bluuebunny/crossref_metadata_2025 huggingface dataset:
Mechanical stress activates NMDA receptors in the absence of agonists
Authors: Maneshi Mohammad Mehdi , Maki Bruce , Gnanasambandam Radhakrishnan , Belin Sophie , Popescu Gabriela K. , Sachs Frederick , Hua Susan Z.
Published: January 2017

While studying the physiological response of primary rat astrocytes to fluid shear stress in a model of traumatic brain injury (TBI), we found that shear stress induced Ca2+ entry. The influx was inhibited by MK-801, a specific pore blocker of N-Methyl-D-aspartic acid receptor (NMDAR) channels, and this occurred in the absence of agonists. Other NMDA open channel blockers ketamine and memantine showed a similar effect. The competitive glutamate antagonists AP5 and GluN2B-selective inhibitor ifenprodil reduced NMDA-activated currents, but had no effect on the mechanically induced Ca2+ influx. Extracellular Mg2+ at 2 mM did not significantly affect the shear induced Ca2+ influx, but at 10 mM it produced significant inhibition. Patch clamp experiments showed mechanical activation of NMDAR and inhibition by MK-801. The mechanical sensitivity of NMDARs may play a role in the normal physiology of fluid flow in the glymphatic system and it has obvious relevance to TBI.
Complex Roles of Solution Chemistry on Graphene Oxide Coagulation onto Titanium Dioxide: Batch Experiments, Spectroscopy Analysis and Theoretical Calculation
Authors: Yu Shujun , Wang Xiangxue , Zhang Rui , Yang Tongtong , Ai Yuejie , Wen Tao , Huang Wei , Hayat Tasawar , Alsaedi Ahmed , Wang Xiangke
Published: January 2017

Although graphene oxide (GO) has been used in multidisciplinary areas due to its excellent physicochemical properties, its environmental behavior and fate are still largely unclear. In this study, batch experiments, spectroscopy analysis and theoretical calculations were addressed to promote a more comprehensive understanding toward the coagulation behavior of GO onto TiO2 under various environmental conditions (pH, co-existing ions, temperature, etc.). The results indicated that neutral pH was beneficial to the removal of GO due to the electrostatic interaction. The presence of cations accelerated GO coagulation significantly owing to the influence of electrical double layer compression. On the contrary, the presence of anions improved the stability of GO primarily because of electrostatic repulsion and steric hindrance. Results of XRD, FTIR and XPS analysis indicated that the coagulation of GO on TiO2 was mainly dominated by electrostatic interactions and hydrogen bonds, which were further evidenced by DFT calculations. The high binding energy further indicated the stability of GO + TiO2 system, suggesting that TiO2 can be used as an effective coagulant for the efficient elimination and coagulation of GO from aqueous solutions. These findings might likely lead to a better understanding of the migration and transformation of carbon nanomaterials in the natural environment.
Intrinsic Origins of Crack Generation in Ni-rich LiNi0.8Co0.1Mn0.1O2 Layered Oxide Cathode Material
Authors: Lim Jin-Myoung , Hwang Taesoon , Kim Duho , Park Min-Sik , Cho Kyeongjae , Cho Maenghyo
Published: January 2017

Ni-rich LiNi0.8Co0.1Mn0.1O2 layered oxide cathodes have been highlighted for large-scale energy applications due to their high energy density. Although its specific capacity is enhanced at higher voltages as Ni ratio increases, its structural degradation due to phase transformations and lattice distortions during cycling becomes severe. For these reasons, we focused on the origins of crack generation from phase transformations and structural distortions in Ni-rich LiNi0.8Co0.1Mn0.1O2 using multiscale approaches, from first-principles to meso-scale phase-field model. Atomic-scale structure analysis demonstrated that opposite changes in the lattice parameters are observed until the inverse Li content x = 0.75; then, structure collapses due to complete extraction of Li from between transition metal layers. Combined-phase investigations represent the highest phase barrier and steepest chemical potential after x = 0.75, leading to phase transformations to highly Li-deficient phases with an inactive character. Abrupt phase transformations with heterogeneous structural collapse after x = 0.81 (~220 mAh g−1) were identified in the nanodomain. Further, meso-scale strain distributions show around 5% of anisotropic contraction with lower critical energy release rates, which cause not only micro-crack generations of secondary particles on the interfaces between the contracted primary particles, but also mechanical instability of primary particles from heterogeneous strain changes.
The Fall of Sleep K-Complex in Alzheimer Disease
Authors: De Gennaro Luigi , Gorgoni Maurizio , Reda Flaminia , Lauri Giulia , Truglia Ilaria , Cordone Susanna , Scarpelli Serena , Mangiaruga Anastasia , D’atri Aurora , Lacidogna Giordano , Ferrara Michele , Marra Camillo , Rossini Paolo Maria
Published: January 2017

Although a slowing of electroencephalographic (EEG) activity during wakefulness and –to some extent- sleep of Alzheimer disease (AD) patients (i.e., increased slow-frequency activity) was documented, recent findings in healthy elderly show a decreased 0.6–1 Hz slow wave activity (SWA) during NREM, which was associated to β-amyloid deposition and impaired hippocampal memory consolidation. We hypothesize that the apparent contradiction may be explained by the partial overlap between 0.6–1 Hz EEG activity and K-Complex (KC). According to this view, we studied both frontal KCs and SWA in 20 AD patients and 20 healthy age-matched controls (HC) during nightly sleep, under the hypothesis that KCs better discriminate patients from healthy elderly than ≤1 Hz SWA. A drastic decrease of KC density during stage 2 NREM was found in AD compared to HC. Patients show more than 40% reduction of the KC density, allowing a correct classification of 80%. On the other hand, ≤1 Hz SWA of AD patients is slightly (not significantly) higher in most cortical areas compared to HC. Although no significant changes of ≤1 Hz SWA are detectable over frontal areas in AD, KC density decreases over the same location, and its decrease is related to the cognitive decline.
Host plant species determines symbiotic bacterial community mediating suppression of plant defenses
Authors: Chung Seung Ho , Scully Erin D. , Peiffer Michelle , Geib Scott M. , Rosa Cristina , Hoover Kelli , Felton Gary W.
Published: January 2017

