bluuebunny/crossref_metadata_2025 huggingface dataset:
A phenome-wide examination of neural and cognitive function
Authors: Poldrack R.A. , Congdon E. , Triplett W. , Gorgolewski K.J. , Karlsgodt K.H. , Mumford J.A. , Sabb F.W. , Freimer N.B. , London E.D. , Cannon T.D. , Bilder R.M.
Published: December 2016

This data descriptor outlines a shared neuroimaging dataset from the UCLA Consortium for Neuropsychiatric Phenomics, which focused on understanding the dimensional structure of memory and cognitive control (response inhibition) functions in both healthy individuals (130 subjects) and individuals with neuropsychiatric disorders including schizophrenia (50 subjects), bipolar disorder (49 subjects), and attention deficit/hyperactivity disorder (43 subjects). The dataset includes an extensive set of task-based fMRI assessments, resting fMRI, structural MRI, and high angular resolution diffusion MRI. The dataset is shared through the OpenfMRI project, and is formatted according to the Brain Imaging Data Structure (BIDS) standard.
Correction: Corrigendum: A database of marine phytoplankton abundance, biomass and species composition in Australian waters
Authors: Davies Claire H. , Coughlan Alex , Hallegraeff Gustaaf , Ajani Penelope , Armbrecht Linda , Atkins Natalia , Bonham Prudence , Brett Steve , Brinkman Richard , Burford Michele , Clementson Lesley , Coad Peter , Coman Frank , Davies Diana , Dela-Cruz Jocelyn , Devlin Michelle , Edgar Steven , Eriksen Ruth , Furnas Miles , Hassler Christel , Hill David , Holmes Michael , Ingleton Tim , Jameson Ian , Leterme Sophie C. , Lønborg Christian , McLaughlin James , McEnnulty Felicity , McKinnon A. David , Miller Margaret , Murray Shauna , Nayar Sasi , Patten Renee , Pausina Sarah A. , Pritchard Tim , Proctor Roger , Purcell-Meyerink Diane , Raes Eric , Rissik David , Ruszczyk Jason , Slotwinski Anita , Swadling Kerrie M. , Tattersall Katherine , Thompson Peter , Thomson Paul , Tonks Mark , Trull Thomas W. , Uribe-Palomino Julian , Waite Anya M. , Yauwenas Rouna , Zammit Anthony , Richardson Anthony J.
Published: December 2016

Scientific Data 3:160043 doi:10.1038/sdata.2016.43 (2016); Published 21 Jun 2016; Updated 6 Dec 2016 A series of errors in our database were brought to our attention by readers, and have been corrected in an updated version of this database, which is accessible via the AODN at the following link: https://portal.
Umbilical Cord-derived Mesenchymal Stem Cells Instruct Monocytes Towards an IL10-producing Phenotype by Secreting IL6 and HGF
Authors: Deng Yinan , Zhang Yingcai , Ye Linsen , Zhang Tong , Cheng Jintao , Chen Guihua , Zhang Qi , Yang Yang
Published: December 2016

Human UC-MSCs are regarded as an attractive alternative to BM-MSCs for clinical applications due to their easy preparation, higher proliferation and lower immunogenicity. However, the mechanisms underlying immune suppression by UC-MSCs are still unclear. We studied the mechanism of inhibition by UC-MSCs during the differentiation of monocytes into DCs and focused on the specific source and the role of the involved cytokines. We found that UC-MSCs suppressed monocyte differentiation into DCs and instructed monocytes towards other cell types, with clear decreases in the expression of co-stimulatory molecules, in the secretion of inflammatory factors and in allostimulatory capacity. IL6, HGF and IL10 might be involved in this process because they were detected at higher levels in a coculture system. UC-MSCs produce IL-6 and HGF, and neutralization of IL-6 and HGF reversed the suppressive effect of UC-MSCs. IL10 was not produced by UC-MSCs but was exclusively produced by monocytes after exposure to UC-MSCs, IL-6 or HGF. In summary, we found that the UC-MSC-mediated inhibitory effect was dependent on IL6 and HGF secreted by UC-MSCs and that this effect induced monocyte-derived cells to produce IL10, which might indirectly strengthen the suppressive effect of UC-MSCs.
Exploring experimental cerebral malaria pathogenesis through the characterisation of host-derived plasma microparticle protein content
Authors: Tiberti Natalia , Latham Sharissa L. , Bush Stephen , Cohen Amy , Opoka Robert O. , John Chandy C. , Juillard Annette , Grau Georges E. , Combes Valéry
Published: December 2016

Cerebral malaria (CM) is a severe complication of Plasmodium falciparum infection responsible for thousands of deaths in children in sub-Saharan Africa. CM pathogenesis remains incompletely understood but a number of effectors have been proposed, including plasma microparticles (MP). MP numbers are increased in CM patients’ circulation and, in the mouse model, they can be localised within inflamed vessels, suggesting their involvement in vascular damage. In the present work we define, for the first time, the protein cargo of MP during experimental cerebral malaria (ECM) with the overarching hypothesis that this characterisation could help understand CM pathogenesis. Using qualitative and quantitative high-throughput proteomics we compared MP proteins from non-infected and P. berghei ANKA-infected mice. More than 360 proteins were identified, 60 of which were differentially abundant, as determined by quantitative comparison using TMTTM isobaric labelling. Network analyses showed that ECM MP carry proteins implicated in molecular mechanisms relevant to CM pathogenesis, including endothelial activation. Among these proteins, the strict association of carbonic anhydrase I and S100A8 with ECM was verified by western blot on MP from DBA/1 and C57BL/6 mice. These results demonstrate that MP protein cargo represents a novel ECM pathogenic trait to consider in the understanding of CM pathogenesis.
Comparison of cell behavior on pva/pva-gelatin electrospun nanofibers with random and aligned configuration
Authors: Huang Chen-Yu , Hu Keng-Hsiang , Wei Zung-Hang
Published: December 2016

