of RELB and IER3 genes. Unsurprisingly, RELB and IER3 knockdown also inhibited HCC cell viability, growth and migration. Using gene expression profiling of HCC cells following stable NUPR1 knockdown, we found that genes functionally involved in cell death and survival, cellular response to therapies, lipid metabolism, cell growth and proliferation, molecular transport and cellular movement were mostly suppressed. Network analysis of dynamic gene expression identified NF-κB and ERK as downregulated gene nodes, and several HCC-related oncogenes were also suppressed. We identified Runt-related transcription factor 2 (RUNX2) gene as a NUPR1-regulated gene and demonstrated that RUNX2 gene silencing inhibits HCC cell viability, growth, migration and increased cell sensitivity to sorafenib. We propose that the NUPR1/RELB/IER3/RUNX2 pathway has a pivotal role in hepatocarcinogenesis. The identification of the NUPR1/RELB/IER3/RUNX2 pathway as a potential therapeutic target may contribute to the development of new treatment strategies for HCC management.
Junctophilin 3 expresses in pancreatic beta cells and is required for glucose-stimulated insulin secretion
Authors: Li L , Pan Z-F , Huang X , Wu B-W , Li T , Kang M-X , Ge R-S , Hu X-Y , Zhang Y-H , Ge L-J , Zhu D-Y , Wu Y-L , Lou Y-J
Published: June 2016

It is well accepted that junctophilin (JPHs) isoforms act as a physical bridge linking plasma membrane and endoplasmic reticulum (ER) for channel crosstalk in excitable cells. Our purpose is to investigate whether JPHs are involved in the proper communication between Ca2+ influx and subsequent Ca2+ amplification in pancreatic beta cells, thereby participating in regulating insulin secretion. The expression of JPH isoforms was examined in human and mouse pancreatic tissues, and JPH3 expression was found in both the beta cells. In mice, knockdown of Jph3 (si-Jph3) in islets decreased glucose-stimulated insulin secretion (GSIS) accompanied by mitochondrial function impairment. Si-Jph3 lowered the insulin secretory response to Ca2+ signaling in the presence of glucose, and reduced [Ca2+]c transient amplitude triggered by caffeine. Si-Jph3 also attenuated mitofusin 2 expression, thereby disturbing the spatial organization of ER–mitochondria contact in islets. These results suggest that the regulation of GSIS by the KATP channel-independent pathways is partly impaired due to decrease of JPH3 expression in mouse islets. JPH3 also binds to type 2 ryanodine receptors (RyR2) in mouse and human pancreatic tissues, which might contribute to Ca2+ release amplification in GSIS. This study demonstrates some previously unrecognized findings in pancreatic tissues: (1) JPH3 expresses in mouse and human beta cells; (2) si-Jph3 in mouse primary islets impairs GSIS in vitro; (3) impairment in GSIS in si-Jph3 islets is due to changes in RyR2-[Ca2+]c transient amplitude and ER-mitochondria contact.
Multimetallic catalysed radical oxidative C(sp3)–H/C(sp)–H cross-coupling between unactivated alkanes and terminal alkynes
Authors: Tang Shan , Wang Pan , Li Haoran , Lei Aiwen
Published: June 2016

Radical involved transformations are now considered as extremely important processes in modern organic synthetic chemistry. According to the demand by atom-economic and sustainable chemistry, direct C(sp3)–H functionalization through radical oxidative coupling represents an appealing strategy for C–C bond formations. However, the selectivity control of reactive radical intermediates is still a great challenge in these transformations. Here we show a selective radical oxidative C(sp3)–H/C(sp)–H cross-coupling of unactivated alkanes with terminal alkynes by using a combined Cu/Ni/Ag catalytic system. It provides a new way to access substituted alkynes from readily available materials. Preliminary mechanistic studies suggest that this reaction proceeds through a radical process and the C(sp3)–H bond cleavage is the rate-limiting step. This study may have significant implications for controlling selective C–C bond formation of reactive radical intermediates by using multimetallic catalytic systems.
Glacial legacies on interglacial vegetation at the Pliocene-Pleistocene transition in NE Asia
Authors: Herzschuh Ulrike , Birks H. John B. , Laepple Thomas , Andreev Andrei , Melles Martin , Brigham-Grette Julie
Published: June 2016