Herbivore associated bacteria are vital mediators of plant and insect interactions. Host plants play an important role in shaping the gut bacterial community of insects. Colorado potato beetles (CPB;Leptinotarsa decemlineata) use severalSolanumplants as hosts in their natural environment. We previously showed that symbiotic gut bacteria from CPB larvae suppressed jasmonate (JA)-induced defenses in tomato. However, little is known about how changes in the bacterial community may be involved in the manipulation of induced defenses in wild and cultivatedSolanumplants of CPB. Here, we examined suppression of JA-mediated defense in wild and cultivated hosts of CPB by chemical elicitors and their symbiotic bacteria. Furthermore, we investigated associations between the gut bacterial community and suppression of plant defenses using 16 S rRNA amplicon sequencing. Symbiotic bacteria decreased plant defenses in allSolanumhosts and there were different gut bacterial communities in CPB fed on different host plants. When larvae were reared on different hosts, defense suppression differed among host plants. These results demonstrate that host plants influence herbivore gut bacterial communities and consequently affect the herbivore’s ability to manipulate JA-mediated plant defenses. Thus, the presence of symbiotic bacteria that suppress plant defenses might help CPB adapt to host plants.
Carbon monoxide pollution aggravates ischemic heart failure through oxidative stress pathway
Authors: Reboul Cyril , Boissière Julien , André Lucas , Meyer Gregory , Bideaux Patrice , Fouret Gilles , Feillet-Coudray Christine , Obert Philippe , Lacampagne Alain , Thireau Jérôme , Cazorla Olivier , Richard Sylvain
Published: January 2017

Risk of hospital readmission and cardiac mortality increases with atmospheric pollution for patients with heart failure. The underlying mechanisms are unclear. Carbon monoxide (CO) a ubiquitous environmental pollutant could be involved. We explored the effect of daily exposure of CO relevant to urban pollution on post-myocardial infarcted animals. Rats with ischemic heart failure were exposed 4 weeks to daily peaks of CO mimicking urban exposure or to standard filtered air. CO exposure worsened cardiac contractile dysfunction evaluated by echocardiography and at the cardiomyocyte level. In line with clinical reports, the animals exposed to CO also exhibited a severe arrhythmogenic phenotype with numerous sustained ventricular tachycardias as monitored by surface telemetric electrocardiograms. CO did not affect cardiac β–adrenergic responsiveness. Instead, mitochondrial dysfunction was exacerbated leading to additional oxidative stress and Ca2+ cycling alterations. This was reversed following acute antioxidant treatment of cardiomyocytes with N-acetylcysteine confirming involvement of CO-induced oxidative stress. Exposure to daily peaks of CO pollution aggravated cardiac dysfunction in rats with ischemic heart failure by specifically targeting mitochondria and generating ROS-dependent alterations. This pathway may contribute to the high sensibility and vulnerability of individuals with cardiac disease to environmental outdoor air quality.
Profile of upregulated inflammatory proteins in sera of Myasthenia Gravis patients
Authors: Molin Carl Johan , Westerberg Elisabet , Punga Anna Rostedt
Published: January 2017

This study describes specific patterns of elevated inflammatory proteins in clinical subtypes of myasthenia gravis (MG) patients. MG is a chronic, autoimmune neuromuscular disease with antibodies most commonly targeting the acetylcholine receptors (AChRab), which causes fluctuating skeletal muscle fatigue. MG pathophysiology includes a strong component of inflammation, and a large proportion of patients with early onset MG additionally present thymus hyperplasia. Due to the fluctuating nature and heterogeneity of the disease, there is a great need for objective biomarkers as well as novel potential inflammatory targets. We examined the sera of 45 MG patients (40 AChRab seropositive and 5 AChRab seronegative), investigating 92 proteins associated with inflammation. Eleven of the analysed proteins were significantly elevated compared to healthy controls, out of which the three most significant were: matrix metalloproteinase 10 (MMP-10; p = 0.0004), transforming growth factor alpha (TGF-α; p = 0.0017) and extracellular newly identified receptor for advanced glycation end-products binding protein (EN-RAGE) (also known as protein S100-A12; p = 0.0054). Further, levels of MMP-10, C-X-C motif ligand 1 (CXCL1) and brain derived neurotrophic factor (BDNF) differed between early and late onset MG. These novel targets provide valuable additional insight into the systemic inflammatory response in MG.
Elucidating the genetic basis of an oligogenic birth defect using whole genome sequence data in a non-model organism, Bubalus bubalis
Authors: Whitacre Lynsey K. , Hoff Jesse L. , Schnabel Robert D. , Albarella Sara , Ciotola Francesca , Peretti Vincenzo , Strozzi Francesco , Ferrandi Chiara , Ramunno Luigi , Sonstegard Tad S. , Williams John L. , Taylor Jeremy F. , Decker Jared E.
Published: January 2017