Electrospinning technique is able to create nanofibers with specific orientation. Poly(vinyl alcohol) (PVA) have good mechanical stability but poor cell adhesion property due to the low affinity of protein. In this paper, extracellular matrix, gelatin is incorporated into PVA solution to form electrospun PVA-gelatin nanofibers membrane. Both randomly oriented and aligned nanofibers are used to investigate the topography-induced behavior of fibroblasts. Surface morphology of the fibers is studied by optical microscopy and scanning electron microscopy (SEM) coupled with image analysis. Functional group composition in PVA or PVA-gelatin is investigated by Fourier Transform Infrared (FTIR). The morphological changes, surface coverage, viability and proliferation of fibroblasts influenced by PVA and PVA-gelatin nanofibers with randomly orientated or aligned configuration are systematically compared. Fibroblasts growing on PVA-gelatin fibers show significantly larger projected areas as compared with those cultivated on PVA fibers which p-value is smaller than 0.005. Cells on PVA-gelatin aligned fibers stretch out extensively and their intracellular stress fiber pull nucleus to deform. Results suggest that instead of the anisotropic topology within the scaffold trigger the preferential orientation of cells, the adhesion of cell membrane to gelatin have substantial influence on cellular behavior.
DNA intercalation optimized by two-step molecular lock mechanism
Authors: Almaqwashi Ali A. , Andersson Johanna , Lincoln Per , Rouzina Ioulia , Westerlund Fredrik , Williams Mark C.
Published: December 2016

The diverse properties of DNA intercalators, varying in affinity and kinetics over several orders of magnitude, provide a wide range of applications for DNA-ligand assemblies. Unconventional intercalation mechanisms may exhibit high affinity and slow kinetics, properties desired for potential therapeutics. We used single-molecule force spectroscopy to probe the free energy landscape for an unconventional intercalator that binds DNA through a novel two-step mechanism in which the intermediate and final states bind DNA through the same mono-intercalating moiety. During this process, DNA undergoes significant structural rearrangements, first lengthening before relaxing to a shorter DNA-ligand complex in the intermediate state to form a molecular lock. To reach the final bound state, the molecular length must increase again as the ligand threads between disrupted DNA base pairs. This unusual binding mechanism results in an unprecedented optimized combination of high DNA binding affinity and slow kinetics, suggesting a new paradigm for rational design of DNA intercalators.
Relocation of active site carboxylates in major facilitator superfamily multidrug transporter LmrP reveals plasticity in proton interactions
Authors: Nair Asha V. , Singh Himansha , Raturi Sagar , Neuberger Arthur , Tong Zhen , Ding Ning , Agboh Kelvin , van Veen Hendrik W.
Published: December 2016

The expression of polyspecific membrane transporters is one important mechanism by which cells can obtain resistance to structurally different antibiotics and cytotoxic agents. These transporters reduce intracellular drug concentrations to subtoxic levels by mediating drug efflux across the cell envelope. The major facilitator superfamily multidrug transporter LmrP from Lactococcus lactis catalyses drug efflux in a membrane potential and chemical proton gradient-dependent fashion. To enable the interaction with protons and cationic substrates, LmrP contains catalytic carboxyl residues on the surface of a large interior chamber that is formed by transmembrane helices. These residues co-localise together with polar and aromatic residues, and are predicted to be present in two clusters. To investigate the functional role of the catalytic carboxylates, we generated mutant proteins catalysing membrane potential-independent dye efflux by removing one of the carboxyl residues in Cluster 1. We then relocated this carboxyl residue to six positions on the surface of the interior chamber, and tested for restoration of wildtype energetics. The reinsertion at positions towards Cluster 2 reinstated the membrane potential dependence of dye efflux. Our data uncover a remarkable plasticity in proton interactions in LmrP, which is a consequence of the flexibility in the location of key residues that are responsible for proton/multidrug antiport.
Parity Deformed Jaynes-Cummings Model: “Robust Maximally Entangled States”
Authors: Dehghani A. , Mojaveri B. , Shirin S. , Faseghandis S. Amiri
Published: December 2016

The parity-deformations of the quantum harmonic oscillator are used to describe the generalized Jaynes-Cummings model based on the λ-analog of the Heisenberg algebra. The behavior is interestingly that of a coupled system comprising a two-level atom and a cavity field assisted by a continuous external classical field. The dynamical characters of the system is explored under the influence of the external field. In particular, we analytically study the generation of robust and maximally entangled states formed by a two-level atom trapped in a lossy cavity interacting with an external centrifugal field. We investigate the influence of deformation and detuning parameters on the degree of the quantum entanglement and the atomic population inversion. Under the condition of a linear interaction controlled by an external field, the maximally entangled states may emerge periodically along with time evolution. In the dissipation regime, the entanglement of the parity deformed JCM are preserved more with the increase of the deformation parameter, i.e. the stronger external field induces better degree of entanglement.
Heterotrophy promotes the re-establishment of photosynthate translocation in a symbiotic coral after heat stress
Authors: Tremblay Pascale , Gori Andrea , Maguer Jean François , Hoogenboom Mia , Ferrier-Pagès Christine
Published: December 2016