Broad-scale climate control of vegetation is widely assumed. Vegetation-climate lags are generally thought to have lasted no more than a few centuries. Here our palaeoecological study challenges this concept over glacial–interglacial timescales. Through multivariate analyses of pollen assemblages from Lake El’gygytgyn, Russian Far East and other data we show that interglacial vegetation during the Plio-Pleistocene transition mainly reflects conditions of the preceding glacial instead of contemporary interglacial climate. Vegetation–climate disequilibrium may persist for several millennia, related to the combined effects of permafrost persistence, distant glacial refugia and fire. In contrast, no effects from the preceding interglacial on glacial vegetation are detected. We propose that disequilibrium was stronger during the Plio-Pleistocene transition than during the Mid-Pliocene Warm Period when, in addition to climate, herbivory was important. By analogy to the past, we suggest today’s widespread larch ecosystem on permafrost is not in climate equilibrium. Vegetation-based reconstructions of interglacial climates used to assess atmospheric CO2–temperature relationships may thus yield misleading simulations of past global climate sensitivity.
Correction: Corrigendum: Inhibition of NF-κB by deoxycholic acid induces miR-21/PDCD4-dependent hepatocellular apoptosis
Authors: Rodrigues Pedro M. , Afonso Marta B. , Simão André L. , Borralho Pedro M. , Rodrigues Cecília M. P. , Castro Rui E.
Published: June 2016

Scientific Reports 5: Article number: 17528; published online: 01 December 2015; updated: 24 June 2016 The original version of this Article contained an error in the title of the paper, where the word “hepatocellular” was incorrectly given as “hepatocelular”. This has now been corrected in the PDF and HTML versions of the Article.
Transcriptome sequencing uncovers a three–long noncoding RNA signature in predicting breast cancer survival
Authors: Guo Wenna , Wang Qiang , Zhan Yueping , Chen Xijia , Yu Qi , Zhang Jiawei , Wang Yi , Xu Xin-jian , Zhu Liucun
Published: June 2016

Long noncoding RNAs (lncRNAs) play a crucial role in tumorigenesis. The aim of this study is to identify lncRNA signature that can predict breast cancer patient survival. RNA expression data from 1064 patients were downloaded from The Cancer Genome Atlas project. Cox regression, Kaplan–Meier, and receiver operating characteristic (ROC) analyses were performed to construct a model for predicting the overall survival (OS) of patients and evaluate it. A model consisting of three lncRNA genes (CAT104, LINC01234, and STXBP5-AS1) was identified. The Kaplan–Meier analysis and ROC curves proved that the model could predict the prognostic survival with good sensitivity and specificity in both the validation set (AUC = 0.752, 95% confidence intervals (CI): 0.651–0.854) and the microarray dataset (AUC = 0.714, 95%CI: 0.615–0.814). Further study showed the three-lncRNA signature was not only pervasive in different breast cancer stages, subtypes and age groups, but also provides more accurate prognostic information than some widely known biomarkers. The results suggested that RNA-seq transcriptome profiling provides that the three-lncRNA signature is an independent prognostic biomarker, and have clinical significance. In addition, lncRNA, miRNA, and mRNA interaction network indicated lncRNAs may intervene in breast cancer pathogenesis by binding to miR-190b, acting as competing endogenous RNAs.
Correction: Corrigendum: Recurrent hormone-binding domain truncated ESR1 amplifications in primary endometrial cancers suggest their implication in hormone independent growth
Authors: Holst Frederik , Hoivik Erling A. , Gibson William J. , Taylor-Weiner Amaro , Schumacher Steven E. , Asmann Yan W. , Grossmann Patrick , Trovik Jone , Necela Brian M. , Thompson E. Aubrey , Meyerson Matthew , Beroukhim Rameen , Salvesen Helga B. , Cherniack Andrew D.
Published: June 2016

Scientific Reports 6: Article number: 25521; published online: 10 May 2016; updated: 24 June 2016 In the original version of this Article, there were errors in Affiliation 2 which was incorrectly given as ‘KG Jebsen Center for Precision Medicine in Gynecologic Cancer, Department of Gynecology and Obstetrics, Haukeland University Hospital Bergen, Norway’.
Two conformational states in D-shaped DNA: Effects of local denaturation
Authors: Lee O.-chul , Kim Cheolhee , Kim Jae-Yeol , Lee Nam Ki , Sung Wokyung
Published: June 2016