Recent strong selection for dairy traits in water buffalo has been associated with higher levels of inbreeding, leading to an increase in the prevalence of genetic diseases such as transverse hemimelia (TH), a congenital developmental abnormality characterized by absence of a variable distal portion of the hindlimbs. Limited genomic resources available for water buffalo required an original approach to identify genetic variants associated with the disease. The genomes of 4 bilateral and 7 unilateral affected cases and 14 controls were sequenced. A concordance analysis of SNPs and INDELs requiring homozygosity unique to all unilateral and bilateral cases revealed two genes, WNT7A and SMARCA4, known to play a role in embryonic hindlimb development. Additionally, SNP alleles in NOTCH1 and RARB were homozygous exclusively in the bilateral cases, suggesting an oligogenic mode of inheritance. Homozygosity mapping by whole genome de novo assembly also supported oligogenic inheritance; implicating 13 genes involved in hindlimb development in bilateral cases and 11 in unilateral cases. A genome-wide association study (GWAS) predicted additional modifier genes. Although our data show a complex inheritance of TH, we predict that homozygous variants in WNT7A and SMARCA4 are necessary for expression of TH and selection against these variants should eradicate TH.
Spatio-temporal patterns of stream methane and carbon dioxide emissions in a hemiboreal catchment in Southwest Sweden
Authors: Natchimuthu Sivakiruthika , Wallin Marcus B. , Klemedtsson Leif , Bastviken David
Published: January 2017

Global stream and river greenhouse gas emissions seem to be as large as the oceanic C uptake. However, stream and river emissions are uncertain until both spatial and temporal variability have been quantified. Here we investigated in detail the stream CH4 and CO2 emissions within a hemiboreal catchment in Southwest Sweden primarily covered by coniferous forest. Gas transfer velocities (k600), CH4 and CO2 concentrations were measured with multiple methods. Our data supported modelling approaches accounting for various stream slopes, water velocities and discharge. The results revealed large but partially predictable spatio-temporal variabilities in k600, dissolved gas concentrations, and emissions. The variability in CO2 emission was best explained by the variability in k, while dissolved CH4 concentrations explained most of the variability in CH4 emission, having implications for future measurements. There were disproportionately large emissions from high slope stream reaches including waterfalls, and from high discharge events. In the catchment, stream reaches with low slope and time periods of moderate discharge dominated (90% of area and 69% of time). Measurements in these stream areas and time periods only accounted for <36% of the total estimated emissions. Hence, not accounting for local or episodic high emissions can lead to substantially underestimated emissions.
Pulsation-limited oxygen diffusion in the tumour microenvironment
Authors: Milotti Edoardo , Stella Sabrina , Chignola Roberto
Published: January 2017

Hypoxia is central to tumour evolution, growth, invasion and metastasis. Mathematical models of hypoxia based on reaction-diffusion equations provide seemingly incomplete descriptions as they fail to predict the measured oxygen concentrations in the tumour microenvironment. In an attempt to explain the discrepancies, we consider both the inhomogeneous distribution of oxygen-consuming cells in solid tumours and the dynamics of blood flow in the tumour microcirculation. We find that the low-frequency oscillations play an important role in the establishment of tumour hypoxia. The oscillations interact with consumption to inhibit oxygen diffusion in the microenvironment. This suggests that alpha-blockers–a class of drugs used to treat hypertension and stress disorders, and known to lower or even abolish low-frequency oscillations of arterial blood flow –may act as adjuvant drugs in the radiotherapy of solid tumours by enhancing the oxygen effect.
miRNA and mRNA expression analysis reveals potential sex-biased miRNA expression
Authors: Guo Li , Zhang Qiang , Ma Xiao , Wang Jun , Liang Tingming
Published: January 2017

Recent studies suggest that mRNAs may be differentially expressed between males and females. This study aimed to perform expression analysis of mRNA and its main regulatory molecule, microRNA (miRNA), to discuss the potential sex-specific expression patterns using abnormal expression profiles from The Cancer Genome Atlas database. Generally, deregulated miRNAs and mRNAs had consistent expression between males and females, but some miRNAs may be oppositely expressed in specific diseases: up-regulated in one group and down-regulated in another. Studies of miRNA gene families and clusters further confirmed that these sequence or location related miRNAs might have opposing expression between sexes. The specific miRNA might have greater expression divergence across different groups, suggesting flexible expression across different individuals, especially in tumor samples. The typical analysis regardless of the sex will ignore or balance these sex-specific deregulated miRNAs. Compared with flexible miRNAs, their targets of mRNAs showed relative stable expression between males and females. These relevant results provide new insights into miRNA-mRNA interaction and sex difference.
Sex-related difference in human white matter volumes studied: Inspection of the corpus callosum and other white matter by VBM
Authors: Shiino Akihiko , Chen Yen-wei , Tanigaki Kenji , Yamada Atsushi , Vigers Piers , Watanabe Toshiyuki , Tooyama Ikuo , Akiguchi Ichiro
Published: January 2017

It has been contended that any observed difference of the corpus callosum (CC) size between men and women is not sex-related but brain-size-related. A recent report, however, showed that the midsagittal CC area was significantly larger in women in 37 brain-size-matched pairs of normal young adults. Since this constituted strong evidence of sexual dimorphism and was obtained from publicly available data in OASIS, we examined volume differences within the CC and in other white matter using voxel-based morphometry (VBM). We created a three-dimensional region of interest of the CC and measured its volume. The VBM statistics were analyzed by permutation test and threshold-free cluster enhancement (TFCE) with the significance levels at FWER < 0.05. The CC volume was significantly larger in women in the same 37 brain-size-matched pairs. We found that the CC genu was the subregion showing the most significant sex-related difference. We also found that white matter in the bilateral anterior frontal regions and the left lateral white matter near to Broca’s area were larger in women, whereas there were no significant larger regions in men. Since we used brain-size-matched subjects, our results gave strong volumetric evidence of localized sexual dimorphism of white matter.
A second generation SNP and SSR integrated linkage map and QTL mapping for the Chinese mitten crab Eriocheir sinensis
Authors: Qiu Gao-Feng , Xiong Liang-Wei , Han Zhi-Ke , Liu Zhi-Qiang , Feng Jian-Bin , Wu Xu-Gan , Yan Yin-Long , Shen Hong , Huang Long , Chen Li
Published: January 2017