Symbiotic scleractinian corals are particularly affected by climate change stress and respond by bleaching (losing their symbiotic dinoflagellate partners). Recently, the energetic status of corals is emerging as a particularly important factor that determines the corals’ vulnerability to heat stress. However, detailed studies of coral energetic that trace the flow of carbon from symbionts to host are still sparse. The present study thus investigates the impact of heat stress on the nutritional interactions between dinoflagellates and coral Stylophora pistillata maintained under auto- and heterotrophy. First, we demonstrated that the percentage of autotrophic carbon retained in the symbionts was significantly higher during heat stress than under non-stressful conditions, in both fed and unfed colonies. This higher photosynthate retention in symbionts translated into lower rates of carbon translocation, which required the coral host to use tissue energy reserves to sustain its respiratory needs. As calcification rates were positively correlated to carbon translocation, a significant decrease in skeletal growth was observed during heat stress. This study also provides evidence that heterotrophic nutrient supply enhances the re-establishment of normal nutritional exchanges between the two symbiotic partners in the coral S. pistillata, but it did not mitigate the effects of temperature stress on coral calcification.
13-Methylberberine, a berberine analogue with stronger anti-adipogenic effects on mouse 3T3-L1 cells
Authors: Chow Yit-Lai , Sogame Mami , Sato Fumihiko
Published: December 2016

Lipid metabolism modulation is a main focus of metabolic syndrome research, an area in which many natural and synthetic chemicals are constantly being screened for in vitro and in vivo activity. Berberine, a benzylisoquinoline plant alkaloid, has been extensively investigated for its anti-obesity effects and as a potential cholesterol and triglyceride-lowering drug. We screened 11 protoberberine and 2 benzophenanthridine alkaloids for their anti-adipogenic effects on 3T3-L1 adipocytes and found that 13-methylberberine exhibited the most potent activity. 13-Methylberberine down-regulated the expression of the main adipocyte differentiation transcription factors, peroxisome proliferator-activated receptor gamma (PPARγ) and CCAAT enhancer binding protein alpha (C/EBPα), as well as their target genes. PPARγ, C/EBPα, and sterol regulatory element binding protein 1 (SREBP-1) protein levels were reduced, and this lipid-reducing effect was attenuated by an AMP-activated protein kinase (AMPK) inhibitor, indicating that the effect of this compound requires the AMPK signaling pathway. Decreased Akt phosphorylation suggested reduced de novo lipid synthesis. C-13 methyl substitution of berberine increased its accumulation in treated cells, suggesting that 13-methylberberine has improved absorption and higher accumulation compared to berberine. Our findings suggest that 13-methylberberine has potential as an anti-obesity drug.
OsSGL, a novel pleiotropic stress-related gene enhances grain length and yield in rice
Authors: Wang Manling , Lu Xuedan , Xu Guoyun , Yin Xuming , Cui Yanchun , Huang Lifang , Rocha Pedro S. C. F. , Xia Xinjie
Published: December 2016

Abiotic stress seriously affects the yield of rice (Oryza sativaL.). Grain yield in rice is multiplicatively determined by the number of panicles, number of grains per panicle, and grain weight. Here, we describe the molecular and functional characterization ofSTRESS_tolerance and GRAIN_LENGTH (OsSGL), a rice gene strongly up-regulated by a wide spectrum of abiotic stresses.OsSGLencodes a putative member of the DUF1645 protein family of unknown function. Overexpression ofOsSGLsignificantly altered certain development processes greatly and positively affecting an array of traits in transgenic rice plants, including increased grain length, grain weight and grain number per panicle, resulting in a significant increase in yield. Microscopical analysis showed that the enhancedOsSGLexpression promoted cell division and grain filling. Microarray and quantitative real-time PCR (qRT-PCR) analyses revealed that a large number of genes involved in stress-response, cell cycle and cytokinin signaling processes were induced or suppressed inOsSGL-overexpressing plants. Together, our results suggest thatOsSGLmay regulate stress-tolerance and cell growth by acting via a cytokinin signaling pathway. This study not only contributes to our understanding of the underlying mechanism regulating rice stress-tolerance and grain length, but also provides a strategy for tailor-made crop yield improvement.
Fish DNA-modified clays: Towards highly flame retardant polymer nanocomposite with improved interfacial and mechanical performance
Authors: Zabihi Omid , Ahmadi Mojtaba , Khayyam Hamid , Naebe Minoo
Published: December 2016

Deoxyribonucleic Acid (DNA) has been recently found to be an efficient renewable and environmentally-friendly flame retardant. In this work, for the first time, we have used waste DNA from fishing industry to modify clay structure in order to increase the clay interactions with epoxy resin and take benefit of its additional thermal property effect on thermo-physical properties of epoxy-clay nanocomposites. Intercalation of DNA within the clay layers was accomplished in a one-step approach confirmed by FT-IR, XPS, TGA, and XRD analyses, indicating that d-space of clay layers was expanded from ~1.2 nm for pristine clay to ~1.9 nm for clay modified with DNA (d-clay). Compared to epoxy nanocomposite containing 2.5%wt of Nanomer I.28E organoclay (m-clay), it was found that at 2.5%wt d-clay loading, significant enhancements of ~14%, ~6% and ~26% in tensile strength, tensile modulus, and fracture toughness of epoxy nanocomposite can be achieved, respectively. Effect of DNA as clay modifier on thermal performance of epoxy nanocomposite containing 2.5%wt d-clay was evaluated using TGA and cone calorimetry analysis, revealing significant decreases of ~4000 kJ/m2 and ~78 kW/m2 in total heat release and peak of heat release rate, respectively, in comparison to that containing 2.5%wt of m-clay.
Implementing a benchmarking and feedback concept decreases postoperative pain after total knee arthroplasty: A prospective study including 256 patients
Authors: Benditz A. , Drescher J. , Greimel F. , Zeman F. , Grifka J. , Meißner W. , Völlner F.
Published: December 2016