The bending of double-stranded(ds) DNA on the nano-meter scale plays a key role in many cellular processes such as nucleosome packing, transcription-control, and viral-genome packing. In our recent study, a nanometer-sized dsDNA bent into a D shape was formed by hybridizing a circular single-stranded(ss) DNA and a complementary linear ssDNA. Our fluorescence resonance energy transfer (FRET) measurement of D-DNA revealed two types of conformational states: a less-bent state and a kinked state, which can transform into each other. To understand the origin of the two deformed states of D-DNA, here we study the presence of open base-pairs in the ds portion by using the breathing-DNA model to simulate the system. We provide strong evidence that the two states are due to the emergence of local denaturation, i.e., a bubble in the middle and two forks at ends of the dsDNA portion. We also study the system analytically and find that the free-energy landscape is bistable with two minima representative of the two states. The kink and fork sizes estimated by the analytical calculation are also in excellent agreement with the results of the simulation. Thus, this combined experimental-simulation-analytical study corroborates that highly bent D-DNA reduces bending stress via local denaturation.
De novo intrachromosomal gene conversion from OPN1MW to OPN1LW in the male germline results in Blue Cone Monochromacy
Authors: Buena-Atienza Elena , Rüther Klaus , Baumann Britta , Bergholz Richard , Birch David , De Baere Elfride , Dollfus Helene , Greally Marie T. , Gustavsson Peter , Hamel Christian P. , Heckenlively John R. , Leroy Bart P. , Plomp Astrid S. , Pott Jan Willem R. , Rose Katherine , Rosenberg Thomas , Stark Zornitza , Verheij Joke B. G. M. , Weleber Richard , Zobor Ditta , Weisschuh Nicole , Kohl Susanne , Wissinger Bernd
Published: June 2016

X-linked cone dysfunction disorders such as Blue Cone Monochromacy and X-linked Cone Dystrophy are characterized by complete loss (of) or reduced L- and M- cone function due to defects in the OPN1LW/OPN1MW gene cluster. Here we investigated 24 affected males from 16 families with either a structurally intact gene cluster or at least one intact single (hybrid) gene but harbouring rare combinations of common SNPs in exon 3 in single or multiple OPN1LW and OPN1MW gene copies. We assessed twelve different OPN1LW/MW exon 3 haplotypes by semi-quantitative minigene splicing assay. Nine haplotypes resulted in aberrant splicing of ≥20% of transcripts including the known pathogenic haplotypes (i.e. ‘LIAVA’, ‘LVAVA’) with absent or minute amounts of correctly spliced transcripts, respectively. De novo formation of the ‘LIAVA’ haplotype derived from an ancestral less deleterious ‘LIAVS’ haplotype was observed in one family with strikingly different phenotypes among affected family members. We could establish intrachromosomal gene conversion in the male germline as underlying mechanism. Gene conversion in the OPN1LW/OPN1MW genes has been postulated, however, we are first to demonstrate a de novo gene conversion within the lineage of a pedigree.
A Synthetic Pseudo-Rh: NOx Reduction Activity and Electronic Structure of Pd–Ru Solid-solution Alloy Nanoparticles
Authors: Sato Katsutoshi , Tomonaga Hiroyuki , Yamamoto Tomokazu , Matsumura Syo , Zulkifli Nor Diana Binti , Ishimoto Takayoshi , Koyama Michihisa , Kusada Kohei , Kobayashi Hirokazu , Kitagawa Hiroshi , Nagaoka Katsutoshi
Published: June 2016

Rh is one of the most important noble metals for industrial applications. A major fraction of Rh is used as a catalyst for emission control in automotive catalytic converters because of its unparalleled activity toward NOxreduction. However, Rh is a rare and extremely expensive element; thus, the development of Rh alternative composed of abundant elements is desirable. Pd and Ru are located at the right and left of Rh in the periodic table, respectively, nevertheless this combination of elements is immiscible in the bulk state. Here, we report a Pd–Ru solid-solution-alloy nanoparticle (PdxRu1-xNP) catalyst exhibiting better NOxreduction activity than Rh. Theoretical calculations show that the electronic structure of Pd0.5Ru0.5is similar to that of Rh, indicating that Pd0.5Ru0.5can be regarded as a pseudo-Rh. Pd0.5Ru0.5exhibits better activity than natural Rh, which implies promising applications not only for exhaust-gas cleaning but also for various chemical reactions.
Conditioning adaptive combination of P-values method to analyze case-parent trios with or without population controls
Authors: Lin Wan-Yu , Liang Yun-Chieh
Published: June 2016