The Chinese mitten crabEriocheir sinensisis the most economically important cultivated crab species in China, and its genome has a high number of chromosomes (2n = 146). To obtain sufficient markers for construction of a dense genetic map for this species, we employed the recently developed specific-locus amplified fragment sequencing (SLAF-seq) method for large-scale SNPs screening and genotyping in a F1 full-sib family of 149 individuals. SLAF-seq generated 127,677 polymorphic SNP markers, of which 20,803 valid markers were assigned into five segregation types and were used together with previous SSR markers for linkage map construction. The final integrated genetic map included 17,680 SNP and 629 SSR markers on the 73 linkage groups (LG), and spanned 14,894.9 cM with an average marker interval of 0.81 cM. QTL mapping localized three significant growth-related QTL to a 1.2 cM region in LG53 as well as 146 sex-linked markers in LG48. Genome-wide QTL-association analysis further identified four growth-related QTL genes named LNX2, PAK2, FMRFamide and octopamine receptors. These genes are involved in a variety of different signaling pathways including cell proliferation and growth. The map and SNP markers described here will be a valuable resource for theE. sinensisgenome project and selective breeding programs.
Feature selection and classification of urinary mRNA microarray data by iterative random forest to diagnose renal fibrosis: a two-stage study
Authors: Zhou Le-Ting , Cao Yu-Han , Lv Lin-Li , Ma Kun-Ling , Chen Ping-Sheng , Ni Hai-Feng , Lei Xiang-Dong , Liu Bi-Cheng
Published: January 2017

Renal fibrosis is a common pathological pathway of progressive chronic kidney disease (CKD). However, kidney function parameters are suboptimal for detecting early fibrosis, and therefore, novel biomarkers are urgently needed. We designed a 2-stage study and constructed a targeted microarray to detect urinary mRNAs of CKD patients with renal biopsy and healthy participants. We analysed the microarray data by an iterative random forest method to select candidate biomarkers and produce a more accurate classifier of renal fibrosis. Seventy-six and 49 participants were enrolled into stage I and stage II studies, respectively. By the iterative random forest method, we identified a four-mRNA signature in urinary sediment, including TGFβ1, MMP9, TIMP2, and vimentin, as important features of tubulointerstitial fibrosis (TIF). All four mRNAs significantly correlated with TIF scores and discriminated TIF with high sensitivity, which was further validated in the stage-II study. The combined classifiers showed excellent sensitivity and outperformed serum creatinine and estimated glomerular filtration rate measurements in diagnosing TIF. Another four mRNAs significantly correlated with glomerulosclerosis. These findings showed that urinary mRNAs can serve as sensitive biomarkers of renal fibrosis, and the random forest classifier containing urinary mRNAs showed favourable performance in diagnosing early renal fibrosis.
CTCF interacts with the lytic HSV-1 genome to promote viral transcription
Authors: Lang Fengchao , Li Xin , Vladimirova Olga , Hu Benxia , Chen Guijun , Xiao Yu , Singh Vikrant , Lu Danfeng , Li Lihong , Han Hongbo , Wickramasinghe J. M. A. S. P. , Smith Sheryl T. , Zheng Chunfu , Li Qihan , Lieberman Paul M. , Fraser Nigel W. , Zhou Jumin
Published: January 2017

CTCF is an essential chromatin regulator implicated in important nuclear processes including in nuclear organization and transcription. Herpes Simplex Virus-1 (HSV-1) is a ubiquitous human pathogen, which enters productive infection in human epithelial and many other cell types. CTCF is known to bind several sites in the HSV-1 genome during latency and reactivation, but its function has not been defined. Here, we report that CTCF interacts extensively with the HSV-1 DNA during lytic infection by ChIP-seq, and its knockdown results in the reduction of viral transcription, viral genome copy number and virus yield. CTCF knockdown led to increased H3K9me3 and H3K27me3, and a reduction of RNA pol II occupancy on viral genes. Importantly, ChIP-seq analysis revealed that there is a higher level of CTD Ser2P modified RNA Pol II near CTCF peaks relative to the Ser5P form in the viral genome. Consistent with this, CTCF knockdown reduced the Ser2P but increased Ser5P modified forms of RNA Pol II on viral genes. These results suggest that CTCF promotes HSV-1 lytic transcription by facilitating the elongation of RNA Pol II and preventing silenced chromatin on the viral genome.
Diabetes, cardiac disorders and asthma as risk factors for severe organ involvement among adult dengue patients: A matched case-control study
Authors: Pang Junxiong , Hsu Jung Pu , Yeo Tsin Wen , Leo Yee Sin , Lye David C.
Published: January 2017

Progression to severe organ involvement due to dengue infection has been associated with severe dengue disease, intensive care treatment, and mortality. However, there is a lack of understanding of the impact of pre-existing comorbidities and other risk factors of severe organ involvement among dengue adults. The aim of this retrospective case-control study is to characterize and identify risk factors that predispose dengue adults at risk of progression with severe organ involvement. This study involved 174 dengue patients who had progressed with severe organ involvement and 865 dengue patients without severe organ involvement, matched by the year of presentation of the cases, who were admitted to Tan Tock Seng Hospital between year 2005 and 2008. Age group of 60 years or older, diabetes, cardiac disorders, asthma, and having two or more pre-existing comorbidities were independent risk factors of severe organ involvement. Abdominal pain, clinical fluid accumulation, and hematocrit rise and rapid platelet count drop at presentation were significantly associated with severe organ involvement. These risk factors, when validated in a larger study, will be useful for triage by clinicians for prompt monitoring and clinical management at first presentation, to minimize the risk of severe organ involvement and hence, disease severity.
Simplifying multidimensional fermentation dataset analysis and visualization: One step closer to capturing high-quality mutant strains
Authors: Zhou Xiang , Xu Dan , Jiang Ting-Ting
Published: January 2017