Perioperative pain reduction, particularly during the first two days, is highly important for patients after total knee arthroplasty (TKA). Problems are not only caused by medical issues but by organization and hospital structure. The present study shows how the quality of pain management can be increased by implementing a standardized pain concept and simple, consistent benchmarking. All patients included into the study had undergone total knee arthroplasty. Outcome parameters were analyzed by means of a questionnaire on the first postoperative day. A multidisciplinary team implemented a regular procedure of data analyzes and external benchmarking by participating in a nationwide quality improvement project. At the beginning of the study, our hospital ranked 16th in terms of activity-related pain and 9th in patient satisfaction among 47 anonymized hospitals participating in the benchmarking project. At the end of the study, we had improved to 1st activity-related pain and to 2nd in patient satisfaction. Although benchmarking started and finished with the same standardized pain management concept, results were initially pure. Beside pharmacological treatment, interdisciplinary teamwork and benchmarking with direct feedback mechanisms are also very important for decreasing postoperative pain and for increasing patient satisfaction after TKA.
Blood-borne phagocytes internalize urate microaggregates and prevent intravascular NETosis by urate crystals
Authors: Pieterse Elmar , Jeremic Ivica , Czegley Christine , Weidner Daniela , Biermann Mona H.C. , Veissi Susan , Maueröder Christian , Schauer Christine , Bilyy Rostyslav , Dumych Tetiana , Hoffmann Markus , Munoz Luis E. , Bengtsson Anders A. , Schett Georg , van der Vlag Johan , Herrmann Martin
Published: December 2016

Hyperuricemia is strongly linked to cardiovascular complications including atherosclerosis and thrombosis. In individuals with hyperuricemia, needle-shaped monosodium urate crystals (nsMSU) frequently form within joints or urine, giving rise to gouty arthritis or renal calculi, respectively. These nsMSU are potent instigators of neutrophil extracellular trap (NET) formation. Little is known on the mechanism(s) that prevent nsMSU formation within hyperuricemic blood, which would potentially cause detrimental consequences for the host. Here, we report that complement proteins and fetuins facilitate the continuous clearance by blood-borne phagocytes and resident macrophages of small urate microaggregates (UMA; <1 μm in size) that initially form in hyperuricemic blood. If this clearance fails, UMA exhibit bipolar growth to form typical full-sized nsMSU with a size up to 100 μm. In contrast to UMA, nsMSU stimulated neutrophils to release NETs. Under conditions of flow, nsMSU and NETs formed densely packed DNase I-resistant tophus-like structures with a high obstructive potential, highlighting the importance of an adequate and rapid removal of UMA from the circulation. Under pathological conditions, intravascularly formed nsMSU may hold the key to the incompletely understood association between NET-driven cardiovascular disease and hyperuricemia.
Blood hsa-miR-122-5p and hsa-miR-885-5p levels associate with fatty liver and related lipoprotein metabolism—The Young Finns Study
Authors: Raitoharju Emma , Seppälä Ilkka , Lyytikäinen Leo-Pekka , Viikari Jorma , Ala-Korpela Mika , Soininen Pasi , Kangas Antti J. , Waldenberger Melanie , Klopp Norman , Illig Thomas , Leiviskä Jaana , Loo Britt-Marie , Oksala Niku , Kähönen Mika , Hutri-Kähönen Nina , Laaksonen Reijo , Raitakari Olli , Lehtimäki Terho
Published: December 2016

MicroRNAs are involved in disease development and may be utilized as biomarkers. We investigated the association of blood miRNA levels and a) fatty liver (FL), b) lipoprotein and lipid pathways involved in liver lipid accumulation and c) levels of predicted mRNA targets in general population based cohort. Blood microRNA profiling (TaqMan OpenArray), genome-wide gene expression arrays and nuclear magnetic resonance metabolomics were performed for Young Finns Study participants aged 34–49 years (n = 871). Liver fat status was assessed ultrasonographically. Levels of hsa-miR-122-5p and -885-5p were up-regulated in individuals with FL (fold change (FC) = 1.55, p = 1.36 * 10−14 and FC = 1.25, p = 4.86 * 10−4, respectively). In regression model adjusted with age, sex and BMI, hsa-miR-122-5p and -885-5p predicted FL (OR = 2.07, p = 1.29 * 10−8 and OR = 1.41, p = 0.002, respectively). Together hsa-miR-122-5p and -885-5p slightly improved the detection of FL beyond established risk factors. These miRNAs may be associated with FL formation through the regulation of lipoprotein metabolism as hsa-miR-122-5p levels associated with small VLDL, IDL, and large LDL lipoprotein subclass components, while hsa-miR-885-5p levels associated inversely with XL HDL cholesterol levels. Hsa-miR-885-5p levels correlated inversely with oxysterol-binding protein 2 (OSBPL2) expression (r = −0.143, p = 1.00 * 10−4) and suppressing the expression of this lipid receptor and sterol transporter could link hsa-miR-885-5p with HDL cholesterol levels.
A century of temporal stability of genetic diversity in wild bumblebees
Authors: Maebe Kevin , Meeus Ivan , Vray Sarah , Claeys Thomas , Dekoninck Wouter , Boevé Jean-Luc , Rasmont Pierre , Smagghe Guy
Published: December 2016