Detection of rare causal variants can help uncover the etiology of complex diseases. Recruiting case-parent trios is a popular study design in family-based studies. If researchers can obtain data from population controls, utilizing them in trio analyses can improve the power of methods. The transmission disequilibrium test (TDT) is a well-known method to analyze case-parent trio data. It has been extended to rare-variant association testing (abbreviated as “rvTDT”), with the flexibility to incorporate population controls. The rvTDT method is robust to population stratification. However, power loss may occur in the conditioning process. Here we propose a “conditioning adaptive combination of P-values method” (abbreviated as “conADA”), to analyze trios with/without unrelated controls. By first truncating the variants with larger P-values, we decrease the vulnerability of conADA to the inclusion of neutral variants. Moreover, because the test statistic is developed by conditioning on parental genotypes, conADA generates valid statistical inference in the presence of population stratification. With regard to statistical methods for next-generation sequencing data analyses, validity may be hampered by population stratification, whereas power may be affected by the inclusion of neutral variants. We recommend conADA for its robustness to these two factors (population stratification and the inclusion of neutral variants).
STARD6 on steroids: solution structure, multiple timescale backbone dynamics and ligand binding mechanism
Authors: Létourneau Danny , Bédard Mikaël , Cabana Jérôme , Lefebvre Andrée , LeHoux Jean-Guy , Lavigne Pierre
Published: June 2016

START domain proteins are conserved α/β helix-grip fold that play a role in the non-vesicular and intracellular transport of lipids and sterols. The mechanism and conformational changes permitting the entry of the ligand into their buried binding sites is not well understood. Moreover, their functions and the identification of cognate ligands is still an active area of research. Here, we report the solution structure of STARD6 and the characterization of its backbone dynamics on multiple time-scales through15N spin-relaxation and amide exchange studies. We reveal for the first time the presence of concerted fluctuations in the Ω1loop and the C-terminal helix on the microsecond-millisecond time-scale that allows for the opening of the binding site and ligand entry. We also report that STARD6 binds specifically testosterone. Our work represents a milestone for the study of ligand binding mechanism by other START domains and the elucidation of the biological function of STARD6.
Dual-pump Kerr Micro-cavity Optical Frequency Comb with varying FSR spacing
Authors: Wang Weiqiang , Chu Sai T. , Little Brent E. , Pasquazi Alessia , Wang Yishan , Wang Leiran , Zhang Wenfu , Wang Lei , Hu Xiaohong , Wang Guoxi , Hu Hui , Su Yulong , Li Feitao , Liu Yuanshan , Zhao Wei
Published: June 2016

In this paper, we demonstrate a novel dual-pump approach to generate robust optical frequency comb with varying free spectral range (FSR) spacing in a CMOS-compatible high-Q micro-ring resonator (MRR). The frequency spacing of the comb can be tuned by an integer number FSR of the MRR freely in our dual-pump scheme. The dual pumps are self-oscillated in the laser cavity loop and their wavelengths can be tuned flexibly by programming the tunable filter embedded in the cavity. By tuning the pump wavelength, broadband OFC with the bandwidth of >180 nm and the frequency-spacing varying from 6 to 46-fold FSRs is realized at a low pump power. This approach could find potential and practical applications in many areas, such as optical metrology, optical communication and signal processing systems, for its excellent flexibility and robustness.
Different Effects of sgRNA Length on CRISPR-mediated Gene Knockout Efficiency
Authors: Zhang Jian-Ping , Li Xiao-Lan , Neises Amanda , Chen Wanqiu , Hu Lin-Ping , Ji Guang-Zhen , Yu Jun-Yao , Xu Jing , Yuan Wei-Ping , Cheng Tao , Zhang Xiao-Bing
Published: June 2016

CRISPR-Cas9 is a powerful genome editing technology, yet with off-target effects. Truncated sgRNAs (17nt) have been found to decrease off-target cleavage without affecting on-target disruption in 293T cells. However, the potency of 17nt sgRNAs relative to the full-length 20nt sgRNAs in stem cells, such as human mesenchymal stem cells (MSCs) and induced pluripotent stem cells (iPSCs), has not been assessed. Using a GFP reporter system, we found that both 17nt and 20nt sgRNAs expressed by lentiviral vectors induce ~95% knockout (KO) in 293T cells, whereas the KO efficiencies are significantly lower in iPSCs (60–70%) and MSCs (65–75%). Furthermore, we observed a decrease of 10–20 percentage points in KO efficiency with 17nt sgRNAs compared to full-length sgRNAs in both iPSCs and MSCs. Off-target cleavage was observed in 17nt sgRNAs with 1-2nt but not 3-4nt mismatches; whereas 20nt sgRNAs with up to 5nt mismatches can still induce off-target mutations. Of interest, we occasionally observed off-target effects induced by the 17nt but not the 20nt sgRNAs. These results indicate the importance of balancing on-target gene cleavage potency with off-target effects: when efficacy is a major concern such as genome editing in stem cells, the use of 20nt sgRNAs is preferable.
Evolution of 2009 H1N1 influenza viruses during the pandemic correlates with increased viral pathogenicity and transmissibility in the ferret model
Authors: Otte Anna , Marriott Anthony C. , Dreier Carola , Dove Brian , Mooren Kyra , Klingen Thorsten R. , Sauter Martina , Thompson Katy-Anne , Bennett Allan , Klingel Karin , van Riel Debby , McHardy Alice C. , Carroll Miles W. , Gabriel Gülsah
Published: June 2016