In this study, we analyzed mutants of Clostridium acetobutylicum, an organism used in a broad range of industrial processes related to biofuel production, to facilitate future studies of bioreactor and bioprocess design and scale-up, which are very important research projects for industrial microbiology applications. To accomplish this, we generated 329 mutant strains and applied principal component analysis (PCA) to fermentation data gathered from these strains to identify a core set of independent features for comparison. By doing so, we were able to explain the differences in the mutant strains’ fermentation expression states and simplify the analysis and visualization of the multidimensional datasets related to the strains. Our study has produced a high-efficiency PCA application based on a data analytics tool that is designed to visualize screening results and to support several hundred sets of data on fermentation interactions to assist researchers in more precisely screening and capturing high-quality mutant strains. More importantly, although this study focused on the use of PCA in microbial fermentation engineering, its results are broadly applicable.
PHF14: an innate inhibitor against the progression of renal fibrosis following folic acid-induced kidney injury
Authors: Yang Bo , Chen Sixiu , Wu Ming , Zhang Lin , Ruan Mengna , Chen Xujiao , Chen Zhengjun , Mei Changlin , Mao Zhiguo
Published: January 2017

PHF14 is a newly identified regulator of mesenchyme growth in embryonic tissues. Previous studies have shown that phf14-null mutants die just after birth due to interstitial tissue hyperplasia in major organs, including the kidneys. The aim of this study was to investigate PHF14 function in renal fibrosis. By studying the chronic kidney injury mouse model, we found that PHF14 was upregulated in fibrotic kidneys after renal insults induced by folic acid administration. Compared with wild-type mice, PHF14-null mice showed more severe renal fibrosis after pro-fibrotic stimuli. Moreover, PHF14 in rat renal fibroblasts was upregulated by transforming growth factor-β (TGF-β) stimulation; while this upregulation was inhibited when smad3 phosphorylation was blocked. A chromatin immunoprecipitation (ChIP) assay further indicated that phospho-smad3 (p-smad3) acted as a transcription factor to enhance PHF14 expression. A lack of PHF14 expression enhanced collagen I and α-smooth muscle actin (α-SMA) synthesis induced by TGF-β in vitro. PHF14 was involved in inhibition of platelet-derived growth factor (PDGF) signaling overactivation by selectively repressing PDGF receptor-α (PDGFR-α) transcription. In summary, PHF14 expression was upregulated in fibrotic models in vivo and in vitro, and the TGF-β/smad3/PHF14 pathway acted as a self-limiting mechanism in the TGF-β-dominated renal pro-fibrotic process by suppressing PDGFR-α expression.
Increased Uterine NK cell numbers and perforin expression during the implantation phase in IVF Cycles with GnRH Antagonist Protocol
Authors: Xu Bufang , Wang Jingwen , Xia Lan , Zhang Dan , Wu Xian , Zhang Aijun
Published: January 2017

GnRH antagonist negatively affects endometrial receptivity inin vitrofertilization (IVF) cycles, however, its underlying mechanism remains unclear. To explore its target molecules, we studied endometria in the window phase of fixed GnRH antagonist, low-dose flexible GnRH antagonist, GnRH agonist long protocol, and untreated control groups. There were 384 differentially expressed genes (DEGs) in the fixed antagonist group with greater than twofold expression change compared with the control group and 197 DEGs between the fixed antagonist and agonist groups, the majority of which were associated with the natural killer (NK) cell-mediated cytotoxicity pathway. We then analysed the PRF1 and FASLG protein levels. The perforin level were significantly higher in both the antagonist groups than in other two groups, and was higher in the fixed antagonist group. Similarly, the uNK cell numbers were higher in the antagonist groups, and the highest uNK cell number occurred in the fixed group (p < 0.05). No significant differences existed in the Fas ligand levels and apoptosis rates among the three treatment groups, but were higher in the treatment groups than the control group. Together, these data indicate that GnRH antagonist may increase the uNK cell numbers and perforin expression, and this effect may be dose-dependent.
Batch effects and the effective design of single-cell gene expression studies
Authors: Tung Po-Yuan , Blischak John D. , Hsiao Chiaowen Joyce , Knowles David A. , Burnett Jonathan E. , Pritchard Jonathan K. , Gilad Yoav
Published: January 2017

Single-cell RNA sequencing (scRNA-seq) can be used to characterize variation in gene expression levels at high resolution. However, the sources of experimental noise in scRNA-seq are not yet well understood. We investigated the technical variation associated with sample processing using the single-cell Fluidigm C1 platform. To do so, we processed three C1 replicates from three human induced pluripotent stem cell (iPSC) lines. We added unique molecular identifiers (UMIs) to all samples, to account for amplification bias. We found that the major source of variation in the gene expression data was driven by genotype, but we also observed substantial variation between the technical replicates. We observed that the conversion of reads to molecules using the UMIs was impacted by both biological and technical variation, indicating that UMI counts are not an unbiased estimator of gene expression levels. Based on our results, we suggest a framework for effective scRNA-seq studies.
Social harassment induces anxiety-like behaviour in crayfish
Authors: Bacqué-Cazenave Julien , Cattaert Daniel , Delbecque Jean-Paul , Fossat Pascal
Published: January 2017