Since the 1950s, bumblebee (Bombus) species are showing a clear decline worldwide. Although many plausible drivers have been hypothesized, the cause(s) of this phenomenon remain debated. Here, genetic diversity in recentversushistorical populations of bumblebee species was investigated by selecting four currently restricted and four currently widespread species. Specimens from five locations in Belgium were genotyped at 16 microsatellite loci, comparing historical specimens (1913–1915) with recent ones (2013–2015). Surprisingly, our results showed temporal stability of genetic diversity in the restricted species. Furthermore, both historical and recent populations of restricted species showed a significantly lower genetic diversity than found in populations of co-occurring widespread species. The difference in genetic diversity between species was thus already present before the alleged recent drivers of bumblebee decline could have acted (from the 1950’s). These results suggest that the alleged drivers are not directly linked with the genetic variation of currently declining bumblebee populations. A future sampling in the entire distribution range of these species will infer if the observed link between low genetic diversity and population distribution on the Belgium scale correlates with species decline on a global scale.
Small molecules increase direct neural conversion of human fibroblasts
Authors: Pfisterer Ulrich , Ek Fredrik , Lang Stefan , Soneji Shamit , Olsson Roger , Parmar Malin
Published: December 2016

The generation of human induced neurons (hiNs) via exogenous delivery of neural transcription factors represents a novel technique to obtain disease and patient specific neurons. These cells have the potential to be used for disease modeling, diagnostics and drug screening, and also to be further developed for brain repair. In the present study, we utilized hiNs to develop an unbiased screening assay for small molecules that increase the conversion efficiency. Using this assay, we screened 307 compounds from five annotated libraries and identified six compounds that were very potent in potentiating the reprogramming process. When combined in an optimal combination and dose, these compounds increased the reprogramming efficiency of human fibroblasts more than 6-fold. Global gene expression and CellNet analysis at different timepoints during the reprogramming process revealed that neuron-specific genes and gene regulatory networks (GRNs) became progressively more activated while converting cells shut down fibroblast-specific GRNs. Further bioinformatics analysis revealed that the addition of the six compound resulted in the accelerated upregulation of a subset of neuronal genes, and also increased expression of genes associated with transcriptional activity and mediation of cellular stress response.
New Insights into Molecular Organization of Human Neuraminidase-1: Transmembrane Topology and Dimerization Ability
Authors: Maurice Pascal , Baud Stéphanie , Bocharova Olga V. , Bocharov Eduard V. , Kuznetsov Andrey S. , Kawecki Charlotte , Bocquet Olivier , Romier Beatrice , Gorisse Laetitia , Ghirardi Maxime , Duca Laurent , Blaise Sébastien , Martiny Laurent , Dauchez Manuel , Efremov Roman G. , Debelle Laurent
Published: December 2016

Neuraminidase 1 (NEU1) is a lysosomal sialidase catalyzing the removal of terminal sialic acids from sialyloconjugates. A plasma membrane-bound NEU1 modulating a plethora of receptors by desialylation, has been consistently documented from the last ten years. Despite a growing interest of the scientific community to NEU1, its membrane organization is not understood and current structural and biochemical data cannot account for such membrane localization. By combining molecular biology and biochemical analyses with structural biophysics and computational approaches, we identified here two regions in human NEU1 - segments 139–159 (TM1) and 316–333 (TM2) - as potential transmembrane (TM) domains. In membrane mimicking environments, the corresponding peptides form stable α-helices and TM2 is suited for self-association. This was confirmed with full-size NEU1 by co-immunoprecipitations from membrane preparations and split-ubiquitin yeast two hybrids. The TM2 region was shown to be critical for dimerization since introduction of point mutations within TM2 leads to disruption of NEU1 dimerization and decrease of sialidase activity in membrane. In conclusion, these results bring new insights in the molecular organization of membrane-bound NEU1 and demonstrate, for the first time, the presence of two potential TM domains that may anchor NEU1 in the membrane, control its dimerization and sialidase activity.
Association of MTDH immunohistochemical expression with metastasis and prognosis in female reproduction malignancies: a systematic review and meta-analysis
Authors: Hou Yongbin , Yu Lihua , Mi Yonghua , Zhang Jiwang , Wang Ke , Hu Liyi
Published: December 2016