There is increasing evidence that 2009 pandemic H1N1 influenza viruses have evolved after pandemic onset giving rise to severe epidemics in subsequent waves. However, it still remains unclear which viral determinants might have contributed to disease severity after pandemic initiation. Here, we show that distinct mutations in the 2009 pandemic H1N1 virus genome have occurred with increased frequency after pandemic declaration. Among those, a mutation in the viral hemagglutinin was identified that increases 2009 pandemic H1N1 virus binding to human-like α2,6-linked sialic acids. Moreover, these mutations conferred increased viral replication in the respiratory tract and elevated respiratory droplet transmission between ferrets. Thus, our data show that 2009 H1N1 influenza viruses have evolved after pandemic onset giving rise to novel virus variants that enhance viral replicative fitness and respiratory droplet transmission in a mammalian animal model. These findings might help to improve surveillance efforts to assess the pandemic risk by emerging influenza viruses.
SAS6-like protein in Plasmodium indicates that conoid-associated apical complex proteins persist in invasive stages within the mosquito vector
Authors: Wall Richard J. , Roques Magali , Katris Nicholas J. , Koreny Ludek , Stanway Rebecca R. , Brady Declan , Waller Ross F. , Tewari Rita
Published: June 2016

The SAS6-like (SAS6L) protein, a truncated paralogue of the ubiquitous basal body/centriole protein SAS6, has been characterised recently as a flagellum protein in trypanosomatids, but associated with the conoid in apicomplexan Toxoplasma. The conoid has been suggested to derive from flagella parts, but is thought to have been lost from some apicomplexans including the malaria-causing genus Plasmodium. Presence of SAS6L in Plasmodium, therefore, suggested a possible role in flagella assembly in male gametes, the only flagellated stage. Here, we have studied the expression and role of SAS6L throughout the Plasmodium life cycle using the rodent malaria model P. berghei. Contrary to a hypothesised role in flagella, SAS6L was absent during gamete flagellum formation. Instead, SAS6L was restricted to the apical complex in ookinetes and sporozoites, the extracellular invasive stages that develop within the mosquito vector. In these stages SAS6L forms an apical ring, as we show is also the case in Toxoplasma tachyzoites. The SAS6L ring was not apparent in blood-stage invasive merozoites, indicating that the apical complex is differentiated between the different invasive forms. Overall this study indicates that a conoid-associated apical complex protein and ring structure is persistent in Plasmodium in a stage-specific manner.
Photochromic switching of the DNA helicity induced by azobenzene derivatives
Authors: Deiana Marco , Pokladek Ziemowit , Olesiak-Banska Joanna , Młynarz Piotr , Samoc Marek , Matczyszyn Katarzyna
Published: June 2016

The photochromic properties of azobenzene, involving conformational changes occurring upon interaction with light, provide an excellent tool to establish new ways of selective regulation applied to biosystems. We report here on the binding of two water-soluble 4-(phenylazo)benzoic acid derivatives (Azo-2N and Azo-3N) with double stranded DNA and demonstrate that the photoisomerization of Azo-3N leads to changes in DNA structure. In particular, we show that stabilization and destabilization of the B-DNA secondary structure can be photochemically induced in situ by light. This photo-triggered process is fully reversible and could be an alternative pathway to control a broad range of biological processes. Moreover, we found that the bicationic Azo-3N exhibited a higher DNA-binding constant than the monocationic Azo-2N pointing out that the number of positive charges along the photosensitive polyamines chain plays a pivotal role in stabilizing the photochrome-DNA complex.
Gene Expression Profiling of Breast Cancer Brain Metastasis
Authors: Lee Ji Yun , Park Kyunghee , Lee Eunjin , Ahn TaeJin , Jung Hae Hyun , Lim Sung Hee , Hong Mineui , Do In-Gu , Cho Eun Yoon , Kim Duk-Hwan , Kim Ji-Yeon , Ahn Jin Seok , Im Young-Hyuck , Park Yeon Hee
Published: June 2016