Social interactions leading to dominance hierarchies often elicit psychological disorders in mammals including harassment and anxiety. Here, we demonstrate that this sequence also occurs in an invertebrate, the crayfish Procambarus clarkii. When placed in the restricted space of an aquarium, crayfish dyads generally fight until one of the opponents suddenly escapes, thereafter clearly expressing a submissive behaviour. Nevertheless, the winner frequently keeps on displaying excessive aggressive acts, having deleterious consequences in losers and interpreted as harassment behaviour. We indeed observed that, contrary to winners, losers expressed anxiety-like behaviour (ALB) in correlation with the stress intensity they suffered during the harassment period mainly. Injections of an anxiolytic abolished ALB, confirming its homology with anxiety. A serotonin (5-HT) antagonist had the same effect, suggesting a role for 5-HT, whose brain concentrations increased much more in losers than in winners. Our findings suggest that the bases of harassment and of its anxiogenic consequences have emerged very early during evolution, and emphasize crayfish as an unexpected but potentially fruitful model for the study of these social disorders.
Chrna7 deficient mice manifest no consistent neuropsychiatric and behavioral phenotypes
Authors: Yin Jiani , Chen Wu , Yang Hongxing , Xue Mingshan , Schaaf Christian P.
Published: January 2017

The alpha7 nicotinic acetylcholine receptor, encoded by theCHRNA7gene, has been implicated in various psychiatric and behavioral disorders, including schizophrenia, bipolar disorder, epilepsy, autism, Alzheimer’s disease, and Parkinson’s disease, and is considered a potential target for therapeutic intervention. 15q13.3 microdeletion syndrome is a rare genetic disorder, caused by submicroscopic deletions on chromosome 15q.CHRNA7is the only gene in this locus that has been deleted entirely in cases involving the smallest microdeletions. Affected individuals manifest variable neurological and behavioral phenotypes, which commonly include developmental delay/intellectual disability, epilepsy, and autism spectrum disorder. Subsets of patients have short attention spans, aggressive behaviors, mood disorders, or schizophrenia. Previous behavioral studies suggested thatChrna7deficient mice had attention deficits, but were normal in baseline behavioral responses, learning, memory, and sensorimotor gating. Given a growing interest inCHRNA7-related diseases and a better appreciation of its associated human phenotypes, an in-depth behavioral characterization of theChrna7deficient mouse model appeared prudent. This study was designed to investigate whetherChrna7deficient mice manifest phenotypes related to those seen in human individuals, using an array of 12 behavioral assessments and electroencephalogram (EEG) recordings on freely-moving mice. Examined phenotypes included social interaction, compulsive behaviors, aggression, hyperactivity, anxiety, depression, and somatosensory gating. Our data suggests that mouse behavior and EEG recordings are not sensitive to decreasedChrna7copy number.
Bromodomain protein Brd3 promotes Ifnb1 transcription via enhancing IRF3/p300 complex formation and recruitment to Ifnb1 promoter in macrophages
Authors: Ren Wenhui , Wang Chunmei , Wang Qinlan , Zhao Dezhi , Zhao Kai , Sun Donghao , Liu Xingguang , Han Chaofeng , Hou Jin , Li Xia , Zhang Qian , Cao Xuetao , Li Nan
Published: January 2017

As members of bromodomain and extra-terminal motif protein family, bromodomain-containing proteins regulate a wide range of biological processes including protein scaffolding, mitosis, cell cycle progression and transcriptional regulation. The function of these bromodomain proteins (Brds) in innate immune response has been reported but the role of Brd3 remains unclear. Here we find that virus infection significantly downregulate Brd3 expression in macrophages and Brd3 knockout inhibits virus-triggered IFN-β production. Brd3 interacts with both IRF3 and p300, increases p300-mediated acetylation of IRF3, and enhances the association of IRF3 with p300 upon virus infection. Importantly, Brd3 promotes the recruitment of IRF3/p300 complex to the promoter of Ifnb1, and increases the acetylation of histone3/histone4 within the Ifnb1 promoter, leading to the enhancement of type I interferon production. Therefore, our work indicated that Brd3 may act as a coactivator in IRF3/p300 transcriptional activation of Ifnb1 and provided new epigenetic mechanistic insight into the efficient activation of the innate immune response.
TFP5 peptide, derived from CDK5-activating cofactor p35, provides neuroprotection in early-stage of adult ischemic stroke
Authors: Ji Ya-Bin , Zhuang Pei-Pei , Ji Zhong , Wu Yong-Ming , Gu Yong , Gao Xiao-Ya , Pan Su-Yue , Hu Ya-Fang
Published: January 2017

Cyclin-dependent kinase 5 (CDK5) is a multifaceted protein shown to play important roles in the central nervous system. Abundant evidence indicates that CDK5 hyperactivities associated with neuronal apoptosis and death following ischemic stroke. CDK5 activity increases when its cofactor p35 cleaves into p25 during ischemia. Theoretically, inhibition of CDK5/p25 activity or reduction of p25 would be neuroprotective. TFP5, a modified 24-aa peptide (Lys254-Ala277) derived from p35, was found to effectively inhibit CDK5 hyperactivity and improve the outcomes of Alzheimer’s disease and Parkinson’s disease in vivo. Here, we showed that intraperitoneal injection of TFP5 significantly decreased the size of ischemia in early-stage of adult ischemic stroke rats. Relative to controls, rats treated with TFP5 displayed reduced excitotoxicity, neuroinflammation, apoptosis, astrocytes damage, and blood-brain barrier disruption. Our findings suggested that TFP5 might serve as a potential therapeutic candidate for acute adult ischemic stroke.
The effects of Lactobacillus plantarum on small intestinal barrier function and mucosal gene transcription; a randomized double-blind placebo controlled trial
Authors: Mujagic Zlatan , de Vos Paul , Boekschoten Mark V. , Govers Coen , Pieters Harm-Jan H. M. , de Wit Nicole J. W. , Bron Peter A. , Masclee Ad A. M. , Troost Freddy J.
Published: January 2017