Various literatures have demonstrated that overexpression of Metadherin (MTDH) is correlated with tumor metastasis and it can predict poor survival outcomes in female reproduction malignancies. In order to enhance the statistical power and reach a recognized conclusion, we conducted a systematic review and meta-analysis to thoroughly investigate the association of MTDH expression with tumor metastasis and survival outcomes following PRISMA guidelines. Odds ratios (ORs) and hazard ratios (HRs) were used to demonstrate the impact of MTDH on tumor metastasis and prognosis respectively. Data were pooled with appropriate effects model on STATA12.0. Our results indicated that high MTDH expression is significantly correlated with higher mortality for breast, ovarian and cervical cancer. High immunohistochemical expression of MTDH is remarkably associated with shorter disease-free survival (DFS) in breast cancer but not in ovarian cancer. The pooled results suggested that high level of MTDH significantly predicted distant metastasis and lymph node metastasis in breast cancer. Strong associations were observed between MTDH expression and lymph node metastasis in ovarian and cervical cancer. In conclusion, MTDH might be a novel biomarker which can effectively reflect metastasis status and prognosis of breast cancer. However, its application in clinical practice needs more prospective studies with large samples.
Characteristics of NH4+ and NO3− fluxes in tea (Camellia sinensis) roots measured by scanning ion-selective electrode technique
Authors: Ruan Li , Wei Kang , Wang Liyuan , Cheng Hao , Zhang Fen , Wu Liyun , Bai Peixian , Zhang Chengcai
Published: December 2016

As a vital beverage crop, tea has been extensively planted in tropical and subtropical regions. Nitrogen (N) levels and forms are closely related to tea quality. Based on different N levels and forms, we studied changes in NO3− and NH4+ fluxes in tea roots utilizing scanning ion-selective electrode technique. Our results showed that under both single and mixed N forms, influx rates of NO3− were much lower than those of NH4+, suggesting a preference for NH4+ in tea. With the increase in N concentration, the influx rate of NO3− increased more than that of NH4+. The NH4+ influx rates in a solution without NO3− were much higher than those in a solution with NO3−, while the NO3− influx rates in a solution without NH4+ were much lower than those in a solution with NH4+. We concluded that (1) tea roots showed a preference for NH4+, (2) presence of NO3− had a negative effect on NH4+ influx, and (3) NH4+ had a positive effect on NO3− influx. Our findings not only may help advance hydroponic tea experiments but also may be used to develop efficient fertilization protocols for soil-grown tea in the future.
Establishment of a gastric cancer subline with high metastatic potential using a novel microfluidic system
Authors: Chen Zhe-zhou , Li Wan-ming , Zhang Yu , Yu Min , Shan Lian-feng , Yuan De-zheng , Liu Fu-rong , Fang Jin
Published: December 2016

Metastasis is an important hallmark of malignant tumors. In this study, we developed a microfluidic system to screen highly metastatic sublines via differential resolution of cell invasiveness. The system was composed of a PDMS-glass device connected with a syringe pump and a Petri dish. To facilitate the selection process, a long-term cell invasion driving force based on a chemotactic factor gradient was created using the Petri dish-based liquid supply pattern, and the invasive cells were collected for round-by-round selection via an open region in the chip. Using the system, we established an SGC-7901/B2 subline from the human gastric cancer SGC-7901 cell line by only two rounds of selection. In vitro assays showed that the SGC-7901/B2 cells were superior to the parental cells in proliferation and invasiveness. Furthermore, an in vivo tumorigenicity assay demonstrated that compared with the parental cells, the subline had stronger spontaneous metastatic and proliferative capability, which led to a shorter survival duration. Additionally, the protein expression differences including E-cadherin and Smad3 between the subline and parental cells were revealed. In conclusion, this microfluidic system is a highly effective tool for selecting highly metastatic sublines, and SGC-7901/B2 cells could serve as a potential model for tumor metastasis research.
Synergistically strengthened 3D micro-scavenger cage adsorbent for selective removal of radioactive cesium
Authors: Jang Sung-Chan , Kang Sung-Min , Haldorai Yuvaraj , Giribabu Krishnan , Lee Go-Woon , Lee Young-Chul , Hyun Moon Seop , Han Young-Kyu , Roh Changhyun , Huh Yun Suk
Published: December 2016

A novel microporous three-dimensional pomegranate-like micro-scavenger cage (P-MSC) composite has been synthesized by immobilization of iron phyllosilicates clay onto a Prussian blue (PB)/alginate matrix and tested for the removal of radioactive cesium from aqueous solution. Experimental results show that the adsorption capacity increases with increasing the inactive cesium concentration from 1 ppm to 30 ppm, which may be attributed to greater number of adsorption sites and further increase in the inactive cesium concentration has no effect. The P-MSC composite exhibit maximum adsorption capacity of 108.06 mg of inactive cesium per gram of adsorbent. The adsorption isotherm is better fitted to the Freundlich model than the Langmuir model. In addition, kinetics studies show that the adsorption process is consistent with a pseudo second-order model. Furthermore, at equilibrium, the composite has an outstanding adsorption capacity of 99.24% for the radioactive cesium from aqueous solution. This may be ascribed to the fact that the AIP clay played a substantial role in protecting PB release from the P-MSC composite by cross-linking with alginate to improve the mechanical stability. Excellent adsorption capacity, easy separation, and good selectivity make the adsorbent suitable for the removal of radioactive cesium from seawater around nuclear plants and/or after nuclear accidents.
Novel human mutation and CRISPR/Cas genome-edited mice reveal the importance of C-terminal domain of MSX1 in tooth and palate development
Authors: Mitsui Silvia Naomi , Yasue Akihiro , Masuda Kiyoshi , Naruto Takuya , Minegishi Yoshiyuki , Oyadomari Seiichi , Noji Sumihare , Imoto Issei , Tanaka Eiji
Published: December 2016