The biology of breast cancer brain metastasis (BCBM) is poorly understood. We aimed to explore genes that are implicated in the process of brain metastasis of primary breast cancer (BC). NanoString nCounter Analysis covering 252 target genes was used for comparison of gene expression levels between 20 primary BCs that relapsed to brain and 41 BCBM samples. PAM50-based intrinsic subtypes such as HER2-enriched and basal-like were clearly over-represented in BCBM. A panel of 22 genes was found to be significantly differentially expressed between primary BC and BCBM. Five of these genes,CXCL12,MMP2,MMP11,VCAM1, andMME, which have previously been associated with tumor progression, angiogenesis, and metastasis, clearly discriminated between primary BC and BCBM. Notably, the five genes were significantly upregulated in primary BC compared to BCBM. Conversely,SOX2andOLIG2genes were upregulated in BCBM. These genes may participate in metastatic colonization but not in primary tumor development. Among patient-matched paired samples (n = 17), a PAM50 molecular subtype conversion was observed in eight cases (47.1%), with a trend toward unfavorable subtypes in patients with the distinct gene expression. Our findings, although not conclusive, reveal differentially expressed genes that might mediate the brain metastasis process.
Systems pathway engineering of Corynebacterium crenatum for improved L-arginine production
Authors: Man Zaiwei , Xu Meijuan , Rao Zhiming , Guo Jing , Yang Taowei , Zhang Xian , Xu Zhenghong
Published: June 2016

L-arginine is an important amino acid in food and pharmaceutical industries. Until now, the main production method of L-arginine in China is the highly polluting keratin acid hydrolysis. The industrial level L-arginine production by microbial fermentation has become an important task. In previous work, we obtained a new L-arginine producing Corynebacterium crenatum (subspecies of Corynebacterium glutamicum) through screening and mutation breeding. In this work, we performed systems pathway engineering of C. crenatum for improved L-arginine production, involving amplification of L-arginine biosynthetic pathway flux by removal of feedback inhibition and overexpression of arginine operon; optimization of NADPH supply by modulation of metabolic flux distribution between glycolysis and pentose phosphate pathway; increasing glucose consumption by strengthening the preexisting glucose transporter and exploitation of new glucose uptake system; channeling excess carbon flux from glycolysis into tricarboxylic acid cycle to alleviate the glucose overflow metabolism; redistribution of carbon flux at α-ketoglutarate metabolic node to channel more flux into L-arginine biosynthetic pathway; minimization of carbon and cofactor loss by attenuation of byproducts formation. The final strain could produce 87.3 g L−1 L-arginine with yield up to 0.431 g L-arginine g−1 glucose in fed-batch fermentation.
Ventromedial prefrontal cortex, adding value to autobiographical memories
Authors: Lin Wen-Jing , Horner Aidan J. , Burgess Neil
Published: June 2016

The medial prefrontal cortex (mPFC) has been consistently implicated in autobiographical memory recall and decision making. Its function in decision making tasks is believed to relate to value representation, but its function in autobiographical memory recall is not yet clear. We hypothesised that the mPFC represents the subjective value of elements during autobiographical memory retrieval. Using functional magnetic resonance imaging during an autobiographical memory recall task, we found that the blood oxygen level dependent (BOLD) signal in ventromedial prefrontal cortex (vmPFC) was parametrically modulated by the affective values of items in participants’ memories when they were recalling and evaluating these items. An unrelated modulation by the participant’s familiarity with the items was also observed. During retrieval of the event, the BOLD signal in the same region was modulated by the personal significance and emotional intensity of the memory, which was correlated with the values of the items within them. These results support the idea that vmPFC processes self-relevant information and suggest that it is involved in representing the personal emotional values of the elements comprising autobiographical memories.
REAC technology and hyaluron synthase 2, an interesting network to slow down stem cell senescence
Authors: Maioli Margherita , Rinaldi Salvatore , Pigliaru Gianfranco , Santaniello Sara , Basoli Valentina , Castagna Alessandro , Fontani Vania , Ventura Carlo
Published: June 2016

Hyaluronic acid (HA) plays a fundamental role in cell polarity and hydrodynamic processes, affording significant modulation of proliferation, migration, morphogenesis and senescence, with deep implication in the ability of stem cells to execute their differentiating plans. The Radio Electric Asymmetric Conveyer (REAC) technology is aimed to optimize the ions fluxes at the molecular level in order to optimize the molecular mechanisms driving cellular asymmetry and polarization. Here, we show that treatment with 4-methylumbelliferone (4-MU), a potent repressor of type 2 HA synthase and endogenous HA synthesis, dramatically antagonized the ability of REAC to recover the gene and protein expression of Bmi1, Oct4, Sox2, and Nanog in ADhMSCs that had been made senescent by prolonged culture up to the 30th passage. In senescent ADhMSCs, 4-MU also counteracted the REAC ability to rescue the gene expression of TERT, and the associated resumption of telomerase activity. Hence, the anti-senescence action of REAC is largely dependent upon the availability of endogenous HA synthesis. Endogenous HA and HA-binding proteins with REAC technology create an interesting network that acts on the modulation of cell polarity and intracellular environment. This suggests that REAC technology is effective on an intracellular niche level of stem cell regulation.
Using oriented peptide array libraries to evaluate methylarginine-specific antibodies and arginine methyltransferase substrate motifs
Authors: Gayatri Sitaram , Cowles Martis W. , Vemulapalli Vidyasiri , Cheng Donghang , Sun Zu-Wen , Bedford Mark T.
Published: June 2016