The aim of this study was to investigate the effects of three Lactobacillus plantarum strains on in-vivo small intestinal barrier function and gut mucosal gene transcription in human subjects. The strains were selected for their differential effects on TLR signalling and tight junction protein rearrangement, which may lead to beneficial effects in a stressed human gut mucosa. Ten healthy volunteers participated in four different intervention periods: 7-day oral intake of either L. plantarum WCFS1, CIP104448, TIFN101 or placebo, proceeded by a 4 weeks wash-out period. Lactulose-rhamnose ratio (an indicator of small intestinal permeability) increased after intake of indomethacin, which was given as an artificial stressor of the gut mucosal barrier (mean ratio 0.06 ± 0.04 to 0.10 ± 0.06, p = 0.001), but was not significantly affected by the bacterial interventions. However, analysis in small intestinal biopsies, obtained by gastroduodenoscopy, demonstrated that particularly L. plantarum TIFN101 modulated gene transcription pathways related to cell-cell adhesion with high turnover of genes involved in tight- and adhesion junction protein synthesis and degradation (e.g. actinin alpha-4, metalloproteinase-2). These effects were less pronounced for L. plantarum WCFS1 and CIP104448. In conclusion, L. plantarum TIFN101 induced the most pronounced probiotic properties with specific gene transcriptional effects on repair processes in the compromised intestine of healthy subjects.
Methylomic profiling of cortex samples from completed suicide cases implicates a role for PSORS1C3 in major depression and suicide
Authors: Murphy T M , Crawford B , Dempster E L , Hannon E , Burrage J , Turecki G , Kaminsky Z , Mill J
Published: January 2017

Major depressive disorder (MDD) represents a major social and economic health issue and constitutes a major risk factor for suicide. The molecular pathology of suicidal depression remains poorly understood, although it has been hypothesised that regulatory genomic processes are involved in the pathology of both MDD and suicidality. In this study, genome-wide patterns of DNA methylation were assessed in depressed suicide completers (n=20) and compared with non-psychiatric, sudden-death controls (n=20) using tissue from two cortical brain regions (Brodmann Area 11 (BA11) and Brodmann Area 25 (BA25)). Analyses focused on identifying differentially methylated regions (DMRs) associated with suicidal depression and epigenetic variation were explored in the context of polygenic risk scores for major depression and suicide. Weighted gene co-methylation network analysis was used to identify modules of co-methylated loci associated with depressed suicide completers and polygenic burden for MDD and suicide attempt. We identified a DMR upstream of the PSORS1C3 gene, subsequently validated using bisulfite pyrosequencing and replicated in a second set of suicide samples, which is characterised by significant hypomethylation in both cortical brain regions in MDD suicide cases. We also identified discrete modules of co-methylated loci associated with polygenic risk burden for suicide attempt, but not major depression. Suicide-associated co-methylation modules were enriched among gene networks implicating biological processes relevant to depression and suicidality, including nervous system development and mitochondria function. Our data suggest that there are coordinated changes in DNA methylation associated with suicide that may offer novel insights into the molecular pathology associated with depressed suicide completers.
Construction and application of a new cell electrochemical detecting system based on the hyposmotic principle
Authors: Cui Ji-Wen , Wang Qian , Bi Sheng , Zhang Jing , Zhu Jin-Ling , Liu Ji-Guang , Wu Dong-mei
Published: January 2017

A new electrochemical detecting system has been constructed, in which the detection limits have been improved by one order of magnitude.
Accurate measurement of long range proton–carbon scalar coupling constants
Authors: Dickson Claire L. , Blundell Charles D. , Butts Craig P. , Felton Alice , Jeffreys Alex , Takacs Zoltan
Published: January 2017

The accuracy and ease-of-use of various experimental NMR methods for measuringnJCHvalues is assessed.
Fluorescence suppression of MPA stabilized CdTe QDs for direct determination of propranolol
Authors: Zhang Fan , Chen Miaomiao , Zhang Haiqing , Xiong Huayu , Wen Wei , Zhang Xiuhua , Wang Shengfu
Published: January 2017

A sensitive, convenient and rapid fluorescent sensor for effectively and directly detecting propranolol was proposed based on the fluorescence suppression of 3-mercaptopropionic acid stabilized CdTe quantum dots.
Magnesium, zinc, aluminium and gallium hydride complexes of the transition metals
Authors: Butler Michael J. , Crimmin Mark R.
Published: January 2017

Here we survey and organise the state-of-the-art understanding of the TM–H–M linkage (M = Mg, Zn, Al, Ga). We discuss the structure and bonding in these complexes, their known reactivity, and their largely unrealised potential in catalysis.
Control of bulk homochirality and proton conductivity in isostructural chiral metal–organic frameworks
Authors: Song Bai-Qiao , Chen Da-Qin , Ji Zhenguo , Tang Junhong , Wang Xin-Long , Zang Hong-Ying , Su Zhong-Min
Published: January 2017

Two enantiomeric pairs of isostructural homochiral metal–organic frameworks (MOFs) have been synthesized directly from chiral ligands and indirectly from achiral ligandsviaspontaneous resolution combined with cooperative chirality induction, respectively.
Surface-mounted MOF templated fabrication of homochiral polymer thin film for enantioselective adsorption of drugs
Authors: Gu Zhi-Gang , Fu Wen-Qiang , Liu Min , Zhang Jian
Published: January 2017