Several mutations, located mainly in the MSX1 homeodomain, have been identified in non-syndromic tooth agenesis predominantly affecting premolars and third molars. We identified a novel frameshift mutation of the highly conserved C-terminal domain of MSX1, known as Msx homology domain 6 (MH6), in a Japanese family with non-syndromic tooth agenesis. To investigate the importance of MH6 in tooth development, Msx1 was targeted in mice with CRISPR/Cas system. Although heterozygous MH6 disruption did not alter craniofacial development, homozygous mice exhibited agenesis of lower incisors with or without cleft palate at E16.5. In addition, agenesis of the upper third molars and the lower second and third molars were observed in 4-week-old mutant mice. Although the upper second molars were present, they were abnormally small. These results suggest that the C-terminal domain of MSX1 is important for tooth and palate development, and demonstrate that that CRISPR/Cas system can be used as a tool to assess causality of human disorders in vivo and to study the importance of conserved domains in genes.
Global DNA methylation variations after short-term heat shock treatment in cultured microspores of Brassica napus cv. Topas
Authors: Li Jun , Huang Qian , Sun Mengxiang , Zhang Tianyao , Li Hao , Chen Biyun , Xu Kun , Gao Guizhen , Li Feng , Yan Guixin , Qiao Jiangwei , Cai Yongping , Wu Xiaoming
Published: December 2016

Heat stress can induce the cultured microspores into embryogenesis. In this study, whole genome bisulphite sequencing was employed to study global DNA methylation variations after short-term heat shock (STHS) treatments in cultured microspores of Brassica napus cv. Topas. Our results indicated that treatment on cultured Topas microspores at 32 °C for 6 h triggered DNA hypomethylation, particularly in the CG and CHG contexts. And the total number of T32 (Topas 32 °C for 6 h) vs. T0 (Topas 0 h) differentially methylated region-related genes (DRGs) was approximately two-fold higher than that of T18 (Topas 18 °C for 6 h) vs. T0 DRGs, which suggested that 32 °C might be a more intense external stimulus than 18 °C resulting in more changes in the DNA methylation status of cultured microspores. Additionally, 32 °C treatment for 6 h led to increased CHG differential methylations of transposons (DMTs), which were mainly constituted by overlaps between the hypomethylated differentially methylated regions (hypo-DMRs) and transposon elements (TEs). Further analysis demonstrated that the DRGs and their paralogs exhibited differential methylated/demethylated patterns. To summarize, the present study is the first methylome analysis of cultured microspores in response to STHS and may provide valuable information on the roles of DNA methylation in heat response.
Distinct epigenomes in CD4+ T cells of newborns, middle-ages and centenarians
Authors: Zhao Ming , Qin Jian , Yin Hanqi , Tan Yixin , Liao Wei , Liu Qian , Luo Shuangyan , He Min , Liang Gongping , Shi Yajing , Zhang Qing , Cai Wenjun , Yin Guangliang , Zhou Yin , Wang Jing , Li Mengying , Huang Yi , Liu Aiyun , Wu Haijing , Zhang Zhiyong , Lu Qianjin
Published: December 2016

Age-related variations in genes and microRNAs expression and DNA methylation have been reported respectively; however, their interactions during aging are unclear. We therefore investigated alterations in the transcriptomes, miRNAomes and DNA methylomes in the same CD4+T cells from newborn (NB), middle-aged (MA) and long-lived (LL) individuals to elucidate the molecular changes and their interactions. A total 659 genes showed significantly expression changes across NB, MA and LL individuals, in which we identified four age-related co-expression modules with three hub networks of co-expressed genes and non-coding RNAs. Moreover, we identified 9835 differentially methylated regions (DMRs) including 7015 hypermethylated and 2820 hypomethylated DMRs in the NB compared with the MA, and 12,362 DMRs including 4809 hypermethylated and 7553 hypomethylated DMRs in the MA compared with the LL. The integrated analysis revealed a potential relationship between genes transcription and DNA methylation for many age- or immune-related genes, suggesting that DNA methylation-dependent transcription regulation is involved in development and functions of T cells during aging. Our results reveals age-related transcription and methylation changes and their interactions in human T cells from the cradle to the grave. Longitudinal work is required to establish the relationship between identified age-associated genes/DNA methylation and T cells aging phenotypes.
Functional complexity emerging from anatomical constraints in the brain: the significance of network modularity and rich-clubs
Authors: Zamora-López Gorka , Chen Yuhan , Deco Gustavo , Kringelbach Morten L. , Zhou Changsong
Published: December 2016

The large-scale structural ingredients of the brain and neural connectomes have been identified in recent years. These are, similar to the features found in many other real networks: the arrangement of brain regions into modules and the presence of highly connected regions (hubs) forming rich-clubs. Here, we examine how modules and hubs shape the collective dynamics on networks and we find that both ingredients lead to the emergence of complex dynamics. Comparing the connectomes of C. elegans, cats, macaques and humans to surrogate networks in which either modules or hubs are destroyed, we find that functional complexity always decreases in the perturbed networks. A comparison between simulated and empirically obtained resting-state functional connectivity indicates that the human brain, at rest, lies in a dynamical state that reflects the largest complexity its anatomical connectome can host. Last, we generalise the topology of neural connectomes into a new hierarchical network model that successfully combines modular organisation with rich-club forming hubs. This is achieved by centralising the cross-modular connections through a preferential attachment rule. Our network model hosts more complex dynamics than other hierarchical models widely used as benchmarks.
Basigin can be a therapeutic target to restore the retinal vascular barrier function in the mouse model of diabetic retinopathy
Authors: Arima Mitsuru , Cui Dan , Kimura Tokuhiro , Sonoda Koh-Hei , Ishibashi Tatsuro , Matsuda Satoshi , Ikeda Eiji
Published: December 2016