Signal transduction in response to stimuli relies on the generation of cascades of posttranslational modifications that promote protein-protein interactions and facilitate the assembly of distinct signaling complexes. Arginine methylation is one such modification, which is catalyzed by a family of nine protein arginine methyltransferases, or PRMTs. Elucidating the substrate specificity of each PRMT will promote a better understanding of which signaling networks these enzymes contribute to. Although many PRMT substrates have been identified and their methylation sites mapped, the optimal target motif for each of the nine PRMTs has not been systematically addressed. Here we describe the use of Oriented Peptide Array Libraries (OPALs) to methodically dissect the preferred methylation motifs for three of these enzymes – PRMT1, CARM1 and PRMT9. In parallel, we show that an OPAL platform with a fixed methylarginine residue can be used to validate the methyl-specific and sequence-specific properties of antibodies that have been generated against different PRMT substrates and can also be used to confirm the pan nature of some methylarginine-specific antibodies.
Photo-derived transformation from modified chitosan@calcium carbonate nanohybrids to nanosponges
Authors: Byeon Jeong Hoon
Published: June 2016

Zwitterionic chitosan (ZC)@calcium carbonate (CC) nanoparticles were conveniently obtained and transformed to biocompatible nanosponges by continuous gas-phase photo-derived transformation in a single-pass configuration, and their potential use for biomedical applications was investigated. The mean diameter of the ZC@CC sponges was ~166 nm (~72 nm for CC and, ~171 nm for ZC), and the sponges had a mesoporous structure (i.e., an average pore diameter of ~13 nm). Measurements of the sponge cytotoxicity were performed and only a slight decrease was observed (>78% in cell viability) when compared with pure ZC (>80%). The ZC@CC sponges had a similar transfection ability to lipofectamine (~2.7 × 109RLU mg−1protein) at a 50:1 ratio of sponge:DNA weight. Because of a porous structure, the sponges showed remarkably higher transfection efficiencies than pure ZC.
The dynamics of human behavior in the public goods game with institutional incentives
Authors: Dong Yali , Zhang Boyu , Tao Yi
Published: June 2016

The empirical research on the public goods game (PGG) indicates that both institutional rewards and institutional punishment can curb free-riding and that the punishment effect is stronger than the reward effect. Self-regarding models that are based on Nash equilibrium (NE) strategies or evolutionary game dynamics correctly predict which incentives are best at promoting cooperation, but individuals do not play these rational strategies overall. The goal of our study is to investigate the dynamics of human decision making in the repeated PGG with institutional incentives. We consider that an individual’s contribution is affected by four factors, which are self-interest, the behavior of others, the reaction to rewards and the reaction to punishment. We find that people on average do not react to rewards and punishment and that self-interest and the behavior of others sufficiently explain the dynamics of human behavior. Further analysis suggests that institutional incentives promote cooperation by affecting the self-regarding preference and that the other-regarding preference seems to be independent of incentive schemes. Because individuals do not change their behavioral patterns even if they were not rewarded or punished, the mere potential to punish defectors and reward cooperators can lead to considerable increases in the level of cooperation.
A colorimetric and fluorometric sensor for the determination of norepinephrine
Authors: Menon Shalini , Jose Ammu Rosin , Jesny S. , Kumar Krishnapillai Girish
Published: June 2016

Visual detection of brown silver NPs formed from silver nitrate in the presence of NE exhibiting strong metal enhanced fluorescence signals.
Multifunctional supramolecular vesicles based on the complex of ferrocenecarboxylic acid capped pillar[5]arene and a galactose derivative for targeted drug delivery
Authors: Chang Yincheng , Hou Chenxi , Ren Jingli , Xin Xiaoting , Pei Yuxin , Lu Yuchao , Cao Shoupeng , Pei Zhichao
Published: June 2016