A chiral porous polymer thin film has been prepared using a template of SURMOF, showing an enantioselective adsorption of naproxen.
Facile synthesis of N-acyl 2-aminobenzothiazoles by NHC-catalyzed direct oxidative amidation of aldehydes
Authors: Premaletha Sethulekshmy , Ghosh Arghya , Joseph Sumi , Yetra Santhivardhana Reddy , Biju Akkattu T.
Published: January 2017

NHC-catalyzed direct amidation of aldehydes with 2-aminobenzothiazoles allowed the synthesis of N-acyl 2-aminobenzothiazoles proceeding via acyl azolium intermediates.
A pH-responsive molecular capsule with an acridine shell: catch and release of large hydrophobic compounds
Authors: Kishimoto Mai , Kondo Kei , Akita Munetaka , Yoshizawa Michito
Published: January 2017

Reversible assembly and disassembly of a supramolecular capsule bearing multiple acridine panels occur in water under neutral and acidic conditions, respectively. The pH-responsive capsule encapsulates various hydrophobic compounds in neutral water and subsequently releases them by simple acidification.
Morphology transition in helical tubules of a supramolecular gel driven by metal ions
Authors: Lalitha Krishnamoorthy , Sridharan Vellaisamy , Maheswari C. Uma , Vemula Praveen Kumar , Nagarajan Subbiah
Published: January 2017

We report a chiral molecular packing with α-helical tubules, and chiral symmetry-breaking upon exposure to metal ions that generated the final ordered structure via an in situ morphological transition without undergoing any phase change.
A photo-auxiliary approach – enabling excited state classical phototransformations with metal free visible light irradiation
Authors: Iyer Akila , Jockusch Steffen , Sivaguru Jayaraman
Published: January 2017

To address the problem of using UV light to initiate traditional photoreactions, hydrazide based chromophores are evaluated as a “photo-auxiliary“ with visible light using a metal free photocatalyst to afford photoproducts in high yields.
Biomimetic mineralization of metal–organic frameworks around polysaccharides
Authors: Liang Kang , Wang Ru , Boutter Manon , Doherty Cara M. , Mulet Xavier , Richardson Joseph J.
Published: January 2017

Biomimetic mineralization exploits natural biomineralization processes for the design and fabrication of synthetic functional materials.
A novel aggregation-induced emission platform from 2,3-diphenylbenzo[b]thiophene S,S-dioxide
Authors: Guo Jingjing , Hu Shimin , Luo Wenwen , Hu Rongrong , Qin Anjun , Zhao Zujin , Tang Ben Zhong
Published: January 2017

The steric hindrance and electronic push–pull effect greatly influence the aggregation-induced emission (AIE) properties of 2,3-diphenylbenzo[b]thiophene S,S-dioxide.
Adsorbing the 3d-transition metal atoms to effectively modulate the electronic and magnetic behaviors of zigzag SiC nanoribbons
Authors: Li Hui , Chen Wei , Shen Xiaopeng , Liu Jingwei , Huang Xuri , Yu Guangtao
Published: January 2017

The surface-adsorbing 3d-transition metal atoms can be used as an effective strategy to tune the electronic and magnetic behaviors of zSiCNRs.
Oligomerization of FVFLM peptides and their ability to inhibit beta amyloid peptides aggregation: consideration as a possible model
Authors: Kouza M. , Banerji A. , Kolinski A. , Buhimschi I. A. , Kloczkowski A.
Published: January 2017

This paper explores how and why FVFLM peptides can be used as model systems to inhibit beta-amyloid aggregation.
Tuning of intrinsic antiferromagnetic to ferromagnetic ordering in microporous α-MnO2 by inducing tensile strain
Authors: Kruthika G. , Karthikeyan J. , Murugan P.
Published: January 2017

Tensile strain (introduced either by mechanical or chemical means) is able to tune the intrinsic antiferromagnetic property of α-MnO2 to ferromagnetic in an effective way compared to the effects of an oxygen vacancy.
Ten-gram scale SiC@SiO2 nanowires: high-yield synthesis towards industrialization, in situ growth mechanism and their peculiar photoluminescence and electromagnetic wave absorption properties
Authors: Li Z. J. , Yu H. Y. , Song G. Y. , Zhao J. , Zhang H. , Zhang M. , Meng A. L. , Li Q. D.
Published: January 2017

SiC@SiO2 nanowires, as a functional nanocomposite, have attracted widespread attention due to their fascinating performance and broad application prospect.
Synthesis-driven, structure-dependent optical behavior in phase-tunable NaYF4:Yb,Er-based motifs and associated heterostructures
Authors: Liu Haiqing , Han Jinkyu , McBean Coray , Lewis Crystal S. , Kumar Routh Prahlad , Cotlet Mircea , Wong Stanislaus S.
Published: January 2017

FRET efficiency between CdSe QDs and NaYF4 is affected by the amount of QDs loaded onto the underlying 0D, 1D, and 3D NaYF4 host materials.
Understanding room-temperature π-dimerisation of radical ions: intramolecular π-[TTF]22+ in functionalised calix[4]arenes
Authors: Fumanal Maria , Capdevila-Cortada Marçal , Novoa Juan J.
Published: January 2017

Room-temperature π-[TTF]22+ dimers in calix[4]arene derivatives unravelled by means of DFT calculations.
Influence of NO and (NO)2 adsorption on the properties of Fe-N4 porphyrin-like graphene sheets
Authors: Ashori Elham , Nazari Fariba , Illas Francesc
Published: January 2017

Fe-N4 porphyrin-like graphene catalysis and spin filter characteristics toward NO and (NO)2 dimer adsorption.