Despite the advance in medical technology, diabetic retinopathy (DR) is still an intractable disease which leads to the damage of retinal cells and finally the visual loss. Impairment of retinal vascular barrier triggered by an admixture of multiple inflammatory cytokines is a core of pathophysiology of DR. Therefore, the molecules involved commonly in multiple cytokines-induced impairment of vascular barrier would be the targets of curative treatment of DR. Here, we demonstrate that basigin, a transmembrane molecule expressed in neural barrier-forming endothelial cells, is the molecule essential for vascular barrier impairment which is shared by various triggers including VEGF, TNFα and IL-1β. In vitro data with neural microvascular endothelial cells indicated that stimulation with cytokines decreases the levels of claudin-5 in cell membranes and consequently impairs the barrier function in a manner dependent on the interaction of claudin-5 with basigin and caveolin-1. In addition, the increased vascular permeability in retinas of streptozotocin-induced diabetic mice was shown to be clearly normalized by intravitreous injection of siRNAs specific for basigin. This study has highlighted basigin as a common essential molecule for various stimuli-induced impairment of retinal vascular barrier, which can be a target for strategies to establish a curative treatment of DR.
Adsorption of methylene blue on an agro-waste oiltea shell with and without fungal treatment
Authors: Liu Jiayang , Li Enzhong , You Xiaojuan , Hu Changwei , Huang Qingguo
Published: December 2016

A lignocellulosic waste oiltea shell (OTS) was evaluated as an inexpensive sorbent to remove methylene blue (MB) from aqueous solution. Fungal treatment of OTS increased the MB adsorption by modifying the physicochemical properties of OTS and simultaneously produced laccase as a beneficial co-product. Without fungal treatment, the maximum amount of adsorption (qm) of MB by OTS was 64.4 mg/g, whereas the treatment with fungus Pycnoporus sp. and Trametes versicolor increased qm up to 72.5 mg/g and 85.7 mg/g, respectively. This is because of the improved surface area and pore sizes as well as altered chemical compositions. The equilibrium sorption data for OTS both with and without treatment fitted to the Langmuir model, and the sorption rate data well fitted to the pseudo second-order kinetic model. The changes in free energy (ΔG°) and separation factor (RL) indicated that the sorption was spontaneous and favorable. Scanning electron microscopy and Fourier transform infrared spectroscopy showed the changes in the surface morphology and functional groups of OTS after fungal treatment. The agro-waste OTS could be utilized as a low-cost adsorbent for efficient dye removal, and fungal treatment can serve as a mild and clean technique to increase the adsorptive capacity of OTS.
The Core Subunit of A Chromatin-Remodeling Complex, ZmCHB101, Plays Essential Roles in Maize Growth and Development
Authors: Yu Xiaoming , Jiang Lili , Wu Rui , Meng Xinchao , Zhang Ai , Li Ning , Xia Qiong , Qi Xin , Pang Jinsong , Xu Zheng-Yi , Liu Bao
Published: December 2016

ATP-dependent chromatin remodeling complexes play essential roles in the regulation of diverse biological processes by formulating a DNA template that is accessible to the general transcription apparatus. Although the function of chromatin remodelers in plant development has been studied in A. thaliana, how it affects growth and development of major crops (e.g., maize) remains uninvestigated. Combining genetic, genomic and bioinformatic analyses, we show here that the maize core subunit of chromatin remodeling complex, ZmCHB101, plays essential roles in growth and development of maize at both vegetative and reproductive stages. Independent ZmCHB101 RNA interference plant lines displayed abaxially curling leaf phenotype due to increase of bulliform cell numbers, and showed impaired development of tassel and cob. RNA-seq-based transcriptome profiling revealed that ZmCHB101 dictated transcriptional reprogramming of a significant set of genes involved in plant development, photosynthesis, metabolic regulation, stress response and gene expressional regulation. Intriguingly, we found that ZmCHB101 was required for maintaining normal nucleosome density and 45 S rDNA compaction. Our findings suggest that the SWI3 protein, ZmCHB101, plays pivotal roles in maize normal growth and development via regulation of chromatin structure.
Robust increase in extreme summer rainfall intensity during the past four decades observed in China
Authors: Xiao Chan , Wu Peili , Zhang Lixia , Song Lianchun
Published: December 2016

Global warming increases the moisture holding capacity of the atmosphere and consequently the potential risks of extreme rainfall. Here we show that maximum hourly summer rainfall intensity has increased by about 11.2% on average, using continuous hourly gauge records for 1971–2013 from 721 weather stations in China. The corresponding event accumulated precipitation has on average increased by more than 10% aided by a small positive trend in events duration. Linear regression of the 95th percentile daily precipitation intensity with daily mean surface air temperature shows a negative scaling of −9.6%/K, in contrast to a positive scaling of 10.6%/K for hourly data. This is made up of a positive scaling below the summer mean temperature and a negative scaling above. Using seasonal means instead of daily means, we find a consistent scaling rate for the region of 6.7–7%/K for both daily and hourly precipitation extremes, about 10% higher than the regional Clausius-Clapeyron scaling of 6.1%/K based on a mean temperature of 24.6 °C. With up to 18% further increase in extreme precipitation under continuing global warming towards the IPCC’s 1.5 °C target, risks of flash floods will exacerbate on top of the current incapability of urban drainage systems in a rapidly urbanizing China.