Supramolecular vesicles have been constructed based on the host–guest complexation, which show dual-responsiveness and cancer cells targetability.
Tin-based composite anodes for potassium-ion batteries
Authors: Sultana Irin , Ramireddy Thrinathreddy , Rahman Md Mokhlesur , Chen Ying , Glushenkov Alexey M.
Published: June 2016

An anode based on the tetragonal tin (Sn) phase that can alloy electrochemically with potassium is demonstrated for potassium-ion batteries.
A novel iridium/acid co-catalyzed transfer hydrogenative C(sp3)–H bond alkylation to access functionalized N-heteroaromatics
Authors: Tan Zhenda , Jiang Huanfeng , Zhang Min
Published: June 2016

A transfer hydrogenative coupling strategy, enabling direct alkylation of C(sp3)–H bonds and atom-economic access to functionalized N-heteroaromatics, has been demonstrated.
MnO nanoparticles embedded in a carbon matrix as high performance lithium-ion battery anodes: preparation, microstructure and electrochemistry
Authors: Ma Shaojun , Chen Dongming , Wang Wen-lou
Published: June 2016

Nano-sized MnO intimately embedded in a porous carbon matrix has been synthesized by a facile method where the manganese-salts/glycerol sol was used as the precursor.
Fluorescence enhancement in visible light: dielectric or noble metal?
Authors: Sun S. , Wu L. , Bai P. , Png C. E.
Published: June 2016

A comprehensive comparison is conducted between a dielectric and plasmonic metal to evaluate their capability and applicability in fluorescence enhancement.
Energy transfer and tunable multicolor emission and paramagnetic properties of GdF3:Dy3+,Tb3+,Eu3+ phosphors
Authors: Guan Hongxia , Sheng Ye , Xu Chengyi , Dai Yunzhi , Xie Xiaoming , Zou Haifeng
Published: June 2016

GdF3:RE3+ (RE = Dy3+, Tb3+, Eu3+) phosphors can realize multicolor emission including white light. Simultaneously, GdF3:RE3+ (RE = Dy3+, Tb3+, Eu3+) phosphors also exhibit paramagnetic properties at room temperature and low temperatures.
Aqueous biphasic systems composed of ionic liquids and polypropylene glycol: insights into their liquid–liquid demixing mechanisms
Authors: Neves Catarina M. S. S. , Shahriari Shahla , Lemus Jesus , Pereira Jorge F. B. , Freire Mara G. , Coutinho João A. P.
Published: June 2016

Comprehensive analysis on the molecular level mechanisms ruling the formation of aqueous biphasic systems.
Synthetic analogues of Fe(ii)–Fe(iii) minerals containing a pentagonal ‘Cairo’ magnetic lattice
Authors: Cumby J. , Bayliss R. D. , Berry F. J. , Greaves C.
Published: June 2016

Synthesis, properties and chemical modification of low-dimensional minerals.
Calorimetric studies of the interactions of metalloenzyme active site mimetics with zinc-binding inhibitors
Authors: Robinson Sophia G. , Burns Philip T. , Miceli Amanda M. , Grice Kyle A. , Karver Caitlin E. , Jin Lihua
Published: June 2016

The binding of drugs to metalloenzymes is an intricate process that involves several interactions, including binding of the drug to the enzyme active site metal, as well as multiple interactions between the drug and the enzyme residues.
Transformation kinetics of silver nanoparticles and silver ions in aquatic environments revealed by double stable isotope labeling
Authors: Yu Sujuan , Yin Yongguang , Zhou Xiaoxia , Dong Lijie , Liu Jingfu
Published: June 2016

A double stable isotope labeling method (107AgNPs and 109AgNO3) was used to track the transformation kinetics of AgNPs and Ag+ in aquatic environments.
Designing a multicolor long range nanoscopic ruler for the imaging of heterogeneous tumor cells
Authors: Chavva Suhash Reddy , Viraka Nellore Bhanu Priya , Pramanik Avijit , Sinha Sudarson Sekhar , Jones Stacy , Ray Paresh Chandra
Published: June 2016

Multicolor NSET probes are capable of selective and simultaneous detection of cancer stem cells and epithelial cells.
A bimodal fluorescent and photocytotoxic naphthalene diimide for theranostic applications
Authors: Salvati Erica , Doria Filippo , Manoli Francesco , D'Angelo Carmen , Biroccio Annamaria , Freccero Mauro , Manet Ilse
Published: June 2016

We describe the bimodal activity of a water-soluble tetracationic naphthalene diimide as red light emitter for fluorescence imaging, including fluorescence-lifetime imaging, and singlet oxygen photosensitizer, inducing photocytotoxicity in cancer cells.